Nature , IF:49.962 , 2023 Jan , V613 (7942) : P145-152 doi: 10.1038/s41586-022-05529-9
NLR surveillance of pathogen interference with hormone receptors induces immunity.
Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.; Howard Hughes Medical Institute, Department of Biology, Duke University, Durham, NC, USA.; Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, CA, USA.; Key Laboratory of Plant Immunity, Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China. taoxiaorong@njau.edu.cn.
Phytohormone signalling pathways have an important role in defence against pathogens mediated by cell-surface pattern recognition receptors and intracellular nucleotide-binding leucine-rich repeat class immune receptors(1,2) (NLR). Pathogens have evolved counter-defence strategies to manipulate phytohormone signalling pathways to dampen immunity and promote virulence(3). However, little is known about the surveillance of pathogen interference of phytohormone signalling by the plant innate immune system. The pepper (Capsicum chinense) NLR Tsw, which recognizes the effector nonstructural protein NSs encoded by tomato spotted wilt orthotospovirus (TSWV), contains an unusually large leucine-rich repeat (LRR) domain. Structural modelling predicts similarity between the LRR domain of Tsw and those of the jasmonic acid receptor COI1, the auxin receptor TIR1 and the strigolactone receptor partner MAX2. This suggested that NSs could directly target hormone receptor signalling to promote infection, and that Tsw has evolved a LRR resembling those of phytohormone receptors LRR to induce immunity. Here we show that NSs associates with COI1, TIR1 and MAX2 through a common repressor-TCP21-which interacts directly with these phytohormone receptors. NSs enhances the interaction of COI1, TIR1 or MAX2 with TCP21 and blocks the degradation of corresponding transcriptional repressors to disable phytohormone-mediated host immunity to the virus. Tsw also interacts directly with TCP21 and this interaction is enhanced by viral NSs. Downregulation of TCP21 compromised Tsw-mediated defence against TSWV. Together, our findings reveal that a pathogen effector targets TCP21 to inhibit phytohormone receptor function, promoting virulence, and a plant NLR protein has evolved to recognize this interference as a counter-virulence strategy, thereby activating immunity.
PMID: 36517600
Trends Plant Sci , IF:18.313 , 2023 Jan doi: 10.1016/j.tplants.2022.12.004
Auxin-cytokinin interplay shapes root functionality under low-temperature stress.
Department of Agronomy, Kansas State University, Manhattan, KA 66506, USA. Electronic address: manishtiwari@ksu.edu.; Department of Agronomy, Kansas State University, Manhattan, KA 66506, USA.; Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57006, USA.; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA.; Department of Agronomy, Kansas State University, Manhattan, KA 66506, USA; Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79410, USA. Electronic address: kjagadish.sv@ttu.edu.
Low-temperature stress alters root system architecture. In particular, changes in the levels and response to auxin and cytokinin determine the fate of root architecture and function under stress because of their vital roles in regulating root cell division, differentiation, and elongation. An intricate nexus of genes encoding components of auxin and cytokinin biosynthesis, signaling, and transport components operate to counteract stress and facilitate optimum development. We review the role of auxin transport and signaling and its regulation by cytokinin during root development and stem cell maintenance under low-temperature stress. We highlight intricate mechanisms operating in root stem cells to minimize DNA damage by altering phytohormone levels, and discuss a working model for cytokinin in low-temperatures stress response.
PMID: 36599768
Trends Plant Sci , IF:18.313 , 2023 Feb , V28 (2) : P131-134 doi: 10.1016/j.tplants.2022.10.007
Growth or stress responses: TMK-FER balancing act.
State Key Laboratory of Crop Biology, Engineering Center of Saline-Alkali Soil Plant - Microbial Joint Restoration, Shandong Agricultural University, Tai'an 271018, China.; State Key Laboratory of Crop Biology, Engineering Center of Saline-Alkali Soil Plant - Microbial Joint Restoration, Shandong Agricultural University, Tai'an 271018, China. Electronic address: shizhong@sdau.edu.cn.; State Key Laboratory of Crop Biology, Engineering Center of Saline-Alkali Soil Plant - Microbial Joint Restoration, Shandong Agricultural University, Tai'an 271018, China. Electronic address: cczheng@sdau.edu.cn.
Transmembrane kinases (TMKs) and Feronia (FER) belong to the leucine-rich repeat receptor-like kinase family. Recent studies reveal that they coordinate plant growth and stress responses by regulating the balance between acidification and alkalization and crosstalk between auxin and abscisic acid, revealing a dynamic equilibrium in the regulation of the TMK-FER module in plants.
PMID: 36371397
Trends Plant Sci , IF:18.313 , 2023 Jan , V28 (1) : P54-73 doi: 10.1016/j.tplants.2022.08.019
Is auxin enough? Cytokinins and margin patterning in simple leaves.
Instituto de Bioingenieria, Universidad Miguel Hernandez, Campus de Elche, 03202 Elche, Alicante, Spain.; Instituto de Bioingenieria, Universidad Miguel Hernandez, Campus de Elche, 03202 Elche, Alicante, Spain. Electronic address: jlmicol@umh.es.
The interplay between auxin and cytokinins affects facets of plant development as different as ovule formation and lateral root initiation. Moreover, cytokinins favor complexity in the development of Solanum lycopersicum and Cardamine hirsuta compound leaves. Nevertheless, no role has been proposed for cytokinins in patterning the margins of the simple leaves of Arabidopsis thaliana, a process that is assumed to be sufficiently explained by auxin localization. Here, we discuss evidence supporting the hypothesis that cytokinins play a role in simple leaf margin morphogenesis via crosstalk with auxin, as occurs in other plant developmental events. Indeed, mutant or transgenic arabidopsis plants defective in cytokinin biosynthesis or signaling, or with increased cytokinin degradation have leaf margins less serrated than the wild type.
PMID: 36180378
Trends Plant Sci , IF:18.313 , 2022 Dec , V27 (12) : P1196-1198 doi: 10.1016/j.tplants.2022.08.011
Spatiotemporal imaging clarifies leaf primordium patterning.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences and Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Peking University, Beijing 100871, China. Electronic address: yuling.jiao@pku.edu.cn.
The first step in organ morphogenesis is the subdivision of a primordium into discrete regions by patterning genes. Recently, Burian et al. used live imaging and cell-lineage tracing to illuminate early patterning events during the establishment of leaf primordium adaxial-abaxial (dorsoventral) polarity, which clarifies controversies in the field.
PMID: 36055917
Trends Plant Sci , IF:18.313 , 2022 Dec , V27 (12) : P1209-1217 doi: 10.1016/j.tplants.2022.06.002
Towards a hierarchical gene regulatory network underlying somatic embryogenesis.
National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; University of Chinese Academy of Sciences (UCAS), Shanghai 200032, PR China.; National Key Laboratory of Plant Molecular Genetics (NKLPMG), CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology (SIPPE), Chinese Academy of Sciences (CAS), 200032 Shanghai, PR China; ShanghaiTech University, Shanghai 200031, PR China. Electronic address: jwwang@sippe.ac.cn.
Genome-editing technologies have advanced in recent years but designing future crops remains limited by current methods of improving somatic embryogenesis (SE) capacity. In this Opinion, we provide an update on the molecular event by which the phytohormone auxin promotes the acquisition of plant cell totipotency through evoking massive changes in transcriptome and chromatin accessibility. We propose that the chromatin states and individual totipotency-related transcription factors (TFs) from disparate gene families organize into a hierarchical gene regulatory network underlying SE. We conclude with a discussion of the practical paths to probe the cellular origin of the somatic embryo and the epigenetic landscape of the totipotent cell state in the era of single-cell genomics.
PMID: 35810071
Nat Plants , IF:15.793 , 2022 Dec , V8 (12) : P1408-1422 doi: 10.1038/s41477-022-01274-z
Genome-wide dissection of changes in maize root system architecture during modern breeding.
College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China.; Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China.; Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China.; Cereal Crops Research Institute, Pirsabak, Nowshera, Pakistan.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.; College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China. caucfj@cau.edu.cn.; Sanya Institute of China Agricultural University, Sanya, China. caucfj@cau.edu.cn.; College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China. yuanlixing@cau.edu.cn.; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China. yuanlixing@cau.edu.cn.; College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, China. panqingchun@cau.edu.cn.; Sanya Institute of China Agricultural University, Sanya, China. panqingchun@cau.edu.cn.
Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.
PMID: 36396706
Nat Commun , IF:14.919 , 2023 Jan , V14 (1) : P423 doi: 10.1038/s41467-023-36200-0
A phosphoinositide hub connects CLE peptide signaling and polar auxin efflux regulation.
Department of Plant Molecular Biology, University of Lausanne, CH-1015, Lausanne, Switzerland.; Institute of Plant and Microbial Biology, University of Zurich, Zurich-Basel Plant Science Center, CH-8008, Zurich, Switzerland.; Department of Biology, Western University, London, Canada.; Department of Plant Molecular Biology, University of Lausanne, CH-1015, Lausanne, Switzerland. christian.hardtke@unil.ch.
Auxin efflux through plasma-membrane-integral PIN-FORMED (PIN) carriers is essential for plant tissue organization and tightly regulated. For instance, a molecular rheostat critically controls PIN-mediated auxin transport in developing protophloem sieve elements of Arabidopsis roots. Plasma-membrane-association of the rheostat proteins, BREVIS RADIX (BRX) and PROTEIN KINASE ASSOCIATED WITH BRX (PAX), is reinforced by interaction with PHOSPHATIDYLINOSITOL-4-PHOSPHATE-5-KINASE (PIP5K). Genetic evidence suggests that BRX dampens autocrine signaling of CLAVATA3/EMBRYO SURROUNDING REGION-RELATED 45 (CLE45) peptide via its receptor BARELY ANY MERISTEM 3 (BAM3). How excess CLE45-BAM3 signaling interferes with protophloem development and whether it does so directly or indirectly remains unclear. Here we show that rheostat polarity is independent of PIN polarity, but interdependent with PIP5K. Catalytically inactive PIP5K confers rheostat polarity without reinforcing its localization, revealing a possible PIP5K scaffolding function. Moreover, PIP5K and PAX cooperatively control local PIN abundance. We further find that CLE45-BAM3 signaling branches via RLCK-VII/PBS1-LIKE (PBL) cytoplasmic kinases to destabilize rheostat localization. Our data thus reveal antagonism between CLE45-BAM3-PBL signaling and PIP5K that converges on auxin efflux regulation through dynamic control of PAX polarity. Because second-site bam3 mutation suppresses root as well as shoot phenotypes of pip5k mutants, CLE peptide signaling likely modulates phosphoinositide-dependent processes in various developmental contexts.
PMID: 36702874
Sci Adv , IF:14.136 , 2023 Jan , V9 (1) : Peade2493 doi: 10.1126/sciadv.ade2493
Auxin promotes hypocotyl elongation by enhancing BZR1 nuclear accumulation in Arabidopsis.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, Shandong, China.
Auxin and brassinosteroids (BRs) are two major growth-promoting phytohormones that shape hypocotyl elongation; however, the cross-talk between auxin and BR in this process is not fully understood. In this study, we found that auxin-induced hypocotyl elongation is dependent on brassinazole-resistant 1 (BZR1), a core BR signaling component. Auxin promotes BZR1 nuclear accumulation in hypocotyl cells, a process dependent on mitogen-activated protein kinase 3 (MPK3) and MPK6, which are both activated by auxin and whose encoding genes are highly expressed in hypocotyls. We determined that MPK3/MPK6 phosphorylate and reduce the protein stability of general regulatory factor 4 (GRF4), a member of the 14-3-3 family of proteins that retain BZR1 in the cytoplasm. In summary, this study reveals the molecular mechanism by which auxin promotes hypocotyl elongation by enhancing BZR1 nuclear accumulation via MPK3/MPK6-regulated GRF4 protein stability.
PMID: 36598987
Sci Adv , IF:14.136 , 2022 Dec , V8 (49) : Peabq2047 doi: 10.1126/sciadv.abq2047
Endoreplication mediates cell size control via mechanochemical signaling from cell wall.
Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90187 Umea, Sweden.; IRBV, Department of Biological Sciences, University of Montreal, 4101 Sherbrooke Est, Montreal H1X 2B2, QC, Canada.; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium.; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.; Laboratoire Reproduction et Developpement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69364 Lyon, France.
Endoreplication is an evolutionarily conserved mechanism for increasing nuclear DNA content (ploidy). Ploidy frequently scales with final cell and organ size, suggesting a key role for endoreplication in these processes. However, exceptions exist, and, consequently, the endoreplication-size nexus remains enigmatic. Here, we show that prolonged tissue folding at the apical hook in Arabidopsis requires endoreplication asymmetry under the control of an auxin gradient. We identify a molecular pathway linking endoreplication levels to cell size through cell wall remodeling and stiffness modulation. We find that endoreplication is not only permissive for growth: Endoreplication reduction enhances wall stiffening, actively reducing cell size. The cell wall integrity kinase THESEUS plays a key role in this feedback loop. Our data thus explain the nonlinearity between ploidy levels and size while also providing a molecular mechanism linking mechanochemical signaling with endoreplication-mediated dynamic control of cell growth.
PMID: 36490331
Mol Plant , IF:13.164 , 2023 Jan doi: 10.1016/j.molp.2023.01.010
Ca(2+)-dependent TaCCD1 cooperates with TaSAUR215 to enhance plasma membrane H(+)-ATPase activity and alkali stress tolerance by inhibiting PP2C-mediated dephosphorylation of TaHA2 in wheat.
Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China.; Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Science, Shandong University, Qingdao 266237, China. Electronic address: lshuwei@sdu.edu.cn.
Alkali stress is a major constraint for crop production in large regions of saline-alkali land. However, little is known about the mechanisms through which wheat responds to alkali stress. In this study, we identified a calcium ion-binding protein from wheat, TaCCD1, which is critical for regulating the plasma membrane (PM) H(+)-ATPase-mediated alkali stress response. Plasma membrane H(+)-ATPase activity is closely related to alkali tolerance in the wheat variety Shanrong 4 (SR4). We found that two D-clade type 2C protein phosphatases, TaPP2C.D1 and TaPP2C.D8 (TaPP2C.D1/8), negatively modulated alkali stress tolerance by inhibiting PM H(+)-ATPase activity via dephosphorylating the penultimate threonine residue (Thr926) of TaHA2. Alkali stress induced the expression of TaCCD1 in SR4, and TaCCD1 interacted with TaSAUR215, an early auxin-responsive protein. These responses were both dependent on calcium signaling triggered by alkali stress. TaCCD1 enhanced the inhibitory effect of TaSAUR215 on TaPP2C.D1/8 activity, thereby promoting the activity of the PM H(+)-ATPase TaHA2 and alkali stress tolerance in wheat. Functional and genetic analyses verified the effects of these genes in response to alkali stress and indicated that TaPP2C.D1/8 are located downstream of TaSAUR215 and TaCCD1. In conclusion, this study describes a comprehensive signaling pathway for the regulation of wheat responses to alkali stress. In this pathway, Ca(2+)-dependent TaCCD1 cooperates with TaSAUR215 to enhance PM H(+)-ATPase activity and alkali stress tolerance by inhibiting the TaPP2C.D1/8-mediated dephosphorylation of the penultimate threonine residue of PM H(+)-ATPase TaHA2 in wheat.
PMID: 36681864
Mol Plant , IF:13.164 , 2022 Dec doi: 10.1016/j.molp.2022.12.013
Natural variations of OsAUX5, a target gene of OsWRKY78, control the neutral essential amino acid content in rice grains.
Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.; Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China. Electronic address: jincheng@hainanu.edu.cn.; Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China. Electronic address: jie.luo@hainanu.edu.cn.
Grain essential amino acid (EAA) levels contribute to rice nutritional quality. However, the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear. Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene, OsAUX5, which encodes an amino acid transporter that functions in uptake of multiple amino acids. We identified an elite haplotype of Pro::OsAUX5(Hap2) that enhances grain EAA accumulation without an apparent negative effect on agronomic traits. Natural variations of OsAUX5 occur in the cis elements of its promoter, which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box, contributing to grain EAA variation among rice varieties. The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors, which contributed to the divergence between japonica and indica. Introduction of the indica-type Pro::OsAUX5(Hap2) genotype into japonica could significantly increase EAA levels, indicating that indica-type Pro::OsAUX5(Hap2) can be utilized to increase grain EAAs of japonica varieties. Collectively, our study uncovers an WRKY78-OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.
PMID: 36540024
Mol Plant , IF:13.164 , 2022 Dec , V15 (12) : P1838-1840 doi: 10.1016/j.molp.2022.11.012
Adenylate cyclase activity of TIR1/AFB links cAMP to auxin-dependent responses.
Department of Biology, College of Science and Technology, Wenzhou-Kean University, 88 Daxue Road, Ouhai, Wenzhou 325060, Zhejiang Province, China; Wenzhou Municipal Key Lab for Applied Biomedical and Biopharmaceutical Informatics, Ouhai, Wenzhou 325060, Zhejiang Province, China; Zhejiang Bioinformatics International Science and Technology Cooperation Center, Ouhai, Wenzhou 325060, Zhejiang Province, China.; Department of Chemistry, Biology & Biotechnology, University of Perugia, Perugia 06121, Italy. Electronic address: christophandreas.gehring@UniPG.it.
PMID: 36419358
Mol Plant , IF:13.164 , 2022 Dec , V15 (12) : P1947-1961 doi: 10.1016/j.molp.2022.11.001
Submergence promotes auxin-induced callus formation through ethylene-mediated post-transcriptional control of auxin receptors.
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea.; Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, Korea.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Korea; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea. Electronic address: hyojunlee@kribb.re.kr.
Plant cells in damaged tissue can be reprogrammed to acquire pluripotency and induce callus formation. However, in the aboveground organs of many species, somatic cells that are distal to the wound site become less sensitive to auxin-induced callus formation, suggesting the existence of repressive regulatory mechanisms that are largely unknown. Here we reveal that submergence-induced ethylene signals promote callus formation by releasing post-transcriptional silencing of auxin receptor transcripts in non-wounded regions. We determined that short-term submergence of intact seedlings induces auxin-mediated cell dedifferentiation across the entirety of Arabidopsis thaliana explants. The constitutive triple response 1-1 (ctr1-1) mutation induced callus formation in explants without submergence, suggesting that ethylene facilitates cell dedifferentiation. We show that ETHYLENE-INSENSITIVE 2 (EIN2) post-transcriptionally regulates the abundance of transcripts for auxin receptor genes by facilitating microRNA393 degradation. Submergence-induced calli in non-wounded regions were suitable for shoot regeneration, similar to those near the wound site. We also observed submergence-promoted callus formation in Chinese cabbage (Brassica rapa), indicating that this may be a conserved mechanism in other species. Our study identifies previously unknown regulatory mechanisms by which ethylene promotes cell dedifferentiation and provides a new approach for boosting callus induction efficiency in shoot explants.
PMID: 36333910
Mol Plant , IF:13.164 , 2023 Jan , V16 (1) : P260-278 doi: 10.1016/j.molp.2022.09.004
The protein-protein interaction landscape of transcription factors during gynoecium development in Arabidopsis.
Unidad de Genomica Avanzada (UGA-LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, Mexico.; Departamento de Biotecnologia y Bioquimica, Unidad Irapuato, CINVESTAV-IPN, Irapuato, Guanajuato 36824, Mexico.; Instituto de Fisica, Universidad de San Luis Potosi, San Luis Potosi, SLP 78290, Mexico.; Unidad de Genomica Avanzada (UGA-LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, Mexico. Electronic address: stefan.defolter@cinvestav.mx.
Flowers are composed of organs whose identity is defined by the combinatorial activity of transcription factors (TFs). The interactions between MADS-box TFs and protein complex formation have been schematized in the floral quartet model of flower development. The gynoecium is the flower's female reproductive part, crucial for fruit and seed production and, hence, for reproductive success. After the establishment of carpel identity, many tissues arise to form a mature gynoecium. TFs have been described as regulators of gynoecium development, and some interactions and complexes have been identified. However, broad knowledge about the interactions among these TFs and their participation during development remains scarce. In this study, we used a systems biology approach to understand the formation of a complex reproductive unit-as the gynoecium-by mapping binary interactions between well-characterized TFs. We analyzed almost 4500 combinations and detected more than 250 protein-protein interactions (PPIs), resulting in a process-specific interaction map. Topological analyses suggest hidden functions and novel roles for many TFs. In addition, we observed a close relationship between TFs involved in auxin and cytokinin-signaling pathways and other TFs. Furthermore, we analyzed the network by combining PPI data, expression, and genetic data, which helped us to dissect it into several dynamic spatio-temporal subnetworks related to gynoecium development processes. Finally, we generated an extended PPI network that predicts new players in gynoecium development. Taken together, all these results serve as a valuable resource for the plant community.
PMID: 36088536
Plant Cell , IF:11.277 , 2023 Jan doi: 10.1093/plcell/koad012
Hormone synergy: Auxin and jasmonate boost abscisic acid signaling via ARF10 and ARF16.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; Department of Cell and Developmental Biology, University of California San Diego, La Jolla, 92093, USA.
PMID: 36651138
Plant Cell , IF:11.277 , 2023 Jan doi: 10.1093/plcell/koad004
Gateway to morphogenesis: TIR1 auxin receptor is essential for cellular differentiation and organ formation in Marchantia polymorpha.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; Laboratory of Biochemistry, Wageningen University and Research, Wageningen, the Netherlands.
PMID: 36648106
Plant Cell , IF:11.277 , 2022 Dec doi: 10.1093/plcell/koac369
Cytokinin-responsive MdTCP17 interacts with MdWOX11 to repress adventitious root primordium formation in apple rootstocks.
College of Horticulture, Yangling Sub-Center of National Center for Apple Improvement, Northwest A&F University, Yangling, 712100, Shaanxi, P. R. China.
Adventitious root (AR) formation plays an important role in vegetatively propagated plants. Cytokinin (CK) inhibits AR formation, but the molecular mechanisms driving this process remain unknown. In this study, we confirmed that CK content is related to AR formation and further revealed that a high auxin/CK ratio was beneficial to AR formation in apple (Malus domestica). A correlation between expression of CK-responsive TEOSINTE BRANCHED1, CYCLOIDEA, and PCF17 (MdTCP17) and AR formation in response to CK was identified, and overexpression of MdTCP17 in transgenic apple inhibited AR formation. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays revealed an interaction between MdTCP17 and WUSCHEL-RELATED HOMEOBOX11 (MdWOX11), and a significant correlation between the expression of MdWOX11 and AR ability. Overexpression of MdWOX11 promoted AR primordium formation in apple, while interference of MdWOX11 inhibited AR primordium production. Moreover, a positive correlation was found between MdWOX11 and LATERAL ORGAN BOUNDARIES DOMAIN29 (MdLBD29) expression, and yeast one-hybrid, dual luciferase reporter, and ChIP-qPCR assays verified the binding of MdWOX11 to the MdLBD29 promoter with a WOX-box element in the binding sequence. Furthermore, MdTCP17 reduced the binding of MdWOX11 and MdLBD29 promoters, and co-expression of MdTCP17 and MdWOX11 reduced MdLBD29 expression. Together, these results explain the function and molecular mechanism of MdTCP17-mediated CK inhibition of AR primordium formation, which could be used to improve apple rootstocks genetically.
PMID: 36544357
Plant Cell , IF:11.277 , 2022 Dec doi: 10.1093/plcell/koac367
Auxin signaling is essential for organogenesis but not for cell survival in the liverwort Marchantia polymorpha.
Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto 606-8502, Japan.; Graduate School of Life Sciences, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai, 980-8577, Japan.; Graduate School of Science, Kobe University, 1-1, Rokkodai-cho, Nada-ku, Kobe, 657-8501, Japan.; Graduate School of Science and Engineering, Ehime University, 2-5, Bunkyo-cho, Matsuyama, 790-8577, Japan.; Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Noda 278-8510, Japan.
Auxin plays pleiotropic roles in plant development via gene regulation upon its perception by the receptors TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFBs). This auxin-regulated transcriptional control mechanism originated in the common ancestor of land plants. Although the complete loss of TIR1/AFBs causes embryonic lethality in Arabidopsis thaliana, it is unclear whether the requirement for TIR1-mediated auxin perception in cell viability can be generalized. The model liverwort Marchantia polymorpha has a minimal auxin signaling system with only a single TIR1/AFB, MpTIR1. Here we show by genetic, biochemical, and transcriptomic analyses that MpTIR1 functions as an evolutionarily conserved auxin receptor. Null mutants and conditionally knocked-out mutants of MpTIR1 were viable but incapable of forming any organs and grew as cell masses. Principal component analysis performed using transcriptomes at various developmental stages indicated that MpTIR1 is involved in the developmental transition from spores to organized thalli, during which apical notches containing stem cells are established. In Mptir1 cells, stem-cell- and differentiation-related genes were up- and down-regulated, respectively. Our findings suggest that, in M. polymorpha, auxin signaling is dispensable for cell division but is essential for three-dimensional patterning of the plant body by establishing pluripotent stem cells for organogenesis, a derived trait of land plants.
PMID: 36529527
Plant Cell , IF:11.277 , 2022 Dec doi: 10.1093/plcell/koac362
Auxin contributes to jasmonate-mediated regulation of abscisic acid signaling during seed germination in Arabidopsis.
CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.; College of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China.
Abscisic acid (ABA) represses seed germination and post-germinative growth in Arabidopsis thaliana. Auxin and jasmonic acid (JA) stimulate ABA function; however, the possible synergistic effects of auxin and JA on ABA signaling and the underlying molecular mechanisms remain elusive. Here, we show that exogenous auxin works synergistically with JA to enhance the ABA-induced delay of seed germination. Auxin biosynthesis, perception, and signaling are crucial for JA-promoted ABA responses. The auxin-dependent transcription factors AUXIN RESPONSE FACTOR10 (ARF10) and ARF16 interact with JASMONATE ZIM-DOMAIN (JAZ) repressors of JA signaling. ARF10 and ARF16 positively mediate JA-increased ABA responses, and overaccumulation of ARF16 partially restores the hyposensitive phenotype of JAZ-accumulating plants defective in JA signaling in response to combined ABA and JA treatment. Furthermore, ARF10 and ARF16 physically associate with ABSCISIC ACID INSENSITIVE5 (ABI5), a critical regulator of ABA signaling, and the ability of ARF16 to stimulate JA-mediated ABA responses is mainly dependent on ABI5. ARF10 and ARF16 activate the transcriptional function of ABI5, whereas JAZ repressors antagonize their effects. Collectively, our results demonstrate that auxin contributes to the synergetic modulation of JA on ABA signaling, and explain the mechanism by which ARF10/16 coordinate with JAZ and ABI5 to integrate the auxin, JA, and ABA signaling pathways.
PMID: 36516412
Plant Cell , IF:11.277 , 2023 Jan , V35 (1) : P390-408 doi: 10.1093/plcell/koac316
Brassinosteroids promote etiolated apical structures in darkness by amplifying the ethylene response via the EBF-EIN3/PIF3 circuit.
School of Life Sciences, Southwest University, Chongqing 400715, China.; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China.; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.; Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China.; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China.
Germinated plants grow in darkness until they emerge above the soil. To help the seedling penetrate the soil, most dicot seedlings develop an etiolated apical structure consisting of an apical hook and folded, unexpanded cotyledons atop a rapidly elongating hypocotyl. Brassinosteroids (BRs) are necessary for etiolated apical development, but their precise role and mechanisms remain unclear. Arabidopsis thaliana SMALL AUXIN UP RNA17 (SAUR17) is an apical-organ-specific regulator that promotes production of an apical hook and closed cotyledons. In darkness, ethylene and BRs stimulate SAUR17 expression by transcription factor complexes containing PHYTOCHROME-INTERACTING FACTORs (PIFs), ETHYLENE INSENSITIVE 3 (EIN3), and its homolog EIN3-LIKE 1 (EIL1), and BRASSINAZOLE RESISTANT1 (BZR1). BZR1 requires EIN3 and PIFs for enhanced DNA-binding and transcriptional activation of the SAUR17 promoter; while EIN3, PIF3, and PIF4 stability depends on BR signaling. BZR1 transcriptionally downregulates EIN3-BINDING F-BOX 1 and 2 (EBF1 and EBF2), which encode ubiquitin ligases mediating EIN3 and PIF3 protein degradation. By modulating the EBF-EIN3/PIF protein-stability circuit, BRs induce EIN3 and PIF3 accumulation, which underlies BR-responsive expression of SAUR17 and HOOKLESS1 and ultimately apical hook development. We suggest that in the etiolated development of apical structures, BRs primarily modulate plant sensitivity to darkness and ethylene.
PMID: 36321994
Plant Cell , IF:11.277 , 2023 Jan , V35 (1) : P453-468 doi: 10.1093/plcell/koac297
The RAC/ROP GTPase activator OsRopGEF10 functions in crown root development by regulating cytokinin signaling in rice.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou 510642, China.; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts 01003, USA.
RAC/Rho of plant (ROP) GTPases are major molecular switches that control diverse signaling cascades for plant growth, development, and defense. Here, we discovered a signaling node that connects RAC/ROPs to cytokinins. Rice (Oryza sativa) plants develop a fibrous root system mainly composed of crown roots. Cytokinin signaling via a phosphorelay system is critical for crown root development. We show that OsRopGEF10, which activates RAC/ROPs, acts upstream of the cytoplasmic-nuclear shuttling phosphotransfer proteins AHPs of the cytokinin signaling pathway to promote crown root development. Mutations of OsRopGEF10 induced hypersensitivity to cytokinin, whereas overexpressing this gene reduced the cytokinin response. Loss of OsRopGEF10 function reduced the expression of the response regulator gene OsRR6, a repressor of cytokinin signaling, and impaired crown root development. Mutations in OsAHP1/2 led to increased crown root production and rescued the crown root defect of Osropgef10. Furthermore, auxin activates the ROP GTPase OsRAC3, which attenuates cytokinin signaling for crown root initiation. Molecular interactions between OsRopGEF10, OsRAC3, and OsAHP1/2 implicate a mechanism whereby OsRopGEF10-activated OsRAC3 recruits OsAHP1/2 to the cortical cytoplasm, sequestering them from their phosphorelay function in the nucleus. Together, our findings uncover the OsRopGEF10-OsRAC3-OsAHP1/2 signaling module, establish a link between RAC/ROPs and cytokinin, and reveal molecular crosstalk between auxin and cytokinin during crown root development.
PMID: 36190337
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Jan , V120 (3) : Pe2209781120 doi: 10.1073/pnas.2209781120
CPR5-mediated nucleo-cytoplasmic localization of IAA12 and IAA19 controls lateral root development during abiotic stress.
Department of Life Sciences, Pohang University of Science and Technology, Pohang 37673, Korea.; Department of Systems Biology, Yonsei University, Seoul 03722, Korea.; Institute for Convergence Research and Education in Advanced Technology, Yonsei University, Incheon 21983, Korea.
Plasticity of the root system architecture (RSA) is essential in enabling plants to cope with various environmental stresses and is mainly controlled by the phytohormone auxin. Lateral root development is a major determinant of RSA. Abiotic stresses reduce auxin signaling output, inhibiting lateral root development; however, how abiotic stress translates into a lower auxin signaling output is not fully understood. Here, we show that the nucleo-cytoplasmic distribution of the negative regulators of auxin signaling AUXIN/INDOLE-3-ACETIC ACID INDUCIBLE 12 (AUX/IAA12 or IAA12) and IAA19 determines lateral root development under various abiotic stress conditions. The cytoplasmic localization of IAA12 and IAA19 in the root elongation zone enforces auxin signaling output, allowing lateral root development. Among components of the nuclear pore complex, we show that CONSTITUTIVE EXPRESSOR OF PATHOGENESIS-RELATED GENES 5 (CPR5) selectively mediates the cytoplasmic translocation of IAA12/19. Under abiotic stress conditions, CPR5 expression is strongly decreased, resulting in the accumulation of nucleus-localized IAA12/19 in the root elongation zone and the suppression of lateral root development, which is reiterated in the cpr5 mutant. This study reveals a regulatory mechanism for auxin signaling whereby the spatial distribution of AUX/IAA regulators is critical for lateral root development, especially in fluctuating environmental conditions.
PMID: 36623191
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Dec , V119 (50) : Pe2210338119 doi: 10.1073/pnas.2210338119
Transcriptional repressor RST1 controls salt tolerance and grain yield in rice by regulating gene expression of asparagine synthetase.
College of Life Sciences, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.; Jiangsu Coastal Area Institute of Agricultural Science, Yancheng 224002, China.; State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.; Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.; Department of Integrative Biological Sciences and Industry, Sejong University, Seoul 05006, Korea.
Salt stress impairs nutrient metabolism in plant cells, leading to growth and yield penalties. However, the mechanism by which plants alter their nutrient metabolism processes in response to salt stress remains elusive. In this study, we identified and characterized the rice (Oryza sativa) rice salt tolerant 1 (rst1) mutant, which displayed improved salt tolerance and grain yield. Map-based cloning revealed that the gene RST1 encoded an auxin response factor (OsARF18). Molecular analyses showed that RST1 directly repressed the expression of the gene encoding asparagine synthetase 1 (OsAS1). Loss of RST1 function increased the expression of OsAS1 and improved nitrogen (N) utilization by promoting asparagine production and avoiding excess ammonium (NH(4)(+)) accumulation. RST1 was undergoing directional selection during domestication. The superior haplotype RST1(Hap III) decreased its transcriptional repression activity and contributed to salt tolerance and grain weight. Together, our findings unravel a synergistic regulator of growth and salt tolerance associated with N metabolism and provide a new strategy for the development of tolerant cultivars.
PMID: 36472959
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Dec , V119 (50) : Pe2215569119 doi: 10.1073/pnas.2215569119
Polar auxin transport modulates early leaf flattening.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.; Centro de Biotecnologia y Genomica de Plantas (CBGP), Universidad Politecnica de Madrid (UPM), Centro Nacional Instituto de Investigacion y Tecnologia Agraria y Alimentaria (INIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcon, 28223, Madrid, Spain.; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Peking University, Beijing 100871, China.; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China.
The flattened leaf form is an important adaptation for efficient photosynthesis, and the developmental process of flattened leaves has been intensively studied. Classic microsurgery studies in potato and tomato suggest that the shoot apical meristem (SAM) communicates with the leaf primordia to promote leaf blade formation. More recently, it was found that polar auxin transport (PAT) could mediate this communication. However, it is unclear how the expression of leaf patterning genes is tailored by PAT routes originating from SAM. By combining experimental observations and computer model simulations, we show that microsurgical incisions and local inhibition of PAT in tomato interfere with auxin transport toward the leaf margins, reducing auxin response levels and altering the leaf blade shape. Importantly, oval auxin responses result in the bipolar expression of SlLAM1 that determines leaf blade formation. Furthermore, wounding caused by incisions promotes degradation of SlREV, a known regulator of leaf polarity. Additionally, computer simulations suggest that local auxin biosynthesis in early leaf primordia could remove necessity for external auxin supply originating from SAM, potentially explaining differences between species. Together, our findings establish how PAT near emerging leaf primordia determines spatial auxin patterning and refines SlLAM1 expression in the leaf margins to guide leaf flattening.
PMID: 36469773
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Dec , V119 (49) : Pe2212881119 doi: 10.1073/pnas.2212881119
Mitochondrial GPAT-derived LPA controls auxin-dependent embryonic and postembryonic development.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing 210014, China.; Ministry of Agriculture (MOA) Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing 210095, China.
Membrane properties are emerging as important cues for the spatiotemporal regulation of hormone signaling. Lysophosphatidic acid (LPA) evokes multiple biological responses by activating G protein-coupled receptors in mammals. In this study, we demonstrated that LPA derived from the mitochondrial glycerol-3-phosphate acyltransferases GPAT1 and GPAT2 is a critical lipid-based cue for auxin-controlled embryogenesis and plant growth in Arabidopsis thaliana. LPA levels decreased, and the polarity of the auxin efflux carrier PIN-FORMED1 (PIN1) at the plasma membrane (PM) was defective in the gpat1 gpat2 mutant. As a consequence of distribution defects, instructive auxin gradients and embryonic and postembryonic development are severely compromised. Further cellular and genetic analyses revealed that LPA binds directly to PIN1, facilitating the vesicular trafficking of PIN1 and polar auxin transport. Our data support a model in which LPA provides a lipid landmark that specifies membrane identity and cell polarity, revealing an unrecognized aspect of phospholipid patterns connecting hormone signaling with development.
PMID: 36454754
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Dec , V119 (49) : Pe2209256119 doi: 10.1073/pnas.2209256119
Chemical genetic screening identifies nalacin as an inhibitor of GH3 amido synthetase for auxin conjugation.
Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.; Institute for Advanced Studies, Wuhan University, Wuhan 430072, P.R. China.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 1138657, Japan.; Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA 92093.; Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
Auxin inactivation is critical for plant growth and development. To develop plant growth regulators functioning in auxin inactivation pathway, we performed a phenotype-based chemical screen in Arabidopsis and identified a chemical, nalacin, that partially mimicked the effects of auxin. Genetic, pharmacological, and biochemical approaches demonstrated that nalacin exerts its auxin-like activities by inhibiting indole-3-acetic acid (IAA) conjugation that is mediated by Gretchen Hagen 3 (GH3) acyl acid amido synthetases. The crystal structure of Arabidopsis GH3.6 in complex with D4 (a derivative of nalacin) together with docking simulation analysis revealed the molecular basis of the inhibition of group II GH3 by nalacin. Sequence alignment analysis indicated broad bioactivities of nalacin and D4 as inhibitors of GH3s in vascular plants, which were confirmed, at least, in tomato and rice. In summary, our work identifies nalacin as a potent inhibitor of IAA conjugation mediated by group II GH3 that plays versatile roles in hormone-regulated plant development and has potential applications in both basic research and agriculture.
PMID: 36454752
Curr Biol , IF:10.834 , 2023 Jan , V33 (1) : P75-85.e5 doi: 10.1016/j.cub.2022.11.045
Local light signaling at the leaf tip drives remote differential petiole growth through auxin-gibberellin dynamics.
Plant-Environment Signaling, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.; Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.; Plant-Environment Signaling, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands.; Laboratory for Molecular Biology, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, the Netherlands.; Laboratory of Biochemistry, Wageningen University, Stippeneng 4, 6708 WE Wageningen, the Netherlands.; Plant-Environment Signaling, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. Electronic address: r.pierik@uu.nl.
Although plants are immobile, many of their organs are flexible to move in response to environmental cues. In dense vegetation, plants detect neighbors through far-red light perception with their leaf tip. They respond remotely, with asymmetrical growth between the abaxial and adaxial sides of the leafstalk, the petiole. This results in upward movement that brings the leaf blades into better lit zones of the canopy. The plant hormone auxin is required for this response, but it is not understood how non-differential leaf tip-derived auxin can remotely regulate movement. Here, we show that remote signaling of far-red light promotes auxin accumulation in the abaxial petiole. This local auxin accumulation is facilitated by reinforcing an intrinsic directionality of the auxin transport protein PIN3 on the petiole endodermis, as visualized with a PIN3-GFP line. Using an auxin biosensor, we show that auxin accumulates in all cell layers from endodermis to epidermis in the abaxial petiole, upon far-red light signaling in the remote leaf tip. In the petiole, auxin elicits a response to both auxin itself as well as a second growth promoter; gibberellin. We show that this dual regulation is necessary for hyponastic leaf movement in response to light. Our data indicate that gibberellin is required to permit cell growth, whereas differential auxin accumulation determines which cells can grow. Our results reveal how plants can spatially relay information about neighbor proximity from their sensory leaf tips to the petiole base, thus driving adaptive growth.
PMID: 36538931
J Hazard Mater , IF:10.588 , 2023 Mar , V445 : P130530 doi: 10.1016/j.jhazmat.2022.130530
Pre treatment of melatonin rescues cotton seedlings from cadmium toxicity by regulating key physio-biochemical and molecular pathways.
State Key Laboratory of Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China; School of Life Science and Technology, Henan Institute of Science and Technology, Hualan St. 90, Xinxiang 453003, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 450000, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya 572024, China.; School of Life Science and Technology, Henan Institute of Science and Technology, Hualan St. 90, Xinxiang 453003, China.; Faculty of Science, University Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei Darussalam.; Institute of Ecology and Evolution, 5289 University of Oregon, Eugene, OR 97403, USA.; Sinopharm Wuhan Plasma-derived Biotherapies Co., Ltd, Wuhan, China.; School of Life Science and Technology, Henan Institute of Science and Technology, Hualan St. 90, Xinxiang 453003, China. Electronic address: ruiyangzh@gmail.com.; State Key Laboratory of Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China. Electronic address: xiongyc@lzu.edu.cn.
Melatonin, a plant/animal origin hormone, regulates plant response to abiotic stresses by protecting them from oxidative damage. This study identified physiochemical and molecular mechanism of melatonin-induced cadmium (Cd) stress tolerance and detoxification in cotton seedlings. Cotton seedlings, with or without melatonin (15 microM) pretreatment, were subjected to Cd (100 microM) stress in a hydroponic medium for eight days. We found that higher cellular Cd accumulation in leaf tissues significantly inhibited the growth and physiology of cotton seedlings. In contrast, melatonin-treated seedlings maintained leaf photosynthetic capacity, producing relatively higher fresh (17.4%) and dry (19.3%) weights than non-melatonin-treated plants under Cd-contaminated environments. The improved growth and leaf functioning were strongly linked with the melatonin-induced repression of Cd transporter genes (LOC107894197, LOC107955631, LOC107899273) in roots. Thus, melatonin induced downregulation of the Cd transporter genes further inhibited Cd ion transport towards leaf tissues. This suggests that the differentially expressed transporter genes (DEG) are key drivers of the melatonin-mediated regulation of Cd transportation and sequestration in cotton. Melatonin also protected cotton seedlings from Cd-induced oxidative injury by reducing tissues malondialdehyde (MDA) and hydrogen peroxide (H(2)O(2)) levels and increasing the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), and ascorbate peroxidase (APX) enzymes. Transcriptomic analysis revealed that melatonin activated mitogen-activated protein kinase (MAPK) signaling pathways to simulate stomatal adjustment and photosynthesis in Cd-stressed leaves. Further, melatonin protects intercellular organs, particularly ribosomes, from Cd-induced oxidative damage by promoting ribosomal biosynthesis and improving translational efficiency. The findings elucidated the molecular basis of melatonin-mediated Cd stress tolerance in plants and provided a key for the effective strategy of Cd accumulation in cotton.
PMID: 36463746
J Hazard Mater , IF:10.588 , 2023 Feb , V444 (Pt A) : P130427 doi: 10.1016/j.jhazmat.2022.130427
Transcriptome reveals the exposure effects of CeO(2) nanoparticles on pakchoi (Brassica chinensis L.) photosynthesis.
College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China. Electronic address: jhong@zjut.edu.cn.; College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.; College of Life Sciences, Shanxi Agricultural University, Taigu, Shanxi 030801, China.; Department of Chemistry and Biochemistry, The University of Texas, El Paso, TX 79968, United States.
In this study, soil-grown pakchoi after 2 weeks seedling cultivation were exposed to CeO(2) nanoparticles (CeO(2) NPs) at 0.7, 7, 70, and 350 mg kg(-1) for 30 days. Results showed that chlorophyll content and photosynthetic assimilation rate were decreased significantly under all treatments with the largest decrease of 34.16% (0.7 mg kg(-1) CeO(2) NPs), however, sub-stomatal CO(2) was increased dramatically under low dose of CeO(2) NPs (0.7 mg kg(-1)). There were 4576, 3548, 2787, and 2514 genes up/down regulated significantly by 0.7, 7, 70, and 350 mg kg(-1) CeO(2) NPs, respectively, and 767 genes affected under all treatments. In addition, 0.7 mg kg(-1) CeO(2) NPs up-regulated 10 chlorophyll synthesis genes, 20 photosynthesis genes, and 10 carbon fixation enzyme genes; while 350 mg kg(-1) CeO(2) NPs down-regulated 5 photosynthesis genes and 28 auxin-activated genes. Among the key genes of photosynthesis, Ferredoxin-NADP reductase (PetH) was upregulated in 0.7, 7 and 70 mg kg(-1) treatments, while Photosystem II lipoprotein (Psb27) was downregulated under 7, 70 and 350 mg kg(-1) treatments. Top 20 metabolic pathways affected by CeO(2) NPs including plant hormone, amino acids, and glutathione, and carbon metabolism These results provide information about utilizing CeO(2) NPs more safely and effectively in the future.
PMID: 36410248
J Hazard Mater , IF:10.588 , 2023 Jan , V441 : P129843 doi: 10.1016/j.jhazmat.2022.129843
Changes in the m6A RNA methylome accompany the promotion of soybean root growth by rhizobia under cadmium stress.
College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China.; Daqing Branch, Heilongjiang Academy of Agricultural Sciences, Daqing 163316, Heilongjiang, People's Republic of China.; College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China. Electronic address: qshchen@126.com.; College of Agriculture, Northeast Agricultural University, Harbin 150030, Heilongjiang, People's Republic of China. Electronic address: qizhaoming1860@126.com.
Cadmium (Cd) is the most widely distributed heavy metal pollutant in soil and has significant negative effects on crop yields and human health. Rhizobia can enhance soybean growth in the presence of heavy metals, and the legume-rhizobia symbiosis has been used to promote heavy-metal phytoremediation, but much remains to be learned about the molecular networks that underlie these effects. Here, we demonstrated that soybean root growth was strongly suppressed after seven days of Cd exposure but that the presence of rhizobia largely eliminated this effect, even prior to nodule development. Moreover, rhizobia did not appear to promote root growth by limiting plant Cd uptake: seedlings with and without rhizobia had similar root Cd concentrations. Previous studies have demonstrated a role for m6A RNA methylation in the response of rice and barley to Cd stress. We therefore performed transcriptome-wide m6A methylation profiling to investigate changes in the soybean RNA methylome in response to Cd with and without rhizobia. Here, we provide some of the first data on transcriptome-wide m6a RNA methylation patterns in soybean; m6A modifications were concentrated at the 3' UTR of transcripts and showed a positive relationship with transcript abundance. Transcriptome-wide m6A RNA methylation peaks increased in the presence of Cd, and the integration of m6A methylome and transcriptome results enabled us to identify 154 genes whose transcripts were both differentially methylated and differentially expressed in response to Cd stress. Annotation results suggested that these genes were associated with Ca(2+) homeostasis, ROS pathways, polyamine metabolism, MAPK signaling, hormones, and biotic stress responses. There were 176 differentially methylated and expressed transcripts under Cd stress in the presence of rhizobia. In contrast to the Cd-only gene set, they were also enriched in genes related to auxin, jasmonic acid, and brassinosteroids, as well as abiotic stress tolerance. They contained fewer genes related to Ca(2+) homeostasis and also included candidates with known functions in the legume-rhizobia symbiosis. These findings offer new insights into how rhizobia promote soybean root growth under Cd stress; they provide candidate genes for research on plant heavy metal responses and for the use of legumes in phytoremediation.
PMID: 36113351
J Nanobiotechnology , IF:10.435 , 2023 Jan , V21 (1) : P2 doi: 10.1186/s12951-022-01753-7
Silica nanoparticles promote wheat growth by mediating hormones and sugar metabolism.
MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China.; Key Laboratory of Integrated Pest Management of Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Institute of Plant Protection and Soil Science, Insect Pests and Weeds Control, Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China.; MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China. yinjunliang@yangtzeu.edu.cn.; MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, Hubei, China. yongxingzhu@yangtzeu.edu.cn.
BACKGROUND: Silica nanoparticles (SiNPs) have been demonstrated to have beneficial effects on plant growth and development, especially under biotic and abiotic stresses. However, the mechanisms of SiNPs-mediated plant growth strengthening are still unclear, especially under field condition. In this study, we evaluated the effect of SiNPs on the growth and sugar and hormone metabolisms of wheat in the field. RESULTS: SiNPs increased tillers and elongated internodes by 66.7% and 27.4%, respectively, resulting in a larger biomass. SiNPs can increase the net photosynthetic rate by increasing total chlorophyll contents. We speculated that SiNPs can regulate the growth of leaves and stems, partly by regulating the metabolisms of plant hormones and soluble sugar. Specifically, SiNPs can increase auxin (IAA) and fructose contents, which can promote wheat growth directly or indirectly. Furthermore, SiNPs increased the expression levels of key pathway genes related to soluble sugars (SPS, SUS, and alpha-glucosidase), chlorophyll (CHLH, CAO, and POR), IAA (TIR1), and abscisic acid (ABA) (PYR/PYL, PP2C, SnRK2, and ABF), whereas the expression levels of genes related to CTKs (IPT) was decreased after SiNPs treatment. CONCLUSIONS: This study shows that SiNPs can promote wheat growth and provides a theoretical foundation for the application of SiNPs in field conditions.
PMID: 36593514
New Phytol , IF:10.151 , 2023 Jan doi: 10.1111/nph.18774
Somatic embryo initiation by rice BABY BOOM1 involves activation of zygote-expressed auxin biosynthesis genes.
Department of Plant Sciences, University of California, Davis, CA, 95616, USA.; Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA.; Department of Plant Biology, University of California, Davis, CA, 95616, USA.; Present address: Department of Plant Pathology, University of California Davis, CA, 95616, USA.
Plant embryogenesis results from the fusion of male and female gametes but can also be induced in somatic cells. The molecular pathways for embryo initiation are poorly understood, especially in monocots. In rice, the male gamete expressed BABY BOOM1 (OsBBM1) transcription factor functions as an embryogenic trigger in the zygote, and can also promote somatic embryogenesis when ectopically expressed in somatic tissues. We used gene editing, transcriptome profiling, and chromatin immunoprecipitation to determine the molecular players involved in embryo initiation downstream of OsBBM1. We identify OsYUCCA (OsYUC) auxin biosynthesis genes as direct targets of OsBBM1. Unexpectedly, these OsYUC targets in zygotes are expressed only from the maternal genome, whereas the paternal genome exclusively provides functional OsBBM1 to initiate embryogenesis. Induction of somatic embryogenesis by exogenous auxin requires OsBBM genes as well as downstream OsYUC targets. Ectopic OsBBM1 initiates somatic embryogenesis without exogenous auxins but requires functional OsYUC genes. Thus, an OsBBM-OsYUC module is a key player for both somatic and zygotic embryogenesis in rice. Zygotic embryo initiation involves a partnership of male and female genomes, through which paternal OsBBM1 activates maternal OsYUC genes. In somatic embryogenesis, exogenous auxin triggers OsBBM1 expression, which then activates endogenous auxin biosynthesis OsYUC genes.
PMID: 36707918
New Phytol , IF:10.151 , 2023 Jan doi: 10.1111/nph.18691
A Physcomitrella PIN protein acts in spermatogenesis and sporophyte retention.
Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.; Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104, Freiburg, Germany.; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany.; Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, 79110, Freiburg, Germany.
The auxin efflux PIN-FORMED (PIN) proteins are conserved in all land plants and important players in plant development. In the moss Physcomitrella (Physcomitrium patens), three canonical PINs (PpPINA-C) are expressed in the leafy shoot (gametophore). PpPINA and PpPINB show functional activity in vegetative growth and sporophyte development. Here, we examined the role of PpPINC in the life cycle of Physcomitrella. We established reporter and knockout lines for PpPINC and analysed vegetative and reproductive tissues using microscopy and transcriptomic sequencing of moss gametangia. PpPINC is expressed in immature leaves, mature gametangia and during sporophyte development. The sperm cells (spermatozoids) of pinC knockout mutants exhibit increased motility and an altered flagella phenotype. Furthermore, the pinC mutants have a higher portion of differentially expressed genes related to spermatogenesis, increased fertility and an increased abortion rate of premeiotic sporophytes. Here, we show that PpPINC is important for spermatogenesis and sporophyte retention. We propose an evolutionary conserved way of polar growth during early moss embryo development and sporophyte attachment to the gametophore while suggesting the mechanical function in sporophyte retention of a ring structure, the Lorch ring.
PMID: 36696950
New Phytol , IF:10.151 , 2023 Jan doi: 10.1111/nph.18733
Local Auxin Biosynthesis Regulates Brace Root Angle and Lodging Resistance in Maize.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; HainanYazhou Bay Seed Lab, Sanya, 572025, China.; Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Helsinki, 00790, Finland.; College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China.; Shimadzu (China) Co., Ltd. Shenzhen Branch, Shenzhen, 518042, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
Root lodging poses a major threat to maize production, resulting in reduced grain yield and quality, and increased harvest costs. Here, we combined expressional, genetic and cytological studies to demonstrate a role of ZmYUC2 and ZmYUC4 in regulating gravitropic response of the brace root and lodging resistance in maize. We show that both ZmYUC2 and ZmYUC4 are preferentially expressed in root tips with partially overlapping expression patterns, and the protein products of ZmYUC2 and ZmYUC4 are localized in the cytoplasm and endoplasmic reticulum (ER), respectively. The Zmyuc4 single mutant and Zmyuc2/4 double mutant exhibit enlarged brace root angle compared to the wild type plants, with larger brace root angle being observed in the Zmyuc2/4 double mutant. Consistently, the brace root tips of the Zmyuc4 single mutant and Zmyuc2/4 double mutant accumulate less auxin and are defective in proper reallocation of auxin in response to gravi-stimuli. Further, we show that the Zmyuc4 single mutant and the Zmyuc2/4 double mutant display obviously enhanced root lodging resistance. Our combined results demonstrate that ZmYUC2- and ZmYUC4-mediated local auxin biosynthesis is required for normal gravity response of the brace roots and provide effective targets for breeding root lodging resistant maize cultivars.
PMID: 36636793
New Phytol , IF:10.151 , 2023 Feb , V237 (4) : P1115-1121 doi: 10.1111/nph.18602
Extranuclear auxin signaling: a new insight into auxin's versatility.
Department of Botany and Plant Sciences, Institute of Integrated Genome Biology, University of California, Riverside, CA, 92521, USA.; FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Auxin phytohormone has a role in most aspects of the life of a land plant and is found even in ancient plants such as single-cell green algae. Auxin's ubiquitous but specific effects have been mainly explained by the extraordinary ability of plants to interpret spatiotemporal patterns of auxin concentrations via the regulation of gene transcription. This is thought to be achieved through the combinatorial effects of two families of nuclear coreceptor proteins, that is the TRANSPORT INHIBITOR RESPONSE1 and AUXIN-SIGNALING F-BOX (TIR1/AFB) and AUXIN/INDOLE ACETIC ACID. Recent evidence has suggested transcription-independent roles of TIR1/AFBs localized outside the nucleus and TRANSMEMBRANE KINASE (TMK)-based auxin signaling occurring in the plasma membrane. Furthermore, emerging evidence supports a coordinated action of the intra- and extranuclear auxin signaling pathways to regulate specific auxin responses. Here, we highlight how auxin signaling acts inside and outside the nucleus for the regulation of growth and morphogenesis and propose that the future direction of auxin biology lies in the elucidation of a new collaborative paradigm of intra- and extranuclear auxin signaling.
PMID: 36336825
New Phytol , IF:10.151 , 2023 Feb , V237 (4) : P1320-1332 doi: 10.1111/nph.18600
Soilborne bacterium Klebsiella pneumoniae promotes cluster root formation in white lupin through ethylene mediation.
Joint International Research Laboratory of Water and Nutrient in Crop, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Department of Biology, Hong Kong Baptist University and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China.
Cluster roots of white lupin are induced by low phosphorus (LP) to efficiently access unavailable P, but how soilborne microbes are associated with cluster root formation (CRF) is unclear. We investigated the roles of soilborne bacteria in CRF response to LP by high-throughput sequencing and root-bacteria interactions. Cluster root number was significantly decreased in plants grown in sterilized soil compared with nonsterilized soil. Proteobacteria was enriched in CR, as shown by microbiome analysis of soil (bulk, rhizosphere, and rhizosheath) and roots (main, lateral, and CR). Large-scale gene expression level implicated ethylene mediation in CRF. Klebsiella pneumoniae (P7), a soilborne bacterium belonging to Proteobacteria, was isolated from CR. Among 11 isolated strains, P7 exhibited the highest 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity; this enzyme inhibits the biosynthesis of ethylene in plants by the cleavage of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid and promotes CRF under LP. We constructed an ACCD-deficit mutant accd in the P7 genetic background. The loss-of-function mutation failed to promote CRF under LP conditions. Also, auxin responses may be involved in K. pneumoniae-ethylene-mediated CRF. Overall, we propose that the soilborne bacterium K. pneumoniae promotes CRF of white lupin in response to LP by ethylene mediation.
PMID: 36336781
New Phytol , IF:10.151 , 2023 Feb , V237 (4) : P1391-1404 doi: 10.1111/nph.18589
A GT-1 and PKc domain-containing transcription regulator SIMPLE LEAF1 controls compound leaf development in woodland strawberry.
Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China.; Hubei Hongshan Laboratory, Wuhan, 430070, China.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, 20742, USA.
Leaves are strikingly diverse in terms of shapes and complexity. The wild and cultivated strawberry plants mostly develop trifoliate compound leaves, yet the underlying genetic basis remains unclear in this important fruit crop in Rosaceae. Here, we identified two EMS mutants designated simple leaf1 (sl1-1 and sl1-2) and one natural simple-leafed mutant monophylla in Fragaria vesca. Their causative mutations all reside in SL1 (FvH4_7g28640) causing premature stop codon at different positions in sl1-1 and sl1-2 and an eight-nucleotide insertion (GTTCATCA) in monophylla. SL1 encodes a transcription regulator with the conserved DNA-binding domain GT-1 and the catalytic domain of protein kinases PKc. Expression of SL1pro::SL1 in sl1-1 completely restored compound leaf formation. The 35S::SL1 lines developed palmate-like leaves with four or five leaflets at a low penetrance. However, overexpressing the truncated SL1(DeltaPK) caused no phenotypes, probably due to the disruption of homodimerization. SL1 is preferentially expressed at the tips of leaflets and serrations. Moreover, SL1 is closely associated with the auxin pathway and works synergistically with FveLFYa in leaf morphogenesis. Overall, our work uncovered a new type of transcription regulator that promotes compound leaf formation in the woodland strawberry and shed new lights on the diversity of leaf complexity control.
PMID: 36319612
New Phytol , IF:10.151 , 2023 Feb , V237 (3) : P807-822 doi: 10.1111/nph.18570
Root architecture plasticity in response to endoparasitic cyst nematodes is mediated by damage signaling.
Laboratory of Nematology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; Laboratory of Molecular Biology, Cluster of Plant Developmental Biology, Wageningen University & Research, 6708 PB, Wageningen, the Netherlands.; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.; Institute of Crop Science and Resource Conservation (INRES), Molecular Phytomedicine, University of Bonn, 53115, Bonn, Germany.
Plant root architecture plasticity in response to biotic stresses has not been thoroughly investigated. Infection by endoparasitic cyst nematodes induces root architectural changes that involve the formation of secondary roots at infection sites. However, the molecular mechanisms regulating secondary root formation in response to cyst nematode infection remain largely unknown. We first assessed whether secondary roots form in a nematode density-dependent manner by challenging wild-type Arabidopsis plants with increasing numbers of cyst nematodes (Heterodera schachtii). Next, using jasmonate-related reporter lines and knockout mutants, we tested whether tissue damage by nematodes triggers jasmonate-dependent secondary root formation. Finally, we verified whether damage-induced secondary root formation depends on local auxin biosynthesis at nematode infection sites. Intracellular host invasion by H. schachtii triggers a transient local increase in jasmonates, which activates the expression of ERF109 in a COI1-dependent manner. Knockout mutations in COI1 and ERF109 disrupt the nematode density-dependent increase in secondary roots observed in wild-type plants. Furthermore, ERF109 regulates secondary root formation upon H. schachtii infection via local auxin biosynthesis. Host invasion by H. schachtii triggers secondary root formation via the damage-induced jasmonate-dependent ERF109 pathway. This points at a novel mechanism underlying plant root plasticity in response to biotic stress.
PMID: 36285401
New Phytol , IF:10.151 , 2023 Jan , V237 (2) : P563-575 doi: 10.1111/nph.18552
Root placement patterns in allelopathic plant-plant interactions.
College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China.; Department of Biological Sciences, Eastern Illinois University, Charleston, IL, 61920, USA.
Plants actively respond to their neighbors by altering root placement patterns. Neighbor-modulated root responses involve root detection and interactions mediated by root-secreted functional metabolites. However, chemically mediated root placement patterns and their underlying mechanisms remain elusive. We used an allelopathic wheat model system challenged with 60 target species to identify root placement responses in window rhizobox experiments. We then tested root responses and their biochemical mechanisms in incubation experiments involving the addition of activated carbon and functional metabolites with amyloplast staining and auxin localization in roots. Wheat and each target species demonstrated intrusive, avoidant or unresponsive root placement, resulting in a total of nine combined patterns. Root placement patterns were mediated by wheat allelochemicals and (-)-loliolide signaling of neighbor species. In particular, (-)-loliolide triggered wheat allelochemical production that altered root growth and placement, degraded starch grains in the root cap and induced uneven distribution of auxin in target species roots. Root placement patterns in wheat-neighbor interactions were perception dependent and species dependent. Signaling (-)-loliolide induced the production and release of wheat allelochemicals that modulated root placement patterns. Therefore, root placement patterns are generated by both signaling chemicals and allelochemicals in allelopathic plant-plant interactions.
PMID: 36263726
New Phytol , IF:10.151 , 2023 Jan , V237 (2) : P483-496 doi: 10.1111/nph.18556
The RhLOL1-RhILR3 module mediates cytokinin-induced petal abscission in rose.
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193, China.; Crops Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, 95616, USA.; Department of Plant Sciences, University of California at Davis, Davis, CA, 95616, USA.
In many plant species, petal abscission can be considered the final step of petal senescence. Cytokinins (CKs) are powerful suppressors of petal senescence; however, their role in petal abscission is ambiguous. Here, we observed that, in rose (Rosa hybrida), biologically active CK is accumulated during petal abscission and acts as an accelerator of the abscission process. Using a combination of reverse genetics, and molecular and biochemical techniques, we explored the roles of a LESION SIMULATING DISEASE1 (LSD1) family member RhLOL1 interacting with a bHLH transcription factor RhILR3 in CK-induced petal abscission. Silencing RhLOL1 delays rose petal abscission, while the overexpression of its ortholog SlLOL1 in tomato (Solanum lycopersicum) promotes pedicel abscission, indicating the conserved function of LOL1 in activating plant floral organ abscission. In addition, we identify a bHLH transcription factor, RhILR3, that interacts with RhLOL1. We show that RhILR3 binds to the promoters of the auxin signaling repressor auxin/indole-3-acetic acid (Aux/IAA) genes to inhibit their expression; however, the interaction of RhLOL1 with RhILR3 activates the expression of the Aux/IAA genes including RhIAA4-1. Silencing RhIAA4-1 delays rose petal abscission. Our results thus reveal a RhLOL1-RhILR3 regulatory module involved in CK-induced petal abscission via the regulation of the expression of the Aux/IAA genes.
PMID: 36263705
New Phytol , IF:10.151 , 2023 Jan , V237 (1) : P78-87 doi: 10.1111/nph.18536
SUE4, a novel PIN1-interacting membrane protein, regulates acropetal auxin transport in response to sulfur deficiency.
Division of Life Sciences and Medicine, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China.; Division of Molecular & Cell Biophysics, Hefei National Science Center for Physical Sciences at the Microscale, University of Science and Technology of China, The Innovation Academy of Seed Design, Chinese Academy of Sciences, Hefei, Anhui Province, 230027, China.; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, 350002, China.; State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.; College of Environmental and Resources Sciences, Zhejiang University, Hangzhou, Zhejiang Province, 310058, China.; Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China.
Sulfur (S) is an essential macronutrient for plants and a signaling molecule in abiotic stress responses. It is known that S availability modulates root system architecture; however, the underlying molecular mechanisms are largely unknown. We previously reported an Arabidopsis gain-of-function mutant sulfate utilization efficiency4 (sue4) that could tolerate S deficiency during germination and early seedling growth with faster primary root elongation. Here, we report that SUE4, a novel plasma membrane-localized protein, interacts with the polar auxin transporter PIN1, resulting in reduced PIN1 protein levels and thus decreasing auxin transport to the root tips, which promotes primary root elongation. Moreover, SUE4 is induced by sulfate deficiency, consistent with its role in root elongation. Further analyses showed that the SUE4-PIN1 interaction decreased PIN1 levels, possibly through 26 S proteasome-mediated degradation. Taken together, our finding of SUE4-mediated root elongation is consistent with root adaptation to highly mobile sulfate in soil, thus revealing a novel component in the adaptive response of roots to S deficiency.
PMID: 36226797
New Phytol , IF:10.151 , 2022 Dec , V236 (6) : P2216-2232 doi: 10.1111/nph.18491
Osa-miR160a confers broad-spectrum resistance to fungal and bacterial pathogens in rice.
State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
Rice production is threatened by multiple pathogens. Breeding cultivars with broad-spectrum disease resistance is necessary to maintain and improve crop production. Previously we found that overexpression of miR160a enhanced rice blast disease resistance. However, it is unclear whether miR160a also regulates resistance against other pathogens, and what the downstream signaling pathways are. Here, we demonstrate that miR160a positively regulates broad-spectrum resistance against the causative agents of blast, leaf blight and sheath blight in rice. Mutations of miR160a-targeted Auxin Response Factors result in different alteration of resistance conferred by miR160a. miR160a enhances disease resistance partially by suppressing ARF8, as mutation of ARF8 in MIM160 background partially restores the compromised resistance resulting from MIM160. ARF8 protein binds directly to the promoter and suppresses the expression of WRKY45, which acts as a positive regulator of rice immunity. Mutation of WRKY45 compromises the enhanced blast resistance and bacterial leaf blight resistance conferred by arf8 mutant. Overall, our results reveal that a microRNA coordinates rice broad-spectrum disease resistance by suppressing multiple target genes that play different roles in disease resistance, and uncover a new regulatory pathway mediated by the miR160a-ARF8 module. These findings provide new resources to potentially improve disease resistance for breeding in rice.
PMID: 36101507
New Phytol , IF:10.151 , 2023 Jan , V237 (2) : P408-413 doi: 10.1111/nph.18487
Systemic control of plant regeneration and wound repair.
The Institute of Plant Sciences, Faculty of Agriculture, The Hebrew University, Rehovot, 761000, Israel.
Plants have a broad capacity to regenerate damaged organs. The study of wounding in multiple developmental systems has uncovered many of the molecular properties underlying plants' competence for regeneration at the local cellular level. However, in nature, wounding is rarely localized to one place, and plants need to coordinate regeneration responses at multiple tissues with environmental conditions and their physiological state. Here, we review the evidence for systemic signals that regulate regeneration on a plant-wide level. We focus on the role of auxin and sugars as short- and long-range signals in natural wounding contexts and discuss the varied origin of these signals in different regeneration scenarios. Together, this evidence calls for a broader, system-wide view of plant regeneration competence.
PMID: 36101501
New Phytol , IF:10.151 , 2022 Dec , V236 (6) : P2265-2281 doi: 10.1111/nph.18483
Nodule INception-independent epidermal events lead to bacterial entry during nodule development in peanut (Arachis hypogaea).
National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.; Amity University Haryana, Amity Education Valley, Panchgaon, Manesar, Haryana, 122412, India.
Legumes can host nitrogen-fixing rhizobia inside root nodules. In model legumes, rhizobia enter via infection threads (ITs) and develop nodules in which the infection zone contains a mixture of infected and uninfected cells. Peanut (Arachis hypogaea) diversified from model legumes c. 50-55 million years ago. Rhizobia enter through 'cracks' to form nodules in peanut roots where cells of the infection zone are uniformly infected. Phylogenomic studies have indicated symbiosis as a labile trait in peanut. These atypical features prompted us to investigate the molecular mechanism of peanut nodule development. Combining cell biology, genetics and genomic tools, we visualized the status of hormonal signaling in peanut nodule primordia. Moreover, we dissected the signaling modules of Nodule INception (NIN), a master regulator of both epidermal infection and cortical organogenesis. Cytokinin signaling operates in a broad zone, from the epidermis to the pericycle inside nodule primordia, while auxin signaling is narrower and focused. Nodule INception is involved in nodule organogenesis, but not in crack entry. Nodulation Pectate Lyase, which remodels cell walls during IT formation, is not required. By contrast, Nodule enhanced Glycosyl Hydrolases (AhNGHs) are recruited for cell wall modification during crack entry. While hormonal regulation is conserved, the function of the NIN signaling modules is diversified in peanut.
PMID: 36098671
New Phytol , IF:10.151 , 2022 Dec , V236 (5) : P1637-1654 doi: 10.1111/nph.18474
Gravity sensing and responses in the coordination of the shoot gravitropic setpoint angle.
Division of Plant Environmental Responses, National Institute for Basic Biology, Myodaiji, Okazaki, 444-8556, Japan.
Gravity is one of the fundamental environmental cues that affect plant development. Indeed, the plant architecture in the shoots and roots is modulated by gravity. Stems grow vertically upward, whereas lateral organs, such as the lateral branches in shoots, tend to grow at a specific angle according to a gravity vector known as the gravitropic setpoint angle (GSA). During this process, gravity is sensed in specialised gravity-sensing cells named statocytes, which convert gravity information into biochemical signals, leading to asymmetric auxin distribution and driving asymmetric cell division/expansion in the organs to achieve gravitropism. As a hypothetical offset mechanism against gravitropism to determine the GSA, the anti-gravitropic offset (AGO) has been proposed. According to this concept, the GSA is a balance of two antagonistic growth components, that is gravitropism and the AGO. Although the nature of the AGO has not been clarified, studies have suggested that gravitropism and the AGO share a common gravity-sensing mechanism in statocytes. This review discusses the molecular mechanisms underlying gravitropism as well as the hypothetical AGO in the control of the GSA.
PMID: 36089891
New Phytol , IF:10.151 , 2022 Dec , V236 (5) : P1762-1778 doi: 10.1111/nph.18467
Phosphorylation status of Bbeta subunit acts as a switch to regulate the function of phosphatase PP2A in ethylene-mediated root growth inhibition.
Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA.; Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.; Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
The various combinations and regulations of different subunits of phosphatase PP2A holoenzymes underlie their functional complexity and importance. However, molecular mechanisms governing the assembly of PP2A complex in response to external or internal signals remain largely unknown, especially in Arabidopsis thaliana. We found that the phosphorylation status of Bbeta of PP2A acts as a switch to regulate the activity of PP2A. In the absence of ethylene, phosphorylated Bbeta leads to an inactivation of PP2A; the substrate EIR1 remains to be phosphorylated, preventing the EIR1-mediated auxin transport in epidermis, leading to normal root growth. Upon ethylene treatment, the dephosphorylated Bbeta mediates the formation of the A2-C4-Bbeta protein complex to activate PP2A, resulting in the dephosphorylation of EIR1 to promote auxin transport in epidermis of elongation zone, leading to root growth inhibition. Altogether, our research revealed a novel molecular mechanism by which the dephosphorylation of Bbeta subunit switches on PP2A activity to dephosphorylate EIR1 to establish EIR1-mediated auxin transport in the epidermis in elongation zone for root growth inhibition in response to ethylene.
PMID: 36073540
New Phytol , IF:10.151 , 2022 Dec , V236 (5) : P1748-1761 doi: 10.1111/nph.18459
Karrikin signaling regulates hypocotyl shade avoidance response by modulating auxin homeostasis in Arabidopsis.
Laboratory of Photosynthesis and Environment, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.; University of Chinese Academy of Sciences, Beijing, 100039, China.
Shade affects all aspects of plant growth and development, including seed germination, hypocotyl elongation, petiole growth, leaf hyponasty, and flowering time. Here, we found that mutations in the key Arabidopsis karrikins signal perception-associated KARRIKIN INSENSITIVE 2 (KAI2) gene, encoding an alpha/beta-fold hydrolase, and the MORE AXILLARY GROWTH 2 (MAX2) gene, encoding an F-box protein, led to greater hypocotyl elongation under shade avoidance conditions. We further verified that these phenotypes were caused by perception of the endogenous KAI2-ligands (KLs), and that this phenotype is independent of strigolactone biosynthetic or signaling pathways. Upon perception of a KL, it is probable that the target protein forms a complex with the KAI2/MAX2 proteins, which are degraded through the action of the 26S proteasome. We demonstrated that SUPPRESSOR OF MAX2-1 (SMAX1) is the degradation target for the KAI2/MAX2 complex in the context of shade avoidance. KAI2 and MAX2 require SMAX1 to limit the hypocotyl growth associated with shade avoidance. Treatment with l-kynurenine, an inhibitor of auxin accumulation, partially restored elongation of kai2 mutant hypocotyls under simulated shade. Furthermore, KAI2 is involved in regulating auxin accumulation and polar auxin transport, which may contribute to the hypocotyl shade response. In addition, SMAX1 gene overexpression promoted the hypocotyl shade response. RNA-sequencing analysis revealed that SMAX1-overexpression affected the expression of many auxin homeostasis genes, especially under simulated shade. Altogether, our data support the conclusion that KL signaling regulates shade avoidance by modulating auxin homeostasis in the hypocotyl.
PMID: 36068957
New Phytol , IF:10.151 , 2022 Dec , V236 (5) : P1734-1747 doi: 10.1111/nph.18448
Bipartite phosphoinositide-dependent modulation of auxin signaling during xylem differentiation in Arabidopsis thaliana roots.
Department of Biology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8092, Zurich, Switzerland.
Efficient root-to-shoot delivery of water and nutrients in plants relies on the correct differentiation of xylem cells into hollow elements. While auxin is integral to the formation of xylem cells, it remains poorly characterized how each subcellular pool of this hormone regulates this process. Combining genetic and cell biological approaches, we investigated the bipartite activity of nucleoplasmic vs plasma membrane-associated phosphatidylinositol 4-phosphate kinases PIP5K1 and its homolog PIP5K2 in Arabidopsis thaliana roots and uncovered a novel mechanism by which phosphoinositides integrate distinct aspects of the auxin signaling cascade and, in turn, regulate the onset of xylem differentiation. The appearance of undifferentiated cells in protoxylem strands of pip5k1 pip5k2 is phenomimicked in auxin transport and perception mutants and can be partially restored by the nuclear residence of PIP5K1. By contrast, exclusion of PIP5K1 from the nucleus hinders the auxin-mediated induction of the xylem master regulator VASCULAR RELATED NAC DOMAIN (VND) 7. A xylem-specific increase of auxin levels abolishes pip5k1 pip5k2 vascular defects, indicating that the establishment of auxin maxima is required to activate VND7-mediated xylem differentiation. Our results describe a new mechanism by which distinct subcellular pools of phosphoinositides integrate auxin transport and perception to initiate xylem differentiation in a spatiotemporal manner.
PMID: 36039703
New Phytol , IF:10.151 , 2022 Dec , V236 (5) : P1721-1733 doi: 10.1111/nph.18440
Feedback regulation of auxin signaling through the transcription of H2A.Z and deposition of H2A.Z to SMALL AUXIN UP RNAs in Arabidopsis.
Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200032, China.
Auxin is a critical phytohormone that is involved in the regulation of most plant growth and developmental responses. In particular, epigenetic mechanisms, like histone modifications and DNA methylation, were reported to affect auxin biosynthesis and transport. However, the involvement of other epigenetic factors, such as histone variant H2A.Z, in the auxin-related developmental regulation remains unclear. We report that the histone variant H2A.Z knockdown mutant in Arabidopsis Col-0 ecotype, h2a.z-kd, has more lateral roots and weak gravitational responses related to auxin-regulated growth performances. Further study revealed that auxin promotes the eviction of H2A.Z from the auxin-responsive genes SMALL AUXIN-UP RNAs (SAURs) to activate their transcriptions. We found that IAA promotes the transcription of H2A.Z genes through HOMEOBOX PROTEIN 22/25 (AtHB22/25) transcription factors which work as downstream targets of ARF7/19 in auxin signaling. Double mutant of hb22 hb25 showed similar lateral root and gravitropism phenotypes to h2a.z-kd. Our results shed light on a reciprocal regulation hub through INOSITOL AUXOTROPHY 80-mediated H2A.Z eviction and ARF7/19-HB22/25-mediated H2A.Z transcription to modulate the activation of SAURs and plant growth in Arabidopsis.
PMID: 36017638
Plant Biotechnol J , IF:9.803 , 2022 Dec doi: 10.1111/pbi.13974
Profiling of phytohormone-specific microRNAs and characterization of the miR160-ARF1 module involved in glandular trichome development and artemisinin biosynthesis in Artemisia annua.
Medical School of Nantong University, Nantong, China.; School of Food and Bioengineering, Fujian Polytechnic Normal University, Fuqing, China.; Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai, China.; Research and Development Center of Chinese Medicine Resources and Biotechnology, Shanghai University of Traditional Chinese Medicine, Shanghai, China.; Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, National Engineering Research Center of Edible Fungi, Shanghai, China.; Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Shanghai, China.; Innovative Drug R&D Center, College of Life Sciences, Huaibei Normal University, Huaibei, China.
MicroRNAs (miRNAs) play crucial roles in plant development and secondary metabolism through different modes of sequence-specific interaction with their targets. Artemisinin biosynthesis is extensively regulated by phytohormones. However, the function of phytohormone-responsive miRNAs in artemisinin biosynthesis remains enigmatic. Thus, we combined the analysis of transcriptomics, small RNAs, and the degradome to generate a comprehensive resource for identifying key miRNA-target circuits involved in the phytohormone-induced process of artemisinin biosynthesis in Artemisia annua. In total, 151 conserved and 52 novel miRNAs and their 4132 targets were determined. Based on the differential expression analysis, miR160 was selected as a potential miRNA involved in artemisinin synthesis. Overexpressing MIR160 significantly impaired glandular trichome formation and suppressed artemisinin biosynthesis in A. annua, while repressing its expression resulted in the opposite effect, indicating that miR160 negatively regulates glandular trichome development and artemisinin biosynthesis. RNA ligase-mediated 5' RACE and transient transformation assays showed that miR160 mediates the RNA cleavage of Auxin Response Factor 1 (ARF1) in A. annua. Furthermore, ARF1 was shown to increase artemisinin synthesis by activating AaDBR2 expression. Taken together, our results reveal the intrinsic link between the miR160-ARF1 module and artemisinin biosynthesis, and may expedite the innovation of metabolic engineering approaches for high and stable production of artemisinin in the future.
PMID: 36478140
Plant Biotechnol J , IF:9.803 , 2023 Jan , V21 (1) : P122-135 doi: 10.1111/pbi.13930
A HST1-like gene controls tiller angle through regulating endogenous auxin in common wheat.
National Key Laboratory of Wheat and Maize Crop Science / CIMMYT-China Wheat and Maize Joint Research Center /Agronomy College, Henan Agricultural University, Zhengzhou, China.
Tiller angle is one of the most important agronomic traits and one key factor for wheat ideal plant architecture, which can both increase photosynthetic efficiency and greatly enhance grain yield. Here, a deacetylase HST1-like (TaHST1L) gene controlling wheat tiller angle was identified by the combination of a genome-wide association study (GWAS) and bulked segregant analysis (BSA). Ethyl methane sulfonate (EMS)-mutagenized tetraploid wheat lines with the premature stop codon of TaHST1L exhibited significantly smaller tiller angles than the wild type. TaHST1L-overexpressing (OE) plants exhibited significantly larger tiller angles and increased tiller numbers in both winter and spring wheat, while TaHST1L-silenced RNAi plants displayed significantly smaller tiller angles and decreased tiller numbers. Moreover, TaHST1L strongly interacted with TaIAA17 and inhibited its expression at the protein level, and thus possibly improved the content of endogenous auxin in the basal tissue of tillers. The transcriptomics and metabolomics results indicated that TaHST1L might change plant architecture by mediating auxin signal transduction and regulating endogenous auxin levels. In addition, a 242-bp insertion/deletion (InDel) in the TaHST1L-A1 promoter altered transcriptional activity and TaHST1L-A1b allele with the 242-bp insertion widened the tiller angle of TaHST1L-OE transgenic rice plants. Wheat varieties with TaHST1L-A1b allele possessed the increased tiller angle and grain yield. Further analysis in wheat and its progenitors indicated that the 242-bp InDel possibly originated from wild emmer and was strongly domesticated in the current varieties. Therefore, TaHST1L involved in the auxin signalling pathway showed the big potential to improve wheat yield by controlling plant architecture.
PMID: 36128872
Cell Rep , IF:9.423 , 2022 Dec , V42 (1) : P111913 doi: 10.1016/j.celrep.2022.111913
Control of lateral root initiation by DA3 in Arabidopsis.
School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore.; State Key Laboratory of Plant Cell and Chromosome, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore.; School of Science, Anhui Agricultural University, Hefei 230036, China.; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore. Electronic address: dbsyuhao@nus.edu.sg.
Lateral root (LR) initiation is controlled by the pericycle and the neighboring endodermis in Arabidopsis. Here, we demonstrate that UBIQUITIN-SPECIFIC PROTEASE14/DA3 regulates LR initiation by modulating auxin signaling in the pericycle and endodermis. DA3 negatively affects the mRNA and protein levels of AUXIN RESPONSE FACTOR7 (ARF7) and ARF19 in the pericycle and endodermis but positively regulates the protein stability of SHORT HYPOCOTYL 2 (SHY2/IAA3), an auxin signaling repressor, in the endodermis. We show that DA3 interacts with ARF7 and ARF19, inhibiting their binding to the locus of LATERAL ORGAN BOUNDARY DOMAIN16 (LBD16) to repress its expression in the pericycle. SHY2 also interacts with ARF7 and ARF19 in the endodermis and enhances the DA3 repressive effect on ARF7 and ARF19, thus modulating LBD16 expression in the pericycle. Overall, our findings show that DA3 acts with SHY2, ARF7, and ARF19 to coordinate auxin signaling in the pericycle and endodermis to control LR initiation in Arabidopsis.
PMID: 36640335
Plant Physiol , IF:8.34 , 2023 Jan doi: 10.1093/plphys/kiad038
Causes and consequences of endogenous hypoxia on growth and metabolism of developing maize kernels.
Leibniz-Institut fur Pflanzengenetik und Kulturpflanzenforschung, Corrensstrasse, 06466 Seeland-Gatersleben, Germany.; University of Florida, Horticultural Sciences Department, Fifield Hall, 2550 Hull Rd., PO Box 110690, Gainesville, FL, 32611, USA.; KU Leuven - University of Leuven, BIOSYST-MeBioS, Willem de Croylaan 42, B-3001 Leuven, Belgium.
Maize (Zea mays) kernels are the largest cereal grains, and their endosperm is severely oxygen deficient during grain fill. The causes, dynamics, and mechanisms of acclimation to hypoxia are minimally understood. Here, we demonstrate that hypoxia develops in the small, growing endosperm, but not the nucellus, and becomes the standard state, regardless of diverse structural and genetic perturbations in modern maize (B73, popcorn, sweet corn), mutants (sweet4c, glossy6, waxy), and non-domesticated wild relatives (teosintes and Tripsacum species). We also uncovered an interconnected void space at the chalazal pericarp, providing superior oxygen supply to the placental tissues and basal endosperm transfer layer. Modelling indicated a very high diffusion resistance inside the endosperm, which, together with internal oxygen consumption, could generate steep oxygen gradients at the endosperm surface. Manipulation of oxygen supply induced reciprocal shifts in gene expression implicated in controlling mitochondrial functions (23.6 kDa Heat-Shock Protein, Voltage Dependent Anion Channel 2) and multiple signalling pathways (core hypoxia genes, cyclic nucleotide metabolism, ethylene synthesis). Metabolite profiling revealed oxygen-dependent shifts in mitochondrial pathways, ascorbate metabolism, starch synthesis, and auxin degradation. Long-term elevated oxygen supply enhanced the rate of kernel development. Altogether, evidence here supports a mechanistic framework for the establishment of and acclimation to hypoxia in the maize endosperm.
PMID: 36691698
Plant Physiol , IF:8.34 , 2023 Jan doi: 10.1093/plphys/kiad034
Auxin-independent effects of apical dominance induce changes in phytohormones correlated with bud outgrowth.
ARC Centre of Excellence for Plant Success in Nature and Agriculture, School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.; School of Biological Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
The inhibition of shoot branching by the growing shoot tip of plants, termed apical dominance, was originally thought to be mediated by auxin. Recently the importance of the shoot tip sink strength during apical dominance has re-emerged with recent studies highlighting roles for sugars in promoting branching. This raises many unanswered questions on the relative roles of auxin and sugars in apical dominance. Here we show that auxin depletion after decapitation is not always the initial trigger of rapid cytokinin increases in buds that are instead correlated with enhanced sugars. Auxin may also act through strigolactones which have been shown to suppress branching after decapitation, but here we show that strigolactones do not have a significant effect on initial bud outgrowth after decapitation. We report here that when sucrose or cytokinin is abundant, strigolactones are less inhibitory during the bud release stage compared to during later stages and that strigolactone treatment rapidly inhibits cytokinin accumulation in pea (Pisum sativum) axillary buds of intact plants. After initial bud release, we find an important role of gibberellin in promoting sustained bud growth downstream of auxin. We are therefore able to suggest a model of apical dominance that integrates auxin, sucrose, strigolactones, cytokinins and gibberellins and describes differences in signalling across stages of bud release to sustained growth.
PMID: 36690819
Plant Physiol , IF:8.34 , 2023 Jan doi: 10.1093/plphys/kiad006
Roles of very-long-chain fatty acids in compound leaf patterning in Medicago truncatula.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266101, China.; Grassland Agri-Husbandry Research Center, Qingdao Agricultural University, Qingdao 266109, China.; College of Life Sciences, Shandong Normal University, Jinan 250014, China.; State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.; Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Provincial Key Laboratory for Crop Germplasm Innovation and Utilization, Hunan Agricultural University, Changsha 410128, China.; Institute of Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA.
Plant cuticles are composed of hydrophobic cuticular waxes and cutin. Very long-chain fatty acids (VLCFAs) are components of epidermal waxes and the plasma membrane and are involved in organ morphogenesis. By screening a barrelclover (Medicago truncatula) mutant population tagged by the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified two types of mutants with unopened flower phenotypes, named unopened flower1 (uof1) and uof2. Both UOF1 and UOF2 encode enzymes that are involved in the biosynthesis of VLCFAs and cuticular wax. Comparative analysis of the mutants indicated that the mutation in UOF1, but not UOF2, leads to increased number of leaflets in M. truncatula. UOF1 was specifically expressed in the outermost cell layer (L1) of the shoot apical meristem (SAM) and leaf primordia. The uof1 mutants displayed defects in VLCFAs-mediated plasma membrane integrity, resulting in the disordered localization of the PIN-FORMED1 (PIN1) ortholog SMOOTH LEAF MARGIN1 (SLM1) in M. truncatula. Our work demonstrates that the UOF1-mediated biosynthesis of VLCFAs in L1 is critical for compound leaf patterning, which is associated with the polarization of the auxin efflux carrier in M. truncatula.
PMID: 36617225
Plant Physiol , IF:8.34 , 2022 Dec doi: 10.1093/plphys/kiac581
The Mediator complex subunit MED25 interacts with HDA9 and PIF4 to regulate thermomorphogenesis.
Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.; Temasek Life Science Laboratory, 1 Research Link, National University of Singapore, Singapore.; Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.; Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Centre, S.S. Ionica, km 419.5, 75026 Rotondella (Matera), Italy.
Thermomorphogenesis is, among other traits, characterised by enhanced hypocotyl elongation due to induction of auxin biosynthesis genes like YUCCA8 by transcription factors, most notably PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Efficient binding of PIF4 to the YUCCA8 locus under warmth depends on HISTONE DEACETYLASE 9 (HDA9) activity, which mediates histone H2A.Z depletion at the YUCCA8 locus. However, HDA9 lacks intrinsic DNA binding capacity, and how HDA9 is recruited to YUCCA8, and possibly other PIF4-target sites, is currently not well-understood. The Mediator complex functions as a bridge between transcription factors bound to specific promoter sequences and the basal transcription machinery containing RNA polymerase II. Mutants of Mediator component Mediator25 (MED25) exhibit reduced hypocotyl elongation and reduced expression of YUCCA8 at 27 degrees C. In line with a proposed role for MED25 in thermomorphogenesis in Arabidopsis (Arabidopsis thaliana), we demonstrated enhanced association of MED25 to the YUCCA8 locus under warmth and interaction of MED25 with both PIF4 and HDA9. Genetic analysis confirmed that MED25 and HDA9 operate in the same pathway. Intriguingly, we also showed that MED25 destabilises HDA9 protein. Based on our findings, we propose that MED25 recruits HDA9 to the YUCCA8 locus by binding to both PIF4 and HDA9.
PMID: 36537119
Plant Physiol , IF:8.34 , 2022 Dec doi: 10.1093/plphys/kiac586
Abscisic acid promotes auxin biosynthesis to inhibit primary root elongation in rice.
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China.
Soil compaction is a global problem causing inadequate rooting and poor yield in crops. Accumulating evidence indicates that phytohormones coordinately regulate root growth via regulating specific growth processes in distinct tissues. However, how abscisic acid (ABA) signaling translates into auxin production to control root growth during adaptation to different soil environments is unclear. In this study, we report that ABA has biphasic effects on primary root growth in rice (Oryza sativa) through an auxin biosynthesis-mediated process, causing suppression of root elongation and promotion of root swelling in response to soil compaction. We found that ABA treatment induced the expression of auxin biosynthesis genes and auxin accumulation in roots. Conversely, blocking auxin biosynthesis reduced ABA sensitivity in roots, showing longer and thinner primary roots with larger root meristem size and smaller root diameter. Further investigation revealed that the transcription factor basic region and leucine zipper 46 (OsbZIP46), involved in ABA signaling, can directly bind to the YUCCA8/rice ethylene-insensitive 7 (OsYUC8/REIN7) promoter to activate its expression, and genetic analysis revealed that OsYUC8/REIN7 is located downstream of OsbZIP46. Moreover, roots of mutants defective in ABA or auxin biosynthesis displayed the enhanced ability to penetrate compacted soil. Thus, our results disclose the mechanism in which ABA employs auxin as a downstream signal to modify root elongation and radial expansion, resulting in short and swollen roots impaired in their ability to penetrate compacted soil. These findings provide avenues for breeders to select crops resilient to soil compaction.
PMID: 36535001
Plant Physiol , IF:8.34 , 2022 Dec doi: 10.1093/plphys/kiac553
SUMO E3 ligase AtMMS21-dependent SUMOylation of AUXIN/INDOLE-3-ACETIC ACID 17 regulates auxin signaling.
Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Science, South China Normal University, Guangzhou 510631, PR China.
Changes in plant auxin levels can be perceived and converted into cellular responses by auxin signal transduction. AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins are auxin transcriptional inhibitors that play important roles in regulating auxin signal transduction. The stability of Aux/IAA proteins is important for transcription initiation and downstream auxin-related gene expression. Here, we report that the Aux/IAA protein IAA17 interacts with the small ubiquitin-related modifier (SUMO) E3 ligase METHYL METHANESULFONATE-SENSITIVE 21 (AtMMS21) in Arabidopsis (Arabidopsis thaliana). AtMMS21 regulated the SUMOylation of IAA17 at the K41 site. Notably, root length was suppressed in plants overexpressing IAA17, whereas the roots of K41-mutated IAA17 transgenic plants were not significantly different from wild-type roots. Biochemical data indicated that K41-mutated IAA17 or IAA17 in the AtMMS21 knock-out mutant was more likely to be degraded compared to non-mutated IAA17 in wild-type plants. In conclusion, our data revealed a role for SUMOylation in the maintenance of IAA17 protein stability, which contributes to improving our understanding of the mechanisms of auxin signaling.
PMID: 36464768
Plant Physiol , IF:8.34 , 2022 Dec doi: 10.1093/plphys/kiac535
Wheat AUXIN RESPONSE FACTOR 15 delays senescence through competitive interaction at the TaNAM1 locus.
Department of Plant Biology and Genome Center, University of California, Davis, California 95616.
PMID: 36454670
Plant Physiol , IF:8.34 , 2023 Jan , V191 (1) : P496-514 doi: 10.1093/plphys/kiac516
The B-box transcription factor IbBBX29 regulates leaf development and flavonoid biosynthesis in sweet potato.
Key Laboratory of Sweet Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.; Sanya Institute of China Agricultural University, Hainan 572025, China.; Provincial Key Laboratory of Agrobiology, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210000, China.; Institute of Grain and Oil Crops, Yantai Academy of Agricultural Sciences, Yantai 265500, China.; College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China.
Plant flavonoids are valuable natural antioxidants. Sweet potato (Ipomoea batatas) leaves are rich in flavonoids, regenerate rapidly, and can adapt to harsh environments, making them an ideal material for flavonoid biofortification. Here, we demonstrate that the B-box (BBX) family transcription factor IbBBX29 regulates the flavonoid contents and development of sweet potato leaves. IbBBX29 was highly expressed in sweet potato leaves and significantly induced by auxin (IAA). Overexpression of IbBBX29 contributed to a 21.37%-70.94% increase in leaf biomass, a 12.08%-21.85% increase in IAA levels, and a 31.33%-63.03% increase in flavonoid accumulation in sweet potato, whereas silencing this gene produced opposite effects. Heterologous expression of IbBBX29 in Arabidopsis (Arabidopsis thaliana) led to a dwarfed phenotype, along with enhanced IAA and flavonoid accumulation. RNA-seq analysis revealed that IbBBX29 modulates the expression of genes involved in the IAA signaling and flavonoid biosynthesis pathways. Chromatin immunoprecipitation-quantitative polymerase chain reaction and electrophoretic mobility shift assay indicated that IbBBX29 targets key genes of IAA signaling and flavonoid biosynthesis to activate their expression by binding to specific T/G-boxes in their promoters, especially those adjacent to the transcription start site. Moreover, IbBBX29 physically interacted with developmental and phenylpropanoid biosynthesis-related proteins, such as AGAMOUS-LIKE 21 protein IbAGL21 and MYB308-like protein IbMYB308L. Finally, overexpressing IbBBX29 also increased flavonoid contents in sweet potato storage roots. These findings indicate that IbBBX29 plays a pivotal role in regulating IAA-mediated leaf development and flavonoid biosynthesis in sweet potato and Arabidopsis, providing a candidate gene for flavonoid biofortification in plants.
PMID: 36377782
Plant Physiol , IF:8.34 , 2023 Jan , V191 (1) : P463-478 doi: 10.1093/plphys/kiac513
Transcription factors KNAT3 and KNAT4 are essential for integument and ovule formation in Arabidopsis.
The State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China.; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea 90183, Sweden.; Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China.; Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki, Japan.; Guangdong Laboratory of Lingnan Modern Agriculture, Guangzhou 510642, China.
Integuments form important protective cell layers surrounding the developing ovules in gymno- and angiosperms. Although several genes have been shown to influence the development of integuments, the transcriptional regulatory mechanism is still poorly understood. In this work, we report that the Class II KNOTTED1-LIKE HOMEOBOX (KNOX II) transcription factors KNOTTED1-LIKE HOMEBOX GENE 3 (KNAT3) and KNAT4 regulate integument development in Arabidopsis (Arabidopsis thaliana). KNAT3 and KNAT4 were co-expressed in inflorescences and especially in young developing ovules. The loss-of-function double mutant knat3 knat4 showed an infertility phenotype, in which both inner and outer integuments of the ovule are arrested at an early stage and form an amorphous structure as in the bell1 (bel1) mutant. The expression of chimeric KNAT3- and KNAT4-EAR motif repression domain (SRDX repressors) resulted in severe seed abortion. Protein-protein interaction assays demonstrated that KNAT3 and KNAT4 interact with each other and also with INNER NO OUTER (INO), a key transcription factor required for the outer integument formation. Transcriptome analysis showed that the expression of genes related with integument development is influenced in the knat3 knat4 mutant. The knat3 knat4 mutant also had a lower indole-3-acetic acid (IAA) content, and some auxin signaling pathway genes were downregulated. Moreover, transactivation analysis indicated that KNAT3/4 and INO activate the auxin signaling gene IAA INDUCIBLE 14 (IAA14). Taken together, our study identified KNAT3 and KNAT4 as key factors in integument development in Arabidopsis.
PMID: 36342216
Plant Physiol , IF:8.34 , 2023 Jan , V191 (1) : P772-788 doi: 10.1093/plphys/kiac511
HEAT-RESPONSIVE PROTEIN regulates heat stress via fine-tuning ethylene/auxin signaling pathways in cotton.
Institute of Crop Science, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.; Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan, Pakistan.; National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
Plants sense and respond to fluctuating temperature and light conditions during the circadian cycle; however, the molecular mechanism underlying plant adaptability during daytime warm conditions remains poorly understood. In this study, we reveal that the ectopic regulation of a HEAT RESPONSIVE PROTEIN (GhHRP) controls the adaptation and survival of cotton (Gossypium hirsutum) plants in response to warm conditions via modulating phytohormone signaling. Increased ambient temperature promptly enhanced the binding of the phytochrome interacting factor 4 (GhPIF4)/ethylene-insensitive 3 (GhEIN3) complex to the GhHRP promoter to increase its mRNA level. The ectopic expression of GhHRP promoted the temperature-dependent accumulation of GhPIF4 transcripts and hypocotyl elongation by triggering thermoresponsive growth-related genes. Notably, the upregulation of the GhHRP/GhPIF4 complex improved plant growth via modulating the abundance of Arabidopsis thaliana auxin biosynthetic gene YUCCA8 (AtYUC8)/1-aminocyclopropane-1-carboxylate synthase 8 (AtACS8) for fine-tuning the auxin/ethylene interplay, ultimately resulting in decreased ethylene biosynthesis. GhHRP thus protects chloroplasts from photo-oxidative bursts via repressing AtACS8 and AtACS7 and upregulating AtYUC8 and the heat shock transcription factors (HSFA2), heat shock proteins (HSP70 and HSP20). Strikingly, the Deltahrp disruption mutant exhibited compromised production of HSP/YUC8 that resulted in an opposite phenotype with the loss of the ability to respond to warm conditions. Our results show that GhHRP is a heat-responsive signaling component that assists plants in confronting the dark phase and modulates auxin signaling to rescue growth under temperature fluctuations.
PMID: 36342207
Plant Physiol , IF:8.34 , 2023 Jan , V191 (1) : P610-625 doi: 10.1093/plphys/kiac464
Transition to ripening in tomato requires hormone-controlled genetic reprogramming initiated in gel tissue.
Laboratoire de Recherche en Sciences Vegetales-Genomique et Biotechnologie des Fruits-UMR5546, Universite de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France.; Universite de Toulouse, INRAe/INP Toulouse, Genomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France.; Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610065, China.; Institute of Biosciences, Department of Botany, Universidade de Sao Paulo, Sao Paulo, 11461 Brazil.; Departamento de Alimentos e Nutricao Experimental, Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.; Metatoul-AgromiX platform, LRSV, Universite de Toulouse, CNRS, UPS, Toulouse INP, France.; MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, 31077, France.
Ripening is the last stage of the developmental program in fleshy fruits. During this phase, fruits become edible and acquire their unique sensory qualities and post-harvest potential. Although our knowledge of the mechanisms that regulate fruit ripening has improved considerably over the past decades, the processes that trigger the transition to ripening remain poorly deciphered. While transcriptomic profiling of tomato (Solanum lycopersicum L.) fruit ripening to date has mainly focused on the changes occurring in pericarp tissues between the Mature Green and Breaker stages, our study addresses the changes between the Early Mature Green and Late Mature Green stages in the gel and pericarp separately. The data showed that the shift from an inability to initiate ripening to the capacity to undergo full ripening requires extensive transcriptomic reprogramming that takes place first in the locular tissues before extending to the pericarp. Genome-wide transcriptomic profiling revealed the wide diversity of transcription factor (TF) families engaged in the global reprogramming of gene expression and identified those specifically regulated at the Mature Green stage in the gel but not in the pericarp, thereby providing potential targets toward deciphering the initial factors and events that trigger the transition to ripening. The study also uncovered an extensive reformed homeostasis for most plant hormones, highlighting the multihormonal control of ripening initiation. Our data unveil the antagonistic roles of ethylene and auxin during the onset of ripening and show that auxin treatment delays fruit ripening via impairing the expression of genes required for System-2 autocatalytic ethylene production that is essential for climacteric ripening. This study unveils the detailed features of the transcriptomic reprogramming associated with the transition to ripening of tomato fruit and shows that the first changes occur in the locular gel before extending to pericarp and that a reformed auxin homeostasis is essential for the ripening to proceed.
PMID: 36200876
Plant Physiol , IF:8.34 , 2023 Jan , V191 (1) : P335-351 doi: 10.1093/plphys/kiac462
Factor of DNA methylation 1 affects woodland strawberry plant stature and organ size via DNA methylation.
Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China.; Hubei Hongshan Laboratory, Wuhan 430070, China.; College of Horticulture, Anhui Agricultural University, Hefei 230036, China.; Department of Cell Biology and Molecular Genetics, University of Maryland, Mary land 20742, USA.
RNA-directed DNA methylation (RdDM) is an epigenetic process that directs silencing to specific genomic regions and loci. The biological functions of RdDM are not well studied in horticultural plants. Here, we isolated the ethyl methane-sulfonate-induced mutant reduced organ size (ros) producing small leaves, flowers, and fruits in woodland strawberry (Fragaria vesca) due to reduced cell numbers compared with that in the wild-type (WT). The candidate mutation causes a premature stop codon in FvH4_6g28780, which shares high similarity to Arabidopsis (Arabidopsis thaliana) Factor of DNA Methylation1 (FDM1) encoding an RdDM pathway component and was named FveFDM1. Consistently, the fvefdm1CR mutants generated by CRISPR/Cas9 also produced smaller organs. Overexpressing FveFDM1 in an Arabidopsis fdm1-1 fdm2-1 double mutant restored DNA methylation at the RdDM target loci. FveFDM1 acts in a protein complex with its homolog Involved in De Novo 2 (FveIDN2). Furthermore, whole-genome bisulfite sequencing revealed that DNA methylation, especially in the CHH context, was remarkably reduced throughout the genome in fvefdm1. Common and specific differentially expressed genes were identified in different tissues of fvefdm1 compared to in WT tissues. DNA methylation and expression levels of several gibberellic acid (GA) biosynthesis and cell cycle genes were validated. Moreover, the contents of GA and auxin were substantially reduced in the young leaves of fvefdm1 compared to in the WT. However, exogenous application of GA and auxin could not recover the organ size of fvefdm1. In addition, expression levels of FveFDM1, FveIDN2, Nuclear RNA Polymerase D1 (FveNRPD1), Domains Rearranged Methylase 2 (FveDRM2), and cell cycle genes were greatly induced by GA treatment. Overall, our work demonstrated the critical roles of FveFDM1 in plant growth and development via RdDM-mediated DNA methylation in horticultural crops.
PMID: 36200851
Plant Physiol , IF:8.34 , 2023 Jan , V191 (1) : P542-557 doi: 10.1093/plphys/kiac447
Abscisic acid modulates neighbor proximity-induced leaf hyponasty in Arabidopsis.
Faculty of Biology and Medicine, Centre for Integrative Genomics, University of Lausanne, Genopode Building, Lausanne CH-1015, Switzerland.; Plant Biochemistry, Department of Biology, ETH Zurich, Universitat-Str. 2, CH-8092 Zurich, Switzerland.; Department of Plant Sciences, Downing Street, Cambridge, University of Cambridge, CB2 3EA, UK.
Leaves of shade-avoiding plants such as Arabidopsis (Arabidopsis thaliana) change their growth pattern and position in response to low red to far-red ratios (LRFRs) encountered in dense plant communities. Under LRFR, transcription factors of the phytochrome-interacting factor (PIF) family are derepressed. PIFs induce auxin production, which is required for promoting leaf hyponasty, thereby favoring access to unfiltered sunlight. Abscisic acid (ABA) has also been implicated in the control of leaf hyponasty, with gene expression patterns suggesting that LRFR regulates the ABA response. Here, we show that LRFR leads to a rapid increase in ABA levels in leaves. Changes in ABA levels depend on PIFs, which regulate the expression of genes encoding isoforms of the enzyme catalyzing a rate-limiting step in ABA biosynthesis. Interestingly, ABA biosynthesis and signaling mutants have more erect leaves than wild-type Arabidopsis under white light but respond less to LRFR. Consistent with this, ABA application decreases leaf angle under white light; however, this response is inhibited under LRFR. Tissue-specific interference with ABA signaling indicates that an ABA response is required in different cell types for LRFR-induced hyponasty. Collectively, our data indicate that LRFR triggers rapid PIF-mediated ABA production. ABA plays a different role in controlling hyponasty under white light than under LRFR. Moreover, ABA exerts its activity in multiple cell types to control leaf position.
PMID: 36135791
Plant Physiol , IF:8.34 , 2023 Jan , V191 (1) : P265-279 doi: 10.1093/plphys/kiac407
Abscisic acid inhibits primary root growth by impairing ABI4-mediated cell cycle and auxin biosynthesis.
School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710129, China.; College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.; Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu 611130, China.
Cell cycle progression and the phytohormones auxin and abscisic acid (ABA) play key roles in primary root growth, but how ABA mediates the transcription of cell cycle-related genes and the mechanism of crosstalk between ABA and auxin requires further research. Here, we report that ABA inhibits primary root growth by regulating the ABA INSENSITIVE4 (ABI4)-CYCLIN-DEPENDENT KINASE B2;2 (CDKB2;2)/CYCLIN B1;1 (CYCB1;1) module-mediated cell cycle as well as auxin biosynthesis in Arabidopsis (Arabidopsis thaliana). ABA induced ABI4 transcription in the primary root tip, and the abi4 mutant showed an ABA-insensitive phenotype in primary root growth. Compared with the wild type (WT), the meristem size and cell number of the primary root in abi4 increased in response to ABA. Further, the transcription levels of several cell-cycle positive regulator genes, including CDKB2;2 and CYCB1;1, were upregulated in abi4 primary root tips. Subsequent chromatin immunoprecipitation (ChIP)-seq, ChIP-qPCR, and biochemical analysis revealed that ABI4 repressed the expression of CDKB2;2 and CYCB1;1 by physically interacting with their promoters. Genetic analysis demonstrated that overexpression of CDKB2;2 or CYCB1;1 fully rescued the shorter primary root phenotype of ABI4-overexpression lines, and consistently, abi4/cdkb2;2-cr or abi4/cycb1;1-cr double mutations largely rescued the ABA-insensitive phenotype of abi4 with regard to primary root growth. The expression levels of DR5promoter-GFP and PIN1promoter::PIN1-GFP in abi4 primary root tips were significantly higher than those in WT after ABA treatment, with these changes being consistent with changes in auxin concentration and expression patterns of auxin biosynthesis genes. Taken together, these findings indicated that ABA inhibits primary root growth through ABI4-mediated cell cycle and auxin-related regulatory pathways.
PMID: 36047837
Environ Pollut , IF:8.071 , 2023 Jan : P121140 doi: 10.1016/j.envpol.2023.121140
Enhanced detoxification via Cyt-P450 governs cross-tolerance to ALS-inhibiting herbicides in weed species of centaurea.
Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014, Cordoba, Spain.; Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014, Cordoba, Spain. Electronic address: z82vagaj@uco.es.; Biosciences Department, Polytechnic Institute of Beja, Beja, Portugal; VALORIZA-Research Centre for Endogenous Resource Valorization, Polytechnic Institute of Portalegre, Portalegre, Portugal.; Department of Agroforestry Sciences, Campus El Carmen, University of Huelva, 21007, Huelva, Spain.; Centro de Ciencias da Natureza, Campus Lagoa Do Sino, Universidade Federal de Sao Carlos, Buri, 18290-000, Brazil.; Plant Protection Department, Extremadura Scientific and Technological Research Center (CICYTEX), Ctra. de AV, Km 372, Badajoz, 06187, Guadajira, Spain.; Department D'Hortofructicultura, Botanica i Jardineria, Agrotecnio-CERCA Center, Universitat de Lleida, Lleida, Spain.
Centaurea is a genus of winter weeds with a similar life cycle and competitive traits, which occurs in small-grains production fields in the central-southern of the Iberian Peninsula. However, most of herbicides recommended for weed management in wheat show poor control of Centaurea species. This study summarizes the biology, herbicide tolerance to acetolactate synthase (ALS) inhibitors, and recommended chemical alternatives for the control of Centaurea species. Four species (C. cyanus L., C. diluta Aiton, C. melitensis L. and C. pullata L. subsp. baetica Talavera), taxonomically characterized, were found as the main important broadleaf weeds in small-grains production fields of the Iberian Peninsula. These species showed innate tolerance to tribenuron-methyl (TM), showing LD(50) values (mortality of 50% of a population) higher than the field dose of TM (20 g ai ha(-1)). The order of tolerance was C. diluta (LD(50) = 702 g ha(-1)) >> C. pullata (LD(50) = 180 g ha(-1)) >> C. cyanus (LD(50) = 65 g ha(-1)) > C. melitensis (LD(50) = 32 g ha(-1)). Centaurea cyanus and C. melitensis presented higher foliar retention (150-180 muL herbicide solution), absorption (14-28%) and subsequent translocation (7-12%) of TM with respect to the other two species. Centaurea spp. plants were able to metabolize (14)C-TM into non-toxic forms (hydroxylated OH-metsulfuron-methyl and conjugated-metsulfuron-methyl), with cytochrome P450 monooxygenases being responsible for herbicide detoxification. Centaurea cyanus and C. mellitensis metabolized up to 25% of TM, while C. diluta and C. pullata metabolized more than 50% of the herbicide. Centaurea species showed 80-100% survival when treated with of florasulam, imazamox and/or metsulfuron-methyl, i.e., these weeds present cross-tolerance to ALS inhibitors. In contrast, auxin mimics herbicides (2,4-D, clopyralid, dicamba, fluroxypir and MCPA) efficiently controlled the four Centaurea species. In addition, the mixture of ALS-inhibitors and auxin mimics also proved to be an interesting alternative for the control of Centaurea. These results show that plants of the genus Centaurea found in the winter cereal fields of the Iberian Peninsula have an innate tolerance to TM and cross-resistance to other ALS-inhibiting herbicides, governed by reduced absorption and translocation, but mainly by the metabolization of the herbicide via Cyt-P450.
PMID: 36706859
Sci Total Environ , IF:7.963 , 2023 Jan , V855 : P158888 doi: 10.1016/j.scitotenv.2022.158888
Regulation of rhizospheric microbial network to enhance plant growth and resist pollutants: Unignorable weak electric field.
MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China.; College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.; MOE Key Laboratory of Pollution Processes and Environmental Criteria, Tianjin Key Laboratory of Environmental Remediation and Pollution Control, College of Environmental Science and Engineering, Nankai University, No. 38 Tongyan Road, Jinnan District, Tianjin 300350, China. Electronic address: tianli1@nankai.edu.cn.
The union of Plant Growth-Promoting Bacteria (PGPB) and rhizosphere confers a series of functions beneficial to plant. However, the lack of an opearable in situ method limits the further understanding on the mechanism. In this study, a weak electric field was designed to regulate rhizospheric microflora in a constructed root-splitting reactor. Compared with the control, the aboveground and underground biomass of rice seedling increased by 17 % and 18 % (p < 0.05) respectively under the exist of weak electric field of 0.14 V/cm. The joint action of rhizosphere and PGPB displayed the detoxification ability in the condition of soluble petroleum hydrocarbons, where the height, stem diameter, biomass and root vigor of the plant was increased by 58 %, 32 %, 43 % and 48 % respectively than the control. The selective reproduction of endophytes and ectophytes (denitrifying, auxin-producing, hydrocarbon-degrading and electroactive bacteria) was observed under applied weak electric field, which enhanced the nitrogen utilization, cellular metabolic activity and resistance to toxic organics of plant. This was further confirmed by the up-regulated OTUs related to the hydrocarbon degradation function, tryptophan metabolism and metabolism of nicotinate and nicotinamide. Moreover, the weak electric field also enhanced the transfer ability of partial endophytes grown in the root to improve plant stress resistance. The results in this work inspired an exercisable method for in situ enrichment of PGPB in the rhizosphere to cope with food crisis and provided a new way to deal with sudden environmental events.
PMID: 36165908
Sci Total Environ , IF:7.963 , 2022 Dec , V851 (Pt 2) : P158287 doi: 10.1016/j.scitotenv.2022.158287
Perfluorooctanoic acid and perfluorooctane sulfonic acid inhibit plant growth through the modulation of phytohormone signalling pathways: Evidence from molecular and genetic analysis in Arabidopsis.
College of Horticulture, Shanxi Agricultural University, Taigu 030801, China.; College of Horticulture, Shanxi Agricultural University, Taigu 030801, China. Electronic address: xujin@sxau.edu.cn.
Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonic acid (PFOS) are the most representative perfluoroalkyl substances that accumulate in the food chain and are harmful to the environment. The uptake, translocation and physiological effects of PFOA and PFOS in plants have been reported in recent years; however, the regulatory mechanisms underlying PFOA- and PFOS-mediated plant growth and development remain largely unclear. Here, using Arabidopsis thaliana as the study material, we showed that both PFOA and PFOS inhibited plant growth; PFOS showed a stronger inhibitory effect on primary root (PR) growth, whereas PFOA exerted a stronger inhibitory effect on photosynthesis. Transcriptome analysis revealed that PFOA- and PFOS-modulated plant growth and development were correlated with the phytohormones auxin and abscisic acid (ABA). Further genetic analyses using mutants related to auxin biosynthesis, receptors and transport and mutants related to ABA biosynthesis and signalling transduction revealed that both PFOA and PFOS inhibited PR growth by modulating auxin biosynthesis and signalling pathways, and the ABA signalling pathway was also involved in PFOS-mediated PR growth inhibition. Collectively, these results shed new light on the molecular mechanisms of PFOA- and PFOS-mediated root system growth and their effects on phytohormone signalling pathways in plants.
PMID: 36030856
mBio , IF:7.867 , 2023 Jan : Pe0336322 doi: 10.1128/mbio.03363-22
Emergence of an Auxin Sensing Domain in Plant-Associated Bacteria.
Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain.; Department of Biotechnology and Environmental Protection, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain.; Department of Biochemistry and Molecular Biology B and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence Campus Mare Nostrum, Murcia, Spain.; Bioinformatics Research Center, Pavlov First Saint Petersburg Medical State University, St. Petersburg, Russia.; Molecular Biology Institute of Barcelona, CSIC, Barcelona, Spain.; The Center of Bio- and Chemoinformatics, I. M. Sechenov First Moscow State Medical University, Moscow, Russia.; Department of Microbiology, The Ohio State University, Columbus, Ohio, USA.
Bacteria have evolved a sophisticated array of signal transduction systems that allow them to adapt their physiology and metabolism to changing environmental conditions. Typically, these systems recognize signals through dedicated ligand binding domains (LBDs) to ultimately trigger a diversity of physiological responses. Nonetheless, an increasing number of reports reveal that signal transduction receptors also bind antagonists to inhibit responses mediated by agonists. The mechanisms by which antagonists block the downstream signaling cascade remain largely unknown. To advance our knowledge in this field, we used the LysR-type transcriptional regulator AdmX as a model. AdmX activates the expression of an antibiotic biosynthetic cluster in the rhizobacterium Serratia plymuthica. AdmX specifically recognizes the auxin phytohormone indole-3-acetic acid (IAA) and its biosynthetic intermediate indole-3-pyruvic acid (IPA) as signals. However, only IAA, but not IPA, was shown to regulate antibiotic production in S. plymuthica. Here, we report the high-resolution structures of the LBD of AdmX in complex with IAA and IPA. We found that IAA and IPA compete for binding to AdmX. Although IAA and IPA binding does not alter the oligomeric state of AdmX, IPA binding causes a higher degree of compactness in the protein structure. Molecular dynamics simulations revealed significant differences in the binding modes of IAA and IPA by AdmX, and the inspection of the three-dimensional structures evidenced differential agonist- and antagonist-mediated structural changes. Key residues for auxin binding were identified and an auxin recognition motif defined. Phylogenetic clustering supports the recent evolutionary emergence of this motif specifically in plant-associated enterobacteria. IMPORTANCE Although antagonists were found to bind different bacterial signal transduction receptors, we are still at the early stages of understanding the molecular details by which these molecules exert their inhibitory effects. Here, we provide insight into the structural changes resulting from the binding of an agonist and an antagonist to a sensor protein. Our data indicate that agonist and antagonist recognition is characterized by small conformational differences in the LBDs that can be efficiently transmitted to the output domain to modulate the final response. LBDs are subject to strong selective pressures and are rapidly evolving domains. An increasing number of reports support the idea that environmental factors drive the evolution of sensor domains. Given the recent evolutionary history of AdmX homologs, as well as their narrow phyletic distribution within plant-associated bacteria, our results are in accordance with a plant-mediated evolutionary process that resulted in the emergence of receptor proteins that specifically sense auxin phytohormones.
PMID: 36602305
Curr Opin Plant Biol , IF:7.834 , 2023 Jan , V73 : P102336 doi: 10.1016/j.pbi.2023.102336
Compounds from rhizosphere microbes that promote plant growth.
Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo. Edificio B3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacan, Mexico.; Facultad de Quimico Farmacobiologia, Universidad Michoacana de San Nicolas de Hidalgo, C. P. 58240, Morelia, Michoacan, Mexico.; Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo. Edificio B3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacan, Mexico. Electronic address: jbucio@umich.mx.
The rhizosphere is the soil-plant interface colonized by bacterial and fungal species that exert growth-promoting and adaptive benefits. The plant-bacteria relationships rely upon the perception of volatile organic compounds (VOCs), canonical phytohormones such as auxins and cytokinins, and the bacterial quorum sensing-related N-acyl-L-homoserine lactones and cyclodipeptides. On the other hand, plant-beneficial Trichoderma fungi emit highly active VOCs, including 6-pentyl-2H-pyran-2-one (6-PP), and beta-caryophyllene, which contribute to plant morphogenesis, but also into how these microbes spread over roots or live as endophytes. Here, we describe recent findings concerning how compounds from beneficial bacteria and fungi affect root architecture and advance into the signaling events that mediate microbial recognition.
PMID: 36716513
Food Chem , IF:7.514 , 2023 May , V408 : P135215 doi: 10.1016/j.foodchem.2022.135215
A multiomics integrative analysis of color de-synchronization with softening of 'Hass' avocado fruit: A first insight into a complex physiological disorder.
Escuela de Agronomia, Facultad de Ciencias Agronomicas y de los Alimentos, Pontificia Universidad Catolica de Valparaiso, Quillota, Chile.; KU Leuven, Facility for Systems Biology based Mass Spectrometry SYBIOMA, Leuven, Belgium; Biodiversity International, Biodiversity for Food and Agriculture, Leuven, Belgium.; Department of Analytical Chemistry, Faculty of Sciences, University of Granada, Granada, Spain.; Universidad Nacional Agraria La Molina, Instituto de Biotecnologia, Lima, Peru.; Centro de Estudios Postcosecha, Facultad de Ciencias Agronomicas, Universidad de Chile, Santiago, Chile.; Departamento de Fruticultura y Enologia, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Santiago, Chile; Departamento de Genetica Molecular y Microbiologia, Facultad de Ciencias Biologicas, Pontificia Universidad Catolica de Chile, Santiago, Chile; ANID-Millennium Science Initiative Program - Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile; Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile. Electronic address: claudio.meneses@uc.cl.; Escuela de Agronomia, Facultad de Ciencias Agronomicas y de los Alimentos, Pontificia Universidad Catolica de Valparaiso, Quillota, Chile; Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile. Electronic address: romina.pedreschi@pucv.cl.
Exocarp color de-synchronization with softening of 'Hass' avocado is a relevant recurrent problem for the avocado supply chain. This study aimed to unravel the mechanisms driving this de-synchronization integrating omics datasets from avocado exocarp of different storage conditions and color phenotypes. In addition, we propose potential biomarkers to predict color synchronized/de-synchronized fruit. Integration of transcriptomics, proteomics and metabolomics and network analysis revealed eight transcription factors associated with differentially regulated genes between regular air (RA) and controlled atmosphere (CA) and twelve transcription factors related to avocado fruit color de-synchronization control in ready-to-eat stage. CA was positively correlated to auxins, ethylene, cytokinins and brassinosteroids-related genes, while RA was characterized by enrichment of cell wall remodeling and abscisic acid content associated genes. At ready-to-eat higher contents of flavonoids, abscisic acid and brassinosteroids were associated with color-softening synchronized avocados. In contrast, de-synchronized fruit revealed increases of jasmonic acid, salicylic acid and auxin levels.
PMID: 36528992
Free Radic Biol Med , IF:7.376 , 2023 Jan , V196 : P93-107 doi: 10.1016/j.freeradbiomed.2023.01.015
Responses of individual and combined polystyrene and polymethyl methacrylate nanoplastics on hormonal content, fluorescence/photochemistry of chlorophylls and ROS scavenging capacity in Lemna minor under arsenic-induced oxidative stress.
Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, 42090, Konya, Turkey. Electronic address: cozfidan@erbakan.edu.tr.; Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey. Electronic address: eytugay@selcuk.edu.tr.; Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey. Electronic address: busra.arikan@selcuk.edu.tr.; Department of Biotechnology, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey. Electronic address: fatmanur.alp@selcuk.edu.tr.; Department of Agricultural Trade and Management, Faculty of Economy and Administrative Sciences, Yeditepe University, 34755, Istanbul, Turkey. Electronic address: metinturan@yeditepe.edu.tr.; Department of Physics, Faculty of Science, Selcuk University, Selcuklu, 42130, Konya, Turkey. Electronic address: hcavusoglu@selcuk.edu.tr.; Graduate School of Natural and Applied Sciences, Nanotechnology and Advanced Materials, Selcuk University, Selcuklu, 42130, Konya, Turkey. Electronic address: huseyinsakalak@gmail.com.
Nanoplastics alter the adverse impacts of hazardous contaminants such as heavy metals by changing their adsorption and accumulation. Few findings are available on the interaction between nanoplastic and heavy metals in plants. However, there is no report on the mechanisms for removing metal stress-mediated oxidative damage by the combination treatments of nanoplastics. To address this lack of information, polystyrene nanoplastic (PS, 100 mg L(-1)) and polymethyl methacrylate (PMMA, 100 mg L(-1)) were hydroponically applied to Lemna minor exposed to arsenate (As, 100 muM) for 7 days. PS or PMMA caused a reduction in the contents of N, P, K, Ca, Mg and Mn, but the improved contents were detected in the presence of PS or PMMA plus As stress. The hormone contents (auxin, gibberellic acid, cytokinin, salicylic acid and jasmonic acid) reduced by stress were re-arranged through PS or PMMA applications. Based on chlorophyll efficiency, fluorescence kinetics and performance of PSII, the impaired photosynthesis by As stress was improved via PS or PMMA applications. This alleviation did not continue under the combined form of PS and PMMA in As-applied plants. All analyzed antioxidant activity (superoxide dismutase (SOD), catalase (CAT), peroxidase (POX), ascorbate peroxidase (APX), glutathione reductase (GR), glutathione S-transferase (GST), glutathione peroxidase (GPX), monodehydroascorbate reductase (MDHAR) and dehydroascorbate reductase (DHAR)) decreased or unchanged under As, PS or PMMA. Due to the inactivation of the defense system, L. minor had high levels of hydrogen peroxide (H(2)O(2)) and thiobarbituric acid reactive substances (TBARS), showing lipid peroxidation. After As toxicity, induvial applications of PS or PMMA indicated the activated enzyme capacity (SOD, POX, GST and GPX) and upregulated AsA/DHA, GSH/GSSG and redox state of GSH, which facilitated the removal of radical accumulation. The efficiency of the antioxidant system in As + PS + PMMA-applied L. minor was not enough to remove damage induced by As stress; hereby, TBARS and H(2)O(2) contents were similar to the As-treated group. Our findings from alone or combined application of PS and PMMA provide new information to advance the tolerance mechanism against As exposure in L. minor.
PMID: 36657731
Plant Cell Environ , IF:7.228 , 2023 Jan doi: 10.1111/pce.14548
Low light stress promotes new tiller regeneration by changing source-sink relationship and activating expression of expansin genes in wheat.
Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 286 Huaizhong Road, Shijiazhuang, 050021, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Jilin Da'an Agro-ecosystem National Observation Research Station, Changchun Jingyuetan Remote Sensing Experiment Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China.
Low light stress seriously decreased wheat grain number through the formation of aborted spike during the reproductive period, and induced new tiller regeneration to offset the loss of grain number. However, the mechanism by which plants coordinate spike aborted growth and the regeneration of new tillers remains unknown. To better understand this coordinated process, morphological, physiological, and transcriptomic analyses were performed under low light stress at the young microspore stage. Our findings indicated that leaves exhausted most stored carbohydrate in one day of darkness. However, spike and uppermost internode (UI) were converted from sink to source, due to increased abscisic acid (ABA) content and decreased cytokinin content. During this process, genes encoding amylases, Sugars Will Eventually be Exported Transporters (SWEET) and sucrose transporters or sucrose carriers (SUT/SUC) were up-regulated in spike and UI, which degraded starch into soluble sugars and loaded them into phloem. Subsequently, soluble sugars were transported to tiller node (TN) where cytokinin and auxin content increased and ABA content decreased, followed by unloading into TN cells by up-regulated cell wall invertase (CWINV) genes and highly expressed H(+) /hexose symporter genes. Finally, expansin genes integrated the sugar pathway and hormone pathway, and regulate the formation of new tillers directly. This article is protected by copyright. All rights reserved.
PMID: 36695201
Plant Cell Environ , IF:7.228 , 2022 Dec doi: 10.1111/pce.14517
ZmBET5L1 inhibits primary root growth and decreases osmotic stress tolerance by mediating vesicle aggregation and tethering in maize.
National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.; State Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Shandong, Tai-An, China.; Key Laboratory of Plant Development and Environmental Adaption Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China.
Improving osmotic stress tolerance is critical to help crops to thrive and maintain high yields in adverse environments. Here, we characterized a core subunit of the transport protein particle (TRAPP) complex, ZmBET5L1, in maize using knowledge-driven data mining and genome editing. We found that ZmBET5L1 can interact with TRAPP I complex subunits and act as a tethering factor to mediate vesicle aggregation and targeting from the endoplasmic reticulum to the Golgi apparatus. ZmBET5L1 knock-out increased the primary root elongation rate under 20% polyethylene glycol-simulated osmotic stress and the survival rate under drought stress compared to wild-type seedlings. In addition, we found that ZmBET5L1 moderates PIN1 polar localization and auxin flow to maintain normal root growth. ZmBET5L1 knock-out optimized auxin flow to the lateral side of the root and promoted its growth to generate a robust root, which may be related to improved osmotic stress tolerance. Together, these findings demonstrate that ZmBET5L1 inhibits primary root growth and decreases osmotic stress tolerance by regulating vesicle transport and auxin distribution. This study has improved our understanding of the role of tethering factors in response to abiotic stresses and identified desirable variants for breeding osmotic stress tolerance in maize.
PMID: 36515184
Plant Cell Environ , IF:7.228 , 2022 Dec doi: 10.1111/pce.14508
Wheat genome architecture influences interactions with phytobeneficial microbial functional groups in the rhizosphere.
Univ Lyon, Universite Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France.; Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.
Wheat has undergone a complex evolutionary history, which led to allopolyploidization and the hexaploid bread wheat Triticum aestivum. However, the significance of wheat genomic architecture for beneficial plant-microbe interactions is poorly understood, especially from a functional standpoint. In this study, we tested the hypothesis that wheat genomic architecture was an overriding factor determining root recruitment of microorganisms with particular plant-beneficial traits. We chose five wheat species representing genomic profiles AA (Triticum urartu), BB SS (Aegilops speltoides), DD (Aegilops tauschii), AABB (Triticum dicoccon) and AABBDD (Triticum aestivum) and assessed by quantitative polymerase chain reaction their ability to interact with free-nitrogen fixers, 1-aminocyclopropane-1-carboxylate deaminase producers, 2,4-diacetylphloroglucinol producers and auxin producers via the phenylpyruvate decarboxylase pathway, in combination with Illumina MiSeq metabarcoding analysis of N fixers (and of the total bacterial community). We found that the abundance of the microbial functional groups could fluctuate according to wheat genomic profile, as did the total bacterial abundance. N fixer diversity and total bacterial diversity were also influenced significantly by wheat genomic profile. Often, rather similar results were obtained for genomes DD (Ae. tauschii) and AABBDD (T. aestivum), pointing for the first time that the D genome could be particularly important for wheat-bacteria interactions.
PMID: 36494920
Plant Cell Environ , IF:7.228 , 2023 Feb , V46 (2) : P498-517 doi: 10.1111/pce.14491
ABA-responsive AREB1/ABI3-1/ABI5 cascade regulates IAA oxidase gene SlDAO2 to inhibit hypocotyl elongation in tomato.
Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Beijing, People's Republic of China.; Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.
Hypocotyl elongation is dramatically influenced by environmental factors and phytohormones. Indole-3-acetic acid (IAA) plays a prominent role in hypocotyl elongation, whereas abscisic acid (ABA) is regarded as an inhibitor through repressing IAA synthesis and signalling. However, the regulatory role of ABA in local IAA deactivation remains largely uncharacterized. In this study, we confirmed the antagonistic interplay of ABA and IAA during the hypocotyl elongation of tomato (Solanum lycopersicum) seedlings. We identified an IAA oxidase enzyme DIOXYGENASE FOR AUXIN OXIDATION2 (SlDAO2), and its expression was induced by both external and internal ABA signals in tomato hypocotyls. Moreover, the overexpression of SlDAO2 led to a reduced sensitivity to IAA, and the knockout of SlDAO2 alleviated the inhibitory effect of ABA on hypocotyl elongation. Furthermore, an ABA-responsive regulatory SlAREB1/SlABI3-1/SlABI5 cascade was identified to act upstream of SlDAO2 and to precisely control its expression. SlAREB1 directly bound to the ABRE present in the SlDAO2 promoter to activate SlDAO2 expression, and SlABI3-1 enhanced while SlABI5 inhibited the activation ability of SlAREB1 by directly interacting with SlAREB1. Our findings revealed that ABA might induce local IAA oxidation and deactivation via SlDAO2 to modulate IAA homoeostasis and thereby repress hypocotyl elongation in tomato.
PMID: 36369997
Plant Cell Environ , IF:7.228 , 2023 Feb , V46 (2) : P567-591 doi: 10.1111/pce.14486
Low iron ameliorates the salinity-induced growth cessation of seminal roots in wheat seedlings.
School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.; School of Life Sciences, Zhengzhou University, Zhengzhou, China.
Wheat plants are ubiquitously simultaneously exposed to salinity and limited iron availability caused by soil saline-alkalisation. Through this study, we found that both low Fe and NaCl severely inhibited the growth of seminal roots in wheat seedlings; however, sufficient Fe caused greater growth cessation of seminal roots than low Fe under salt stress. Low Fe improved the root meristematic division activity, not altering the mature cell sizes compared with sufficient Fe under salt stress. Foliar Fe spray and split-root experiments showed that low Fe-alleviating the salinity-induced growth cessation of seminal roots was dependent on local low Fe signals in the roots. Ionomics combined with TEM/X-ray few differences in the root Na(+) uptake and vacuolar Na(+) sequestration between two Fe levels under salt stress. Phytohormone profiling and metabolomics revealed salinity-induced overaccumulation of ACC/ethylene and tryptophan/auxin in the roots under sufficient Fe than under low Fe. Differential gene expression, pharmacological inhibitor addition and the root growth performance of transgenic wheat plants revealed that the rootward auxin efflux and was responsible for the low Fe-mediated amelioration of the salinity-induced growth cessation of seminal roots. Our findings will provide novel insights into the modulation of crop root growth under salt stress.
PMID: 36358019
Plant Cell Environ , IF:7.228 , 2023 Jan , V46 (1) : P306-321 doi: 10.1111/pce.14460
Integrated transcriptomic and metabolomic profiles reveal adaptive responses of three poplar varieties against the bacterial pathogen Lonsdalea populi.
National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China.; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.; The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing, China.
Different poplar varieties vary in their tolerance to certain pathogens. However, knowledge about molecular regulation and critical responses of resistant poplars during pathogen infection remains scarce. To investigate adaptive responses to canker disease caused by the bacterium Lonsdalea populi, we screened three poplar varieties with contrasting tolerance, including Populus deltoides. 'Zhonglin 2025' (2025), Populus x Euramericana. '74/76' (107) and Populus tomentosa cv 'henan' (P. tomentosa). Transcriptomic analysis revealed significant changes in the expression levels of defence-related genes in different poplar varieties in response to infection, which reshaped the PTI and ETI processes. Intriguingly, photosynthesis-related genes were found to be highly expressed in the resistant variety, whereas the opposite was observed in the susceptible variety. Susceptible poplars maintained the activation of defence-related genes during early period of onset, which restricted the expression of photosynthesis-related and auxin signal-related genes. Furthermore, combined with metabolomic analysis, differences in the content of antibacterial substances and key differentially expressed genes in phenylpropane and flavonoid biosynthesis pathways were identified. Delayed induction of catechin in the susceptible variety and it's in vitro antibacterial activity were considered to be one of the important reasons for the differences in resistance to L. populi compared with the resistant variety, which is of practical interest for tree breeding. Moreover, the trade-off between growth and defence observed among the three poplar varieties during infection provides new insights into the multilevel regulatory circuits in tree-pathogen interactions.
PMID: 36217265
Plant Cell Environ , IF:7.228 , 2023 Jan , V46 (1) : P215-238 doi: 10.1111/pce.14451
Impacts of iron on phosphate starvation-induced root hair growth in Arabidopsis.
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China and University of Chinese Academy of Sceinces, Beijing, China.; Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China.
In Arabidopsis, phosphate starvation (-Pi)-induced responses of primary root and lateral root growth are documented to be correlated with ambient iron (Fe) status. However, whether and how Fe participates in -Pi-induced root hair growth (RHG) remains unclear. Here, responses of RHG to different Fe concentrations under Pi sufficiency/deficiency were verified. Generally, distinct dosage effects of Fe on RHG appeared at both Pi levels, due to the generation of reactive oxygen species. Following analyses using auxin mutants and the phr1 mutant revealed that auxin and the central regulator PHR1 are required for Fe-triggered RHG under -Pi. A further proteomic study indicated that processes of vesicle trafficking and auxin synthesis and transport were affected by Fe under -Pi, which were subsequently validated by using a vesicle trafficking inhibitor, brefeldin A, and an auxin reporter, R2D2. Moreover, vesicle trafficking-mediated recycling of PIN2, an auxin efflux transporter, was notably affected by Fe under -Pi. Correspondingly, root hairs of pin2 mutant displayed attenuated responses to Fe under -Pi. Together, we propose that Fe affects auxin signalling probably by modulating vesicle trafficking, chiefly the PIN2 recycling, which might work jointly with PHR1 on modulating -Pi-induced RHG.
PMID: 36174546
Chemosphere , IF:7.086 , 2023 Feb , V313 : P137571 doi: 10.1016/j.chemosphere.2022.137571
Toxicity effects of nanoplastics on soybean (Glycine max L.): Mechanisms and transcriptomic analysis.
Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.; Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China.; Engineering Research Center of Chinese Ministry of Education for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun 130118, China. Electronic address: hanxuerong@jlau.edu.cn.; Key Laboratory of Wetland Ecology and Environment, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China. Electronic address: yuhw@iga.ac.cn.
Microplastic (MP) pollution has become a major concern in recent years. In agricultural production, MPs can not only affect the growth of crops but also affect yield. Compared with micron-sized MPs, nanoplastics (NPs) may be more harmful to plants. However, the effects of NPs on plant growth and development have attracted relatively little attention. As such, research has currently plateaued at the level of morphology and physiology, and the molecular mechanisms are still unclear. In this study, soybeans (Glycine max L.) were treated with polystyrene nanoplastics (PS-NPs) to observe phenotypic changes and measure the effects of PS-NPs on diverse aspects of soybeans. Compared to the control group, the soybean stem and root lengths were inhibited by 11.78% and 12.58%, respectively. The reactive oxygen species content and the antioxidant enzyme activities changed significantly (p < 0.05). The accumulation of manganese (Mn) and magnesium (Mg) in the roots revealed that root transmembrane transport was affected by PS-NPs stress. The content of salicylic acid 2-O-beta-glucoside was inhibited whereas the accumulation of l-tryptophan, the precursor of auxin synthesis, was significantly increased (p < 0.05) in leaves. Transcriptomic analysis showed that PS-NPs could affect soybean DNA repair, membrane protein transport, and hormone synthesis and response. This study revealed the toxicity of NPs to soybeans and that NPs affected a variety of biological processes through transcriptome and hormone metabolome analysis, which provides a theoretical basis to further study the molecular mechanism of the effects on plants.
PMID: 36535503
J Integr Plant Biol , IF:7.061 , 2023 Jan doi: 10.1111/jipb.13460
ESCRT-III component OsSNF7.2 modulates leaf rolling by trafficking and endosomal degradation of auxin biosynthetic enzyme OsYUC8 in rice.
State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, 225009, China.; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
The endosomal sorting complex required for transport (ESCRT) is highly conserved in eukaryotic cells and plays an essential role in the biogenesis of multivesicular bodies and cargo degradation to the plant vacuole or lysosomes. Although ESCRT components affect a variety of plant growth and development processes, their impact on leaf development is rarely reported. Here, we found that OsSNF7.2, an ESCRT-III component, controls leaf rolling in rice (Oryza sativa). The Ossnf7.2 mutant rolled leaf 17 (rl17) has adaxially rolled leaves due to the decreased number and size of the bulliform cells. OsSNF7.2 is expressed ubiquitously in all tissues, and its protein is localized in the endosomal compartments. OsSNF7.2 homologs, including OsSNF7, OsSNF7.3, and OsSNF7.4, can physically interact with OsSNF7.2, but their single mutation did not result in leaf rolling. Other ESCRT complex subunits, namely OsVPS20, OsVPS24, and OsBRO1, also interact with OsSNF7.2. Further assays revealed that OsSNF7.2 interacts with OsYUC8 and aids its vacuolar degradation. Both Osyuc8 and rl17 Osyuc8 showed rolled leaves, indicating that OsYUC8 and OsSNF7.2 function in the same pathway, conferring leaf development. This study reveals a new biological function for the ESCRT-III components, and provides new insights into the molecular mechanisms underlying leaf rolling. This article is protected by copyright. All rights reserved.
PMID: 36702785
J Integr Plant Biol , IF:7.061 , 2022 Dec doi: 10.1111/jipb.13441
To curve for survival: Apical hook development.
Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology (SUSTech), Shenzhen, Guangdong, 518055, China.
Apical hook is a simple curved structure formed at the upper part of hypocotyls when dicot seeds germinate in darkness. The hook structure is transient but essential for seedlings' survival during soil emergence due to its efficient protection of the delicate shoot apex from mechanical injury. As a superb model system for studying plant differential growth, apical hook has fascinated botanists as early as the Darwin age, and significant advances have been achieved at both the morphological and molecular levels to understand how apical hook development is regulated. Here, we will mainly summarize the research progresses at these two regards. We will also briefly compare the growth dynamics between apical hook and hypocotyl gravitropic bending at early seed germination phase, with the aim to deduce certain consensus on their connections. Finally, we will outline the remaining questions and future research perspectives for apical hook development. This article is protected by copyright. All rights reserved.
PMID: 36562414
J Integr Plant Biol , IF:7.061 , 2022 Dec , V64 (12) : P2425-2437 doi: 10.1111/jipb.13387
High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis.
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Plant Synthetic Biology Center, FAFU-UCR Joint Center for Horticultural Biology and Metabolomics, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.; Basic Forestry and Proteomics Research Center, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China.
Callus induction, which results in fate transition in plant cells, is considered as the first and key step for plant regeneration. This process can be stimulated in different tissues by a callus-inducing medium (CIM), which contains a high concentration of phytohormone auxin. Although a few key regulators for callus induction have been identified, the multiple aspects of the regulatory mechanism driven by high levels of auxin still need further investigation. Here, we find that high auxin induces callus through a H3K36 histone methylation-dependent mechanism, which requires the methyltransferase SET DOMAIN GROUP 8 (SDG8). During callus induction, the increased auxin accumulates SDG8 expression through a TIR1/AFBs-based transcriptional regulation. SDG8 then deposits H3K36me3 modifications on the loci of callus-related genes, including a master regulator WOX5 and the cell proliferation-related genes, such as CYCB1.1. This epigenetic regulation in turn is required for the transcriptional activation of these genes during callus formation. These findings suggest that the massive transcriptional reprogramming for cell fate transition by auxin during callus formation requires epigenetic modifications including SDG8-mediated histone H3K36 methylation. Our results provide insight into the coordination between auxin signaling and epigenetic regulation during fundamental processes in plant development.
PMID: 36250442
J Integr Plant Biol , IF:7.061 , 2023 Jan , V65 (1) : P82-99 doi: 10.1111/jipb.13366
Transmembrane kinase 1-mediated auxin signal regulates membrane-associated clathrin in Arabidopsis roots.
Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.; College of Life Sciences, Shaoxing University, Shaoxing, 312000, China.
Clathrin-mediated endocytosis (CME) is the major endocytic pathway in eukaryotic cells that directly regulates abundance of plasma membrane proteins. Clathrin triskelia are composed of clathrin heavy chains (CHCs) and light chains (CLCs), and the phytohormone auxin differentially regulates membrane-associated CLCs and CHCs, modulating the endocytosis and therefore the distribution of auxin efflux transporter PIN-FORMED2 (PIN2). However, the molecular mechanisms by which auxin regulates clathrin are still poorly understood. Transmembrane kinase (TMKs) family proteins are considered to contribute to auxin signaling and plant development; it remains unclear whether they are involved in PIN transport by CME. We assessed TMKs involvement in the regulation of clathrin by auxin, using genetic, pharmacological, and cytological approaches including live-cell imaging and immunofluorescence. In tmk1 mutant seedlings, auxin failed to rapidly regulate abundance of both CHC and CLC and to inhibit PIN2 endocytosis, leading to an impaired asymmetric distribution of PIN2 and therefore auxin. Furthermore, TMK3 and TMK4 were shown not to be involved in regulation of clathrin by auxin. In summary, TMK1 is essential for auxin-regulated clathrin recruitment and CME. TMK1 therefore plays a critical role in the establishment of an asymmetric distribution of PIN2 and an auxin gradient during root gravitropism.
PMID: 36114789
J Integr Plant Biol , IF:7.061 , 2023 Jan , V65 (1) : P25-44 doi: 10.1111/jipb.13365
Cowpea NAC1/NAC2 transcription factors improve growth and tolerance to drought and heat in transgenic cowpea through combined activation of photosynthetic and antioxidant mechanisms.
Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India.; Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu, 501-1193,, Japan.
NAC (NAM/ATAF1/2/CUC2) transcription factors are central switches of growth and stress responses in plants. However, unpredictable interspecies conservation of function and regulatory targets makes the well-studied NAC orthologs inapt for pulse engineering. The knowledge of suitable NAC candidates in hardy pulses like cowpea (Vigna unguiculata (L.) Walp.) is still in infancy, hence warrants immediate biotechnological intervention. Here, we showed that overexpression of two native NAC genes (VuNAC1 and VuNAC2) promoted germinative, vegetative, and reproductive growth and conferred multiple abiotic stress tolerance in a commercial cowpea variety. The transgenic lines displayed increased leaf area, thicker stem, nodule-rich denser root system, early flowering, higher pod production ( approximately 3.2-fold and approximately 2.1-fold), and greater seed weight (10.3% and 6.0%). In contrast, transient suppression of VuNAC1/2 caused severe growth retardation and flower inhibition. The overexpressor lines showed remarkable tolerance to major yield-declining terminal stresses, such as drought, salinity, heat, and cold, and recovered growth and seed production by boosting photosynthetic activity, water use efficiency, membrane integrity, Na(+) /K(+) homeostasis, and antioxidant activity. The comparative transcriptome study indicated consolidated activation of genes involved in chloroplast development, photosynthetic complexes, cell division and expansion, cell wall biogenesis, nutrient uptake and metabolism, stress response, abscisic acid, and auxin signaling. Unlike their orthologs, VuNAC1/2 direct synergistic transcriptional tuning of stress and developmental signaling to avoid unwanted trade-offs. Their overexpression governs the favorable interplay of photosynthesis and reactive oxygen species regulation to improve stress recovery, nutritional sufficiency, biomass, and production. This unconventional balance of strong stress tolerance and agronomic quality is useful for translational crop research and molecular breeding of pulses.
PMID: 36107155
J Exp Bot , IF:6.992 , 2022 Dec doi: 10.1093/jxb/erac508
Fine-Tuned Nitric Oxide And Hormone Interface In Plant Root Development And Regeneration.
Dpto. de Botanica y Fisiologia Vegetal. Instituto de Investigacion en Agrobiotecnologia (CIALE). Facultad de Biologia. Universidad de Salamanca. C/ Rio Duero 12, 37185 Salamanca, Spain.; Universidad Politecnica de Madrid, Madrid, Spain.
Plant root growth and developmental capacities reside in a few stem cells of the root apical meristem (RAM). Maintenance of these stem cells requires regenerative divisions of the initial stem cell niche (SCN) cells, self-maintenance, and proliferative divisions of the daughter cells. This ensures sufficient cell diversity to guarantee the development of complex root tissues in the plant. Damage in the root during growth involves the formation of a new post-embryonic root, a process known as regeneration. Post-embryonic root development and organogenesis processes include primary root (PR) development and SCN maintenance, plant regeneration and the development of adventitious and lateral roots. These developmental processes require a fine-tuned balance between cell proliferation and maintenance. An important regulator during root development and regeneration is the gasotransmitter nitric oxide (NO). In this review we have sought to compile how NO regulates cell rate proliferation, cell differentiation, and quiescence of SCNs, usually through interaction with phytohormones, or other molecular mechanisms involved in cellular redox homeostasis. NO exerts a role on molecular components of the auxin (Aux) and cytokinin (CK) signaling pathways in PR that affects cell proliferation and maintenance of the RAM. During root regeneration, a peak of Aux and CKs triggers specific molecular programs. Moreover, NO participates in adventitious root formation through its interaction with players of the brassinosteroids (BRs) and CKs signaling cascade. Lately, NO has been implicated in root regeneration under hypoxia conditions by regulating stem cell specification through phytoglobins.
PMID: 36548145
J Exp Bot , IF:6.992 , 2023 Jan , V74 (1) : P364-376 doi: 10.1093/jxb/erac421
Metabolic link between auxin production and specialized metabolites in Sorghum bicolor.
Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL 32611, USA.; Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.; Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL 32608, USA.; Department of Microbiology & Cell Science, Gainesville, FL 32611, USA.; UF Genetics Institute, University of Florida, Gainesville, FL 32611, USA.; Florida Center for Renewable Chemicals and Fuels, University of Florida, Gainesville, FL 32611, USA.
Aldoximes are amino acid derivatives that serve as intermediates for numerous specialized metabolites including cyanogenic glycosides, glucosinolates, and auxins. Aldoxime formation is mainly catalyzed by cytochrome P450 monooxygenases of the 79 family (CYP79s) that can have broad or narrow substrate specificity. Except for SbCYP79A1, aldoxime biosynthetic enzymes in the cereal sorghum (Sorghum bicolor) have not been characterized. This study identified nine CYP79-encoding genes in the genome of sorghum. A phylogenetic analysis of CYP79 showed that SbCYP79A61 formed a subclade with maize ZmCYP79A61, previously characterized to be involved in aldoxime biosynthesis. Functional characterization of this sorghum enzyme using transient expression in Nicotiana benthamiana and stable overexpression in Arabidopsis thaliana revealed that SbCYP79A61 catalyzes the production of phenylacetaldoxime (PAOx) from phenylalanine but, unlike the maize enzyme, displays no detectable activity against tryptophan. Additionally, targeted metabolite analysis after stable isotope feeding assays revealed that PAOx can serve as a precursor of phenylacetic acid (PAA) in sorghum and identified benzyl cyanide as an intermediate of PAOx-derived PAA biosynthesis in both sorghum and maize. Taken together, our results demonstrate that SbCYP79A61 produces PAOx in sorghum and may serve in the biosynthesis of other nitrogen-containing phenylalanine-derived metabolites involved in mediating biotic and abiotic stresses.
PMID: 36300527
J Exp Bot , IF:6.992 , 2023 Jan , V74 (1) : P265-282 doi: 10.1093/jxb/erac416
GhROP6 GTPase modulates auxin accumulation in cotton fibers by regulating cell-specific GhPIN3a localization.
Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, PR China.; Academy of Agricultural Sciences, Southwest University, Chongqing, PR China.; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, PR China.
PIN-FORMED- (PIN) mediated polar auxin transport plays a predominant role in most auxin-triggered organogenesis in plants. Global control of PIN polarity at the plasma membrane contributes to the essential establishment of auxin maxima in most multicellular tissues. However, establishment of auxin maxima in single cells is poorly understood. Cotton fibers, derived from ovule epidermal cells by auxin-triggered cell protrusion, provide an ideal model to explore the underlying mechanism. Here, we report that cell-specific degradation of GhPIN3a, which guides the establishment of the auxin gradient in cotton ovule epidermal cells, is associated with the preferential expression of GhROP6 GTPase in fiber cells. In turn, GhROP6 reduces GhPIN3a abundance at the plasma membrane and facilitates intracellular proteolysis of GhPIN3a. Overexpression and activation of GhROP6 promote cell elongation, resulting in a substantial improvement in cotton fiber length.
PMID: 36255218
J Exp Bot , IF:6.992 , 2023 Jan , V74 (1) : P233-250 doi: 10.1093/jxb/erac406
RsCLE22a regulates taproot growth through an auxin signaling-related pathway in radish (Raphanus sativus L.).
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOAR, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.
CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are a class of small molecules involved in plant growth and development. Although radish (Raphanus sativus) is an important root vegetable crop worldwide, the functions of CLE peptides in its taproot formation remain elusive. Here, a total of 48 RsCLE genes were identified from the radish genome. RNA in situ hybridization showed that RsCLE22a gene was highly expressed in the vascular cambium. Overexpression of RsCLE22a inhibited root growth by impairing stem cell proliferation in Arabidopsis, and radish plants with exogenous supplementation of RsCLE22 peptide (CLE22p) showed a similar phenotype. The vascular cambial activity was increased in RsCLE22a-silenced plants. Transcriptome analysis revealed that CLE22p altered the expression of several genes involved in meristem development and hormone signal transduction in radish. Immunolocalization results showed that CLE22p increased auxin accumulation in vascular cambium. Yeast one-hybrid and dual-luciferase assays showed that the WUSCHEL-RELATED HOMEOBOX 4 (RsWOX4) binds to RsCLE22a promoter and activates its transcription. The expression level of RsWOX4 was related to vascular cambial activity and was regulated by auxin. Furthermore, a RsCLE22a-RsWOX4 module is proposed to regulate taproot vascular cambium activity through an auxin signaling-related pathway in radish. These findings provide novel insights into the regulation of root growth in a horticultural crop.
PMID: 36239471
Int J Biol Macromol , IF:6.953 , 2023 Jan , V230 : P123165 doi: 10.1016/j.ijbiomac.2023.123165
Gnawing pressure led to the expansion of JAZ genes in angiosperms.
Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences & Ministry of Water Resource, Yangling 712100, China; University of the Chinese Academy of Sciences, Beijing 100049, China.; Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China.; Tasly R&D Institute, Tasly Holding Group Co. Ltd, Tianjin 300410, China; Tasly R&D Institute, State Key Laboratory of Core Technology in Innovative Chinese Medicine, Tianjin 300410, China.; Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China. Electronic address: xpg_xpg@zstu.edu.cn.; Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Institute of Soil and Water Conservation, Chinese Academy of Sciences & Ministry of Water Resource, Yangling 712100, China; University of the Chinese Academy of Sciences, Beijing 100049, China. Electronic address: liangzs@zstu.edu.cn.
A long-standing problem in evolutionary biology is why some populations differentiate into many species while the majority do not. Angiosperms is an excellent group for investigating this problem because their diversity is unevenly distributed in space and phylogeny. Plant hormone participates in growth, development and defense. However, jasmonic acid (JA) was the only hormone response to bites. We first searched jasmonate ZIM-domain (JAZ), AUXIN/INDOLE ACETIC ACID (IAA / aux), PYR/PYL/RCAR (PYL), DELLA, and SUPPRESSOR OF MAX2 1-like (SMAX) in 272 plant species. We found the gene number change trends were consistent with origination rates and species numbers of angiosperms. So, 26 representative species were selected as an example for further analysis. The results showed JAZ had experienced two lineage-specific gene expansion events in angiosperms, which coincided with increases in mammalian body size and dental diversity. The proliferation of large herbivores as a results of mammalian prosperity after dinosaur extinction may be related to angiosperm evolution and bursting. The proliferation of large herbivores as the result of mammalian prosperity after the extinction of the dinosaurs was related to angiosperm evolution and bursting. Overall, our study uncovered a previously unknown co-evolution mechanism in terrestrial plants exposed to extreme environmental conditions.
PMID: 36623623
Int J Biol Macromol , IF:6.953 , 2022 Dec , V232 : P123081 doi: 10.1016/j.ijbiomac.2022.12.300
Genome wide analysis of BREVIS RADIX gene family from wheat (Triticum aestivum): A conserved gene family differentially regulated by hormones and abiotic stresses.
ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India; Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India.; ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, Kerala 695017, India.; Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201301, India.; ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi 110012, India. Electronic address: Monika.Dalal@icar.gov.in.
BREVIS RADIX is a plant specific gene family with unique protein-protein interaction domain. It regulates developmental processes viz. root elongation and tiller angle which are pertinent for crop improvement. In the present study, five BRX family genes were identified in wheat genome and clustered into five sub-groups. Phylogenetic and synteny analyses revealed evolutionary conservation among BRX proteins from monocot species. Expression analyses showed abundance of TaBRXL1 transcripts in vegetative and reproductive tissues except flag leaf. TaBRXL2, TaBRXL3 and TaBRXL4 showed differential, tissue specific and lower level expression as compared to TaBRXL1. TaBRXL5-A expressed exclusively in stamens. TaBRXL1 was upregulated under biotic stresses while TaBRXL2 expression was enhanced under abiotic stresses. TaBRXL2 and TaBRXL3 were upregulated by ABA and IAA in roots. In shoot, TaBRXL2 was upregulated by ABA while TaBRXL3 and TaBRXL4 were upregulated by IAA. Expression levels, tissue specificity and response time under different conditions suggest distinct as well as overlapping functions of TaBRX genes. This was also evident from global co-expression network of these genes. Further, TaBRX proteins exhibited homotypic and heterotypic interactions which corroborated with the role of BRX domain in protein-protein interaction. This study provides leads for functional characterization of TaBRX genes.
PMID: 36592856
Int J Biol Macromol , IF:6.953 , 2022 Dec , V229 : P791-802 doi: 10.1016/j.ijbiomac.2022.12.230
Genome-wide identification and characterization of PIN-FORMED (PIN) and PIN-LIKES (PILS) gene family reveals their role in adventitious root development in tea nodal cutting (Camellia Sinensis).
International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China.; Department of Biotechnology, PSG College of Arts & Science, Coimbatore 14, Tamilnadu, India.; International Institute of Tea Industry Innovation for "the Belt and Road", Nanjing Agricultural University, Nanjing 210095, Jiangsu, PR China. Electronic address: lxh@njau.edu.cn.
Auxin affects all aspects of plant growth and development, including morphogenesis and adaptive responses. Auxin transmembrane transport is promoted by PIN formation (PIN) and a structurally similar PIN-like (PILS) gene family, which jointly controls the directional transport of the auxin between plant cells, and the accumulation of intracellular auxin. At present, there is no study investigating the roles of CslPIN and CslPILS gene family in root development in the tea plant (Camellia sinensis). In this study, 8 CslPIN and 10 CslPILS genes were identified in the tea plant, and their evolutionary relationships, physical and chemical properties, conserved motifs, cis-acting elements, chromosome location, collinearity, and expression characteristics were analyzed. The mechanism of CslPIN and CslPILS in the formation of tea adventitious roots (ARs) was studied by the AR induction system. Through functional verification, the regulation of CslPIN3 gene on root growth and development of tea plant was studied by over-expression of CslPIN3 in Arabidopsis thaliana and in situ hybridization in Camellia sinensis. The results confirmed CslPIN3 was involved in the regulation of root growth and development as well as auxin accumulation. This study provides a better insight into the regulatory mechanism of CslPIN and CslPILS gene family on the formation of AR in tea plant.
PMID: 36572081
Int J Biol Macromol , IF:6.953 , 2023 Feb , V227 : P285-296 doi: 10.1016/j.ijbiomac.2022.12.175
Genome-wide evolutionary analysis of AUX/IAA gene family in wheat identifies a novel gene TaIAA15-1A regulating flowering time by interacting with ARF.
College of Agronomy, Liaocheng University, Liaocheng 252059, PR China. Electronic address: pssu2014@163.com.; College of Agronomy, Liaocheng University, Liaocheng 252059, PR China.; Lianyungang Academy of Agricultural Sciences, Lianyungang 222000, PR China.; Key Laboratory of Huang-Huai-Hai Smart Agricultural Technology of the Ministry of Agriculture and Rural Affairs, College of Information Science and Engineering, Shandong Agricultural University, Tai'an, Shandong 271018, PR China. Electronic address: xinsinian2006@163.com.; College of Agronomy, Liaocheng University, Liaocheng 252059, PR China. Electronic address: guoshangjing@lcu.edu.cn.
Flowering time is a critical agronomic trait that has strong effects on crop yields. Auxin signaling pathway plays an important role in various development processes, such as flowering, grain development. However, no Aux/IAA gene had been reported to have functions involving in wheat flowering time. Here, we systematically performed genome-wide identification, classification, domain distribution, exon-intron structure, chromosome locations and global expression pattern of Aux/IAA gene family in 14 plant genomes (including Triticum aestivum). A phylogenetic model was proposed to infer the Aux/IAA evolutionary history involving in a central exon-intron structure "2121" during evolution. Overexpression of TaIAA15-1A caused an early flowering time in Brachypodium. RNA-seq analysis showed that TaIAA15-1A overexpression alters various pathways including phytohormone signaling pathway, flowering-related pathway, and polyamine biosynthesis pathway. Screening of auxin response factor (ARF) genes identified BdARF16 that interacted with TaIAA15-1A. Exogenous polyamine (spermidine and spermine) treatments promoted early flowering and (putrescine and DCHA) delayed flowering time of WT plants. Our finding will provide insights on mechanisms of Aux/IAAs gene family and TaIAA15-1A, illustrating the potential during crop improvement programs.
PMID: 36549029
Development , IF:6.868 , 2022 Dec , V149 (24) doi: 10.1242/dev.200370
Surface-localized glycoproteins act through class C ARFs to fine-tune gametophore initiation in Physcomitrium patens.
Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec.2, Academia Rd., Nankang, Taipei 11529, Taiwan.; Department of Biological Sciences, Faculty of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan.; Graduate School of Life Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo 060-0810, Japan.; Division of Life Science, Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan.
Arabinogalactan proteins are functionally diverse cell wall structural glycoproteins that have been implicated in cell wall remodeling, although the mechanistic actions remain elusive. Here, we identify and characterize two AGP glycoproteins, SLEEPING BEAUTY (SB) and SB-like (SBL), that negatively regulate the gametophore bud initiation in Physcomitrium patens by dampening cell wall loosening/softening. Disruption of SB and SBL led to accelerated gametophore formation and altered cell wall compositions. The function of SB is glycosylation dependent and genetically connected with the class C auxin response factor (ARF) transcription factors PpARFC1B and PpARFC2. Transcriptomics profiling showed that SB upregulates PpARFC2, which in turn suppresses a range of cell wall-modifying genes that are required for cell wall loosening/softening. We further show that PpARFC2 binds directly to multiple AuxRE motifs on the cis-regulatory sequences of PECTIN METHYLESTERASE to suppress its expression. Hence, our results demonstrate a mechanism by which the SB modulates the strength of intracellular auxin signaling output, which is necessary to fine-tune the timing of gametophore initials formation.
PMID: 36520083
Development , IF:6.868 , 2022 Dec , V149 (23) doi: 10.1242/dev.199773
Position of meristems and the angles of the cell division plane regulate the uniqueness of lateral organ shape.
Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.; Department of Micro Engineering, Kyoto University, Kyoto 615-8540, Japan.; Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan.
Leaf meristem is a cell proliferative zone present in the lateral organ primordia. In this study, we examined how cell proliferative zones in primordia of planar floral organs and polar auxin transport inhibitor (PATI)-treated leaf organs differ from those of non-treated foliage leaves of Arabidopsis thaliana, with a focus on the accumulation pattern of ANGUSTIFOLIA3 (AN3) protein, a key element for leaf meristem positioning. We found that PATI-induced leaf shape changes were correlated with cell division angle but not with meristem positioning/size or AN3 localisation. In contrast, different shapes between sepals and petals compared with foliage leaves were associated with both altered meristem position, due to altered AN3 expression patterns, and different distributions of cell division angles. A numerical simulation showed that meristem position majorly affected the final shape but biased cell division angles had a minor effect. Taken together, these results suggest that the unique shapes of different lateral organs depend on the position of the meristem in the case of floral organs and cell division angles in the case of leaf organs with different auxin flow.
PMID: 36373561
Cells , IF:6.6 , 2023 Jan , V12 (2) doi: 10.3390/cells12020295
The Histone H3K27 Demethylase REF6 Is a Positive Regulator of Light-Initiated Seed Germination in Arabidopsis.
Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
Seed germination is the first step in initiating a new life cycle in seed plants. Light is a major environmental factor affecting seed germination. Phytochrome B (phyB) is the primary photoreceptor promoting germination during the initial phase of imbibition. Post-translational histone methylation occurring at both lysine and arginine residues plays a crucial role in transcriptional regulation in plants. However, the role of histone lysine demethylation in light-initiated seed germination is not yet reported. Here, we identified that Relative of Early Flowering 6 (REF6)/Jumonji Domain-containing Protein 12 (JMJ12), a histone H3 lysine 27 (H3K27) demethylase, acts as a positive regulator of light-initiated seed germination. The loss of function of REF6 in Arabidopsis inhibits phyB-dependent seed germination. Genome-wide RNA-sequencing analysis revealed that REF6 regulates about half of the light-responsive transcriptome in imbibed seeds, including genes related to multiple hormonal signaling pathways and cellular processes. Phenotypic analyses indicated that REF6 not only regulates seed germination through GA (gibberellin) and ABA (abscisic acid) processes but also depends on the auxin signaling pathway. Furthermore, REF6 directly binds to and decreases the histone H3K27me3 levels of auxin-signaling- and cell-wall-loosening-related genes, leading to the activated expression of these genes in imbibed seeds. Taken together, our study identifies REF6 as the first histone lysine demethylase required for light-initiated seed germination. Our work also reveals the important role of REF6-mediated histone H3K27 demethylation in transcriptional reprogramming in the light-initiated seed germination process.
PMID: 36672228
Plant J , IF:6.417 , 2023 Jan doi: 10.1111/tpj.16118
Role of reactive oxygen species in the modulation of auxin flux and root development in Arabidopsis thaliana.
Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, University of Freiburg, 79104, Freiburg, Germany.; Instituto de Bioingenieria, Universidad Miguel Hernandez, 03202, Elche, Spain.; Centre for BioSystems Analysis, BIOSS Centre for Biological Signalling Studies; University of Freiburg, 79104, Freiburg, Germany.; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China.; ScreenSYS GmbH, Engesserstr. 4, 79108, Freiburg, Germany.
Reactive oxygen species (ROS) play a dual role in plant biology, acting as important signal transduction molecules and as toxic byproducts of aerobic metabolism that accumulate in cells upon exposure to different stressors and lead to cell death. In plants, root architecture is regulated by the distribution and intercellular flow of the phytohormone auxin. In this study, we identified ROS as an important modulator of auxin distribution and response in the root. ROS production is necessary for root growth, proper tissue patterning, cell growth, and lateral root (LR) induction. Alterations in ROS balance led to altered auxin distribution and response in SOD and RHD2 loss-of-function mutants. Treatment of Arabidopsis seedlings with additional sources of ROS (hydrogen peroxide) or an ROS production inhibitor (diphenylene iodonium) induced phenocopies of the mutants studied. Simultaneous application of auxin and ROS increased LR primordia induction, and PIN-FORMED protein immunolocalization further demonstrated the existing link between auxin and ROS in orchestrating cell division and auxin flux during root development.
PMID: 36700340
Plant J , IF:6.417 , 2023 Jan doi: 10.1111/tpj.16109
Biosynthesis- and transport-mediated dynamic auxin distribution during seed development controls seed size in Arabidopsis.
Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
Auxin is indispensable to the fertilization-induced coordinated development of the embryo, endosperm, and seed coat. However, little attention has been given to the distribution pattern, maintenance mechanism, and function of auxin throughout the process of seed development. In the present study, we found that auxin response signals display a dynamic distribution pattern during Arabidopsis seed development. Shortly after fertilization, strong auxin response signals were observed at the funiculus, chalaza, and micropylar integument where the embryo attaches. Later, additional signals appeared at the middle layer of the inner integument (ii1') above the chalaza and the whole inner layer of the outer integument (oi1). These signals peaked when the seed was mature, then declined upon desiccation and disappeared in the dried seed. Auxin biosynthesis genes, including ASB1, TAA1, YUC1, YUC4, YUC8, and YUC9, contributed to the accumulation of auxin in the funiculus and seed coat. Auxin efflux carrier PIN3 and influx carrier AUX1 also contributed to the polar auxin distribution in the seed coat. PIN3 was expressed in the ii1 (innermost layer of the inner integument) and oi1 layers of the integument and showed polar localization. AUX1 was expressed in both layers of the outer integument and the endosperm and displayed a uniform localization. Further research demonstrated that the accumulation of auxin in the seed coat regulates seed size. Transgenic plants that specifically express the YUC8 gene in the oi2 or ii1 seed coat produced larger seeds. These results provide useful tools for cultivating high-yielding crops.
PMID: 36648165
Plant J , IF:6.417 , 2023 Jan doi: 10.1111/tpj.16103
CLE3 and its homologs share overlapping functions in the modulation of lateral root formation through CLV1 and BAM1 in Arabidopsis thaliana.
Graduate School of Science and Technology, Kumamoto University, Kumamoto, 860-8555, Japan.; Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan.; International Research Organization for Advanced Science and Technology (IROAST), Kumamoto University, Kumamoto, 860-8555, Japan.; International Research Center for Agriculture and Environmental Biology, Kumamoto University, Kumamoto, 860-8555, Japan.
Lateral roots are important for a wide range of processes, including uptake of water and nutrients. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) 1 ~ 7 peptide family and their cognate receptor CLV1 have been shown to negatively regulate lateral root formation under low-nitrate conditions. However, little is known about how CLE signaling regulates lateral root formation. A persistent obstacle in CLE peptide research is their functional redundancies, which makes functional analyses difficult. To address this problem, we generate the cle1 ~ 7 septuple mutant (cle1 ~ 7-cr1, cr stands for mutant allele generated with CRISPR/Cas9). cle1 ~ 7-cr1 exhibits longer lateral roots under normal conditions. Specifically, in cle1 ~ 7-cr1, the lateral root density is increased, and lateral root primordia initiation is found to be accelerated. Further analysis shows that cle3 single mutant exhibits slightly longer lateral roots. On the other hand, plants that overexpress CLE2 and CLE3 exhibit decreased lateral root lengths. To explore cognate receptor(s) of CLE2 and CLE3, we analyze lateral root lengths in clv1 barely any meristem 1(bam1) double mutant. Mutating both the CLV1 and BAM1 causes longer lateral roots, but not in each single mutant. In addition, genetic analysis reveals that CLV1 and BAM1 are epistatic to CLE2 and CLE3. Furthermore, gene expression analysis shows that the LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) genes, which promote lateral root formation, are upregulated in cle1 ~ 7-cr1 and clv1 bam1. We therefore propose that CLE2 and CLE3 peptides are perceived by CLV1 and BAM1 to mediate lateral root formation through LBDs regulation.
PMID: 36628476
Plant J , IF:6.417 , 2023 Jan doi: 10.1111/tpj.16095
The Arabidopsis D27-LIKE1 is a cis/cis/trans-beta-carotene isomerase that contributes to Strigolactone biosynthesis and negatively impacts ABA level.
The BioActives Lab, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia.; Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Jeddah, 23955, Saudi Arabia.; Department of Biology, Faculty of Applied Sciences, Umm Al-Qura University, 8XH2+XVP, Mecca, 24382, Saudi Arabia.; Agriculture and Agri-Food Canada, Kentville Research and Development Centre, 32 Main Street, Kentville, NS, B4N 1J5, Canada.; The Laboratory of Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Jeddah, 23955, Saudi Arabia.
The enzyme DWARF27 (D27) catalyzes the reversible isomerization of all-trans- into 9-cis-beta-carotene, initiating strigolactone (SL) biosynthesis. Genomes of higher plants encode two D27-homologs, D27-like1 and -like2, with unknown functions. Here, we investigated the enzymatic activity and biological function of the Arabidopsis D27-like1. In vitro enzymatic assays and expression in Synechocystis sp. PCC6803 revealed an unreported 13-cis/15-cis/9-cis- and a 9-cis/all-trans-beta-carotene isomerization. Although disruption of AtD27-like1 did not cause SL deficiency phenotypes, overexpression of AtD27-like1 in the d27 mutant restored the more-branching phenotype, indicating a contribution of AtD27-like1 to SL biosynthesis. Accordingly, generated d27 d27like1 double mutants showed a more pronounced branching phenotype compared to d27. The contribution of AtD27-like1 to SL biosynthesis is likely a result of its formation of 9-cis-beta-carotene that was present at higher levels in AtD27-like1 overexpressing lines. By contrast, AtD27-like1 expression correlated negatively with the content of 9-cis-violaxanthin, a precursor of ABA, in shoots. Consistently, ABA levels were higher in shoots and also in dry seeds of the d27like1 and d27 d27like1 mutants. Transgenic lines expressing GUS driven by the AtD27LIKE1 promoter and transcript analysis of hormone-treated Arabidopsis seedlings revealed that AtD27LIKE1 is expressed in different tissues and affects ABA and auxin. Taken together, our work reports a cis/cis-beta-carotene isomerase that affects the content of both cis-carotenoid-derived plant hormones, ABA and SLs.
PMID: 36602437
Plant J , IF:6.417 , 2023 Jan doi: 10.1111/tpj.16089
The full-length Auxin Response Factor 8 isoform ARF8.1 controls pollen cell wall formation and directly regulates TDF1, AMS and MS188 expression.
Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Sapienza Universita di Roma, 00185, Rome, Italy.; Dipartimento di Biologia e Biotecnologie 'Charles Darwin', Sapienza Universita di Roma, 00185, Rome, Italy.; Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, 13416-000, Piracicaba, Brazil.
Auxin Response Factor 8 plays a key role in late stamen development: its splice variants ARF8.4 and ARF8.2 control stamen elongation and anther dehiscence. Here, we characterized the role of ARF8 isoforms in pollen fertility. By phenotypic and ultrastructural analysis of arf8-7 mutant stamens, we found defects in pollen germination and viability caused by alterations in exine structure and pollen coat deposition. Furthermore, tapetum degeneration, a prerequisite for proper pollen wall formation, is delayed in arf8-7 anthers. In agreement, the genes encoding the transcription factors TDF1, AMS, MS188 and MS1, required for exine and pollen coat formation, and tapetum development, are downregulated in arf8-7 stamens. Consistently, the sporopollenin content is decreased, and the expression of sporopollenin synthesis/transport and pollen coat protein biosynthetic genes, regulated by AMS and MS188, is reduced. Inducible expression of the full-length isoform ARF8.1 in arf8-7 inflorescences complements the pollen (and tapetum) phenotype and restores the expression of the above transcription factors. Chromatin immunoprecipitation-quantitative polymerase chain reaction assay revealed that ARF8.1 directly targets the promoters of TDF1, AMS and MS188. In conclusion, the ARF8.1 isoform controls pollen and tapetum development acting directly on the expression of TDF1, AMS and MS188, which belong to the pollen/tapetum genetic pathway.
PMID: 36597651
Plant J , IF:6.417 , 2023 Jan doi: 10.1111/tpj.16093
Folate shapes plant root architecture by affecting auxin distribution.
Key Laboratory of Horticultural Plant Biology, MOE, and Key Laboratory of Horticultural Crop Biology and Genetic Improvement (Central Region), MOA, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.; College of Horticulture, Henan Agricultural University, Zhengzhou, Henan, 450002, China.; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.
Folate (vitamin B9) is important for plant root development, but the mechanism is largely unknown. Here we characterized a root defective mutant, folb2, in Arabidopsis, which has severe developmental defects in the primary root. The root apical meristem of the folb2 mutant is impaired, and adventitious roots are frequently found at the root-hypocotyl junction. Positional cloning revealed that a 61-bp deletion is present in the predicted junction region of the promoter and the 5' untranslated region of AtFolB2, a gene encoding a dihydroneopterin aldolase that functions in folate biosynthesis. This mutation leads to a significant reduction in the transcript level of AtFolB2. Liquid chromatography-mass spectrometry analysis showed that the contents of the selected folate compounds were decreased in folb2. Arabidopsis AtFolB2 knockdown lines phenocopy the folb2 mutant. On the other hand, the application of exogenous 5-formyltetrahydrofolic acid could rescue the root phenotype of folb2, indicating that the root phenotype is indeed related to the folate level. Further analysis revealed that folate could promote rootward auxin transport through auxin transporters and that folate may affect particular auxin/indole-3-acetic acid proteins and auxin response factors. Our findings provide new insights into the important role of folic acid in shaping root structure.
PMID: 36587293
Plant J , IF:6.417 , 2023 Jan , V113 (2) : P225-245 doi: 10.1111/tpj.16042
A genome-wide association study identifies novel players in Na and Fe homeostasis in Arabidopsis thaliana under alkaline-salinity stress.
Plant Physiology Laboratory, Bioscience Faculty, Universitat Autonoma de Barcelona, C/de la Vall Moronta s/n, E-08193, Bellaterra, Spain.; Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland.; Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
In nature, multiple stress factors occur simultaneously. The screening of natural diversity panels and subsequent Genome-Wide Association Studies (GWAS) is a powerful approach to identify genetic components of various stress responses. Here, the nutritional status variation of a set of 270 natural accessions of Arabidopsis thaliana grown on a natural saline-carbonated soil is evaluated. We report significant natural variation on leaf Na (LNa) and Fe (LFe) concentrations in the studied accessions. Allelic variation in the NINJA and YUC8 genes is associated with LNa diversity, and variation in the ALA3 is associated with LFe diversity. The allelic variation detected in these three genes leads to changes in their mRNA expression and correlates with plant differential growth performance when plants are exposed to alkaline salinity treatment under hydroponic conditions. We propose that YUC8 and NINJA expression patters regulate auxin and jasmonic signaling pathways affecting plant tolerance to alkaline salinity. Finally, we describe an impairment in growth and leaf Fe acquisition associated with differences in root expression of ALA3, encoding a phospholipid translocase active in plasma membrane and the trans Golgi network which directly interacts with proteins essential for the trafficking of PIN auxin transporters, reinforcing the role of phytohormonal processes in regulating ion homeostasis under alkaline salinity.
PMID: 36433704
Plant J , IF:6.417 , 2023 Jan , V113 (1) : P106-126 doi: 10.1111/tpj.16039
RAV1 mediates cytokinin signaling for regulating primary root growth in Arabidopsis.
Department of Biotechnology, St Xavier's College, 30, Mother Teresa Sarani, Kolkata, 700016, India.; Department of Mechanical Engineering, Indian Institute of Technology, Surjyamukhi Road, Amingaon, Guwahati, Assam, 781039, India.
Root growth dynamics is an outcome of complex hormonal crosstalk. The primary root meristem size, for example, is determined by antagonizing actions of cytokinin and auxin. Here we show that RAV1, a member of the AP2/ERF family of transcription factors, mediates cytokinin signaling in roots to regulate meristem size. The rav1 mutants have prominently longer primary roots, with a meristem that is significantly enlarged and contains higher cell numbers, compared with wild-type. The mutant phenotype could be restored on exogenous cytokinin application or by inhibiting auxin transport. At the transcript level, primary cytokinin-responsive genes like ARR1, ARR12 were significantly downregulated in the mutant root, indicating impaired cytokinin signaling. In concurrence, cytokinin induced regulation of SHY2, an Aux/IAA gene, and auxin efflux carrier PIN1 was hindered in rav1, leading to altered auxin transport and distribution. This effectively altered root meristem size in the mutant. Notably, CRF1, another member of the AP2/ERF family implicated in cytokinin signaling, is transcriptionally repressed by RAV1 to promote cytokinin response in roots. Further associating RAV1 with cytokinin signaling, our results demonstrate that cytokinin upregulates RAV1 expression through ARR1, during post-embryonic root development. Regulation of RAV1 expression is a part of secondary cytokinin response that eventually represses CRF1 to augment cytokinin signaling. To conclude, RAV1 functions in a branch pathway downstream to ARR1 that regulates CRF1 expression to enhance cytokinin action during primary root development in Arabidopsis.
PMID: 36423224
Plant J , IF:6.417 , 2023 Jan , V113 (1) : P92-105 doi: 10.1111/tpj.16036
CRISPR/Cas9 genome-editing applied to MdPGT1 in apple results in reduced foliar phloridzin without impacting plant growth.
Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy.; C3A Center Agriculture Food Environment, University of Trento, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy.; The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland, 1025, New Zealand.; Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Hans-Knoll-Strasse 8, Jena, 07745, Germany.; Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Palacky University, Slechtitelu 19, Olomouc, CZ-783 71, Czech Republic.
Phloridzin is the most abundant polyphenolic compound in apple (Malus x domestica Borkh.), which results from the action of a key phloretin-specific UDP-2'-O-glucosyltransferase (MdPGT1). Here, we simultaneously assessed the effects of targeting MdPGT1 by conventional transgenesis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing. To this end, we conducted transcriptomic and metabolic analyses of MdPGT1 RNA interference knockdown and genome-edited lines. Knockdown lines exhibited characteristic impairment of plant growth and leaf morphology, whereas genome-edited lines exhibited normal growth despite reduced foliar phloridzin. RNA-sequencing analysis identified a common core of regulated genes, involved in phenylpropanoid and flavonoid pathways. However, we identified genes and processes differentially modulated in stunted and genome-edited lines, including key transcription factors and genes involved in phytohormone signalling. Therefore, we conducted a phytohormone profiling to obtain insight into their role in the phenotypes observed. We found that salicylic and jasmonic acid were increased in dwarf lines, whereas auxin and ABA showed no correlation with the growth phenotype. Furthermore, bioactive brassinosteroids were commonly up-regulated, whereas gibberellin GA(4) was distinctively altered, showing a sharp decrease in RNA interference knockdown lines. Expression analysis by reverse transcriptase-quantitative polymerase chain reaction expression analysis further confirmed transcriptional regulation of key factors involved in brassinosteroid and gibberellin interaction. These findings suggest that a differential modulation of phytohormones may be involved in the contrasting effects on growth following phloridzin reduction. The present study also illustrates how CRISPR/Cas9 genome editing can be applied to dissect the contribution of genes involved in phloridzin biosynthesis in apple.
PMID: 36401738
Plant J , IF:6.417 , 2022 Dec , V112 (6) : P1462-1472 doi: 10.1111/tpj.16027
Arabidopsis cyclin-dependent kinase C2 interacts with HDA15 and is involved in far-red light-mediated hypocotyl cell elongation.
Institute of Plant Biology, National Taiwan University, Taipei, 10617, Taiwan.
Histone deacetylases (HDAs) regulate many aspects of plant development and responses to environmental changes. Previous studies have demonstrated that the Arabidopsis histone deacetylase HDA15 is a positive regulator in far-red (FR) light-mediated inhibition of hypocotyl elongation. Furthermore, HDA15 can be phosphorylated and its enzymatic activity is negatively regulated by phosphorylation. However, the kinases that can phosphorylate HDA15 are still unknown. Cyclin-dependent kinases (CDKs) are a large family of serine/threonine protein kinases and have been identified as major regulators of the cell cycle and transcription. In this study, we show that the cyclin-dependent kinase CDKC2 interacts with HDA15 both in vitro and in vivo. In vitro kinase assays show that CDKC2 phosphorylates HDA15. Genetic evidence suggests that HDA15 acts downstream of CDKC2 in hypocotyl elongation under FR light. Furthermore, HDA15 and CDKC2 function synergistically in the regulation of FR-mediated cell elongation. The expression of cell wall organization- and auxin signaling-related genes under FR light is increased in hda15 and cdkc2/hda15 mutants. Taken together, our study indicates that CDKC2 can phosphorylate HDA15 and plays an important role in FR light-regulated hypocotyl elongation.
PMID: 36367383
Plant J , IF:6.417 , 2023 Jan , V113 (1) : P7-22 doi: 10.1111/tpj.16024
Endogenous auxin maintains embryonic cell identity and promotes somatic embryo development in Arabidopsis.
Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, The Netherlands.; Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
Somatic embryogenesis (SE), or embryo development from in vitro cultured vegetative explants, can be induced in Arabidopsis by the synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) or by overexpression of specific transcription factors, such as AT-HOOK MOTIF NUCLEAR LOCALIZED 15 (AHL15). Here, we explored the role of endogenous auxin [indole-3-acetic acid (IAA)] during 2,4-D and AHL15-induced SE. Using the pWOX2:NLS-YFP reporter, we identified three distinct developmental stages for 2,4-D and AHL15-induced SE in Arabidopsis, with these being (i) acquisition of embryo identity; (ii) formation of pro-embryos; and (iii) somatic embryo patterning and development. The acquisition of embryo identity coincided with enhanced expression of the indole-3-pyruvic acid auxin biosynthesis YUCCA genes, resulting in an enhanced pDR5:GFP-reported auxin response in the embryo-forming tissues. Chemical inhibition of the indole-3-pyruvic acid pathway did not affect the acquisition of embryo identity, but significantly reduced or completely inhibited the formation of pro-embryos. Co-application of IAA with auxin biosynthesis inhibitors in the AHL15-induced SE system rescued differentiated somatic embryo formation, confirming that increased IAA levels are important during the last two stages of SE. Our analyses also showed that polar auxin transport, with AUXIN/LIKE-AUX influx and PIN-FORMED1 efflux carriers as important drivers, is required for the transition of embryonic cells to proembryos and, later, for correct cell fate specification and differentiation. Taken together, our results indicate that endogenous IAA biosynthesis and its polar transport are not required for the acquisition of embryo identity, but rather to maintain embryonic cell identity and for the formation of multicellular proembryos and their development into histodifferentiated embryos.
PMID: 36345646
Plant J , IF:6.417 , 2022 Dec , V112 (5) : P1127-1140 doi: 10.1111/tpj.15993
Auxin triggers pectin modification during rootlet emergence in white lupin.
IPSiM, Univ Montpellier, CNRS, INRAE, Supagro, 34060, Montpellier, France.; Umea Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83, Umea, Sweden.; UMR INRAE 1158 BioEcoAgro, BIOPI Biologie des Plantes et Innovation, SFR Condorcet FR CNRS 3417, Universite de Picardie, 80039, Amiens, France.
Emergence of secondary roots through parental tissue is a highly controlled developmental process. Although the model plant Arabidopsis has been useful to uncover the predominant role of auxin in this process, its simple root structure is not representative of how emergence takes place in most plants, which display more complex root anatomy. White lupin is a legume crop producing structures called cluster roots, where closely spaced rootlets emerge synchronously. Rootlet primordia push their way through several cortical cell layers while maintaining the parent root integrity, reflecting more generally the lateral root emergence process in most multilayered species. In this study, we showed that lupin rootlet emergence is associated with an upregulation of cell wall pectin modifying and degrading genes under the active control of auxin. Among them, we identified LaPG3, a polygalacturonase gene typically expressed in cells surrounding the rootlet primordium and we showed that its downregulation delays emergence. Immunolabeling of pectin epitopes and their quantification uncovered a gradual pectin demethylesterification in the emergence zone, which was further enhanced by auxin treatment, revealing a direct hormonal control of cell wall properties. We also report rhamnogalacturonan-I modifications affecting cortical cells that undergo separation as a consequence of primordium outgrowth. In conclusion, we describe a model of how external tissues in front of rootlet primordia display cell wall modifications to allow for the passage of newly formed rootlets.
PMID: 36178138
Commun Biol , IF:6.268 , 2022 Dec , V5 (1) : P1410 doi: 10.1038/s42003-022-04313-9
Significance of NatB-mediated N-terminal acetylation of auxin biosynthetic enzymes in maintaining auxin homeostasis in Arabidopsis thaliana.
MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.; Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China.; Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.; Basic Forestry and Proteomics Research Center, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China. leiwu@lzu.edu.cn.; Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China. leiwu@lzu.edu.cn.; MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China. gqguo@lzu.edu.cn.; Gansu Province Key Laboratory of Gene Editing for Breeding, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China. gqguo@lzu.edu.cn.
The auxin IAA (Indole-3-acetic acid) plays key roles in regulating plant growth and development, which depends on an intricate homeostasis that is determined by the balance between its biosynthesis, metabolism and transport. YUC flavin monooxygenases catalyze the rate-limiting step of auxin biosynthesis via IPyA (indole pyruvic acid) and are critical targets in regulating auxin homeostasis. Despite of numerous reports on the transcriptional regulation of YUC genes, little is known about those at the post-translational protein level. Here, we show that loss of function of CKRC3/TCU2, the auxiliary subunit (Naa25) of Arabidopsis NatB, and/or of its catalytic subunit (Naa20), NBC, led to auxin-deficiency in plants. Experimental evidences show that CKRC3/TCU2 can interact with NBC to form a NatB complex, catalyzing the N-terminal acetylation (NTA) of YUC proteins for their intracellular stability to maintain normal auxin homeostasis in plants. Hence, our findings provide significantly new insight into the link between protein NTA and auxin biosynthesis in plants.
PMID: 36550195
Int J Mol Sci , IF:5.923 , 2023 Jan , V24 (2) doi: 10.3390/ijms24021603
Genome-Wide Identification, Expression Analysis, and Potential Roles under Abiotic Stress of the YUCCA Gene Family in Mungbean (Vigna radiata L.).
Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China.; College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.
YUCCA, belonging to the class B flavin-dependent monooxygenases, catalyzes the rate-limiting step for endogenous auxin synthesis and is implicated in plant-growth regulation and stress response. Systematic analysis of the YUCCA gene family and its stress response benefits the dissection of regulation mechanisms and breeding applications. In this study, 12 YUCCA genes were identified from the mungbean (Vigna radiata L.) genome and were named based on their similarity to AtYUCCAs. Phylogenetic analysis revealed that the 12 VrYUCCAs could be divided into 4 subfamilies. The evidence from enzymatic assays in vitro and transgenetic Arabidopsis in vivo indicated that all the isolated VrYUCCAs had biological activity in response to IAA synthesis. Expression pattern analysis showed that functional redundancy and divergence existed in the VrYUCCA gene family. Four VrYUCCAs were expressed in most tissues, and five VrYUCCAs were specifically highly expressed in the floral organs. The response toward five stresses, namely, auxin (indole-3-acetic acid, IAA), salinity, drought, high temperatures, and cold, was also investigated here. Five VrYUCCAs responded to IAA in the root, while only VrYUCCA8a was induced in the leaf. VrYUCCA2a, VrYUCCA6a, VrYUCCA8a, VrYUCCA8b, and VrYUCCA10 seemed to dominate under abiotic stresses, due to their sensitivity to the other four treatments. However, the response modes of the VrYUCCAs varied, indicating that they may regulate different stresses in distinct ways to finely adjust IAA content. The comprehensive analysis of the VrYUCCAs in this study lays a solid foundation for further investigation of VrYUCCA genes' mechanisms and applications in breeding.
PMID: 36675117
Int J Mol Sci , IF:5.923 , 2023 Jan , V24 (2) doi: 10.3390/ijms24021540
Low-Speed Clinorotation of Brachypodium distachyon and Arabidopsis thaliana Seedlings Triggers Root Tip Curvatures That Are Reminiscent of Gravitropism.
Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706, USA.; Kate Baldwin LLC, Analytical Design, Cross Plains, WI 53528, USA.
Clinostats are instruments that continuously rotate biological specimens along an axis, thereby averaging their orientation relative to gravity over time. Our previous experiments indicated that low-speed clinorotation may itself trigger directional root tip curvature. In this project, we have investigated the root curvature response to low-speed clinorotation using Arabidopsis thaliana and Brachypodium distachyon seedlings as models. We show that low-speed clinorotation triggers root tip curvature in which direction is dictated by gravitropism during the first half-turn of clinorotation. We also show that the angle of root tip curvature is modulated by the speed of clinorotation. Arabidopsis mutations affecting gravity susception (pgm) or gravity signal transduction (arg1, toc132) are shown to affect the root tip curvature response to low-speed clinorotation. Furthermore, low-speed vertical clinorotation triggers relocalization of the PIN3 auxin efflux facilitator to the lateral membrane of Arabidopsis root cap statocytes, and creates a lateral gradient of auxin across the root tip. Together, these observations support a role for gravitropism in modulating root curvature responses to clinorotation. Interestingly, distinct Brachypodium distachyon accessions display different abilities to develop root tip curvature responses to low-speed vertical clinorotation, suggesting the possibility of using genome-wide association studies to further investigate this process.
PMID: 36675054
Int J Mol Sci , IF:5.923 , 2023 Jan , V24 (2) doi: 10.3390/ijms24021182
Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize.
National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.; The Shennong Laboratory, Zhengzhou 450002, China.
Increasing grain yield is required to meet the rapidly expanding demands for food, feed, and fuel. Inflorescence meristems are central to plant growth and development. However, the question concerning whether inflorescence development can be regulated to improve grain yield remains unclear. Here, we describe a naturally occurring single recessive mutation called fea5 that can increase grain yield in maize. Using bulk segregant analysis sequencing (BSA-seq), the candidate region was initially mapped to a large region on chromosome 4 (4.68 Mb-11.26 Mb). Transcriptome sequencing (RNA-seq) revealed a total of 1246 differentially expressed genes (DEGs), of which 835 were up-regulated and 411 were down-regulated. Further analysis revealed the enrichment of DEGs in phytohormone signal transduction. Consistently, phytohormone profiling indicated that auxin (IAA), jasmonic acid (JA), ethylene (ETH), and cytokinin (CK) levels increased significantly, whereas the gibberellin (GA) level decreased significantly in fea5. By integrating BSA-seq with RNA-seq, we identified Zm00001d048841 as the most likely candidate gene. Our results provide valuable insight into this new germplasm resource and the molecular mechanism underlying fasciated ears that produce a higher kernel row number in maize.
PMID: 36674701
Int J Mol Sci , IF:5.923 , 2023 Jan , V24 (1) doi: 10.3390/ijms24010843
Regulation of PIN-FORMED Protein Degradation.
Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing 400715, China.; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing 400715, China.
Auxin action largely depends on the establishment of auxin concentration gradient within plant organs, where PIN-formed (PIN) auxin transporter-mediated directional auxin movement plays an important role. Accumulating studies have revealed the need of polar plasma membrane (PM) localization of PIN proteins as well as regulation of PIN polarity in response to developmental cues and environmental stimuli, amongst which a typical example is regulation of PIN phosphorylation by AGCVIII protein kinases and type A regulatory subunits of PP2A phosphatases. Recent findings, however, highlight the importance of PIN degradation in reestablishing auxin gradient. Although the underlying mechanism is poorly understood, these findings provide a novel aspect to broaden the current knowledge on regulation of polar auxin transport. In this review, we summarize the current understanding on controlling PIN degradation by endosome-mediated vacuolar targeting, autophagy, ubiquitin modification and the related E3 ubiquitin ligases, cytoskeletons, plant hormones, environmental stimuli, and other regulators, and discuss the possible mechanisms according to recent studies.
PMID: 36614276
Int J Mol Sci , IF:5.923 , 2023 Jan , V24 (1) doi: 10.3390/ijms24010756
Identification and Functional Validation of Auxin-Responsive Tabzip Genes from Wheat Leaves in Arabidopsis.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China.; State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University, Xianyang 712100, China.
Leaves are an essential and unique organ of plants, and many studies have proved that auxin has significant impacts on the architecture of leaves, thus the manipulation of the three-dimensional structure of a leaf could provide potential strategies for crop yields. In this study, 32 basic leucine zipper transcription factors (bZIP TFs) which responded to 50 muM of indole-acetic acid (IAA) were identified in wheat leaves by transcriptome analysis. Phylogenetic analysis indicated that the 32 auxin-responsive TabZIPs were classified into eight groups with possible different functions. Phenotypic analysis demonstrated that knocking out the homologous gene of the most down-regulated auxin-responsive TabZIP6D_20 in Arabidopsis (AtHY5) decreased its sensitivity to 1 and 50 muM IAA, while the TabZIP6D_20/hy5 complementary lines recovered its sensitivity to auxin as a wild type (Wassilewskija), suggesting that the down-regulated TabZIP6D_20 was a negative factor in the auxin-signaling pathway. These results demonstrated that the auxin-responsive TabZIP genes might have various and vital functions in the architecture of a wheat leaf under auxin response.
PMID: 36614202
Int J Mol Sci , IF:5.923 , 2023 Jan , V24 (1) doi: 10.3390/ijms24010740
Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.; Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150080, China.; Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.
Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.
PMID: 36614182
Int J Mol Sci , IF:5.923 , 2022 Dec , V24 (1) doi: 10.3390/ijms24010624
Genome-Wide Analysis of the AAAP Gene Family in Populus and Functional Analysis of PsAAAP21 in Root Growth and Amino Acid Transport.
State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
The adventitious root (AR) is the basis for successful propagation by plant cuttings and tissue culture and is essential for maintaining the positive traits of a variety. Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolisms and have few studies on root growth and amino acid transport. In this study, with a systematic bioinformatics analysis of the Populus AAAP family, 83 PtrAAAPs were identified from Populus trichocarpa and grouped into 8 subfamilies. Subsequently, chromosomal distribution, genetic structure, cis-elements analysis, and expression pattern analysis of the AAAP family were performed and the potential gene AAAP21 regulating root development was screened by combining the results of RNA-Seq and QTL mapping. PsAAAP21 was proven as promoting root development by enhancing AR formation. Differentially expressed genes (DEGs) from RNA-seq results of overexpressing lines were enriched to multiple amino acid-related pathways, and the amino acid treatment to transgenic lines indicated that PsAAAP21 regulated amino acid transport, including tyrosine, methionine, and arginine. Analysis of the AAAP gene family provided a theoretical basis for uncovering the functions of AAAP genes. The identification of PsAAAP21 on root promotion and amino acid transport in Populus will help with breeding new woody plant species with strong rooting ability.
PMID: 36614067
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (24) doi: 10.3390/ijms232416146
Comparative Analysis of Physiological, Hormonal and Transcriptomic Responses Reveal Mechanisms of Saline-Alkali Tolerance in Autotetraploid Rice (Oryza sativa L.).
Faculty of Agronomy, Jilin Agricultural University, Changchun 130118, China.
Saline-alkali soil has posed challenges to the growth of agricultural crops, while polyploidy often show greater adaptability in diverse and extreme environments including saline-alkali stress, but its defense mechanisms in rice remain elusive. Herein, we explored the mechanisms of enhanced saline-alkali tolerance of autotetraploid rice 93-11T relative to diploid rice 93-11D, based on physiological, hormonal and transcriptomic profilings. Physiologically, the enhanced saline-alkali tolerance in 93-11T was manifested in higher soluble sugar accumulation and stronger superoxide dismutase (SOD) and peroxidase (POD) activities in leaves during 24 h after saline-alkali shock. Furthermore, various hormone levels in leaves of 93-11T altered greatly, such as the negative correlation between salicylic acid (SA) and the other four hormones changed to positive correlation due to polyploidy. Global transcriptome profiling revealed that the upregulated differentially expressed genes (DEGs) in leaves and roots of 93-11T were more abundant than that in 93-11D, and there were more DEGs in roots than in leaves under saline-alkali stress. Genes related to phytohormone signal transduction of auxin (AUX) and SA in roots, lignin biosynthesis in leaves or roots, and wax biosynthesis in leaves were obviously upregulated in 93-11T compared with 93-11D under saline-alkali condition. Collectively, 93-11T subjected to saline-alkali stress possibly possesses higher osmotic regulation ability due to cuticular wax synthesis, stronger negative regulation of reactive oxygen species (ROS) production by increasing the SA levels and maintaining relative lower levels of IAA, and higher antioxidant capacity by increasing activities of SOD and POD, as well as lignin biosynthesis. Our research provides new insights for exploring the mechanisms of saline-alkali tolerance in polyploid rice and discovering new gene targets for rice genetic improvement.
PMID: 36555786
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (24) doi: 10.3390/ijms232416112
Identification of Transcriptional Networks Involved in De Novo Organ Formation in Tomato Hypocotyl Explants.
Instituto de Bioingenieria, Universidad Miguel Hernandez, 03202 Elche, Spain.
Some of the hormone crosstalk and transcription factors (TFs) involved in wound-induced organ regeneration have been extensively studied in the model plant Arabidopsis thaliana. In previous work, we established Solanum lycopersicum "Micro-Tom" explants without the addition of exogenous hormones as a model to investigate wound-induced de novo organ formation. The current working model indicates that cell reprogramming and founder cell activation requires spatial and temporal regulation of auxin-to-cytokinin (CK) gradients in the apical and basal regions of the hypocotyl combined with extensive metabolic reprogramming of some cells in the apical region. In this work, we extended our transcriptomic analysis to identify some of the gene regulatory networks involved in wound-induced organ regeneration in tomato. Our results highlight a functional conservation of key TF modules whose function is conserved during de novo organ formation in plants, which will serve as a valuable resource for future studies.
PMID: 36555756
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (24) doi: 10.3390/ijms232415950
Induction of Somatic Embryogenesis in Plants: Different Players and Focus on WUSCHEL and WUS-RELATED HOMEOBOX (WOX) Transcription Factors.
Department of Agriculture Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy.
In plants, other cells can express totipotency in addition to the zygote, thus resulting in embryo differentiation; this appears evident in apomictic and epiphyllous plants. According to Haberlandt's theory, all plant cells can regenerate a complete plant if the nucleus and the membrane system are intact. In fact, under in vitro conditions, ectopic embryos and adventitious shoots can develop from many organs of the mature plant body. We are beginning to understand how determination processes are regulated and how cell specialization occurs. However, we still need to unravel the mechanisms whereby a cell interprets its position, decides its fate, and communicates it to others. The induction of somatic embryogenesis might be based on a plant growth regulator signal (auxin) to determine an appropriate cellular environment and other factors, including stress and ectopic expression of embryo or meristem identity transcription factors (TFs). Still, we are far from having a complete view of the regulatory genes, their target genes, and their action hierarchy. As in animals, epigenetic reprogramming also plays an essential role in re-establishing the competence of differentiated cells to undergo somatic embryogenesis. Herein, we describe the functions of WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors in regulating the differentiation-dedifferentiation cell process and in the developmental phase of in vitro regenerated adventitious structures.
PMID: 36555594
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (24) doi: 10.3390/ijms232415918
Genome-Wide Identification of Wheat KNOX Gene Family and Functional Characterization of TaKNOX14-D in Plants.
College of Agronomy, Northwest A&F University, Xianyang 712100, China.
The KNOX genes play important roles in maintaining SAM and regulating the development of plant leaves. However, the TaKNOX genes in wheat are still not well understood, especially their role in abiotic stress. In this study, a total of 36 KNOX genes were identified, and we demonstrated the function of the TaKNOX14-D gene under mechanical injury and cold stress. Thirty-six TaKNOX genes were divided into two groups, and thirty-four TaKNOX genes were predicted to be located in the nucleus by Cell-PLoc. These genes contained five tandem duplications. Fifteen collinear gene pairs were exhibited in wheat and rice, one collinear gene pair was exhibited in wheat and Arabidopsis. The phylogenetic tree and motif analysis suggested that the TaKNOX gene appeared before C3 and C4 diverged. Gene structure showed that the numbers of exons and introns in TaKNOX gene are different. Wheat TaKNOX genes showed different expression patterns during the wheat growth phase, with seven TaKNOX genes being highly expressed in the whole growth period. These seven genes were also highly expressed in most tissues, and also responded to most abiotic stress. Eleven TaKNOX genes were up-regulated in the tillering node during the leaf regeneration period after mechanical damage. When treating the wheat with different hormones, the expression patterns of TaKNOX were changed, and results showed that ABA promoted TaKNOX expression and seven TaKNOX genes were up-regulated under cytokinin and auxin treatment. Overexpression of the TaKNOX14-D gene in Arabidopsis could increase the leaf size, plant height and seed size. This gene overexpression in Arabidopsis also increased the compensatory growth capacity after mechanical damage. Overexpression lines also showed high resistance to cold stress. This study provides a better understanding of the TaKNOX genes.
PMID: 36555558
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (24) doi: 10.3390/ijms232415729
Genome-Wide Identification and Expression Analysis of the Aux/IAA Gene Family of the Drumstick Tree (Moringa oleifera Lam.) Reveals Regulatory Effects on Shoot Regeneration.
College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural University, Guangzhou 510642, China.; Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou 510642, China.
Auxin plays a critical role in organogenesis in plants. The classical auxin signaling pathway holds that auxin initiates downstream signal transduction by degrading Aux/IAA transcription repressors that interact with ARF transcription factors. In this study, 23 MoIAA genes were identified in the drumstick tree genome. All MoIAA genes were located within five subfamilies based on phylogenetic evolution analysis; the gene characteristics and promoter cis-elements were also analyzed. The protein interaction network between the MoIAAs with MoARFs was complex. The MoIAA gene family responded positively to NAA treatment, exhibiting different patterns and degrees, notably for MoIAA1, MoIAA7 and MoIAA13. The three genes expressed and functioned in the nucleus; only the intact encoding protein of MoIAA13 exhibited transcriptional activation activity. The shoot regeneration capacity in the 35S::MoIAA13-OE transgenic line was considerably lower than in the wild type. These results establish a foundation for further research on MoIAA gene function and provide useful information for improved tissue culture efficiency and molecular breeding of M. oleifera.
PMID: 36555370
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (24) doi: 10.3390/ijms232415718
Transcriptional Regulation of zma-MIR528a by Action of Nitrate and Auxin in Maize.
Departamento de Bioquimica, Facultad de Quimica, Universidad Nacional Autonoma de Mexico, Ciudad de Mexcio 04510, Mexico.; Department of Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden.; Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, Av. Universidad 2001, Cuernavaca 62210, Mexico.; Instituto de Ecologia, Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 04510, Mexico.
In recent years, miR528, a monocot-specific miRNA, has been assigned multifaceted roles during development and stress response in several plant species. However, the transcription regulation and the molecular mechanisms controlling MIR528 expression in maize are still poorly explored. Here we analyzed the zma-MIR528a promoter region and found conserved transcription factor binding sites related to diverse signaling pathways, including the nitrate (TGA1/4) and auxin (AuxRE) response networks. Accumulation of both pre-miR528a and mature miR528 was up-regulated by exogenous nitrate and auxin treatments during imbibition, germination, and maize seedling establishment. Functional promoter analyses demonstrated that TGA1/4 and AuxRE sites are required for transcriptional induction by both stimuli. Overall, our findings of the nitrogen- and auxin-induced zma-MIR528a expression through cis-regulatory elements in its promoter contribute to the knowledge of miR528 regulome.
PMID: 36555358
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (24) doi: 10.3390/ijms232415600
Auxin Biosynthesis Genes in Allotetraploid Oilseed Rape Are Essential for Plant Development and Response to Drought Stress.
Oil Crops Research Institute of Chinese Academy of Agricultural Sciences/Key Laboratory for Biological Sciences and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China.
Crucial studies have verified that IAA is mainly generated via the two-step pathway in Arabidopsis, in which tryptophan aminotransferase (TAA) and YUCCA (YUC) are the two crucial enzymes. However, the role of the TAA (or TAR) and YUC genes in allotetraploid oilseed rape underlying auxin biosynthesis and development regulation remains elusive. In the present study, all putative TAR and YUC genes were identified in B. napus genome. Most TAR and YUC genes were tissue that were specifically expressed. Most YUC and TAR proteins contained trans-membrane regions and were confirmed to be endoplasmic reticulum localizations. Enzymatic activity revealed that YUC and TAR protein members were involved in the conversion of IPA to IAA and Trp to IPA, respectively. Transgenic plants overexpressing BnaYUC6a in both Arabidopsis and B. napus displayed high auxin production and reduced plant branch angle, together with increased drought resistance. Moreover, mutation in auxin biosynthesis BnaTARs genes by CRISPR/Cas9 caused development defects. All these results suggest the convergent role of BnaYUC and BnaTAR genes in auxin biosynthesis. Different homoeologs of BnaYUC and BnaTAR may be divergent according to sequence and expression variation. Auxin biosynthesis genes in allotetraploid oilseed rape play a pivotal role in coordinating plant development processes and stress resistance.
PMID: 36555242
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (23) doi: 10.3390/ijms232315436
Arabidopsis Cys2/His2 Zinc Finger Transcription Factor ZAT18 Modulates the Plant Growth-Defense Tradeoff.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.
Plant defense responses under unfavorable conditions are often associated with reduced growth. However, the mechanisms underlying the growth-defense tradeoff remain to be fully elucidated, especially at the transcriptional level. Here, we revealed a Cys2/His2-type zinc finger transcription factor, namely, ZAT18, which played dual roles in plant immunity and growth by oppositely regulating the signaling of defense- and growth-related hormones. ZAT18 was first identified as a salicylic acid (SA)-inducible gene and was required for plant responses to SA in this study. In addition, we observed that ZAT18 enhanced the plant immunity with growth penalties that may have been achieved by activating SA signaling and repressing auxin signaling. Further transcriptome analysis of the zat18 mutant showed that the biological pathways of defense-related hormones, including SA, ethylene and abscisic acid, were repressed and that the biological pathways of auxin and cytokinin, which are growth-related hormones, were activated by abolishing the function of ZAT18. The ZAT18-mediated regulation of hormone signaling was further confirmed using qRT-PCR. Our results explored a mechanism by which plants handle defense and growth at the transcriptional level under stress conditions.
PMID: 36499767
Int J Mol Sci , IF:5.923 , 2022 Dec , V23 (23) doi: 10.3390/ijms232315246
Transcriptome Analysis Reveals the Molecular Regularity Mechanism Underlying Stem Bulblet Formation in Oriental Lily 'Siberia'; Functional Characterization of the LoLOB18 Gene.
Institute of Biotechnology, Fujian Academy of Agricultural Sciences, Fuzhou 350003, China.; College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
The formation of underground stem bulblets in lilies is a complex biological process which is key in their micropropagation. Generally, it involves a stem-to-bulblet transition; however, the underlying mechanism remains elusive. It is important to understand the regulatory mechanism of bulblet formation for the reproductive efficiency of Lilium. In this study, we investigated the regulatory mechanism of underground stem bulblet formation under different conditions regarding the gravity point angle of the stem, i.e., vertical (control), horizontal, and slanting. The horizontal and slanting group displayed better formation of bulblets in terms of quality and quantity compared with the control group. A transcriptome analysis revealed that sucrose and starch were key energy sources for bulblet formation, auxin and cytokinin likely promoted bulblet formation, and gibberellin inhibited bulblet formation. Based on transcriptome analysis, we identified the LoLOB18 gene, a homolog to AtLOB18, which has been proven to be related to embryogenic development. We established the stem bud growth tissue culture system of Lilium and silenced the LoLOb18 gene using the VIGS system. The results showed that the bulblet induction was reduced with down-regulation of LoLOb18, indicating the involvement of LoLOb18 in stem bulblet formation in lilies. Our research lays a solid foundation for further molecular studies on stem bulblet formation of lilies.
PMID: 36499579
J Fungi (Basel) , IF:5.816 , 2023 Jan , V9 (1) doi: 10.3390/jof9010090
Epichloe Endophytes Shape the Foliar Endophytic Fungal Microbiome and Alter the Auxin and Salicylic Acid Phytohormone Levels in Two Meadow Fescue Cultivars.
Department of Biology, University of Turku, 20014 Turku, Finland.; Biodiversity Unit, University of Turku, 20014 Turku, Finland.; Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojova 263, 16502 Prague, Czech Republic.
Plants harbor a large diversity of endophytic microbes. Meadow fescue (Festuca pratensis) is a cool-season grass known for its symbiotic relationship with the systemic and vertically-via seeds-transmitted fungal endophyte Epichloe uncinata, yet its effects on plant hormones and the microbial community is largely unexplored. Here, we sequenced the endophytic bacterial and fungal communities in the leaves and roots, analyzing phytohormone concentrations and plant performance parameters in Epichloe-symbiotic (E+) and Epichloe-free (E-) individuals of two meadow fescue cultivars. The endophytic microbial community differed between leaf and root tissues independent of Epichloe symbiosis, while the fungal community was different in the leaves of Epichloe-symbiotic and Epichloe-free plants in both cultivars. At the same time, Epichloe symbiosis decreased salicylic acid and increased auxin concentrations in leaves. Epichloe-symbiotic plants showed higher biomass and higher seed mass at the end of the season. Our results demonstrate that Epichloe symbiosis alters the leaf fungal microbiota, which coincides with changes in phytohormone concentrations, indicating that Epichloe endophytes affect both plant immune responses and other fungal endophytes. Whether the effect of Epichloe endophytes on other fungal endophytes is connected to changes in phytohormone concentrations remains to be elucidated.
PMID: 36675911
J Fungi (Basel) , IF:5.816 , 2022 Dec , V9 (1) doi: 10.3390/jof9010024
Reprogramming of Fundamental miRNA and Gene Expression during the Barley-Piriformospora indica Interaction.
School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin 300401, China.; Tianjin Key Laboratory of Structure and Performance for Functional Molecules, College of Chemistry, Tianjin Normal University, Tianjin 300387, China.
The interactions between plants and microorganisms, which are widely present in the microbial-dominated rhizosphere, have been studied. This association is highly beneficial to the organisms involved, as plants benefit soil microorganisms by providing them with metabolites, while microorganisms promote plant growth and development by promoting nutrient uptake and/or protecting the plant from biotic and abiotic stresses. Piriformospora indica, an endophytic fungus of Sebacinales, colonizes the roots of a wide range of host plants and establishes various benefits for the plants. In this work, an interaction between barley and the P. indica was established to elucidate microRNA (miRNA)-based regulatory changes in miRNA profiles and gene expression that occurred during the symbiosis. Growth promotion and vigorous root development were confirmed in barley colonized by P. indica. The genome-wide expression profile analysis of miRNAs in barley root showed that 7,798,928, 6,418,039 and 7,136,192 clean reads were obtained from the libraries of mock, 3 dai and 7 dai roots, respectively. Sequencing of the barley genome yielded in 81 novel miRNA and 450 differently expressed genes (DEGs). Additionally, 11, 24, 6 differentially expressed microRNAs (DEMs) in barley were found in the three comparison groups, including 3 dai vs. mock, 7 dai vs. mock and 7 dai vs. 3 dai, respectively. The predicted target genes of these miRNAs are mainly involved in transcription, cell division, auxin signal perception and transduction, photosynthesis and hormone stimulus. Transcriptome analysis of P. indica identified 667 and 594 differentially expressed genes (DEG) at 3 dai and 7 dai. Annotation and GO (Gene Ontology) analysis indicated that the DEGs with the greatest changes were concentrated in oxidoreductase activity, ion transmembrane transporter activity. It implies that reprogramming of fundamental miRNA and gene expression occurs both in barley and P. indica. Analysis of global changes in miRNA profiles of barley colonized with P. indica revealed that several putative endogenous barley miRNAs expressed upon colonization belonging to known micro RNA families involved in growth and developmental regulation.
PMID: 36675845
Front Plant Sci , IF:5.753 , 2022 , V13 : P1054821 doi: 10.3389/fpls.2022.1054821
Morphophysiological and transcriptome analysis reveal that reprogramming of metabolism, phytohormones and root development pathways governs the potassium (K(+)) deficiency response in two contrasting chickpea cultivars.
National Institute of Plant Genome Research, New Delhi, India.
Potassium (K(+)) is an essential macronutrient for plant growth and development. K(+) deficiency hampers important plant processes, such as enzyme activation, protein synthesis, photosynthesis and stomata movement. Molecular mechanism of K(+) deficiency tolerance has been partly understood in model plants Arabidopsis, but its knowledge in legume crop chickpea is missing. Here, morphophysiological analysis revealed that among five high yielding desi chickpea cultivars, PUSA362 shows stunted plant growth, reduced primary root growth and low K(+) content under K(+) deficiency. In contrast, PUSA372 had negligible effect on these parameters suggesting that PUSA362 is K(+) deficiency sensitive and PUSA372 is a K(+) deficiency tolerant chickpea cultivar. RNA-seq based transcriptome analysis under K(+) deficiency revealed a total of 820 differential expressed genes (DEG's) in PUSA362 and 682 DEGs in PUSA372. These DEGs belongs to different functional categories, such as plant metabolism, signal transduction components, transcription factors, ion/nutrient transporters, phytohormone biosynthesis and signalling, and root growth and development. RNA-seq expression of randomly selected 16 DEGs was validated by RT-qPCR. Out of 16 genes, 13 showed expression pattern similar to RNA-seq expression, that verified the RNA-seq expression data. Total 258 and 159 genes were exclusively up-regulated, and 386 and 347 genes were down-regulated, respectively in PUSA362 and PUSA372. 14 DEGs showed contrasting expression pattern as they were up-regulated in PUSA362 and down-regulated in PUSA372. These include somatic embryogenesis receptor-like kinase 1, thaumatin-like protein, ferric reduction oxidase 2 and transcription factor bHLH93. Nine genes which were down-regulated in PUSA362 found to be up-regulated in PUSA372, including glutathione S-transferase like, putative calmodulin-like 19, high affinity nitrate transporter 2.4 and ERF17-like protein. Some important carbohydrate metabolism related genes, like fructose-1,6-bisphosphatase and sucrose synthase, and root growth related Expansin gene were exclusively down-regulated, while an ethylene biosynthesis gene 1-aminocyclopropane-1-carboxylate oxidase 1 (ACO1) was up-regulated in PUSA362. Interplay of these and several other genes related to hormones (auxin, cytokinin, GA etc.), signal transduction components (like CBLs and CIPKs), ion transporters and transcription factors might underlie the contrasting response of two chickpea cultivars to K(+) deficiency. In future, some of these key genes will be utilized in genetic engineering and breeding programs for developing chickpea cultivars with improved K(+) use efficiency (KUE) and K(+) deficiency tolerance traits.
PMID: 36714783
Front Plant Sci , IF:5.753 , 2022 , V13 : P1096645 doi: 10.3389/fpls.2022.1096645
Salicylic acid delays pear fruit senescence by playing an antagonistic role toward ethylene, auxin, and glucose in regulating the expression of PpEIN3a.
College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China.
Salicylic acid (SA) and ethylene (ET) are crucial fruit senescence hormones. SA inhibited ET biosynthesis. However, the mechanism of SA delaying fruit senescence is less known. ETHYLENE INSENSITIVE 3 (EIN3), a key positive switch in ET perception, functions as a transcriptional activator and binds to the primary ET response element that is present in the promoter of the ETHYLENE RESPONSE FACTOR1 gene. In this study, a gene encoding putative EIN3 protein was cloned from sand pear and designated as PpEIN3a. The deduced PpEIN3a contains a conserved EIN3 domain. The evolutionary analysis results indicated that PpEIN3a belonged to the EIN3 superfamily. Real-time quantitative PCR analysis revealed that the accumulation of PpEIN3a transcripts were detected in all tissues of this pear. Moreover, PpEIN3a expression was regulated during fruit development. Interestingly, the expression of PpEIN3a was downregulated by SA but upregulated by ET, auxin, and glucose. Additionally, the contents of free and conjugated SA were higher than those of the control after SA treatment. While the content of ET and auxin (indole-3-acetic acid, IAA) dramatically decreased after SA treatment compared with control during fruit senescence. The content of glucose increased when fruit were treated by SA for 12 h and then there were no differences between SA treatment and control fruit during the shelf life. SA also delayed the decrease in sand pear (Pyrus pyrifolia Nakai. 'Whangkeumbae') fruit firmness. The soluble solid content remained relatively stable between the SA treated and control fruits. This study showed that SA plays an antagonistic role toward ET, auxin, and glucose in regulating the expression of PpEIN3a to delay fruit senescence.
PMID: 36714736
Front Plant Sci , IF:5.753 , 2022 , V13 : P1088278 doi: 10.3389/fpls.2022.1088278
The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI regulates primary root growth and lateral root elongation.
School of Life Sciences, Jiangsu Normal University, Xuzhou, Jiangsu, China.; Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China.; Technical Services and Sales Department, Zhengzhou Xuanyuan Biotechnology Co. LTD, Zhengzhou, Henan, China.
Roots are the main organs through which plants absorb water and nutrients. As the key phytohormone involved in root growth, auxin functions in plant environmental responses by modulating auxin synthesis, distribution and polar transport. The Arabidopsis thaliana trehalose-6-phosphate phosphatase gene AtTPPI can improve root architecture, and tppi1 mutants have significantly shortened primary roots. However, the mechanism underlying the short roots of the tppi1 mutant and the upstream signaling pathway and downstream genes regulated by AtTPPI are unclear. Here, we demonstrated that the AtTPPI gene could promote auxin accumulation in AtTPPI-overexpressing plants. By comparing the transcriptomic data of tppi1 and wild-type roots, we found several upregulations of auxin-related genes, including GH3.3, GH3.9 and GH3.12, may play an important role in the AtTPPI gene-mediated auxin transport signaling pathway, ultimately leading to changes in auxin content and primary root length. Moreover, increased AtTPPI expression can regulate primary root growth and lateral root elongation under different concentration of nitrate conditions. Overall, constitutive expression of AtTPPI increased auxin contents and improved lateral root elongation, constituting a new method for improving the nitrogen utilization efficiency of plants.
PMID: 36714693
Front Plant Sci , IF:5.753 , 2022 , V13 : P1097998 doi: 10.3389/fpls.2022.1097998
Characterization of cadmium accumulation mechanism between eggplant (Solanum melongena L.) cultivars.
Research Center for Environmental Pollution Control Technology, School of Chemical and Environmental Engineering, Hunan Institute of Technology, Hengyang, China.
Excessive cadmium (Cd) accumulation in vegetables due to farmland pollution constitutes a serious threat to human health. Eggplant has a tendency to accumulate Cd. To investigate the mechanism of the differences in Cd accumulation levels between high-Cd (BXGZ) and low-Cd (MYQZ) eggplant cultivar, physiological and biochemical indicators and mRNA expression of eggplant were examined using photosynthetic apparatus, biochemical test kits, Fourier transform infrared (FTIR) spectroscopy and transcriptome sequencing, etc. The results of biochemical test kits and FTIR revealed that MYQZ enhanced pectin methylesterase (PME) activity, and lignin and pectin content in the root cell wall, which was associated with the upregulation of PME, cinnamyl-alcohol dehydrogenase and peroxidase (PODs). Higher levels of cysteine and glutathione (GSH) contents and upregulation of genes associated with sulfur metabolism, as well as higher expression of ATP-binding cassette transporters (ABCs), cation exchangers (CAX) and metal tolerance proteins (MTPs) were observed in MYQZ. In BXGZ, the higher stomatal density and stomatal aperture as well as higher levels of Ca(2+) binding protein-1 (PCaP1) and aquaporins and lower levels of A2-type cyclins (CYCA2-1) are consistent with an enhanced transpiration rate in BXGZ. Furthermore, a more developed root system was shown to be associated with higher levels of auxin response factor (ARF19), GATA transcription factors (GATA4, 5 and 11) and auxin efflux carrier component (PIN5) in BXGZ. In conclusion, highly active PME, and higher levels of lignin and pectin in MYQZ are expected to reduce Cd toxicity, while Cd translocation can be inhibited with the help of ABC and other Cd transporters. As for BXGZ, the uptake and translocation of Cd were enhanced by the developed root system and stronger transpiration.
PMID: 36699861
Front Plant Sci , IF:5.753 , 2022 , V13 : P1043757 doi: 10.3389/fpls.2022.1043757
Combined metabolomic and transcriptomic analysis reveals key components of OsCIPK17 overexpression improves drought tolerance in rice.
School of Life Sciences, Nantong University, Nantong, China.
Oryza Sativa is one of the most important food crops in China, which is easily affected by drought during its growth and development. As a member of the calcium signaling pathway, CBL-interacting protein kinase (CIPK) plays an important role in plant growth and development as well as environmental stress. However, there is no report on the function and mechanism of OsCIPK17 in rice drought resistance. We combined transcriptional and metabonomic analysis to clarify the specific mechanism of OsCIPK17 in response to rice drought tolerance. The results showed that OsCIPK17 improved drought resistance of rice by regulating deep roots under drought stress; Response to drought by regulating the energy metabolism pathway and controlling the accumulation of citric acid in the tricarboxylic acid (TCA) cycle; Our exogenous experiments also proved that OsCIPK17 responds to citric acid, and this process involves the auxin metabolism pathway; Exogenous citric acid can improve the drought resistance of overexpression plants. Our research reveals that OsCIPK17 positively regulates rice drought resistance and participates in the accumulation of citric acid in the TCA cycle, providing new insights for rice drought resistance.
PMID: 36699859
Front Plant Sci , IF:5.753 , 2022 , V13 : P1058421 doi: 10.3389/fpls.2022.1058421
Microspore embryogenesis induction by mannitol and TSA results in a complex regulation of epigenetic dynamics and gene expression in bread wheat.
Departamento de Genetica y Produccion Vegetal, Estacion Experimental de Aula Dei, Consejo Superior de Investigaciones Cientificas (EEAD-CSIC), Zaragoza, Spain.; Departamento de Patologia, Anatomia y Fisiologia, Facultad de Ciencias, Universidad de Navarra, Pamplona, Spain.
Reprogramming of microspores development towards embryogenesis mediated by stress treatment constitutes the basis of doubled haploid production. Recently, compounds that alter histone post-translational modifications (PTMs) have been reported to enhance microspore embryogenesis (ME), by altering histones acetylation or methylation. However, epigenetic mechanisms underlying ME induction efficiency are poorly understood. In this study, the epigenetic dynamics and the expression of genes associated with histone PTMs and ME induction were studied in two bread wheat cultivars with different ME response. Microspores isolated at 0, 3 and 5 days, treated with 0.7M mannitol (MAN) and 0.7M mannitol plus 0.4microM trichostatin A (TSA), which induced ME more efficiently, were analyzed. An additional control of gametophytic development was included. Microspores epigenetic state at the onset of ME induction was distinctive between cultivars by the ratio of H3 variants and their acetylated forms, the localization and percentage of labeled microspores with H3K9ac, H4K5ac, H4K16ac, H3K9me2 and H3K27me3, and the expression of genes related to pollen development. These results indicated that microspores of the high responding cultivar could be at a less advanced stage in pollen development. MAN and TSA resulted in a hyperacetylation of H3.2, with a greater effect of TSA. Histone PTMs were differentially affected by both treatments, with acetylation being most concerned. The effect of TSA was observed in the H4K5ac localization pattern at 3dT in the mid-low responding cultivar. Three gene networks linked to ME response were identified. TaHDT1, TaHAG2, TaYAO, TaNFD6-A, TabZIPF1 and TaAGO802-B, associated with pollen development, were down-regulated. TaHDA15, TaHAG3, TaHAM, TaYUC11D, Ta-2B-LBD16 TaMS1 and TaDRM3 constituted a network implicated in morphological changes by auxin signaling and cell wall modification up-regulated at 3dT. The last network included TaHDA18, TaHAC1, TaHAC4, TaABI5, TaATG18fD, TaSDG1a-7A and was related to ABA and ethylene hormone signaling pathways, DNA methylation and autophagy processes, reaching the highest expression at 5dT. The results indicated that TSA mainly modified the regulation of genes related to pollen and auxin signaling. This study represents a breakthrough in identifying the epigenetic dynamics and the molecular mechanisms governing ME induction efficiency, with relevance to recalcitrant wheat genotypes and other crops.
PMID: 36699843
Front Plant Sci , IF:5.753 , 2022 , V13 : P1035157 doi: 10.3389/fpls.2022.1035157
Genome sequencing and resequencing identified three horizontal gene transfers and uncovered the genetic mechanism on the intraspecies adaptive evolution of Gastrodia elata Blume.
School of Health and Life Science, Kaili University, Kaili, Guizhou, China.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.; Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, China.; College of Agriculture, South China Agricultural University, Guangzhou, Guangdong, China.
Horizontal gene transfer is a rare and useful genetic mechanism in higher plants. Gastrodia elata Blume (GE) (Orchidaceae), well known as traditional medicinal material in East Asia, adopts a heterotrophic lifestyle, thus being considered to be more prone to horizontal gene transfer (HGT). GE is a "polytypic species" that currently comprised of five recognized forms according to the plant morphology. G. elata Blume forma elata (GEE) and G. elata Bl.f.glauca (GEG) are two common forms that naturally grow in different habitats with difference in altitude and latitude. G. elata Bl.f.viridis (GEV) often occurs sporadically in cultivated populations of GEE and GEG. However, the genetic relationships and genetic mechanism underpinned the divergent ecological adaptations of GEE and GEG have not been revealed. Here, we assembled a chromosome-level draft genome of GEE with 1.04 Gb. Among predicted 17,895 protein coding genes, we identified three HGTs. Meanwhile, we resequenced 10 GEE accessions, nine GEG accessions, and 10 GEV accessions, and identified two independent genetic lineages: GEG_pedigree (GEG individuals and GEV individuals collected from GEG populations) and GEE_pedigree (GEE individuals and GEV individuals collected from GEE populations), which strongly support the taxonomic status of GEE and GEG as subspecies, not as different forms. In highly differentiated genomic regions of GEE_pedigree and GEG_pedigree, three chalcone synthase-encoding genes and one Phox/Bem1p (PB1) domain of encoding Auxin (AUX)/Indoleacetic acid (IAA) were identified in selection sweeping genome regions, which suggested that differentiation between GEE_pedigree and GEG_pedigree was promoted by the selection of genes related to photoresponse and growth and development. Overall, this new genome would be helpful for breeding and utilization of GE and the new findings would deepen the understanding about ecological adaptation and evolution of GE.
PMID: 36684780
Front Plant Sci , IF:5.753 , 2022 , V13 : P1019152 doi: 10.3389/fpls.2022.1019152
Effects of exogenous auxin on yield in foxtail millet (Setaria italica L.) when applied at the grain-filling stage.
Shanxi Agricultural University, Taiyuan, Shanxi, China.
Foxtail millet (Setaria italica L.) is of high nutritious value, which is an important crop in arid and semi-arid regions. The objective of this experiment was to explore the effects of the synthetic auxin naphthalene acetic acid (NAA) on the physiological processes of foxtail millet, and to provide a theoretical basis and technical approaches for its efficient use in millet cultivation. Two foxtail millet varieties ('Jingu 21' and 'Zhangzagu 5') were treated with six concentrations of NAA from 0-144 mg L(-1) at the grain-filling stage in field experiments. The photosynthetic pigment contents, gas exchange parameters, chlorophyll fluorescence parameters, and grain yield were measured in foxtail millet. The results showed that low concentrations of NAA (18-36 mg L(-1)) increased the contents of photosynthetic pigments, and increased the activities of antioxidant enzymes, the photosynthetic rate, and the activity of photosystem system II (PS II). At higher NAA concentrations, the facilitation effect of the treatments diminished, showing a clear concentration effect. In this study, yield was significantly and positively correlated with PS II effective quantum yield (Y(II)) and the PSII electron transport rate (ETR), and the net photosynthetic rate (Pn) was significantly and positively correlated with chlorophyll content, stomatal conductance (Gs), Y(II), and ETR. These results also indicated that exogenous NAA application promotes the production of ATP and NADPH by increasing the efficiency of electron transfer within the photosystems and also improved photochemical utilization, which facilitates the fixation and reduction of carbon, ultimately leading to an increase in Pn and increasing grain yield in foxtail millet.
PMID: 36684766
Front Plant Sci , IF:5.753 , 2022 , V13 : P1060965 doi: 10.3389/fpls.2022.1060965
Genome-wide identification and expression analysis of AUX/LAX family genes in Chinese hickory (Carya cathayensis Sarg.) Under various abiotic stresses and grafting.
State Key Laboratory of Subtropical Silviculture, Zhejiang Agriculture and Forestry (A&F) University, Hangzhou, China.; Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang Agriculture and Forestry (A&F) University, Hangzhou, China.; College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, China.; Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, Pennsylvania State University, Hershey, PA, United States.
Auxin is essential for regulating plant growth and development as well as the response of plants to abiotic stresses. AUX/LAX proteins are auxin influx transporters belonging to the amino acid permease family of proton-driven transporters, and are involved in the transport of indole-3-acetic acid (IAA). However, how AUX/LAX genes respond to abiotic stresses in Chinese hickory is less studied. For the first time identification, structural characteristics as well as gene expression analysis of the AUX/LAX gene family in Chinese hickory were conducted by using techniques of gene cloning and real-time fluorescent quantitative PCR. Eight CcAUX/LAXs were identified in Chinese hickory, all of which had the conserved structural characteristics of AUX/LAXs. CcAUX/LAXs were most closely related to their homologous proteins in Populus trichocarpa , which was in consistence with their common taxonomic character of woody trees. CcAUX/LAXs exhibited different expression profiles in different tissues, indicating their varying roles during growth and development. A number of light-, hormone-, and abiotic stress responsive cis-acting regulatory elements were detected on the promoters of CcAUX/LAX genes. CcAUX/LAX genes responded differently to drought and salt stress treatments to varying degrees. Furthermore, CcAUX/LAX genes exhibited complex expression changes during Chinese hickory grafting. These findings not only provide a valuable resource for further functional validation of CcAUX/LAXs, but also contribute to a better understanding of their potential regulatory functions during grafting and abiotic stress treatments in Chinese hickory.
PMID: 36684757
Front Plant Sci , IF:5.753 , 2022 , V13 : P1023088 doi: 10.3389/fpls.2022.1023088
Root pruning improves maize water-use efficiency by root water absorption.
State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China.; College of Forestry, Northwest Agriculture and Forestry University, Yangling, Shaanxi, China.; School of Pharmacy, Weifang Medical University, Weifang, China.; Geography and Environmental Engineering Department, Baoji University of Arts and Sciences, Baoji, China.; The University of Western Australia Institute of Agriculture, and University of Western Australia School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia.; Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest Agriculture and Forestry University, Yangling, China.
Root systems are an important component of plants that impact crop water-use efficiency (WUE) and yield. This study examined the effects of root pruning on maize yield, WUE, and water uptake under pot and hydroponic conditions. The pot experiment showed that root pruning significantly decreased root/shoot ratio. Both small root pruning (cut off about 1/5 of the root system, RP1) and large root pruning (cut off about 1/3 of the root system, RP2) improved WUE and root hydraulic conductivity (Lpr) in the residual root system. Compared with that in the un-cut control, at the jointing stage, RP1 and RP2 increased Lpr by 43.9% and 31.5% under well-watered conditions and 27.4% and 19.8% under drought stress, respectively. RP1 increased grain yield by 12.9% compared with that in the control under well-watered conditions, whereas both pruning treatments did not exhibit a significant effect on yield under drought stress. The hydroponic experiment demonstrated that root pruning did not reduce leaf water potential but increased residual root hydraulic conductivity by 26.2% at 48 h after root pruning under well-watered conditions. The foregoing responses may be explained by the upregulation of plasma membrane intrinsic protein gene and increases in abscisic acid and jasmonic acid in roots. Increased auxin and salicylic acid contributed to the compensated lateral root growth. In conclusion, root pruning improved WUE in maize by root water uptake.
PMID: 36684736
Front Plant Sci , IF:5.753 , 2022 , V13 : P994268 doi: 10.3389/fpls.2022.994268
Integrated analysis of transcriptome and microRNAs associated with exogenous calcium-mediated enhancement of hypoxic tolerance in cucumber seedlings (Cucumis sativus L.).
Shanghai Key Lab of Protected Horticultural Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China.; Shanghai Dushi Green Engineering Co., Ltd., Shanghai, China.
Plants often suffer from hypoxic stress due to flooding caused by extreme weather. Hypoxia usually leads to restricted oxygen supply and alters metabolic patterns from aerobic to anaerobic. Cucumber roots are fragile and highly sensitive to damage from hypoxic stress. The purpose of this study was to investigate the regulatory mechanism of exogenous calcium alleviating hypoxic stress in cucumber through transcriptome and small RNAs analysis. Three treatments were performed in this paper, including untreated-control (CK), hypoxic stress (H), and hypoxic stress + exogenous calcium treatment (H + Ca(2+)). A large number of differentially expressed genes (DEGs) were identified, 1,463 DEGs between CK vs H, 3,399 DEGs between H vs H + Ca(2+), and 5,072 DEGs between CK vs H + Ca(2+), respectively. KEGG analysis of DEGs showed that exogenous calcium could activate hormone signaling pathways (ethylene, ABA, IAA and cytokinin), transcription factors (MYB, MYB-related, bHLH, bZIP, and WRKY), calcium signaling and glycolysis pathway to mitigating hypoxic stress in cucumber seedlings. Additionally, miRNA and their target genes were detected and predicted between treatments. The target genes of these miRNAs revealed that auxin, cellulose synthase, and mitochondrial ribosomal related genes (Csa2G315390, Csa6G141390, Csa4G053280, and Csa6G310480) probably play in the improvement of the hypoxic tolerance of cucumber seedlings through exogenous calcium application. In short, our data adds new information to the mechanism of exogenous calcium mitigation of hypoxic stress injury in cucumber seedlings at transcriptional and post-transcriptional levels.
PMID: 36684729
Front Plant Sci , IF:5.753 , 2022 , V13 : P1061747 doi: 10.3389/fpls.2022.1061747
Uninterrupted embryonic growth leading to viviparous propagule formation in woody mangrove.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.; Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, United States.
Vivipary is a rare sexual reproduction phenomenon where embryos germinate directly on the maternal plants. However, it is a common genetic event of woody mangroves in the Rhizophoraceae family. The ecological benefits of vivipary in mangroves include the nurturing of seedlings in harsh coastal and saline environments, but the genetic and molecular mechanisms of vivipary remain unclear. Here we investigate the viviparous embryo development and germination processes in mangrove Kandelia obovata by a transcriptomic approach. Many key biological pathways and functional genes were enriched in different tissues and stages, contributing to vivipary. Reduced production of abscisic acid set a non-dormant condition for the embryo to germinate directly. Genes involved in the metabolism of and response to other phytohormones (gibberellic acid, brassinosteroids, cytokinin, and auxin) are expressed precociously in the axis of non-vivipary stages, thus promoting the embryo to grow through the seed coat. Network analysis of these genes identified the central regulatory roles of LEC1 and FUS3, which maintain embryo identity in Arabidopsis. Moreover, photosynthesis related pathways were significantly up-regulated in viviparous embryos, and substance transporter genes were highly expressed in the seed coat, suggesting a partial self-provision and maternal nursing. We conclude that the viviparous phenomenon is a combinatorial result of precocious loss of dormancy and enhanced germination potential during viviparous seed development. These results shed light on the relationship between seed development and germination, where the continual growth of the embryo replaces a biphasic phenomenon until a mature propagule is established.
PMID: 36684724
Front Plant Sci , IF:5.753 , 2022 , V13 : P1098820 doi: 10.3389/fpls.2022.1098820
The genome wide analysis of Tryptophan Aminotransferase Related gene family, and their relationship with related agronomic traits in Brassica napus.
College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.; Key Laboratory of Molecular Biophysics, the Ministry of Education of China, Wuhan, China.
Tryptophan Aminotransferase of Arabidopsis1/Tryptophan Aminotransferase-Related (TAA1/TAR) proteins are the enzymes that involved in auxin biosynthesis pathway. The TAA1/TAR gene family has been systematically characterized in several plants but has not been well reported in Brassica napus. In the present study, a total of 102 BnTAR genes with different number of introns were identified. It was revealed that these genes are distributed unevenly and occurred as clusters on different chromosomes except for A4, A5, A10 and C4 in B. napus. Most of the these BnTAR genes are conserved despite of existing of gene loss and gene gain. In addition, the segmental replication and whole-genome replication events were both play an important role in the BnTAR gene family formation. Expression profiles analysis indicated that the expression of BnTAR gene showed two patterns, part of them were mainly expressed in roots, stems and leaves of vegetative organs, and the others were mainly expressed in flowers and seeds of reproductive organs. Further analysis showed that many of BnTAR genes were located in QTL intervals of oil content or seed weight, for example BnAMI10 was located in cqOC-C5-4 and cqSW-A2-2, it indicated that some of the BnTAR genes might have relationship with these two characteristics. This study provides a multidimensional analysis of the TAA1/TAR gene family and a new insight into its biological function in B. napus.
PMID: 36618649
Front Plant Sci , IF:5.753 , 2022 , V13 : P1079212 doi: 10.3389/fpls.2022.1079212
Transcriptome and metabolome analyses reveal the key genes related to grain size of big grain mutant in Tartary Buckwheat (Fagopyrum tartaricum).
College of Agronomy and Biotechnology, Southwest University, Chongqing, China.; Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China.; Baicheng Academy of Agricultural Sciences of Jilin Province, Baicheng, Jilin, China.
Grain size with high heritability and stability is an important selection target during Tartary buckwheat breeding. However, the mechanisms that regulate Tartary buckwheat grain development are unknown. We generated transcriptome and metabolome sequencing from 10 and 15 days past anthesis (DPA) grains of big grain mutant (bg1) and WT, and identified 4108 differentially expressed genes (DEGs) including 93 significantly up-regulated differential genes and 85 significantly down-regulated genes in both stages, simultaneously. Meanwhile, we identified DEGs involved in ubiquitin-proteasome pathway, HAI-KU (IKU) pathway, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone (auxin, brassinosteroids and cytokinins) transduction pathway and five transcription factor families, including APETALA (AP2), GROWTH-REGULATING FACTORS (GRF), AUXIN RESPONSE FACTOR (ARF), WRKY and MYB. Weighted gene co-expression network analysis (WGCNA) was performed and obtained 9 core DEGs. Conjoint analyses of transcriptome and metabolome sequencing screened out 394 DEGs. Using a combined comprehensive analysis, we identified 24 potential candidate genes that encode E3 ubiquitin-protein ligase HIP1, EMBRYO-DEFECTIVE (EMB) protein, receptor-like protein kinase FERONIA (FER), kinesin-4 protein SRG1, and so on, which may be associated with the big-grain mutant bg1. Finally, a quantitative real-time Polymerase Chain Reaction (qRT-PCR) assay was conducted to validate the identified DEGs. Our results provide additional knowledge for identification and functions of causal candidate genes responsible for the variation in grain size and will be an invaluable resource for the genetic dissection of Tartary buckwheat high-yield molecular breeding.
PMID: 36618631
Front Plant Sci , IF:5.753 , 2022 , V13 : P1098787 doi: 10.3389/fpls.2022.1098787
Synergistic effects of nitrogen metabolites on auxin regulating plant growth and development.
College of Resources, Sichuan Agricultural University, Chengdu, China.
Nitrogen is one of the important nutrients required for plant growth and development. There is increasing evidences that almost all types of nitrogen metabolites affect, at least to some extent, auxin content and/or signaling in plants, which in turn affects seed germination, plant root elongation, gravitropism, leaf expansion and floral transition. This opinion focuses on the roles of nitrogen metabolites, NO3- , NH4+ , tryptophan and NO and their synergistic effects with auxin on plant growth and development. Nitrate reductase (NR) converts nitrate into nitrite, and was roughly positive-correlated with the root auxin level, suggesting a crosstalk between nitrate signaling and auxin signaling. Abscisic Acid Responsive Element Binding Factor 3 (AFB3) and Tryptophan Aminotransferase of Arabidopsis 1 (TAA1) are also the key enzymes involved in nitrogen metabolite-regulated auxin biosynthesis. Recent advances in the crosstalk among NO3- , NH4+ , tryptophan and NO in regulation to NR, AFB3 and TAA1 are also summarized.
PMID: 36605959
Front Plant Sci , IF:5.753 , 2022 , V13 : P1066736 doi: 10.3389/fpls.2022.1066736
Transgenic tobacco plant overexpressing ginkgo dihydroflavonol 4-reductase gene GbDFR6 exhibits multiple developmental defects.
Key Laboratory of Hangzhou City for Quality and Safety of Agricultural Products, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China.; Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, Hangzhou Normal University, Hangzhou, China.; College of Science and Technology, Ningbo University, Ningbo, China.
Dihydroflavonol Q 4-reductase (DFR), a key enzyme in the flavonoid biosynthetic pathway in plants, significantly influences plant survival. However, the roles of DFR in the regulation of plant development are largely unknown. In the present study, phenotypes of transgenic tobacco plants overexpressing the Ginkgo biloba DFR gene, GbDFR6, were investigated. Transgenic tobacco seedlings exhibited relatively low fresh weights, long primary roots, decreased lateral root numbers, and impaired root gravitropic responses when compared to wild-type tobacco plants. Adult transgenic tobacco plants exhibited a considerably high percentage of wrinkled leaves when compared to the wild-type tobacco plants. In addition to the auxin-related phenotypic changes, transgenic tobacco plants exhibited delayed flowering phenotypes under short-day conditions. Gene expression analysis revealed that the delayed flowering in transgenic tobacco plants was caused by the low expression levels of NtFT4. Finally, variations in anthocyanin and flavonoid contents in transgenic tobacco plants were evaluated. The results revealed that the levels of most anthocyanins identified in transgenic tobacco leaves increased. Specifically, cyanidin-3,5-O-diglucoside content increased by 9.8-fold in transgenic tobacco plants when compared to the wild-type tobacco plants. Pelargonidin-3-O-(coumaryl)-glucoside was only detected in transgenic tobacco plants. Regarding flavonoid compounds, one flavonoid compound (epicatechin gallate) was upregulated, whereas seven flavonoid compounds (Tamarixetin-3-O-rutinoside; Sexangularetin-3-O-glucoside-7-O-rhamnoside; Kaempferol-3-O-neohesperidoside; Engeletin; 2'-Hydoxy,5-methoxyGenistein-O-rhamnosyl-glucoside; Diosmetin; Hispidulin) were downregulated in both transgenic tobacco leaves and roots. The results indicate novel and multiple roles of GbDFR6 in ginkgo and provide a valuable method to produce a late flowering tobacco variety in tobacco industry.
PMID: 36589135
Front Plant Sci , IF:5.753 , 2022 , V13 : P1064556 doi: 10.3389/fpls.2022.1064556
Identification of a major QTL, Parth6.1 associated with parthenocarpic fruit development in slicing cucumber genotype, Pusa Parthenocarpic Cucumber-6.
Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, India.; Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.; ICAR-Indian Institute of Vegetable Research, Varanasi, India.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.; Division of Sample Survey, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.
Parthenocarpy is an extremely important trait that revolutionized the worldwide cultivation of cucumber under protected conditions. Pusa Parthenocarpic Cucumber-6 (PPC-6) is one of the important commercially cultivated varieties under protected conditions in India. Understanding the genetics of parthenocarpy, molecular mapping and the development of molecular markers closely associated with the trait will facilitate the introgression of parthenocarpic traits into non-conventional germplasm and elite varieties. The F(1), F(2) and back-crosses progenies with a non-parthenocarpic genotype, Pusa Uday indicated a single incomplete dominant gene controlling parthenocarpy in PPC-6. QTL-seq comprising of the early parthenocarpy and non-parthenocarpic bulks along with the parental lines identified two major genomic regions, one each in chromosome 3 and chromosome 6 spanning over a region of 2.7 Mb and 7.8 Mb, respectively. Conventional mapping using F(2:3) population also identified two QTLs, Parth6.1 and Parth6.2 in chromosome 6 which indicated the presence of a major effect QTL in chromosome 6 determining parthenocarpy in PPC-6. The flanking markers, SSR01148 and SSR 01012 for Parth6.1 locus and SSR10476 and SSR 19174 for Parth6.2 locus were identified and can be used for introgression of parthenocarpy through the marker-assisted back-crossing programme. Functional annotation of the QTL-region identified two major genes, Csa_6G396640 and Csa_6G405890 designated as probable indole-3-pyruvate monooxygenase YUCCA11 and Auxin response factor 16, respectively associated with auxin biosynthesis as potential candidate genes. Csa_6G396640 showed only one insertion at position 2179 in the non-parthenocarpic parent. In the case of Csa_6G405890, more variations were observed between the two parents in the form of SNPs and InDels. The study provides insight about genomic regions, closely associated markers and possible candidate genes associated with parthenocarpy in PPC-6 which will be instrumental for functional genomics study and better understanding of parthenocarpy in cucumber.
PMID: 36589066
Front Plant Sci , IF:5.753 , 2022 , V13 : P1057993 doi: 10.3389/fpls.2022.1057993
Melatonin regulates gene expressions through activating auxin synthesis and signaling pathways.
State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
BACKGROUND: Both melatonin and indole-3-acetic acid (IAA) are derived from tryptophan. And the most interesting and unsolved puzzle in melatonin research is that what is the relationship between melatonin and auxin? METHODS: In this study, we performed transcriptome analysis with a time series method to disclose the connection of the two metabolites in soybean. RESULTS: Our results reveal that melatonin and IAA treatments cause substantial overlaps in gene expression changes. Common genes of melatonin and IAA treatments could be sorted into clusters with very similar expression tendency. A KEGG assay showed that exogenous applied melatonin enriched differentially expressed genes in auxin biosynthesis and signaling pathways. For details, melatonin up-regulates several YUCCA genes which participate in auxin biosynthesis; melatonin also enhances expression levels of auxin receptor coding genes, such as TIR1, AFB3 and AFB5; dozens of genes involved in auxin transport, such as AUXI and PIN, are regulated by melatonin similarly as by auxin; auxin-responsive genes, such as IAA, ARF, GH3 and SAUR-like genes, intensively respond to melatonin as well as to auxin. A DR5 promoter mediated GUS staining assay showed that low concentration of melatonin could induce auxin biosynthesis in a dosage manner, whereas high concentration of melatonin would eliminate such effect. At last, gene ontology (GO) analysis suggests that melatonin treatment has similar characteristics as auxin treatment in many processes. However, the two molecules still keep their own features respectively. For example, melatonin takes part in stress responses, while IAA treatment enriches the GO terms that related to cell growth. CONCLUSION: Taken together, exogenous applied melatonin, if not exceeds the appropriate concentration, could promote auxin responses range from biosynthesis to signaling transduction. Thus, our research is a key part to explain the auxin-like roles of melatonin in regulating plant growth.
PMID: 36582645
Front Plant Sci , IF:5.753 , 2022 , V13 : P1049144 doi: 10.3389/fpls.2022.1049144
Alkaline stress reduces root waving by regulating PIN7 vacuolar transport.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.; Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.; Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.; State Key Laboratory of Crop Genetics and Germplasm Enhancement and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing Agricultural University, Nanjing, China.; Institute of Biology II/Molecular Plant Physiology, Faculty of Biology, Albert-Ludwigs-University of Freiburg, Schanzlestr. 1, Freiburg, Germany.
Root development and plasticity are assessed via diverse endogenous and environmental cues, including phytohormones, nutrition, and stress. In this study, we observed that roots in model plant Arabidopsis thaliana exhibited waving and oscillating phenotypes under normal conditions but lost this pattern when subjected to alkaline stress. We later showed that alkaline treatment disturbed the auxin gradient in roots and increased auxin signal in columella cells. We further demonstrated that the auxin efflux transporter PIN-FORMED 7 (PIN7) but not PIN3 was translocated to vacuole lumen under alkaline stress. This process is essential for root response to alkaline stress because the pin7 knockout mutants retained the root waving phenotype. Moreover, we provided evidence that the PIN7 vacuolar transport might not depend on the ARF-GEFs but required the proper function of an ESCRT subunit known as FYVE domain protein required for endosomal sorting 1 (FREE1). Induced silencing of FREE1 disrupted the vacuolar transport of PIN7 and reduced sensitivity to alkaline stress, further highlighting the importance of this cellular process. In conclusion, our work reveals a new role of PIN7 in regulating root morphology under alkaline stress.
PMID: 36582637
Front Plant Sci , IF:5.753 , 2022 , V13 : P1090072 doi: 10.3389/fpls.2022.1090072
Identification of genomic regions associated with soybean responses to off-target dicamba exposure.
Fisher Delta Research, Extension, and Education Center, Division of Plant Science and Technology, University of Missouri, Portageville, MO, United States.; Agronomy Department, University of Florida, Gainesville, FL, United States.; Biological Systems Engineering, University of Wisconsin-Madison, Madison, WI, United States.; Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States.; Department of Crop Sciences, University of Illinois, Urbana, IL, United States.; Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri, Columbia, MO, United States.
The widespread adoption of genetically modified (GM) dicamba-tolerant (DT) soybean was followed by numerous reports of off-target dicamba damage and yield losses across most soybean-producing states. In this study, a subset of the USDA Soybean Germplasm Collection consisting of 382 genetically diverse soybean accessions originating from 15 countries was used to identify genomic regions associated with soybean response to off-target dicamba exposure. Accessions were genotyped with the SoySNP50K BeadChip and visually screened for damage in environments with prolonged exposure to off-target dicamba. Two models were implemented to detect significant marker-trait associations: the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) and a model that allows the inclusion of population structure in interaction with the environment (GxE) to account for variable patterns of genotype responses in different environments. Most accessions (84%) showed a moderate response, either moderately tolerant or moderately susceptible, with approximately 8% showing tolerance and susceptibility. No differences in off-target dicamba damage were observed across maturity groups and centers of origin. Both models identified significant associations in regions of chromosomes 10 and 19. The BLINK model identified additional significant marker-trait associations on chromosomes 11, 14, and 18, while the GxE model identified another significant marker-trait association on chromosome 15. The significant SNPs identified by both models are located within candidate genes possessing annotated functions involving different phases of herbicide detoxification in plants. These results entertain the possibility of developing non-GM soybean cultivars with improved tolerance to off-target dicamba exposure and potentially other synthetic auxin herbicides. Identification of genetic sources of tolerance and genomic regions conferring higher tolerance to off-target dicamba may sustain and improve the production of other non-DT herbicide soybean production systems, including the growing niche markets of organic and conventional soybean.
PMID: 36570921
Front Plant Sci , IF:5.753 , 2022 , V13 : P1025422 doi: 10.3389/fpls.2022.1025422
Transcriptional profiling of defense responses to Botrytis cinerea infection in leaves of Fragaria vesca plants soil-drenched with beta-aminobutyric acid.
Division of Biotechnology and Plant Health, Norwegian Institute of Bioeconomy Research, As, Norway.; Department of Plant Sciences, Norwegian University of Life Sciences (NMBU), As, Norway.; Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.; Department of Genetics, Genomics and Breeding, National Institute of Agricultural Botany- East Malling Research Station, East Malling, United Kingdom.
Grey mold caused by the necrotrophic fungal pathogen Botrytis cinerea can affect leaves, flowers, and berries of strawberry, causing severe pre- and postharvest damage. The defense elicitor beta-aminobutyric acid (BABA) is reported to induce resistance against B. cinerea and many other pathogens in several crop plants. Surprisingly, BABA soil drench of woodland strawberry (Fragaria vesca) plants two days before B. cinerea inoculation caused increased infection in leaf tissues, suggesting that BABA induce systemic susceptibility in F. vesca. To understand the molecular mechanisms involved in B. cinerea susceptibility in leaves of F. vesca plants soil drenched with BABA, we used RNA sequencing to characterize the transcriptional reprogramming 24 h post-inoculation. The number of differentially expressed genes (DEGs) in infected vs. uninfected leaf tissue in BABA-treated plants was 5205 (2237 upregulated and 2968 downregulated). Upregulated genes were involved in pathogen recognition, defense response signaling, and biosynthesis of secondary metabolites (terpenoid and phenylpropanoid pathways), while downregulated genes were involved in photosynthesis and response to auxin. In control plants not treated with BABA, we found a total of 5300 DEGs (2461 upregulated and 2839 downregulated) after infection. Most of these corresponded to those in infected leaves of BABA-treated plants but a small subset of DEGs, including genes involved in 'response to biologic stimulus', 'photosynthesis' and 'chlorophyll biosynthesis and metabolism', differed significantly between treatments and could play a role in the induced susceptibility of BABA-treated plants.
PMID: 36570914
Front Plant Sci , IF:5.753 , 2022 , V13 : P1049681 doi: 10.3389/fpls.2022.1049681
Proteome-wide analysis of hydrogen peroxide-induced protein carbonylation in Arabidopsis thaliana.
Groupe de Recherche et Biologie Vegetale (GRBV), Department of Chemistry, Biochemistry and Physics, Universite du Quebec a Trois-Rivieres, Trois-Rivieres, QC, Canada.
INTRODUCTION: Protein carbonylation is a non-enzymatic and irreversible post-translational modification that occurs naturally in living organisms under the direct or indirect effect of reactive oxygen species (ROS). In animals, signaling pathways involving numerous carbonylated proteins have been identified, highlighting the dual role of these molecules in ROS signal transduction. In plants, studies on phytohormone signaling (auxin, methyl jasmonate, abscisic acid) have shown that reactive carbonyl species (RCS: acrolein, malondialdehyde, 4-hydroxynonenal, etc.), derived from the action of ROS on lipids, play important roles in secondary root formation and stomatal closure. However, the carbonylated proteins involved in these signaling pathways remain to be identified. METHODS: In this study, we analyzed proteins responsive to carbonylation by exogenous hydrogen peroxide (H2O2) by profiling the carbonyl proteome extracted from Arabidopsis thaliana leaves after H2O2 treatment. Carbonylated proteins were enriched at the peptide level and analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). RESULTS AND DISCUSSION: We identified 35 and 39 uniquely carbonylated proteins in the untreated and the H2O2-treated plant samples, respectively. In comparison to the control treatment, gene ontology enrichment analysis revealed that most of the carbonylated proteins identified in the H2O2-treated plant samples are related to sulfate adenylyl transferases and amidophosphoribosyl transferases involved in the immune system response, defense response, and external stimulus-response. These results indicated that exogenous H2O2 caused a change in the pattern of protein carbonylation in A. thaliana leaves. Protein carbonylation may thus influence the plant transcriptome and metabolism in response to H2O2 and ROS-triggering external stimuli.
PMID: 36544875
Front Plant Sci , IF:5.753 , 2022 , V13 : P1059559 doi: 10.3389/fpls.2022.1059559
Characterization and expression profiling of PIN auxin efflux transporters reveal their role in developmental and abiotic stress conditions in rice.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India.; Department of Botany, Christ Church College, Kanpur, India.
The auxin efflux transporter proteins called PINs ferry auxin from its source to sinks in particular directions depending on their polar localizations in the plasma membrane, thus facilitating the development of the entire plant architecture. The rice genome has 12 PIN genes distributed over eight chromosomes. To study their roles in plant development, abiotic stress responsiveness, and shaping an auxin-dependent root architecture, a genome-wide analysis was carried out. Based on phylogeny, cellular localization, and hydrophilic loop domain size, the PINs were categorized into canonical and noncanonical PINs. PINs were found expressed in all of the organs of plants that emphasized their indispensable role throughout the plant's life cycle. We discovered that PIN5C and PIN9 were upregulated during salt and drought stress. We also found that regardless of its cellular level, auxin functioned as a molecular switch to turn on auxin biosynthesis genes. On the contrary, although PIN expression was upregulated upon initial treatment with auxin, prolonged auxin treatment not only led to their downregulation but also led to the development of auxin-dependent altered root formation in rice. Our study paves the way for developing stress-tolerant rice and plants with a desirable root architecture by genetic engineering.
PMID: 36531415
Front Plant Sci , IF:5.753 , 2022 , V13 : P1035022 doi: 10.3389/fpls.2022.1035022
Improving berry quality and antioxidant ability in 'Ruidu Hongyu' grapevine through preharvest exogenous 2,4-epibrassinolide, jasmonic acid and their signaling inhibitors by regulating endogenous phytohormones.
Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.; College of Chemistry and Chemical Engineering, Zhongkai University of Agricultural Engineering, Guangzhou, China.; Grape and Wine Institute, Guangxi Academy of Agricultural Sciences, Nanning, Guangxi, China.
Grape berries contain a variety of metabolites, such as anthocyanins, sugars, fatty acids, and antioxidants. Endogenous phytohormones strongly influence these metabolites, which regulate berry quality improvement. In this study, we evaluated the effects of 2,4-epibrassinolide (EBR, brassinolide (BR)-like growth regulator), jasmonic acid (JA), and their signaling inhibitors brassinazole (Brz), and sodium diethyldithiocarbamate (DIECA) on berry quality and antioxidant ability. Overall, the pre-harvest application of 0.5 mg L(-1) EBR and 100 mumol L(-1) JA significantly influences the quality of the grape berry. Results showed that EBR was superior to other treatments at enhancing the content of different metabolites, including anthocyanins, fructose, glucose, and a variety of fatty acids, in grapes. EBR and JA also enhanced the synthesis of gibberellin(3) (GA(3)), cytokinin (CTK), salicylic acid (SA), JA, methyl jasmonate (MeJA), BR, and abscisic acid (ABA), while inhibiting the synthesis of auxin (IAA). Most genes related to BR/JA and anthocyanins/sugars/fatty acids biosynthesis were up-regulated. The effects of Brz and DIECA on the grape berry quality were totally reversed throughout the study, as shown by EBR and JA. According to correlation analysis, EBR and JA have a beneficial positive interaction that promotes the formation of strong coherences in grape berries between ABA/IAA/ZT-fruit expansion, BR/JA/MeJA/GA(3)/ZR-biochemical characteristics development, JA/MeJA/ABA/GA(3)/SA/ZR-antioxidant capacity enhancement, and JA/MeJA/IAA/GA(3)/ZT/ZR-fatty acids accumulation. In this regard, we concluded that preharvest exogenous 0.5 mg L(-1) EBR and 100 mumol L(-1) JA is a successful way to improve grape berry quality.
PMID: 36531411
Front Plant Sci , IF:5.753 , 2022 , V13 : P1065253 doi: 10.3389/fpls.2022.1065253
Knockout of a papain-like cysteine protease gene OCP enhances blast resistance in rice.
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; University of Chinese Academy of Sciences, Beijing, China.; College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua, China.
Papain-like cysteine proteases (PLCPs) play an important role in the immune response of plants. In Arabidopsis, several homologous genes are known to be involved in defending against pathogens. However, the effects of PLCPs on diseases that afflict rice are largely unknown. In this study, we show that a PLCP, an oryzain alpha chain precursor (OCP), the ortholog of the Arabidopsis protease RD21 (responsive to dehydration 21), participates in regulating resistance to blast disease with a shorter lesion length characterizing the knockout lines (ocp-ko), generated via CRISPR/Cas9 technology. OCP was expressed in all rice tissues and mainly located in the cytoplasm. We prove that OCP, featuring cysteine protease activity, interacts with OsRACK1A (receptor for activated C kinase 1) and OsSNAP32 (synaptosome-associated protein of 32 kD) physically in vitro and in vivo, and they co-locate in the rice cytoplasm but cannot form a ternary complex. Many genes related to plant immunity were enriched in the ocp-ko1 line whose expression levels changed significantly. The expression of jasmonic acid (JA) and ethylene (ET) biosynthesis and regulatory genes were up-regulated, while that of auxin efflux transporters was down-regulated in ocp-ko1. Therefore, OCP negatively regulates blast resistance in rice by interacting with OsRACK1A or OsSNAP32 and influencing the expression profiles of many resistance-related genes. Moreover, OCP might be the cornerstone of blast resistance by suppressing the activation of JA and ET signaling pathways as well as promoting auxin signaling pathways. Our research provides a comprehensive resource of PLCPs for rice plants in defense against pathogens that is also of potential breeding value.
PMID: 36531367
Front Plant Sci , IF:5.753 , 2022 , V13 : P1060228 doi: 10.3389/fpls.2022.1060228
Molecular mechanism of leaf adaxial upward curling caused by BpPIN3 suppression in Betula pendula.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China.; Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States.
Leaves are one of the vegetative organs of plants that are essential for plant growth and development. PIN-FORMED (PINs) gene is an indoleacetic acid (IAA) transporter that plays a critical role in leaf development. To determine the function of BpPIN3 in leaf polarity formation in Betula pendula, the transgenic lines with BpPIN3 overexpression (OE) and BpPIN3-reduced expression (RE) were analyzed using the Agrobacterium-mediated method. The RE lines displayed the characteristics of leaf margin adaxial upward curling, with lower expression of BpPIN3 resulting in greater rolling. Tissue localization of IAA in the auxin GUS reporter system proved that auxin in the RE was mainly distributed in the secondary veins, palisade tissues, and epidermal cells in the leaf margin area. The auxin content in the leaf margin area was significantly greater than that in the main vein tissue. The cell density of the palisade tissue and the ratio of palisade tissue to spongy tissue in the curled leaf margin of the RE lines were found to be significantly decreased. RNA-seq analysis revealed that the RE hormone-signaling pathway genes were significantly enriched compared with those of the OE and WT lines; in particular, the auxin response-related genes SAURs (i.e., SAUR23, SAUR24, SAUR28, and SAUR50) and GH3.10 were found to be significantly upregulated. qRT-PCR analysis indicated that BpPIN3 expression at the leaf margin was significantly lower than that near the main vein in the RE lines. In contrast, the expression levels of SAURs and GH3.10 were significantly higher than those near the midrib. In conclusion, BpPIN3 regulates the expression of auxin response-related genes and the polar transport of auxin to change the polar form of the proximal and distal axes of birch leaves.
PMID: 36531359
Theor Appl Genet , IF:5.699 , 2022 Dec , V135 (12) : P4457-4468 doi: 10.1007/s00122-022-04231-8
BSA‑seq and genetic mapping identified candidate genes for branching habit in peanut.
Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China.; College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.; College of Agricultural Science and Technology, Shandong Agriculture and Engineering University, Jinan, 250100, People's Republic of China.; Cash Crop Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.; Henan Academy of Crop Molecular Breeding, Henan Academy of Agricultural Sciences/Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture/Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, 450002, People's Republic of China.; Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, Australia.; Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China. xingjunw@hotmail.com.; College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China. xingjunw@hotmail.com.; Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100, People's Republic of China. chuanzhiz@126.com.; College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China. chuanzhiz@126.com.
The candidate gene AhLBA1 controlling lateral branch angel of peanut was fine-mapped to a 136.65-kb physical region on chromosome 15 using the BSA-seq and QTL mapping. Lateral branch angel (LBA) is an important plant architecture trait of peanut, which plays key role in lodging, peg soil penetration and pod yield. However, there are few reports of fine mapping and quantitative trait loci (QTLs)/cloned genes for LBA in peanut. In this project, a mapping population was constructed using a spreading variety Tifrunner and the erect variety Fuhuasheng. Through bulked segregant analysis sequencing (BSA-seq), a major gene related to LBA, named as AhLBA1, was preliminarily mapped at the region of Chr.15: 150-160 Mb. Then, using traditional QTL approach, AhLBA1 was narrowed to a 1.12 cM region, corresponding to a 136.65-kb physical interval of the reference genome. Of the nine genes housed in this region, three of them were involved in hormone metabolism and regulation, including one "F-box protein" and two "2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase (2OG oxygenase)" encoding genes. In addition, we found that the level of some classes of cytokinin (CK), auxin and ethylene showed significant differences between spreading and erect peanuts at the junction of main stem and lateral branch. These findings will aid further elucidation of the genetic mechanism of LBA in peanut and facilitating marker-assisted selection (MAS) in the future breeding program.
PMID: 36181525
Front Microbiol , IF:5.64 , 2022 , V13 : P1026991 doi: 10.3389/fmicb.2022.1026991
Characterization of plant growth promoting activities of indigenous bacteria of phosphate mine wastes, a first step toward revegetation.
Center of Research Plants and Microbial Biotechnologies, Biodiversity and Environment, Team of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.; HSM, University of Montpellier, CNRS, IRD, Montpellier, France.; Laboratoire des Materiaux Innovants, Energie et Developpement Durable (IMED)_Laboratory, Faculty of Science and Technology, Cadi Ayyad University, Marrakesh, Morocco.; Geology & Sustainable Mining Institute (GSMI), Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco.
Morocco holds the vast majority of the world's phosphate reserves, but due to the processes involved in extracting and commercializing these reserves, large quantities of de-structured, nutritionally deficient mine phosphate wastes are produced each year. In a semi-arid climate, these wastes severely hamper plant growth and development leading to huge unvegetated areas. Soil indigenous Plant Growth-Promoting Bacteria (PGPB) play a pivotal role in restauration of these phosphate mining wastes by revegetation, by increasing plants development, soil functioning, and nutrient cycling. The development of a vegetative cover above the degraded phosphate wastes, could stabilize and reintegrate these wastes in the surrounding environment. The current study's objectives were to isolate, characterize, and identify indigenous bacterial strains, and test their PGP activity in vitro and, for the best-performing strains in planta, in order to assess their potential for acting as biofertilizers. A quantitative test for the synthesis of auxin and the production of siderophores as well as a qualitative test for the solubilization of phosphate were performed on all isolated bacterial strains. The production of hydrogen cyanide (HCN), exopolysaccharides (EPS), and enzymes were also examined. Three bacteria, selected among the best PGPB of this study, were tested in planta to determine whether such indigenous bacteria could aid plant growth in this de-structured and nutrient-poor mining soil. Using 16S rRNA gene sequencing, 41 bacterial strains were isolated and 11 genera were identified: Acinetobacter, Agrococcus, Bacillus, Brevibacterium, Microbacterium, Neobacillus, Paenibacillus, Peribacillus, Pseudarthrobacter, Stenotrophomonas, and Raoultella. Among the three best performing bacteria (related to Bacillus paramycoides, Brevibacterium anseongense, and Stenotrophomonas rhizophila), only Stenotrophomonas rhizophila and Brevibacterium anseongense were able to significantly enhance Lupinus albus L. growth. The best inoculation results were obtained using the strain related to Stenotrophomonas rhizophila, improving the plant's root dry weight and chlorophyll content. This is also, to our knowledge, the first study to show a PGP activity of Brevibacterium anseongense.
PMID: 36590425
J Agric Food Chem , IF:5.279 , 2022 Dec , V70 (51) : P16229-16240 doi: 10.1021/acs.jafc.2c07072
Novel Plant Growth Regulator Guvermectin from Plant Growth-Promoting Rhizobacteria Boosts Biomass and Grain Yield in Rice.
Key Laboratory of Agricultural Microbiology of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China.; State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.; Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China.; Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
Food is a fundamental human right, and global food security is threatened by crop production. Plant growth regulators (PGRs) play an essential role in improving crop yield and quality, and this study reports on a novel PGR, termed guvermectin (GV), isolated from plant growth-promoting rhizobacteria, which can promote root and coleoptile growth, tillering, and early maturing in rice. GV is a nucleoside analogue like cytokinin (CK), but it was found that GV significantly promoted root and hypocotyl growth, which is different from the function of CK in Arabidopsis. The Arabidopsis CK receptor triple mutant ahk2-2 ahk3-3 cre1-12 still showed a GV response. Moreover, GV led different growth-promoting traits from auxin, gibberellin (GA), and brassinosteroid (BR) in Arabidopsis and rice. The results from a four-year field trial involving 28 rice varieties showed that seed-soaking treatment with GV increased the yields by 6.2 to 19.6%, outperforming the 4.0 to 10.8% for CK, 1.6 to 16.9% for BR, and 2.2 to 7.1% for GA-auxin-BR mixture. Transcriptome analysis demonstrated that GV induced different transcriptome patterns from CK, auxin, BR, and GA, and SAUR genes may regulate GV-mediated plant growth and development. This study suggests that GV represents a novel PGR with a unique signal perception and transduction pathway in plants.
PMID: 36515163
J Agric Food Chem , IF:5.279 , 2022 Dec , V70 (49) : P15380-15389 doi: 10.1021/acs.jafc.2c05908
Identification of a Novel 2,4-D Metabolic Detoxification Pathway in 2,4-D-Resistant Waterhemp (Amaranthus tuberculatus).
Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, United States.; Department of Chemistry, Materials and Molecular Analysis Center, Colorado State University, Fort Collins, Colorado 80523, United States.
A 2,4-dichlorophenoxyactic acid (2,4-D)-resistant population of Amaranthus tuberculatus (common waterhemp) from Nebraska, USA, was previously found to have rapid metabolic detoxification of the synthetic auxin herbicide 2,4-D. We purified the main 2,4-D metabolites from resistant and susceptible plants, solved their structures by nuclear magnetic resonance (NMR) and high-resolution mass spectrometry (HRMS), and synthesized the metabolites to determine their in planta toxicity. Susceptible plants conjugated 2,4-D to aspartate to form 2,4-D-aspartic acid (2,4-D-Asp), while resistant plants had a unique metabolic profile where 2,4-D was hydroxylated into 5-OH-2,4-D, followed by conjugation into a sugar metabolite (2,4-D-5-O-d-glucopyranoside) and subsequent malonylation into 2,4-D-(6'-O-malonyl)-5-O-d-glucopyranoside. Toxicological studies on waterhemp and Arabidopsis thaliana confirmed that the hydroxylated metabolite lost its auxinic action and toxicity. In contrast, the 2,4-D-Asp metabolite found in susceptible plants retained some auxinic action and toxicity. These results demonstrate that 2,4-D-resistant A. tuberculatus evolved novel detoxification reactions not present in susceptible plants to rapidly metabolize 2,4-D, potentially mediated by cytochrome P450 enzymes that perform the initial 5-hydroxylation reaction. This novel mechanism is more efficient to detoxify 2,4-D and produces metabolites with lower toxicity compared to the aspartic acid conjugation found in susceptible waterhemp.
PMID: 36453610
Biology (Basel) , IF:5.079 , 2023 Jan , V12 (1) doi: 10.3390/biology12010095
The Strigolactone Pathway Is a Target for Modifying Crop Shoot Architecture and Yield.
Waite Research Institute, School of Agriculture Food & Wine, The University of Adelaide, Adelaide, SA 5064, Australia.; Australian Research Council Centre of Excellence in Plants for Space, The University of Adelaide, Adelaide, SA 5064, Australia.; Australian Research Council Training Centre for Future Crops Development, The University of Adelaide, Adelaide, SA 5064, Australia.; Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD 4072, Australia.
Due to their sessile nature, plants have developed the ability to adapt their architecture in response to their environment. Branching is an integral component of plant architecture, where hormonal signals tightly regulate bud outgrowth. Strigolactones (SLs), being a novel class of phytohormone, are known to play a key role in branching decisions, where they act as a negative regulator of bud outgrowth. They can achieve this by modulating polar auxin transport to interrupt auxin canalisation, and independently of auxin by acting directly within buds by promoting the key branching inhibitor TEOSINTE BRANCHED1. Buds will grow out in optimal conditions; however, when conditions are sub-optimal, SL levels increase to restrict branching. This can be a problem in agricultural applications, as reductions in branching can have deleterious effects on crop yield. Variations in promoter elements of key SL-related genes, such as IDEAL PLANT ARCHITECTURE1, have been identified to promote a phenotype with enhanced yield performance. In this review we highlight how this knowledge can be applied using new technologies to develop new genetic variants for improving crop shoot architecture and yield.
PMID: 36671787
Metabolites , IF:4.932 , 2022 Dec , V12 (12) doi: 10.3390/metabo12121231
In Vivo Low-Temperature Plasma Ionization Mass Spectrometry (LTP-MS) Reveals Regulation of 6-Pentyl-2H-Pyran-2-One (6-PP) as a Physiological Variable during Plant-Fungal Interaction.
Department of Biotechnology and Biochemistry, Center for Research and Advanced Studies (CINVESTAV), Irapuato 36824, Mexico.; UGA-Langebio, Center for Research and Advanced Studies (CINVESTAV) Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-Leon, Irapuato 36824, Mexico.; Department of Biochemical Engineering, Nacional Technological Institute, Celaya 38010, Mexico.
Volatile organic compounds (VOCs) comprises a broad class of small molecules (up to ~300 g/mol) produced by biological and non-biological sources. VOCs play a vital role in an organism's metabolism during its growth, defense, and reproduction. The well-known 6-pentyl-alpha-pyrone (6-PP) molecule is an example of a major volatile biosynthesized by Trichoderma atroviride that modulates the expression of PIN auxin-transport proteins in primary roots of Arabidopsis thaliana during their relationship. Their beneficial relation includes lateral root formation, defense induction, and increased plant biomass production. The role of 6-PP has been widely studied due to its relevance in this cross-kingdom relationship. Conventional VOCs measurements are often destructive; samples require further preparation, and the time resolution is low (around hours). Some techniques enable at-line or real-time analyses but are highly selective to defined compounds. Due to these technical constraints, it is difficult to acquire relevant information about the dynamics of VOCs in biological systems. Low-temperature plasma (LTP) ionization allows the analysis of a wide range of VOCs by mass spectrometry (MS). In addition, LTP-MS requires no sample preparation, is solvent-free, and enables the detection of 6-PP faster than conventional analytical methods. Applying static statistical methods such as Principal Component Analysis (PCA) and Discriminant Factorial Analysis (DFA) leads to a loss of information since the biological systems are dynamic. Thus, we applied a time series analysis to find patterns in the signal changes. Our results indicate that the 6-PP signal is constitutively emitted by T. atroviride only; the signal shows high skewness and kurtosis. In A. thaliana grown alone, no signal corresponding to 6-PP is detected above the white noise level. However, during T. atroviride-A. thaliana interaction, the signal performance showed reduced skewness and kurtosis with high autocorrelation. These results suggest that 6-PP is a physiological variable that promotes homeostasis during the plant-fungal relationship. Although the molecular mechanism of this cross-kingdom control is still unknown, our study indicates that 6-PP has to be regulated by A. thaliana during their interaction.
PMID: 36557269
Plant Cell Physiol , IF:4.927 , 2023 Jan doi: 10.1093/pcp/pcad007
Wound-induced rooting in plants - A big BIG ROle emerges for calcium and auxin.
Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 Japan.
PMID: 36688580
Plant Cell Physiol , IF:4.927 , 2023 Jan , V63 (12) : P2045 doi: 10.1093/pcp/pcac169
Editor's Note: The Impact of Tobamovirus Infection on Root Development Involves Induction of Auxin Response Factor 10a in Tomato.
PMID: 36625085
Plant Cell Physiol , IF:4.927 , 2023 Jan , V63 (12) : P1943-1953 doi: 10.1093/pcp/pcac150
Silicon Palliates Chromium Toxicity through the Formation of Root Hairs in Rice (Oryza sativa) Mediated by GSH and IAA.
Crop Nanobiology and Molecular Stress Physiology Lab, Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida 201313, India.; Department of Biotechnology, Motilal Nehru National Institute of Technology Allahabad, Prayagraj, UP 211004, India.; Department of Biology, Saint Joseph's University, University City Campus, 600 S. 43rd St., Philadelphia, PA 19104, USA.; Department of Stress, Development and Signaling in Plants, Group of Antioxidants, Free Radicals and Nitric Oxide in Biotechnology, Food and Agriculture, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas (CSIC), Profesor Albareda 1, Granada 18008, Spain.; Plant Physiology Laboratory, Department of Botany, C.M.P. Degree College, A Constituent Post Graduate College of University of Allahabad, Prayagraj 211002, India.
Along with the rapidly increasing environmental contamination by heavy metals, the exposure of plants to chromium has also magnified, resulting in a declined productivity. Hexavalent chromium [Cr(VI)], the most toxic form of Cr, brings about changes in plant processes at morpho-physiological and biochemical levels. However, silicon (Si) is known to mitigate the impact of abiotic stresses in plants. Here, we demonstrate Si-mediated alleviation of Cr(VI) toxicity and its effects on root hair formation in rice seedlings. Reduced glutathione (GSH) and indole-3 acetic acid (IAA, an important auxin) were assessed for their involvement in root hair formation after the application of Si to Cr(VI)-stressed plants, and our results confirmed their crucial significance in such developmental processes. The expression analysis of genes involved in GSH biosynthesis (OsGS2) and regeneration (OsGR1), and auxin biosynthesis (OsTAA1 and OsYUCCA1) and transport (OsAUX1 and OsPIN1) corroborated their positive role in Si-mediated root hair formation in Cr(VI)-stressed rice seedlings. Moreover, the results indicated that nitric oxide (NO) seems a probable but not fundamental component in Si-mediated formation of roots in rice during exposure to Cr(VI) stress. In this study, the indispensable role of GSH and IAA, redox homeostasis of GSH and IAA biosynthesis and transport are discussed with regard to Si-mediated formation of root hairs in rice under Cr(VI) stress. The results of the study suggest that Si is a protective agent against Cr(VI) stress in rice, and the findings can be used to develop Cr(VI) stress-tolerant varieties of rice with enhanced productivity.
PMID: 36264202
Plant Cell Physiol , IF:4.927 , 2023 Jan , V63 (12) : P1848-1856 doi: 10.1093/pcp/pcac149
Integration of Auxin, Brassinosteroid and Cytokinin in the Regulation of Rice Yield.
Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, 77 Cheongam-Ro, Namgu, Pohang-si 37673, South Korea.; Department of Botany, Hindu Girls College, Maharshi Dayanand University, Sonipat 131001, India.; Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, TX 79409, Vietnam.; Department of Plant and Soil Science, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79409, USA.
Crop varieties with a high yield are most desirable in the present context of the ever-growing human population. Mostly, the yield traits are governed by a complex of numerous molecular and genetic facets modulated by various quantitative trait loci (QTLs). With the identification and molecular characterizations of yield-associated QTLs over recent years, the central role of phytohormones in regulating plant yield is becoming more apparent. Most often, different groups of phytohormones work in close association to orchestrate yield attributes. Understanding this cross talk would thus provide new venues for phytohormone pyramiding by editing a single gene or QTL(s) for yield improvement. Here, we review a few important findings to integrate the knowledge on the roles of auxin, brassinosteroid and cytokinin and how a single gene or a QTL could govern cross talk among multiple phytohormones to determine the yield traits.
PMID: 36255097
Plant Cell Physiol , IF:4.927 , 2023 Jan , V63 (12) : P1814-1825 doi: 10.1093/pcp/pcac138
Auxin Crosstalk with Reactive Oxygen and Nitrogen Species in Plant Development and Abiotic Stress.
Department of Botany, D D Pant Interdisciplinary Research Laboratory, University of Allahabad, Prayagraj-211002, India.; Crop Nanobiology and Molecular Stress Physiology Lab, Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida 201313, India.; Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, Prayagraj-211004, India.; Department of Botany, Plant Physiology Laboratory, CMP, Degree Collage, University of Allahabad, Prayagraj-211002, India.; Department of Biology, Technische Universitat Dresden, Dresden 01062, Germany.; Department of Biochemistry, Cell and Molecular Biology, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas (CSIC), C/Professor Albareda, 1, Granada 18008, Spain.
The phytohormone auxin acts as an important signaling molecule having regulatory functions during the growth and development of plants. Reactive oxygen species (ROS) are also known to perform signaling functions at low concentrations; however, over-accumulation of ROS due to various environmental stresses damages the biomolecules and cell structures and leads to cell death, and therefore, it can be said that ROS act as a double-edged sword. Nitric oxide (NO), a gaseous signaling molecule, performs a wide range of favorable roles in plants. NO displays its positive role in photomorphogenesis, root growth, leaf expansion, seed germination, stomatal closure, senescence, fruit maturation, mitochondrial activity and metabolism of iron. Studies have revealed the early existence of these crucial molecules during evolution. Moreover, auxin, ROS and NO together show their involvement in various developmental processes and abiotic stress tolerance. Redox signaling is a primary response during exposure of plants to stresses and shows a link with auxin signaling. This review provides updated information related to crosstalk between auxin, ROS and NO starting from their evolution during early Earth periods and their interaction in plant growth and developmental processes as well as in the case of abiotic stresses to plants.
PMID: 36208156
Plant Cell Physiol , IF:4.927 , 2023 Jan , V63 (12) : P1806-1813 doi: 10.1093/pcp/pcac084
Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize.
Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India.
The evolution of root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, and thus a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus adventitious root types display species-specific diversity. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of the actions and interactions of crucial genetic and hormonal regulators. In this review, we provide a comprehensive view of the key regulators involved during the different stages of adventitious root development in two important crop plants, rice and maize. We have reviewed the roles of major phytohormones, microRNAs and transcription factors and their crosstalk during adventitious root development in these cereal crops.
PMID: 35713294
Plant Cell Physiol , IF:4.927 , 2023 Jan , V63 (12) : P1980-1993 doi: 10.1093/pcp/pcab179
The Impact of Tobamovirus Infection on Root Development Involves Induction of Auxin Response Factor 10a in Tomato.
Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Institute, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel.; The Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, PO Box 12, Rehovot 761001, Israel.; Plant Sciences Institute, Agricultural Research Organization, The Volcani Institute, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel.
Plant viruses cause systemic diseases that severely impair plant growth and development. While the accumulation of viruses in the root system has long been established, little is known as to how viruses affect root architecture. Here, we examined how the emerging tobamovirus, tomato brown rugose fruit virus (ToBRFV), alters root development in tomato. We found that ToBRFV and tobacco mosaic virus both invaded root systems during the first week of infection. ToBRFV infection of tomato plants resulted in a significant decrease in root biomass and elongation and root-to-shoot ratio and a marked suppression of root branching. Mutation in RNA-dependent RNA polymerase 6 increased the susceptibility of tomato plants to ToBRFV, resulting in severe reduction of various root growth parameters including root branching. Viral root symptoms were associated with the accumulation of auxin response factor 10a (SlARF10a) transcript, a homolog of Arabidopsis ARF10, a known suppressor of lateral root development. Interestingly, loss-of-function mutation in SlARF10a moderated the effect of ToBRFV on root branching. In contrast, downregulation of sly-miR160a, which targets SlARF10a, was associated with constitutive suppression root branching independent of viral infection. In addition, overexpression of a microRNA-insensitive mutant of SlARF10a mimicked the effect of ToBRFV on root development, suggesting a specific role for SlARF10a in ToBRFV-mediated suppression of root branching. Taken together, our results provide new insights into the impact of tobamoviruses on root development and the role of ARF10a in the suppression of root branching in tomato.
PMID: 34977939
Plant Cell Physiol , IF:4.927 , 2023 Jan , V63 (12) : P1968-1979 doi: 10.1093/pcp/pcab155
Auxin-Responsive (Phospho)proteome Analysis Reveals Key Biological Processes and Signaling Associated with Shoot-Borne Crown Root Development in Rice.
Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee, Uttarakhand 247667, India.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent 9052, Belgium.; VIB Center for Plant Systems Biology, Ghent 9052, Belgium.
The rice root system is primarily composed of shoot-borne adventitious/crown roots (ARs/CRs) that develop from the coleoptile base, and therefore, it is an excellent model system for studying shoot-to-root trans-differentiation process. We reveal global changes in protein and metabolite abundance and protein phosphorylation in response to an auxin stimulus during CR development. The liquid chromatography-tandem mass spectrometry (LC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) analyses of developing crown root primordia (CRP) and emerged CRs identified 334 proteins and 12 amino acids, respectively, that were differentially regulated upon auxin treatment. Gene ontology enrichment analysis of global proteome data uncovered the biological processes associated with chromatin conformational change, gene expression and cell cycle that were regulated by auxin signaling. Spatial gene expression pattern analysis of differentially abundant proteins disclosed their stage-specific dynamic expression pattern during CRP development. Further, our tempo-spatial gene expression and functional analyses revealed that auxin creates a regulatory module during CRP development and activates ethylene biosynthesis exclusively during CRP initiation. Further, the phosphoproteome analysis identified 8,220 phosphosites, which could be mapped to 1,594 phosphoproteins and of which 66 phosphosites were differentially phosphorylated upon auxin treatment. Importantly, we observed differential phosphorylation of the cyclin-dependent kinase G-2 (OsCDKG;2) and cell wall proteins, in response to auxin signaling, suggesting that auxin-dependent phosphorylation may be required for cell cycle activation and cell wall synthesis during root organogenesis. Thus, our study provides evidence for the translational and post-translational regulation during CR development downstream of the auxin signaling pathway.
PMID: 34679169
Pest Manag Sci , IF:4.845 , 2022 Dec doi: 10.1002/ps.7294
The differential binding and biological efficacy of auxin herbicides.
School of Life Sciences, University of Warwick, Coventry, UK.; Corteva Agriscience, Crop Protection Discovery & Development, Indianapolis, Indiana, USA.
BACKGROUND: Auxin herbicides have been used for selective weed control for 75 years and they continue to be amongst the most widely used weed control agents globally. The auxin herbicides fall into five chemical classes, with two herbicides not classified, and in all cases it is anticipated that recognition in the plant starts with binding to the Transport Inhibitor Response 1 (TIR1) family of auxin receptors. There is evidence that some classes of auxins act selectively with certain clades of receptors, although a comprehensive structure-activity relationship has not been available. RESULTS: Using purified receptor proteins to measure binding efficacy we have conducted quantitative structure activity relationship (qSAR) assays using representative members of the three receptor clades in Arabidopsis, TIR1, AFB2 and AFB5. Complementary qSAR data for biological efficacy at the whole-plant level using root growth inhibition and foliar phytotoxicity assays have also been analyzed for each family of auxin herbicides, including for the afb5-1 receptor mutant line. CONCLUSIONS: Comparisons of all these assays highlight differences in receptor selectivity and some systematic differences between results for binding in vitro and activity in vivo. The results could provide insights into weed spectrum differences between the different classes of auxin herbicides, as well as the potential resistance and cross-resistance implications for this herbicide class. (c) 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
PMID: 36458868
Plant Sci , IF:4.729 , 2023 Jan , V329 : P111606 doi: 10.1016/j.plantsci.2023.111606
pin2 mutant agravitropic root phenotype is conditional and nutrient-sensitive.
IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France.; Univ New Hampshire, Durham, USA.; IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France. Electronic address: benjamin.peret@cnrs.fr.
Plants have the capacity to sense and adapt to environmental factors using the phytohormone auxin as a major regulator of tropism and development. Among these responses, gravitropism is essential for plant roots to grow downward in the search for nutrients and water. We discovered a new mutant allele of the auxin efflux transporter PIN2 that revealed that pin2 agravitropic root mutants are conditional and nutrient-sensitive. We describe that nutrient composition of the medium, rather than osmolarity, can revert the agravitropic root phenotype of pin2. Indeed, on phosphorus- and nitrogen-deprived media, the agravitropic root defect was restored independently of primary root growth levels. Slow and fast auxin responses were evaluated using DR5 and R2D2 probes, respectively, and revealed a strong modulation by nutrient composition of the culture medium. We evaluated the role of PIN and AUX auxin transporters and demonstrated that neither PIN3 nor AUX1 are involved in this process. However, we observed the ectopic expression of PIN1 in the epidermis in the pin2 mutant background associated with permissive, but not restrictive, conditions. This ectopic expression was associated with a restoration of the asymmetric accumulation of auxin necessary for the reorientation of the root according to gravity. These observations suggest a strong regulation of auxin distribution by nutrients availability, directly impacting root's ability to drive their gravitropic response.
PMID: 36706868
Plant Sci , IF:4.729 , 2023 Feb , V327 : P111536 doi: 10.1016/j.plantsci.2022.111536
A 2-bp deletion in the protein kinase domain region of the ERECTA-like receptor kinase gene in cucumber results in short internode phenotype.
School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China.; School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China.; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, Jiangsu 210014, China.; School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou, Jiangsu 225009, China. Electronic address: xhchen@yzu.edu.cn.
Cucumber varieties with shortend internodes require less space than regular vining varieties, thus have great significance for germplasm improvement. Here, we found a novel spontaneous cucumber mutant si107 that exhibited short intenodes (si), smaller leaves, fruits, and seeds. The decrease in longitudinal cell length led to the shortened internodes of si107. The genetic analysis revealed a single recessive gene si-2 that was responsible for the mutation. Through multiple lines of evidence, we demonstrated that CsSI is the possible candidate gene for si-2, which encodes an ERECTA leucine-rich repeat receptor-like kinase. The shortened internode in si107 is attributed to a 2-bp deletion in the protein kinase domain region of this gene. The expression of CsSI was higher in the internodes, petioles, and fruit peels of si107 than in the wild type (WT). The transcriptome analysis between the si107 mutant and WT indicated that differentially expressed genes were significantly enriched in the plant hormone signal transduction pathway, in which auxin signal genes comprised the largest group, and all were downregulated in si107. Phytohormone quantitation confirmed that endogenous auxin levels in the stems of si107 were decreased. Our results provide new insights into the molecular mechanisms underlying the internode length control in cucumber.
PMID: 36402238
Plant Sci , IF:4.729 , 2023 Jan , V326 : P111522 doi: 10.1016/j.plantsci.2022.111522
Transcription factor NtWRKY33a modulates the biosynthesis of polyphenols by targeting NtMYB4 and NtHCT genes in tobacco.
China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China.; Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China.; Technology Center, China Tobacco Hunan Industrial Co., Ltd., Changsha 410007, China. Electronic address: hpj3508@126.com.; China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute of CNTC, Zhengzhou 450001, China. Electronic address: yangjun@ztri.com.cn.
There are abundant polyphenols in tobacco leaves mainly including chlorogenic acid (CGA), rutin, and scopoletin, which not only influence plant growth, development, and environmental adaptation, but also have a great impact on the industrial utilization of tobacco leaves. Few transcription factors regulating the biosynthesis of polyphenols have been identified in tobacco so far. In this study, two NtWRKY33 genes were identified from N. tabacum genome. NtWRKY33a showed higher transcriptional activity than NtWRKY33b, and encoded a nuclear localized protein. Overexpression and knock-out of NtWRKY33a gene revealed that NtWRKY33a inhibited the accumulation of rutin, scopoletin, and total polyphenols, but meanwhile promoted the biosynthesis of CGA. Chromatin immunoprecipitation and Dual-Luc assays indicated that NtWRKY33a could directly bind to the promoters of NtMYB4 and NtHCT, and thus induced the transcription of these two genes. The contents of polyphenols in ntwrky33a, ntmy4, and ntwrky33a/ntmyb4 mutants further confirmed that the repression of NtWRKY33a on the biosynthesis of rutin, scopoletin, and total polyphenols depends on the activity of NtMYB4. Moreover, the promotion of NtHCT by NtWRKY33a modulates the distribution of metabolism flux into the synthesis of CGA. Ectopic expression of NtWRKY33a inhibit the expression of NtSAUR14, NtSAUR59, NtSAUR66, NtIAA4, NtIAA17, and NtIAA19 genes, indicating that NtWRKY33a might be involved in the regulation of plant auxin response. Our study revealed new functions of NtWRKY33a in regulating the synthesis of polyphenols, and provided a promising target for manipulating polyphenols contents in tobacco.
PMID: 36332766
Plant Sci , IF:4.729 , 2022 Dec , V325 : P111500 doi: 10.1016/j.plantsci.2022.111500
Molecular hydrogen positively influences lateral root formation by regulating hydrogen peroxide signaling.
College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.; College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China. Electronic address: wbshenh@njau.edu.cn.
Although a previous study discovered that exogenous molecular hydrogen (H(2)) supplied with hydrogen-rich water (HRW) can mediate lateral root (LR) development, whether or how endogenous H(2) influences LR formation is still elusive. In this report, mimicking the induction responses in tomato seedlings achieved by HRW or exogenous hydrogen peroxide (H(2)O(2); a positive control), transgenic Arabidopsis that overexpressed the hydrogenase1 gene (CrHYD1) from Chlamydomonas reinhardtii not only stimulated endogenous hydrogen peroxide (H(2)O(2)) production, but also markedly promoted LR formation. Above H(2) and H(2)O(2) responses were abolished by the removal of endogenous H(2)O(2). Moreover, the changes in transcriptional patterns of representative cell cycle genes and auxin signaling-related genes during LR development in both tomato and transgenic Arabidopsis thaliana matched with above phenotypes. The alternations in the levels of GUS transcripts driven by the CYCB1 promoter and expression of PIN1 protein further indicated that H(2)O(2) synthesis was tightly linked to LR formation achieved by endogenous H(2), and cell cycle regulation and auxin-dependent pathway might be their targets. There results might provide a reference for molecular mechanism underlying the regulation of root morphogenesis by H(2).
PMID: 36257409
Plant Sci , IF:4.729 , 2022 Dec , V325 : P111462 doi: 10.1016/j.plantsci.2022.111462
Overexpression of SmLAC25 promotes lignin accumulation and decreases salvianolic acid content in Salvia miltiorrhiza.
Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China.; College of Life Science and Food Engineering, Shaanxi Xueqian Normal University, Xi'an 710100, China.; Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China. Electronic address: Zhuxj2018@snnu.edu.cn.; Key Laboratory of the Ministry of Education for Medicinal Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest of China, College of Life Science, Shaanxi Normal University, Xi'an 710062, China. Electronic address: caoxiaoyan@snnu.edu.cn.
Laccase (LAC) is a blue multicopper oxidase that contains four copper ions, which is involved in lignin polymerization and flavonoid biosynthesis in plants. Although dozens of LAC genes have been identified in Salvia miltiorrhiza Bunge (a model medicinal plant), most have not been functionally characterized. Here, we explored the expression patterns and the functionality of SmLAC25 in S. miltiorrhiza. SmLAC25 has a higher expression level in roots and responds to methyl jasmonate, auxin, abscisic acid, and gibberellin stimuli. The SmLAC25 protein is localized in the cytoplasm and chloroplasts. Recombinant SmLAC25 protein could oxidize coniferyl alcohol and sinapyl alcohol, two monomers of G-lignin and S-lignin. To investigate its function, we generated SmLAC25-overexpressed S. miltiorrhiza plantlets and hairy roots. The lignin content increased significantly in all SmLAC25-overexpressed plantlets and hairy roots, compared with the controls. However, the concentrations of rosmarinic acid and salvianolic acid B decreased significantly in all the SmLAC25-overexpressed lines. Further studies revealed that the transcription levels of some key enzyme genes in the lignin synthesis pathway (e.g., SmCCR and SmCOMT) were significantly improved in the SmLAC25-overexpressed lines, while the expression levels of multiple enzyme genes in the salvianolic acid biosynthesis pathway were inhibited. We speculated that the overexpression of SmLAC25 promoted the metabolic flux of lignin synthesis, which resulted in a decreased metabolic flux to the salvianolic acid biosynthesis pathway.
PMID: 36126879
Plant Sci , IF:4.729 , 2022 Dec , V325 : P111461 doi: 10.1016/j.plantsci.2022.111461
Dissection of transcriptome and metabolome insights into the isoquinoline alkaloid biosynthesis during stem development in Phellodendron amurense (Rupr.).
Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China; State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 15004, China. Electronic address: lx2016bjfu@163.com.; State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 15004, China. Electronic address: ckwnefu@163.com.; Linjiang Forestry Bureau of Jilin Province, Linjiang 134600, China. Electronic address: 38047646@qq.com.; Linjiang Forestry Bureau of Jilin Province, Linjiang 134600, China. Electronic address: 67651509@qq.com.; Linjiang Forestry Bureau of Jilin Province, Linjiang 134600, China. Electronic address: 18314591710@163.com.; Linjiang Forestry Bureau of Jilin Province, Linjiang 134600, China. Electronic address: 893483624@qq.com.; Linjiang Forestry Bureau of Jilin Province, Linjiang 134600, China. Electronic address: 1604861006@qq.com.; Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China. Electronic address: xiaonapei2020@163.com.; Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China; State Key Laboratory of Tree Genetics and Breeding, School of Forestry, Northeast Forestry University, Harbin 15004, China. Electronic address: zhaoxyphd@163.com.
Phellodendron amurense (Rupr.) is a well-known medicinal plant with high medicinal value, and its various tissues are enriched in various active pharmaceutical ingredients. Isoquinoline alkaloids are the primary medicinal component of P. amurense and have multiple effects, such as anti-inflammation, antihypertension, and antitumor effects. However, the potential regulatory mechanism of isoquinoline alkaloid biosynthesis during stem development in P. amurense is still poorly understood. In the present study, a total of eight plant hormones for each stem development stage were detected; of those, auxin, gibberellins and brassinosteroids were significantly highly increased in perennial stems and played key roles during stem development in P. amurense. We also investigated the content and change pattern of secondary metabolites and comprehensively identified some key structural genes involved in the isoquinoline alkaloid biosynthesis pathway by combining the transcriptome and metabolomics. A total of 39,978 DEGs were identified in the present study, and six of those had candidate structural genes (NCS, GOT2, TYNA, CODM, TYR, TAT and PSOMT1) that were specifically related to isoquinoline alkaloid biosynthesis in P. amurense. Corydalmine, cyclanoline, dehydroyanhunine, (S)-canadine and corybulbine were the most significantly upregulated metabolites among the different comparative groups. Three differentially expressed metabolites, dopamine, (S)-corytuberine and (S)-canadine, were enriched in the isoquinoline alkaloid biosynthesis pathway. Furthermore, bHLH and WRKY transcription factors play key roles in the isoquinoline alkaloid biosynthesis pathway in P. amurense. The results not only provide comprehensive genetic information for understanding the molecular mechanisms of isoquinoline alkaloid biosynthesis but also lay a foundation for the combinatory usage of the medicinal active ingredient of P. amurense.
PMID: 36122814
Plant Sci , IF:4.729 , 2022 Dec , V325 : P111459 doi: 10.1016/j.plantsci.2022.111459
ZmDWF1 regulates leaf angle in maize.
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China; Henan Academy of Agricultural Science, Zhengzhou, Henan 450002, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China.; College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, No. 15 Longzihu University Park, Zhengdong New Area, Zhengzhou, Henan 450046, China. Electronic address: kulixia0371@163.com.
Leaf angle (LA) is a critical agronomic trait enhancing grain yield under high-density planting in maize. A number of researches have been conducted in recent years to investigate the quantitative trait loci/genes responsible for LA variation, while only a few genes were identified through map-based cloning. Here we cloned the ZmDWF1 gene, which was previously reported to encode Delta24-sterol reductase in the brassinosteroids (BRs) biosynthesis pathway. Overexpression of ZmDWF1 resulted in enlarged LA, indicating that ZmDWF1 is a positive regulator of LA in maize. To reveal the regulatory framework of ZmDWF1, we conducted RNA-Sequencing and yeast-two hybrid (Y2H) screening analysis. RNA-Sequencing analyzing results indicate ZmDWF1 mainly affected expression level of genes involved in cell wall associated metabolism and hormone metabolism including BR, gibberellin, and auxin. Y2H screening with Bi-FC assay confirmed three proteins (ZmPP2C-1, ZmROF1, and ZmTWD1) interacting with ZmDWF1. We revealed a new regulatory network of ZmDWF1 gene in controlling plant architecture in maize.
PMID: 36113675
Plant Sci , IF:4.729 , 2022 Dec , V325 : P111456 doi: 10.1016/j.plantsci.2022.111456
The cytokinin type-B response regulator PeRR12 is a negative regulator of adventitious rooting and salt tolerance in poplar.
Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: HaoranQi@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing 210037, China; Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China. Electronic address: hengcai@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: chicta@163.com.; Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: sianliu@yzu.edu.cn.; State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China. Electronic address: changjunding@caf.ac.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology Ministry of Education, Nanjing Forestry University, Nanjing 210037, China. Electronic address: xum@njfu.edu.cn.
Adventitious root (AR) development is an ecologically and economically important biological process that maintains ecological balance, improves plant survivability, and allows for massive vegetative propagation, but its genetic mechanisms are not well understood. Here, eight Arabidopsis response regulator (ARR) genes were cloned and identified in poplar, most of which were detected in the AR, phloem, and xylem and showed remarkable induction at different time points during AR development. Subcellular localization indicated that most of these PeRR genes are in the nucleus. Based on qRT-PCR expression analysis of some genes related to AR development, we inferred that overexpression of PeRR12 (OE_PeRR12) may inhibited AR formation by suppressing the transcription of PeWOX11, PeWOX5, PePIN1 and PePIN3 in poplar while promoting type-A RR transcripts. Correspondingly, exogenous auxin partially restored the rooting of OE_PeRR12 poplar by inhibiting PeRR12 expression. Moreover, the activities of the antioxidant systems of OE_PeRR12 poplars were lower than those of wild-type poplars under salt stress conditions, indicating that PeRR12 may acts as a repressor that mediates salt tolerance by suppressing the expression of PeHKT1;1. Altogether, these results suggest that PeRR12 plays essential roles in mediating AR formation and salinity tolerance in poplar.
PMID: 36087886
Plant Cell Rep , IF:4.57 , 2022 Dec doi: 10.1007/s00299-022-02965-9
The Aux/IAA protein TaIAA15-1A confers drought tolerance in Brachypodium by regulating abscisic acid signal pathway.
College of Agronomy, Liaocheng University, Liaocheng, 252059, People's Republic of China. pssu2014@163.com.; College of Agronomy, Liaocheng University, Liaocheng, 252059, People's Republic of China.; College of Agronomy, Liaocheng University, Liaocheng, 252059, People's Republic of China. guoshangjing@lcu.edu.cn.
Overexpression of the Aux/IAA protein TaIAA15-1A from wheat improves drought tolerance by regulating the ABA signalling pathway in transgenic Brachypodium. Drought is a major abiotic stress that causes severe crop yield loss. Aux/IAA genes have been shown to be involved in drought stress responses. However, to the best of our knowledge, there has been little research on the molecular mechanism of the wheat Aux/IAA gene in the context of drought tolerance. In this study, we found that expression of the wheat Aux/IAA gene TaIAA15-1A was upregulated by PEG6000, NaCl, SA, JA, IAA and ABA. Transgenic plants overexpressing TaIAA15-1A showed higher drought tolerance than wild-type (WT) plants. The physiological analyses showed that the transgenic lines exhibited a higher survival rate, shoot length, and relative water content than the WT plants. The activities of superoxide dismutase (SOD), catalase (CAT) and peroxidase (POD) were enhanced in transgenic lines, causing a reduction in the hydrogen peroxide (H(2)O(2)) and superoxide anion radical (O(2)(-)) contents. Transcriptome analysis showed that TaIAA15-1A overexpression alters the expression of these genes involved in the auxin signalling pathway, ABA signalling pathway, phenolamides and antioxidant pathways. The results of exogenous ABA treatment suggested that TaIAA15-1A overexpression increased sensitivity to ABA at the germination and postgermination stages compared to WT plants. These results indicate that TaIAA15-1A plays a positive role in plant drought tolerance by regulating ABA-related genes and improving antioxidative stress ability and has potential application in genetically modified crops.
PMID: 36566287
Plant Cell Rep , IF:4.57 , 2022 Dec doi: 10.1007/s00299-022-02956-w
Auxin and CmAP1 regulate the reproductive development of axillary buds in Chinese chestnut (Castanea mollissima).
Engineering and Technology Research Center for Chestnut of National Forestry and Grassland Administration, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Ruiwangfeng No. 12, Haidian, Beijing, 100093, China.; College of Forestry, Shenyang Agriculture University, Shenyang, 110866, Liaoning, China.; Engineering and Technology Research Center for Chestnut of National Forestry and Grassland Administration, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China) of Ministry of Agriculture, Beijing Engineering Research Center for Deciduous Fruit Trees, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Ruiwangfeng No. 12, Haidian, Beijing, 100093, China. lanyanping2000@126.com.
Auxin accumulation upregulates the expression of APETALA1 (CmAP1) and subsequently activates inflorescence primordium development in axillary buds of chestnut. The architecture of fruiting branches is a key determinant of chestnut yield. Normally, axillary buds at the top of mother fruiting branches develop into flowering shoots and bear fruits, and the lower axillary buds develop into vegetative shoots. Decapitation of the upper axillary buds induces the lower buds to develop into flowering shoots. How decapitation modulates the tradeoff between vegetative and reproductive development is unclear. We detected inflorescence primordia within both upper and lower axillary buds on mother fruiting branches. The level of the phytohormones 3-indoleacetic acid (IAA) and trans-zeatin (tZ) increased in the lower axillary buds in response to decapitation. Exogenous application of the synthetic analogues 1-naphthylacetic acid (NAA) or 6-benzyladenine (6-BA) blocked or promoted, respectively, the development of the inflorescence primordia in axillary buds. The transcript levels of the floral identity gene CmAP1 increased in axillary buds following decapitation. An auxin response element TGA-box is present in the CmAP1 promoter and influenced the CmAP1 promoter-driven expression of beta-glucuronidase (GUS) in floral organs in Arabidopsis, suggesting that CmAP1 is induced by auxin. We propose that decapitation releases axillary bud outgrowth from inhibition caused by apical dominance. During this process, decapitation-induced accumulation of auxin induces CmAP1 expression, subsequently promoting the reproductive development of axillary buds.
PMID: 36528704
Plant Cell Rep , IF:4.57 , 2022 Dec doi: 10.1007/s00299-022-02963-x
The AP2/ERF transcription factor SlERF.J2 functions in hypocotyl elongation and plant height in tomato.
Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China.; Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China. chenguoping@cqu.edu.cn.; Room 523, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400030, People's Republic of China. chenguoping@cqu.edu.cn.; Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing, People's Republic of China. huzongli71@163.com.; Room 521, Bioengineering College, Chongqing University, Campus B, 174 Shapingba Main Street, Chongqing, 400030, People's Republic of China. huzongli71@163.com.
Our findings indicated that the SlERF.J2-IAA23 module integrates hormonal signals to regulate hypocotyl elongation and plant height in tomato. Light and phytohormones can synergistically regulate photomorphogenesis-related hypocotyl elongation and plant height in tomato. AP2/ERF family genes have been extensively demonstrated to play a role in light signaling and various hormones. In this study, we identified a novel AP2/ERF family gene in tomato, SlERF.J2. Overexpression of SlERF.J2 inhibits hypocotyl elongation and plant height. However, the plant height in the slerf.j2(ko) knockout mutant was not significantly changed compared with the WT. we found that hypocotyl cell elongation and plant height were regulated by a network involving light, auxin and gibberellin signaling, which is mediated by regulatory relationship between SlERF.J2 and IAA23. SlERF.J2 protein could bind to IAA23 promoter and inhibit its expression. In addition, light-dark alternation can activate the transcription of SlERF.J2 and promote the function of SlERF.J2 in photomorphogenesis. Our findings indicated that the SlERF.J2-IAA23 module integrates hormonal signals to regulate hypocotyl elongation and plant height in tomato.
PMID: 36512035
Plant Cell Rep , IF:4.57 , 2022 Dec , V41 (12) : P2415-2422 doi: 10.1007/s00299-022-02932-4
Ectopic expression of WOX5 promotes cytokinin signaling and de novo shoot regeneration.
Department of Chemistry, Seoul National University, Seoul, 08826, Korea.; Research Institute of Basic Sciences, Seoul National University, Seoul, 08826, Korea.; Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Korea.; Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea.; Division of Horticultural Biotechnology, School of Biotechnology, Hankyong National University, Anseong, 17579, Korea. yuyu1216@hknu.ac.kr.; Department of Chemistry, Seoul National University, Seoul, 08826, Korea. pjseo1@snu.ac.kr.; Research Institute of Basic Sciences, Seoul National University, Seoul, 08826, Korea. pjseo1@snu.ac.kr.; Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea. pjseo1@snu.ac.kr.
WOX5 has a potential in activating cytokinin signaling and shoot regeneration, in addition to its role in pluripotency acquisition. Thus, overexpression of WOX5 maximizes plant regeneration capacity during tissue culture. In vitro plant regeneration involves two steps: callus formation and de novo shoot organogenesis. The WUSCHEL-RELATED HOMEOBOX 5 (WOX5) homeodomain transcription factor is known to be mainly expressed during incubation on callus-inducing medium (CIM) and involved in pluripotency acquisition in callus, but whether WOX5 also affects de novo shoot regeneration on cytokinin-rich shoot-inducing medium (SIM) remains unknown. Based on the recent finding that WOX5 promotes cytokinin signaling, we hypothesized that ectopic expression of WOX5 beyond CIM would further enhance overall plant regeneration capacity, because intense cytokinin signaling is particularly required for shoot regeneration on SIM. Here, we found that overexpression of the WOX5 gene on SIM drastically promoted de novo shoot regeneration from callus with the repression of type-A ARABIDOPSIS RESPONSE REGULATOR (ARR) genes, negative regulators of cytokinin signaling. The enhanced shoot regeneration phenotypes were indeed dependent on cytokinin signaling, which were partially suppressed in the progeny derived from crossing WOX5-overexpressing plants with cytokinin-insensitive 35S:ARR7 plants. The function of WOX5 in enhancing cytokinin-dependent shoot regeneration is evolutionarily conserved, as conditional overexpression of OsWOX5 on SIM profoundly enhanced shoot regeneration in rice callus. Overall, our results provide the technical advance that maximizes in vitro plant regeneration by constitutively expressing WOX5, which unequivocally promotes both callus pluripotency and de novo shoot regeneration.
PMID: 36219248
Plant Cell Rep , IF:4.57 , 2022 Dec , V41 (12) : P2363-2378 doi: 10.1007/s00299-022-02928-0
Switching cell fate by the actin-auxin oscillator in Taxus: cellular aspects of plant cell fermentation.
Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany.; Institute of Pharmacy, Martin-Luther-University, Halle-Wittenberg, Hoher Weg 8, 06120, Halle (Saale), Germany.; Botanical Institute, Karlsruhe Institute of Technology, Fritz-Haber-Weg 4, 76131, Karlsruhe, Germany. peter.nick@kit.edu.
Paclitaxel synthesis in Taxus cells correlates with a cell-fate switch that leads to vacuoles of a glossy appearance and vermiform mitochondria. This switch depends on actin and apoplastic respiratory burst. Plant cell fermentation, the production of valuable products in plant cell culture, has great potential as sustainable alternative to the exploitation of natural resources for compounds of pharmaceutical interest. However, the success of this approach has remained limited, because the cellular aspects of metabolic competence are mostly unknown. The production of the anti-cancer alkaloid Paclitaxel has been, so far, the most successful case for this approach. In the current work, we map cellular aspects of alkaloid synthesis in cells of Taxus chinensis using a combination of live-cell imaging, quantitative physiology, and metabolite analysis. We show evidence that metabolic potency correlates with a differentiation event giving rise to cells with large vacuoles with a tonoplast that is of a glossy appearance, agglomerations of lipophilic compounds, and multivesicular bodies that fuse with the plasma membrane. Cellular features of these glossy cells are bundled actin, more numerous peroxisomes, and vermiform mitochondria. The incidence of glossy cells can be increased by aluminium ions, and this increase is significantly reduced by the actin inhibitor Latrunculin B, and by diphenylene iodonium, a specific inhibitor of the NADPH oxidase Respiratory burst oxidase Homologue (RboH). It is also reduced by the artificial auxin Picloram. This cellular fingerprint matches the implications of a model, where the differentiation into the glossy cell type is regulated by the actin-auxin oscillator that in plant cells acts as dynamic switch between growth and defence.
PMID: 36214871
Plant Cell Rep , IF:4.57 , 2022 Dec , V41 (12) : P2293-2303 doi: 10.1007/s00299-022-02921-7
Disruption of transcription factor RhMYB123 causes the transformation of stamen to malformed petal in rose (Rosa hybrida).
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China.; School of Applied Chemistry and Biotechnology, Shenzhen Polytechnic, Shenzhen, China.; Yunnan Yuntianhua Modern Agriculture Development Co., Ltd, Kunming, China.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing, China.; Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, China. zhouxiaofeng@cau.edu.cn.
We find that the R2R3 MYB transcription factor RhMYB123 has a novel function to regulate stamen-petal organ specification in rose. Rose is one of the ornamental plants with economic importance worldwide. Malformed flower seriously affects the ornamental value and fertility of rose. However, the regulatory mechanism is largely unknown. In this work, we identified a R2R3 MYB transcription factor RhMYB123 from rose, the expression of which significantly decreased from flower differentiation stage to floral organ development stage. Phylogenetic analysis indicated that it belongs to the same subgroup as MYB123 of Arabidopsis and located in nucleus. In addition, RhMYB123 was confirmed to have transcriptional activation function by dual luciferase assay. Silencing RhMYB123 using Virus-Induced Gene Silencing (VIGS) in rose could increase the number of malformed petaloid stamen. Furthermore, we identified 549 differential expressed genes (DEGs) in TRV-RhMYB123 lines compared to TRV controls by RNA-seq of floral buds (flower differentiation stage). Among of those genes, expression of 3 MADS box family genes related to floral organ development reduced in TRV-RhMYB123 lines, including AGAMOUS (RhAG), AGAMOUS LIKE 15 (RhAGL15), and SHATTERPROOF 1 (RhSHP1). Given, previous studies have shown that auxin plays a crucial role in floral meristem initiation and stamen-petal organ specification. We also found 6 DEGs were involved in auxin signal transduction, of which five were reduced expression in TRV-RhMYB123. Taken together, our findings suggested that RhMYB123 may govern the development of malformed petaloid stamen by regulating the expressions of some MADS box family members and auxin signaling pathway elements.
PMID: 35999377
Nitric Oxide , IF:4.427 , 2023 Jan , V130 : P36-57 doi: 10.1016/j.niox.2022.11.004
Say "NO" to plant stresses: Unravelling the role of nitric oxide under abiotic and biotic stress.
Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India. Electronic address: deepdhaka415@gmail.com.; Department of Zoology, Guru Nanak Dev University, Amritsar, 143005, Punjab, India. Electronic address: ohri_puja_11@rediffmail.com.
Nitric oxide (NO) is a diatomic gaseous molecule, which plays different roles in different strata of organisms. Discovered as a neurotransmitter in animals, NO has now gained a significant place in plant signaling cascade. NO regulates plant growth and several developmental processes including germination, root formation, stomatal movement, maturation and defense in plants. Due to its gaseous state, it is unchallenging for NO to reach different parts of cell and counterpoise antioxidant pool. Various abiotic and biotic stresses act on plants and affect their growth and development. NO plays a pivotal role in alleviating toxic effects caused by various stressors by modulating oxidative stress, antioxidant defense mechanism, metal transport and ion homeostasis. It also modulates the activity of some transcriptional factors during stress conditions in plants. Besides its role during stress conditions, interaction of NO with other signaling molecules such as other gasotransmitters (hydrogen sulfide), phytohormones (abscisic acid, salicylic acid, jasmonic acid, gibberellin, ethylene, brassinosteroids, cytokinins and auxin), ions, polyamines, etc. has been demonstrated. These interactions play vital role in alleviating plant stress by modulating defense mechanisms in plants. Taking all these aspects into consideration, the current review focuses on the role of NO and its interaction with other signaling molecules in regulating plant growth and development, particularly under stressed conditions.
PMID: 36460229
Sci Rep , IF:4.379 , 2023 Jan , V13 (1) : P1488 doi: 10.1038/s41598-023-28084-3
Comparative proteomic analysis identified proteins and the phenylpropanoid biosynthesis pathway involved in the response to ABA treatment in cotton fiber development.
Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China.; State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, China.; Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China. yhding@hainanu.edu.cn.; Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China. yhding@hainanu.edu.cn.; Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, 570228, China. huhaiyan@hainanu.edu.cn.; Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China. huhaiyan@hainanu.edu.cn.
Abscisic acid (ABA) is a plant hormone that plays an important role in cotton fiber development. In this study, the physiological changes and proteomic profiles of cotton (Gossypium hirsutum) ovules were analyzed after 20 days of ABA or ABA inhibitor (ABAI) treatment. The results showed that compared to the control (CK), the fiber length was significantly decreased under ABA treatment and increased under ABAI treatment. Using a tandem mass tags-based quantitative technique, the proteomes of cotton ovules were comprehensively analyzed. A total of 7321 proteins were identified, of which 365 and 69 differentially accumulated proteins (DAPs) were identified in ABA versus CK and ABAI versus CK, respectively. Specifically, 345 and 20 DAPs were up- and down-regulated in the ABA group, and 65 and 4 DAPs were up- and down-regulated in the ABAI group, respectively. The DAPs in the ABA group were mainly enriched in the biosynthesis of secondary metabolites, phenylpropanoid biosynthesis and flavonoid secondary metabolism, whereas the DAPs in the ABAI group were mainly enriched in the indole alkaloid biosynthesis and phenylpropanoid biosynthesis pathways. Moreover, 9 proteins involved in phenylpropanoid biosynthesis were upregulated after ABA treatment, suggesting that this pathway might play important roles in the response to ABA, and 3 auxin-related proteins were upregulated, indicating that auxin might participate in the regulation of fiber development under ABAI treatment.
PMID: 36707547
Sci Rep , IF:4.379 , 2022 Dec , V12 (1) : P21124 doi: 10.1038/s41598-022-25731-z
Characteristics of rhizosphere and endogenous bacterial community of Ulleung-sanmaneul, an endemic plant in Korea: application for alleviating salt stress.
Division of Biotechnology, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea.; Wild Plants and Seeds Conservation Department, Baekdudaegan National Arboretum, Bonghwa-gun, Gyeongsangbuk-do, 36209, Republic of Korea.; Division of Biotechnology, Jeonbuk National University, 79 Gobong-ro, Iksan-si, Jeollabuk-do, 54596, Republic of Korea. yonghoonlee@jbnu.ac.kr.; Advanced Institute of Environment and Bioscience, Plant Medical Research Center, and Institute of Bio-Industry, Jeonbuk National University, Jeonju-si, Republic of Korea. yonghoonlee@jbnu.ac.kr.
Microbes influence plant growth and fitness. However, the structure and function of microbiomes associated with rare and endemic plants remain underexplored. To investigate the bacterial community structure of Ulleung-sanmaneul (U-SMN), an endemic plant in Korea, samples were collected from natural and cultivated habitats, and their 16S rDNA was sequenced. The root bacterial community structure differed from those of bulk soil and rhizosphere in both habitats. Endogenous bacteria in cultivated plants were less diverse than wild plants, but Luteibacter rhizovicinus, Pseudomonas fulva, and Sphingomonas pruni were shared. Co-inoculation of Pseudoxanthomonas sp. JBCE485 and Variovorax paradoxus JBCE486 promoted growth and induced salt stress resistance in Arabidopsis and chive. Changes in growth promotion and phenotypes of plants by co-inoculation were mediated by increased auxin production. Each strain colonized the roots without niche competition. The results indicated that host selectivity was influential than environmental factors in formulating endophytic bacterial composition, and domestication simplified the bacterial community diversity. Our results will contribute to the growth and maintenance of endemic U-SMN plants.
PMID: 36476722
Sci Rep , IF:4.379 , 2022 Dec , V12 (1) : P20771 doi: 10.1038/s41598-022-25132-2
Comparative transcriptomics reveals commonalities and differences in the genetic underpinnings of a floral dimorphism.
Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland. giacomo.potente@uzh.ch.; BaseClear BV, Leiden, The Netherlands. giacomo.potente@uzh.ch.; Zurich-Basel Plant Science Center, Zurich, Switzerland. giacomo.potente@uzh.ch.; Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland.; BaseClear BV, Leiden, The Netherlands.; Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.; Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland. peter.szoevenyi@systbot.uzh.ch.; Zurich-Basel Plant Science Center, Zurich, Switzerland. peter.szoevenyi@systbot.uzh.ch.; Department of Systematic and Evolutionary Botany, University of Zurich, Zurich, Switzerland. elena.conti@systbot.uzh.ch.; Zurich-Basel Plant Science Center, Zurich, Switzerland. elena.conti@systbot.uzh.ch.
Distyly, a floral dimorphism associated with heteromorphic self-incompatibility and controlled by the S-locus supergene, evolved independently multiple times. Comparative analyses of the first transcriptome atlas for the main distyly model, Primula veris, with other distylous species produced the following findings. A set of 53 constitutively expressed genes in P. veris did not include any of the housekeeping genes commonly used to normalize gene expression in qPCR experiments. The S-locus gene CYP(T) acquired its role in controlling style elongation via a change in expression profile. Comparison of genes differentially expressed between floral morphs revealed that brassinosteroids and auxin are the main hormones controlling style elongation in P. veris and Fagopyrum esculentum, respectively. Furthermore, shared biochemical pathways might underlie the expression of distyly in the distantly related P. veris, F. esculentum and Turnera subulata, suggesting a degree of correspondence between evolutionary convergence at phenotypic and molecular levels. Finally, we provide the first evidence supporting the previously proposed hypothesis that distyly supergenes of distantly related species evolved via the recruitment of genes related to the phytochrome-interacting factor (PIF) signaling network. To conclude, this is the first study that discovered homologous genes involved in the control of distyly in distantly related taxa.
PMID: 36456708
Ann Bot , IF:4.357 , 2022 Dec doi: 10.1093/aob/mcac161
Specificity in root domain-accumulation of Phytoglobin1 and nitric oxide (NO) determines meristematic viability in water-stressed Brassica napus roots.
Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T 2N2, Canada.; Department of Botany, Faculty of Science, Tanta University, Tanta, 31527, Egypt.
BACKGROUND AND AIMS: Drought reduces plant productivity, especially in the susceptible species Brassica napus. Water stress, mimicked by applications of 10% polyethylene glycol (PEG), elevates nitric oxide (NO) in root cells after a few hours contributing to the degradation of the root apical meristems (RAMs), the function of which relies on auxin and brassinosteroids (BRs). Phytoglobins (Pgbs) are effective NO scavengers induced by the stress. This work examines the effects of BnPgb1 dysregulation in dehydrating B. napus roots, and the spatiotemporal relationship between Pgb1 and activities of auxin and BRs in the regulation of the RAM. METHODS: B. napus lines over-expressing [BnPgb1(S)] or down-regulating [BnPgb1(RNAi)] BnPgb1 were exposed to polyethylene glycol (PEG)-induced water stress. The localization of BnPgb1, NO, auxin and PIN1 were analyzed during the first 48h, while the expression level of biosynthetic auxin and BR genes was measured during the first 24h. Pharmacological treatments were conducted to assess the requirement of auxin and BR in dehydrating roots. KEY RESULTS: During the stress, BnPgb1 protein accumulated preferentially in the peripheral domains of the root elongation zone, exposing the meristem to NO, which inhibits polar auxin transport (PAT), likely by interfering with PIN1 localization and the synthesis of auxin. Diminished auxin at the root tip depressed the synthesis of BR and caused the degradation of the RAMs. The strength of BnPgb1 signal in the elongation zone was increased in BnPgb1(S) roots, where NO was confined to the most apical cells. Consequently, PAT and auxin synthesis were retained, and the definition of RAMs was maintained. The auxin preservation of the RAM required BRs, although BRs alone was not sufficient to fully rescue drought-damaged RAMs in auxin depleted environments. CONCLUSIONS: The tissue-specific localization of BnPgb1 and NO are determinant for B. napus root response to water stress. A model is proposed where auxin and BRs act as downstream components of BnPgb1 signalling in the preservation of RAMs in dehydrating roots.
PMID: 36571296
Ann Bot , IF:4.357 , 2022 Dec , V130 (6) : P869-882 doi: 10.1093/aob/mcac122
Cytokinins and auxins in organs of aquatic carnivorous plants: what do they reflect?
Institute of Botany of the Czech Academy of Sciences, Dukelska 135, CZ-379 01 Trebon, Czech Republic.; Laboratory of Growth Regulators, Faculty of Science, Palacky University & Institute of Experimental Botany AS CR, Slechtitelu 27, 78371 Olomouc, Czech Republic.; Department of Chemical Biology, Faculty of Science, Palacky University, Slechtitelu 27, 78371 Olomouc, Czech Republic.
BACKGROUND AND AIMS: Aquatic carnivorous plants have typical rootless linear shoots bearing traps and exhibit steep physiological polarity with rapid apical growth. The aim was to analyse auxin and cytokinin metabolites in traps, leaves/shoots and shoot apices in several species of genera Aldrovanda and Utricularia to elucidate how the hormonal profiles reflect the specific organ functions and polarity. METHODS: The main auxin and cytokinin metabolites were analysed in miniature samples (>2 mg dry weight) of different organs of Aldrovanda vesiculosa and six Utricularia species using ultraperformance liquid chromatography coupled with triple quadrupole mass spectrometry. KEY RESULTS: Total contents of biologically active forms (free bases, ribosides) of all four main endogenously occurring cytokinin types were consistently higher in traps than in leaves in four Utricularia species with monomorphic shoots and/or higher than in shoots in two Utricularia species with dimorphic shoots. In Aldrovanda traps, the total content of different cytokinin forms was similar to or lower than that in shoots. In U. australis leaves, feeding on prey increased all cytokinin forms, while no consistent differences occurred in Aldrovanda. In four aquatic Utricularia species with monomorphic shoots, the content of four auxin forms was usually higher in traps than in leaves. Zero IAA content was determined in U. australis leaves from a meso-eutrophic site or when prey-fed. CONCLUSIONS: Different cytokinin and auxin profiles estimated in traps and leaves/shoots of aquatic carnivorous plants indicate an association with different dominant functions of these organs: nutrient uptake by traps versus photosynthetic function of traps. Interplay of cytokinins and auxins regulates apical dominance in these plants possessing strong polarity.
PMID: 36215097
Plant Physiol Biochem , IF:4.27 , 2023 Feb , V195 : P362-374 doi: 10.1016/j.plaphy.2023.01.006
Genome-wide analysis of the SAUR gene family and function exploration of DlSAUR32 during early longan somatic embryogenesis.
Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China.; Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China. Electronic address: buliang84@163.com.
The early auxin responsive small auxin up-regulated RNA (SAUR) family is an important gene family in the auxin signal transduction pathway. This study focused on the regulatory mechanism of DlSAUR genes during early somatic embryogenesis (SE) and its response to hormone treatment and abiotic stress. Mining of the available Dimocarpus longan Lour. (D. longan) genome sequence yielded 68 putative SAUR genes. Transcript profiles based on RNA-seq data showed that most of the 24 detected DlSAUR genes were highly expressed in the globular embryos (GE) (10) and most of them responded to heat stress and 2,4-D treatment. The results of qRT-PCR showed that most of DlSAUR genes were up-regulated under auxin inhibitor N-1-naphthylphthalamic acid (NPA) and auxin indole-3-acetic acid (IAA) treatments. Moreover, NPA could promote longan SE. The assay for ATAC-seq data analysis showed that chromatin accessibility of 19 of the 24 DlSAUR genes were open during early SE, and most DlSAUR genes differentially expressed during early SE were not associated with H3K4me1 signal enrichment. The DlSAUR32 was selected for subcellular localization and RNA-seq analysis, which encode a cell nuclear-localized protein. Dual-luciferase assays and transient transformation showed that the transcription factors (TFs) DlWRKY75-1 and DlWRKY75-2 might bind to the DlSAUR32 promoters to inhibition gene transcription. Transient overexpression of DlWRKY75-1 and DlWRKY75-2 decreased IAA content in N. benthamiana leaves. Thus, the regulatory network composed of DlSAUR32 and its related TFs may regulate the early longan SE and be involved in the auxin response regulatory pathway of longan.
PMID: 36682137
Plant Physiol Biochem , IF:4.27 , 2023 Feb , V195 : P330-340 doi: 10.1016/j.plaphy.2023.01.002
Tomato (Solanum lycopersicum) WRKY23 enhances salt and osmotic stress tolerance by modulating the ethylene and auxin pathways in transgenic Arabidopsis.
Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow, 226001, India.; Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Plant Gene Expression Lab, CSIR-National Botanical Research Institute, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. Electronic address: va.sane@nbri.res.in.
Osmotic stress is one of the biggest problems in agriculture, which adversely affects crop productivity. Plants adopt several strategies to overcome osmotic stresses that include transcriptional reprogramming and activation of stress responses mediated by different transcription factors and phytohormones. We have identified a WRKY transcription factor from tomato, SlWRKY23, which is induced by mannitol and NaCl treatment. Over-expression of SlWRKY23 in transgenic Arabidopsis enhances osmotic stress tolerance to mannitol and NaCl and affects root growth and lateral root number. Transgenic Arabidopsis over-expressing SlWRKY23 showed reduced electrolyte leakage and higher relative water content than Col-0 plants upon mannitol and NaCl treatment. These lines also showed better membrane integrity with lower MDA content and higher proline content than Col-0. Responses to mannitol were governed by auxin as treatment with TIBA (auxin transport inhibitor) negatively affected the osmotic tolerance in transgenic lines by inhibiting lateral root growth. Similarly, responses to NaCl were controlled by ethylene as treatment with AgNO(3) (ethylene perception inhibitor) inhibited the stress response to NaCl by suppressing primary and lateral root growth. The study shows that SlWRKY23, a osmotic stress inducible gene in tomato, imparts tolerance to mannitol and NaCl stress through interaction of the auxin and ethylene pathways.
PMID: 36669348
Plant Physiol Biochem , IF:4.27 , 2023 Feb , V195 : P193-205 doi: 10.1016/j.plaphy.2023.01.010
Polyamine metabolizing rhizobacteria Pseudomonas sp. GBPI_506 modulates hormone signaling to enhance lateral roots and nicotine biosynthesis in Nicotiana benthamiana.
Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India. Electronic address: r.jain@uva.nl.; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, Uttar Pradesh, India. Electronic address: pari169396@gmail.com.; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India. Electronic address: shwetaguleria000@gmail.com.; Graphic Era Deemed to be University, Dehradun, 248002, Uttarakhand, India. Electronic address: anitapandey333@gmail.com.; Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India. Electronic address: sanjaykumar@ihbt.res.in.
Beneficial rhizobacteria in the soil are important drivers of plant health and growth. In this study, we provide the draft genome of a root colonizing and auxin-producing Pseudomonas sp. strain GBPI_506. The bacterium was investigated for its contribution in the growth of Nicotiana benthamiana (Nb) and biosynthesis of nicotine. The bacterium showed chemotaxis towards root exudates potentially mediated by putrescine, a polyamine compound, to colonize the roots of Nb. Application of the bacterium with the roots of Nb, increased plant biomass and total soluble sugars in the leaves, and promoted lateral root (LR) development as compared to the un-inoculated plants. Confocal analysis using transgenic (DR5:GFP) Arabidopsis showed increased auxin trafficking in the LR of inoculated plants. Upregulation of nicotine biosynthesis genes and genes involved in salicylic acid (SA) and jasmonic acid (JA) signaling in the roots of inoculated plants suggested increased nicotine biosynthesis as a result of bacterial application. An increased JA content in roots and nicotine accumulation in leaves provided evidence on JA-mediated upregulation of nicotine biosynthesis in the bacterized plants. The findings suggested that the bacterial root colonization triggered networking between auxin, SA, and JA to facilitate LR development leading to enhanced plant growth and nicotine biosynthesis in Nb.
PMID: 36641943
Plant Physiol Biochem , IF:4.27 , 2023 Jan , V194 : P685-695 doi: 10.1016/j.plaphy.2022.12.018
The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions.
School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China.; School of Life Sciences, Jiangsu University, Zhenjiang, 212013, Jiangsu, China. Electronic address: cjinfor@163.com.
Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.
PMID: 36565613
Plant Physiol Biochem , IF:4.27 , 2023 Jan , V194 : P182-192 doi: 10.1016/j.plaphy.2022.11.018
Nitric oxide acts as an inducer of Strategy-I responses to increase Fe availability and mobilization in Fe-starved broccoli (Brassica oleracea var. oleracea).
Department of Genetics, University of Georgia, GA 30602, USA; Molecular Plant Physiology Laboratory, University of Rajshahi, Rajshahi, 6205, Bangladesh. Electronic address: ahmad.kabir@uga.edu.; Molecular Plant Physiology Laboratory, University of Rajshahi, Rajshahi, 6205, Bangladesh.; Grassland and Forage Division, National Institute of Animal Science, Rural Development Administration, Cheonan, 31000, Republic of Korea.; Plant Nutrition Laboratory, Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
Iron (Fe) deficiency causes reduced growth and yield in broccoli. This study elucidates how sodium nitroprusside (SNP), known as nitric oxide (NO) donor, mitigates the retardation caused by Fe deficiency in broccoli. The SNP caused substantial nitric oxide accumulation in the roots of Fe-deficient plants, which resulted in a significant improvement in chlorophyll levels, photosynthetic efficiency, and morphological growth parameters, showing that it has a favorable influence on recovering broccoli health. Ferric reductase activity and the expression of BoFRO1 (ferric chelate reductase) gene in roots were consistently increased by SNP under Fe deficiency, which likely resulted in increased Fe mobilization. Furthermore, proton (H(+)) extrusion and BoHA2 (H(+)-ATPase 2) expression were significantly increased, suggesting that they may be involved in lowering rhizospheric pH to restore Fe mobilization in roots of bicarbonate-treated broccoli plants. The levels of Fe in root and shoot tissues and the expression of BoIRT1 (Fe-regulated transporter) both increased dramatically after SNP supplementation under Fe deprivation. Furthermore, SNP-induced increase in citrate and malate concentrations suggested a role of NO in improved Fe chelation in Fe-deficient broccoli. A NO scavenger (cPTIO) ceased the elevated FCR activity and IAA (indole-3-acetic acid) concentration in Fe-starved plants treated with SNP. These findings suggest that SNP may play a role in initiating Fe availability by elevated IAA concentration and BoEIR1 (auxin efflux carrier) expression in the roots of broccoli during Fe shortage. Therefore, SNP may improve Fe availability and mobilization by increasing Strategy-I Fe uptake pathways, which may help broccoli tolerate Fe deficiency.
PMID: 36423388
BMC Plant Biol , IF:4.215 , 2023 Jan , V23 (1) : P35 doi: 10.1186/s12870-022-04025-6
Responses of roots and rhizosphere of female papaya to the exogenous application of GA(3).
Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.; Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. rayming@illinois.edu.
Exogenous GAs have an indeterminate effect on root development. Our current study used female papaya to reveal how the roots and rhizosphere respond to the exogenous application of GA(3) by investigating the transcriptome profile in roots, metabolic profile and microbial community in both roots and rhizosphere of GA(3)-treated and control female papaya. The results demonstrated that exogenous GA(3) treatment enhanced female papaya lateral root development, which gave plants physical advantages of water and nutrient uptake. In addition, it was likely that GA(3) spraying in papaya shoot apices increased the level of auxin, which was transported to roots by CpPIN1, where auxin upregulated CpLBD16 and repressed CpBP to promote the lateral root initiation and development. In papaya roots, corresponding transporters (CpTMT3, CpNRT1:2, CpPHT1;4, CpINT2, CpCOPT2, CpABCB11, CpNIP4;1) were upregulated and excretion transporters were downregulated such as CpNAXT1 for water and nutrients uptake with exogenous GA(3) application. Moreover, in GA(3)-treated papaya roots, CpALS3 and CpMYB62 were downregulated, indicating a stronger abiotic resistance to aluminum toxic and phosphate starvation. On the other hand, BRs and JAs, which involve in defense responses, were enriched in the roots and rhizosphere of GA(3)-treated papayas. The upregulation of the two hormones might result in the reduction of pathogens in roots and rhizosphere such as Colletotrichum and Verticillium. GA(3)-treated female papaya increased the abundance of beneficial bacteria species including Mycobacterium, Mitsuaria, and Actinophytocola, but decreased that of the genera Candidatus and Bryobacter for that it required less nitrate. Overall, the roots and rhizosphere of female papaya positively respond to exogenous application of GA(3) to promote development and stress tolerance. Treatment of female papaya with GA3 might result in the promotion of lateral root formation and development by upregulating CpLBD16 and downregulating CpBP. GA(3)-treated papaya roots exhibited feedback control of brassinolide and jasmonate signaling in root development and defense. These findings revealed complex response to a growth hormone treatment in papaya roots and rhizosphere and will lead to investigations on the impact of other plant hormones on belowground development in papaya.
PMID: 36642722
BMC Plant Biol , IF:4.215 , 2023 Jan , V23 (1) : P31 doi: 10.1186/s12870-023-04055-8
Genome-wide identification and expression analysis of the SAUR gene family in foxtail millet (Setaria italica L.).
College of Agriculture, Henan University of Science and Technology, Luoyang, 471000, Henan, People's Republic of China.; Henan Academy of Agriculture Sciences, Cereal Crops Institute, Zhengzhou, 450002, Henan, People's Republic of China.; Luoyang Academy of Agriculture and Forestry Sciences, Sweet Potato and Millet Institute, , Luoyang, 471023, Henan, People's Republic of China.; Henan Academy of Agriculture Sciences, Cereal Crops Institute, Zhengzhou, 450002, Henan, People's Republic of China. lijunxia@126.com.
BACKGROUND: Auxin performs important functions in plant growth and development processes, as well as abiotic stress. Small auxin-up RNA (SAUR) is the largest gene family of auxin-responsive factors. However, the knowledge of the SAUR gene family in foxtail millet is largely obscure. RESULTS: In the current study, 72 SiSAUR genes were identified and renamed according to their chromosomal distribution in the foxtail millet genome. These SiSAUR genes were unevenly distributed on nine chromosomes and were classified into three groups through phylogenetic tree analysis. Most of the SiSAUR members from the same group showed similar gene structure and motif composition characteristics. Analysis of cis-acting elements showed that many hormone and stress response elements were identified in the promoter region of SiSAURs. Gene replication analysis revealed that many SiSAUR genes were derived from gene duplication events. We also found that the expression of 10 SiSAURs was induced by abiotic stress and exogenous hormones, which indicated that SiSAUR genes may participated in complex physiological processes. CONCLUSIONS: Overall, these results will be valuable for further studies on the biological role of SAUR genes in foxtail development and response to stress conditions and may shed light on the improvement of the genetic breeding of foxtail millet.
PMID: 36639742
BMC Plant Biol , IF:4.215 , 2023 Jan , V23 (1) : P20 doi: 10.1186/s12870-023-04039-8
The auxin signaling pathway contributes to phosphorus-mediated zinc homeostasis in maize.
College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, People's Republic of China.; National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. liwenxue@caas.cn.; College of Resources and Environmental Sciences; National Academy of Agriculture Green Development; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, Beijing, 100193, People's Republic of China. zcq0206@cau.edu.cn.
Although the interaction between P and Zn has long been recognized in plants, the physiological and molecular mechanisms underlying P and Zn interactions are poorly understood. We show here that P supply decreases the Zn concentration in maize shoots and roots. Compared to +P + Zn (addition of both P and Zn), +P-Zn reduced and -P-Zn increased the total length of 1 degrees lateral roots (LRs). Under +P + Zn, both P and Zn concentrations were lower in the sl1 mutant roots than in wild-type (WT) maize roots, and P accumulation did not reduce the Zn concentration in ll1 mutant roots. Transcriptome profiling showed that the auxin signaling pathway contributed to P-mediated Zn homeostasis in maize. Auxin production and distribution were altered by changes in P and Zn supply. Cytosolic Zn co-localized with auxin accumulation under +P + Zn. Exogenous application of 1-NAA and L-Kyn altered the P-mediated root system architecture (RSA) under Zn deficiency. -P-Zn repressed the expression of miR167. Overexpression of ZmMIR167b increased the lengths of 1 degrees LRs and the concentrations of P and Zn in maize. These results indicate that auxin-dependent RSA is important for P-mediated Zn homeostasis in maize.HighlightAuxin-dependent RSA is important for P-mediated Zn homeostasis in maize.
PMID: 36627574
BMC Plant Biol , IF:4.215 , 2023 Jan , V23 (1) : P11 doi: 10.1186/s12870-022-04012-x
Analysis of co-expression and gene regulatory networks associated with sterile lemma development in rice.
College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China.; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China.; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China. huaanxie@163.com.; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China. huaanxie@163.com.; Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350019, China. jianfzhang@163.com.; Key Laboratory of Germplasm Innovation and Molecular Breeding of Hybrid Rice for South China, Ministry of Agriculture and Affairs P.R. China/Incubator of National Key Laboratory of Germplasm Innovation and Molecular Breeding between Fujian and Ministry of Sciences and Technology/Fuzhou Branch, National Rice Improvement Center of China/Fujian Engineering Laboratory of Crop Molecular Breeding/Fujian Key Laboratory of Rice Molecular Breeding, Fuzhou, 350003, China. jianfzhang@163.com.
BACKGROUND: The sterile lemma is a unique organ of the rice (Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile lemma have not been determined unequivocally, so it is important to elucidate the molecular mechanism of the development of the sterile lemma. RESULTS: In the paper, we outline the regulatory mechanism of sterile lemma development by LONG STERILE LEMMA1 (G1), which has been identified as the gene controlling sterile lemma development. Based on the comprehensive analyses of transcriptome dynamics during sterile lemma development with G1 alleles between wild-type (WT) and mutant (MT) in rice, we obtained co-expression data and regulatory networks related to sterile lemma development. Co-transfection assays of rice protoplasts confirmed that G1 affects the expression of various phytohormone-related genes by regulating a number of critical transcription factors, such as OsLBD37 and OSH1. The hormone levels in sterile lemmas from WT and MT of rice supports the hypotheses that lower auxin, lower gibberellin, and higher cytokinin concentrations are required to maintain a normal phenotype of sterile lemmas. CONCLUSION: The regulatory networks have considerable reference value, and some of the regulatory relationships exhibiting strong correlations are worthy of further study. Taken together, these work provided a detailed guide for further studies into the molecular mechanism of sterile lemma development.
PMID: 36604645
BMC Plant Biol , IF:4.215 , 2022 Dec , V22 (1) : P567 doi: 10.1186/s12870-022-03963-5
Comparative transcriptome profiling of resistant and susceptible foxtail millet responses to Sclerospora graminicola infection.
College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.; College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.; College of Agriculture, Shanxi Agricultural University, Taigu, 030801, Shanxi, China. hanyuanhuai@sxau.edu.cn.; Shanxi Key Laboratory of Germplasm Innovation and Molecular Breeding of Minor Crop, Taiyuan, 030031, China. hanyuanhuai@sxau.edu.cn.; College of Plant Protection, Shanxi Agricultural University, Taigu, 030801, Shanxi, China. jm.w@163.com.
BACKGROUND: Downy mildew of foxtail millet, which is caused by the biotrophic oomycete Sclerospora graminicola (Sacc.) Schroeter, is one of the most disruptive diseases. The foxtail millet-S. graminicola interaction is largely unexplored. Transcriptome sequencing technology can help to reveal the interaction mechanism between foxtail millet and its pathogens. RESULTS: Transmission electron microscopy observations of leaves infected with S. graminicola showed that the structures of organelles in the host cells gradually became deformed and damaged, or even disappeared from the 3- to 7-leaf stages. However, organelles in the leaves of resistant variety were rarely damaged. Moreover, the activities of seven cell wall degrading enzymes in resistant and susceptible varieties were also quite different after pathogen induction and most of enzymes activities were significantly higher in the susceptible variety JG21 than in the resistant variety G1 at all stages. Subsequently, we compared the transcriptional profiles between the G1 and JG21 in response to S. graminicola infection at 3-, 5-, and 7-leaf stages using RNA-Seq technology. A total of 473 and 1433 differentially expressed genes (DEGs) were identified in the resistant and susceptible varieties, respectively. The pathway analysis of the DEGs showed that the highly enriched categories were related to glutathione metabolism, plant hormone signalling, phenylalanine metabolism, and cutin, suberin and wax biosynthesis. Some defence-related genes were also revealed in the DEGs, including leucine-rich protein kinase, Ser/Thr protein kinase, peroxidase, cell wall degrading enzymes, laccases and auxin response genes. Our results also confirmed the linkage of transcriptomic data with qRT-PCR data. In particular, LRR protein kinase encoded by Seita.8G131800, Ser/Thr protein kinase encoded by Seita.2G024900 and Seita. 2G024800, which have played an essential resistant role during the infection by S. graminicola. CONCLUSIONS: Transcriptome sequencing revealed that host resistance to S. graminicola was likely due to the activation of defence-related genes, such as leucine-rich protein kinase and Ser/Thr protein kinase. Our study identified pathways and genes that contribute to the understanding of the interaction between foxtail millet and S. graminicola at the transcriptomic level. The results will help us better understand the resistance mechanism of foxtail millet against S. graminicola.
PMID: 36471245
BMC Plant Biol , IF:4.215 , 2022 Dec , V22 (1) : P562 doi: 10.1186/s12870-022-03918-w
Leaf transcriptome analysis of Medicago ruthenica revealed its response and adaptive strategy to drought and drought recovery.
Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China.; Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China. nmczysfl@126.com.
BACKGROUND: Drought is one of the main causes of losses in forage crop yield and animal production. Medicago ruthenica (L.) cv. Zhilixing is a high-yielding alfalfa cultivar also known for its high tolerance to drought. We analyzed the transcriptome profile of this cultivar throughout drought stress and recovery and we were able to describe its phased response through the expression profiles of overlapping gene networks and drought-specific genes. RESULTS: The ABA and auxin signal transduction pathways are overlapping pathways in response to drought and drought recovery in forage crops. Medicago ruthenica (L.) cv. Zhilixing adopts different strategies at different degrees of drought stress. On the 9th day of drought, transcriptional regulations related to osmoregulation are enhanced mainly through increased activities of carbohydrate and amino acid metabolism, while photosynthetic activities were reduced to slow down growth. With drought prolonging, on the 12th day of drought, the synthesis of proline and other stored organic substances was suppressed in general. After recovery, Medicago ruthenica synthesizes flavonoids through the flavonoid biosynthesis pathway to remove accumulated ROS and repair the oxidative damage from water stress. In addition, the regulation of circadian rhythm seems to accelerate the drought recovery process. CONCLUSIONS: Medicago ruthenica adapts to drought by regulating the osmoregulatory system and photosynthesis, which appears to involve the ABA and auxin signaling pathways as key regulators. Furthermore, the synthesis of flavonoids and the regulation of the circadian rhythm can accelerate the recovery process. These results enriched our knowledge of molecular responses to drought and drought recovery in Medicago ruthenica and provide useful information for the development of new legume forage grass varieties with improved adaptability to drought stress.
PMID: 36460952
Tree Physiol , IF:4.196 , 2022 Dec , V42 (12) : P2627-2639 doi: 10.1093/treephys/tpac089
The dark septate endophyte Phialocephala sphaeroides suppresses conifer pathogen transcripts and promotes root growth of Norway spruce.
College of Forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China.; Department of Forest Sciences, University of Helsinki, PO Box 27, Helsinki FIN-00014, Finland.
Plant-associated microbes including dark septate endophytes (DSEs) of forest trees play diverse functional roles in host fitness including growth promotion and increased defence. However, little is known about the impact on the fungal transcriptome and metabolites during tripartite interaction involving plant host, endophyte and pathogen. To understand the transcriptional regulation of endophyte and pathogen during co-infection, Norway spruce (Picea abies) seedlings were infected with DSE Phialocephala sphaeroides, or conifer root-rot pathogen Heterobasidion parviporum, or both. Phialocephala sphaeroides showed low but stable transcripts abundance (a decrease of 40%) during interaction with Norway spruce and conifer pathogen. By contrast, H. parviporum transcripts were significantly reduced (92%) during co-infection. With RNA sequencing analysis, P. sphaeroides experienced a shift from cell growth to anti-stress and antagonistic responses, while it repressed the ability of H. parviporum to access carbohydrate nutrients by suppressing its carbohydrate/polysaccharide-degrading enzyme machinery. The pathogen on the other hand secreted cysteine peptidase to restrict free growth of P. sphaeroides. The expression of both DSE P. sphaeroides and pathogen H. parviporum genes encoding plant growth promotion products were equally detected in both dual and tripartite interaction systems. This was further supported by the presence of tryptophan-dependent indolic compound in liquid culture of P. sphaeroides. Norway spruce and Arabidopsis seedlings treated with P. sphaeroides culture filtrate exhibited auxin-like phenotypes, such as enhanced root hairs, and primary root elongation at low concentration but shortened primary root at high concentration. The results suggested that the presence of the endophyte had strong repressive or suppressive effect on H. parviporum transcripts encoding genes involved in nutrient acquisition.
PMID: 35878416
Anal Bioanal Chem , IF:4.142 , 2023 Jan doi: 10.1007/s00216-023-04529-6
A 3D-printed analytical device seamlessly integrating sample treatment for electrochemical detection of IAA in Marchantia polymorpha.
School of Public Health, Nantong University, 9 Seyuan Rd., Nantong, 226019, Jiangsu, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China. liuwu@cemps.ac.cn.; School of Public Health, Nantong University, 9 Seyuan Rd., Nantong, 226019, Jiangsu, China. hxl362349@ntu.edu.cn.; School of Public Health, Nantong University, 9 Seyuan Rd., Nantong, 226019, Jiangsu, China. ningbao@ntu.edu.cn.
Because of the pivotal point of Marchantia polymorpha (M. polymorpha) in plant evolution, its auxin (mainly indole-3-acetic acid, IAA) levels could provide useful evidence for the study of the evolution of IAA. However, M. polymorpha could not be easily pretreated for electrochemical detection because they are at the entry level of land plants. Herein, we designed a three-dimensional (3D)-printed analytical device for seamless integration of sample treatment and electrochemical detection. Specifically, the electrochemical cell could be used as a mortar in which a tiny plant sample could be ground with a 3D-printed pestle, followed by mixing with the buffer solution under vibration for electrochemical detection of IAA with a disposable working electrode at the bottom of the cell. Using our strategy, the limits of quantification could reach 0.05 mumol L(-1) after optimization of parameters. We were able to demonstrate that IAA in different tissues of wild-type and mutant M. polymorpha could be successfully differentiated after they were treated with the 3D-printed analytical device. The obtained results were comparable to the samples blended with zirconium beads while the differences of IAA levels in different tissues of M. polymorpha agreed well with previous reports. This study suggested the potential of sample treatment integrated with electrochemical detection for analysis of IAA using the 3D printing techniques and their possible applications in the research of plants and other fields.
PMID: 36705731
Microorganisms , IF:4.128 , 2022 Dec , V10 (12) doi: 10.3390/microorganisms10122472
Bacillus velezensis BY6 Promotes Growth of Poplar and Improves Resistance Contributing to the Biocontrol of Armillaria solidipes.
Heilongjiang Provincial Key Laboratory of Forest Sustainable Management and Environmental Microbial Engineering, Northeast Forestry University, Harbin 150040, China.
To improve the application of endophyte Bacillus velezensis BY6 from the xylem of poplar, the effect of BY6 on the growth of diseased Populus davidiana x Populus. alba var. pyramidalis Louche (Pdpap poplar) seedlings and the biological control effect on the pathogen Armillaria solidipes were tested using a plant split-root experiment. After applying BY6 to the roots of diseased Pdpap poplar seedlings, the results show that plant growth indicators (dry mass, fresh mass, and plant height) were significantly increased (p < 0.05), and genes related to auxin hormone signal transcription were activated. BY6 indicated a surprising control effect after the inoculation of diseased Pdpap poplar seedlings. Compared to the infected control group, the treated disease index of the diseased Pdpap poplar seedlings in the treatment group were reduced by 49.53% on the 20th day. The relative staining areas of diaminobenzidine (DAB) and Trypan blue decreased by 3.37 and 7.31 times, respectively. The physiological indicators (soluble sugar and protein) and oxidase indicators were significantly increased (p < 0.05). The expression levels of defense genes related to salicylic acid (SA) and jasmonic acid (JA) signaling pathways were significantly increased (p < 0.05). Amazingly, the results indicate that BY6 simultaneously activates induced systemic resistance (ISR) and systemic acquired resistance (SAR) in diseased Pdpap poplar seedlings and promotes growth. The results indicate that BY6 is a promising candidate for developing forest tree biofertilizers and biopesticides.
PMID: 36557725
Planta , IF:4.116 , 2022 Dec , V257 (1) : P23 doi: 10.1007/s00425-022-04058-z
Auxin homeostasis in maize (Zea mays) is regulated via 1-O-indole-3-acetyl-myo-inositol synthesis at early stages of seedling development and under abiotic stress.
Department of Biochemistry, Nicolaus Copernicus University, Lwowska 1, 87-100, Torun, Poland. anciar@umk.pl.; Department of Biochemistry, Nicolaus Copernicus University, Lwowska 1, 87-100, Torun, Poland.; Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University, Lwowska 1, 87-100, Torun, Poland.
Indole-3-acetyl-myo-inositol biosynthesis is regulated during maize seedling development and in response to drought and cold stress. The main purpose of this pathway is maintenance of auxin homeostasis. Indole-3-acetic acid (IAA) conjugation to myo-inositol is a part of a mechanism controlling free auxin level in maize. In this work, we investigated changes in the indole-3-acetyl-myo-inositol (IAInos) biosynthesis pathway in 3-d- and 6-d-old maize seedlings and germinating seeds as well as in seedlings subjected to drought and cold stress to evaluate a role of this pathway in maize development and stress response. In germinating seeds, activity of the enzymes involved in IAInos biosynthesis remains unchanged between 3-d- and 6-d-old material but increases in coleoptiles and radicles of the seedlings. Under cold stress, in germinating seeds and in coleoptiles, activity of the enzymes decreases and increases, respectively; however, it does not entail changes in auxin level. In drought-exposed germinating maize seeds, totally diminished activities of IAInos synthesis pathway enzymes resulted in almost twofold increase of free IAA content. Similar increase of auxin level was observed in radicles of drought-subjected seedlings together with lack of catalytic activity of the first enzyme of the pathway. Exogenous IAInos has no effect on the level of non-enzymatic antioxidant, ascorbate. It has also either no effect on the protein carbonylation and lipid peroxidation, or it affects it in a similar way as exogenously applied IAA and myo-inositol, which are products of IAInos hydrolysis. Thus, IAInos biosynthesis pathway acts in maize development and stress responses by regulation of free IAA concentration, as IAInos itself does not appear to have a distinct role in these processes.
PMID: 36539632
Genes (Basel) , IF:4.096 , 2023 Jan , V14 (1) doi: 10.3390/genes14010181
A Genome-Wide View of the Transcriptome Dynamics of Fresh-Cut Potato Tubers.
Provincial Key Laboratory of Crops Genetic Improvement, Research Institute of Crops, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.
Fresh fruits and vegetable products are easily perishable during postharvest handling due to enzymatic browning reactions. This phenomenon has contributed to a significant loss of food. To reveal the physiological changes in fresh-cut potato tubers at the molecular level, a transcriptome analysis of potato tubers after cutting was carried out. A total of 10,872, 10,449, and 11,880 differentially expressed genes (DEGs) were identified at 4 h, 12 h and 24 h after cutting, respectively. More than 87.5% of these DEGs were classified into the categories of biological process (BP) and molecular function (MF) based on Gene Ontology (GO) analysis. There was a difference in the response to cutting at different stages after the cutting of potato tubers. The genes related to the phenol and fatty biosynthesis pathways, which are responsible for enzymatic browning and wound healing in potato tubers, were significantly enriched at 0-24 h after cutting. Most genes related to the enzymatic browning of potato tubers were up-regulated in response to cut-wounding. Plant hormone biosynthesis, signal molecular biosynthesis and transduction-related genes, such as gibberelin (GA), cytokinin (CK), ethylene (ET), auxin (IAA), jasmonic acid (JA), salicylic (SA), and Respiratory burst oxidase (Rboh) significantly changed at the early stage after cutting. In addition, the transcription factors involved in the wound response were the most abundant at the early stage after cutting. The transcription factor with the greatest response to injury was MYB, followed by AP2-EREBP, C3H and WRKY. This study revealed the physiological changes at the molecular level of fresh-cut potato tubers after cutting. This information is needed for developing a better approach to enhancing the postharvest shelf life of fresh processed potato and the breeding of potato plants that are resistant to enzymatic browning.
PMID: 36672922
Plant Mol Biol , IF:4.076 , 2022 Dec doi: 10.1007/s11103-022-01318-0
High temporal-resolution transcriptome landscapes of maize embryo sac and ovule during early seed development.
State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China.; Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China.; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, People's Republic of China.; Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, Beijing, People's Republic of China.; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China.; State Key Laboratory of Plant Physiology and Biochemistry, China Agricultural University, Beijing, People's Republic of China. jianchen@cau.edu.cn.; Department of Plant Genetics and Breeding, National Maize Improvement Center, China Agricultural University, Beijing, People's Republic of China. jianchen@cau.edu.cn.; Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, People's Republic of China. jianchen@cau.edu.cn.
Here we provided a high temporal-resolution transcriptome atlas of maize embryo sac and ovule to reveal the gene activity dynamic during early seed development. The early maize (Zea mays) seed development is initiated from double fertilization in the embryo sac and needs to undergo a highly dynamic and complex development process to form the differentiated embryo and endosperm. Despite the importance of maize seed for food, feed, and biofuel, many regulators responsible for controlling its early development are not known yet. Here, we reported a high temporal-resolution transcriptome atlas of embryo sac and ovule based on 44 time point samples collected within the first four days of seed development. A total of 25,187 genes including 1598 transcription factors (TFs) involved in early seed development were detected. Global comparisons of the expressions of these genes revealed five distinct development stages of early seed, which are mainly related to double fertilization, asymmetric cell division of the zygote, as well as coenocyte formation, cellularization and differentiation in endosperm. We identified 3327 seed-specific genes, which more than one thousand seed-specific genes with main expressions during early seed development were newly identified here, including 859 and 186 genes predominantly expressed in the embryo sac and ovule, respectively. Combined with the published transcriptome data of seed, we uncovered the dominant auxin biosynthesis, transport and signaling related genes at different development stages and subregions of seed. These results are helpful for understanding the genetic control of early seed development.
PMID: 36508138
Plant Mol Biol , IF:4.076 , 2023 Jan , V111 (1-2) : P21-36 doi: 10.1007/s11103-022-01308-2
The involvement of AtMKK1 and AtMKK3 in plant-deleterious microbial volatile compounds-induced defense responses.
Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan.; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan.; Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.; Department of Plant Systems Physiology, Radboud University, Nijmegen, The Netherlands.; Kaohsiung District Agricultural Research and Extension Station, Pingtung, Taiwan.; Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan. haojen@mail.ncku.edu.tw.; Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan. haojen@mail.ncku.edu.tw.; Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan. haojen@mail.ncku.edu.tw.
Plant-deleterious microbial volatiles activate the transactivation of hypoxia, MAMPs and wound responsive genes in Arabidopsis thaliana. AtMKK1 and AtMKK3 are involved in the plant-deleterious microbial volatiles-induced defense responses. Microbial volatile compounds (mVCs) are a collection of volatile metabolites from microorganisms with biological effects on all living organisms. mVCs function as gaseous modulators of plant growth and plant health. In this study, the defense events induced by plant-deleterious mVCs were investigated. Enterobacter aerogenes VCs lead to growth inhibition and immune responses in Arabidopsis thaliana. E. aerogenes VCs negatively regulate auxin response and transport gene expression in the root tip, as evidenced by decreased expression of DR5::GFP, PIN3::PIN3-GFP and PIN4::PIN4-GFP. Data from transcriptional analysis suggests that E. aerogenes VCs trigger hypoxia response, innate immune responses and metabolic processes. In addition, the transcript levels of the genes involved in the synthetic pathways of antimicrobial metabolites camalexin and coumarin are increased after the E. aerogenes VCs exposure. Moreover, we demonstrate that MKK1 serves as a regulator of camalexin biosynthesis gene expression in response to E. aerogenes VCs, while MKK3 is the regulator of coumarin biosynthesis gene expression. Additionally, MKK1 and MKK3 mediate the E. aerogenes VCs-induced callose deposition. Collectively, these studies provide molecular insights into immune responses by plant-deleterious mVCs.
PMID: 36109466
Plant Mol Biol , IF:4.076 , 2022 Dec , V110 (6) : P531-543 doi: 10.1007/s11103-022-01304-6
Combined analysis of mRNA and miRNA reveals the banana potassium absorption regulatory network and validation of miRNA160a.
Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China.; Institute of Fruit Tree ResearchKey Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural AffairsGuangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China.; School of Agriculture and Environment, The UWA Institute of Agriculture, The University of Western Australia, Perth, 6009 WA, Australia.; Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China. w_mingyuan@163.com.; Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China. 907153549@qq.com.; Institute of Horticulture Science and Engineering, Huaqiao University, Xiamen, 361021, China. yuhailing1989@163.com.
Potassium (K) has an important effect on the growth and development of plants. Banana contains higher K content than many other fruits, and its plant requires more K nutrient in soil. However, the soil in the banana-producing areas in China is generally deficient in K. Therefore, understanding the mechanism of banana K absorption may assist in providing effective strategy to solve this problem. This study used two banana varieties with contrasting K tolerance, 'Guijiao No. 1' (low-K tolerant), and 'Brazilian banana' (low-K sensitive)to investigate K absorption mechanisms in response to low-K stress through miRNA and mRNA sequencing analysis. Under low-K condition, 'Guijiao No.1' showed higher plant height, dry weight, tissue K content and ATPase activity. Analysis of transcription factors showed that they were mainly in the types or classes of MYB, AP-EREBP, bHLH, etc. The sequencing results showed that 'Guijiao No. 1' had 776 differentially expressed genes (DEGs) and 27 differentially expressed miRNAs (DEMs), and 'Brazilian banana' had 71 DEGs and 14 DEMs between normal and low K treatments. RT-qPCR results showed that all miRNAs and mRNAs showed similar expression patterns with RNA-Seq and transcriptome. miRNA regulatory network was constructed by integrated analysis of miRNA-mRNA data. miR160a was screened out as a key miRNA, and preliminary functional validation was performed. Arabidopsis overexpressing miR160a showed reduced tolerance to low K, and inhibited phenotypic traits such as shorter root length, and reduced K accumulation. The overexpressed miR160a had a targeting relationship with ARF10 and ARF16 in Arabidopsis. These results indicate that miR160a may regulate K absorption in bananas through the auxin pathway. This study provides a theoretical basis for further study on the molecular mechanism of banana response to low potassium stress.
PMID: 35962899
Phytochemistry , IF:4.072 , 2023 Feb , V206 : P113531 doi: 10.1016/j.phytochem.2022.113531
Labdane diterpenoids from the heartwood of Leucosceptrum canum that impact on root growth and seed germination of Arabidopsis thaliana.
State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China.; State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China.; State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, PR China; State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, PR China. Electronic address: shli@cdutcm.edu.cn.
Eleven undescribed diterpenoids possessing labdane, 3,18-cyclo-labdane, 19 (4 --> 3)-labdane and 12-nor-labdane skeletons, named leucolactones A-K, were isolated from the heartwood of a large woody Lamiaceae plant, Leucosceptrum canum. Their structures were determined by NMR, MS, and in the case of leucolactones A by single crystal X-ray diffraction analysis. Plausible biosynthetic pathway of leucolactones were proposed. Leucolactones showed significant inhibitory effects against seed germination and root elongation of Arabidopsis thaliana in the Petri dish bioassay. Among them, the diastereomeric leucolactones G and H were the most potent, with EC(50) values for root elongation of 6.53 +/- 1.35 and 9.75 +/- 1.25 muM, respectively. The preliminary structure-activity relationship of leucolactones was discussed. The increase of auxin reporter activity in A. thaliana DR5::GUS roots by leucolactone H was observed, indicating that leucolactones altered auxin accumulation and distribution. These findings suggested that leucolactones might be involved in regulation of plant growth and development through altering auxin accumulation and distribution, presumably contributing to the heartwood formation in L. canum.
PMID: 36464100
BMC Genomics , IF:3.969 , 2023 Jan , V24 (1) : P41 doi: 10.1186/s12864-022-09098-z
Global transcriptome profiling reveals differential regulatory, metabolic and hormonal networks during somatic embryogenesis in Coffea arabica.
Nestle Research - Plant Science Research Unit, Tours, France. rayan.awada@cirad.fr.; UMR DIADE, CIRAD, Montpellier, France. rayan.awada@cirad.fr.; UMR DIADE, Universite de Montpellier, CIRAD, Montpellier, IRD, France. rayan.awada@cirad.fr.; Nestle Research - Plant Science Research Unit, Tours, France.; Nestle Research, Societe Des Produits Nestle SA, Lausanne, Switzerland.; Sophia Genetics, Geneve, Switzerland.; UMR DIADE, Universite de Montpellier, CIRAD, Montpellier, IRD, France.; UMR DIADE, IRD, Montpellier, France.; UMR DIADE, CIRAD, Montpellier, France.; Max Planck Institute for Molecular Plant Physiology, Golm, Germany.; School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
BACKGROUND: Somatic embryogenesis (SE) is one of the most promising processes for large-scale dissemination of elite varieties. However, for many plant species, optimizing SE protocols still relies on a trial and error approach. We report the first global scale transcriptome profiling performed at all developmental stages of SE in coffee to unravel the mechanisms that regulate cell fate and totipotency. RESULTS: RNA-seq of 48 samples (12 developmental stages x 4 biological replicates) generated 90 million high quality reads per sample, approximately 74% of which were uniquely mapped to the Arabica genome. First, the statistical analysis of transcript data clearly grouped SE developmental stages into seven important phases (Leaf, Dedifferentiation, Primary callus, Embryogenic callus, Embryogenic cell clusters, Redifferentiation and Embryo) enabling the identification of six key developmental phase switches, which are strategic for the overall biological efficiency of embryo regeneration. Differential gene expression and functional analysis showed that genes encoding transcription factors, stress-related genes, metabolism-related genes and hormone signaling-related genes were significantly enriched. Second, the standard environmental drivers used to control SE, i.e. light, growth regulators and cell density, were clearly perceived at the molecular level at different developmental stages. Third, expression profiles of auxin-related genes, transcription factor-related genes and secondary metabolism-related genes were analyzed during SE. Gene co-expression networks were also inferred. Auxin-related genes were upregulated during dedifferentiation and redifferentiation while transcription factor-related genes were switched on from the embryogenic callus and onward. Secondary metabolism-related genes were switched off during dedifferentiation and switched back on at the onset of redifferentiation. Secondary metabolites and endogenous IAA content were tightly linked with their respective gene expression. Lastly, comparing Arabica embryogenic and non-embryogenic cell transcriptomes enabled the identification of biological processes involved in the acquisition of embryogenic capacity. CONCLUSIONS: The present analysis showed that transcript fingerprints are discriminating signatures of cell fate and are under the direct influence of environmental drivers. A total of 23 molecular candidates were successfully identified overall the 12 developmental stages and can be tested in many plant species to optimize SE protocols in a rational way.
PMID: 36694132
BMC Genomics , IF:3.969 , 2022 Dec , V23 (1) : P846 doi: 10.1186/s12864-022-09078-3
Transcriptomic analysis reveals the formation mechanism of anemone-type flower in chrysanthemum.
Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education Ministry, School of Landscape Architecture, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, 100083, China.; National Bot Garden, Beijing, 100093, China.; Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Education Ministry, School of Landscape Architecture, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, 100083, China. 101navy@163.com.
BACKGROUND: The ray and disc florets on the chrysanthemum capitulum are morphologically diverse and have remarkably abundant variant types, resulting in a rich variety of flower types. An anemone shape with pigmented and elongated disk florets is an important trait in flower shape breeding of chrysanthemums. The regulatory mechanism of their anemone-type disc floret formation was not clear, thus limiting the directional breeding of chrysanthemum flower types. In this study, we used morphological observation, transcriptomic analysis, and gene expression to investigate the morphogenetic processes and regulatory mechanisms of anemone-type chrysanthemum. RESULT: Scanning electron microscopy (SEM) observation showed that morphological differences between non-anemone-type disc florets and anemone-type disc florets occurred mainly during the petal elongation period. The anemone-type disc florets elongated rapidly in the later stages of development. Longitudinal paraffin section analysis revealed that the anemone-type disc florets were formed by a great number of cells in the middle layer of the petals with vigorous division. We investigated the differentially expressed genes (DEGs) using ray and disc florets of two chrysanthemum cultivars, 082 and 068, for RNA-Seq and their expression patterns of non-anemone-type and anemone-type disc florets. The result suggested that the CYCLOIDEA2 (CYC2s), MADS-box genes, and phytohormone signal-related genes appeared significantly different in both types of disc florets and might have important effects on the formation of anemone-type disc florets. In addition, it is noteworthy that the auxin and jasmonate signaling pathways might play a vital role in developing anemone-type disc florets. CONCLUSIONS: Based on our findings, we propose a regulatory network for forming non-anemone-type and anemone-type disc florets. The results of this study lead the way to further clarify the mechanism of the anemone-type chrysanthemum formation and lay the foundation for the directive breeding of chrysanthemum petal types.
PMID: 36544087
BMC Genomics , IF:3.969 , 2022 Dec , V23 (1) : P814 doi: 10.1186/s12864-022-09039-w
A comparative transcriptomic analysis reveals a coordinated mechanism activated in response to cold acclimation in common vetch (Vicia sativa L.).
Department of Grassland Science, College of Animal Science, Guizhou University, Guiyang, China.; Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang, China.; School of Tropical Crops, Hainan University, Haikou, China.; State Key Laboratory of Grassland Agro-ecosystems, China, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.; Grassland Technology Experiment and Extension Station, Guiyang, China.; College of Agriculture, Guizhou University, Guiyang, China. hejin0811@163.com.
BACKGROUND: Due to its strong abiotic stress tolerance, common vetch is widely cultivated as a green manure and forage crop in grass and crop rotation systems. The comprehensive molecular mechanisms activated in common vetch during cold adaptation remain unknown. RESULTS: We investigated physiological responses and transcriptome profiles of cold-sensitive (Lanjian No. 1) and cold-tolerant (Lanjian No. 3) cultivars during cold acclimation to explore the molecular mechanisms of cold acclimation. In total, 2681 and 2352 differentially expressed genes (DEGs) were identified in Lanjian No. 1 and Lanjian No. 3, respectively; 7532 DEGs were identified in both lines. DEGs involved in "plant hormone signal transduction" were significantly enriched during cold treatment, and 115 DEGs involved in cold-processed hormone signal transduction were identified. Common vetch increased the level of indoleacetic acid (IAA) by upregulating the transcriptional regulator Aux/IAA and downregulating GH3, endowing it with stronger cold tolerance. An auxin-related DEG was overexpressed in yeast and shown to possess a biological function conferring cold tolerance. CONCLUSION: This study identifies specific genes involved in Ca(2+) signaling, redox regulation, circadian clock, plant hormones, and transcription factors whose transcriptional differentiation during cold acclimation may improve cold tolerance and contributes to the understanding of common and unique molecular mechanisms of cold acclimation in common vetch. The candidate genes identified here also provide valuable resources for further functional genomic and breeding studies.
PMID: 36482290
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020413
New Paradigms in Brassinosteroids, Strigolactones, Sphingolipids, and Nitric Oxide Interaction in the Control of Lateral and Adventitious Root Formation.
Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy.; Department of Biosciences, University of Milan, 20133 Milan, Italy.
The root system is formed by the primary root (PR), which forms lateral roots (LRs) and, in some cases, adventitious roots (ARs), which in turn may produce their own LRs. The formation of ARs is also essential for vegetative propagation in planta and in vitro and for breeding programs. Root formation and branching is coordinated by a complex developmental network, which maximizes the plant's ability to cope with abiotic stress. Rooting is also a response caused in a cutting by wounding and disconnection from the donor plant. Brassinosteroids (BRs) are steroid molecules perceived at the cell surface. They act as plant-growth-regulators (PGRs) and modulate plant development to provide stress tolerance. BRs and auxins control the formation of LRs and ARs. The auxin/BR interaction involves other PGRs and compounds, such as nitric oxide (NO), strigolactones (SLs), and sphingolipids (SPLs). The roles of these interactions in root formation and plasticity are still to be discovered. SLs are carotenoid derived PGRs. SLs enhance/reduce LR/AR formation depending on species and culture conditions. These PGRs possibly crosstalk with BRs. SPLs form domains with sterols within cellular membranes. Both SLs and SPLs participate in plant development and stress responses. SPLs are determinant for auxin cell-trafficking, which is essential for the formation of LRs/ARs in planta and in in vitro systems. Although little is known about the transport, trafficking, and signaling of SPLs, they seem to interact with BRs and SLs in regulating root-system growth. Here, we review the literature on BRs as modulators of LR and AR formation, as well as their crosstalk with SLs and SPLs through NO signaling. Knowledge on the control of rooting by these non-classical PGRs can help in improving crop productivity and enhancing AR-response from cuttings.
PMID: 36679126
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020409
Auxin Transporter OsPIN1b, a Novel Regulator of Leaf Inclination in Rice (Oryza sativa L.).
Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot 010030, China.; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.; State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.; College of Life Science and Technology, Inner Mongolia Normal University, Hohhot 010022, China.
Leaf inclination is one of the most important components of the ideal architecture, which effects yield gain. Leaf inclination was shown that is mainly regulated by brassinosteroid (BR) and auxin signaling. Here, we reveal a novel regulator of leaf inclination, auxin transporter OsPIN1b. Two CRISPR-Cas9 homozygous mutants, ospin1b-1 and ospin1b-2, with smaller leaf inclination compared to the wild-type, Nipponbare (WT/NIP), while overexpression lines, OE-OsPIN1b-1 and OE-OsPIN1b-2 have opposite phenotype. Further cell biological observation showed that in the adaxial region, OE-OsPIN1b-1 has significant bulge compared to WT/NIP and ospin1b-1, indicating that the increase in the adaxial cell division results in the enlarging of the leaf inclination in OE-OsPIN1b-1. The OsPIN1b was localized on the plasma membrane, and the free IAA contents in the lamina joint of ospin1b mutants were significantly increased while they were decreased in OE-OsPIN1b lines, suggesting that OsPIN1b might action an auxin transporter such as AtPIN1 to alter IAA content and leaf inclination. Furthermore, the OsPIN1b expression was induced by exogenous epibrassinolide (24-eBL) and IAA, and ospin1b mutants are insensitive to BR or IAA treatment, indicating that the effecting leaf inclination is regulated by OsPIN1b. This study contributes a new gene resource for molecular design breeding of rice architecture.
PMID: 36679122
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020378
SlIAA9 Mutation Maintains Photosynthetic Capabilities under Heat-Stress Conditions.
Master Program of Agronomy, Faculty of Agriculture, Universitas Padjadjaran, Sumedang 45363, Indonesia.; Under Graduate Program of Agrotechnology, Faculty of Agriculture, Universitas Padjadjaran, Sumedang 45363, Indonesia.; Department of Agronomy, Faculty of Agriculture, Universitas Padjadjaran, Sumedang 45363, Indonesia.; Department of Biology, Institut Teknologi Sepuluh Nopember, Surabaya 60111, Indonesia.; Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia.; Department of Agronomy and Horticulture, Faculty of Agriculture, IPB University, Bogor 16680, Indonesia.; Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8577, Japan.; Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8577, Japan.
Tomato is one of the most widely consumed horticultural products. However, tomato is very sensitive to changes in temperature. Daily average temperatures above 32 degrees C severely reduced tomato plant growth, development, and productivity. Therefore, climate change-induced global warming is a major threat to future tomato production. Good photosynthetic capability under heat stress conditions is known to be a major sign of heat tolerance. Tomato INDOLE-ACETIC-ACID (SlIAA9) is a transcriptional repressor in auxin signaling. SlIAA9 mutation caused heightened endogenous auxin response and biosynthesis within plant tissues. In this study, we studied the photosynthetic capability of iaa9-3 and iaa9-5 mutants under heat-stress conditions. We discovered that both iaa9-3 and iaa9-5 could maintain their photosynthetic capability after 14 days of heat treatment (>40 degrees C), differing from Wild Type-Micro-Tom (WT-MT) tomato. Both iaa9 mutants had higher net photosynthetic rate, stomatal conductance, leaf total chlorophyll, leaf carotenoids, Fv/Fm value, and lower leaf MDA than WT-MT. These results suggested that the SlIAA9 mutation benefits plant adaptation to heat stress.
PMID: 36679090
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020371
The Arabidopsis LHT1 Amino Acid Transporter Contributes to Pseudomonas simiae-Mediated Plant Growth Promotion by Modulating Bacterial Metabolism in the Rhizosphere.
Department of Biology, University of Virginia, Charlottesville, VA 22904, USA.; Department of Molecular Biology & Biotechnology, School of Biological Sciences, College of Agriculture & Natural Sciences, University of Cape Coast, UC, Cape Coast P.O. Box 5007, Ghana.
The root microbiome structure ensures optimal plant host health and fitness, and it is, at least in part, defined by the plant genotype. It is well documented that root-secreted amino acids promote microbial chemotaxis and growth in the rhizosphere. However, whether the plant-mediated re-uptake of amino acids contributes to maintaining optimal levels of amino acids in the root exudates, and, in turn, microbial growth and metabolism, remains to be established. Here, we show that Lysine-Histidine Transporter-1 (LHT1), an amino acid inward transporter expressed in Arabidopsis thaliana roots, limits the growth of the plant-growth-promoting bacteria Pseudomonas simiae WCS417r (Ps WCS417r). The amino acid profiling of the lht1 mutant root exudates showed increased levels of glutamine, among other amino acids. Interestingly, lht1 exudates or Gln-supplemented wild-type exudates enhance Ps WCS417r growth. However, despite promoting bacterial growth and robust root colonization, lht1 exudates and Gln-supplemented wild-type exudates inhibited plant growth in a Ps WCS417r-dependent manner. The transcriptional analysis of defense and growth marker genes revealed that plant growth inhibition was not linked to the elicitation of plant defense but likely to the impact of Ps WCS417r amino acids metabolism on auxin signaling. These data suggest that an excess of amino acids in the rhizosphere impacts Ps WCS417r metabolism, which, in turn, inhibits plant growth. Together, these results show that LHT1 regulates the amino-acid-mediated interaction between plants and Ps WCS417r and suggest a complex relationship between root-exuded amino acids, root colonization by beneficial bacteria, bacterial metabolism, and plant growth promotion.
PMID: 36679084
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020354
Characterization and Transcriptome Analysis of Maize Small-Kernel Mutant smk7a in Different Development Stages.
College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.; National Engineering Research Center of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China.
The kernel serves as a storage organ for various nutrients and determines the yield and quality of maize. Understanding the mechanisms regulating kernel development is important for maize production. In this study, a small-kernel mutant smk7a of maize was characterized. Cytological observation suggested that the development of the endosperm and embryo was arrested in smk7a in the early development stage. Biochemical tests revealed that the starch, zein protein, and indole-3-acetic acid (IAA) contents were significantly lower in smk7a compared with wild-type (WT). Consistent with the defective development phenotype, transcriptome analysis of the kernels 12 and 20 days after pollination (DAP) revealed that the starch, zein, and auxin biosynthesis-related genes were dramatically downregulated in smk7a. Genetic mapping indicated that the mutant was controlled by a recessive gene located on chromosome 2. Our results suggest that disrupted nutrition accumulation and auxin synthesis cause the defective endosperm and embryo development of smk7a.
PMID: 36679067
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020330
ATANN3 Is Involved in Extracellular ATP-Regulated Auxin Distribution in Arabidopsis thaliana Seedlings.
Ministry of Education Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.
Extracellular ATP (eATP) plays multiple roles in plant growth and development, and stress responses. It has been revealed that eATP suppresses growth and alters the growth orientation of the root and hypocotyl of Arabidopsis thaliana by affecting auxin transport and localization in these organs. However, the mechanism of the eATP-stimulated auxin distribution remains elusive. Annexins are involved in multiple aspects of plant cellular metabolism, while their role in response to apoplastic signals remains unclear. Here, by using the loss-of-function mutations, we investigated the role of AtANN3 in the eATP-regulated root and hypocotyl growth. Firstly, the inhibitory effects of eATP on root and hypocotyl elongation were weakened or impaired in the AtANN3 null mutants (atann3-1 and atann3-2). Meanwhile, the distribution of DR5-GUS and DR5-GFP indicated that the eATP-induced asymmetric distribution of auxin in the root tips or hypocotyl cells occurred in wild-type control plants, while in atann3-1 mutant seedlings, it was not observed. Further, the eATP-induced asymmetric distribution of PIN2-GFP in root-tip cells or that of PIN3-GFP in hypocotyl cells was reduced in atann3-1 seedlings. Finally, the eATP-induced asymmetric distribution of cytoplasmic vesicles in root-tip cells was impaired in atann3-1 seedlings. Based on these results, we suggest that AtANN3 may be involved in eATP-regulated seedling growth by regulating the distribution of auxin and auxin transporters in vegetative organs.
PMID: 36679043
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020289
IBA Delivery Technique and Media Salts Affected In Vitro Rooting and Acclimatization of Eight Prunus Genotypes.
Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA.; Department of Mathematics, Clemson University, Clemson, SC 29634, USA.
Difficult-to-root plants often perform poorly during acclimatization and in vitro rooting can increase the survival and quality of plants. The influence of auxin application and mineral nutrition on in vitro rooting and subsequent effects on plant quality in eight Prunus genotypes were investigated. Microshoots were rooted in vitro on Murashige and Skoog (MS), (1/2) MS, Driver and Kuniyuki (DKW), or New Prunus Medium (NPM) media formulations in combination with 15 microM indole-3-butyric acid (IBA), 4-day 15 microM IBA pulse, 1 mM 30 s quick-dip, or IBA-free treatments. Shoots were observed pre- and post-acclimatization to determine rooting methods to maximize quality and minimize labor. A genotype-specific response to auxin application was observed with seven of eight genotypes achieving 100% survival when paired with the recommended IBA treatment. Peaches performed best when treated with 4-day IBA pulse or 30 s quick-dip. Rooting of P. cerasifera, it's hybrid to P. persica, and P. munsoniana all benefitted from IBA application. Shoots rooted with 15 microM IBA were smaller and lower quality in most genotypes. DKW maximized size and quality in six genotypes. Better shoots and larger root systems during in vitro rooting produced better plants in the greenhouse with no detrimental effect of callus growth. Rooting techniques to maximize plant quality while reducing labor are specified.
PMID: 36679002
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020266
Occurrence, Function, and Biosynthesis of the Natural Auxin Phenylacetic Acid (PAA) in Plants.
Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL 32611, USA.; Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.; Genetic Institute, University of Florida, Gainesville, FL 32611, USA.
Auxins are a class of plant hormones playing crucial roles in a plant's growth, development, and stress responses. Phenylacetic acid (PAA) is a phenylalanine-derived natural auxin found widely in plants. Although the auxin activity of PAA in plants was identified several decades ago, PAA homeostasis and its function remain poorly understood, whereas indole-3-acetic acid (IAA), the most potent auxin, has been used for most auxin studies. Recent studies have revealed unique features of PAA distinctive from IAA, and the enzymes and intermediates of the PAA biosynthesis pathway have been identified. Here, we summarize the occurrence and function of PAA in plants and highlight the recent progress made in PAA homeostasis, emphasizing PAA biosynthesis and crosstalk between IAA and PAA homeostasis.
PMID: 36678978
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020227
Transcriptomic Insights into Functions of LkABCG36 and LkABCG40 in Nicotiana tabacum.
College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China.; State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.; National Engineering Laboratory for Tree Breeding, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083, China.
ATP-binding cassette transporters (ABC transporters) play crucial physiological roles in plants, such as being involved in the growth and development of organs, nutrient acquisition, response to biotic and abiotic stress, disease resistance, and the interaction of the plant with its environment. The ABCG subfamily of proteins are involved in the process of plant vegetative organ development. In contrast, the functions of the ABCG36 and ABCG40 transporters have received considerably less attention. Here, we investigated changes in the transcriptomic data of the stem tissue of transgenic tobacco (Nicotiana tabacum) with LkABCG36 and LkABCG40 (Larix kaempferi) overexpression, and compared them with those of the wild type (WT). Compared with the WT, we identified 1120 and 318 differentially expressed genes (DEGs) in the LkABCG36 and LkABCG40 groups, respectively. We then annotated the function of the DEGs against the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The results showed enrichment in cell wall biogenesis and hormone signal transduction functional classes in transgenic LkABCG36 tobacco. In transgenic LkABCG40 tobacco, the enrichment was involved in metabolic and biosynthetic processes, mainly those related to environmental adaptation. In addition, among these DEGs, many auxin-related genes were significantly upregulated in the LkABCG36 group, and we found key genes involved in environmental adaptation in the LkABCG40 group, including an encoding resistance protein and a WRKY transcription factor. These results suggest that LkABCG36 and LkABCG40 play important roles in plant development and environmental adaptation. LkABCG36 may promote plant organ growth and development by increasing auxin transport, whereas LkABCG40 may inhibit the expression of WRKY to improve the resistance of transgenic tobacco. Our results are beneficial to researchers pursuing further study of the functions of ABCG36 and ABCG40.
PMID: 36678941
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (2) doi: 10.3390/plants12020225
Optimized Recovery of Cryostored Dormant Buds of Mulberry Germplasm.
Seed Science and Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India.; Tissue Culture and Cryopreservation Unit, ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi 110012, India.; Central Sericultural Germplasm Resources Center, Hosur 635109, India.
A two-step freezing cryoprotocol preceded by desiccation to 15 to 25% moisture content was developed and successfully applied to winter dormant buds of mulberry (different Morus spp.) of a core set comprising 238 accessions studies in our laboratory. The survival and recovery percentage of diverse accessions cryobanked for various periods were tested under in vitro conditions, and several factors were analyzed to determine their role in optimizing the recovery of low-viability accessions. The effect of rates of freezing and thawing (both fast and slow), were tested and recovery compared. Recovery conditions such as dark incubation and rehydration in sterile moist moss grass for different durations after cryopreservation led to a higher survival percentage compared to controls. Two different recovery culture media were compared for their efficiency in survival. On average, the survival under in vitro culture conditions using optimized conditions was high: above 60% in majority of the accessions. Dormant buds showed viability in the range of 25 to 100% with an average of 50.4%. The recovery percentage of winter dormant buds after cryopreservation via slow freezing and slow thawing with rehydration by moist moss grass for 2 h was recorded in the range from 63.3 to 90.9% with an average of 81.05%. Without rehydration, it ranged from 50 to 75% with an average of 60.4%. Regeneration of cryopreserved mulberry germplasm after 6 years of storage indicated no survival loss over different years of storage, and 33-40% of the accessions showed viability above 40%, up to a maximum of 100%. Maximum shoot formation (100%) was obtained from Morus alba. The majority of the accessions were rooted in vitro within 20-25 days of subculture in the auxin rich rooting media, except in wild species M. latifolia and M. laevigata, which took longer (45 to 60 days) for root development. All the rooted plantlets were then transferred to the field and successfully established in a glasshouse.
PMID: 36678937
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (1) doi: 10.3390/plants12010201
Grafting Causes Physiological Changes and Promotes Adventitious Root Formation in Rejuvenated Soft Shoots of Taxodium hybrid 'Zhongshanshan'.
Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.; Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing 210014, China.; Jingjiang Greening Engineering Co., Ltd., Jingjiang 214500, China.; College of Forestry and Agriculture, Stephen F. Austin State University, Nacogdoches, TX 75962, USA.
Taxodium hybrid 'Zhongshanshan' has been widely used as a timber tree in river network areas and coastal regions and is mainly propagated by cuttings. However, when trees age, their capacity to form adventitious roots becomes weaker. We successfully enhanced the rooting ability of shoots in T. hybrid 'Zhongshanshan 302' by their rejuvenation based on grafting. We recorded temporal variation in endogenous auxin, abscisic acid (ABA), gibberellins (GAs), trans-zeatin-riboside (TZR), soluble sugar and H(2)O(2) after root induction. Auxin, soluble sugars and H(2)O(2) levels were higher in rejuvenated shoots than in mature shoots, whereas the opposite was true for ABA and GAs. Notably, indole-3-acetic acid (IAA) and GA3 presented higher contents with more obvious differences in T. hybrid 'Zhongshanshan 302' rejuvenated shoots vs. mature shoots compared with other kinds of auxin and GAs. The evident improvement in the rooting ability of rejuvenated shoots after grafting likely resulted from the differential regulation of plant hormones, carbohydrates and redox signaling. In addition to the physiological basis of improved rooting ability by grafting, this study provided a theoretical basis for the optimization of subsequent propagation techniques in T. hybrid 'Zhongshanshan' and potentially other Taxodium spp.
PMID: 36616329
Plants (Basel) , IF:3.935 , 2023 Jan , V12 (1) doi: 10.3390/plants12010186
Characterizing Root Morphological Responses to Exogenous Tryptophan in Soybean (Glycine max) Seedlings Using a Scanner-Based Rhizotron System.
Department of International Agricultural Development, Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan.; Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, 14625 CR 672, Wimauma, FL 33598, USA.
Tryptophan is a precursor of indole-3-acetic acid (IAA), which is the major auxin involved in the regulation of lateral root formation. In this study, we used a scanner-based rhizotron system to examine root growth and morphological responses of soybean (Glycine max, 'Golden Harvest') seedlings to exogenous tryptophan. Seeds were sown directly in the rhizotron filled with field soil. Tryptophan was applied at 1.9 and 3.8 mg plant(-1) by soil drenching or foliar spray. Canopy and root projected area were monitored by analyzing canopy and rhizotron images using ImageJ software. Seedlings were sampled at the first trifoliate stage, 18 days after sowing (DAS), and root morphology was determined by analyzing washed root images using WinRHIZO software. According to contrast analysis, when all tryptophan treatments were pooled, tryptophan application increased canopy and root projected area by 13% to 14% compared with the control at 18 DAS. Tryptophan application also increased root dry matter accumulation by 26%, root:shoot ratio by 24%, and secondary root number by 13%. Tryptophan applied by soil drenching also increased root length and surface area of fine roots (<0.2 mm diameter) by 25% and 21%, respectively, whereas it slightly inhibited primary root elongation. The efficacy of tryptophan soil drenching in stimulating root formation became greater with increasing the application rate. These results suggest that exogenous tryptophan induces auxin-like activities in root development. Soil drenching of tryptophan appears to be an effective strategy in improving the establishment of soybean. Importantly, this strategy is easily implementable by commercial growers with no negative side effect.
PMID: 36616315
Plants (Basel) , IF:3.935 , 2022 Dec , V12 (1) doi: 10.3390/plants12010117
Meta-QTL Analysis for Yield Components in Common Bean (Phaseolus vulgaris L.).
Departamento de Ciencias Vegetales, Facultad de Agronomia e Ingenieria Forestal, Pontificia Universidad Catolica de Chile, Santiago 7820436, Chile.; Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile.; Departamento de Produccion Agricola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile.
Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.
PMID: 36616246
Plants (Basel) , IF:3.935 , 2022 Dec , V12 (1) doi: 10.3390/plants12010108
Chayote Fruit (Sechium edule var. virens levis) Development and the Effect of Growth Regulators on Seed Germination.
Colegio de Postgraduados, Campus Montecillo, Km. 36.5 Carretera Mexico-Texcoco, Montecillo 56230, Mexico.; Colegio de Postgraduados, Campus San Luis Potosi, San Iturbide No. 73, Salinas de Hidalgo, San Luis Potosi 78600, Mexico.; Red de Estudios Moleculares Avanzados, Cluster Biomimic(R), Instituto de Ecologia, A. C. Carretera Antigua a Coatepec 351, Xalapa, Veracruz 91073, Mexico.
The chayote fruit is a nontraditional vegetable belonging to the Cucurbitaceae family. The fruit has an endocarpic recalcitrant seed that emerges postharvest, drastically shortening its shelf life. In this study, the changes during fruit and seed development before and after harvest (ah) are reported. Additionally, in order to investigate how growth regulators (GRs) affect seed germination, 2-cloroethylphosphonic acid (CPA) (200 microL L(-1)), gibberellic acid (GA(3)) (100 and 200 mg L(-1)), auxin (2,4-D) (0.5 and 1.0 mM), and abscisic acid (ABA) (0.5 and 1.0 mM) were applied after harvest. The results showed that the chayote fruit reached horticultural maturity at 21 days after anthesis, with a sigmoid trend: phase I featured slow growth and high transpiration; in phase II, growth was accelerated and accumulation of endosperm was observed; and in phase III, both growth rate and transpiration were reduced, soluble sugars increased, and the seed showed 25% cotyledon development. At day 13 ah, CPA, GA(3), and 2,4-D (0.5 mM) increased seed germination, with values between 10 and 15 mm of the embryonary axis, and the treatments with 2,4-D (1 mM) and ABA (0.5 and 1.0 mM) retarded their growth (2-6 mm). This research allowed us to reveal the phenological phases and the shelf life of the chayote fruit, as well as the results of possible postharvest treatment with GRs; our results suggest that strategies to delay viviparism and prolong the shelf life of the fruit should be applied before 10 days ah, when the embryonic axis of the seed has not developed.
PMID: 36616239
Plants (Basel) , IF:3.935 , 2022 Dec , V12 (1) doi: 10.3390/plants12010071
An Evidence Theory and Fuzzy Logic Combined Approach for the Prediction of Potential ARF-Regulated Genes in Quinoa.
National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China.; CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.; Laboratory of Advanced Technology and Intelligent Systems, National Engineering School of Sousse, Sousse 4023, Tunisia.; Department of Agronomy and Plant Biotechnology, National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajene, University of Carthage-Tunis, Tunis 1082, Tunisia.; Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, B.P. 901, Hammam Lif 2050, Tunisia.; Higher Institute of Applied Biology Medenine, University of Gabes, Medenine 4119, Tunisia.; Laboratory of Molecular and Cellular Screening Processes, Sfax Biotechnology Center, B.P 1177, Sfax 3018, Tunisia.
Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental factors. Quinoa was selected as among the model crops destined for bio-saline agriculture that could contribute to the staple food security for an ever-growing worldwide population under various climate change scenarios. The auxin response factors (ARFs) constitute the main contributors in the plant adaptation to severe environmental conditions. Thus, the determination of the ARF-binding sites represents the major step that could provide promising insights helping in plant breeding programs and improving agronomic traits. Hence, determining the ARF-binding sites is a challenging task, particularly in species with large genome sizes. In this report, we present a data fusion approach based on Dempster-Shafer evidence theory and fuzzy set theory to predict the ARF-binding sites. We then performed an "In-silico" identification of the ARF-binding sites in Chenopodium quinoa. The characterization of some known pathways implicated in the auxin signaling in other higher plants confirms our prediction reliability. Furthermore, several pathways with no or little available information about their functions were identified to play important roles in the adaptation of quinoa to environmental conditions. The predictive auxin response genes associated with the detected ARF-binding sites may certainly help to explore the biological roles of some unknown genes newly identified in quinoa.
PMID: 36616201
Plants (Basel) , IF:3.935 , 2022 Dec , V12 (1) doi: 10.3390/plants12010033
Genome-Wide Identification of PIN and PILS Gene Families in Areca catechu and the Potential Role of AcPIN6 in Lateral Brace Root Formation.
Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou 570228, China.
PIN-FORMED (PIN) and PIN-LIKES (PILS) are two families of auxin transporters that control the directional cell-to-cell transport and intracellular accumulation of auxin, thereby influencing plant growth and development. Most knowledge of PINs and PILSs was obtained from the dicot model plant Arabidopsis thaliana. Here, we focus on the distribution and expression of the PIN and PILS gene families in areca palm (Areca catechu), a monocot tree. The whole genomic dataset of areca palm was used to identify twelve AcPINs and eight AcPILSs, and a phylogenetic tree was constructed of PINS and PILS together with several other palm species, including the date palm (Phoenix dactylifera), oil palm (Elaeis guineensis), and coconut (Cocos nucifera). We further analyzed the expression patterns of AcPIN and AcPILS in areca palm, and found that AcPIN6 displayed an extremely high transcriptional abundance in the brace roots and was extremely stimulated in the lateral root primordium. This result implies that AcPIN6 plays an important role in the growth and formation of brace roots, especially in lateral root initiation. We also overexpressed AcPIN6 and AcPIN6-eGFP in Arabidopsis, and the results revealed that the PIN6 localized on the plasma membrane and affected auxin-related phenomena. Taken together, we analyzed the evolutionary relationships of PINs and PILSs in palm species, and the roles of PIN6 in areca palm root formation. The results will improve the understanding of root system construction in large palm trees.
PMID: 36616161
Plants (Basel) , IF:3.935 , 2022 Dec , V11 (24) doi: 10.3390/plants11243572
Histone Acetyltransferase GCN5 Affects Auxin Transport during Root Growth by Modulating Histone Acetylation and Gene Expression of PINs.
Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.; Postgraduate Program Studies "Applications of Biology-Biotechnology, Molecular and Microbial Analysis of Food and Products", School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.; Natural Products Research Centre of Excellence (NatPro-AUTh), Center of Interdisciplinary Research and Innovation of Aristotle University of Thessaloniki (CIRI-AUTh), 57001 Thessaloniki, Greece.
General Control Non-Derepressible 5 (GCN5) is a histone acetyltransferase that targets multiple genes and is essential for the acetylation of Lysine residues in the N-terminal tail of histone H3 in Arabidopsis. GCN5 interacts with the transcriptional coactivator Alteration/Deficiency in Activation 2b (ADA2b), which enhances its activity functioning in multiprotein complexes, such as the Spt-Ada-Gcn5-Acetyltransferase complex (SAGA). Mutations in GCN5 and ADA2b result in pleiotropic phenotypes, including alterations in the growth of roots. Auxin is known to regulate root development by modulating gene expression patterns. Auxin moves polarly during plant growth via the Pin-formed (PIN) auxin efflux transport proteins. The effect of GCN5 and ADA2b on auxin distribution at different stages of early root growth (4 to 7 days post-germination) was studied using the reporter lines DR5rev::GFP and PIN1::PIN1-GFP. In wild-type plants, auxin efflux transporter PIN1 expression increases from the fourth to the seventh day of root growth. The PIN1 expression was reduced in the roots of gcn5-1 and ada2b-1 compared to the wild type. The expression of PIN1 in ada2b-1 mutants is confined only to the meristematic zone, specifically in the stele cells, whereas it is almost abolished in the elongation zone. Gene expression analysis showed that genes associated with auxin transport, PIN1, PIN3 and PIN4, are downregulated in gcn5-1 and ada2b-1 mutants relative to the wild type. As a result, auxin accumulation was also reduced in gcn5-1 and ada2b-1 compared to wild-type roots. Furthermore, acetylation of Lysine 14 of histone H3 (H3K14) was also affected in the promoter and coding region of PIN1, PIN3 and PIN4 genes during root growth of Arabidopsis in gcn5 mutants. In conclusion, GCN5 acts as a positive regulator of auxin distribution in early root growth by modulating histone H3 acetylation and the expression of auxin efflux transport genes.
PMID: 36559684
Plants (Basel) , IF:3.935 , 2022 Dec , V11 (24) doi: 10.3390/plants11243555
Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis).
Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China.; Columbian College of Arts & Sciences, Phillips Hall, The George Washington University, 801 22nd St. NW., Washington, DC 20052, USA.; College of Life Sciences, Shandong Normal University, Jinan 250061, China.; College of Life Science, Huangshan University, Huangshan 245061, China.
Chinese cabbage tipburn is characterized by the formation of necrotic lesions on the margin of leaves, including on the insides of the leafy head. This physiological disorder is associated with a localized calcium deficiency during leaf development. However, little information is available regarding the molecular mechanisms governing Ca-deficiency-triggered tipburn. This study comprehensively analysed the transcriptomic comparison between control and calcium treatments (CK and 0 mM Ca) in Chinese cabbage to determine its molecular mechanism in tipburn. Our analysis identified that the most enriched gene ontology (GO) categories are photosynthesis, thylakoid and cofactor binding. Moreover, the KEGG pathway was most enriched in photosynthesis, carbon metabolism and carbon fixation. We also analyzed the co-expression network by functional categories and identified ten critical hub differentially expressed genes (DEGs) in each gene regulatory network (GRN). These DEGs might involve abiotic stresses, developmental processes, cell wall metabolism, calcium distribution, transcription factors, plant hormone biosynthesis and signal transduction pathways. Under calcium deficiency, CNX1, calmodulin-binding proteins and CMLs family proteins were downregulated compared to CK. In addition, plant hormones such as GA, JA, BR, Auxin and ABA biosynthesis pathways genes were downregulated under calcium treatment. Likewise, HATs, ARLs and TCP transcription factors were reported as inactive under calcium deficiency, and potentially involved in the developmental process. This work explores the specific DEGs' significantly different expression levels in 0 mM Ca and the control involved in plant hormones, cell wall developments, a light response such as chlorophylls and photosynthesis, transport metabolism and defence mechanism and redox. Our results provide critical evidence of the potential roles of the calcium signal transduction pathway and candidate genes governing Ca-deficiency-triggered tipburn in Chinese cabbage.
PMID: 36559667
Plants (Basel) , IF:3.935 , 2022 Dec , V11 (24) doi: 10.3390/plants11243512
The Role of gamma-Aminobutyric Acid (GABA) in the Occurrence of Adventitious Roots and Somatic Embryos in Woody Plants.
State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, The Chinese Academy of Forestry, Beijing 100091, China.; College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China.; Key Laboratory of Forest Ecology and Environment of National Forestry and Grassland Administration, Research Institute of Forest Ecology, Environment and Protection, The Chinese Academy of Forestry, Beijing 100091, China.
The occurrence of adventitious roots and somatic embryos is a crucial step in micropropagation that frequently limits the application of this technique in woody plants. Recent studies demonstrated that they can be negatively or positively regulated with gamma-aminobutyric acid (GABA), which is a four-carbon non-proteinous amino acid that not only acts as a main inhibitory neurotransmitter in mammals. It has been reported that GABA affects plant growth and their response to stress although its mode of action is still unclear. This review dealt with the effects of GABA on adventitious root formation and growth as well as on somatic embryogenesis. Furthermore, we focused on discussing the interaction of GABA with phytohormones, such as auxin, ethylene, abscisic acid, and gibberellin, as well as with the carbon and nitrogen metabolism during adventitious root development. We suggested that research on GABA will contribute to the application of micropropagation in the recalcitrant fruit and forest species.
PMID: 36559624
Plants (Basel) , IF:3.935 , 2022 Dec , V11 (24) doi: 10.3390/plants11243486
Transcriptomics Analysis Reveals a Putative Role for Hormone Signaling and MADS-Box Genes in Mature Chestnut Shoots Rooting Recalcitrance.
Mision Biologica de Galicia, Consejo Superior de Investigaciones Cientificas, 15780 Santiago de Compostela, Spain.; Department of Horticulture, University of Sirnak, 73100 Sirnak, Turkey.
Maturation imposes several changes in plants, which are particularly drastic in the case of trees. In recalcitrant woody species, such as chestnut (Castanea sativa Mill.), one of the major maturation-related shifts is the loss of the ability to form adventitious roots in response to auxin treatment as the plant ages. To analyze the molecular mechanisms underlying this phenomenon, an in vitro model system of two different lines of microshoots derived from the same field-grown tree was established. While juvenile-like shoots root readily when treated with exogenous auxin, microshoots established from the crown of the tree rarely form roots. In the present study, a transcriptomic analysis was developed to compare the gene expression patterns in both types of shoots 24 h after hormone and wounding treatment, matching the induction phase of the process. Our results support the hypothesis that the inability of adult chestnut tissues to respond to the inductive treatment relies in a deep change of gene expression imposed by maturation that results in a significant transcriptome modification. Differences in phytohormone signaling seem to be the main cause for the recalcitrant behavior of mature shoots, with abscisic acid and ethylene negatively influencing the rooting ability of the chestnut plants. We have identified a set of related MADS-box genes whose expression is modified but not suppressed by the inductive treatment in mature shoots, suggesting a putative link of their activity with the rooting-recalcitrant behavior of this material. Overall, distinct maturation-derived auxin sensibility and homeostasis, and the related modifications in the balance with other phytohormones, seem to govern the outcome of the process in each type of shoots.
PMID: 36559597
Plants (Basel) , IF:3.935 , 2022 Dec , V11 (24) doi: 10.3390/plants11243457
Combined Transcriptomic and Metabolomic Analysis Reveals Insights into Resistance of Arabidopsis bam3 Mutant against the Phytopathogenic Fungus Fusarium oxysporum.
Laboratory of Mycology, Scientific Department of Phytopathology, Benaki Phytopathological Institute, 8 St. Delta Street, 145 61 Athens, Greece.; Laboratory of Pesticide Science, Agricultural University of Athens, 75 Iera Odos Street, 118 55 Athens, Greece.; Laboratory of Plant Pathology, Agricultural University of Athens, 75 Iera Odos Street, 118 55 Athens, Greece.
The wilt-inducing strains of Fusarium oxysporum are responsible for severe damage to many economically important plant species. The most cost-effective and environmentally safe method for the management of Fusarium wilt is the use of resistant cultivars when they are available. In the present study, the Arabidopsis genotype with disruptions in the beta-amylase 3 (BAM3) gene, which encodes the major hydrolytic enzyme that degrades starch to maltose, had significantly lower susceptibility to Fusarium oxysporum f. sp. raphani (For) compared to wild-type (wt) plants. It showed the lowest disease severity and contained reduced quantities of fungal DNA in the plant vascular tissues when analyzed with real-time PCR. Through metabolomic analysis using gas chromatography (GC)-mass spectrometry (MS) and gene-expression analysis by reverse-transcription quantitative PCR (RT-qPCR), we observed that defense responses of Arabidopsis bam3 mutants are associated with starch-degradation enzymes, the corresponding modification of the carbohydrate balance, and alterations in sugar (glucose, sucrose, trehalose, and myo-inositol) and auxin metabolism.
PMID: 36559570
Am J Bot , IF:3.844 , 2023 Jan , V110 (1) : Pe16102 doi: 10.1002/ajb2.16102
What determines root-sprouting ability: Injury or phytohormones?
Department of Experimental and Functional Morphology, Institute of Botany of the Czech Academy of Sciences, Dukelska 135, CZ-379 82, Trebon, Czech Republic.; Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojova 263, 165 02 Prague 6, Czech Republic.; Department of Ecology and Environmental Sciences, Palacky University, Slechtitelu 241/27, CZ-783 71, Olomouc, Czech Republic.; Department of Botany, Faculty of Science, Charles University, Benatska 2, CZ-128 01 Praha 2, Czech Republic.
PREMISE: Root-sprouting (RS) is an evolutionarily independent alternative to axillary stem branching for a plant to attain its architecture. Root-sprouting plants are better adapted to disturbance than non-RS plants, and their vigor is frequently boosted by biomass removal. Nevertheless, RS plants are rarer than plants that are not root-sprouters, possibly because they must overcome developmental barriers such as intrinsic phytohormonal balance or because RS ability is conditioned by injury to the plant body. The objective of this study was to identify whether phytohormones or injury enable RS. METHODS: In a greenhouse experiment, growth variables, root respiration, and phytohormones were analyzed in two closely related clonal herbs that differ in RS ability (spontaneously RS Inula britannica and rhizomatous non-RS I. salicina) with and without severe biomass removal. RESULTS: As previously reported, I. britannica is a root-sprouter, but injury did not boost its RS ability. Root respiration did not differ between the two species and decreased continuously with time irrespectively of injury, but their phytohormone profiles differed significantly. In RS species, the auxins-to-cytokinins ratio was low, and injury further decreased it. CONCLUSIONS: This first attempt to test drivers behind different plant growth forms suggests that intrinsic phytohormone regulation, especially the auxins-to-cytokinins ratio, might be behind RS ability. Injury, causing a phytohormonal imbalance, seems to be less important in spontaneously RS species than expected for RS species in general.
PMID: 36371783
Life (Basel) , IF:3.817 , 2023 Jan , V13 (1) doi: 10.3390/life13010170
Comparative Proteomics Analysis between Maize and Sorghum Uncovers Important Proteins and Metabolic Pathways Mediating Drought Tolerance.
Department of Biotechnology, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa.; Centre for Bioinformatics and Computational Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7500, South Africa.; DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Robert Sobukwe Road, Bellville 7530, South Africa.
Drought severely affects crop yield and yield stability. Maize and sorghum are major crops in Africa and globally, and both are negatively impacted by drought. However, sorghum has a better ability to withstand drought than maize. Consequently, this study identifies differences between maize and sorghum grown in water deficit conditions, and identifies proteins associated with drought tolerance in these plant species. Leaf relative water content and proline content were measured, and label-free proteomics analysis was carried out to identify differences in protein expression in the two species in response to water deficit. Water deficit enhanced the proline accumulation in sorghum roots to a higher degree than in maize, and this higher accumulation was associated with enhanced water retention in sorghum. Proteomic analyses identified proteins with differing expression patterns between the two species, revealing key metabolic pathways that explain the better drought tolerance of sorghum than maize. These proteins include phenylalanine/tyrosine ammonia-lyases, indole-3-acetaldehyde oxidase, sucrose synthase and phenol/catechol oxidase. This study highlights the importance of phenylpropanoids, sucrose, melanin-related metabolites and indole acetic acid (auxin) as determinants of the differences in drought stress tolerance between maize and sorghum. The selection of maize and sorghum genotypes with enhanced expression of the genes encoding these differentially expressed proteins, or genetically engineering maize and sorghum to increase the expression of such genes, can be used as strategies for the production of maize and sorghum varieties with improved drought tolerance.
PMID: 36676117
J Appl Microbiol , IF:3.772 , 2022 Dec doi: 10.1093/jambio/lxac013
Not just passengers, but co-pilots! Non-rhizobial nodule-associated bacteria promote cowpea growth and symbiosis with (brady)rhizobia.
Colegiado de Farmacia, Universidade Federal do Vale do Sao Francisco (Univasf), Petrolina, PE 56304-205, Brazil.; Universidade Estadual da Paraiba (UEPB), Campina Grande, PB 58429-500, Brazil.; Universidade Estadual de Feira de Santana (UEFS), Feira de Santana, Novo Horizonte, BA 44036-900, Brazil.; Instituto Federal de Educacao, Ciencia e Tecnologia do Para (IFPA), Campus Itaituba, Itaituba, PA 68183-300, Brazil.; Helmholtz Munich, German Research Center for Environmental Health, Neuherberg, Munich 85764, Germany.; Fundacao de Amparo a Pesquisa do Estado de Pernambuco (Facepe), Recife, PE 50720-001, Brazil.; Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq), Brasilia, DF 71605-001, Brazil.; Embrapa Semiarido, Petrolina, PE 56302-970, Brazil.; Embrapa Agrobiologia, Seropedica, RJ 23897-970, Brazil.
AIMS: To isolate and characterize non-rhizobial nodule-associated bacteria (NAB) from cowpea root-nodules regarding their performance of plant-growth-promoting mechanisms and their ability to enhance cowpea growth and symbiosis when co-inoculated with bradyrhizobia. METHODS AND RESULTS: Sixteen NAB were isolated, identified, and in vitro evaluated for plant growth promotion traits. The ability to promote cowpea growth was analyzed when co-inoculated with Bradyrhizobium pachyrhizi BR 3262 in sterile and non-sterile substrates. The 16S rRNA gene sequences analysis revealed that NAB belonged to the genera Chryseobacterium (4), Bacillus (3), Microbacterium (3), Agrobacterium (1), Escherichia (1), Delftia (1), Pelomonas (1), Sphingomonas (1), and Staphylococcus (1). All strains produced different amounts of auxin siderophores and formed biofilms. Twelve out of the 16 strains carried the nifH, a gene associated with nitrogen fixation. Co-inoculation of NAB (ESA 424 and ESA 29) with Bradyrhizobium pachyrhizi BR 3262 significantly promoted cowpea growth, especially after simultaneous inoculation with the three strains. CONCLUSIONS: NAB are efficient cowpea growth promoters and can improve the efficiency of the symbiosis between cowpea and the N2-fixing microsymbiont B. pachyrhizi BR 3262, mainly under a specific triple microbial association.
PMID: 36626727
Gene , IF:3.688 , 2023 Jan , V851 : P146982 doi: 10.1016/j.gene.2022.146982
Molecular characterization of the GH3 family in alfalfa under abiotic stress.
Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou 570228, People's Republic of China; School of Tropical Crops, Hainan University, Haikou 570228, People's Republic of China.; College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, People's Republic of China.; Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou 570228, People's Republic of China.; Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia.; Hainan University Archives, Haikou 570228, People's Republic of China.; Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou 570228, People's Republic of China; School of Tropical Crops, Hainan University, Haikou 570228, People's Republic of China. Electronic address: zhangrui@hainanu.edu.cn.; Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou 570228, People's Republic of China. Electronic address: yhchen@hainanu.edu.cn.
The phytohormone auxin plays a pivotal role in regulating plant growth, development, and abiotic stress responses by promptly controlling the expression of auxin response genes. The Gretchen Hagen3 (GH3) genes are a major early auxin response gene family that contribute to auxin homeostasis by conjugating excess auxins to amino acids. To our knowledge, a genome-wide investigation of the GH3 genes in alfalfa has never been reported. Here, we present a comprehensive bioinformatics analysis of the MsGH3 gene family, including chromosomal locations, phylogenetic relationships, gene structures, conserved motifs and Gene Ontology annotation. Interestingly, the analysis revealed 31 MsGH3 genes in the alfalfa genome. These genes were classified phylogenetically into the GH3-I, GH3-II, and GH3-III subgroups. Additionally, the data analysis showed that most MsGH3 genes are tissue specific and responsive to environmental stress-related hormones. Furthermore, the analysis of cis elements and potential biological functions revealed that the MsGH3 genes play potential roles in various stress responses. Notably, qRT-PCR results following exposure to high temperature, drought, and salt treatments demonstrated that most of the MsGH3 family genes, especially MsGH3-12, MsGH3-13, and MsGH3-15, play important roles in stress responses. These findings provide invaluable insight for future practical analyses and genetic improvement of alfalfa abiotic stress tolerance.
PMID: 36270456
J Plant Physiol , IF:3.549 , 2023 Jan , V282 : P153919 doi: 10.1016/j.jplph.2023.153919
Auxin alleviates cadmium toxicity by increasing vacuolar compartmentalization and decreasing long-distance translocation of cadmium in Poa pratensis.
College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China.; College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Lanzhou, Gansu, 730070, China. Electronic address: mahl@gsau.edu.cn.
Kentucky bluegrass (Poa pratensis L.) hyperaccumulates cadmium (Cd) and exhibits a hypertolerance. Thus, it has potential for the phytoremediation of Cd-containing soil. Auxin signaling is involved in the response to Cd stress. However, the mechanisms of auxin-mediated detoxification and Cd translocation in plants remain unclear. This study aimed to investigate the effects of exogenous application of indole-3-acetic acid (IAA) on the Cd translocation, subcellular Cd distribution, chemical forms of Cd, and transcriptional regulation of Kentucky bluegrass. The results showed that the exogenous application of IAA increased the amount of organelle-bound Cd and vacuole-compartmentalized Cd in root cells, reduced the Cd concentration in the leaf tissues (epidermis, mesophyll, and vascular bundle) and root tissues (rhizodermis and cortex) but increased in the stele, and alleviate Cd-induced leaf chlorosis and growth inhibition. The expression of genes associated with Cd transporters (ABCs, ZIPs, NASs, OPTs, and YSLs), phosphatases, oxalate decarboxylases and lignin biosynthesis were significantly regulated by exogenous IAA under Cd stress. A positive regulation of phosphatases and oxalate decarboxylases genes related to an increase in phosphate- and oxalate-bound Cd, as well as a decrease in pectate- and protein-bound Cd and inorganic Cd, thereby contributing to a decrease in Cd phytotoxicity. The significant regulation of Cd transporters associated with decreasing the long-distance translocation of Cd, and the activation of lignin biosynthesis may contribute to the development of root endodermal barriers and increase the deposition of undissolved Cd phosphates and oxalate-bound Cd in the stele. These results revealed the important role of auxin in Cd detoxification and translocation in Kentucky bluegrass and they provide a theoretical basis for the phytoremediation of Cd-containing soil.
PMID: 36706576
J Plant Physiol , IF:3.549 , 2023 Feb , V281 : P153920 doi: 10.1016/j.jplph.2023.153920
Transcriptome and anatomical studies reveal alterations in leaf thickness under long-term drought stress in tobacco.
Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China.; Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China. Electronic address: maxinghua@caas.cn.; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, 666 Wusu Street, Hangzhou, 311300, China.; Guangxi Key Laboratory of Agric-Environment and Agric-Products Safety, Agricultural College of Guangxi University, Nanning, 530004, China.; Department of Agronomy, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan.; Key Laboratory of Tobacco Biology and Processing, Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China. Electronic address: shiyi@caas.cn.
Drought is one of the foremost environmental factors that limit the growth of plants. Leaf thickness (LT) is an important quantitative trait in plant physiology. The experiment was carried out in a growth room and the plants were divided into two groups such as well-watered and drought-stressed. This work investigated leaf growth in terms of leaf surface growth and expansion rate, leaf stomata traits, LT, anticlinal growth, and leaf cell layers. The results showed that the leaf area and leaf surface expansion rate were decreased by drought stress (DS). Similarly, LT, anticlinal expansion rate, palisade and spongy tissue thickness, and their related expansion rates were also decreased at different days' time points (DTP) of DS. However, a steady increase was observed in the aforementioned parameters after 12 DTP of DS. The stomatal density increased while stomata size decreased at 3 DTP and 12 DTP (low leaf water potential and relative leaf water content at these time points) and vice versa at 24 DTP compared with the well-watered plants indicating adaptations in these traits in response to DS, and thus the leaf water status played a role in the regulation of leaf stomata traits. The cell length decreased in the upper epidermis, palisade and spongy tissues by DS up to 12 DTP led to lower LT while an increase was observed after 12 DTP that resulted in higher LT. The increase in the LT was supported by the upregulation of starch and sucrose metabolism, glycerolipid metabolism, protein processing in endoplasmic reticulum pathways at 18 DTP along with the differentially expressed genes induced that were related to cell wall remodeling (cellulose, expansin, xyloglucans) and cell expansion (auxin response factors and aquaporin). The results explain the response of leaf thickness to drought stress and show alterations in LT and leaf stomatal traits. This study might serve as a valuable source of gene information for functional studies and provide a theoretical basis to understand leaf growth in terms of leaf anatomy and leaf stomatal traits under drought stress.
PMID: 36680840
J Plant Physiol , IF:3.549 , 2023 Jan , V280 : P153891 doi: 10.1016/j.jplph.2022.153891
The nitrification inhibitor 1,9-decanediol from rice roots promotes root growth in Arabidopsis through involvement of ABA and PIN2-mediated auxin signaling.
State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China. Electronic address: yflu@issas.ac.cn.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China.; School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia.; Amway (China) Botanical R&D Center, Wuxi, 214115, China.; State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, China; University of Chinese Academy of Sciences, Beijing, 100049, China. Electronic address: wmshi@issas.ac.cn.
1,9-decanediol (1,9-D) is a biological nitrification inhibitor secreted in roots, which effectively inhibits soil nitrifier activity and reduces nitrogen loss from agricultural fields. However, the effects of 1,9-D on plant root growth and the involvement of signaling pathways in the plant response to 1,9-D have not been investigated. Here, we report that 1,9-D, in the 100-400 muM concentration range, promotes primary root length in Arabidopsis seedlings at 3d and 5d, by 10.1%-33.3% and 6.9%-32.6%, and, in a range of 50-200 muM, leads to an increase in the number of lateral roots. 150 muM 1,9-D was found optimum for the positive regulation of root growth. qRT-PCR analysis reveals that 1,9-D can significantly increase AtABA3 gene expression and that a mutation in ABA3 results in insensitivity of root growth to 1,9-D. Moreover, through pharmacological experiments, we show that exogenous addition of ABA (abscisic acid) with 1,9-D enhances primary root length by 23.5%-63.3%, and an exogenous supply of 1,9-D with the ABA inhibitor Flu reduces primary root length by 1.0%-14.3%. Primary root length of the pin2/eir1-1 is shown to be insensitive to both exogenous addition of 1,9-D and ABA, indicating that the auxin carrier PIN2/EIR1 is involved in promotion of root growth by 1,9-D. These results suggest a novel for 1,9-D in regulating plant root growth through ABA and auxin signaling.
PMID: 36495813
Funct Integr Genomics , IF:3.41 , 2022 Dec , V23 (1) : P14 doi: 10.1007/s10142-022-00928-7
Leaf rust responsive miRNA and their target genes in wheat.
Division of Genetics, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, 110012, India.; Regional Station, ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India.; Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India.; Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, 250004, India. pkgupta36@gmail.com.
Small RNA sequencing (sRNA-seq) and degradome analysis were used for the identification of miRNAs and their target host genes in a pair of near-isogenic lines (NILs), which differed for the presence of leaf rust resistance gene Lr28. The study led to identification of (i) 506 known and 346 novel miRNAs; and (ii) 5054 target genes including 4557 in silico predicted and 497 degradome-based genes using 105 differentially expressed (DE) miRNAs. A subset of 128 targets (67 in silico + 61 degradome-based) was differentially expressed in RNA-seq data that was generated by us earlier using the same pair of NILs; among these 128 targets, 58 target genes exhibited an inverse relationship with the DE miRNAs (expression of miRNAs and activation/suppression of target genes). Eight miRNAs which belonged to the conserved miRNA families and were known to be induced in response to fungal diseases in plants included the following: miR156, miR158, miR159, miR168, miR169, miR172, miR319, miR396. The target genes belonged to the following classes of genes known to be involved in downstream disease resistance pathways; peroxidases, sugar transporters, auxin response signaling, oxidation-reduction, etc. It was also noticed that although a majority of miRNAs and target genes followed the above classical inverse relationship, there were also examples, where no such relationship was observed. Among the target genes, there were also 51 genes that were not only regulated by miRNAs, but were also differentially methylated at sequences including the following segments: promotors, introns, TSS, exons. The results of the present study suggest a complex interplay among miRNA genes, target genes, and various epigenetic controls, which regulate the expression of genes involved in downstream pathways for disease resistance.
PMID: 36550370
Protoplasma , IF:3.356 , 2023 Jan doi: 10.1007/s00709-022-01833-3
Auxin- and pH-induced guttation in Phycomyces sporangiophores: relation between guttation and diminished elongation growth.
Institute for Multidisciplinary Research, University of Belgrade, Kneza Viseslava 1, 11030, Belgrade, Serbia. vunduk@imsi.bg.ac.rs.; Max Planck Institute for Evolutionary Biology, Department of Evolutionary Biology, August Thienemann Str. 2, 24306, Plon, Germany.; Institute for Multidisciplinary Research, University of Belgrade, Kneza Viseslava 1, 11030, Belgrade, Serbia.; Singidunum University, Danijelova 32, 11010, Belgrade, Serbia.; Faculty of Biology, Philipps-University Marburg, Karl-Von-Frisch Str. 8, 35032, Marburg, Germany.
Guttation, the formation of exudation water, is widespread among plants and fungi, yet the underlying mechanisms remain largely unknown. We describe the conditions for inducing guttation in sporangiophores of the mucoracean fungus, Phycomyces blakesleeanus. Cultivation on peptone-enriched potato dextrose agar elicits vigorous guttation mainly below the apical growing zone, while sporangiophores raised on a glucose-mineral medium manifest only moderate guttation. Mycelia do not guttate irrespective of the employed media. The topology of guttation droplets allows identifying the non-growing part of the sporangiophore as a guttation zone, which responds to humidity and medium composition in ways that become relevant for turgor homeostasis and thus the sensor physiology of the growing zone. Apparently, the entire sporangiophore, rather than exclusively the growing zone, participates in signal reception and integration to generate a common growth output. Exogenous auxin applied to the growing zones elicits two correlated responses: (i) formation of guttation droplets in the growing and transition zones below the sporangium and (ii) a diminution of the growth rate. In sporangiophore populations, guttation-induction by exogenous control buffer occurs at low frequencies; the bias for guttation increases with increasing auxin concentration. Synthetic auxins and the transport inhibitor NPA suppress guttation completely, but leave growth rates largely unaffected. Mutants C2 carA and C148 carA madC display higher sensitivities for auxin-induced guttation compared to wild type. A working model for guttation includes aquaporins and mechanosensitive ion channels that we identified in Phycomyces by sequence domain searches.
PMID: 36622433
Protoplasma , IF:3.356 , 2023 Jan , V260 (1) : P257-270 doi: 10.1007/s00709-022-01773-y
Genome-wide identification of Aux/IAA and ARF gene families in bread wheat (Triticum aestivum L.).
Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.; Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India. param@genomeindia.org.
Wheat (Triticum aestivum L.) is one of the most important food crops in the world. Somatic embryogenesis is an event that is triggered by the presence of auxin hormone for the induction of somatic cells to get converted to embryonic cells. Somatic embryogenesis represents the most important process of totipotency of plants. The role of auxins is widely understood during various stages of embryogenesis including polarity establishment, de-differentiation, re-differentiations, and morphogenesis. Many of the Aux/IAAs and ARFs which are part of auxin signaling components have been identified to play various roles during embryogenesis. In this analysis, the Aux/IAAs and ARFs of T. aestivum have been analyzed at the genome-scale; their structure, function, and evolutionary relatedness were determined. Several Aux/IAAs and ARFs components of T. aestivum have been found to exclusively regulate axis formation, meristem commitment, and other re-differentiation processes by differential expression studies.
PMID: 35606614
Funct Plant Biol , IF:3.101 , 2023 Jan , V50 (1) : P58-70 doi: 10.1071/FP22002
Crucial role of Arabidopsis glutaredoxin S17 in heat stress response revealed by transcriptome analysis.
State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, P. R. China.; USDA/ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA.
Heat stress can have detrimental effects on plant growth and development. However, the mechanisms by which the plant is able to perceive changes in ambient temperature, transmit this information, and initiate a temperature-induced response are not fully understood. Previously, we showed that heterologous expression of an Arabidopsis thaliana L. monothiol glutaredoxin AtGRXS17 enhances thermotolerance in various crops, while disruption of AtGRXS17 expression caused hypersensitivity to permissive temperature. In this study, we extend our investigation into the effect of AtGRXS17 and heat stress on plant growth and development. Although atgrxs17 plants were found to exhibit a slight decrease in hypocotyl elongation, shoot meristem development, and root growth compared to wild-type when grown at 22 degrees C, these growth phenotypic differences became more pronounced when growth temperatures were raised to 28 degrees C. Transcriptome analysis revealed significant changes in genome-wide gene expression in atgrxs17 plants compared to wild-type under conditions of heat stress. The expression of genes related to heat stress factors, auxin response, cellular communication, and abiotic stress were altered in atgrxs17 plants in response to heat stress. Overall, our findings indicate that AtGRXS17 plays a critical role in controlling the transcriptional regulation of plant heat stress response pathways.
PMID: 36099929
Plant Direct , IF:3.038 , 2022 Dec , V6 (12) : Pe465 doi: 10.1002/pld3.465
Opposing effects of trans- and cis-cinnamic acid during rice coleoptile elongation.
Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium.; VIB-UGent Center for Plant Systems Biology Ghent Belgium.; Laboratory of Plant Growth Analysis Ghent University Global Campus Incheon South Korea.; VIB Metabolomics Core Ghent Ghent Belgium.; Department of Biotechnology Ghent University Ghent Belgium.; Department of Green Chemistry and Technology Ghent University Ghent Belgium.
The phenylpropanoid cinnamic acid (CA) is a plant metabolite that can occur under a trans- or cis-form. In contrast to the proven bioactivity of the cis-form (c-CA), the activity of trans-CA (t-CA) is still a matter of debate. We tested both compounds using a submerged rice coleoptile assay and demonstrated that they have opposite effects on cell elongation. Notably, in the tip of rice coleoptile t-CA showed an inhibiting and c-CA a stimulating activity. By combining transcriptomics and (untargeted) metabolomics with activity assays and genetic and pharmacological experiments, we aimed to explain the underlying mechanistic processes. We propose a model in which c-CA treatment activates proton pumps and stimulates acidification of the apoplast, which in turn leads to the loosening of the cell wall, necessary for elongation. We hypothesize that c-CA also inactivates auxin efflux transporters, which might cause a local auxin accumulation in the tip of the coleoptile. For t-CA, the phenotype can partially be explained by a stimulation of cell wall polysaccharide feruloylation, leading to a more rigid cell wall. Metabolite profiling also demonstrated that salicylic acid (SA) derivatives are increased upon t-CA treatment. As SA is a known antagonist of auxin, the shift in SA homeostasis provides an additional explanation of the observed t-CA-mediated restriction on cell growth.
PMID: 36545006
PeerJ , IF:2.984 , 2023 , V11 : Pe14581 doi: 10.7717/peerj.14581
Stem transcriptome screen for selection in wild and cultivated pitahaya (Selenicereus undatus): an epiphytic cactus with edible fruit.
Universidad Autonoma Metropolitana Iztapalapa, Ciudad de Mexico, Mexico.; INBIOTECA, Universidad Veracruzana, Xalapa, Veracruz, Mexico.; Biologia Evolutiva, Instituto de Ecologia AC, Xalapa, Veracruz, Mexico.
Dragon fruit, pitahaya or pitaya are common names for the species in the Hylocereus group of Selenicereus that produce edible fruit. These Neotropical epiphytic cacti are considered promising underutilized crops and are currently cultivated around the world. The most important species, S. undatus, has been managed in the Maya domain for centuries and is the focus of this article. Transcriptome profiles from stems of wild and cultivated plants of this species were compared. We hypothesized that differences in transcriptomic signatures could be associated with genes related to drought stress. De novo transcriptome assembly and the analysis of differentially expressed genes (DEGs) allowed us to identify a total of 9,203 DEGs in the Hunucma cultivar relative of wild Mozomboa plants. Of these, 4,883 represent up-regulated genes and 4,320, down-regulated genes. Additionally, 6,568 DEGs were identified from a comparison between the Uman cultivar and wild plants, revealing 3,286 up-regulated and 3,282 down-regulated genes. Approximately half of the DEGs are shared by the two cultivated plants. Differences between the two cultivars that were collected in the same region could be the result of differences in management. Metabolism was the most representative functional category in both cultivars. The up-regulated genes of both cultivars formed a network related to the hormone-mediated signaling pathway that includes cellular responses to auxin stimulus and to hormone stimulus. These cellular reactions have been documented in several cultivated plants in which drought-tolerant cultivars modify auxin transport and ethylene signaling, resulting in a better redistribution of assimilates.
PMID: 36632141
PeerJ , IF:2.984 , 2023 , V11 : Pe14617 doi: 10.7717/peerj.14617
Integrative genomic and transcriptomic analyses of a bud sport mutant 'Jinzao Wuhe' with the phenotype of large berries in grapevines.
The Research Institute of Forestry and Pomology, Tianjin Academy of Agricultural Sciences, Tianjin, China.; Institute of Crop Germplasm and Biotechnology, Tianjin Academy of Agricultural Sciences, Tianjin, China.; College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.; College of Horticulture and Gardening, Tianjin Agricultural University, Tianjin, China.
BACKGROUND: Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. 'Jinzao Wuhe' is a bud sport of the elite cultivar 'Himord Seedless' with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear. METHODS: Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for 'Jinzao Wuhe' and its maternal plant 'Himord Seedless' were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation. RESULTS: In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between 'Himord Seedless' and 'Jinzao Wuhe' harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine. CONCLUSION: Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars.
PMID: 36620751
Ecotoxicology , IF:2.823 , 2023 Jan , V32 (1) : P1-11 doi: 10.1007/s10646-022-02613-8
Pea root responses under naproxen stress: changes in the formation of structural barriers in the primary root in context with changes of auxin and abscisic acid levels.
Section of Experimental Plant Biology, Department of Experimental Biology, Faculty of Science, Masaryk University Brno, Kotlarska 2, 611 37, Brno, Czech Republic.; Section of Experimental Plant Biology, Department of Experimental Biology, Faculty of Science, Masaryk University Brno, Kotlarska 2, 611 37, Brno, Czech Republic. zezulka@sci.muni.cz.; Department of Plant Physiology, Faculty of Natural Science, Comenius University in Bratislava, Mlynska dolina B2, 842 15, Bratislava, Slovakia.; Institute of Plant Biology, Faculty of Agronomy, Mendel University Brno, Zemedelska 1, 613 00, Brno, Czech Republic.; Laboratory of Metabolomics and Isotope Analyses, Global Change Research Institute, Czech Academy of Sciences, Belidla 986/4a, 603 00, Brno, Czech Republic.
Pharmaceuticals belong to pseudo-persistent pollutants because of constant entry into the environment and hazardous potential for non-target organisms, including plants, in which they can influence biochemical and physiological processes. Detailed analysis of results obtained by microscopic observations using fluorescent dyes (berberine hemisulphate, Fluorol Yellow 088), detection of phytohormone levels (radioimmunoassay, enzyme-linked immune sorbent assay) and thermogravimetric analysis of lignin content proved that the drug naproxen (NPX) can stimulate the formation of root structural barriers. In the primary root of plants treated with 0.5, 1, and 10 mg/L NPX, earlier Casparian strip formation and development of the whole endodermis circle closer to its apex were found after five days of cultivation (by 9-20% as compared to control) and after ten days from 0.1 mg/L NPX (by 8-63%). Suberin lamellae (SL) were deposited in endodermal cells significantly closer to the apex under 10 mg/L NPX by up to 75%. Structural barrier formation under NPX treatment can be influenced indirectly by auxin-supported cell division and differentiation caused by its eight-times higher level under 10 mg/L NPX and directly by stimulated SL deposition induced by abscisic acid (higher from 0.5 mg/L NPX), as proved by the higher proportion of cells with SL in the primary root base (by 8-44%). The earlier modification of endodermis in plant roots can help to limit the drug transfer and maintain the homeostasis of the plant.
PMID: 36542231
Mol Biotechnol , IF:2.695 , 2023 Jan doi: 10.1007/s12033-023-00653-x
Loss-of-Function Mutation of ACTIN-RELATED PROTEIN 6 (ARP6) Impairs Root Growth in Response to Salinity Stress.
Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh, Vietnam.; National Institute of Medicinal Materials, Hanoi, Vietnam.; Faculty of Biotechnology, Ho Chi Minh City Open University, 97 Vo Van Tan Street, District 3, Ho Chi Minh, Vietnam.; Faculty of Biotechnology, Ho Chi Minh City Open University, 97 Vo Van Tan Street, District 3, Ho Chi Minh, Vietnam. nguyen.nhoai@ou.edu.vn.
H2A.Z-containing nucleosomes have been found to function in various developmental programs in Arabidopsis (e.g., floral transition, warm ambient temperature, and drought stress responses). The SWI2/SNF2-Related 1 Chromatin Remodeling (SWR1) complex is known to control the deposition of H2A.Z, and it has been unraveled that ACTIN-RELATED PROTEIN 6 (ARP6) is one component of this SWR1 complex. Previous studies showed that the arp6 mutant exhibited some distinguished phenotypes such as early flowering, leaf serration, elongated hypocotyl, and reduced seed germination rate in response to osmotic stress. In this study, we aimed to investigate the changes of arp6 mutant when the plants were grown in salt stress condition. The phenotypic observation showed that the arp6 mutant was more sensitive to salt stress than the wild type. Upon salt stress condition, this mutant exhibited attenuated root phenotypes such as shorter primary root length and fewer lateral root numbers. The transcript levels of stress-responsive genes, ABA INSENSITIVE 1 (ABI1) and ABI2, were found to be impaired in the arp6 mutant in comparison with wild-type plants in response to salt stress. In addition, a meta-analysis of published data indicated a number of genes involved in auxin response were induced in arp6 mutant grown in non-stress condition. These imply that the loss of H2A.Z balance (in arp6 mutant) may lead to change stress and auxin responses resulting in alternative root morphogenesis upon both normal and salinity stress conditions.
PMID: 36627550
Arch Microbiol , IF:2.552 , 2022 Dec , V205 (1) : P45 doi: 10.1007/s00203-022-03358-y
Molecular identification and characterization of phytobeneficial osmotolerant endophytic bacteria inhabiting root nodules of the Saharan tree Vachellia tortilis subsp. raddiana.
Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco.; Microbiology and Molecular Biology Team, Center of Plant and Microbial Biotechnology, Biodiversity and Environment, Faculty of Sciences, Mohammed V University in Rabat, Avenue Ibn Battouta, BP 1014, 10000, Rabat, Morocco. jamal.aurag@fsr.um5.ac.ma.
Nodular endophytes of drought-tolerant legumes are understudied. For this reason, we have isolated and studied non-symbiotic endophytic bacteria from nodules of Vachellia tortilis subsp. raddiana, a leguminous tree adapted to the harsh arid climate of Southern Morocco. Rep-PCR analysis followed by 16S rDNA sequencing revealed two main genera, Pseudomonas and Bacillus. Isolates responded variably to salt and water stresses, and mostly produced exopolysaccharides. Differences concerned also plant growth-promoting activities: phosphate, potassium, and zinc solubilization; biological nitrogen fixation; auxin, siderophore, ammonia, and HCN production; and ACC deaminase activity. Some strains exhibited antagonistic activities against phytopathogenic fungi (Fusarium oxysporum and Botrytis cinerea) and showed at least two enzymatic activities (cellulase, protease, chitinase). Four selected strains inoculated to vachellia plants under controlled conditions have shown significant positive impacts on plant growth parameters. These strains are promising bio-inoculants for vachellia plants to be used in reforestation programs in arid areas increasingly threatened by desertification.
PMID: 36576567
Biol Open , IF:2.422 , 2022 Dec , V11 (12) doi: 10.1242/bio.059668
Reevaluating the relationship between EGL-43 (EVI1) and LIN-12 (Notch) during C. elegans anchor cell invasion.
Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA.; Howard Hughes Medical Institute, Department of Biology, Stanford University, Stanford, CA 94305, USA.
Development of the Caenorhabditis elegans reproductive tract is orchestrated by the anchor cell (AC). This occurs in part through a cell invasion event that connects the uterine and vulval tissues. Several key transcription factors regulate AC invasion, such as EGL-43, HLH-2, and NHR-67. Specifically, these transcription factors function together to maintain the post-mitotic state of the AC, a requirement for AC invasion. Recently, a mechanistic connection has been made between loss of EGL-43 and AC cell-cycle entry. The current model states that EGL-43 represses LIN-12 (Notch) expression to prevent AC proliferation, suggesting that Notch signaling has mitogenic effects in the invasive AC. To reexamine the relationship between EGL-43 and LIN-12, we first designed and implemented a heterologous co-expression system called AIDHB that combines the auxin-inducible degron (AID) system of plants with a live cell-cycle sensor based on human DNA helicase B (DHB). After validating AIDHB using AID-tagged GFP, we sought to test it by using AID-tagged alleles of egl-43 and lin-12. Auxin-induced degradation of either EGL-43 or LIN-12 resulted in the expected AC phenotypes. Lastly, we seized the opportunity to pair AIDHB with RNAi to co-deplete LIN-12 and EGL-43, respectively, which revealed that LIN-12 is not required for AC proliferation following loss of EGL-43.
PMID: 36445013
Physiol Mol Biol Plants , IF:2.391 , 2022 Dec , V28 (11-12) : P1997-2009 doi: 10.1007/s12298-022-01268-3
Volatile organic compounds from Lysinibacillus macroides regulating the seedling growth of Arabidopsis thaliana.
College of Life Sciences, Shandong Agricultural University, Tai'an, 271018 China. GRID: grid.440622.6. ISNI: 0000 0000 9482 4676; Shandong Key Laboratory of Agricultural Microbiology, Tai'an, 271018 China.; Shandong Engineering Research Center of Plant-Microbia Restoration for Saline-Alkali Land, Tai'an, 271018 China.
Volatile organic compounds (VOCs) have the characteristics of long distance propagation, low concentration, perception, and indirect contact between organisms. In this experiment, Lysinibacillus macroides Xi9 was isolated from cassava residue, and the VOCs produced by this strain were analyzed by the SPME-GC-MS method, mainly including alcohols, esters, and alkanes. By inoculation of L. macroides Xi9, VOCs can promote the growth and change the root-system architecture of Arabidopsis seedlings. The results showed that the number of lateral roots, root density, and fresh weight of Arabidopsis seedlings were significantly higher (p
PMID: 36573143
Int J Genomics , IF:2.326 , 2022 , V2022 : P2093029 doi: 10.1155/2022/2093029
A Genomic Analysis of Bacillus megaterium HT517 Reveals the Genetic Basis of Its Abilities to Promote Growth and Control Disease in Greenhouse Tomato.
State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory for Farmland Eco-Environment of Hebei Province, Hebei Collaborative Innovation Center for Green & Efficient Vegetable Industry, College of Resources and Environmental Science, Hebei Industrial Technology Institute of Microbial Fertilizers, Hebei Agricultural University, Baoding 071000, China.; College of Plant Protection, Hebei Agricultural University, Baoding 071000, China.; Agricultural and Rural Bureau of Yongqing, Hebei Province 065600, China.; Centre for Soil and Environmental Research, Lincoln University, Christchurch 7647, New Zealand.
Bacillus megaterium is well known as a plant growth-promoting rhizobacterium, but the relevant molecular mechanisms remain unclear. This study aimed to elucidate the effects of B. megaterium HT517 on the growth and development of and the control of disease in greenhouse tomato and its mechanism of action. A pot experiment was conducted to determine the effect of B. megaterium on tomato growth, and this experiment included the HT517 group (3.2 x 10(8) cfu/pot) and the control group (inoculated with the same amount of sterilized suspension). An antagonistic experiment and a plate confrontation experiment were conducted to study the antagonistic effect of B. megaterium and Fusarium oxysporum f.sp. lycopersici. Liquid chromatography-mass spectrometry was used to determine the metabolite composition and metabolic pathway of HT517. PacBio+Illumina HiSeq sequencing was utilized for map sequencing of the samples. An in-depth analysis of the functional genes related to the secretion of these substances by functional bacteria was conducted. HT517 could secrete organic acids that solubilize phosphorus, promote root growth, secrete auxin, which that promotes early flowering and fruiting, and alkaloids, which control disease, and reduce the incidence of crown rot by 51.0%. The complete genome sequence indicated that the strain comprised one circular chromosome with a length of 5,510,339 bp (including four plasmids in the genome), and the GC content accounted for 37.95%. Seven genes (pyk, aceB, pyc, ackA, gltA, buk, and aroK) related to phosphate solubilization, five genes (trpA, trpB, trpS, TDO2, and idi) related to growth promotion, eight genes (hpaB, pheS, pheT, ileS, pepA, iucD, paaG, and kamA) related to disease control, and one gene cluster of synthetic surfactin were identified in this research. The identification of molecular biological mechanisms for extracellular secretion by the HT517 strain clarified that its organic acids solubilized phosphorus, that auxin promoted growth, and that alkaloids controlled tomato diseases.
PMID: 36605453
Mol Biol Rep , IF:2.316 , 2022 Dec , V49 (12) : P11273-11280 doi: 10.1007/s11033-022-07712-7
Determination of genotoxic damages of picloram and dicamba with comet assay in Allium cepa rooted in tissue culture and distilled water.
Faculty of Gazi Education, Department of Biology Education, Gazi University, Ankara, Turkey. cigdemozel@gazi.edu.tr.; Science Faculty, Department of Biology, Gazi University, Ankara, Turkey.; Vocational School of Technical Sciences, Amasya University, Amasya, Turkey.; Faculty of Gazi Education, Department of Biology Education, Gazi University, Ankara, Turkey.
BACKGROUND: Many genotoxicity tests allow us to understand the mechanism of damages on genetic material occurring in living organisms against various physical and chemical agents. One of them is the Comet test. The current study aimed to evaluate genotoxic caused by picloram and dicamba to root meristems of Allium cepa utilizing comet assay. METHODS: Two different protocols were used for rooting and auxin/pesticide application. (i) A. cepa bulbs were rooted in MS medium and then treated with Murashige and Skoog (MS) medium (control) and 0.67, 1.34, 2.01, 2.68, 3.35, 4.02, and 8.04 mg/L of picloram and dicamba using aseptic tissue culture techniques. (ii) A. cepa bulbs were then rooted in bidistilled water and treated with 0 (control), 0.67, 1.34, 2.01, 2.68, 3.35, 4.02, and 8.04 mg/L of picloram and dicamba in distilled water. The A. cepa root tip cells in both treatment groups were examined using comet test to find the possible DNA damaging effects of picloram and dicamba. RESULTS: The results obtained at all the concentrations were statistically compared with their control groups. Almost at all the concentrations of Picloram and dicamba increased comet tail intensity (%) and tail moment in roots treated in MS medium. Two highest concentrations revealed toxic effect. On the other hand, DNA damaging effect of both auxins was only noted on the highest (> 4.02 mg/L) in roots treated in distilled water. CONCLUSIONS: This study approve and confirm genotoxic effects of how growth regulators on plants. These findings give an evidence of DNA damage in A. cepa. Therefore, both picloram and dicamba should only be used in appropriate and recommended concentrations in agriculture to conserve ecosystem and to pose minimum threat to life.
PMID: 35804213
J Basic Microbiol , IF:2.281 , 2023 Jan , V63 (1) : P17-25 doi: 10.1002/jobm.202200463
Transcriptome analysis of Armillaria gallica 012 m in response to auxin.
Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, Kunming, China.; Department of Chemistry, School of Chemistry and Environment, Yunnan Minzu University, Kunming, China.; Life Science College, Southwest Forestry University, Kunming, China.; Kunming Xianghao Technology Co. Ltd., Kunming, China.
Gastrodia elata is an achlorophyllous and fully mycoheterotrophic orchid which obtains carbon and other nutrients from Armillaria species in its life cycle. Many researchers suggested that plant hormones, as signing molecules, play a central role in the plant-fungi interaction. In the process of Armillaria gallica 012 m cultivation, both exogenous indole-3-acetic acid (IAA) and indole-3-butyric acid (IBA) distinctly stimulated the growth of mycelia in solid media. The differential expression genes (DEGs) of A. gallica 012 m with IAA versus blank control (BK) and IBA versus BK were investigated. The results showed that more than 80% of DEGs of the IAA group were coincident with the DEGs of the IBA group, and more than half of upregulated DEGs and most of the downregulated DEGs of the IAA group coincided with those DEGs of the IBA group. Above research implied that A. gallica 012 m could perceive IAA and IBA, and possess similar responses and signaling pathways to IAA and IBA. The overlapping differential genes of the IAA group and IBA group were analyzed by GO term, and the results showed that several DEGs identified were related to biological processes including positive regulation of the biological process and biological process. The downregulated NmrA-like and FKBP_C genes might be benefit to the growth of mycelia. Those results can explain that exiguous IAA and IBA improved the growth of A. gallica to some extent. We speculate that IAA and IBA are signaling molecules, and regulate the expression of growth-related genes of A. gallica 012 m by the same signaling pathway.
PMID: 36449692
Antonie Van Leeuwenhoek , IF:2.271 , 2022 Dec doi: 10.1007/s10482-022-01800-1
Devosia oryzisoli sp. nov., a novel moderately halotolerant bacterium isolated from the roots of rice plants and genome mining revealed the biosynthesis potential as plant growth promoter.
Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea.; Department of Life Science, Dongguk University-Seoul, 10326, Goyang, South Korea. tseo@dongguk.edu.
A Gram-stain-negative, halotolerant bacterium designated as PTR5(T) was isolated from the roots of rice plants, collected in Ilsan, South Korea. Cells were, aerobic, asporogenous, motile, rod-shaped, white in color, and grew at 5-38 degrees C (optimum 30 degrees C), at pH 5.0-0-8.0 (optimum, 7.0) and tolerates up to 10% (w/v) NaCl (optimum, 0% NaCl). According to the EZbioCloud server the most closely related Devosia species to strain PTR5(T) based on 16 S rRNA gene sequence comparison are Devosia crocina (97.4%), followed by D. soli (97.2%), D. lucknowensis (96.9%) and D. marina (96.5%). The respiratory quinone was identified as Q-10. The major polar lipids were phosphatidylglycerol and diphosphatidylglycerol. C(16:0), C(18:1) omega7c 11-methyl and summed feature 8 (comprising C(18:1) omega7c/C(18:1) omega6c) constituted the main cellular fatty acids. The draft genome sequence of strain PTR5(T) was 3,689,283 bp in size. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and amino acid identity (AAI) values between strain PTR5(T) and its close relative were 72.8-76.8%, 19-20.7% and 70.3-75%, respectively. The G + C content was 63.7%. Strain PTR5(T) was able to produce siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Genes for siderophore production, auxin responsive and tryptophan biosynthesis were present in the genome of novel strain. Also, gene clusters involved in detoxification of various metal pollutants and antibiotics were also revealed in the genome of novel strain PTR5(T), this suggest that novel strain can facilitate bioremediation of heavy metals and antibiotics in contaminated areas. This study aimed to determine the detailed taxonomic position of the strain PTR5(T) using the modern polyphasic approach. On the basis of evidence presented in this study, strain PTR5(T) is considered to represent a novel species of the genus Devosia, for which the name Devosia oryzisoli sp. nov. (type strain PTR5(T) (KCTC 82691(T) = TBRC 15163(T)) is proposed.
PMID: 36525157
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2163342 doi: 10.1080/15592324.2022.2163342
Cloning and expression study of a high-affinity nitrate transporter gene from Zea mays L.
Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China.; Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China.; Aulin College, Northeast Forestry University, Harbin, Heilongjiang, China.
A nitrate transporter gene, named B46NRT2.1, from salt-tolerant Zea mays L. B46 has been cloned. B46NRT2.1 contained the same domain belonging to the major facilitator superfamily (PLN00028). The results of the phylogenetic tree indicated that B46NRT2.1 exhibits sequence similarity and the closest relationship with those known nitrate transporters of the NRT2 family. Through RT-qPCR, we found that the expression of B46NRT2.1 mainly happens in the root and leaf. Moreover, the treatment with NaCl, Na(2)CO(3), and NaHCO(3) could significantly increase the expression of B46NRT2.1. B46NRT2.1 was located in the plasma membrane. Through the study of yeast and plant salt response brought by B46NRT2.1 overexpression, we have preliminary knowledge that the expression of B46NRT2.1 makes yeast and plants respond to salt shock. There are 10 different kinds of cis-acting regulatory elements (CRES) in the promotor sequences of B46NRT2.1 gene using the PlantCARE web server to analyze. It mainly includes hormone response, abscisic acid, salicylic acid, gibberellin, methyl jasmonate, and auxin. The B46NRT2.1 gene's co-expression network showed that it was co-expressed with a number of other genes in several biological pathways, including regulation of NO(3) long-distance transit, modulation of nitrate sensing and metabolism, nitrate assimilation, and transduction of Jasmonic acid-independent wound signal. The results of this work should serve as a good scientific foundation for further research on the functions of the NRT2 gene family in plants (inbred line B46), and this research adds to our understanding of the molecular mechanisms under salt tolerance.
PMID: 36645908
Plant Signal Behav , IF:2.247 , 2022 Dec , V17 (1) : P2096780 doi: 10.1080/15592324.2022.2096780
GIGANTEA regulates lateral root formation by modulating auxin signaling in Arabidopsis thaliana.
Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
Lateral root (LR) formation is a vital organogenetic process that determines the root architecture in plants. The number of root branches governs the degree of anchorage, efficiency of nutrients acquisition, and water uptake. The molecular pathways involved in LR formation have been extensively studied in Arabidopsis thaliana (At). A plant hormone, Auxin, is a key regulator of root development and promotes LR formation in plants. A plethora of Arabidopsis genes have been identified to regulate LR initiation, patterning, and emergence processes. Recently, the involvement of flowering time control pathways and circadian clock pathways in LR development has come to light, but the connecting link between these processes is still missing. We have established that GIGANTEA (GI), a key component of photoperiodic flowering, can regulate the formation of LRs in Arabidopsis. GI is known to be involved in red light signaling and circadian clock signaling pathways. Here, we report that over-expression of GI enhances LR formation in red light in At. Real-time PCR analysis shows that GI positively regulates the transcription of TRANSPORT INHIBITOR RESPONSE 1 (TIR1) which is an upstream component of auxin signaling. Furthermore, gi-100 mutant downregulates the LR initiation signaling gene, AUXIN RESPONSE FACTOR 7 (ARF7), and its downstream target gene, LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16). Hence, GI acts as a positive regulator of IAA14-ARF7-LBD16 modules during LR initiation. We have also checked the effect of GI on the expression of NAC1 and AIR3 genes which are controlled by TIR1 during LR formation. Our results show that GI induces the NAC1 transcription and its downstream gene, AIR3 expression, which leads to the enhancement of LR initiation. Taken together, our results suggest that GI controls the expression of TIR1 to govern auxin signaling during LR formation in presence of red light and GI can act as a link between circadian clock signaling, flowering time control pathways, light signaling, and lateral root development pathways.
PMID: 35822517
Plant Signal Behav , IF:2.247 , 2022 Dec , V17 (1) : P2095143 doi: 10.1080/15592324.2022.2095143
Chemically defined elicitors activate priming in tomato seedlings.
Department of Research and Development, Zero Gravity Solutions, Inc., Boca Raton, FL, USA.
Tomato (Solanum lycopersicum L.) is an important crop that possesses about 35,000 genes. The treatment of plants with elicitors or pathogen attacks causes a cascade of defense reactions. We investigated tomato responses to the BamFX(TM) solution containing Zn and Cu elicitors and report the results of comparative transcriptome analysis of tomato seeds treated with Zn and Cu elicitors. The seeds were treated with optimum concentrations of Bam-FX solutions and subjected to cold methanolic extraction methods to obtain the secondary metabolites produced within them at different time intervals post-Bam-FX treatment. The metabolite mixture was analyzed using gas chromatography-mass spectrometry (GCMS). In transcriptome sequencing, GO and KEGG analyses revealed that the majority of the DEGs in BamFx-treated tomato was associated with primary and secondary metabolism, plant hormone signal transduction, TF regulation, transport, and responses to stimuli.The secondary metabolites found in the BamFX treated tomato seedlings - Esters of Fumaric acid, Succinic acid etc. The transcript levels of most auxin transporter-encoding genes changed significantly in the BamFX-treated seedlings (e.g., Solyc01g007010.3, a RING-type E3 ubiquitin transferase). The gene Solyc07g061720.3 for Gibberellin 2-oxidase and the Phorbol-ester/DAG-type domain-containing protein (Solyc02g068680.1) associated with the intracellular signaling genes were found upregulated in the BamFx-treated seeds. The time-dependent effect of the BamFX (1:500 for 60 min) was found to be regulating Abscisic acid signaling pathway genes (Solyc09g015380.1). This study identified many candidate genes for future functional analyses and laid a theoretical foundation for an improved understanding of the molecular mechanisms involved in the BamFx treatment of tomatoes to improve stress resistance.
PMID: 35770510
Plant Signal Behav , IF:2.247 , 2022 Dec , V17 (1) : P2065432 doi: 10.1080/15592324.2022.2065432
Functional redundancy of OsPIN1 paralogous genes in regulating plant growth and development in rice.
Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.; Agricultural Experiment Station of Zhejiang University, Hangzhou, Zhejiang, China.
The OsPIN1 paralogous genes (OsPIN1a-1d) are important for root and panicle development in rice (Oryza sativa L.). However, the specific role of OsPIN1 paralogous genes is still not clear. To understand the specific roles of PIN1 paralogs in rice, we generated pin1 triple and quadruple mutants by crossing the pin1a pin1b and pin1c pin1d double mutants which we previously created. Compared with the 7-day-old wild type, the pin1a pin1c pin1d and pin1b pin1c pin1d triple mutants showed no obvious phenotype variation except that the pin1a pin1c pin1d triple mutant had shorter primary root and shoot. The pin1a pin1b pin1c and pin1a pin1b pin1d triple mutants exhibited a series of developmental abnormalities, including shorter primary roots, longer root hairs, fewer crown roots and lateral roots, shorter and curved shoots. Furthermore, the pin1a pin1b pin1c pin1d quadruple mutant displayed more severe phenotypic defects which was lethal. In addition, the expression levels of some hormone signal transduction and crown root development related genes, such as OsIAAs, OsARFs, OsRRs, and OsCRLs, were significantly altered in the stem base of all examined pin1 multiple mutants. Taken together, our results demonstrated that the four OsPIN1 paralogous genes function redundantly in regulating rice growth and development.
PMID: 35442849
Plant Signal Behav , IF:2.247 , 2022 Dec , V17 (1) : P2031784 doi: 10.1080/15592324.2022.2031784
The epigenetic regulator ULTRAPETALA1 suppresses de novo root regeneration from Arabidopsis leaf explants.
Key Laboratory of Saline-Alkali Vegetation Ecology Restoration Ministry of Education, Northeast Forestry University, Harbin, China.; College of Life Science, Institute of Genetics, Northeast Forestry University, Harbin, China.; Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China.
Plants have the potency to regenerate adventitious roots from aerial organs after detachment. In Arabidopsis thaliana, de novo root regeneration (DNRR) from leaf explants is triggered by wounding signaling that rapidly induces the expression of the ETHYLENE RESPONSE FACTOR (ERF) transcription factors ERF109 and ABR1 (ERF111). In turn, the ERFs promote the expression of ASA1, an essential enzyme of auxin biosynthesis, which contributes to rooting by providing high levels of auxin near the wounding side of the leaf. Here, we show that the loss of the epigenetic regulator ULTRAPETALA1 (ULT1), which interacts with Polycomb and Trithorax Group proteins, accelerates and reinforces adventitious root formation. Expression of ERF109 and ASA1 was increased in ult1 mutants, whereas ABR1 was not significantly changed. Cultivation of explants on media with exogenous auxin equates adventitious root formation in wild-type with ult1 mutants, suggesting that ULT1 negatively regulates DNRR by suppressing auxin biosynthesis. Based on these findings, we propose that ULT1 is involved in a novel mechanism that prevents overproliferation of adventitious roots during DNRR.
PMID: 35164655
Folia Microbiol (Praha) , IF:2.099 , 2022 Dec , V67 (6) : P899-911 doi: 10.1007/s12223-022-00985-2
Predicting interactions of the frass-associated yeast Hyphopichia heimii with Olea europaea subsp. cuspidata and twig-boring bark beetles.
Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.; Department of Conservation Ecology and Entomology, Stellenbosch University, Stellenbosch, 7602, South Africa.; Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa. abo@sun.ac.za.
Bark beetles are destructive insect pests known to form symbioses with different fungal taxa, including yeasts. The aim of this study was to (1) determine the prevalence of the rare yeast Hyphopichia heimii in bark beetle frass from wild olive trees in South Africa and to (2) predict the potential interaction of this yeast with trees and bark beetles. Twenty-eight culturable yeast species were isolated from frass in 35 bark beetle galleries, including representatives of H. heimii from nine samples. Physiological characterization of H. heimii isolates revealed that none was able to degrade complex polymers present in hemicellulose; however, all were able to assimilate sucrose and cellobiose, sugars associated with an arboreal habitat. All isolates were able to produce the auxin indole acetic acid, indicative of a potential symbiosis with the tree. Sterol analysis revealed that the isolates possessed ergosterol quantities ranging from 3.644 +/- 0.119 to 13.920 +/- 1.230 mg/g dry cell weight, which suggested that H. heimii could serve as a source of sterols in bark beetle diets, as is known for other bark beetle-associated fungi. In addition, gas chromatography-mass spectrometry demonstrated that at least one of the isolates, Hyphopichia heimii CAB 1614, was able to convert the insect pheromone cis-verbenol to the anti-aggregation pheromone verbenone. This indicated that H. heimii could potentially influence beetle behaviour. These results support the contention of a tripartite symbiosis between H. heimii, olive trees, and bark beetles.
PMID: 35767213
Life Sci Space Res (Amst) , IF:2.082 , 2023 Feb , V36 : P138-146 doi: 10.1016/j.lssr.2022.10.005
Comprehensive analyses of plant hormones in etiolated pea and maize seedlings grown under microgravity conditions in space: Relevance to the International Space Station experiment "Auxin Transport".
Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan. Electronic address: yamazaki.chiaki@jaxa.jp.; Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan. Electronic address: yamazaki.tomokazu@jaxa.jp.; Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. Electronic address: mikiko@riken.jp.; Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan. Electronic address: yumiko.takebayashi@riken.jp.; Mass Spectrometry and Microscopy Unit, RIKEN Center for Sustainable Resource Science (CSRS), Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan; Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan. Electronic address: sakaki@agr.nagoya-u.ac.jp.; Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: ueda-f@basil.ocn.ne.jp.; Faculty of Agriculture, Tottori University, 4-101 Koyamacho-minami, Tottori 680-8553, Japan. Electronic address: m.oka@muses.tottori-u.ac.jp.; Future Development Division, Advanced Engineering Services Co., Ltd., 1-6-1 Takezono, Tsukuba, Ibaraki 305-0032, Japan. Electronic address: kamada.motoshi@jaxa.jp.; Technology and Research Promotion Department, Japan Space Forum, Shin-Otemachi Bldg. 7F, 2-2-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan. Electronic address: shimazu@spacelife.tokyo.; Utilization Engineering Department, Japan Manned Space System Corporation, Space Station Test Building, Tsukuba Space Center, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan. Electronic address: kasahara.haruo@jaxa.jp.; Utilization Engineering Department, Japan Manned Space System Corporation, Space Station Test Building, Tsukuba Space Center, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan. Electronic address: sano.hiromi@jaxa.jp.; Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan. Electronic address: suzuki.tomomi@jaxa.jp.; Japan Aerospace Exploration Agency, 2-1-1 Sengen, Tsukuba, Ibaraki 305-8505, Japan. Electronic address: higashibata.akira@jaxa.jp.; Faculty of Liberal Arts and Sciences, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: k.miyamoto@omu.ac.jp.; Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan. Electronic address: w21913n@omu.ac.jp.
Functional relationships between endogenous levels of plant hormones in the growth and development of shoots in etiolated Alaska pea and etiolated Golden Cross Bantam maize seedlings under different gravities were investigated in the "Auxin Transport" experiment aboard the International Space Station (ISS). Comprehensive analyses of 31 species of plant hormones of pea and maize seedlings grown under microgravity (mug) in space and 1 g conditions were conducted. Principal component analysis (PCA) and a multiple regression analysis with the dataset from the plant hormone analysis of the etiolated pea seedlings grown under mug and 1 g conditions in the presence and absence of 2,3,5-triiodobenzoic acid (TIBA) revealed endogenous levels of auxin correlated positively with bending and length of epicotyls. Endogenous cytokinins correlated negatively with them. These results suggest an interaction of auxin and cytokinins in automorphogenesis and growth inhibition of etiolated Alaska pea epicotyls grown under mug conditions in space. Less polar auxin transport with reduced endogenous levels of auxin increased endogenous levels of cytokinins, resulting in changing the growth direction of epicotyls and inhibiting growth. On the other hand, almost no close relationship between endogenous plant hormone levels and growth and development in etiolated maize seedlings grown was observed under mug conditions in space, as per Schulze et al. (1992). However, endogenous levels of IAA in the seedlings grown under mug conditions in space were significantly higher than those grown on Earth, similar to the cases of polar auxin transport already reported.
PMID: 36682823
Methods Enzymol , IF:1.6 , 2023 , V680 : P35-83 doi: 10.1016/bs.mie.2022.07.034
Biochemical characterization of plant aromatic aminotransferases.
Department of Botany, University of Wisconsin-Madison, Madison, WI, United States. Electronic address: koper@wisc.edu.; Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.; Department of Botany, University of Wisconsin-Madison, Madison, WI, United States.; Department of Botany, University of Wisconsin-Madison, Madison, WI, United States. Electronic address: maeda2@wisc.edu.
Aromatic aminotransferases (Aro ATs) are pyridoxal-5-phosphate (PLP)-dependent enzymes that catalyze the transamination reactions of an aromatic amino acid (AAA) or a keto acid. Aro ATs are involved in biosynthesis or degradation of AAAs and play important functions in controlling the production of plant hormones and secondary metabolites, such as auxin, tocopherols, flavonoids, and lignin. Most Aro ATs show substrate promiscuity and can accept multiple aromatic and non-aromatic amino and keto acid substrates, which complicates and limits our understanding of their in planta functions. Considering the critical roles Aro ATs play in plant primary and secondary metabolism, it is important to accurately determine substrate specificity and kinetic properties of Aro ATs. This chapter describes various methodologies of protein expression, purification and enzymatic assays, which can be used for biochemical characterization of Aro ATs.
PMID: 36710018
Vavilovskii Zhurnal Genet Selektsii , 2022 Dec , V26 (8) : P721-732 doi: 10.18699/VJGB-22-88
Molecular mechanisms of vascular tissue patterning in Arabidopsis thaliana L. roots.
Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia.; Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
A vascular system in plants is a product of aromorphosis that enabled them to colonize land because it delivers water, mineral and organic compounds to plant organs and provides effective communications between organs and mechanical support. Vascular system development is a common object of fundamental research in plant development biology. In the model plant Arabidopsis thaliana, early stages of vascular tissue formation in the root are a bright example of the self-organization of a bisymmetric (having two planes of symmetry) pattern of hormone distribution, which determines vascular cell fates. In the root, vascular tissue development comprises four stages: (1) specification of progenitor cells for the provascular meristem in early embryonic stages, (2) the growth and patterning of the embryo provascular meristem, (3) postembryonic maintenance of the cell identity in the vascular tissue initials within the root apical meristem, and (4) differentiation of their descendants. Although the anatomical details of A. thaliana root vasculature development have long been known and described in detail, our knowledge of the underlying molecular and genetic mechanisms remains limited. In recent years, several important advances have been made, shedding light on the regulation of the earliest events in provascular cells specification. In this review, we summarize the latest data on the molecular and genetic mechanisms of vascular tissue patterning in A. thaliana root. The first part of the review describes the root vasculature ontogeny, and the second reconstructs the sequence of regulatory events that underlie this histogenesis and determine the development of the progenitors of the vascular initials in the embryo and organization of vascular initials in the seedling root.
PMID: 36694717
Microbiol Resour Announc , 2023 Jan : Pe0104622 doi: 10.1128/mra.01046-22
Draft Genome Sequences of Four Plant Growth-Promoting Rhizobacteria Isolated from Saffron (Crocus sativus L.) Rhizosphere in Morocco.
Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, Morocco.; Biotechnology Laboratory, Bioinova Research Center, Rabat Medical and Pharmacy School, Mohammed V University in Rabat, Rabat, Morocco.
We report the draft genome sequences of plant growth-promoting Rahnella perminowiae strain S11P1, Variovorax sp. strain S12S4, and Pseudomonas sp. strains S11A4 and S11P7, which were isolated from saffron (Crocus sativus L.) rhizosphere. Several genes were predicted to be involved in auxin production, phosphate solubilization, and other specialized functions in plant growth and defense.
PMID: 36633434
Genomics Inform , 2022 Dec , V20 (4) : Pe45 doi: 10.5808/gi.22056
Application of data fusion modeling for the prediction of auxin response elements in Zea mays for food security purposes.
Laboratory of Advanced Technology and Intelligent Systems, National Engineering School of Sousse, Sousse 4023, Tunisia.; Department of Agronomy and Plant Biotechnology, National Institute of Agronomy of Tunisia (INAT), 43 Avenue Charles Nicolle, 1082 El Mahrajene, University of Carthage-Tunis, Tunisia.; Laboratory of Extremophile Plants, Centre of Biotechnology of Borj-Cedria, B.P. 901, Hammam Lif 2050, Tunisia.; Laboratory of Molecular and Cellular Screening Processes, Sfax Biotechnology Center, B.P 1177, Sfax 3018, Tunisia.
Food security will be affected by climate change worldwide, particularly in the developingworld, where the most important food products originate from plants. Plants are often exposed to environmental stresses that may affect their growth, development, yield, and foodquality. Auxin is a hormone that plays a critical role in improving plants' tolerance of environmental conditions. Auxin controls the expression of many stress-responsive genes inplants by interacting with specific cis-regulatory elements called auxin-responsive elements (AuxREs). In this work, we performed an in silico prediction of AuxREs in promotersof five auxin-responsive genes in Zea mays. We applied a data fusion approach based onthe combined use of Dempster-Shafer evidence theory and fuzzy sets. Auxin has a directimpact on cell membrane proteins. The short-term auxin response may be represented bythe regulation of transmembrane gene expression. The detection of an AuxRE in the promoter of prolyl oligopeptidase (POP) in Z. mays and the 3-fold overexpression of this geneunder auxin treatment for 30 min indicated the role of POP in maize auxin response. POP isregulated by auxin to perform stress adaptation. In addition, the detection of two AuxRETGTCTC motifs in the upstream sequence of the bx1 gene suggests that bx1 can be regulated by auxin. Auxin may also be involved in the regulation of dehydration-responsive element-binding and some members of the protein kinase superfamily.
PMID: 36617652
Cell Regen , 2023 Jan , V12 (1) : P1 doi: 10.1186/s13619-022-00140-9
WOX11: the founder of plant organ regeneration.
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China.; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai, 200032, China. xulin@cemps.ac.cn.
De novo organ regeneration is the process in which adventitious roots or shoots regenerate from detached or wounded organs. De novo organ regeneration can occur either in natural conditions, e.g. adventitious root regeneration from the wounded sites of detached leaves or stems, or in in-vitro tissue culture, e.g. organ regeneration from callus. In this review, we summarize recent advances in research on the molecular mechanism of de novo organ regeneration, focusing on the role of the WUSCHEL-RELATED HOMEOBOX11 (WOX11) gene in the model plant Arabidopsis thaliana. WOX11 is a direct target of the auxin signaling pathway, and it is expressed in, and regulates the establishment of, the founder cell during de novo root regeneration and callus formation. WOX11 activates the expression of its target genes to initiate root and callus primordia. Therefore, WOX11 links upstream auxin signaling to downstream cell fate transition during regeneration. We also discuss the role of WOX11 in diverse species and its evolution in plants.
PMID: 36596978
Heliyon , 2022 Dec , V8 (12) : Pe11969 doi: 10.1016/j.heliyon.2022.e11969
Prediction of In vitro organogenesis of Bacopa monnieri using artificial neural networks and regression models.
Agricultural Research Station, Fort Valley State University, Fort Valley, GA 31030, USA.; Department of Bioinformatics, Boston University, Boston, MA 02115, USA.; Houston County High School, Warner Robins, GA 31088, USA.; Department of Agricultural Sciences, College of Agriculture, Family Sciences and Technology, Fort Valley State University, Fort Valley, GA 31030, USA.
This study was conducted to determine if artificial neural networks (ANN) can be used to accurately predict in vitro organogenesis of Bacopa monnieri compared with statistical regression. Prediction models were developed for shoot and root organogenesis (outputs) on two culture media (Murashige and Skoog and Gamborg B5) affected by two explant types (leaf and node) and two cytokinins (6-Benzylaminopurine and Thidiazuron at 1.0, 5.0, and 10.0 muM levels) with and without the addition of auxin (1-Naphthaleneacetic acid 0.1 muM) (inputs). Categorical data were encoded in numeric form using one-hot encoding technique. Backpropagation (BP) and Kalman filter (KF) learning algorithms were used to develop nonparametric models between inputs and outputs. Correlations between predicted and observed outputs (validation dataset) were similar in both ANN-BP (R values = 0.77, 0.71, 0.68, and 0.48), and ANN-KF (R values = 0.79, 0.68, 0.75, and 0.49), and were higher than regression (R values = 0.13, 0.48, 0.39, and 0.37) models for shoots and roots from leaf and node explants, respectively. Because ANN models have the ability to interpolate from unseen data, they could be used as an effective tool in accurately predicting the in vitro growth kinetics of Bacopa cultures.
PMID: 36544836
Biotechnol Genet Eng Rev , 2022 Dec : P1-22 doi: 10.1080/02648725.2022.2157949
Comparison of diversity and zinc solubilizing efficiency of rhizobacteria obtained from solanaceous crops under polyhouse and open field conditions.
Department of Biotechnology, Chandigarh University, Mohali, Punjab, India.; Department of Agricultural Sciences, Chandigarh University, Mohali, Punjab, India.; Department of Chemistry, University Institute of Science, Chandigarh University, Mohali, Punjab, India.; Department of Environmental Science, Veer Bahadur Singh Purvanchal University, Jaunpur, Uttar Pradesh, India.; Biotechnology Program, Dr. Rammanohar Lohia Avadh University, Ayodhya, Uttar Pradesh, India.
Zinc-solubilizing bacteria (Zn-SB) play a crucial role in regulating soil fertility and plant health by maintaining Zn availability in the rhizosphere. It is uncertain how the Zn-SB population fluctuates across various cultivation systems since varied land-use patterns for agricultural aims may affect microbial activity and plant development effectiveness. The current study aims to examine the Zn-SB potential of various farming systems using Solanum lycopersicum, Solanum melongena, and Capsicum annuum grown in polyhouse soil (PS) and open fields (OF). Only twenty rhizobacterial isolates from PS and two isolates from OF out of 80 showed a strong ability to solubilize Zn, which was evaluated using Atomic Absorption Spectroscopy. Bacterial strain-PS4 solubilized 253.06 ppm of ZnO and produced a high quantity of lactic acid (168.62 g/ml) and acetic acid (470.5 g/ml), whereas bacterial strain OF1 solubilized 16.02 ppm of ZnO by releasing glycolic acid (42.89 g/ml), lactic acid (22.30 g/ml), formic acid (106.03 g/ml), and acetic acid (48.5 microg/ml). Further, in vitro studies demonstrated higher production of auxin, gibberellic acid and siderophore by PS1 as compared to OF1 strain. A large diversity of Zn-SB in the soil was indicated by biochemical analysis, which revealed that isolates belonged to the families Enterobacteriaceae, Bacillaceae, Burkholderiaceae, Streptococcaceae, Paenibacillaceae, Micrococcaceae, Morganellaceae, and Dietziaceae. The isolates PS4 and OF1 were identified as Bacillus cereus and Enterobacter hormaechei, respectively, using 16S rRNA sequencing. The findings show that soil from polyhouses has a greater diversity of Zn-solubilization rhizobacteria than soil from open areas. The findings suggested a potential land-use method for enhancing crop yields by employing microorganisms and polyhouse technology, which could be useful in the future study.
PMID: 36544391
Heliyon , 2022 Dec , V8 (12) : Pe11959 doi: 10.1016/j.heliyon.2022.e11959
Impacts of plant growth regulators in strawberry plant: A review.
G.P. Koirala College of Agriculture and Research Centre (GPCAR), Gothgaun, Morang, Nepal.; Nepal Polytechnic Institute (NPI), Chitwan, Nepal.
Strawberry (Fragaria x ananassa), the family Rosaceae, is a small fruit that has great importance. It is triggered by a number of physiological, genetic, and biochemical processes. Phytohormones or plant growth regulators are organic substances produced naturally in many plants and responsible for controlling growth and other physiological functions. Therefore, plant growth regulators such as Gibberellin, NAA (auxin) and triacontanol, and chlormequat are essential factors that cause strawberry ripening, maturity indices, and determine the quality of fruits. Moreover, Gibberellin stimulates cell division and breaks dormancy whereas NAA (auxin) stimulates root growth. Similarly, triacontanol plays a special role in plant growth and development. Additionally, chlormequat is effective in controlling the height of the plant. The main objective of this review is to study the effect of various plant growth regulators that have a great potential effect on growth, development, and fruit yield.
PMID: 36466575
Methods Mol Biol , 2023 , V2581 : P43-56 doi: 10.1007/978-1-0716-2784-6_4
An In vitro Assay to Recapitulate Hormone-Triggered and SCF-Mediated Protein Ubiquitylation.
Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany.; Molecular Signal Processing Department, Leibniz Institute of Plant Biochemistry (IPB), Halle (Saale), Germany. LuzIrina.Calderon@ipb-halle.de.; KWS Gateway Research Center, LLC, BRDG Park at the Danforth Plant Science Center, St. Louis, MO, USA. LuzIrina.Calderon@ipb-halle.de.
Signaling proteins trigger a sequence of molecular switches in the cell, which permit development, growth, and rapid adaptation to changing environmental conditions. SCF-type E3 ubiquitin ligases recognize signaling proteins prompting changes in their fate, one of these being ubiquitylation followed by degradation by the proteasome. SCFs together with their ubiquitylation targets (substrates) often serve as phytohormone receptors, responding and/or assembling in response to fluctuating intracellular hormone concentrations. Tracing and understanding phytohormone perception and SCF-mediated ubiquitylation of proteins could provide powerful clues on the molecular mechanisms utilized for plant adaptation. Here, we describe an adaptable in vitro system that uses recombinant proteins and enables the study of hormone-triggered SCF-substrate interaction and the dynamics of protein ubiquitylation. This system can serve to predict the requirements for protein recognition and to understand how phytohormone levels have the power to control protein fate.
PMID: 36413309