Nat Rev Mol Cell Biol , IF:94.444 , 2022 Oct , V23 (10) : P680-694 doi: 10.1038/s41580-022-00479-6
Plant hormone regulation of abiotic stress responses.
Institute of Technology, University of Tartu, Tartu, Estonia.; Institut fur Biologie und Biotechnologie der Pflanzen, Westfalische Wilhelms-Universitat Munster, Munster, Germany.; Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.; Graduate School of Environmental and Life Science, Okayama University, Tsushima-Naka, Okayama, Japan.; Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA. jischroeder@ucsd.edu.
Plant hormones are signalling compounds that regulate crucial aspects of growth, development and environmental stress responses. Abiotic stresses, such as drought, salinity, heat, cold and flooding, have profound effects on plant growth and survival. Adaptation and tolerance to such stresses require sophisticated sensing, signalling and stress response mechanisms. In this Review, we discuss recent advances in understanding how diverse plant hormones control abiotic stress responses in plants and highlight points of hormonal crosstalk during abiotic stress signalling. Control mechanisms and stress responses mediated by plant hormones including abscisic acid, auxin, brassinosteroids, cytokinins, ethylene and gibberellins are discussed. We discuss new insights into osmotic stress sensing and signalling mechanisms, hormonal control of gene regulation and plant development during stress, hormone-regulated submergence tolerance and stomatal movements. We further explore how innovative imaging approaches are providing insights into single-cell and tissue hormone dynamics. Understanding stress tolerance mechanisms opens new opportunities for agricultural applications.
PMID: 35513717
Nature , IF:49.962 , 2022 Oct doi: 10.1038/s41586-022-05369-7
Adenylate cyclase activity of TIR1/AFB auxin receptors in plants.
Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.; Department of Plant Physiology and Biotechnology, Nicolaus Copernicus University in Torun, Torun, Poland.; Readiness and Response Directorate, Biosecurity New Zealand, Wellington, New Zealand.; Centre for Fluid and Complex Systems, Coventry University, Coventry, UK.; School of Life Sciences, University of Warwick, Coventry, UK.; Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria. jiri.friml@ist.ac.at.
The phytohormone auxin is the major coordinative signal in plant development(1), mediating transcriptional reprogramming by a well-established canonical signalling pathway. TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB) auxin receptors are F-box subunits of ubiquitin ligase complexes. In response to auxin, they associate with Aux/IAA transcriptional repressors and target them for degradation via ubiquitination(2,3). Here we identify adenylate cyclase (AC) activity as an additional function of TIR1/AFB receptors across land plants. Auxin, together with Aux/IAAs, stimulates cAMP production. Three separate mutations in the AC motif of the TIR1 C-terminal region, all of which abolish the AC activity, each render TIR1 ineffective in mediating gravitropism and sustained auxin-induced root growth inhibition, and also affect auxin-induced transcriptional regulation. These results highlight the importance of TIR1/AFB AC activity in canonical auxin signalling. They also identify a unique phytohormone receptor cassette combining F-box and AC motifs, and the role of cAMP as a second messenger in plants.
PMID: 36289340
Nature , IF:49.962 , 2022 Sep , V609 (7927) : P575-581 doi: 10.1038/s41586-022-05187-x
ABP1-TMK auxin perception for global phosphorylation and auxin canalization.
Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria. jiri.friml@ista.ac.at.; Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.; Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland.; Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.; Institute for Multidisciplinary Research, University of Belgrade, Belgrade, Serbia.; Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent University, Ghent, Belgium.; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czechia.; Graduate School of Science and Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.
The phytohormone auxin triggers transcriptional reprogramming through a well-characterized perception machinery in the nucleus. By contrast, mechanisms that underlie fast effects of auxin, such as the regulation of ion fluxes, rapid phosphorylation of proteins or auxin feedback on its transport, remain unclear(1-3). Whether auxin-binding protein 1 (ABP1) is an auxin receptor has been a source of debate for decades(1,4). Here we show that a fraction of Arabidopsis thaliana ABP1 is secreted and binds auxin specifically at an acidic pH that is typical of the apoplast. ABP1 and its plasma-membrane-localized partner, transmembrane kinase 1 (TMK1), are required for the auxin-induced ultrafast global phospho-response and for downstream processes that include the activation of H(+)-ATPase and accelerated cytoplasmic streaming. abp1 and tmk mutants cannot establish auxin-transporting channels and show defective auxin-induced vasculature formation and regeneration. An ABP1(M2X) variant that lacks the capacity to bind auxin is unable to complement these defects in abp1 mutants. These data indicate that ABP1 is the auxin receptor for TMK1-based cell-surface signalling, which mediates the global phospho-response and auxin canalization.
PMID: 36071161
Cell Res , IF:25.617 , 2022 Oct , V32 (10) : P931-945 doi: 10.1038/s41422-022-00711-0
A spontaneous thermo-sensitive female sterility mutation in rice enables fully mechanized hybrid breeding.
Department of Biology, Hong Kong Baptist University, Hong Kong, China.; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.; Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China.; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.; Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 2-1-2 Kannondai Tsukuba, Ibaraki, Japan.; Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong, China.; College of Horticulture Science and Engineering, Shandong Agricultural University, Taian, Shandong, China.; The Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China.; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA. xuemei.chen@ucr.edu.; Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, Hunan, China. nye@hunau.edu.cn.; Department of Biology, Hong Kong Baptist University, Hong Kong, China. jzhang@hkbu.edu.hk.; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China. jzhang@hkbu.edu.hk.; Department of Biology, Hong Kong Baptist University, Hong Kong, China. gqwang@link.cuhk.edu.hk.; School of Life Sciences and State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China. gqwang@link.cuhk.edu.hk.
Male sterility enables hybrid crop breeding to increase yields and has been extensively studied. But thermo-sensitive female sterility, which is an ideal property that may enable full mechanization in hybrid rice breeding, has rarely been investigated due to the absence of such germplasm. Here we identify the spontaneous thermo-sensitive female sterility 1 (tfs1) mutation that confers complete sterility under regular/high temperature and partial fertility under low temperature as a point mutation in ARGONAUTE7 (AGO7). AGO7 associates with miR390 to form an RNA-Induced Silencing Complex (RISC), which triggers the biogenesis of small interfering RNAs (siRNAs) from TRANS-ACTING3 (TAS3) loci by recruiting SUPPRESSOR OF GENE SILENCING (SGS3) and RNA-DEPENDENT RNA POLYMERASE6 (RDR6) to TAS3 transcripts. These siRNAs are known as tasiR-ARFs as they act in trans to repress auxin response factor genes. The mutant TFS1 (mTFS1) protein is compromised in its ability to load the miR390/miR390* duplex and eject miR390* during RISC formation. Furthermore, tasiR-ARF levels are reduced in tfs1 due to the deficiency in RDR6 but not SGS3 recruitment by mTFS1 RISC under regular/high temperature, while low temperature partially restores mTFS1 function in RDR6 recruitment and tasiR-ARF biogenesis. A miR390 mutant also exhibits female sterility, suggesting that female fertility is controlled by the miR390-AGO7 module. Notably, the tfs1 allele introduced into various elite rice cultivars endows thermo-sensitive female sterility. Moreover, field trials confirm the utility of tfs1 as a restorer line in fully mechanized hybrid rice breeding.
PMID: 36068348
Trends Plant Sci , IF:18.313 , 2022 Sep 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
Nat Microbiol , IF:17.745 , 2022 Nov , V7 (11) : P1817-1833 doi: 10.1038/s41564-022-01244-3
Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome.
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA.; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Division of Oral and Craniofacial Health Sciences, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Plant and Environmental Sciences, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.; Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. redinbo@unc.edu.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. redinbo@unc.edu.; Department of Biochemistry and Biophysics, and the Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. redinbo@unc.edu.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. redinbo@unc.edu.; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. dangl@email.unc.edu.; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. dangl@email.unc.edu.; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. dangl@email.unc.edu.; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. dangl@email.unc.edu.; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. dangl@email.unc.edu.
Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon's MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
PMID: 36266335
Nucleic Acids Res , IF:16.971 , 2022 Oct , V50 (18) : P10544-10561 doi: 10.1093/nar/gkac798
Phosphorylation of the auxin signaling transcriptional repressor IAA15 by MPKs is required for the suppression of root development under drought stress in Arabidopsis.
Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea.
Since plants are sessile organisms, developmental plasticity in response to environmental stresses is essential for their survival. Upon exposure to drought, lateral root development is suppressed to induce drought tolerance. However, the molecular mechanism by which the development of lateral roots is inhibited by drought is largely unknown. In this study, the auxin signaling repressor IAA15 was identified as a novel substrate of mitogen-activated protein kinases (MPKs) and was shown to suppress lateral root development in response to drought through stabilization by phosphorylation. Both MPK3 and MPK6 directly phosphorylated IAA15 at the Ser-2 and Thr-28 residues. Transgenic plants overexpressing a phospho-mimicking mutant of IAA15 (IAA15DD OX) showed reduced lateral root development due to a higher accumulation of IAA15. In addition, MPK-mediated phosphorylation strongly increased the stability of IAA15 through the inhibition of polyubiquitination. Furthermore, IAA15DD OX plants showed the transcriptional downregulation of two key transcription factors LBD16 and LBD29, responsible for lateral root development. Overall, this study provides the molecular mechanism that explains the significance of the MPK-Aux/IAA module in suppressing lateral root development in response to drought.
PMID: 36161329
Nat Commun , IF:14.919 , 2022 Oct , V13 (1) : P5940 doi: 10.1038/s41467-022-33648-4
Variation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip.
Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China.; Hubei Hongshan Laboratory, Wuhan, 430070, China.; Department of Plant Sciences, University of Idaho, Moscow, ID, 83844, USA.; Key Laboratory of Horticultural Plant Biology (MOE) and National Center for Vegetable Improvement (Central China), Huazhong Agricultural University, Wuhan, 430070, China. zhangjunhng@mail.hzau.edu.cn.; Hubei Hongshan Laboratory, Wuhan, 430070, China. zhangjunhng@mail.hzau.edu.cn.
The domestication of tomato has led to striking variations in fruit morphology. Here, we show a genome-wide association study (GWAS) to understand the development of the fruit tip and describe a POINTED TIP (PT) gene that encodes a C2H2-type zinc finger transcription factor. A single nucleotide polymorphism is found to change a histidine (H) to an arginine (R) in the C2H2 domain of PT and the two alleles are referred to as PT(H) and PT(R). Knocking out PT(H) leads to development of pointed tip fruit. PT(H) functions to suppress pointed tip formation by downregulating the transcription of FRUTFULL 2 (FUL2), which alters the auxin transport. Our evolutionary analysis and previous studies by others suggest that the PT(R) allele likely hitch-hiked along with other selected loci during the domestication process. This study uncovers variation in PT and molecular mechanism underlying fruit tip development in tomato.
PMID: 36209204
Trends Biochem Sci , IF:13.807 , 2022 Oct , V47 (10) : P865-874 doi: 10.1016/j.tibs.2022.06.004
Intrinsic and extrinsic regulators of Aux/IAA protein degradation dynamics.
Department of Biology, Duke University, Durham, NC, USA.; Department of Biology, Duke University, Durham, NC, USA. Electronic address: lucia.strader@duke.edu.
The plant hormone auxin acts through regulated degradation of Auxin/INDOLE-3-ACETIC ACID (Aux/IAA) proteins to regulate transcriptional events. In this review, we examine the composition and function of each Aux/IAA structural motif. We then focus on recent characterization of Aux/IAA N-terminal disordered regions, formation of secondary structure within these disordered regions, and post-translational modifications (PTMs) that affect Aux/IAA function and stability. We propose how structural variations between Aux/IAA family members may be tuned for differential transcriptional repression and degradation dynamics.
PMID: 35817652
Mol Plant , IF:13.164 , 2022 Sep doi: 10.1016/j.molp.2022.09.021
Pepper variome reveals the history and key loci associated with fruit domestication and diversification.
Key laboratory of Vegetables Genetics and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences); 12 Zhongguancun South Street, Beijing, 100081, P. R. China.; INRAE, GAFL, Unite de Genetique et Amelioration des Fruits et Legumes; F-84140 Montfavet, France.; Institute of vegetables, Academy of Agricultural Sciences of Guangxi; 174 Daxue East Road, Nanning, 53007, P. R. China.; Dept. of Plant & Env. Sciences, NMSU; Las Cruces, NM 88003, USA.; Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center; Rishon LeZion, Israel.; Biotechnology and Agroindustry Division, ENEA; Italian National Agency for New Technologies, Energy and Sustainable Development; Via Anguillarese 301 - 00123 Roma, Italy. Electronic address: chengfeng@caas.cn.; Key laboratory of Vegetables Genetics and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences); 12 Zhongguancun South Street, Beijing, 100081, P. R. China. Electronic address: chengfeng@caas.cn.
Pepper (Capsicum spp.) is an important vegetable crop, providing a unique pungent sensation when eaten. Through the construction of the pepper variome map, we describe the main groups that emerged during domestication and breeding of C. annuum, their relations and temporal succession, and the molecular events underlying the main transitions. The initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, and the recent appearance of blocky, large, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we describe the identification of Up, a key domestication gene controlling erect vs pendent fruit orientation, encoding a BIG GRAIN protein involved in auxin transport. The up gene gained increased expression especially in the fruit pedicel through a 579 bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. These findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.
PMID: 36176193
Mol Plant , IF:13.164 , 2022 Sep 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
Mol Plant , IF:13.164 , 2022 Oct , V15 (10) : P1543-1557 doi: 10.1016/j.molp.2022.08.008
The regeneration factors ERF114 and ERF115 regulate auxin-mediated lateral root development in response to mechanical cues.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.; Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas alle 5, 756 51 Uppsala, Sweden.; Department of Plant Biochemistry, Center for Plant Molecular Biology (ZMBP), University of Tubingen, 72076 Tubingen, Germany.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium. Electronic address: lieven.deveylder@psb.vib-ugent.be.
Plants show an unparalleled regenerative capacity, allowing them to survive severe stress conditions, such as injury, herbivory attack, and harsh weather conditions. This potential not only replenishes tissues and restores damaged organs but can also give rise to whole plant bodies. Despite the intertwined nature of development and regeneration, common upstream cues and signaling mechanisms are largely unknown. Here, we demonstrate that in addition to being activators of regeneration, ETHYLENE RESPONSE FACTOR 114 (ERF114) and ERF115 govern developmental growth in the absence of wounding or injury. Increased ERF114 and ERF115 activity enhances auxin sensitivity, which is correlated with enhanced xylem maturation and lateral root formation, whereas their knockout results in a decrease in lateral roots. Moreover, we provide evidence that mechanical cues contribute to ERF114 and ERF115 expression in correlation with BZR1-mediated brassinosteroid signaling under both regenerative and developmental conditions. Antagonistically, cell wall integrity surveillance via mechanosensory FERONIA signaling suppresses their expression under both conditions. Taken together, our data suggest a molecular framework in which cell wall signals and mechanical strains regulate organ development and regenerative responses via ERF114- and ERF115-mediated auxin signaling.
PMID: 36030378
Dev Cell , IF:12.27 , 2022 Sep , V57 (17) : P2063-2080.e10 doi: 10.1016/j.devcel.2022.07.017
Mechanical conflict caused by a cell-wall-loosening enzyme activates de novo shoot regeneration.
Indian Institute of Science Education and Research (IISER), Pune 411008, India; IISER, Thiruvananthapuram 695551, India.; Indian Institute of Science Education and Research (IISER), Pune 411008, India; IISER, Thiruvananthapuram 695551, India. Electronic address: mabel.m.mathew@gmail.com.; IISER, Thiruvananthapuram 695551, India.; Indian Institute of Science Education and Research (IISER), Pune 411008, India.; Laboratory of Biochemistry, Wageningen University, Wageningen 6708WE, The Netherlands.; Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki 00014, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki 00014, Finland.; School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.; Indian Institute of Science Education and Research (IISER), Pune 411008, India; IISER, Thiruvananthapuram 695551, India. Electronic address: kalika.prasad@iiserpune.ac.in.
Cellular heterogeneity is a hallmark of multicellular organisms. During shoot regeneration from undifferentiated callus, only a select few cells, called progenitors, develop into shoot. How these cells are selected and what governs their subsequent progression to a patterned organ system is unknown. Using Arabidopsis thaliana, we show that it is not just the abundance of stem cell regulators but rather the localization pattern of polarity proteins that predicts the progenitor's fate. A shoot-promoting factor, CUC2, activated the expression of the cell-wall-loosening enzyme, XTH9, solely in a shell of cells surrounding the progenitor, causing different mechanical stresses in these cells. This mechanical conflict then activates cell polarity in progenitors to promote meristem formation. Interestingly, genetic or physical perturbations to cells surrounding the progenitor impaired the progenitor and vice versa. These suggest a feedback loop between progenitors and their neighbors for shoot regeneration in the absence of tissue-patterning cues.
PMID: 36002002
EMBO J , IF:11.598 , 2022 Oct , V41 (19) : Pe110988 doi: 10.15252/embj.2022110988
ARF2-PIF5 interaction controls transcriptional reprogramming in the ABS3-mediated plant senescence pathway.
State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, China.; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.; Department of Genetics, Harvard Medical School, Boston, MA, USA.; Institute of Future Agriculture, Northwest A&F University, Yangling, China.
One of the hallmarks of plant senescence is the global transcriptional reprogramming coordinated by a plethora of transcription factors (TFs). However, mechanisms underlying the interactions between different TFs in modulating senescence remain obscure. Previously, we discovered that plant ABS3 subfamily MATE transporter genes regulate senescence and senescence-associated transcriptional changes. In a genetic screen for mutants suppressing the accelerated senescence phenotype of the gain-of-function mutant abs3-1D, AUXIN RESPONSE FACTOR 2 (ARF2) and PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) were identified as key TFs responsible for transcriptional regulation in the ABS3-mediated senescence pathway. ARF2 and PIF5 (as well as PIF4) interact directly and function interdependently to promote senescence, and they share common target genes such as key senescence promoting genes ORESARA 1 (ORE1) and STAY-GREEN 1 (SGR1) in the ABS3-mediated senescence pathway. In addition, we discovered reciprocal regulation between ABS3-subfamily MATEs and the ARF2 and PIF5/4 TFs. Taken together, our findings reveal a regulatory paradigm in which the ARF2-PIF5/4 functional module facilitates the transcriptional reprogramming in the ABS3-mediated senescence pathway.
PMID: 35942625
Plant Cell , IF:11.277 , 2022 Oct 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.
RAC/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
Plant Cell , IF:11.277 , 2022 Oct , V34 (11) : P4583-4599 doi: 10.1093/plcell/koac266
The localization of PHRAGMOPLAST ORIENTING KINESIN1 at the division site depends on the microtubule-binding proteins TANGLED1 and AUXIN-INDUCED IN ROOT CULTURES9 in Arabidopsis.
Graduate Group in Biochemistry and Molecular Biology, University of California, Riverside, California, USA.; Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, California, USA.
Proper plant growth and development require spatial coordination of cell divisions. Two unrelated microtubule-binding proteins, TANGLED1 (TAN1) and AUXIN-INDUCED IN ROOT CULTURES9 (AIR9), are together required for normal growth and division plane orientation in Arabidopsis (Arabidopsis thaliana). The tan1 air9 double mutant has synthetic growth and division plane orientation defects, while single mutants lack obvious defects. Here we show that the division site-localized protein, PHRAGMOPLAST ORIENTING KINESIN1 (POK1), was aberrantly lost from the division site during metaphase and telophase in the tan1 air9 mutant. Since TAN1 and POK1 interact via the first 132 amino acids of TAN1 (TAN11-132), we assessed the localization and function of TAN11-132 in the tan1 air9 double mutant. TAN11-132 rescued tan1 air9 mutant phenotypes and localized to the division site during telophase. However, replacing six amino-acid residues within TAN11-132, which disrupted the POK1-TAN1 interaction in the yeast-two-hybrid system, caused loss of both rescue and division site localization of TAN11-132 in the tan1 air9 mutant. Full-length TAN1 with the same alanine substitutions had defects in phragmoplast guidance and reduced TAN1 and POK1 localization at the division site but rescued most tan1 air9 mutant phenotypes. Together, these data suggest that TAN1 and AIR9 are required for POK1 localization, and yet unknown proteins may stabilize TAN1-POK1 interactions.
PMID: 36005863
Plant Cell , IF:11.277 , 2022 Oct , V34 (11) : P4409-4427 doi: 10.1093/plcell/koac262
Auxin and abscisic acid antagonistically regulate ascorbic acid production via the SlMAPK8-SlARF4-SlMYB11 module in tomato.
Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China.; College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, China.
Ascorbic acid (AsA) is a multifunctional phytonutrient that is essential for the human diet as well as plant development. While much is known about AsA biosynthesis in plants, how this process is regulated in tomato (Solanum lycopersicum) fruits remains unclear. Here, we found that auxin treatment inhibited AsA accumulation in the leaves and pericarps of tomato. The auxin response factor gene SlARF4 is induced by auxin to mediate auxin-induced inhibition of AsA accumulation. Specifically, SlARF4 transcriptionally inhibits the transcription factor gene SlMYB11, thereby modulating AsA accumulation by regulating the transcription of the AsA biosynthesis genes l-galactose-1-phosphate phosphatase, l-galactono-1,4-lactone dehydrogenase, and dehydroascorbate. By contrast, abscisic acid (ABA) treatment increased AsA accumulation in tomato under drought stress. ABA induced the expression of the mitogen-activated protein kinase gene SlMAPK8. We demonstrate that SlMAPK8 phosphorylates SlARF4 and inhibits its transcriptional activity, whereas SlMAPK8 phosphorylates SlMYB11 and activates its transcriptional activity. SlMAPK8 functions in ABA-induced AsA accumulation and drought stress tolerance. Moreover, ABA antagonizes the effects of auxin on AsA biosynthesis. Therefore, auxin- and ABA-induced regulation of AsA accumulation is mediated by the SlMAPK8-SlARF4-SlMYB11 module in tomato during fruit development and drought stress responses, shedding light on the roles of phytohormones in regulating AsA accumulation to mediate stress tolerance.
PMID: 36000899
Plant Cell , IF:11.277 , 2022 Oct , V34 (11) : P4124-4125 doi: 10.1093/plcell/koac258
A case of identity: Activation of auxin biosynthesis drives cell reprogramming.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK.
PMID: 35977390
Plant Cell , IF:11.277 , 2022 Oct , V34 (11) : P4388-4408 doi: 10.1093/plcell/koac254
A SlCLV3-SlWUS module regulates auxin and ethylene homeostasis in low light-induced tomato flower abscission.
College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, China.; Crops Pathology and Genetic Research Unit, United States Department of Agriculture Agricultural Research Service, Albany, California 95616, USA.; Department of Plant Sciences, University of California, Los Angeles, California 95616, USA.
Premature abscission of flowers and fruits triggered by low light stress can severely reduce crop yields. However, the underlying molecular mechanism of this organ abscission is not fully understood. Here, we show that a gene (SlCLV3) encoding CLAVATA3 (CLV3), a peptide hormone that regulates stem cell fate in meristems, is highly expressed in the pedicel abscission zone (AZ) in response to low light in tomato (Solanum lycopersicum). SlCLV3 knockdown and knockout lines exhibit delayed low light-induced flower drop. The receptor kinases SlCLV1 and BARELY ANY MERISTEM1 function in the SlCLV3 peptide-induced low light response in the AZ to decrease expression of the transcription factor gene WUSCHEL (SlWUS). DNA affinity purification sequencing identified the transcription factor genes KNOX-LIKE HOMEDOMAIN PROTEIN1 (SlKD1) and FRUITFULL2 (SlFUL2) as SlWUS target genes. Our data reveal that low light reduces SlWUS expression, resulting in higher SlKD1 and SlFUL2 expression in the AZ, thereby perturbing the auxin response gradient and causing increased ethylene production, eventually leading to the initiation of abscission. These results demonstrate that the SlCLV3-SlWUS signaling pathway plays a central role in low light-induced abscission by affecting auxin and ethylene homeostasis.
PMID: 35972422
Plant Cell , IF:11.277 , 2022 Oct , V34 (11) : P4366-4387 doi: 10.1093/plcell/koac250
Rice EIL1 interacts with OsIAAs to regulate auxin biosynthesis mediated by the tryptophan aminotransferase MHZ10/OsTAR2 during root ethylene responses.
State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, 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.; College of Agriculture, South China Agricultural University, Guangzhou 510642, China.; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
Ethylene plays essential roles in adaptive growth of rice (Oryza sativa). Understanding of the crosstalk between ethylene and auxin (Aux) is limited in rice. Here, from an analysis of the root-specific ethylene-insensitive rice mutant mao hu zi 10 (mhz10), we identified the tryptophan aminotransferase (TAR) MHZ10/OsTAR2, which catalyzes the key step in indole-3-pyruvic acid-dependent Aux biosynthesis. Genetically, OsTAR2 acts downstream of ethylene signaling in root ethylene responses. ETHYLENE INSENSITIVE3 like1 (OsEIL1) directly activated OsTAR2 expression. Surprisingly, ethylene induction of OsTAR2 expression still required the Aux pathway. We also show that Os indole-3-acetic acid (IAA)1/9 and OsIAA21/31 physically interact with OsEIL1 and show promotive and repressive effects on OsEIL1-activated OsTAR2 promoter activity, respectively. These effects likely depend on their EAR motif-mediated histone acetylation/deacetylation modification. The special promoting activity of OsIAA1/9 on OsEIL1 may require both the EAR motifs and the flanking sequences for recruitment of histone acetyltransferase. The repressors OsIAA21/31 exhibit earlier degradation upon ethylene treatment than the activators OsIAA1/9 in a TIR1/AFB-dependent manner, allowing OsEIL1 activation by activators OsIAA1/9 for OsTAR2 expression and signal amplification. This study reveals a positive feedback regulation of ethylene signaling by Aux biosynthesis and highlights the crosstalk between ethylene and Aux pathways at a previously underappreciated level for root growth regulation in rice.
PMID: 35972379
Plant Cell , IF:11.277 , 2022 Oct , V34 (11) : P4348-4365 doi: 10.1093/plcell/koac218
Transcriptional activation of auxin biosynthesis drives developmental reprogramming of differentiated cells.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.; Center for Sustainable Resource Science, RIKEN, Yokohama 230-0045, Japan.; Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan.; Division of Evolutionary Biology, National Institute for Basic Biology, Okazaki 444-8585, Japan.; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies, SOKENDAI, Okazaki 444-8585, Japan.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium.; VIB Center for Plant Systems Biology, Ghent B-9052, Belgium.
Plant cells exhibit remarkable plasticity of their differentiation states, enabling regeneration of whole plants from differentiated somatic cells. How they revert cell fate and express pluripotency, however, remains unclear. In this study, we demonstrate that transcriptional activation of auxin biosynthesis is crucial for reprogramming differentiated Arabidopsis (Arabidopsis thaliana) leaf cells. Our data show that interfering with the activity of histone acetyltransferases dramatically reduces callus formation from leaf mesophyll protoplasts. Histone acetylation permits transcriptional activation of PLETHORAs, leading to the induction of their downstream YUCCA1 gene encoding an enzyme for auxin biosynthesis. Auxin biosynthesis is in turn required to accomplish initial cell division through the activation of G2/M phase genes mediated by MYB DOMAIN PROTEIN 3-RELATED (MYB3Rs). We further show that the AUXIN RESPONSE FACTOR 7 (ARF7)/ARF19 and INDOLE-3-ACETIC ACID INDUCIBLE 3 (IAA3)/IAA18-mediated auxin signaling pathway is responsible for cell cycle reactivation by transcriptionally upregulating MYB3R4. These findings provide a mechanistic model of how differentiated plant cells revert their fate and reinitiate the cell cycle to become pluripotent.
PMID: 35922895
Plant Cell , IF:11.277 , 2022 Sep , V34 (10) : P3577-3610 doi: 10.1093/plcell/koac193
Rapid growth of Moso bamboo (Phyllostachys edulis): Cellular roadmaps, transcriptome dynamics, and environmental factors.
Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu 210037, China.; Boyce Thompson Institute, Cornell University, Ithaca, New York 14853, USA.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India.; Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, Institute of Gene Science and Industrialization for Bamboo and Rattan Resources, International Center for Bamboo and Rattan, Beijing 100102, China.; Jiangxi Provincial Key Laboratory for Bamboo Germplasm Resources and Utilization, Jiangxi Agriculture University, Nanchang, Jiangxi 330045, China.; State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.
Moso bamboo (Phyllostachys edulis) shows remarkably rapid growth (114.5 cm/day), but the underlying biological mechanisms remain unclear. After examining more than 12,750 internodes from more than 510 culms from 17 Moso populations, we identified internode 18 as a representative internode for rapid growth. This internode includes a 2-cm cell division zone (DZ), a cell elongation zone up to 12 cm, and a secondary cell wall (SCW) thickening zone. These zones elongated 11.8 cm, produced approximately 570,000,000 cells, and deposited approximately 28 mg g-1 dry weight (DW) lignin and approximately 44 mg g-1 DW cellulose daily, far exceeding vegetative growth observed in other plants. We used anatomical, mathematical, physiological, and genomic data to characterize development and transcriptional networks during rapid growth in internode 18. Our results suggest that (1) gibberellin may directly trigger the rapid growth of Moso shoots, (2) decreased cytokinin and increased auxin accumulation may trigger cell DZ elongation, and (3) abscisic acid and mechanical pressure may stimulate rapid SCW thickening via MYB83L. We conclude that internode length involves a possible tradeoff mediated by mechanical pressure caused by rapid growth, possibly influenced by environmental temperature and regulated by genes related to cell division and elongation. Our results provide insight into the rapid growth of Moso bamboo.
PMID: 35766883
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Oct , V119 (40) : Pe2205757119 doi: 10.1073/pnas.2205757119
Modulation of receptor-like transmembrane kinase 1 nuclear localization by DA1 peptidases in Arabidopsis.
Department of Cell and Developmental Biology, John Innes Centre, Norwich NR4 7UH, United Kingdom.; State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.; University of Chinese Academy of Sciences, Beijing 100039, China.
The cleavage of intracellular domains of receptor-like kinases (RLKs) has an important functional role in the transduction of signals from the cell surface to the nucleus in many organisms. However, the peptidases that catalyze protein cleavage during signal transduction remain poorly understood despite their crucial roles in diverse signaling processes. Here, we report in the flowering plant Arabidopsis thaliana that members of the DA1 family of ubiquitin-regulated Zn metallopeptidases cleave the cytoplasmic kinase domain of transmembrane kinase 1 (TMK1), releasing it for nuclear localization where it represses auxin-responsive cell growth during apical hook formation by phosphorylation and stabilization of the transcriptional repressors IAA32 and IAA34. Mutations in DA1 family members exhibited reduced apical hook formation, and DA1 family-mediated cleavage of TMK1 was promoted by auxin treatment. Expression of the DA1 family-generated intracellular kinase domain of TMK1 by an auxin-responsive promoter fully restored apical hook formation in a tmk1 mutant, establishing the function of DA1 family peptidase activities in TMK1-mediated differential cell growth and apical hook formation. DA1 family peptidase activity therefore modulates TMK1 kinase activity between a membrane location where it stimulates acid cell growth and initiates an auxin-dependent kinase cascade controlling cell proliferation in lateral roots and a nuclear localization where it represses auxin-mediated gene expression and growth.
PMID: 36161927
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Sep , V119 (39) : Pe2209717119 doi: 10.1073/pnas.2209717119
The CsHEC1-CsOVATE module contributes to fruit neck length variation via modulating auxin biosynthesis in cucumber.
State Key Laboratory of Agrobiotechnology, Joint International Research Laboratory of Crop Molecular Breeding, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, Department of Vegetable Sciences, China Agricultural University, Beijing 100193, China.; College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao 066004, China.
Fruit neck is the proximal portion of the fruit with undesirable taste that has detrimental effects on fruit shape and commercial value in cucumber. Despite the dramatic variations in fruit neck length of cucumber germplasms, the genes and regulatory mechanisms underlying fruit neck elongation remain mysterious. In this study, we found that Cucumis sativus HECATE1 (CsHEC1) was highly expressed in fruit neck. Knockout of CsHEC1 resulted in shortened fruit neck and decreased auxin accumulation, whereas overexpression of CsHEC1 displayed the opposite effects, suggesting that CsHEC1 positively regulated fruit neck length by modulating local auxin level. Further analysis showed that CsHEC1 directly bound to the promoter of the auxin biosynthesis gene YUCCA4 (CsYUC4) and activated its expression. Enhanced expression of CsYUC4 resulted in elongated fruit neck and elevated auxin content. Moreover, knockout of CsOVATE resulted in longer fruit neck and higher auxin. Genetic and biochemical data showed that CsOVATE physically interacted with CsHEC1 to antagonize its function by attenuating the CsHEC1-mediated CsYUC4 transcriptional activation. In cucumber germplasms, the expression of CsHEC1 and CsYUC4 positively correlated with fruit neck length, while that of CsOVATE showed a negative correlation. Together, our results revealed a CsHEC1-CsOVATE regulatory module that confers fruit neck length variation via CsYUC4-mediated auxin biosynthesis in cucumber.
PMID: 36122223
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Sep , V119 (36) : Pe2121671119 doi: 10.1073/pnas.2121671119
Auxin regulates source-sink carbohydrate partitioning and reproductive organ development in rice.
National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.; National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Carbohydrate partitioning between the source and sink tissues plays an important role in regulating plant growth and development. However, the molecular mechanisms regulating this process remain poorly understood. In this study, we show that elevated auxin levels in the rice dao mutant cause increased accumulation of sucrose in the photosynthetic leaves but reduced sucrose content in the reproductive organs (particularly in the lodicules, anthers, and ovaries), leading to closed spikelets, indehiscent anthers, and parthenocarpic seeds. RNA sequencing analysis revealed that the expression of AUXIN RESPONSE FACTOR 18 (OsARF18) and OsARF2 is significantly up- and down-regulated, respectively, in the lodicule of dao mutant. Overexpression of OsARF18 or knocking out of OsARF2 phenocopies the dao mutant. We demonstrate that OsARF2 regulates the expression of OsSUT1 through direct binding to the sugar-responsive elements (SuREs) in the OsSUT1 promoter and that OsARF18 represses the expression of OsARF2 and OsSUT1 via direct binding to the auxin-responsive element (AuxRE) or SuRE in their promoters, respectively. Furthermore, overexpression of OsSUT1 in the dao and Osarf2 mutant backgrounds could largely rescue the spikelets' opening and seed-setting defects. Collectively, our results reveal an auxin signaling cascade regulating source-sink carbohydrate partitioning and reproductive organ development in rice.
PMID: 36037381
Curr Biol , IF:10.834 , 2022 Oct doi: 10.1016/j.cub.2022.09.055
Differential growth dynamics control aerial organ geometry.
College of Life 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.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; 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.; Key Laboratory of Microgravity (National Microgravity Laboratory), Center of Biomechanics and Bioengineering, and Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing 100190, China; School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.; 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 Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China. Electronic address: yingwang@ucas.ac.cn.; 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. Electronic address: k.wabnik@upm.es.; 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, Peking-Tsinghua Center for Life Sciences, School of 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. Electronic address: yuling.jiao@pku.edu.cn.
How gene activities and biomechanics together direct organ shapes is poorly understood. Plant leaf and floral organs develop from highly similar initial structures and share similar gene expression patterns, yet they gain drastically different shapes later-flat and bilateral leaf primordia and radially symmetric floral primordia, respectively. We analyzed cellular growth patterns and gene expression in young leaves and flowers of Arabidopsis thaliana and found significant differences in cell growth rates, which correlate with convergence sites of phytohormone auxin that require polar auxin transport. In leaf primordia, the PRESSED-FLOWER-expressing middle domain grows faster than adjacent adaxial domain and coincides with auxin convergence. In contrast, in floral primordia, the LEAFY-expressing domain shows accelerated growth rates and pronounced auxin convergence. This distinct cell growth dynamics between leaf and flower requires changes in levels of cell-wall pectin de-methyl-esterification and mechanical properties of the cell wall. Data-driven computer model simulations at organ and cellular levels demonstrate that growth differences are central to obtaining distinct organ shape, corroborating in planta observations. Together, our study provides a mechanistic basis for the establishment of early aerial organ symmetries through local modulation of differential growth patterns with auxin and biomechanics.
PMID: 36272403
Curr Biol , IF:10.834 , 2022 Sep , V32 (17) : P3838-3846.e5 doi: 10.1016/j.cub.2022.06.064
Apical dominance control by TAR-YUC-mediated auxin biosynthesis is a deep homology of land plants.
Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre for Plant Biology in Uppsala, 750 07 Uppsala, Sweden.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon 69007, France; Experimental Biology Research Group, Institute of Biology, Faculty of Sciences, University of Neuchatel, 2000 Neuchatel, Switzerland.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon 69007, France; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Universite Paris-Saclay, 78000 Versailles, France.; Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, UK.; Universite Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; Universite de Paris, CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, INRIA, Lyon 69007, France. Electronic address: yoan.coudert@cnrs.fr.
A key aim in biology is to identify which genetic changes contributed to the evolution of form through time. Apical dominance, the inhibitory effect exerted by shoot apices on the initiation or outgrowth of distant lateral buds, is a major regulatory mechanism of plant form.(1) Nearly a century of studies in the sporophyte of flowering plants have established the phytohormone auxin as a front-runner in the search for key factors controlling apical dominance,(2)(,)(3) identifying critical roles for long-range polar auxin transport and local auxin biosynthesis in modulating shoot branching.(4-10) A capacity for lateral branching evolved by convergence in the gametophytic shoot of mosses and primed its diversification;(11) however, polar auxin transport is relatively unimportant in this developmental process,(12) the contribution of auxin biosynthesis genes has not been assessed, and more generally, the extent of conservation in apical dominance regulation within the land plants remains largely unknown. To fill this knowledge gap, we sought to identify genetic determinants of apical dominance in the moss Physcomitrium patens. Here, we show that leafy shoot apex decapitation releases apical dominance through massive and rapid transcriptional reprogramming of auxin-responsive genes and altering auxin biosynthesis gene activity. We pinpoint a subset of P. patens TRYPTOPHAN AMINO-TRANSFERASE (TAR) and YUCCA FLAVIN MONOOXYGENASE-LIKE (YUC) auxin biosynthesis genes expressed in the main and lateral shoot apices and show that they are essential for coordinating branch initiation and outgrowth. Our results demonstrate that local auxin biosynthesis acts as a pivotal regulator of apical dominance in moss and constitutes a shared mechanism underpinning shoot architecture control in land plants.
PMID: 35841890
New Phytol , IF:10.151 , 2022 Oct 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, INRES, 53115, Bonn, Germany.
Plant root architecture plasticity in response to biotic stresses has not been thoroughly investigated. Infection by the 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 wildtype Arabidopsis plants with increasing numbers of cyst nematodes (Heterodera schachtii). Next, by using jasmonate-related reporter lines and knock-out mutants, we tested if 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. Knock-out mutations in COI1 and ERF109 disrupt the nematode-density dependent increase of secondary roots observed in wildtype 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 , 2022 Oct 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 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 , 2022 Oct 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. Using 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 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 , 2022 Oct 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, 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 is an essential macronutrient for plants as well as a signaling molecule in abiotic stress responses. It is known that sulfur 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 sulfur 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 26S 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 sulfur deficiency.
PMID: 36226797
New Phytol , IF:10.151 , 2022 Sep 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 Sep 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 Sep 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 Sep 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 Sep 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
Plant Biotechnol J , IF:9.803 , 2022 Sep 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
Plant Physiol , IF:8.34 , 2022 Oct doi: 10.1093/plphys/kiac497
The Auxin response factor TaARF15-A1 negatively regulates senescence in common wheat (Triticum aestivum L.).
Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang Hebei 050000, China.; Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang Henan 455000, China.; Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen Shanxi 041000, China.
Auxin plays an important role in regulating leaf senescence. Auxin response factors (ARFs) are crucial components of the auxin signaling pathway; however, their roles in leaf senescence in cereal crops are unknown. In this study, we identified TaARF15-A1 as a negative regulator of senescence in wheat (Triticum aestivum L.) by analyzing TaARF15-A1 overexpression and RNA interference lines and CRISPR/Cas9-based arf15 mutants. Overexpression of TaARF15-A1 delayed senescence, whereas knockdown lines and knockout mutants showed accelerated leaf senescence and grain ripening. RNA-seq analysis revealed that TaARF15-A1 delays leaf senescence by negatively regulating senescence-promoting processes and positively modulating senescence-delaying genes including senescence-associated phytohormone biosynthesis and metabolism genes as well as transcription factors. We also demonstrated that TaARF15-A1 physically interacts with TaMYC2, a core jasmonic acid (JA) signaling transcription factor that positively modulates wheat senescence. Furthermore, TaARF15-A1 suppressed the expression of TaNAM-1 (TaNAM-A1 and TaNAM-D1) via protein-protein interaction and competition with TaMYC2 for binding to its promoter to regulate senescence. Finally, we identified two haplotypes of TaARF15-A1 in global wheat collections. Association analysis revealed that TaARF15-A1-HapI has undergone strong selection during wheat breeding in China, likely owing to its earlier maturity. Thus, we identify TaARF15-A1 as a negative regulator of senescence in common wheat and present another perspective on the crosstalk between auxin and JA signaling pathways in regulating plant senescence.
PMID: 36282536
Plant Physiol , IF:8.34 , 2022 Oct 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.; 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 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 towards 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 multi-hormonal 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 , 2022 Oct doi: 10.1093/plphys/kiac426
Early defoliation induces auxin redistribution, promoting paradormancy release in pear buds.
College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China.; Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China.; The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China.; Key Laboratory for Silviculture and Conservation, Ministry of Education, Beijing Forestry University, Haidian District, Beijing 100083, China.; Yantai Institute, China Agricultural University, Yantai, Shandong 264670, China.; Hainan Institute of Zhejiang University, Sanya, Hainan 572000, China.
Paradormancy of fruit trees occurs in summer and autumn when signals from adjacent organs stimulate buds to develop slowly. This stage has received less attention that the other stages of dormancy, and the underlying mechanism remains uncharacterized. Early defoliation in late summer and early autumn is usually followed by out-of-season blooming in pear (Pyrus spp.), which substantially decreases the number of buds the following spring and negatively affects fruit production. This early bud flush is an example of paradormancy release. Here, we determined that flower bud auxin content is stable after defoliation; however, polar distribution of the pear (Pyrus pyrifolia) PIN-FORMED auxin efflux carrier 1b (PpyPIN1b) implied that auxin tends to be exported from buds. Transcriptome analysis of floral buds after artificial defoliation revealed changes in auxin metabolism, transport, and signal transduction pathways. Exogenous application of a high concentration of the auxin analog 1-naphthaleneacetic acid (300 mg/L) suppressed PpyPIN1b expression and its protein accumulation in the cell membrane, likely leading to decreased auxin efflux from buds, which hindered flower bud sprouting. Furthermore, carbohydrates and additional hormones also influenced out-of-season flowering. Our results indicate that defoliation-induced auxin efflux from buds accelerates bud paradormancy release. This differs from release of apical-dominance-related lateral bud paradormancy after the apex is removed. Our findings and proposed model further elucidate the mechanism underlying paradormancy and will help researchers to develop methods for inhibiting early defoliation-induced out-of-season bud sprouting.
PMID: 36200868
Plant Physiol , IF:8.34 , 2022 Oct 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, College Park, MD, 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 EMS 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. 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 homologue 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 wild-type 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 wild type. 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 , 2022 Sep 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, United Kingdom.
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 de-repressed. 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 , 2022 Sep doi: 10.1093/plphys/kiac440
Abscisic acid-responsive transcription factors PavDof2/6/15 mediate fruit softening in sweet cherry.
Department of Pomology, College of Horticulture, China Agricultural University, Beijing 100193, China.
Softening is a key step during fruit ripening that is modulated by the interplay between multiple phytohormones. The antagonistic action of abscisic acid (ABA) and auxin determines the rate of fruit ripening and softening. However, the transcription factors that integrate ABA and auxin signals to regulate fruit softening remain to be determined. In this study, we identified several DNA-binding with One Finger (Dof) transcription factors essential for ABA-promoted fruit softening, based on transcriptome analysis of two sweet cherry (Prunus avium L.) varieties with different fruit firmness. We show that PavDof6 directly binds to the promoters of genes encoding cell wall-modifying enzymes to activate their transcription, while PavDof2/15 directly repress their transcription. Transient overexpression of PavDof6 and PavDof2/15 in sweet cherry fruits resulted in precocious and delayed softening, respectively. In addition, we show that the auxin response factor PavARF8, the expression of whose encoding gene is repressed by ABA, activates PavDof2/15 transcription. Furthermore, PavDof2/6/15 and PavARF8 directly bind to the 9-cis-epoxycarotenoid dioxygenase 1 (PavNCED1) promoter and regulate its expression, forming a feedback mechanism for ABA-mediated fruit softening. These findings unveil the physiological framework of fruit softening and establish a direct functional link between the ABA-PavARF8-PavDofs module and cell wall-modifying genes in mediating fruit softening.
PMID: 36130298
Plant Physiol , IF:8.34 , 2022 Sep doi: 10.1093/plphys/kiac441
Ethylene response factor ERF.D7 activates Auxin response factor 2 paralogs to regulate tomato fruit ripening.
Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.; Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
Despite the obligatory role of ethylene in climacteric fruit ripening and the identification of 77 ethylene response factors (ERFs) in the tomato (Solanum lycopersicum) genome, the role of few ERFs has been validated in the ripening process. Here, using a comprehensive morpho-physiological, molecular and biochemical approach, we demonstrate the regulatory role of Ethylene Response Factor D7 (SlERF.D7) in tomato fruit ripening. SlERF.D7 expression positively responded to exogenous ethylene and auxin treatments, most likely in a Ripening Inhibitor (RIN)-independent manner. SlERF.D7 overexpression promoted ripening, and its silencing had the opposite effect. Alterations in its expression modulated ethylene production, pigment accumulation, and fruit firmness. Consistently, genes involved in ethylene biosynthesis and signalling, lycopene biosynthesis, and cell wall loosening were upregulated in the overexpression lines and downregulated in RNAi lines. These transgenic lines also accumulated altered levels of IAA at late-breaker stages. A positive association between Auxin Response Factor 2 (ARF2) paralog's transcripts and SlERF.D7 mRNA levels and that SlARF2A and SlARF2B are direct targets of SlERF.D7 underpinned the perturbed auxin-ethylene crosstalk for the altered ripening program observed in the transgenic fruits. Overall, this study uncovers that SlERF.D7 positively regulates SlARF2A/B abundance to amalgamate auxin and ethylene signalling pathways for controlling tomato fruit ripening.
PMID: 36130295
Plant Physiol , IF:8.34 , 2022 Sep doi: 10.1093/plphys/kiac425
INOSITOL (1,3,4) TRIPHOSPHATE 5/6 KINASE1-Dependent Inositol Polyphosphates Regulate Auxin Responses in Arabidopsis.
Department of Plant Nutrition, Institute of Crop Science and Resource Conservation, Rheinische Friedrich-Wilhelms-Universitat Bonn, 53115 Bonn, Germany.; Department of Physiology & Cell Biology, Leibniz-Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany.; Department of Chemistry and Pharmacy & CIBSS - the Center for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.; Department of Biochemistry, Indian Institute of Science, Bengaluru 560012, India.; Laboratory of Signal Transduction and Plant Resistance, Regional Centre for Biotechnology, NCR-Biotech Science Cluster, Faridabad - 121001. Haryana, India.; Department of Pharmacology, Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.; Medical Research Council Laboratory for Molecular Cell Biology (MRC-LMCB), University College London, London WC1E 6BT, United Kingdom.
The combinatorial phosphorylation of myo-inositol results in the generation of different inositol phosphates (InsPs), of which phytic acid (InsP6) is the most abundant species in eukaryotes. InsP6 is also an important precursor of the higher phosphorylated inositol pyrophosphates (PP-InsPs), such as InsP7 and InsP8, which are characterized by a diphosphate moiety and are also ubiquitously found in eukaryotic cells. While PP-InsPs regulate various cellular processes in animals and yeast, their biosynthesis and functions in plants has remained largely elusive because plant genomes do not encode canonical InsP6 kinases. Recent work has shown that Arabidopsis (Arabidopsis thaliana) INOSITOL (1,3,4) TRIPHOSPHATE 5/6 KINASE1 (ITPK1) and ITPK2 display in vitro InsP6 kinase activity and that, in planta, ITPK1 stimulates 5-InsP7 and InsP8 synthesis and regulates phosphate starvation responses. Here we report a critical role of ITPK1 in auxin-related processes that is independent of the ITPK1-controlled regulation of phosphate starvation responses. Those processes include primary root elongation, root hair development, leaf venation, thermomorphogenic and gravitropic responses, and sensitivity to exogenously applied auxin. We found that the recombinant auxin receptor complex, consisting of the F-Box protein TRANSPORT INHIBITOR RESPONSE1 (TIR1), ARABIDOPSIS SKP1 HOMOLOGUE 1 (ASK1) and the transcriptional repressor INDOLE-3-ACETIC ACID INDUCIBLE 7 (IAA7), binds to anionic inositol polyphosphates with high affinity. We further identified a physical interaction between ITPK1 and TIR1, suggesting a localized production of 5-InsP7, or another ITPK1-dependent InsP/PP-InsP isomer, to activate the auxin receptor complex. Finally, we demonstrate that ITPK1 and ITPK2 function redundantly to control auxin responses, as deduced from the auxin-insensitive phenotypes of itpk1 itpk2 double mutant plants. Our findings expand the mechanistic understanding of auxin perception and suggest that distinct inositol polyphosphates generated near auxin receptors help to fine-tune auxin sensitivity in plants.
PMID: 36124979
Plant Physiol , IF:8.34 , 2022 Sep doi: 10.1093/plphys/kiac418
Root acid phosphatases and rhizobacteria synergistically enhance white lupin and rice phosphorus acquisition.
Joint International Research Laboratory of Water and Nutrient in Crops, Haixia Institute of Ecology and Environmental Engineering, College of Resource and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.; College of Agriculture, Yangzhou University, Yangzhou, 225009, China.; Department of Biology, Hong Kong Baptist University, Stake Key Laboratory of Agrobiotechnology and Chinese University of Hong Kong, Hong Kong.; Institute of Agricultural Sciences, ICA-CSIC, Madrid, Spain.; The UWA Institute of Agriculture and School of Agriculture and Environment, University of Western Australia, Perth, WA 6009, Australia.; College of Horticulture, South China Agricultural University, Guangzhou, China.
The rhizosheath is a belowground area that acts as a communication hub at the root-soil interface to promote water and nutrient acquisition. Certain crops, such as white lupin (Lupinus albus), acquire large amounts of phosphorus (P), owing partially to exudation of acid phosphatases (APases). Plant growth-promoting rhizobacteria also increase soil P availability. However, potential synergistic effects of root APases and rhizosheath-associated microbiota on P acquisition require further research. In this study, we investigated the roles of root purple APases (PAPs) and plant growth-promoting rhizobacteria in rhizosheath formation and P acquisition under conditions of soil drying (SD) and P treatment (+P: soil with P fertilizer; -P: soil without fertilizer). We expressed purple acid phosphatase12 (LaPAP12) in white lupin and rice (Oryza sativa) plants and analyzed the rhizosheath-associated microbiome. Increased or heterologous LaPAP12 expression promoted APase activity and rhizosheath formation, resulting in increased P acquisition mainly under SD-P conditions. It also increased the abundance of members of the genus Bacillus in the rhizosheath-associated microbial communities of white lupin and rice. We isolated a phosphate-solubilizing, auxin-producing Bacillus megaterium strain from the rhizosheath of white lupin and used this to inoculate white lupin and rice plants. Inoculation promoted rhizosheath formation and P acquisition, especially in plants with increased LaPAP12 expression and under SD-P conditions, suggesting a functional role of the bacteria in alleviating P deficit stress via rhizosheath formation. Together, our results suggest a synergistic enhancing effect of LaPAP12 and plant growth-promoting rhizobacteria on rhizosheath formation and P acquisition under SD-P conditions.
PMID: 36066452
Plant Physiol , IF:8.34 , 2022 Sep doi: 10.1093/plphys/kiac412
PHYTOCHROME-INTERACTING FACTOR 4/HEMERA-mediated thermosensory growth requires the Mediator subunit MED14.
Department of Biology, University of Mississippi, Oxford, MS 38677, USA.; Natural Products Utilization Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Oxford, Mississippi, USA.; National Center for Natural Products Research, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA.; Division of Pharmacology, Department of BioMolecular Sciences, School of Pharmacy, University of Mississippi, Oxford, Mississippi, USA.
While moderately elevated ambient temperatures do not trigger stress responses in plants, they do substantially stimulate the growth of specific organs through a process known as thermomorphogenesis. The basic helix-loop-helix transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) plays a central role in regulating thermomorphogenetic hypocotyl elongation in various plant species, including Arabidopsis (Arabidopsis thaliana). Although it is well known that PIF4 and its co-activator HEMERA (HMR) promote plant thermosensory growth by activating genes involved in the biosynthesis and signaling of the phytohormone auxin, the detailed molecular mechanism of such transcriptional activation is not clear. In this report, we investigated the role of the Mediator complex in the PIF4/HMR-mediated thermoresponsive gene expression. Through the characterization of various mutants of the Mediator complex, a tail subunit named MED14 was identified as an essential factor for thermomorphogenetic hypocotyl growth. MED14 was required for the thermal induction of PIF4 target genes but had a marginal effect on the levels of PIF4 and HMR. Further transcriptomic analyses confirmed that the expression of numerous PIF4/HMR-dependent, auxin-related genes required MED14 at warm temperatures. Moreover, PIF4 and HMR physically interacted with MED14 and both were indispensable for the association of MED14 with the promoters of these thermoresponsive genes. While PIF4 did not regulate MED14 levels, HMR was required for the transcript abundance of MED14. Taken together, these results unveil an important thermomorphogenetic mechanism, in which PIF4 and HMR recruit the Mediator complex to activate auxin-related growth-promoting genes when plants sense moderate increases in ambient temperature.
PMID: 36063057
Plant Physiol , IF:8.34 , 2022 Sep , V190 (2) : P1457-1473 doi: 10.1093/plphys/kiac332
Class I TCP transcription factor AtTCP8 modulates key brassinosteroid-responsive genes.
Department of Biological Sciences, Butler University, Indianapolis, Indiana, USA.; Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, USA.; Christopher S. Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, Missouri, USA.; Department of Biology, Marian University, Indianapolis, Indiana, USA.
The plant-specific TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) transcription factor family is most closely associated with regulating plant developmental programs. Recently, TCPs were also shown to mediate host immune signaling, both as targets of pathogen virulence factors and as regulators of plant defense genes. However, comprehensive characterization of TCP gene targets is still lacking. Loss of function of the class I TCP gene AtTCP8 attenuates early immune signaling and, when combined with mutations in AtTCP14 and AtTCP15, additional layers of defense signaling in Arabidopsis (Arabidopsis thaliana). Here, we focus on TCP8, the most poorly characterized of the three to date. We used chromatin immunoprecipitation and RNA sequencing to identify TCP8-bound gene promoters and differentially regulated genes in the tcp8 mutant; these datasets were heavily enriched in signaling components for multiple phytohormone pathways, including brassinosteroids (BRs), auxin, and jasmonic acid. Using BR signaling as a representative example, we showed that TCP8 directly binds and activates the promoters of the key BR transcriptional regulatory genes BRASSINAZOLE-RESISTANT1 (BZR1) and BRASSINAZOLE-RESISTANT2 (BZR2/BES1). Furthermore, tcp8 mutant seedlings exhibited altered BR-responsive growth patterns and complementary reductions in BZR2 transcript levels, while TCP8 protein demonstrated BR-responsive changes in subnuclear localization and transcriptional activity. We conclude that one explanation for the substantial targeting of TCP8 alongside other TCP family members by pathogen effectors may lie in its role as a modulator of BR and other plant hormone signaling pathways.
PMID: 35866682
Plant Physiol , IF:8.34 , 2022 Sep , V190 (2) : P1365-1383 doi: 10.1093/plphys/kiac245
Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration.
Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Utrecht, 3584 CH, The Netherlands.; Department of Botany and Plant Biology, University of Geneva, Geneva 1211, Switzerland.; Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, Freiburg 79104, Germany.; CIBSS-Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany.; Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden AL5 2JQ, UK.; Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, California 92521, USA.; Intelligent Data Ecosystems, Rothamsted Research, Harpenden AL5 2JQ, UK.
Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pretreatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pretreatments reduced this damage. Ethylene pretreatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.
PMID: 35640551
PLoS Biol , IF:8.029 , 2022 Sep , V20 (9) : Pe3001781 doi: 10.1371/journal.pbio.3001781
Leaf vein patterning is regulated by the aperture of plasmodesmata intercellular channels.
Department of Biological Sciences, University of Alberta, Edmonton, Canada.
To form tissue networks, animal cells migrate and interact through proteins protruding from their plasma membranes. Plant cells can do neither, yet plants form vein networks. How plants do so is unclear, but veins are thought to form by the coordinated action of the polar transport and signal transduction of the plant hormone auxin. However, plants inhibited in both pathways still form veins. Patterning of vascular cells into veins is instead prevented in mutants lacking the function of the GNOM (GN) regulator of auxin transport and signaling, suggesting the existence of at least one more GN-dependent vein-patterning pathway. Here we show that in Arabidopsis such a pathway depends on the movement of auxin or an auxin-dependent signal through plasmodesmata (PDs) intercellular channels. PD permeability is high where veins are forming, lowers between veins and nonvascular tissues, but remains high between vein cells. Impaired ability to regulate PD aperture leads to defects in auxin transport and signaling, ultimately leading to vein patterning defects that are enhanced by inhibition of auxin transport or signaling. GN controls PD aperture regulation, and simultaneous inhibition of auxin signaling, auxin transport, and regulated PD aperture phenocopies null gn mutants. Therefore, veins are patterned by the coordinated action of three GN-dependent pathways: auxin signaling, polar auxin transport, and movement of auxin or an auxin-dependent signal through PDs. Such a mechanism of tissue network formation is unprecedented in multicellular organisms.
PMID: 36166438
Sci Total Environ , IF:7.963 , 2022 Sep , 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 Oct , V841 : P156486 doi: 10.1016/j.scitotenv.2022.156486
Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India.
Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.; Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India. Electronic address: psar@bt.iitkgp.ac.in.
Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 x 10(7) gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO4(3-), SO4(2-) and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO4(2-) and NO3(-) reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO4(3-) and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO3(-) reduction to ammonium), and S (assimilatory SO4(2-) reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.
PMID: 35667424
Curr Opin Plant Biol , IF:7.834 , 2022 Oct , V69 : P102293 doi: 10.1016/j.pbi.2022.102293
Reactive oxygen species function as signaling molecules in controlling plant development and hormonal responses.
Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA; Department of Biology and the Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, 27109, USA.; Department of Biology and the Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, 27109, USA.; Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, 27101, USA; Department of Biology and the Center for Molecular Signaling, Wake Forest University, Winston-Salem, NC, 27109, USA. Electronic address: muday@wfu.edu.
Reactive oxygen species (ROS) serve as second messengers in plant signaling pathways to remodel plant growth and development. New insights into how enzymatic ROS-producing machinery is regulated by hormones or localized during development have provided a framework for understanding the mechanisms that control ROS accumulation patterns. Signaling-mediated increases in ROS can then modulate the activity of proteins through reversible oxidative modification of specific cysteine residues. Plants also control the synthesis of antioxidants, including plant-specialized metabolites, to further define when, where, and how much ROS accumulate. The availability of sophisticated imaging capabilities, combined with a growing tool kit of ROS detection technologies, particularly genetically encoded biosensors, sets the stage for improved understanding of ROS as signaling molecules.
PMID: 36099672
Plant Cell Environ , IF:7.228 , 2022 Oct 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 , 2022 Sep 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
Plant Cell Environ , IF:7.228 , 2022 Sep doi: 10.1111/pce.14438
Homeobox transcription factors OsZHD1 and OsZHD2 induce inflorescence meristem activity at floral transition in rice.
Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Miryang, Republic of Korea.; Life and Industry Convergence Research Institute, Pusan National University, Miryang, Republic of Korea.; Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, Republic of Korea.
Floral transition starts in the leaves when florigens respond to various environmental and developmental factors. Among several regulatory genes that are preferentially expressed in the inflorescence meristem during the floral transition, this study examines the homeobox genes OsZHD1 and OsZHD2 for their roles in regulating this transition. Although single mutations in these genes did not result in visible phenotype changes, double mutations in these genes delayed flowering. Florigen expression was not altered in the double mutants, indicating that the delay was due to a defect in florigen signaling. Morphological analysis of shoot apical meristem at the early developmental stage indicated that inflorescence meristem development was significantly delayed in the double mutants. Overexpression of ZHD2 causes early flowering because of downstream signals after the generation of florigens. Expression levels of the auxin biosynthesis genes were reduced in the mutants and the addition of indole-3-acetic acid recovered the defect in the mutants, suggesting that these homeobox genes play a role in auxin biosynthesis. A rice florigen, RICE FLOWERING LOCUS T 1, binds to the promoter regions of homeobox genes. These results indicate that florigens stimulate the expression of homeobox genes, enhancing inflorescence development in the shoot apex.
PMID: 36120845
Plant Cell Environ , IF:7.228 , 2022 Sep doi: 10.1111/pce.14434
Auxin plays a role in the adaptation of rice to anaerobic germination and seedling establishment.
Department of Bioagricultural Sciences, National Chiayi University, Chiayi, Taiwan.; Institute of Biomedical Sciences, National Chung Hsing University, Taichung, Taiwan.
Auxin is well known to stimulate coleoptile elongation and rapid seedling growth in the air. However, its role in regulating rice germination and seedling establishment under submergence is largely unknown. Previous studies revealed that excessive levels of indole-3-acetic acid(IAA) frequently cause the inhibition of plant growth and development. In this study, the high-level accumulation of endogenous IAA is observed under dark submergence, stimulating rice coleoptile elongation but limiting the root and primary leaf growth during anaerobic germination (AG). We found that oxygen and light can reduce IAA levels, promote the seedling establishment and enhance rice AG tolerance. miRNA microarray profiling and RNA gel blot analysis results show that the expression of miR167 is negatively regulated by submergence; it subsequently modulates the accumulation of free IAA through the miR167-ARF-GH3 pathway. The OsGH3-8 encodes an IAA-amido synthetase that functions to prevent free IAA accumulation. Reduced miR167 levels or overexpressing OsGH3-8 increase auxin metabolism, reduce endogenous levels of free IAA and enhance rice AG tolerance. Our studies reveal that poor seed germination and seedling growth inhibition resulting from excessive IAA accumulation would cause intolerance to submergence in rice, suggesting that a certain threshold level of auxin is essential for rice AG tolerance.
PMID: 36071575
J Integr Plant Biol , IF:7.061 , 2022 Oct doi: 10.1111/jipb.13392
Advances in structure and function of auxin response factor in plants.
School of Life Sciences, Inner Mongolia University, Key Laboratory of Herbage & Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage & Endemic Crop Biotechnology, Hohhot, 010000, China.; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
Auxin is a crucial phytohormone that has various effects on the regulators of plant growth and development. Auxin signal transduction is mainly controlled by two gene families: auxin response factor (ARF) and auxin/indole-3-acetic acid (Aux/IAA). ARFs are plant-specific transcription factors that bind directly to auxin response elements in the promoters of auxin-responsive genes. ARF proteins contain three conserved regions: a conserved N-terminal B3 DNA-binding domain, a variable intermediate middle region domain that functions in activation or repression, and a C-terminal domain including the Phox and Bem1p region for dimerization, similar to the III and IV elements of Aux/IAA, which facilitate protein-protein interaction through homodimerization of ARF proteins or heterodimerization of ARF and Aux/IAA proteins. In the two decades following the identification of the first ARF, 23 ARF members have been identified and characterized in Arabidopsis. Using whole-genome sequencing, 22, 25, 23, 25, and 36 ARF genes have been identified in tomato, rice, wheat, sorghum, and maize, respectively, in addition to which the related biofunctions of some ARFs have been reported. ARFs play crucial roles in regulating the growth and development of roots, leaves, flowers, fruits, seeds, responses to biotic and abiotic stresses, and phytohormone signal crosstalk. In this review, we summarize the research progress on the structures and functions of ARFs in Arabidopsis, tomato, and cereal crops, to provide clues for future basic research on phytohormone signaling and the molecular design breeding of crops. This article is protected by copyright. All rights reserved.
PMID: 36263892
J Integr Plant Biol , IF:7.061 , 2022 Oct doi: 10.1111/jipb.13387
High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis.
College of Life Science, 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, Centre for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological 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. This article is protected by copyright. All rights reserved.
PMID: 36250442
J Integr Plant Biol , IF:7.061 , 2022 Sep doi: 10.1111/jipb.13366
TMK1-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, Zhejiang, China.
Clathrin-mediated endocytosis (CME) is the major endocytic pathway in eukaryotic cells that directly regulates abundance of plasma membrane (PM) 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 family proteins (TMKs) 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 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. This article is protected by copyright. All rights reserved.
PMID: 36114789
J Integr Plant Biol , IF:7.061 , 2022 Sep 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 Integr Plant Biol , IF:7.061 , 2022 Oct , V64 (10) : P1916-1934 doi: 10.1111/jipb.13341
The unconventional prefoldin RPB5 interactor mediates the gravitropic response by modulating cytoskeleton organization and auxin transport in Arabidopsis.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China.; Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China.; Sino-German Joint Research Center on Agricultural Biology, College of Life Sciences, Shandong Agricultural University, Daizong Street 61, Tai'an, 271018, China.; Faculty of Biology, Institute of Biology II/Molecular Plant Physiology, Albert-Ludwigs-University of Freiburg, Schanzlestrasse 1, Freiburg, D-79104, Germany.; 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), Shanghai, 200032, China.; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.; Key Laboratory of Plant Molecular Physiology, CAS Center for Excellence in Molecular Plant Sciences, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.
Gravity-induced root curvature involves the asymmetric distribution of the phytohormone auxin. This response depends on the concerted activities of the auxin transporters such as PIN-FORMED (PIN) proteins for auxin efflux and AUXIN RESISTANT 1 (AUX1) for auxin influx. However, how the auxin gradient is established remains elusive. Here we identified a new mutant with a short root, strong auxin distribution in the lateral root cap and an impaired gravitropic response. The causal gene encoded an Arabidopsis homolog of the human unconventional prefoldin RPB5 interactor (URI). AtURI interacted with prefoldin 2 (PFD2) and PFD6, two beta-type PFD members that modulate actin and tubulin patterning in roots. The auxin reporter DR5rev :GFP showed that asymmetric auxin redistribution after gravistimulation is disordered in aturi-1 root tips. Treatment with the endomembrane protein trafficking inhibitor brefeldin A indicated that recycling of the auxin transporter PIN2 is disrupted in aturi-1 roots as well as in pfd mutants. We propose that AtURI cooperates with PFDs to recycle PIN2 and modulate auxin distribution.
PMID: 35943836
J Integr Plant Biol , IF:7.061 , 2022 Oct , V64 (10) : P1901-1915 doi: 10.1111/jipb.13336
FERONIA is involved in phototropin 1-mediated blue light phototropic growth in Arabidopsis.
School of Life Sciences, Central South University, Changsha, 410078, China.; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha, 410082, China.; Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation, Hunan University, Changsha, 410082, China.; Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.; State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.
Plant shoot phototropism is triggered by the formation of a light-driven auxin gradient leading to bending growth. The blue light receptor phototropin 1 (phot1) senses light direction, but how this leads to auxin gradient formation and growth regulation remains poorly understood. Previous studies have suggested phot1's role for regulated apoplastic acidification, but its relation to phototropin and hypocotyl phototropism is unclear. Herein, we show that blue light can cause phot1 to interact with and phosphorylate FERONIA (FER), a known cell growth regulator, and trigger downstream phototropic bending growth in Arabidopsis hypocotyls. fer mutants showed defects in phototropic growth, similar to phot1/2 mutant. FER also interacts with and phosphorylates phytochrome kinase substrates, the phot1 downstream substrates. The phot1-FER pathway acts upstream of apoplastic acidification and the auxin gradient formation in hypocotyl under lateral blue light, both of which are critical for phototropic bending growth in hypocotyls. Our study highlights a pivotal role of FER in the phot1-mediated phototropic cell growth regulation in plants.
PMID: 35924740
J Exp Bot , IF:6.992 , 2022 Oct doi: 10.1093/jxb/erac430
The locoweed endophyte Alternaria oxytropis affects root development in Arabidopsis in vitro through auxin signaling and polar transport.
Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China.; Qinling National Botanical Garden, Xi'an, China.; Shaanxi Institute for Food and Drug, Xi'an, China.; Provincial Key Laboratory of Biotechnology of Shaanxi Province, College of Life Sciences, Northwest University, Xi'an, China.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.; Hubei Hongshan Laboratory, Wuhan, China.; Institute of Biology, Environmental and Rural Science, Aberystwyth University, Aberystwyth SY23 3FL, UK.; Key Laboratory of Grassland Resources of Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China.
Locoweeds are leguminous forbs known for their toxicity to livestock caused by the endophytic fungi Alternaria sect. Undifilum. Unlike the defensive mutualism reported in many toxin producing endophytes and their plant hosts, the benefits that A. sect. Undifilum can confer to it host plants has been unclear. Here we conducted physiological and genetic analyses to show that A. (sect. Undifilum) oxytropis influences the growth, especially root development in its locoweed host and Arabidopsis. A. oxytropis significantly decreased primary root length while increasing the number of lateral roots and root hairs, plant leaf area and fresh weight. It enhanced the levels of plant endogenous auxin, and the expression of key genes in auxin biosynthesis, signaling and transport. Such influence on root development was abolished in auxin signaling and polar transport mutants. A. oxytropis down-regulated PIN1 but increased PIN2, PIN7, and AUX1, which may reflect altered spatial auxin accumulation responsible for the change in root architecture. Plant growth was also insensitive to A. oxytropis when NPA (naphthylphthalamic acid) was applied. Our findings indicate a function of A. oxytropis in promoting the growth and development of Arabidopsis via the regulation of auxin. This suggests the possible role of A. oxytropis to benefit its locoweed hosts, via a process irrelevant to its toxin production.
PMID: 36306203
J Exp Bot , IF:6.992 , 2022 Oct 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.; Horticultural Sciences Department, University of Florida, Gainesville, FL.; Department of Chemistry, University of Florida, Gainesville, FL.; Chemistry Research Unit, Center for Medical, Agricultural and Veterinary Entomology, U.S. Department of Agriculture-Agricultural Research Service, Gainesville, FL.; Department of Microbiology & Cell Science, Gainesville, FL.; UF Genetics Institute, University of Florida, Gainesville, FL.; Florida Center for Renewable Chemicals and Fuels, University of Florida, Gainesville, FL.
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 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 , 2022 Oct doi: 10.1093/jxb/erac416
GhROP6 GTPase promotes cell-specific GhPIN3a degradation in cotton fibers by regulating GhPIN3a localization.
Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, P. R. China.; Academy of Agricultural Sciences, Southwest University, Chongqing, P. R. China.; Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Southwest University, Chongqing, P. R. 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 , 2022 Oct doi: 10.1093/jxb/erac406
RsCLE22a Regulates the Taproot Growth through 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, P.R.China.; College of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China.
CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are a class of small polypeptide molecules involved in plant growth and development. Although radish is an important root vegetable crop worldwide, the functions of CLE peptides in 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 exogenous supplement of RsCLE22 peptide (CLE22p) was shown the similar phenotypes in radish. 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 (Y1H) and dual-luciferase assay (DLA) showed that the RsWOX4 (WUSCHEL-RELATED HOMEOBOX 4) gene binds to RsCLE22a promoter and activated its transcription. Meanwhile, the expression level of RsWOX4 was related to vascular cambial activity and regulated by auxin. Furthermore, a RsCLE22a-RsWOX4 module was proposed to regulate taproot vascular cambium activity through auxin signaling-related pathway in radish. These findings provided novel insight into the regulation of root growth in horticultural crops.
PMID: 36239471
J Exp Bot , IF:6.992 , 2022 Oct , V73 (18) : P6255-6271 doi: 10.1093/jxb/erac280
Actin isovariant ACT7 controls root meristem development in Arabidopsis through modulating auxin and ethylene responses.
Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan.; The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan.; Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada.
The meristem is the most functionally dynamic part in a plant. The shaping of the meristem requires constant cell division and elongation, which are influenced by hormones and the cytoskeletal component, actin. Although the roles of hormones in modulating meristem development have been extensively studied, the role of actin in this process is still elusive. Using the single and double mutants of the vegetative class actin, we demonstrate that actin isovariant ACT7 plays an important role in root meristem development. In the absence of ACT7, but not ACT8 and ACT2, depolymerization of actin was observed. Consistently, the act7 mutant showed reduced cell division, cell elongation, and meristem length. Intracellular distribution and trafficking of auxin transport proteins in the actin mutants revealed that ACT7 specifically functions in the root meristem to facilitate the trafficking of auxin efflux carriers PIN1 and PIN2, and consequently the transport of auxin. Compared with act7, the act7act8 double mutant exhibited slightly enhanced phenotypic response and altered intracellular trafficking. The altered distribution of auxin in act7 and act7act8 affects the response of the roots to ethylene, but not to cytokinin. Collectively, our results suggest that ACT7-dependent auxin-ethylene response plays a key role in controlling Arabidopsis root meristem development.
PMID: 35749807
J Exp Bot , IF:6.992 , 2022 Oct , V73 (18) : P6272-6291 doi: 10.1093/jxb/erac281
MAX2-dependent competence for callus formation and shoot regeneration from Arabidopsis thaliana root explants.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium.; Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium.; Laboratory of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, Yeonsu-Gu, Incheon, Korea.; Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, Universite Paris-Sud, Universite Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette, France.; Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg, Ghent, Belgium.
Although the division of the pericycle cells initiates both lateral root development and root-derived callus formation, these developmental processes are affected differently in the strigolactone and karrikin/KARRIKIN INSENSITIVE 2 (KAI2) ligand signalling mutant more axillary growth 2 (max2). Whereas max2 produces more lateral roots than the wild type, it is defective in the regeneration of shoots from root explants. We suggest that the decreased shoot regeneration of max2 originates from delayed formation of callus primordium, yielding less callus material to regenerate shoots. Indeed, when incubated on callus-inducing medium, the pericycle cell division was reduced in max2 and the early gene expression varied when compared with the wild type, as determined by a transcriptomics analysis. Furthermore, the expression of the LATERAL ORGAN BOUNDARIES DOMAIN genes and of callus-induction genes was modified in correlation with the max2 phenotype, suggesting a role for MAX2 in the regulation of the interplay between cytokinin, auxin, and light signalling in callus initiation. Additionally, we found that the in vitro shoot regeneration phenotype of max2 might be caused by a defect in KAI2, rather than in DWARF14, signalling. Nevertheless, the shoot regeneration assays revealed that the strigolactone biosynthesis mutants max3 and max4 also play a minor role.
PMID: 35738874
J Exp Bot , IF:6.992 , 2022 Oct , V73 (18) : P6334-6351 doi: 10.1093/jxb/erac253
Stress-induced higher vein density in the C3-C4 intermediate Moricandia suffruticosa under drought and heat stress.
Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, People's Republic of China.; Hubei Hongshan Laboratory, Wuhan, Hubei, People's Republic of China.
The evolution of C4 photosynthesis involved multiple anatomical and physiological modifications, yet our knowledge of the genetic regulation involved remains elusive. In this study, systematic analyses were conducted comparing the C3-C4 intermediate Moricandia suffruticosa and its C3 relative Brassica napus (rapeseed). We found that the leaves of M. suffruticosa had significantly higher vein density than those of B. napus, and the vein density was further increased in M. suffruticosa under drought and heat stress. Moreover, the bundle sheath distance, as the mean distance from the outer wall of one bundle sheath to the outer wall of an adjacent one, decreased and the number of centripetal chloroplasts in bundle sheath cells was found to be altered in M. suffruticosa leaves under drought and heat treatments. These results suggest that abiotic stress can induce a change in an intermediate C3-C4 anatomy towards a C4-like anatomy in land plants. By integrating drought and heat factors, co-expression network and comparative transcriptome analyses between M. suffruticosa and B. napus revealed that inducible auxin signaling regulated vascular development, and autophagy-related vesicle trafficking processes were associated with this stress-induced anatomical change. Overexpressing three candidate genes, MsERF02, MsSCL01, and MsDOF01, increased leaf vein density and/or enhanced photosynthetic assimilation and drought adaptability in the transgenic lines. The findings of this study may improve our understanding of the genetic regulation and evolution of C4 anatomy.
PMID: 35675763
J Exp Bot , IF:6.992 , 2022 Sep , V73 (16) : P5758-5772 doi: 10.1093/jxb/erac228
In vitro functional characterization predicts the impact of bacterial root endophytes on plant growth.
Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
Utilizing beneficial microbes for crop improvement is one strategy to achieve sustainable agriculture. However, identifying microbial isolates that promote crop growth is challenging, in part because using bacterial taxonomy to predict an isolate's effect on plant growth may not be reliable. The overall aim of this work was to determine whether in vitro functional traits of bacteria were predictive of their in planta impact. We isolated 183 bacterial endophytes from field-grown roots of two tomato species, Solanum lycopersicum and S. pimpinellifolium. Sixty isolates were screened for six in vitro functional traits: auxin production, siderophore production, phosphate solubilization, antagonism to a soilborne pathogen, and the presence of two antimicrobial metabolite synthesis genes. Hierarchical clustering of the isolates based on the in vitro functional traits identified several groups of isolates sharing similar traits. We called these groups 'functional groups'. To understand how in vitro functional traits of bacteria relate to their impact on plants, we inoculated three isolates from each of the functional groups on tomato seedlings. Isolates within the same functional group promoted plant growth at similar levels, regardless of their host origin or taxonomy. Together, our results demonstrate the importance of examining root endophyte functions for improving crop production.
PMID: 35596672
J Exp Bot , IF:6.992 , 2022 Sep , V73 (17) : P5874-5885 doi: 10.1093/jxb/erac111
Phytomelatonin as a central molecule in plant disease resistance.
Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources, College of Tropical Crops, Hainan University, Haikou, Hainan province, 570228, China.; Department of Cellular and Structural Biology, UT Health San Antonio, Long School of Medicine, San Antonio, TX, USA.
Melatonin is an essential phytohormone in the regulation of many plant processes, including during plant development and in response to stress. Pathogen infections cause serious damage to plants and reduce agricultural production. Recent studies indicate that melatonin plays important roles in alleviating bacterial, fungal, and viral diseases in plants and post-harvest fruits. Herein, we summarize information related to the effects of melatonin on plant disease resistance. Melatonin, reactive oxygen species, and reactive nitrogen species form a complex loop in plant-pathogen interaction to regulate plant disease resistance. Moreover, crosstalk of melatonin with other phytohormones including salicylic acid, jasmonic acid, auxin, and abscisic acid further activates plant defense genes. Melatonin plays an important role not only in plant immunity but also in alleviating pathogenicity. We also summarize the known processes by which melatonin mediates pathogenicity via negatively regulating the expression levels of genes related to cell viability as well as virulence-related genes. The multiple mechanisms underlying melatonin influences on both plant immunity and pathogenicity support the recognition of the essential nature of melatonin in plant-pathogen interactions, highlighting phytomelatonin as a critical molecule in plant immune responses.
PMID: 35298631
Development , IF:6.868 , 2022 Oct doi: 10.1242/dev.200899
A mutation in threonine synthase 1 uncouples proliferation and transition domains of the root apical meristem: experimental evidence and in silico proposed mechanism.
Departamento de Biologia Molecular de Plantas, Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico (UNAM), Av. Universidad, 2001, Cuernavaca 62250, Mexico.; Universidad Tecnologica de Mexico - UNITEC MEXICO - Campus Atizapan, Av. Calacoaya 7, Atizapan de Zaragoza, Estado de Mexico, 52970, Mexico.
A continuum from stem to transit-amplifying and to a differentiated cell state is a common theme in multicellular organisms. In the plant root apical meristem (RAM), transit-amplifying cells are organized in two domains, the proliferation domain (PD) from which the cells are displaced to the transition domain (TD), suggesting that both domains are necessarily coupled. Here we show that in a mutant, affected in threonine (Thr) synthesis (methionine overexpressor2-2), the RAM lacks the PD. Through a combination of cell length profile analysis, mathematical modeling, and molecular markers we establish that the PD and TD can be uncoupled. Remarkably, although the RAM of mto2-2 is represented solely by the TD, the known factors of RAM maintenance and auxin signaling are expressed in the mutant. Mathematical modelling predicts that the stem cell niche critically depends on Thr metabolism, and that when disturbed the normal continuum of cell states becomes aborted.
PMID: 36278862
Development , IF:6.868 , 2022 Sep , V149 (18) doi: 10.1242/dev.200715
The dynamic proteome in Arabidopsis thaliana early embryogenesis.
State Key Laboratory of Agrobiotechnology and School of Life Science, The Chinese University of Hong Kong, 999077 Hong Kong, China.; Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China.
The morphology of the flowering plant is established during early embryogenesis. In recent years, many studies have focused on transcriptional profiling in plant embryogenesis, but the dynamic landscape of the Arabidopsis thaliana proteome remains elusive. In this study, Arabidopsis embryos at 2/4-cell, 8-cell, 16-cell, 32-cell, globular and heart stages were collected for nanoproteomic analysis. In total, 5386 proteins were identified. Of these, 1051 proteins were universally identified in all developmental stages and a range of 27 to 2154 proteins was found to be stage specific. These proteins could be grouped into eight clusters according to their expression levels. Gene Ontology enrichment analysis showed that genes involved in ribosome biogenesis and auxin-activated signalling were enriched during early embryogenesis, indicating that active translation and auxin signalling are important events in Arabidopsis embryo development. Combining RNA-sequencing data with the proteomics analysis, the correlation between mRNA and protein was evaluated. An overall positive correlation was found between mRNA and protein. This work provides a comprehensive landscape of the Arabidopsis proteome in early embryogenesis. Some important proteins/transcription factors identified through network analysis may serve as potential targets for future investigation.
PMID: 35950926
Cells , IF:6.6 , 2022 Sep , V11 (17) doi: 10.3390/cells11172761
Roles of Auxin in the Growth, Development, and Stress Tolerance of Horticultural Plants.
Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 400044, China.
Auxin, a plant hormone, regulates virtually every aspect of plant growth and development. Many current studies on auxin focus on the model plant Arabidopsis thaliana, or on field crops, such as rice and wheat. There are relatively few studies on what role auxin plays in various physiological processes of a range of horticultural plants. In this paper, recent studies on the role of auxin in horticultural plant growth, development, and stress response are reviewed to provide novel insights for horticultural researchers and cultivators to improve the quality and application of horticultural crops.
PMID: 36078168
Plant J , IF:6.417 , 2022 Sep 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
Plant J , IF:6.417 , 2022 Nov , V112 (3) : P860-874 doi: 10.1111/tpj.15987
The Germin-like protein OsGER4 is involved in promoting crown root development under exogenous jasmonic acid treatment in rice.
University of Science and Technology of Hanoi, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.; School of Applied Mathematics and Informatics, University of Science and Technology of Hanoi, 1 Dai Co Viet, Hai Ba Trung, Hanoi, Vietnam.; Institute of Biotechnology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.; Graduate University of Science and Technology, Vietnam Academy of Science and Technology, 18 Hoang Quoc Viet, Cau Giay, Hanoi, 100000, Vietnam.
In rice (Oryza sativa L.), crown roots (CRs) have many important roles in processes such as root system expansion, water and mineral uptake, and adaptation to environmental stresses. Phytohormones such as auxin, cytokinin, and ethylene are known to control CR initiation and development in rice. However, the role of jasmonic acid (JA) in CR development remained elusive. Here, we report that JA promotes CR development by regulating OsGER4, a rice Germin-like protein. Root phenotyping analysis revealed that exogenous JA treatment induced an increase in CR number in a concentration-dependent manner. A subsequent genome-wide association study and gene expression analyses pinpointed a strong association between the Germin-like protein OsGER4 and the increase in CR number under exogenous JA treatment. The ProGER4::GUS reporter line showed that OsGER4 is a hormone-responsive gene involved in various stress responses, mainly confined to epidermal and vascular tissues during CR primordia development and to vascular bundles of mature crown and lateral roots. Notable changes in OsGER4 expression patterns caused by the polar auxin transport inhibitor NPA support its connection to auxin signaling. Phenotyping experiments with OsGER4 knockout mutants confirmed that this gene is required for CR development under exogenous JA treatment. Overall, our results provide important insights into JA-mediated regulation of CR development in rice.
PMID: 36134434
Plant J , IF:6.417 , 2022 Nov , V112 (3) : P812-829 doi: 10.1111/tpj.15983
Multi-omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius).
Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.; Novogene Bioinformatics Institute, Beijing, 100015, China.; Department of Ecology, Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.; Natural Sciences and Science Education, National Institute of Education, Nanyang Technological University, 637616, Singapore.; Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.
Jute (Corchorus sp.) is the most important bast fiber crop worldwide; however, the mechanisms underlying domestication and improvement remain largely unknown. We performed multi-omics analysis by integrating de novo sequencing, resequencing, and transcriptomic and epigenetic sequencing to clarify the domestication and improvement of dark jute Corchorus olitorius. We demonstrated that dark jute underwent early domestication and a relatively moderate genetic bottleneck during improvement breeding. A genome-wide association study of 11 important agronomic traits identified abundant candidate loci. We characterized the selective sweeps in the two breeding stages of jute, prominently, soil salinity differences played an important role in environmental adaptation during domestication, and the strongly selected genes for improvement had an increased frequency of favorable haplotypes. Furthermore, we speculated that an encoding auxin/indole-3-acetic acid protein COS07g_00652 could enhance the flexibility and strength of the stem to improve fiber yield. Our study not only provides valuable genetic resources for future fiber breeding in jute, but also is of great significance for reviewing the genetic basis of early crop breeding.
PMID: 36129373
Plant J , IF:6.417 , 2022 Nov , V112 (3) : P772-785 doi: 10.1111/tpj.15979
N-terminal domain of ARF-GEF GNOM prevents heterodimerization with functionally divergent GNL1 in Arabidopsis.
Center for Plant Molecular Biology (ZMBP), Developmental Genetics, University of Tubingen, Auf der Morgenstelle 32, 72076, Tubingen, Germany.
Evolutionary change following gene duplication can lead to functionally divergent paralogous proteins. If comprising identical subunits their random assortment would also form potentially detrimental heteromeric proteins. In Arabidopsis, the ARF GTPase guanine-nucleotide exchange factor GNOM is essential for polar recycling of auxin-efflux transporter PIN1 from endosomes to the basal plasma membrane whereas its paralog GNL1 mediates retrograde Golgi-endoplasmic reticulum traffic. Here we show that both GNOM and GNL1 form homodimers but no heterodimers. To assess the biological significance of this, we generated transgenic plants expressing engineered heterodimer-compatible GNOM variants. Those plants showed developmental defects such as the failure to produce lateral roots. To identify mechanisms underlying heterodimer prevention, we analyzed interactions of the N-terminal dimerization and cyclophilin-binding (DCB) domain. Each DCB domain interacted with the complementary fragment (DeltaDCB) both of their own and of the paralogous protein. However, only DCB(GNOM) interacted with itself whereas DCB(GNL1) failed to interact with itself and with DCB(GNOM) . GNOM variants in which the DCB domain was removed or replaced by DCB(GNL1) revealed a role for DCB-DCB interaction in the prevention of GNOM-GNL1 heterodimers whereas DCB-DeltaDCB interaction was essential for dimer formation and GNOM function. Our data suggest a model of early DCB-DCB interaction that facilitates GNOM homodimer formation, indirectly precluding formation of detrimental heterodimers.
PMID: 36106415
Plant J , IF:6.417 , 2022 Oct , V112 (2) : P476-492 doi: 10.1111/tpj.15960
Bioenergy sorghum stem growth regulation: intercalary meristem localization, development, and gene regulatory network analysis.
Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843-2128, USA.; ABQMR, Inc., 2301 Yale Blvd. SE, Suite C2, Albuquerque, New Mexico, 87106, USA.; Department of Plant Biology, University of Illinois, Champaign-Urbana, Illinois, 61801, USA.
Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES (SbLOB), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM (dw2) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non-meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin-dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM.
PMID: 36038985
Antioxidants (Basel) , IF:6.312 , 2022 Oct , V11 (10) doi: 10.3390/antiox11102035
Mitochondrial HSC70-1 Regulates Polar Auxin Transport through ROS Homeostasis in Arabidopsis Roots.
Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China.; National 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 200032, China.; College of Life Sciences, Hengshui University, Hengshui 053000, China.
Arabidopsis mitochondrial-localized heat shock protein 70-1 (mtHSC70-1) modulates vegetative growth by assisting mitochondrial complex IV assembly and maintaining reactive oxygen species (ROS) homeostasis. In addition, mtHSC70-1 affects embryo development, and this effect is mediated by auxin. However, whether mtHSC70-1 regulates vegetative growth through auxin and knowledge of the link between ROS homeostasis and auxin distribution remain unclear. Here, we found that mtHSC70-1 knockout seedlings (mthsc70-1a) displayed shortened roots, decreased fresh root weight and lateral root number, increased root width and abnormal root morphology. The introduction of the mtHSC70-1 gene into mthsc70-1a restored the growth and development of roots to the level of the wild type. However, sugar and auxin supplementation could not help the mutant roots restore to normal. Moreover, mthsc70-1a seedlings showed a decrease in meristem length and activity, auxin transport carrier (PINs and AUX1) and auxin abundances in root tips. The application of exogenous reducing agents upregulated the levels of PINs in the mutant roots. The introduction of antioxidant enzyme genes (MSD1 or CAT1) into the mthsc70-1a mutant rescued the PIN and local auxin abundances and root growth and development. Taken together, our data suggest that mtHSC70-1 regulates polar auxin transport through ROS homeostasis in Arabidopsis roots.
PMID: 36290758
Antioxidants (Basel) , IF:6.312 , 2022 Sep , V11 (9) doi: 10.3390/antiox11091792
Exogenous Betaine Enhances the Protrusion Vigor of Rice Seeds under Heat Stress by Regulating Plant Hormone Signal Transduction and Its Interaction Network.
Department of Agronomy, College of Agronomy, Hunan Agricultural University, Changsha 410128, China.; The Key Laboratory of Crop Germplasm Innovation and Resource Utilization of Hunan Province, Hunan Agricultural University, Changsha 410128, China.
Rice is an important food crop. Rice seedlings are mainly composed of root, coleoptile, mesocotyl and euphylla. The elongation of coleoptile and mesocotyl promotes the emergence of rice seedlings. Therefore, analyzing the mechanism of coleoptile and mesocotyl elongation is important for the cultivation of rice varieties. Due to global warming, heat stress is threatening rice yields. Betaine plays an important role in plant resistance to heat stress; however, we lack research on its regulation mechanism of rice seed germination under heat stress. Therefore, we explored the effects of soaking seeds with betaine at different concentrations on rice seed germination under heat stress. According to the results, soaking seeds with 10 mM of betaine could effectively improve the seeds' germination potential and rate under heat stress to promote the germination of rice seeds. To clarify the mitigation mechanism of betaine in heat stress, we measured the antioxidant enzyme activity, malondialdehyde content, soluble protein content and endogenous hormone content of seed protrusion under heat stress. We constructed the cDNA library for transcriptome sequencing. According to the results, 10 mM of betaine improved the activities of the superoxide dismutase, peroxidase and catalase of seed protrusion under heat stress to reduce the malondialdehyde content and increase the soluble protein content to alleviate the effect of heat stress on rice seed germination. The detection of the endogenous hormone content showed that soaking seeds with 10 mM of betaine increased the content of gibberellin and decreased the contents of auxin and abscisic acid of seed protrusion under heat stress. According to the transcriptome analysis, betaine can induce the expressions of key genes in the biosynthesis and metabolism of auxin, abscisic acid and gibberellins in the seed coleoptile and mesocotyl elongation stage, regulate the signal transduction of three hormones and promote the germination of rice seeds under heat stress. This study revealed, for the first time, the physiological and molecular regulation mechanism of betaine promotion of seed germination under heat stress.
PMID: 36139866
Commun Biol , IF:6.268 , 2022 Sep , V5 (1) : P1043 doi: 10.1038/s42003-022-03998-2
The RPN12a proteasome subunit is essential for the multiple hormonal homeostasis controlling the progression of leaf senescence.
Department of Plant Physiology, Umea Plant Science Centre, Umea University, SE-901 87, Umea, Sweden.; Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umea, Sweden.; Department of Plant Physiology, Umea Plant Science Centre, Umea University, SE-901 87, Umea, Sweden. olivier.keech@umu.se.
The 26S proteasome is a conserved multi-subunit machinery in eukaryotes. It selectively degrades ubiquitinated proteins, which in turn provides an efficient molecular mechanism to regulate numerous cellular functions and developmental processes. Here, we studied a new loss-of-function allele of RPN12a, a plant ortholog of the yeast and human structural component of the 19S proteasome RPN12. Combining a set of biochemical and molecular approaches, we confirmed that a rpn12a knock-out had exacerbated 20S and impaired 26S activities. The altered proteasomal activity led to a pleiotropic phenotype affecting both the vegetative growth and reproductive phase of the plant, including a striking repression of leaf senescence associate cell-death. Further investigation demonstrated that RPN12a is involved in the regulation of several conjugates associated with the auxin, cytokinin, ethylene and jasmonic acid homeostasis. Such enhanced aptitude of plant cells for survival in rpn12a contrasts with reports on animals, where 26S proteasome mutants generally show an accelerated cell death phenotype.
PMID: 36180574
Int J Mol Sci , IF:5.923 , 2022 Oct , V23 (20) doi: 10.3390/ijms232012495
Molecular Mechanisms of Diverse Auxin Responses during Plant Growth and Development.
Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin 150500, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.; College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA.; Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, School of Life Sciences, Heilongjiang University, Harbin 150080, China.
The plant hormone auxin acts as a signaling molecule to regulate numerous developmental processes throughout all stages of plant growth. Understanding how auxin regulates various physiological and developmental processes has been a hot topic and an intriguing field. Recent studies have unveiled more molecular details into how diverse auxin responses function in every aspect of plant growth and development. In this review, we systematically summarized and classified the molecular mechanisms of diverse auxin responses, and comprehensively elaborated the characteristics and multilevel regulation mechanisms of the canonical transcriptional auxin response. On this basis, we described the characteristics and differences between different auxin responses. We also presented some auxin response genes that have been genetically modified in plant species and how their changes impact various traits of interest. Finally, we summarized some important aspects and unsolved questions of auxin responses that need to be focused on or addressed in future research. This review will help to gain an overall understanding of and some insights into the diverse molecular mechanisms of auxin responses in plant growth and development that are instrumental in harnessing genetic resources in molecular breeding of extant plant species.
PMID: 36293351
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (19) doi: 10.3390/ijms231911580
Physiological and Comparative Transcriptome Analyses of the High-Tillering Mutant mtn1 Reveal Regulatory Mechanisms in the Tillering of Centipedegrass (Eremochloa ophiuroides (Munro) Hack.).
The National Forestry and Grassland Administration Engineering Research Center for Germplasm Innovation and Utilization of Warm-Season Turfgrasses, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
Tillering is a key factor that determines the reproductive yields of centipedegrass, which is an important perennial warm-season turfgrass. However, the regulatory mechanism of tillering in perennial plants is poorly understood, especially in perennial turfgrasses. In this study, we created and characterised a cold plasma-mutagenised centipedegrass mutant, mtn1 (more tillering number 1). Phenotypic analysis showed that the mtn1 mutant exhibited high tillering, short internodes, long seeds and a heavy 1000-seed weight. Then, a comparative transcriptomic analysis of the mtn1 mutant and wild-type was performed to explore the molecular mechanisms of centipedegrass tillering. The results revealed that plant hormone signalling pathways, as well as starch and sucrose metabolism, might play important roles in centipedegrass tillering. Hormone and soluble sugar content measurements and exogenous treatment results validated that plant hormones and sugars play important roles in centipedegrass tiller development. In particular, the overexpression of the auxin transporter ATP-binding cassette B 11 (EoABCB11) in Arabidopsis resulted in more branches. Single nucleotide polymorphisms (SNPs) were also identified, which will provide a useful resource for molecular marker-assisted breeding in centipedegrass. According to the physiological characteristics and transcriptional expression levels of the related genes, the regulatory mechanism of centipedegrass tillering was systematically revealed. This research provides a new breeding resource for further studies into the molecular mechanism that regulates tillering in perennial plants and for breeding high-tillering centipedegrass varieties.
PMID: 36232880
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (19) doi: 10.3390/ijms231911538
Potential of Rhizobia Nodulating Anthyllis vulneraria L. from Ultramafic Soil as Plant Growth Promoting Bacteria Alleviating Nickel Stress in Arabidopsis thaliana L.
Department of Botany, Institute of Biology, Warsaw University of Life Sciences (SGGW-WULS), Nowoursynowska 159, 02-776 Warsaw, Poland.; Department of Botany and Plant Ecology, Wroclaw University of Environmental and Life Sciences, Grunwaldzki Square 24 A, 50-363 Wroclaw, Poland.; Department of Plant Nutrition, Institute of Soil Science, Plant Nutrition and Environmental Protection, Wroclaw University of Environmental and Life Sciences, Grunwaldzka Street 53, 50-357 Wroclaw, Poland.; Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences (SGGW-WULS), Nowoursynowska 159, Building 37, 02-776 Warsaw, Poland.; Institute of Technology and Life Sciences, Falenty, Al. Hrabska 3, 05-090 Raszyn, Poland.
Rhizobia, which enter into symbiosis with legumes, can also interact with non-legumes and promote plant growth. In this paper, we explored the effects of nickel (Ni, 200 microM) on Arabidopsis thaliana (Col-0) inoculated with plant growth-promoting (PGP) rhizobia nodulating ultramafic Anthyllis vulneraria. The isolated PGP strains tolerant to Ni were identified as Rhizobium sp. and Bradyrhizobium sp. The isolates highly differed in their PGP abilities and Ni resistance. Without Ni-stress, the plants inoculated with most isolates grew better and had higher photosynthetic efficiency than non-inoculated controls. Nickel treatment increased Ni concentration in inoculated plants. Plant growth, leaf anatomy, chloroplast ultrastructure, efficiency of photosynthesis, and antioxidant defense system activity were significantly impaired by Ni, however, the majority of these effects were diminished in plants inoculated with the most effective PGP rhizobia. Real-time PCR revealed an increased expression level of genes involved in auxin and gibberellin biosynthesis in the inoculated, Ni-treated plants, and this may have improved shoot and root growth after inoculation with effective isolates. Our results also suggest a positive correlation between Ni-stress parameters and antioxidant defense system activity, and also between the effectiveness of photosynthesis and plant growth parameters. We showed that the selected rhizobia, naturally nodulating Anthyllis on Ni-rich ultramafic soils can promote Arabidopsis growth and increase plant tolerance to Ni by improving different physiological and biochemical mechanisms.
PMID: 36232842
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (19) doi: 10.3390/ijms231911122
The Identification and Expression Analysis of the Nitraria sibirica Pall. Auxin-Response Factor (ARF) Gene Family.
Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education of China, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.; College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.; Experimental Center of Desert Forestry, Chinese Academy of Forestry, Dengkou 015200, China.
Nitraria sibirica is a shrub that can survive in extreme drought environments. The auxin-response factors (ARFs) are a class of transcription factors that are widely involved in plant growth and development, as well as in the regulation of stress resistance. However, the genome-wide identification of the ARF gene family and its responses to environmental stresses, especially drought stress, in N. sibirica has not yet been reported. Here, we identified a total of 12 ARF genes in the genome of N. sibirica, which were distributed over 10 chromosomes and divided into three clades. Intragenome synteny analysis revealed one collinear gene pair in the ARF gene family, i.e., NsARF9a and NsARF9b. Cis-acting element analysis showed that multiple hormones and stress-responsive cis-acting elements were found in the promoters of NsARFs, suggesting that NsARFs may be involved in multiple biological processes. Quantitative real-time PCR (qRT-PCR) showed that many NsARFs had tissue-specific expression patterns, with the highest expression of NsARF16 in the seedlings of N. sibirica. In addition, most of the NsARFs that were upregulated under drought were independent of endogenous ABA biosynthesis, whereas the response of NsARF5 and NsARF7a to drought was disrupted by the ABA-biosynthesis inhibitor fluridone. These studies provide a basis for further research into how NsARFs in N. sibirica respond to hormonal signaling and environmental stresses.
PMID: 36232423
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (19) doi: 10.3390/ijms231911108
Identification and Characterization of AUXIN Response Factor Gene Family Reveals Their Regulatory Network to Respond the Multi-Hormones Crosstalk during GA-Induced Grape Parthenocarpic Berry.
College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.; Department of Plant Biology, Faculty of Biological Science, Tarbiat Modares University, Tehran 843300, Iran.
Exogenous gibberellin (GA) was widely used to improve berry quality through inducing parthenocarpic seedless berries in grapes. We revealed that auxin response factors (ARFs), the key transcription factors in response to auxin, might respond to GA involving modulation of grape parthenocarpy. However, the underlying molecular mechanism in this process remains yet unclear. Here, a total of 19 VvARF members were identified in the ovaries during GA-induced grapes' parthenocarpy. Interestingly, almost all members were GA-responsive factors, of which 9 could be classified in plant hormone signal transduction (KO04075) and involved in the tryptophan metabolic pathway (K14486). Moreover, VvARFs were predicted to have 310 interacted proteins involved in 19 KEGG pathways. Of them, 32 interacted proteins participated in the KO04075 pathway, including auxin (IAA), salicylic acid (SA), abscisic acid (ABA), cytokinin (CTK), and ethylene signaling pathways by responding to GA-mediated multi-hormone crosstalk. Further analysis demonstrated that VvARF4-2 might be the major factor in the modulation of GA-induced parthenocarpy via the crosstalk of IAA, CTK, SA, and ethylene signaling, followed by VvARF6-1 and VvARF9 involved in SA and ABA signaling pathways, respectively. Finally, we developed a VvARFs-mediated regulatory network by responding to GA-mediated multi-hormone crosstalk during grape parthenocarpy. Collectively, our findings provided novel insights into the regulatory network of VvARFs in GA-guided multi-hormone signaling to modulate grape parthenocarpy, which has great implications for the molecular breeding of high quality seedless grape berries.
PMID: 36232409
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (19) doi: 10.3390/ijms231911045
Whole Transcriptome Analyses of Apricots and Japanese Plum Fruits after 1-MCP (Ethylene-Inhibitor) and Ethrel (Ethylene-Precursor) Treatments Reveal New Insights into the Physiology of the Ripening Process.
Department of Plant Breeding, CEBAS-CSIC, Espinardo, 30100 Murcia, Spain.; Facultad de Medicina Y Ciencia, Universidad San Sebastian, Santiago 7510157, Chile.
The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, 'Goldrich' and 'Santa Rosa'. KEEG and protein-protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in 'Goldrich' and 'Santa Rosa', respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in 'Goldrich' and 'Santa Rosa', respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.
PMID: 36232348
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (18) doi: 10.3390/ijms231810923
Genome-Wide Identification, Evolution, and Expression Analysis of GASA Gene Family in Prunus mume.
Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
The Gibberellic Acid Stimulated Arabidopsis/Gibberellin Stimulated Transcript (GASA/GAST) gene family is a group of plant-specific genes encoding cysteine-rich peptides essential to plant growth, development, and stress responses. Although GASA family genes have been identified in various plant species, their functional roles in Prunus mume are still unknown. In this study, a total of 16 PmGASA genes were identified via a genome-wide scan in Prunus mume and were grouped into three major gene clades based on the phylogenetic tree. All PmGASA proteins possessed the conserved GASA domain, consisting of 12-cysteine residues, but varied slightly in protein physiochemical properties and motif composition. With evolutionary analysis, we observed that duplications and purifying selection are major forces driving PmGASA family gene evolution. By analyzing PmGASA promoters, we detected a number of hormonal-response related cis-elements and constructed a putative transcriptional regulatory network for PmGASAs. To further understand the functional role of PmGASA genes, we analyzed the expression patterns of PmGASAs across different organs and during various biological processes. The expression analysis revealed the functional implication of PmGASA gene members in gibberellic acid-, abscisic acid-, and auxin-signaling, and during the progression of floral bud break in P. mume. To summarize, these findings provide a comprehensive understanding of GASA family genes in P. mume and offer a theoretical basis for future research on the functional characterization of GASA genes in other woody perennials.
PMID: 36142832
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (18) doi: 10.3390/ijms231810642
The Plastidial DIG5 Protein Affects Lateral Root Development by Regulating Flavonoid Biosynthesis and Auxin Transport in Arabidopsis.
Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.; High-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, China.; College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China.; Department of Biology, Hong Kong Baptist University, Kowloon Tang, Hong Kong, China.; Department of Plant Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-713, Korea.; Inner Mongolia Key Laboratory of Plant Stress Physiology and Molecular Biology, Inner Mongolia Agricultural University, Hohhot 010010, China.; State Key Laboratory for Agribiotechnology, Chinese University of Hong Kong, Hong Kong, China.
To reveal the mechanisms underlying root adaptation to drought stress, we isolated and characterized an Arabidopsis mutant, dig5 (drought inhibition of lateral root growth 5), which exhibited increased sensitivity to the phytohormone abscisic acid (ABA) for the inhibition of lateral root growth. The dig5 mutant also had fewer lateral roots under normal conditions and the aerial parts were yellowish with a lower level of chlorophylls. The mutant seedlings also displayed phenotypes indicative of impaired auxin transport, such as abnormal root curling, leaf venation defects, absence of apical hook formation, and reduced hypocotyl elongation in darkness. Auxin transport assays with [(3)H]-labeled indole acetic acid (IAA) confirmed that dig5 roots were impaired in polar auxin transport. Map-based cloning and complementation assays indicated that the DIG5 locus encodes a chloroplast-localized tRNA adenosine deaminase arginine (TADA) that is involved in chloroplast protein translation. The levels of flavonoids, which are naturally occurring auxin transport inhibitors in plants, were significantly higher in dig5 roots than in the wild type roots. Further investigation showed that flavonoid biosynthetic genes were upregulated in dig5. Introduction of the flavonoid biosynthetic mutation transparent testa 4 (tt4) into dig5 restored the lateral root growth of dig5. Our study uncovers an important role of DIG5/TADA in retrogradely controlling flavonoid biosynthesis and lateral root development. We suggest that the DIG5-related signaling pathways, triggered likely by drought-induced chlorophyll breakdown and leaf senescence, may potentially help the plants to adapt to drought stress through optimizing the root system architecture.
PMID: 36142550
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (18) doi: 10.3390/ijms231810596
Integrated Analysis of Transcriptome and Small RNAome Reveals the Regulatory Network for Rapid Growth in Mikania micrantha.
Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China.
M. micrantha has caused huge ecological damage and economic losses worldwide due to its rapid growth and serious invasion. However, the underlying molecular mechanisms of its rapid growth and environmental adaption remain unclear. Here, we performed transcriptome and small RNA sequencing with five tissues of M. micrantha to dissect miRNA-mediated regulation in M. micrantha. WGCNA and GO enrichment analysis of transcriptome identified the gene association patterns and potential key regulatory genes for plant growth in each tissue. The genes highly correlated with leaf and stem tissues were mainly involved in the chlorophyll synthesis, response to auxin, the CAM pathway and other photosynthesis-related processes, which promoted the fast growth of M. micrantha. Importantly, we identified 350 conserved and 192 novel miRNAs, many of which displayed differential expression patterns among tissues. PsRNA target prediction analysis uncovered target genes of both conserved and novel miRNAs, including GRFs and TCPs, which were essential for plant growth and development. Further analysis revealed that miRNAs contributed to the regulation of tissue-specific gene expression in M. micrantha, such as mmi-miR396 and mmi-miR319. Taken together, our study uncovered the miRNA-mRNA regulatory networks and the potential vital roles of miRNAs in modulating the rapid growth of M. micrantha.
PMID: 36142547
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (18) doi: 10.3390/ijms231810548
Plants in Microgravity: Molecular and Technological Perspectives.
Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umea, Sweden.; Doctoral School of Neuroscience, Semmelweis University, H-1083 Budapest, Hungary.; Theoretical Neuroscience and Complex Systems Group, Department of Computational Sciences, Wigner Research Centre for Physics, H-1121 Budapest, Hungary.; Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, Kozep fasor 52, H-6726 Szeged, Hungary.; Biological Research Centre (BRC), Institute of Plant Biology, Eotvos Lorand Research Network (ELKH), H-6726 Szeged, Hungary.
Plants are vital components of our ecosystem for a balanced life here on Earth, as a source of both food and oxygen for survival. Recent space exploration has extended the field of plant biology, allowing for future studies on life support farming on distant planets. This exploration will utilize life support technologies for long-term human space flights and settlements. Such longer space missions will depend on the supply of clean air, food, and proper waste management. The ubiquitous force of gravity is known to impact plant growth and development. Despite this, we still have limited knowledge about how plants can sense and adapt to microgravity in space. Thus, the ability of plants to survive in microgravity in space settings becomes an intriguing topic to be investigated in detail. The new knowledge could be applied to provide food for astronaut missions to space and could also teach us more about how plants can adapt to unique environments. Here, we briefly review and discuss the current knowledge about plant gravity-sensing mechanisms and the experimental possibilities to research microgravity-effects on plants either on the Earth or in orbit.
PMID: 36142459
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (18) doi: 10.3390/ijms231810527
Ustilaginoidea virens Nuclear Effector SCRE4 Suppresses Rice Immunity via Inhibiting Expression of a Positive Immune Regulator OsARF17.
Department of Plant Pathology, The Ministry of Agriculture Key Laboratory of Pest Monitoring and Green Management, and Joint Laboratory for International Cooperation in Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China.; Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China.; State Key Laboratory for Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture of China and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.; College of Plant Protection, Jilin Agricultural University, Changchun 130118, China.
Rice false smut caused by the biotrophic fungal pathogen Ustilaginoidea virens has become one of the most important diseases in rice. The large effector repertory in U. virens plays a crucial role in virulence. However, current knowledge of molecular mechanisms how U. virens effectors target rice immune signaling to promote infection is very limited. In this study, we identified and characterized an essential virulence effector, SCRE4 (Secreted Cysteine-Rich Effector 4), in U. virens. SCRE4 was confirmed as a secreted nuclear effector through yeast secretion, translocation assays and protein subcellular localization, as well as up-regulation during infection. The SCRE4 gene deletion attenuated the virulence of U. virens to rice. Consistently, ectopic expression of SCRE4 in rice inhibited chitin-triggered immunity and enhanced susceptibility to false smut, substantiating that SCRE4 is an essential virulence factor. Furthermore, SCRE4 transcriptionally suppressed the expression of OsARF17, an auxin response factor in rice, which positively regulates rice immune responses and resistance against U. virens. Additionally, the immunosuppressive capacity of SCRE4 depended on its nuclear localization. Therefore, we uncovered a virulence strategy in U. virens that transcriptionally suppresses the expression of the immune positive modulator OsARF17 through nucleus-localized effector SCRE4 to facilitate infection.
PMID: 36142440
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (18) doi: 10.3390/ijms231810360
Proteomic and Biochemical Approaches Elucidate the Role of Millimeter-Wave Irradiation in Wheat Growth under Flooding Stress.
Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.; Research Center for Development of Far-Infrared Region, University of Fukui, Fukui 910-8507, Japan.; Department of Medical Technology, Yokkaichi Nursing and Medical Care University, Yokkaichi 512-8045, Japan.; Institute for Comprehensive Medical Science, Fujita Health University, Toyoake 470-1192, Japan.
Flooding impairs wheat growth and considerably affects yield productivity worldwide. On the other hand, irradiation with millimeter waves enhanced the growth of chickpea and soybean under flooding stress. In the current work, millimeter-wave irradiation notably enhanced wheat growth, even under flooding stress. To explore the protective mechanisms of millimeter-wave irradiation on wheat under flooding, quantitative proteomics was performed. According to functional categorization, proteins whose abundances were changed significantly with and without irradiation under flooding stress were correlated to glycolysis, reactive-oxygen species scavenging, cell organization, and hormonal metabolism. Immunoblot analysis confirmed that fructose-bisphosphate aldolase and beta tubulin accumulated in root and leaf under flooding; however, even in such condition, their accumulations were recovered to the control level in irradiated wheat. The abundance of ascorbate peroxidase increased in leaf under flooding and recovered to the control level in irradiated wheat. Because the abundance of auxin-related proteins changed with millimeter-wave irradiation, auxin was applied to wheat under flooding, resulting in the application of auxin improving its growth, even in such condition. These results suggest that millimeter-wave irradiation on wheat seeds improves the recovery of plant growth from flooding via the regulation of glycolysis, reactive-oxygen species scavenging, and cell organization. Additionally, millimeter-wave irradiation could promote tolerance against flooding through the regulation of auxin contents in wheat.
PMID: 36142271
Int J Mol Sci , IF:5.923 , 2022 Sep , V23 (17) doi: 10.3390/ijms231710183
Genome-Wide Characterization of PIN Auxin Efflux Carrier Gene Family in Mikania micrantha.
Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China.; Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
Mikania micrantha, recognized as one of the world's top 10 pernicious weeds, is a rapidly spreading tropical vine that has invaded the coastal areas of South China, causing serious economic losses and environmental damage. Rapid stem growth is an important feature of M. micrantha which may be related to its greater number of genes involved in auxin signaling and transport pathways and its ability to synthesize more auxin under adverse conditions to promote or maintain stem growth. Plant growth and development is closely connected to the regulation of endogenous hormones, especially the polar transport and asymmetric distribution of auxin. The PIN-FORMED (PIN) auxin efflux carrier gene family plays a key role in the polar transport of auxin and then regulates the growth of different plant tissues, which could indicate that the rapid growth of M. micrantha is closely related to this PIN-dependent auxin regulation. In this study, 11 PIN genes were identified and the phylogenetic relationship and structural compositions of the gene family in M. micrantha were analyzed by employing multiple bioinformatic methods. The phylogenetic analysis indicated that the PIN proteins could be divided into five distinct clades. The structural analysis revealed that three putative types of PIN (canonical, noncanonical and semi-canonical) exist among the proteins according to the length and the composition of the hydrophilic domain. The majority of the PINs were involved in the process of axillary bud differentiation and stem response under abiotic stress, indicating that M. micrantha may regulate its growth, development and stress response by regulating PIN expression in the axillary bud and stem, which may help explain its strong growth ability and environmental adaptability. Our study emphasized the structural features and stress response patterns of the PIN gene family and provided useful insights for further study into the molecular mechanism of auxin-regulated growth and control in M. micrantha.
PMID: 36077586
PLoS Genet , IF:5.917 , 2022 Sep , V18 (9) : Pe1010375 doi: 10.1371/journal.pgen.1010375
SAUR63 stimulates cell growth at the plasma membrane.
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America.; Laboratoire Reproduction et Developpement des Plantes, Universite de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRAE, Lyon, France.; Department of Plant and Microbial Biology, University of Minnesota, St. Paul, Minnesota, United States of America.
In plants, regulated cell expansion determines organ size and shape. Several members of the family of redundantly acting Small Auxin Up RNA (SAUR) proteins can stimulate plasma membrane (PM) H+-ATPase proton pumping activity by inhibiting PM-associated PP2C.D phosphatases, thereby increasing the PM electrochemical potential, acidifying the apoplast, and stimulating cell expansion. Similarly, Arabidopsis thaliana SAUR63 was able to increase growth of various organs, antagonize PP2C.D5 phosphatase, and increase H+-ATPase activity. Using a gain-of-function approach to bypass genetic redundancy, we dissected structural requirements for SAUR63 growth-promoting activity. The divergent N-terminal domain of SAUR63 has a predicted basic amphipathic alpha-helix and was able to drive partial PM association. Deletion of the N-terminal domain decreased PM association of a SAUR63 fusion protein, as well as decreasing protein level and eliminating growth-promoting activity. Conversely, forced PM association restored ability to promote H+-ATPase activity and cell expansion, indicating that SAUR63 is active when PM-associated. Lipid binding assays and perturbations of PM lipid composition indicate that the N-terminal domain can interact with PM anionic lipids. Mutations in the conserved SAUR domain also reduced PM association in root cells. Thus, both the N-terminal domain and the SAUR domain may cooperatively mediate the SAUR63 PM association required to promote growth.
PMID: 36121899
Front Bioeng Biotechnol , IF:5.89 , 2022 , V10 : P1009531 doi: 10.3389/fbioe.2022.1009531
Exogenous hormones supplementation improve adventitious root formation in woody plants.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, Zhejiang, China.; The Engineering Research Institute of Agriculture and Forestry, Ludong University, Yantai, Shandong, China.
PMID: 36177185
Front Plant Sci , IF:5.753 , 2022 , V13 : P958816 doi: 10.3389/fpls.2022.958816
Genome-wide identification of the auxin response factor (ARF) gene family in Magnolia sieboldii and functional analysis of MsARF5.
Department of Forestry, Shenyang Agricultural University, Shenyang, China.; Biotechnology and Analysis Test Center, Liaoning Academy of Forest Science, Shenyang, China.
Auxin plays an essential role in flowering, embryonic development, seed dormancy, and germination. Auxin response factors (ARFs) are plant-specific key transcriptional factors in mediating the gene expression network of auxin signaling. Although ARFs in model plants such as Arabidopsis had been well characterized, their identities and potential roles in non-model plants are less studied. Here, we performed genome-wide identification of ARFs in Magnolia sieboldii K. Koch, a primitive species with high taxonomic importance and medicinal values. We found 25 ARF genes in M. sieboldii, which were widely distributed across multiple chromosomes. Based on sequence similarity, the encoded proteins could be either transcriptional repressors or activators. Gene expression analysis showed a dynamic pattern for many ARFs including MsARF5 during seed germination. In addition, overexpressing of MsARF5 showed that it restores many developmental defects in the Arabidopsis mutant. Moreover, two phenotypically distinct transgenic Arabidopsis lines were obtained, indicating a link between gene expression levels and developmental phenotypes. Taken together, we provided a systematic investigation of the ARF gene family in M. sieboldii and revealed an important role of MsARF5 in mediating auxin signaling.
PMID: 36275560
Front Plant Sci , IF:5.753 , 2022 , V13 : P964003 doi: 10.3389/fpls.2022.964003
A high trans-zeatin nucleoside concentration in corms may promote the multileaf growth of Amorphophallus muelleri.
Yunnan Urban Agricultural Engineering and Technological Research Center, College of Agronomy, Kunming University, Kunming, China.
Amorphophallus muelleri has a multileaf growth pattern different from that of other konjacs; however, the hormonal mechanism underlying this phenomenon is not clear. In this study, the levels of hormones closely related to the sprouting of the axillary bud, including five types of cytokinins, indole-3-acetic acid (IAA) and abscisic acid (ABA) were measured. In the second leaf sprouting stage, the content of trans-zeatin riboside (tZR) in corms increased more than 5000-fold over that in the dormancy period. Surprisingly, although the expression of CYP735A1 and CYP735A2, which synthesize the precursors for tZR was elevated at the second leaf sprouting stage, the expression of IPTs, which have key roles in cytokinin biosynthesis, did not change significantly. In addition, most cytokinin contents in leaves during the same period were significantly lower than those in corms. We speculate that the high cytokinin contents in the corms may not biosynthesized de novo in corms. In addition, the IAA content in the corms also considerably increased during the second leaf sprouting stage. Indole-3-acetaldehyde oxidase (AO1) and auxin efflux carrier PIN1A, presented relatively high expression levels in the same period. In contrast, ABA content, and the expression of NCED1, a rate-limiting enzyme in ABA biosynthesis, were suppressed at the second leaf sprouting stage. It is worth mentioning that N6-(Delta2-isopentenyl) adenosine (iP)-type cytokinins have a high content in corms in the dormant period that significantly decreases after the first leaf sprouting stage, which is completely different from the trend of tZR. By treating dormant corms with iP, the percentage of multibud plants increased, and the growth performance in terms of bud and root length was significantly higher than those of the control. This implies that iP-type cytokinins tend to play a role in promoting first seedling sprouting. Furthermore, there was a remarkable increase of the IAA content in both corms and roots under iP treatment but an inhibitory effect in buds. We speculate that the increase in the IAA content induced by iP is tissue specific. These results will assist in the understanding of the role of hormones, especially cytokinins, in the multileaf growth type of konjac.
PMID: 36275554
Front Plant Sci , IF:5.753 , 2022 , V13 : P979883 doi: 10.3389/fpls.2022.979883
Bacillus amyloliquefaciens GB03 augmented tall fescue growth by regulating phytohormone and nutrient homeostasis under nitrogen deficiency.
State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China.; Guizhou Institute of Prataculture, Guizhou Academy of Agricultural Sciences, Guiyang, China.; School of Life Sciences, Guizhou Normal University, Guiyang, China.; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.
Nitrogen is an important nutrient for plant growth and development. Soil microorganisms have been used to curb the imbalance between the limited content of natural environmental nitrogen and the pollution caused by increasing nitrogen fertilizer use in ecologically fragile areas. Bacillus amyloliquefaciens GB03 has been shown to confer growth promotion and abiotic stress tolerance in Arabidopsis thaliana. This study provided a new insight into the role of the plant growth-promoting rhizobacterium B. amyloliquefaciens GB03 as an initiator of defense against nitrogen deficiency in non-leguminous grass tall fescue (Festuca arundinacea). Two-week-old seedlings of tall fescue were grown with or without GB03 for 4 weeks under total nitrogen (3.75 mM NO3 (-)) or low nitrogen (0.25 mM NO3 (-)) treatment. Growth parameters, chlorophyll content, endogenous total nitrogen, total phosphorus content, and phytohormone content, including those of auxin indole-3-acetic acid, cytokinin, gibberellic acid, and abscisic acid, were determined at the time of harvest. Tall fescue grown in GB03-inoculated soil was more robust than the non-inoculated controls with respect to plant height, root length, plant biomass, chlorophyll concentration, and nutrient (total nitrogen and total phosphorus) contents under total nitrogen treatment. GB03 increased indole acetic acid content by 24.7%, whereas decreased cytokinin and abscisic acid contents by 28.4% and 26.9%, respectively, under a total nitrogen level. Remarkably, GB03 increased indole acetic acid content by more than 80% and inhibited abscisic acid production by nearly 70% under a low nitrogen level. These results showed, for the first time, that GB03 played a crucial role in mediating NO3 (-)dependent regulation of tall fescue growth and development, especially revealing the mechanism of soil bacteria improve resistance to nitrogen deficiency stress in non-nitrogen-fixing species.
PMID: 36275534
Front Plant Sci , IF:5.753 , 2022 , V13 : P995815 doi: 10.3389/fpls.2022.995815
Morphological characterization and transcriptome analysis of leaf angle mutant bhlh112 in maize [Zea mays L.].
College of Agronomy, Gansu Agricultural University, Lanzhou, China.; Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China.; Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China.
Leaf angle is an important agronomic trait in maize [Zea mays L.]. The compact plant phenotype, with a smaller leaf angle, is suited for high-density planting and thus for increasing crop yields. Here, we studied the ethyl methane sulfonate (EMS)-induced mutant bhlh112. Leaf angle and plant height were significantly decreased in bhlh112 compared to the wild-type plants. After treatment of seedlings with exogenous IAA and ABA respectively, under the optimal concentration of exogenous hormones, the variation of leaf angle of the mutant was more obvious than that of the wild-type, which indicated that the mutant was more sensitive to exogenous hormones. Transcriptome analysis showed that the ZmbHLH112 gene was related to the biosynthesis of auxin and brassinosteroids, and involved in the activation of genes related to the auxin and brassinosteroid signal pathways as well as cell elongation. Among the GO enrichment terms, we found many differentially expressed genes (DEGs) enriched in the cell membrane and ribosomal biosynthesis, hormone biosynthesis and signaling pathways, and flavonoid biosynthesis, which could influence cell growth and the level of endogenous hormones affecting leaf angle. Therefore, ZmbHLH112 might regulate leaf angle development through the auxin signaling and the brassinosteroid biosynthesis pathways. 12 genes related to the development of leaf were screened by WGCNA; In GO enrichment and KEGG pathways, the genes were mainly enriched in rRNA binding, ribosome biogenesis, Structural constituent of ribosome; Arabidopsis ribosome RNA methyltransferase CMAL is involved in plant development, likely by modulating auxin derived signaling pathways; The free 60s ribosomes and polysomes in the functional defective mutant rice minute-like1 (rml1) were significantly reduced, resulting in plant phenotypic diminution, narrow leaves, and growth retardation; Hence, ribosomal subunits may play an important role in leaf development. These results provide a foundation for further elucidation of the molecular mechanism of the regulation of leaf angle in maize.
PMID: 36275532
Front Plant Sci , IF:5.753 , 2022 , V13 : P998664 doi: 10.3389/fpls.2022.998664
Transcriptome characteristics during cell wall formation of endosperm cellularization and embryo differentiation in Arabidopsis.
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China.
Embryonic and endosperm development are important biological events during Arabidopsis seed development, and are controlled by dynamic changes in a range of gene expression. Nevertheless, the regulatory mechanisms of endosperm cellularization and embryo differentiation remain unclear. Here, we characterized the early embryo and endosperm development of the naa15 mutant that had abnormal embryo differentiation and incomplete endosperm cellularization compared to WT of Arabidopsis, and comparatively investigated the changes of gene expressions in WT seeds at 3, 4, and 5 days after pollination (3W, 4W, and 5W) and the white homozygous aborted naa15 seeds at 5, 6, and 7 DAP (5M, 6M, and 7M) from naa15-1/+ siliques using RNA sequencing and qPCR assays. The transcriptome analyses showed that there were 2040 and 3630 differentially expressed genes (DEGs) in 4W (at endosperm cellularization initiation stage and heart embryo stage) vs 3W (at syncytium stage and globular embryo stage), and 5W (at end of endosperm cellularization stage and torpedo embryo stage) vs 4W, respectively. The KEGG and GO analyses showed that lipid metabolic processes and transmembrane transport related to cell wall biogenesis, cell division and differentiation, the plant hormone signaling pathway, photosynthesis, and transcription regulator activity were evidently enriched in WT and naa15. The heatmap and qPCR analyses showed that auxin response genes (ARFs), auxin transport genes (PINs) cytokinin synthesis genes (LOGs), cytokinin dehydrogenase genes (CKXs), cytokinin receptor, transcription factors (MYB, bHLH, MADS-box, and ERF) were significantly downregulated in naa15 compared to WT. A series of cell wall genes annotated to xyloglucan endotransglycosylase/hydrolase, pectin methyl esterase, and pectin methyl esterase inhibitor were also identified in these DEGs. Moreover, using an immunofluorescent assay, the features of cell walls displayed that cellulose fluorescence signals in the embryo and endosperm of naa15 were significantly decreased, and the signals of low- and high- methyl esterification of pectin were also obviously decreased in the endosperm of naa15. In summary, we identified a large number of DEGs and investigated the features of cell walls during endosperm cellularization and embryonic differentiation, which provided important information on transcription and gene expression to reveal their regulatory mechanisms.
PMID: 36262665
Front Plant Sci , IF:5.753 , 2022 , V13 : P1021572 doi: 10.3389/fpls.2022.1021572
RNA-seq analysis reveals key genes associated with seed germination of Fritillaria taipaiensis P.Y.Li by cold stratification.
College of Agronomy & Biotechnology, Yunnan Agricultural University, Kunming, China.; Key Laboratory of Medicinal Plant Biology of Yunnan Province, Yunnan Agricultural Waseda University, Fengyuan, Kunming, China.; National & Local Joint Engineering Research Center on Germplasm Innovation & Utilization of Chinese Medicinal Materials in Southwestern China, Yunnan Agricultural University, Kunming, China.; Chongqing Academy of Chinese Materia Medica, Chongqing, China.; Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, United Kingdom.
Seed dormancy is an adaptive strategy for environmental evolution. However, the molecular mechanism of the breaking of seed dormancy at cold temperatures is still unclear, and the genetic regulation of germination initiated by exposure to cold temperature requires further investigation. In the initial phase of the current study, the seed coat characteristics and embryo development of Fritillaria taipaiensis P.Y.Li at different temperatures (0 degrees C, 4 degrees C, 10 degrees C & 25 degrees C) was recorded. The results obtained demonstrated that embryo elongation and the dormancy-breaking was most significantly affected at 4 degrees C. Subsequently, transcriptome analyses of seeds in different states of dormancy, at two stratification temperatures (4 degrees C and 25 degrees C) was performed, combined with weighted gene coexpression network analysis (WGCNA) and metabolomics, to explore the transcriptional regulation of seed germination in F. taipaiensis at the two selected stratification temperatures. The results showed that stratification at the colder temperature (4 degrees C) induced an up-regulation of gene expression involved in gibberellic acid (GA) and auxin biosynthesis and the down-regulation of genes related to the abscisic acid (ABA) biosynthetic pathway. Thereby promoting embryo development and the stimulation of seed germination. Collectively, these data constitute a significant advance in our understanding of the role of cold temperatures in the regulation of seed germination in F. taipaiensis and also provide valuable transcriptomic data for seed dormancy for other non-model plant species.
PMID: 36247582
Front Plant Sci , IF:5.753 , 2022 , V13 : P999990 doi: 10.3389/fpls.2022.999990
Expression analysis of PIN family genes in Chinese hickory reveals their potential roles during grafting and salt stress.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China.; Zhejiang Provincial Key Laboratory of Forest Aromatic Plants-based Healthcare Functions, Zhejiang A&F University, Hangzhou, China.; Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China.
Grafting is an effective way to improve Chinese hickory while salt stress has caused great damage to the Chinese hickory industry. Grafting and salt stress have been regarded as the main abiotic stress types for Chinese hickory. However, how Chinese hickory responds to grafting and salt stress is less studied. Auxin has been proved to play an essential role in the stress response through its re-distribution regulation mediated by polar auxin transporters, including PIN-formed (PIN) proteins. In this study, the PIN gene family in Chinese hickory (CcPINs) was identified and structurally characterized for the first time. The expression profiles of the genes in response to grafting and salt stress were determined. A total of 11 CcPINs with the open reading frames (ORFs) of 1,026-1,983 bp were identified. Transient transformation in tobacco leaves demonstrated that CcPIN1a, CcPIN3, and CcPIN4 were localized in the plasma membrane. There were varying phylogenetic relationships between CcPINs and homologous genes in different species, but the closest relationships were with those in Carya illinoinensis and Juglans regia. Conserved N- and C-terminal transmembrane regions as well as sites controlling the functions of CcPINs were detected in CcPINs. Five types of cis-acting elements, including hormone- and stress-responsive elements, were detected on the promoters of CcPINs. CcPINs exhibited different expression profiles in different tissues, indicating their varied roles during growth and development. The 11 CcPINs responded differently to grafting and salt stress treatment. CcPIN1a might be involved in the regulation of the grafting process, while CcPIN1a and CcPIN8a were related to the regulation of salt stress in Chinese hickory. Our results will lay the foundation for understanding the potential regulatory functions of CcPIN genes during grafting and under salt stress treatment in Chinese hickory.
PMID: 36247577
Front Plant Sci , IF:5.753 , 2022 , V13 : P979141 doi: 10.3389/fpls.2022.979141
Ultrasonication affects the melatonin and auxin levels and the antioxidant system in potato in vitro.
Institute of Food Technology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Debrecen, Hungary.; Centre for Agricultural Genomics and Biotechnology, Faculty of the Agricultural and Food Science and Environmental Management, University of Debrecen, Nyiregyhaza, Hungary.
Melatonin is an ancient hormone whose physiological effects have been extensively studied in animals and human. We now know that it also plays a prominent role in the growth and development of plants. In our present experiment, the relationship between endogenous melatonin and the antioxidant system was investigated in potato plant grown in vitro. Changes in redox homeostasis under ultrasound stress were examined. The concentration of small molecule antioxidants and enzymes of the three-level antioxidant pathway was measured. ELISA method was used to determine the melatonin levels in plant tissues at each growth stage (0 h, 24 h, 48 h, 1 week, and 4 weeks after subculturing the explants) both in control and ultrasound-treated plants. Ultrasound stress activated the three-level defense system and decreased the endogenous melatonin levels. Melatonin was able to provide protection against membrane damage caused by drastic ultrasound treatment. Melatonin at the heart of the redox network is a key component regulating various biochemical, cellular, and physiological responses. It has a dual role, as it is able to act both as a growth regulator and an antioxidant. A close relationship was evidenced between the plant hormone indole-3-acetic acid and melatonin and ascorbic acid.
PMID: 36247572
Front Plant Sci , IF:5.753 , 2022 , V13 : P991548 doi: 10.3389/fpls.2022.991548
A novel function of the key nitrogen-fixation activator NifA in beta-rhizobia: Repression of bacterial auxin synthesis during symbiosis.
Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.; Agroscope, Molecular Ecology and Swiss Institute of Bioinformatics, Zurich, Switzerland.; ETH Zurich, Institute of Molecular Systems Biology, Zurich, Switzerland.
Rhizobia fix nitrogen within root nodules of host plants where nitrogenase expression is strictly controlled by its key regulator NifA. We recently discovered that in nodules infected by the beta-rhizobial strain Paraburkholderia phymatum STM815, NifA controls expression of two bacterial auxin synthesis genes. Both the iaaM and iaaH transcripts, as well as the metabolites indole-acetamide (IAM) and indole-3-acetic acid (IAA) showed increased abundance in nodules occupied by a nifA mutant compared to wild-type nodules. Here, we document the structural changes that a P. phymatum nifA mutant induces in common bean (Phaseolus vulgaris) nodules, eventually leading to hypernodulation. To investigate the role of the P. phymatum iaaMH genes during symbiosis, we monitored their expression in presence and absence of NifA over different stages of the symbiosis. The iaaMH genes were found to be under negative control of NifA in all symbiotic stages. While a P. phymatum iaaMH mutant produced the same number of nodules and nitrogenase activity as the wild-type strain, the nifA mutant produced more nodules than the wild-type that clustered into regularly-patterned root zones. Mutation of the iaaMH genes in a nifA mutant background reduced the presence of these nodule clusters on the root. We further show that the P. phymatum iaaMH genes are located in a region of the symbiotic plasmid with a significantly lower GC content and exhibit high similarity to two genes of the IAM pathway often used by bacterial phytopathogens to deploy IAA as a virulence factor. Overall, our data suggest that the increased abundance of rhizobial auxin in the non-fixing nifA mutant strain enables greater root infection rates and a role for bacterial auxin production in the control of early stage symbiotic interactions.
PMID: 36247538
Front Plant Sci , IF:5.753 , 2022 , V13 : P979033 doi: 10.3389/fpls.2022.979033
OsARF4 regulates leaf inclination via auxin and brassinosteroid pathways in rice.
State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.; Hainan Yazhou Bay Seed Laboratory, Sanya, China.; Key Laboratory of Herbage and Endemic Crop Biology of Ministry of Education, Inner Mongolia Key Laboratory of Herbage and Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, China.
Leaf inclination is a vital agronomic trait and is important for plant architecture that affects photosynthetic efficiency and grain yield. To understand the molecular mechanisms underlying regulation of leaf inclination, we constructed an auxin response factor (arf) rice mutant-osarf4-showing increased leaf inclination using CRISPR/Cas9 gene editing technology. OsARF4 encodes a nuclear protein that is expressed in the lamina joint (LJ) at different developmental stages in rice. Histological analysis indicated that an increase in cell differentiation on the adaxial side resulted in increased leaf inclination in the osarf4 mutants; however, OsARF4-overexpressing lines showed a decrease in leaf inclination, resulting in erect leaves. Additionally, a decrease in the content and distribution of indole-3-acetic acid (IAA) in osarf4 mutant led to a greater leaf inclination, whereas the OsARF4-overexpressing lines showed the opposite phenotype with increased IAA content. RNA-sequencing analysis revealed that the expression of genes related to brassinosteroid (BR) biosynthesis and response was different in the mutants and overexpressing lines, suggesting that OsARF4 participates in the BR signaling pathway. Moreover, BR sensitivity assay revealed that OsARF4-overexpressing lines were more sensitive to exogenous BR treatment than the mutants. In conclusion, OsARF4, a transcription factor in auxin signaling, participates in leaf inclination regulation and links auxin and BR signaling pathways. Our results provide a novel insight into l leaf inclination regulation, and have significant implications for improving rice architecture and grain yield.
PMID: 36247537
Front Plant Sci , IF:5.753 , 2022 , V13 : P1007542 doi: 10.3389/fpls.2022.1007542
The thiol-reductase activity of YUCCA6 enhances nickel heavy metal stress tolerance in Arabidopsis.
Research Institute of Life Sciences, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea.; Division of Applied Life Science (BK21four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea.; Department of Biology, Graduate School of Gyeongsang National University, Jinju, South Korea.; College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea.; Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea.
Anthropogenic activities cause the leaching of heavy metals into groundwater and their accumulation in soil. Excess levels of heavy metals cause toxicity in plants, inducing the production of reactive oxygen species (ROS) and possible death caused by the resulting oxidative stress. Heavy metal stresses repress auxin biosynthesis and transport, inhibiting plant growth. Here, we investigated whether nickel (Ni) heavy metal toxicity is reduced by exogenous auxin application and whether Ni stress tolerance in Arabidopsis thaliana is mediated by the bifunctional enzyme YUCCA6 (YUC6), which functions as an auxin biosynthetic enzyme and a thiol-reductase (TR). We found that an application of up to 1 microM exogenous indole-3-acetic acid (IAA) reduces Ni stress toxicity. yuc6-1D, a dominant mutant of YUC6 with high auxin levels, was more tolerant of Ni stress than wild-type (WT) plants, despite absorbing significantly more Ni. Treatments of WT plants with YUCASIN, a specific inhibitor of YUC-mediated auxin biosynthesis, increased Ni toxicity; however yuc6-1D was not affected by YUCASIN and remained tolerant of Ni stress. This suggests that rather than the elevated IAA levels in yuc6-1D, the TR activity of YUC6 might be critical for Ni stress tolerance. The loss of TR activity in YUC6 caused by the point-mutation of Cys85 abolished the YUC6-mediated Ni stress tolerance. We also found that the Ni stress-induced ROS accumulation was inhibited in yuc6-1D plants, which consequently also showed reduced oxidative damage. An enzymatic assay and transcriptional analysis revealed that the peroxidase activity and transcription of PEROXIREDOXIN Q were enhanced by Ni stress to a greater level in yuc6-1D than in the WT. These findings imply that despite the need to maintain endogenous IAA levels for basal Ni stress tolerance, the TR activity of YUC6, not the elevated IAA levels, plays the predominant role inNi stress tolerance by lowering Ni-induced oxidative stress.
PMID: 36237515
Front Plant Sci , IF:5.753 , 2022 , V13 : P911993 doi: 10.3389/fpls.2022.911993
Overexpression of TaLBD16-4D alters plant architecture and heading date in transgenic wheat.
Shandong Provincial Key Laboratory of Dryland Farming Technology, Qingdao Agricultural University, Qingdao, China.; State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China.
Lateral organ boundaries domain (LBD) proteins, a class of plant-specific transcription factors with a special domain of lateral organ boundaries (LOB), play essential roles in plant growth and development. However, there is little known about the functions of these genes in wheat to date. Our previous study demonstrated that TaLBD16-4D is conducive to increasing lateral root number in wheat. In the present work, we further examined important agronomical traits of the aerial part of transgenic wheat overexpressing TaLBD16-4D. Interestingly, it was revealed that overexpressing TaLBD16-4D could lead to early heading and multiple alterations of plant architecture, including decreased plant height, increased flag leaf size and stem diameter, reduced spike length and tillering number, improved spike density and grain width, and decreased grain length. Moreover, auxin-responsive experiments demonstrated that the expression of TaLBD16-4D in wild-type (WT) wheat plants showed a significant upregulation through 2,4-D treatment. TaLBD16-4D-overexpression lines displayed a hyposensitivity to 2,4-D treatment and reduced shoot gravitropic response. The expressions of a set of auxin-responsive genes were markedly different between WT and transgenic plants. In addition, overexpressing TaLBD16-4D affected the transcript levels of flowering-related genes (TaGI, TaCO1, TaHd1, TaVRN1, TaVRN2, and TaFT1). Notably, the expression of TaGI, TaCO1, TaHd1, TaVRN1, and TaFT1 displayed significant upregulation under IAA treatment. Collectively, our observations indicated that overexpressing TaLBD16-4D could affect aerial architecture and heading time possibly though participating in the auxin pathway.
PMID: 36212357
Front Plant Sci , IF:5.753 , 2022 , V13 : P995855 doi: 10.3389/fpls.2022.995855
De novo transcriptome analysis of high-salinity stress-induced antioxidant activity and plant phytohormone alterations in Sesuvium portulacastrum.
Hainan Academy of Forestry, Hainan Mangrove Research Institute, Haikou, China.; Mangrove Institute, Lingnan Normal University, Zhanjiang, China.
Sesuvium portulacastrum has a strong salt tolerance and can grow in saline and alkaline coastal and inland habitats. This study investigated the physiological and molecular responses of S. portulacastrum to high salinity by analyzing the changes in plant phytohormones and antioxidant activity, including their differentially expressed genes (DEGs) under similar high-salinity conditions. High salinity significantly affected proline (Pro) and hydrogen peroxide (H2O2) in S. portulacastrum seedlings, increasing Pro and H2O2 contents by 290.56 and 83.36%, respectively, compared to the control. Antioxidant activities, including superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT), significantly increased by 83.05, 205.14, and 751.87%, respectively, under high salinity. Meanwhile, abscisic acid (ABA) and gibberellic acid (GA3) contents showed the reverse trend of high salt treatment. De novo transcriptome analysis showed that 36,676 unigenes were matched, and 3,622 salt stress-induced DEGs were identified as being associated with the metabolic and biological regulation processes of antioxidant activity and plant phytohormones. POD and SOD were upregulated under high-salinity conditions. In addition, the transcription levels of genes involved in auxin (SAURs and GH3), ethylene (ERF1, ERF3, ERF114, and ABR1), ABA (PP2C), and GA3 (PIF3) transport or signaling were altered. This study identified key metabolic and biological processes and putative genes involved in the high salt tolerance of S. portulacastrum and it is of great significance for identifying new salt-tolerant genes to promote ecological restoration of the coastal strand.
PMID: 36212296
Front Plant Sci , IF:5.753 , 2022 , V13 : P942217 doi: 10.3389/fpls.2022.942217
Genome-wide identification of calcineurin B-like protein-interacting protein kinase gene family reveals members participating in abiotic stress in the ornamental woody plant Lagerstroemia indica.
School of Life Sciences, Nantong University, Nantong, China.; Key Laboratory of Landscape Plant Genetics and Breeding, Nantong University, Nantong, China.
Calcineurin B-like protein-interacting protein kinases (CIPKs) play important roles in plant responses to stress. However, their function in the ornamental woody plant Lagerstroemia indica is remains unclear. In this study, the LiCIPK gene family was analyzed at the whole genome level. A total of 37 LiCIPKs, distributed across 17 chromosomes, were identified. Conserved motif analysis indicated that all LiCIPKs possess a protein kinase motif (S_TKc) and C-terminal regulatory motif (NAF), while seven LiCIPKs lack a protein phosphatase interaction (PPI) motif. 3D structure analysis further revealed that the N-terminal and C-terminal 3D-structure of 27 members are situated near to each other, while 4 members have a looser structure, and 6 members lack intact structures. The intra- and interspecies collinearity analysis, synonymous substitution rate (K s ) peaks of duplicated LiCIPKs, revealed that approximately 80% of LiCIPKs were retained by the two whole genome duplication (WGD) events that occurred approximately 56.12-61.16 million year ago (MYA) and 16.24-26.34 MYA ago. The promoter of each LiCIPK contains a number of auxin, abscisic acid, gibberellic acid, salicylic acid, and drought, anaerobic, defense, stress, and wound responsive cis-elements. Of the 21 members that were successfully amplified by qPCR, 18 LiCIPKs exhibited different expression patterns under NaCl, mannitol, PEG8000, and ABA treatments. Given that LiCIPK30, the AtSOS2 ortholog, responded to all four types of stress it was selected for functional verification. LiCIPK30 complements the atsos2 phenotype in vivo. 35S:LiCIPK-overexpressing lines exhibit increased leaf area increment, chlorophyll a and b content, reactive oxygen species scavenging enzyme activity, and expression of ABF3 and RD22, while the degree of membrane lipid oxidation decreases under NaCl treatment compared to WT. The evolutionary history, and potential mechanism by which LiCIPK30 may regulate plant tolerance to salt stress were also discussed. In summary, we identified LiCIPK members involved in abiotic stress and found that LiCIPK30 transgenic Arabidopsis exhibits more salt and osmotic stress tolerance than WT. This research provides a theoretical foundation for further investigation into the function of LiCIPKs, and for mining gene resources to facilitate the cultivation and breeding of new L. indica varieties in coastal saline-alkali soil.
PMID: 36204074
Front Plant Sci , IF:5.753 , 2022 , V13 : P953225 doi: 10.3389/fpls.2022.953225
Division of cortical cells is regulated by auxin in Arabidopsis roots.
School of Biological Sciences and Technology, Chonnam National University, Gwangju, South Korea.; Department of Environmental Health Science, Konkuk University, Seoul, South Korea.
The root cortex transports water and nutrients absorbed by the root epidermis into the vasculature and stores substances such as starch, resins, and essential oils. The cortical cells are also deeply involved in determining epidermal cell fate. In Arabidopsis thaliana roots, the cortex is composed of a single cell layer generated by a single round of periclinal division of the cortex/endodermis initials. To further explore cortex development, we traced the development of the cortex by counting cortical cells. Unlike vascular cells, whose number increased during the development of root apical meristem (RAM), the number of cortical cells did not change, indicating that cortical cells do not divide during RAM development. However, auxin-induced cortical cell division, and this finding was confirmed by treatment with the auxin transport inhibitor N-1-naphthylphthalamic acid (NPA) and examining transgenic plants harboring CO2::DeltaARF5, in which cortical expression of truncated AUXIN RESPONSE FACTOR5 (DeltaARF5) induces auxin responses. NPA-induced cortical auxin accumulation and CO2::DeltaARF5-mediated cortical auxin response induced anticlinal and periclinal cell divisions, thus increasing the number of cortical cells. These findings reveal a tight link between auxin and cortical cell division, suggesting that auxin is a key player in determining root cortical cell division.
PMID: 36186058
Front Plant Sci , IF:5.753 , 2022 , V13 : P948099 doi: 10.3389/fpls.2022.948099
Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops.
Faculty of Agronomy, S. Seifullin Kazakh Agro Technical University, Nur-Sultan, Kazakhstan.; A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan.; Kazakh Research Institute of Agriculture and Plant Growing, Almalybak, Kazakhstan.; College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia.
Height from soil at the base of plant to the first pod (HFP) is an important trait for mechanical harvesting of legume crops. To minimise the loss of pods, the HFP must be higher than that of the blades of most combine harvesters. Here, we review the genetic control, morphology, and variability of HFP in legumes and attempt to unravel the diverse terminology for this trait in the literature. HFP is directly related to node number and internode length but through different mechanisms. The phenotypic diversity and heritability of HFP and their correlations with plant height are very high among studied legumes. Only a few publications describe a QTL analysis where candidate genes for HFP with confirmed gene expression have been mapped. They include major QTLs with eight candidate genes for HFP, which are involved in auxin transport and signal transduction in soybean [Glycine max (L.) Merr.] as well as MADS box gene SOC1 in Medicago trancatula, and BEBT or WD40 genes located nearby in the mapped QTL in common bean (Phaseolus vulgaris L.). There is no information available about simple and efficient markers associated with HFP, which can be used for marker-assisted selection for this trait in practical breeding, which is still required in the nearest future. To our best knowledge, this is the first review to focus on this significant challenge in legume-based cropping systems.
PMID: 36186054
Front Plant Sci , IF:5.753 , 2022 , V13 : P1006991 doi: 10.3389/fpls.2022.1006991
Metabolic profiling and gene expression analyses provide insights into cold adaptation of an Antarctic moss Pohlia nutans.
Key Laboratory of Marine Eco-Environmental Science and Technology, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.; School of Advanced Manufacturing, Fuzhou University, Jinjiang, China.; National Glycoengineering Research Center, School of Life Sciences, Shandong University, Qingdao, China.; Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
Antarctica is the coldest, driest, and most windy continent on earth. The major terrestrial vegetation consists of cryptogams (mosses and lichens) and two vascular plant species. However, the molecular mechanism of cold tolerance and relevant regulatory networks were largely unknown in these Antarctic plants. Here, we investigated the global alterations in metabolites and regulatory pathways of an Antarctic moss (Pohlia nutans) under cold stress using an integrated multi-omics approach. We found that proline content and several antioxidant enzyme activities were significantly increased in P. nutans under cold stress, but the contents of chlorophyll and total flavonoids were markedly decreased. A total of 559 metabolites were detected using ultra high-performance liquid chromatography/electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS). We observed 39 and 71 differentially changed metabolites (DCMs) after 24 h and 60 h cold stress, indicating that several major pathways were differentially activated for producing fatty acids, alkaloids, flavonoids, terpenoids, and phenolic acids. In addition, the quantitative transcriptome sequencing was conducted to uncover the global transcriptional profiles of P. nutans under cold stress. The representative differentially expressed genes (DEGs) were identified and summarized to the function including Ca(2+) signaling, ABA signaling, jasmonate signaling, fatty acids biosynthesis, flavonoid biosynthesis, and other biological processes. The integrated dataset analyses of metabolome and transcriptome revealed that jasmonate signaling, auxin signaling, very-long-chain fatty acids and flavonoid biosynthesis pathways might contribute to P. nutans acclimating to cold stress. Overall, these observations provide insight into Antarctic moss adaptations to polar habitats and the impact of global climate change on Antarctic plants.
PMID: 36176693
Front Plant Sci , IF:5.753 , 2022 , V13 : P1006735 doi: 10.3389/fpls.2022.1006735
Tonoplast proton pumps regulate nuclear spacing of female gametophytes via mediating polar auxin transport in Arabidopsis.
Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, The Joint International Research, Shanghai Jiao Tong University, Shanghai, China.; Zhiyuan College, Shanghai Jiao Tong University, Shanghai, China.; Department of Biology, Tokyo Gakugei University, Koganei, Japan.; Shanghai Collaborative Innovation Center of Agri-Seeds/Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai, China.
The vacuole is an important organelle with multiple functions in plants, and the tonoplast that wraps the vacuole also plays essential roles in intracellular trafficking and ion homeostasis. Previous studies found that tonoplast proton pumps regulate embryo development and morphogenesis through their effects on vacuole biogenesis and distribution, as well as polar auxin transport and concomitant auxin gradient. However, the precise roles of the tonoplast proton pumps in gametophyte development remain unclear. Here we demonstrated that the lack of two types of tonoplast proton pumps or the absence of V-ATPase alone leads to abnormal development and nuclear localization of female gametophyte (FG), and slowed endosperm nuclei division after fertilization of the central cell. We further revealed that V-ATPase regulates auxin levels in ovules through coordinating the content and localization of PIN-FORMED 1 (PIN1) protein, hence influencing nuclear spacing between centra cell and egg cell, and subsequent endosperm development. Collectively, our findings revealed a crucial role of V-ATPase in auxin-mediated FG development in Arabidopsis and expanded our understanding of the functions of tonoplast proton pumps in seed plants reproductive development.
PMID: 36176689
Front Plant Sci , IF:5.753 , 2022 , V13 : P989048 doi: 10.3389/fpls.2022.989048
Integrated mRNA and microRNA expression analysis of root response to phosphate deficiency in Medicago sativa.
Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, China.; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
The deficiency of available phosphate significantly limits plant growth and development. This study sought to investigate how alfalfa (Medicago sativa), a high-yielding and high-quality forage widely cultivated worldwide, responds to phosphate deficiency stress by integrating transcriptional and post-transcriptional data. In this study, 6,041 differentially expressed genes (DEGs) were identified in alfalfa roots under phosphate deficiency conditions. Furthermore, psRNATarget, RNAhybrid, and TargetFinder were used to predict the target genes of 137 differentially expressed miRNAs (DEMs) in the root. In total, 3,912 DEGs were predicted as target genes. Pearson correlation analysis revealed 423 pairs of miRNA-mRNA regulatory relationships. MiRNA negatively regulates mRNA involved in regulatory pathways of phosphate deficiency responses in alfalfa. miR156e targeted squamosa promoter-binding-like protein 13A (SPL13), miR160c targeted auxin response factor 18 (ARF18), and miR2587a controlled glycolysis and citrate cycle via Phosphoenolpyruvate carboxykinase (ATP) (PCKA). Novel-miR27 regulated SPX domain-containing protein that controls phosphate transport in alfalfa root, novel-miR3-targeted sulfoquinovosyl transferase SQD2 controlled sulfolipid synthesis and glutathione S-transferase (GST; mediated by miR169j/k and novel-miR159) regulated glutathione metabolism. miR399l regulated auxin-responsive protein SAUR72 involved in IAA signal transduction, while abscisic acid receptor PYL4 (regulated by novel-miR205 and novel-miR83) participated in ABA signal transduction. Combined miRNA-mRNA enrichment analysis showed that most miRNAs regulate the phosphate starvation response of alfalfa by modulating target genes involved in carbohydrate metabolism, sulfolipid metabolism, glutathione metabolism, and hormone signal transduction. Therefore, this study provides new insights into the post-transcriptional regulation mechanism of phosphate deficiency responses and new perspectives on phosphate assimilation pathways in alfalfa and other legumes.
PMID: 36176687
Front Plant Sci , IF:5.753 , 2022 , V13 : P958808 doi: 10.3389/fpls.2022.958808
Comparative transcriptomics analysis of developing peanut (Arachis hypogaea L.) pods reveals candidate genes affecting peanut seed size.
School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China.; Henan Academy of Agricultural Sciences, Henan Academy of Crop Molecular Breeding, State Industrial Innovation Center of Biological Breeding, Key Laboratory of Oil Crops in Huang-Huai-Hai Plains, Ministry of Agriculture, Henan Provincial Key Laboratory for Oil Crops Improvement, Innovation Base of Zhengzhou University, Zhengzhou, Henan, China.; College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China.; College of Agriculture, Henan University of Science and Technology, Luoyang, China.; School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China.
Pod size is one of the most important agronomic features of peanuts, which directly affects peanut yield. Studies on the regulation mechanism underpinning pod size in cultivated peanuts remain hitherto limited compared to model plant systems. To better understand the molecular elements that underpin peanut pod development, we conducted a comprehensive analysis of chronological transcriptomics during pod development in four peanut accessions with similar genetic backgrounds, but varying pod sizes. Several plant transcription factors, phytohormones, and the mitogen-activated protein kinase (MAPK) signaling pathways were significantly enriched among differentially expressed genes (DEGs) at five consecutive developmental stages, revealing an eclectic range of candidate genes, including PNC, YUC, and IAA that regulate auxin synthesis and metabolism, CYCD and CYCU that regulate cell differentiation and proliferation, and GASA that regulates seed size and pod elongation via gibberellin pathway. It is plausible that MPK3 promotes integument cell division and regulates mitotic activity through phosphorylation, and the interactions between these genes form a network of molecular pathways that affect peanut pod size. Furthermore, two variant sites, GCP4 and RPPL1, were identified which are stable at the QTL interval for seed size attributes and function in plant cell tissue microtubule nucleation. These findings may facilitate the identification of candidate genes that regulate pod size and impart yield improvement in cultivated peanuts.
PMID: 36172561
Front Plant Sci , IF:5.753 , 2022 , V13 : P927662 doi: 10.3389/fpls.2022.927662
Auxin-regulated timing of transition from vegetative to reproductive growth in rapeseed (Brassica napus L.) under different nitrogen application rates.
Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.; Huzhou Agricultural Science and Technology Development Center, Huzhou, China.; Institute of Digital Agriculture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
Accelerating the differentiation of floral meristem (FM) from shoot apical meristems (SAM) which determines the conversion from vegetative to reproductive growth is of great significance for the production of rapeseed (Brassica napus L.). In this research, the mechanisms of different nitrogen (N) application rates (low N, N1; normal N, N2; and high N, N3) on different FM development stages triggering the regulation of FM differentiation genes through the auxin biosynthetic and signal transduction were investigated. We found that the stage of FM differentiation, which was identified through a stereomicroscope and scanning electron microscope, came 4 and 7 days earlier under high N rate than under normal and low N levels, with the seed yield increased by 11.1 and 22.6%, respectively. Analysis of the auxin and its derivatives contents showed that the main biosynthesis way of auxin was the indole acetaldehyde oxime (IAOx) pathway, with 3-Indole acetonitrile dramatically accumulated during FM differentiation. At the same time, an obvious decrease of IAA contents at each FM differentiation stage was detected, and then gradually rose. Results of the expression of genes involved in auxin biosynthesis, auxin signaling transduction, and FM identification under five FM differentiation stages and three nitrogen application rates showed that genes involved in auxin biosynthesis were regulated before the FM differentiation stage, while the regulation of FM identity genes appeared mainly at the middle and later periods of the five stages, and the regulation level of genes varied under different N rates. Taken together, a high nitrogen rate could accelerate the initiation of FM differentiation, and auxin involved a lot in this regulation.
PMID: 36161032
Front Plant Sci , IF:5.753 , 2022 , V13 : P931063 doi: 10.3389/fpls.2022.931063
Euryale Small Auxin Up RNA62 promotes cell elongation and seed size by altering the distribution of indole-3-acetic acid under the light.
School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, China.; Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing, China.
Euryale (Euryale ferox Salisb.) is an aquatic crop used as both food and drug in Asia, but its utilization is seriously limited due to low yield. Previously, we hypothesized that Euryale small auxin up RNAs (EuSAURs) regulate seed size, but the underlying biological functions and molecular mechanisms remain unclear. Here, we observed that the hybrid Euryale lines (HL) generate larger seeds with higher indole-3-acetic acid (IAA) concentrations than those in the North Gordon Euryale (WT). Histological analysis suggested that a larger ovary in HL is attributed to longer cells around. Overexpression of EuSAUR62 in rice (Oryza sativa L.) resulted in larger glumes and grains and increased the length of glume cells. Immunofluorescence and protein interaction assays revealed that EuSAUR62 modulates IAA accumulation around the rice ovary by interacting with the rice PIN-FORMED 9, an auxin efflux carrier protein. Euryale basic region/leucine zipper 55 (EubZIP55), which was highly expressed in HL, directly binds to the EuSAUR62 promoter and activated the expression of EuSAUR62. Constant light increased the expression of both EubZIP55 and EuSAUR62 with auxin-mediated hook curvature in HL seedlings. Overall, we proposed that EuSAUR62 is a molecular bridge between light and IAA and plays a crucial role in regulating the size of the Euryale seed.
PMID: 36160968
Front Plant Sci , IF:5.753 , 2022 , V13 : P958833 doi: 10.3389/fpls.2022.958833
LsARF3 mediates thermally induced bolting through promoting the expression of LsCO in lettuce (Lactuca sativa L.).
Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Plant Science and Technology College, Beijing University of Agriculture, Beijing, China.; National Engineering Research Center for Vegetables, Institute of Vegetable Science, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Lettuce (Lactuca sativa L.) is a leafy vegetable whose edible organs usually are leaf or stems, and thus high-temperature induced bolting followed by flower initiation is an undesirable trait in lettuce production. However, the molecular mechanism that controls lettuce bolting and flowering upon thermal treatments is largely unknown. Here, we identified a Lettuce auxin response factor 3 (LsARF3), the expression of which was enhanced by heat and auxin treatments. Interestingly, LsARF3 is preferentially expressed in stem apex, suggesting it might be associated with lettuce bolting. Transgenic lettuce overexpressing LsARF3 displayed early bolting and flowering, whereas knockout of LsARF3 dramatically delayed bolting and flowering in lettuce under normal or high temperature conditions. Furthermore, Exogenous application of IAA failed to rescue the late-bolting and -flowering phenotype of lsarf3 mutants. Several floral integrator genes including LsCO, LsFT, and LsLFY were co-expressed with LsARF3 in the overexpression and knockout lettuce plants. Yeast one-hybrid (Y1H) experiments suggested that LsARF3 could physically interact with the LsCO promoter, which was further confirmed by a dual luciferase assay in tobacco leaves. The results indicated that LsARF3 might directly modulate the expression of LsCO in lettuce. Therefore, these results demonstrate that LsARF3 could promote lettuce bolting in response to the high temperature by directly or indirectly activating the expression of floral genes such as LsCO, which provides new insights into lettuce bolting in the context of ARFs signaling and heat response.
PMID: 36160965
Front Plant Sci , IF:5.753 , 2022 , V13 : P983650 doi: 10.3389/fpls.2022.983650
An APETALA2/ethylene responsive factor transcription factor GmCRF4a regulates plant height and auxin biosynthesis in soybean.
National Center for Soybean Improvement, Key Laboratory of Biology and Genetics and Breeding for Soybean, Ministry of Agriculture and Rural Affairs, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.; The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.
Plant height is one of the key agronomic traits affecting soybean yield. The cytokinin response factors (CRFs), as a branch of the APETALA2/ethylene responsive factor (AP2/ERF) super gene family, have been reported to play important roles in regulating plant growth and development. However, their functions in soybean remain unknown. This study characterized a soybean CRF gene named GmCRF4a by comparing the performance of the homozygous Gmcrf4a-1 mutant, GmCRF4a overexpression (OX) and co-silencing (CS) lines. Phenotypic analysis showed that overexpression of GmCRF4a resulted in taller hypocotyls and epicotyls, more main stem nodes, and higher plant height. While down-regulation of GmCRF4a conferred shorter hypocotyls and epicotyls, as well as a reduction in plant height. The histological analysis results demonstrated that GmCRF4a promotes epicotyl elongation primarily by increasing cell length. Furthermore, GmCRF4a is required for the expression of GmYUCs genes to elevate endogenous auxin levels, which may subsequently enhance stem elongation. Taken together, these observations describe a novel regulatory mechanism in soybean, and provide the basis for elucidating the function of GmCRF4a in auxin biosynthesis pathway and plant heigh regulation in plants.
PMID: 36147224
Front Plant Sci , IF:5.753 , 2022 , V13 : P998698 doi: 10.3389/fpls.2022.998698
Study on exogenous application of thidiazuron on seed size of Brassica napus L.
Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland, Yangtze University, Hubei, China.; College of Life Science, Yangtze University, Hubei, China.; College of Agriculture, Yangtze University, Hubei, China.; Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Hubei, China.
Thidiazuron (TDZ) is a novel and efficient cytokinin commonly used in tissue culture, and numerous studies have demonstrated that TDZ can increase berry size. However, no study to date has explored the effect of TDZ on seed size of Brassica napus and the mechanism. To shed light on the effect of TDZ on the seed size of B. napus, four different concentrations of TDZ were applied to B. napus. Results indicated that TDZ treatment could increase the seed diameter and silique length of B. napus to varying degrees and 100 and 200 mumol/L TDZ treatments were the most effective with a 3.6 and 4.6% increase in seed diameter, respectively. In addition, the yield of B. napus was also substantially increased under TDZ treatment. On the other hand, confocal micrographs of embryos and cotyledon cells suggested that embryos and their cotyledon epidermal cells treated with 200 mumol/L TDZ were obviously larger in size than the control. Furthermore, TDZ promoted the upregulation of some key maternal tissue growth-related genes, including two G-protein signaling genes (AGG3 and RGA1) and two transcriptional regulators (ANT and GS2). The expression analysis of genes related to the auxin metabolic pathways, G-protein signaling, endosperm growth and transcriptional regulators confirmed that treatment with TDZ negatively regulated the key genes ABI5, AGB1, AP2, ARF2, and ARF18 during bud development stage and florescence. The results strongly suggested that TDZ might regulate the transcriptional levels of key genes involved in auxin metabolic pathways, G-protein signaling, endosperm growth and transcriptional regulators, which resulted in bigger cotyledon epidermal cells and seed size in B. napus. This study explored the mechanism of TDZ treatment on the seed size of B. napus and provided an important reference for improving rapeseed yield.
PMID: 36147221
Front Plant Sci , IF:5.753 , 2022 , V13 : P980138 doi: 10.3389/fpls.2022.980138
Auxin and cytokinin control fate determination of cotyledons in the one-leaf plant Monophyllaea glabra.
Graduate School of Science, The University of Tokyo, Tokyo, Japan.
One-leaf plants in the Gesneriaceae family initially have two cotyledons of identical size; one cotyledon stops growing shortly after germination, whereas the other continues indeterminate growth. Factors involved in the unequal growth have been investigated, and a competitive relationship between the two cotyledons was previously proposed. However, questions regarding the fate determination of the two cotyledons remain: Why does only one cotyledon grow indeterminately while the other stops; is the fate of the cotyledons reversible; and what role does light quality play in the fate determination of the cotyledons? In this study, physiological experiments using the one-leaf plant species Monophyllaea glabra suggest that a biased auxin concentration between the two cotyledons and subsequent cytokinin levels may determine the fate of the cotyledons. In addition, observation of relatively mature individuals without hormone treatment and younger individuals with cytokinin treatment under laboratory growth conditions revealed that the fate determination of the microcotyledon is reversible. Although light quality has been suggested to be important for the determination of cotyledon fate in Streptocarpus rexii, an anisocotylous species, we conclude that light quality is not important in M. glabra.
PMID: 36119619
Theor Appl Genet , IF:5.699 , 2022 Oct doi: 10.1007/s00122-022-04231-8
BSAseq 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.
KEY MESSAGE: 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
Theor Appl Genet , IF:5.699 , 2022 Oct , V135 (10) : P3611-3628 doi: 10.1007/s00122-022-04205-w
Genetic dissection of morphological variation in rosette leaves and leafy heads in cabbage (Brassica oleracea var. capitata).
Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands.; Centre for Crop Systems Analysis, Wageningen University and Research, PO Box 430, 6700 AK, Wageningen, The Netherlands.; Biometris, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands.; Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, The Netherlands. guusje.bonnema@wur.nl.
KEY MESSAGE: Correlations between morphological traits of cabbage rosette leaves and heads were found. Genome-wide association studies of these traits identified 50 robust quantitative trait loci in multiple years. Half of these loci affect both organs. Cabbage (Brassica oleracea var. capitata) is an economically important vegetable crop cultivated worldwide. Cabbage plants go through four vegetative stages: seedling, rosette, folding and heading. Rosette leaves are the largest leaves of cabbage plants and provide most of the energy needed to produce the leafy head. To understand the relationship and the genetic basis of leaf development and leafy head formation, 308 cabbage accessions were scored for rosette leaf and head traits in three-year field trials. Significant correlations were found between morphological traits of rosette leaves and heads, namely leaf area with the head area, height and width, and leaf width with the head area and head height, when heads were harvested at a fixed number of days after sowing. Fifty robust quantitative trait loci (QTLs) for rosette leaf and head traits distributed over all nine chromosomes were identified with genome-wide association studies. All these 50 loci were identified in multiple years and generally affect multiple traits. Twenty-five of the QTL were associated with both rosette leaf and leafy head traits. We discuss thirteen candidate genes identified in these QTL that are expressed in heading leaves, with an annotation related to auxin and other phytohormones, leaf development, and leaf polarity that likely play a role in leafy head development or rosette leaf expansion.
PMID: 36057748
Theor Appl Genet , IF:5.699 , 2022 Oct , V135 (10) : P3497-3510 doi: 10.1007/s00122-022-04196-8
Integrated genetic mapping and transcriptome analysis reveal the BnaA03.IAA7 protein regulates plant architecture and gibberellin signaling in Brassica napus L.
College of Agronomy and Biotechnology, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, 400715, China.; Biotechnology Research Center, Southwest University, Chongqing, 400715, China.; State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430070, China.; College of Agronomy and Biotechnology, Academy of Agricultural Sciences, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Southwest University, Chongqing, 400715, China. liezhao@swu.edu.cn.
KEY MESSAGE: A novel mutation in the BnaA03.IAA7 protein reduces plant height and enhances gibberellin signaling in Brassica napus L. Rapeseed (Brassica napus) is an excellent and important source for vegetable oil production, but its production is severely affected by lodging. Lodging hinders mechanization and decreases yield, and an ideal solution is semidwarf breeding. Limited by germplasm resources, semidwarf breeding developed slowly in rapeseed. In the current study, a mutant called sdA03 was isolated from EMS-mutagenized lines of Zhongshuang 11 (ZS11). The inheritance analysis showed that phenotypes of sdA03 were controlled by a single semidominant gene. Genetic mapping, RNA-seq and candidate gene analysis identified BnaA03.IAA7 as a candidate gene, and a function test confirmed that the mutated BnaA03.iaa7 regulates plant architecture in a dose-dependent manner. Yeast two-hybrid and transient expression experiments illustrated the P87L substitution in the GWPPV/I degron motif of BnaA03.iaa7 impaired the interaction between BnaA03.IAA7 and TIR1 proteins, and BnaA03.iaa7 prevented ARF from activating the auxin signaling pathway.The gibberellin (GA) content was higher in sdA03 hypocotyls than in those of ZS11. Further expression analysis showed more active gibberellin signaling in hypocotyl and richer expression of GA synthetic genes in root and cotyledon of sdA03 seedlings. Finally, a marker was developed based on the SNP found in BnaA03.iaa7 and used in molecular breeding. The study enriched our understanding of the architectural regulation of rapeseed and provided germplasm resources for breeding.
PMID: 35962210
Front Microbiol , IF:5.64 , 2022 , V13 : P956018 doi: 10.3389/fmicb.2022.956018
The immunity priming effect of the Arabidopsis phyllosphere resident yeast Protomyces arabidopsidicola strain C29.
Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.
The phyllosphere is a complex habitat for diverse microbial communities. Under natural conditions, multiple interactions occur between host plants and phyllosphere resident microbes, such as bacteria, oomycetes, and fungi. Our understanding of plant associated yeasts and yeast-like fungi lags behind other classes of plant-associated microbes, largely due to a lack of yeasts associated with the model plant Arabidopsis, which could be used in experimental model systems. The yeast-like fungal species Protomyces arabidopsidicola was previously isolated from the phyllosphere of healthy wild-growing Arabidopsis, identified, and characterized. Here we explore the interaction of P. arabidopsidicola with Arabidopsis and found P. arabidopsidicola strain C29 was not pathogenic on Arabidopsis, but was able to survive in its phyllosphere environment both in controlled environment chambers in the lab and under natural field conditions. Most importantly, P. arabidopsidicola exhibited an immune priming effect on Arabidopsis, which showed enhanced disease resistance when subsequently infected with the fungal pathogen Botrytis cinerea. Activation of the mitogen-activated protein kinases (MAPK), camalexin, salicylic acid, and jasmonic acid signaling pathways, but not the auxin-signaling pathway, was associated with this priming effect, as evidenced by MAPK3/MAPK6 activation and defense marker expression. These findings demonstrate Arabidopsis immune defense priming by the naturally occurring phyllosphere resident yeast species, P. arabidopsidicola, and contribute to establishing a new interaction system for probing the genetics of Arabidopsis immunity induced by resident yeast-like fungi.
PMID: 36118213
FEBS J , IF:5.542 , 2022 Oct , V289 (20) : P6172-6186 doi: 10.1111/febs.16132
Meet your MAKR: the membrane-associated kinase regulator protein family in the regulation of plant development.
Department of Plant Molecular Biology, Biophore Building, University of Lausanne, Lausanne, Switzerland.; Institute of Cytology and Genetics, Novosibirsk, Russian Federation.; Novosibirsk State University, Novosibirsk, Russian Federation.; Department of Plant Systems Physiology, Institute for Water and Wetland Research, Faculty of Science, Radboud University, Nijmegen, The Netherlands.; Laboratoire Reproduction et Developpement des Plantes, CNRS, INRAE, Universite de Lyon, Ecole normale superieure de Lyon, Universite Claude Bernard Lyon 1, Lyon, France.
A small family composed of BRI1 KINASE INHIBITOR1 (BKI1) and MEMBRANE-ASSOCIATED KINASE REGULATORS (MAKRs) has recently captured the attention of plant biologists, due to their involvement in developmental processes downstream of hormones and Receptor-Like Kinases (RLK) signalling. BKI1/MAKRs are intrinsically disordered proteins (so-called unstructured proteins) and as such lack specific domains. Instead, they are defined by the presence of two conserved linear motifs involved in the interaction with lipids and proteins, respectively. Here, we first relate the discovery of the MAKR gene family. Then, we review the individual function of characterized family members and discuss their shared and specific modes of action. Finally, we explore and summarize the structural, comparative and functional genomics data available on this gene family. Together, this review aims at building a comprehensive reference about BKI1/MAKR protein function in plants.
PMID: 34288456
iScience , IF:5.458 , 2022 Oct , V25 (10) : P105062 doi: 10.1016/j.isci.2022.105062
PIN-FORMED1 polarity in the plant shoot epidermis is insensitive to the polarity of neighboring cells.
School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.; European Molecular Biology Laboratory, Heidelberg 69117, Germany.
At the Arabidopsis shoot apex, epidermal cells are planar-polarized along an axis marked by the asymmetric localization patterns of several proteins including PIN-FORMED1 (PIN1), which facilitates the directional efflux of the plant hormone auxin to pattern phyllotaxis. While PIN1 polarity is known to be regulated non-cell autonomously via the MONOPTEROS (MP) transcription factor, how this occurs has not been determined. Here, we use mosaic expression of the serine threonine kinase PINOID (PID) to test whether PIN1 polarizes according to the polarity of neighboring cells. Our findings reveal that PIN1 is insensitive to the polarity of PIN1 in neighboring cells arguing against auxin flux or extracellular auxin concentrations acting as a polarity cue, in contrast to previous model proposals.
PMID: 36157591
J Cell Sci , IF:5.285 , 2022 Oct , V135 (19) doi: 10.1242/jcs.260127
Defects in division plane positioning in the root meristematic zone affect cell organization in the differentiation zone.
Graduate Group in Biochemistry and Molecular Biology.; Department of Botany and Plant Sciences, Center for Plant Cell Biology, Institute of Integrative Genome Biology, University of California, Riverside, CA 92521, USA.
Cell-division-plane orientation is critical for plant and animal development and growth. TANGLED1 (TAN1) and AUXIN-INDUCED IN ROOT CULTURES 9 (AIR9) are division-site-localized microtubule-binding proteins required for division-plane positioning. The single mutants tan1 and air9 of Arabidopsis thaliana have minor or no noticeable phenotypes, but the tan1 air9 double mutant has synthetic phenotypes including stunted growth, misoriented divisions and aberrant cell-file rotation in the root differentiation zone. These data suggest that TAN1 plays a role in non-dividing cells. To determine whether TAN1 is required in elongating and differentiating cells in the tan1 air9 double mutant, we limited its expression to actively dividing cells using the G2/M-specific promoter of the syntaxin KNOLLE (pKN:TAN1-YFP). Unexpectedly, in addition to rescuing division-plane defects, expression of pKN:TAN1-YFP rescued root growth and cell file rotation defects in the root-differentiation zone in tan1 air9 double mutants. This suggests that defects that occur in the meristematic zone later affect the organization of elongating and differentiating cells.
PMID: 36074053
Plant Cell Physiol , IF:4.927 , 2022 Oct doi: 10.1093/pcp/pcac153
High Expression of ALTERNATIVE OXIDASE 2 in Latent Axillary Buds Suggests Its Key Role in Quiescence Maintenance in Rosebush.
University of Angers, Institut Agro Rennes-Angers, INRAE, IRHS, SFR QUASAV, Angers F-49000, France.
Most vegetative axes remain quiescent as dormant axillary buds until metabolic and hormonal signals, driven by environmental changes, trigger bud outgrowth. While the resumption of growth activity is well documented, the establishment and maintenance of quiescence is comparatively poorly understood, despite its major importance in the adaptation of plants to the seasonal cycle or in the establishment of their shape. Here, using the rosebush Rosa hybrida 'Radrazz' as plant model, we highlighted that the quiescent state was the consequence of an internal and active energy control of buds, under the influence of hormonal factors previously identified in the bud outgrowth process. We found that the quiescent state in the non-growing vegetative axis of dormant axillary buds displayed a low energy state along with a high expression of the ALTERNATIVE OXIDASE 2 (AOX2) and the accumulation of the corresponding protein. Conversely, AOX2 expression and protein amount strongly decreased during bud burst as energy status shifted to a high state, allowing growth. Since AOX2 can deviate electrons from the cytochrome pathway in the mitochondrial respiratory chain, it could drastically reduce the formation of ATP, which would result in a low energy status unfavorable for growth activities. We provided evidence that the presence/absence of AOX2 in quiescent/growing vegetative axes of buds was under hormonal control, and thus may constitute the mechanistic basis of both quiescence and sink strength manifestation, two important aspects of bud-break.
PMID: 36287074
Plant Cell Physiol , IF:4.927 , 2022 Oct 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, 211004 UP, India.; Department of Biology, Saint Joseph's University, University City Campus, 600 S. 43rd St., Philadelphia, PA 19104, USA.; Department of Biochemistry and Cell and Molecular Biology of 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, 18008, Granada, 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. 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 process. The expression analysis of genes involved in GSH biosynthesis (OsGS2) and regeneration (OsGR1); and auxin biosynthesis (OsTAA1 and OsYUCCA1) and transport (OsAUX1 andOsPIN1) 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 a 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, and redox homeostasis of GSH, 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 suggests Si as 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 , 2022 Oct doi: 10.1093/pcp/pcac146
Auxin-induced WUSCHEL-RELATED HOMEOBOX13 Mediates Asymmetric Activity of Callus Formation upon Cutting.
Department of Biology, Faculty of Science, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-ku, Niigata, Japan.; Advanced Instrumental Analysis Center, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan.; Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya, Tochigi 320-8551, Japan.; Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama-cho, Ikoma, Nara 630-0192, Japan.; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka, Yokohama 244-0813, Japan.; RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.; Department of Biological Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 119-0033, Japan.
Plants have the regenerative ability to reconnect cut organs, which is physiologically important to survive severe tissue damage. The ability to reconnect organs is utilized as grafting to combine two different individuals. Callus formation at the graft junction facilitates organ attachment and vascular reconnection. While it is well documented that local wounding signals provoke callus formation, how callus formation is differentially regulated at each cut end remains elusive. Here, we report that callus formation activity is asymmetrical between the top and bottom cut ends, and is regulated by differential auxin accumulation. Gene expression analyses revealed that cellular auxin response is preferentially up-regulated in the top part of the graft. Disruption of polar auxin transport inhibited callus formation from the top while external application of auxin was sufficient to induce callus formation from the bottom, suggesting that asymmetric auxin accumulation is responsible for active callus formation from the top end. We further found that the expression of a key regulator of callus formation, WUSCHEL-RELATED HOMEOBOX 13 (WOX13) is induced by auxin. The ectopic callus formation from the bottom end, which is triggered by locally supplemented auxin, requires WOX13 function, demonstrating that WOX13 plays a pivotal role in auxin-dependent callus formation. The asymmetric WOX13 expression is observed both in grafted petioles and incised inflorescence stems, underscoring the generality of our findings. We propose that efficient organ reconnection is achieved by a combination of local wounding stimuli and disrupted long-distance signaling.
PMID: 36263676
Plant Cell Physiol , IF:4.927 , 2022 Oct 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, Pohang, 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, Vietnam.; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, 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 crosstalk 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 crosstalk among multiple phytohormones to determine the yield traits.
PMID: 36255097
Plant Cell Physiol , IF:4.927 , 2022 Oct doi: 10.1093/pcp/pcac142
Loss of MYB34 transcription factor supports backward evolution of indole glucosinolate biosynthesis in a subclade of Camelineae tribe and releases feedback loop in this pathway in Arabidopsis.
Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.; Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland.; Department of General Botany, Institute of Experimental Biology, Adam Mickiewicz University, 61-614 Poznan, Poland.
Glucosinolates are specialized defensive metabolites characteristic for the Brassicales order. Among them aliphatic and indolic glucosinolates (IGs) are usually highly abundant in the species from Brassicaceae family. The exception from this trend is constituted by species representing a subclade of Camelineae tribe, including Capsella and Camelina genera, which have reduced capacity to produce and metabolize IGs. Our study addresses contribution of specific glucosinolate-related MYB transcription factors to this unprecedented backward evolution of IG biosynthesis. To this end we performed phylogenomic and functional studies of respective MYB proteins. Obtained results revealed weakened conservation of glucosinolate-related MYB transcription factors, including loss of functional MYB34 protein, in the investigated species. We showed that introduction of functional MYB34 from Arabidopsis thaliana partially restores IG biosynthesis in Capsella rubella indicating that loss of this transcription factor contributes to the backward evolution of this metabolic pathway. Finally, we performed analysis of the impact of particular myb mutations on the feedback loop in IG biosynthesis, which drives auxin overproduction, metabolic dysregulation and strong growth retardation caused by mutations in IG biosynthetic genes. This uncovered unique function of MYB34 among IG-related MYBs in this feedback regulation and consequently in IG conservation in Brassicaceae plants.
PMID: 36222356
Plant Cell Physiol , IF:4.927 , 2022 Oct doi: 10.1093/pcp/pcac138
Auxin crosstalk with reactive oxygen and nitrogen species in plant development and abiotic stress.
D D Pant Interdisciplinary Research Laboratory, Department of Botany, University of Allahabad, India.; Crop Nanobiology and Molecular Stress Physiology Lab,Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, Sector-125, Noida-201313.; Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India.; Plant Physiology Laboratory, Department of Botany, CMP, Degree Collage, University of Allahabad, India.; Institute of Botany, Technische Universitat Dresden, 01062 Dresden, Germany.; Department of Biochemistry, Cell and Molecular Biology, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas (CSIC), C/Professor Albareda, 1, 18008, Granada, 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, cell structures and lead to cell death, 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 favourable roles in plants. NO displays its positive role in photo-morphogenesis, 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 , 2022 Sep doi: 10.1093/pcp/pcac126
The 5'-3' mRNA Decay Pathway Modulates The Plant Circadian Network In Arabidopsis.
Fundacion Instituto Leloir, Instituto de Investigaciones Bioquimicas de Buenos Aires-Consejo Nacional de Investigaciones Cientificas y Tecnicas (CONICET), Buenos Aires, C1405BWE, Argentina.; Department of Biochemistry, University of Otago, Dunedin, 9016, New Zealand.
Circadian rhythms enable organisms to anticipate and adjust their physiology to periodic environmental changes. These rhythms are controlled by biological clocks that consist of a set of clock genes that regulate each other's expression. Circadian oscillations in mRNA levels require regulation of mRNA production and degradation. While transcription factors controlling clock function have been well characterised from cyanobacteria to humans, the role of factors controlling mRNA decay is largely unknown. Here, we show that mutations in LSM1 and XRN4, components of the 5'-3' mRNA decay pathway, alter clock function in Arabidopsis. We found that lsm1 and xrn4 mutants display long-period phenotypes for clock gene expression. In xrn4, these circadian defects were associated with changes in circadian phases of expression, but not overall mRNA levels, of several core clock genes. We then used non-invasive transcriptome-wide mRNA stability analysis to identify genes and pathways regulated by XRN4. Among genes affected in the xrn4 mutant at the transcriptional and post-transcriptional level, we found an enrichment in genes involved in auxin, ethylene, and drought recovery. Large effects were not observed for canonical core-clock genes, although the mRNAs of several auxiliary clock genes that control the pace of the clock, were stabilised in xrn4 mutants. Our results establish that the 5'-3' mRNA decay pathway constitutes a novel post-transcriptional regulatory layer of the circadian gene network, which probably acts through a combination of small effects on mRNA stability of several auxiliary and some core clock genes.
PMID: 36066193
Plant Cell Physiol , IF:4.927 , 2022 Sep , V63 (9) : P1309-1320 doi: 10.1093/pcp/pcac104
OsAMT1;1 and OsAMT1;2 Coordinate Root Morphological and Physiological Responses to Ammonium for Efficient Nitrogen Foraging in Rice.
Key Laboratory of Plant-Soil Interactions, MOE, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China.; State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, No. 866 Yuhangtang Road, Xihu District, Hangzhou City, Zhejiang Province 310058, China.
Optimal plant growth and development rely on morphological and physiological adaptions of the root system to forage heterogeneously distributed nitrogen (N) in soils. Rice grows mainly in the paddy soil where ammonium (NH4+) is present as the major N source. Although root NH4+ foraging behaviors are expected to be agronomically relevant, the underlying mechanism remains largely unknown. Here, we showed that NH4+ supply transiently enhanced the high-affinity NH4+ uptake and stimulated lateral root (LR) branching and elongation. These synergistic physiological and morphological responses were closely related to NH4+-induced expression of NH4+ transporters OsAMT1;1 and OsAMT1;2 in roots. The two independent double mutants (dko) defective in OsAMT1;1 and OsAMT1;2 failed to induce NH4+ uptake and stimulate LR formation, suggesting that OsAMT1s conferred the substrate-dependent root NH4+ foraging. In dko plants, NH4+ was unable to activate the expression of OsPIN2, and the OsPIN2 mutant (lra1) exhibited a strong reduction in NH4+-triggered LR branching, suggesting that the auxin pathway was likely involved in OsAMT1s-dependent LR branching. Importantly, OsAMT1s-dependent root NH4+ foraging behaviors facilitated rice growth and N acquisition under fluctuating NH4+ supply. These results revealed an essential role of OsAMT1s in synergizing root morphological and physiological processes, allowing for efficient root NH4+ foraging to optimize N capture under fluctuating N availabilities.
PMID: 35861152
Appl Microbiol Biotechnol , IF:4.813 , 2022 Nov , V106 (21) : P7027-7037 doi: 10.1007/s00253-022-12194-5
In vitro production of atractylon and beta-eudesmol from Atractylodes chinensis by adventitious root culture.
Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China.; College of Forest Science, Kim Il Sung University, Pyongyang, 999093, Democratic People's Republic of Korea.; College of Life Science, Kim Il Sung University, Pyongyang, 999093, Democratic People's Republic of Korea.; Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China. wjwang225@hotmail.com.; Key Laboratory of Forest Plant Ecology, Ministry of Education, Heilongjiang Provincial Key Laboratory of Ecological Utilization of Forestry-Based Active Substances, College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin, 150040, China. whm0709@163.com.
Atractylodes chinensis is a medicinal plant widely used for the treatment of gastric disorders, and its main bioactive compounds are atractylon and beta-eudesmol. This study was purposed to establish the adventitious root culture system of A. chinensis for in vitro production of atractylon and beta-eudesmol. The main parameters in the adventitious root induction and suspension cultures were optimized to maximize the culture efficiency. Adventitious roots were induced most efficiently from leaf explants on Murashige and Skoog (MS) solid medium containing 1.5 mg/L naphthaleneacetic acid (NAA) and 30 g/L sucrose with the highest root induction rate of approximately 92% and 12.9 roots per explant. During the adventitious root suspension culture, the root biomass and the accumulated content of the target compounds simultaneously increased to reach the maximum values after 8 weeks of culture. The maximum yield of the target compounds (total concentration 3.38 mg/g DW, total yield 2.66 mg) was achieved in the roots cultured in (1/2) MS liquid medium supplemented with 2.0 mg/L IBA, 3.2 mg/L NAA, and 40 g/L sucrose with the inoculum density of 8 g/L. Through the central composite design experiment, it was found that the combined use of different types of auxins in the suspension culture could further improve root growth and metabolite accumulation than the application of only one type of auxin. This work provides a new possibility to have a promising candidate for the industrial production of A. chinensis pharmaceuticals without relying on wild resources or field cultivation. KEY POINTS: * The induction culture was optimized for efficient root induction. * Suspension culture was optimized for the atractylon and beta-eudesmol production. * Combined use of different auxins improves root growth and metabolite accumulation.
PMID: 36171502
Appl Environ Microbiol , IF:4.792 , 2022 Sep , V88 (18) : Pe0088222 doi: 10.1128/aem.00882-22
Elucidating the Effect of Endophytic Entomopathogenic Fungi on Bread Wheat Growth through Signaling of Immune Response-Related Hormones.
Department of Agronomy, ETSIAM, University of Cordoba, Cordoba, Spain.; Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, Spain.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; Center of Plant Systems Biology, VIB, Ghent, Belgium.
Entomopathogenic fungi (EF) provide a potent biocontrol tool; also, their endophytic behavior has broadened their contribution to integrated pest management (IPM) and crop production. In this work, Beauveria bassiana and Metarhizium brunneum were applied to bread wheat (Triticum aestivum) seedlings to elucidate how fungal colonization influences plant growth and the relative expression of 24 genes involved in hormonal syntheses and plant immune mechanisms. A preliminary assay was used to determine the time needed for fungal colonization and assess its effect on wheat growth. Then, plant material collected at various times after inoculation (viz., 2, 8, 20, and 36 h and 9 and 15 days) was used to investigate gene expression by quantitative reverse transcription PCR (RT-qPCR). During the colonization time, B. bassiana and M. brunneum caused strong downregulation of most genes associated with plant immunity and the synthesis of hormones like auxin, cytokinin, and gibberellin. This effect was concomitant with a slowdown of endophytic-colonization-related plant growth until 19 days postinoculation (dpi). However, the wheat started to recover at 15 dpi, simultaneously with upregulation of auxin- and gibberellin-related genes. The results suggest that the EF trigger induced systemic resistance rather than acquired systemic resistance during early plant-microbe cross talk in wheat. Also, they confirm that the hormone and immune responses of wheat triggered by EF inoculation influenced plant growth, which can be useful with a view to optimizing management of these microorganisms for sustainable agriculture. IMPORTANCE Microbial control of insect and mite pests is a key tool to develop integrated pest management (IPM) and sustainable agriculture. Entomopathogenic fungi (EF) may have associations with the plants, playing additional ecological roles in the rhizosphere, in the phylloplane, and as plant endophytes. Beauveria bassiana 04/01TIP and Metarhizium brunneum 01/58Su are two strains that showed very good results either in pest control or plant growth promotion and would be good candidates to develop mycoinsecticides as an alternative to pesticides. However, deep knowledge about their interaction with the plant would let farmers optimize their use and understand the plant response, enhancing and promoting their broader contribution to IPM and crop production.
PMID: 36036583
J Chromatogr A , IF:4.759 , 2022 Oct , V1682 : P463497 doi: 10.1016/j.chroma.2022.463497
Quantification of six types of cytokinins: Integration of an ultra-performance liquid chromatographic-electrospray tandem mass spectrometric method with antibody based immunoaffinity columns equally recognizing cytokinins in free base and nucleoside forms.
College of Agronomy, China Agricultural University, Beijing 100193, People's Republic of China.; Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo 315211, People's Republic of China.; College of Agronomy, China Agricultural University, Beijing 100193, People's Republic of China. Electronic address: yangxiaolin429@cau.edu.cn.; College of Agronomy, China Agricultural University, Beijing 100193, People's Republic of China. Electronic address: wbaomin@263.net.
Cytokinins (CTKs) exist in various types in plants. The accurate quantification of free base and nucleoside types of cytokinins are helpful for better understanding their physiological role. In the present study, antibodies against trans-zeatin riboside (tZR) and N(6)-isopentenyladenine riboside (iPR) antibodies with equal recognition to free base and nucleoside cytokinins were developed. The cross-reactivity of tZR mAb 3G101G7 with tZR, trans-zeatin (tZ), dihydrozeatin riboside (DHZR), dihydrozeatin (DHZ), iPR, and N(6)-isopentenyladenine (iP) was 100.0%, 95.7%, 19.1%, 18.0%, 1.1%, and 0.7%, and that of iPR mAb 5C82F1 with above-mentioned 6 types of cytokinins was 1.5%, 1.4%, 5.7%, 3.1%, 100.0% and 92.6%, respectively. The obtained antibodies were used to prepare two immunoaffinity columns (IAC). The elution efficiencies of tZR 3G101G7-IAC for tZ and tZR, DHZ and DHZR and of iPR 5C82F1-IAC for iP and iPR were almost no difference with the same loading amount on their corresponding IACs. Subsequently, six types of cytokinins in mepiquat chloride (MC)-treated cotton (Gossypium hirsutum L.) roots were determined by IACs combined with ultra-performance liquid chromatography-electrospray tandem mass spectrometry (UPLC-ESI-MS/MS). The contents of tZR, iPR and DHZR were increased by 9.3 approximately 38.5%, 6.6 approximately 23.5%, and 30.1 approximately 110.0%, respectively, whereas those of tZ and iP were reduced by 5.3 approximately 20.0% and 27.7 approximately 32.1%, respectively. The decreased tZ and iP levels led to the ratio of auxin-to-active cytokinins increase to promote lateral root initiation in MC-treated cotton seeding. Integration of the IACs equally recognizing cytokinins in their free base and nucleoside forms with UPLC-ESI-MS/MS can accurately quantify different cytokinins in plant tissues.
PMID: 36166882
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 (H2) supplied with hydrogen-rich water (HRW) can mediate lateral root (LR) development, whether or how endogenous H2 influences LR formation is still elusive. In this report, mimicking the induction responses in tomato seedlings achieved by HRW or exogenous hydrogen peroxide (H2O2; a positive control), transgenic Arabidopsis that overexpressed the hydrogenase1 gene (CrHYD1) from Chlamydomonas reinhardtii not only stimulated endogenous hydrogen peroxide (H2O2) production, but also markedly promoted LR formation. Above H2 and H2O2 responses were abolished by the removal of endogenous H2O2. 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 H2O2 synthesis was tightly linked to LR formation achieved by endogenous H2, 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 H2.
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 Sci , IF:4.729 , 2022 Oct , V323 : P111415 doi: 10.1016/j.plantsci.2022.111415
IbTLD modulates reactive oxygen species scavenging and DNA protection to confer salinity stress tolerance in tobacco.
Agricultural Biotechnology Research Center, Academia Sinica, Taipei 11529, Taiwan. Electronic address: tcch@ucdavis.edu.; Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan. Electronic address: abslwert@gmail.com.; Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan. Electronic address: r98b43022@gmail.com.; Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan. Electronic address: jslin@dragon.nchu.edu.tw.
Plants accumulate reactive oxygen species (ROS) that may damage the cells under prolonged stress conditions. Reduction of the excessive ROS production can alleviate oxidative damage and enhance the survival rates under stress. TLDc-containing protein (TLD) was reported to confer tolerance to oxidative stress, but the regulatory mechanism of TLD remains unclear. In this study, we ectopically overexpressed the Ipomoea batatas TLDc gene (IbTLD) in tobacco and characterized its functions. RNA-sequencing analysis and Gene Ontology term enrichment analysis revealed that IbTLD up-regulates auxin-responsive genes in response to oxidative stress. Under salinity stress, the IbTLD transgenic lines showed higher germination rates, chlorophyll contents, and root lengths than wild type (W38). In addition, the IbTLD transgenic lines showed higher expression of ROS scavenging genes, nudix hydrolases, ROS scavenging enzyme activity, and lesser DNA damage compared to W38 under salinity stress. Therefore, our results suggest that IbTLD activates the expression of ROS scavenging genes and confers tolerance to salinity stress in planta.
PMID: 35963494
Plant Sci , IF:4.729 , 2022 Oct , V323 : P111409 doi: 10.1016/j.plantsci.2022.111409
PpPIF8, a DELLA2-interacting protein, regulates peach shoot elongation possibly through auxin signaling.
College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China.; College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China. Electronic address: jcheng2007@163.com.; College of Horticulture, Henan Agricultural University, 95 Wenhua Road, Zhengzhou 450002, China. Electronic address: jcfeng@henau.edu.cn.
Rapid growth of branches in a peach tree restricts the light penetration and air ventilation within the orchard, which lowers fruit quality and promotes the occurrence of diseases and insects. Our previous works showed that PpDELLA1 and PpDELLA2 repress the rapid growth of annual shoots. Proteins that interact with DELLA are vital for its function. In this study, seven PpPIFs (PpPIF1, -2, -3, -4, -6, -7 and -8) were identified in the peach genome and contain a conserved bHLH domain. Among the seven PpPIFs, PpPIF8 interacted with PpDELLA2 through an unknown motif in the C-terminal and/or the bHLH domain. Overexpression of PpPIF8 in Arabidopsis promotes plant height and branch numbers. Hypocotyl elongation was significantly enhanced by PpPIF8 under weak light intensity. PpPIF8 overexpressed in Arabidopsis and transiently expressed in peach seedlings upregulated the transcription of YUCCA and SAUR19 and downregulated SHY1 and -2. Additionally, PpPIF4 and -8 were significantly induced by weak light. Phylogentic analysis and intron patterns of the bHLH domain strongly suggested that PIFs from six species could be divided into two groups of different evolutionary origins. These results lay a foundation for the further study of the repression of shoot growth by PpDELLA2 through protein interaction with PpPIF8 in peach.
PMID: 35934255
Plant Sci , IF:4.729 , 2022 Oct , V323 : P111408 doi: 10.1016/j.plantsci.2022.111408
Overexpression of a SHORT-ROOT transcriptional factor enhances the auxin mediated formation of adventitious roots and lateral roots in poplar trees.
School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Nankai District, Tianjin 300072, China.. Electronic address: 2441909790@qq.com.; School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Nankai District, Tianjin 300072, China.. Electronic address: 1501661988@qq.com.; School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Nankai District, Tianjin 300072, China.. Electronic address: 18700944808@163.com.; School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Nankai District, Tianjin 300072, China.. Electronic address: shaohuiyang77@tju.edu.cn.; School of Environmental Science and Engineering, Tianjin University, Weijin Rd. 92, Nankai District, Tianjin 300072, China.. Electronic address: jiehuawang@tju.edu.cn.
SHORT-ROOT (SHR) defines root stem cells and maintains radial patterning, but its involvement in adventitious root (AR) formation has not been reported. In this study, we showed that PtSHR2 was transcriptionally upregulated by excision before the formation of AR and responded dynamically to auxin. PtSHR2 overexpression (SHR2B(OE)) in hybrid poplars resulted in an increased number of ARs with an initial delay. Despite a lower endogenous content in the stems than in wild-type plants, indole-3-acetic acid (IAA) content at the SHR2B(OE) basal stem increased rapidly after cutting and reached a higher maximum than in wild-type plants, which was accompanied by a more sustained and stronger induction of AR formation marker genes. In addition, the higher auxin content in SHR2B(OE) ARs resulted in more and longer lateral roots (LRs). Application of auxin abolished the early delay in the formation of AR and largely other AR phenotypes of SHR2B(OE) plants, whereas the polar auxin transport inhibitor N-1-naphthylphthalamic acid completely inhibited both AR and LR abnormalities. Since the enhanced rooting ability of SHR2B(OE) stem cuttings in hydroponics was clearly confirmed, our results suggest a novel role of poplar SHR2 as a positive regulator during the organogenesis of AR and LR by affecting local auxin homeostasis.
PMID: 35932828
Plant Sci , IF:4.729 , 2022 Oct , V323 : P111401 doi: 10.1016/j.plantsci.2022.111401
The Citrus sinensis TILLER ANGLE CONTROL 1 (CsTAC1) gene regulates tree architecture in sweet oranges by modulating the endogenous hormone content.
Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA. Electronic address: manjul@ufl.edu.; Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Pomology Department, Faculty of Agriculture, Mansoura University, Mansoura 35516, Egypt.; Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31512, Egypt.; Citrus Research and Education Center, IFAS, University of Florida, Lake Alfred, FL 33850, USA.
Citrus is a major fruit crop cultivated on a global scale. Citrus trees are long lived perennials with a large canopy. Understanding the genetic control of tree architecture could provide tools for breeding and selection of citrus cultivars suitable for high density planting with improved light exposure. Tree architecture is modulated by the TILLER ANGLE CONTROL 1 (TAC1) gene which plays an important role in the regulation of the shoot angle. Herein, we used CRISPR/Cas9 technology to knockout the CsTAC1 gene for the biochemical and molecular analysis of its function. Nine transgenic lines were obtained, and five edited plants were confirmed based on T7EI mismatch detection assay and Sanger sequencing. The transgenic citrus lines exhibited pleiotropic phenotypes, including differences in branch angle and stem growth. Additionally, silencing CsTAC1 led to enhanced CsLAZY1 transcript levels in the tested lines. Analysis of the phytohormonal profile revealed that TAC1-edited plants exhibited lower auxin contents and increased cytokinin levels in the leaves compared to the wild-type plants. The GA7 gibberellin level was enhanced in most of the edited lines. Collectively, TAC1 affects branch angle in association with hormone signals in citrus.
PMID: 35905898
Front Genet , IF:4.599 , 2022 , V13 : P1001195 doi: 10.3389/fgene.2022.1001195
Integration of transcriptome and metabolome analyses reveals key lodging-resistance-related genes and metabolic pathways in maize.
Hebei Key Laboratory of Quality and Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China.; School of Medicine, Nankai University, Tianjin, China.
Stalk lodging, or breakage of the stalk at or below the ear, is one of the vital factors causing substantial yield losses in maize (Zea mays. L). Lodging affects maize plants' physiological and molecular processes, eventually impacting plant growth and productivity. Despite this known fact, few researchers have investigated the genetic architecture underlying lodging in maize. Herein, through integrated transcriptome, metabolome, and phenotypic analyses of stalks of three diverse hybrid cultivars (highly resistant JNK738, mildly resistant JNK728, and lowly resistant XY335) at the tasseling (10 days to silking, 10 DTS) stage, we identified key genes and metabolic pathways modulating lodging resistance in maize. Based on the RNA-Seq analysis, a total of 10093 differentially expressed genes (DEGs) were identified from the comparison of the three varieties in pairs. Additionally, key lodging resistance-related metabolic pathways were obtained by KEGG enrichment analysis, and the DEGs were found predominantly enriched in phenylpropanoid and secondary metabolites biosynthesis pathways in the L_vs._H and M_vs._H comparison groups. Moreover, K-means analysis clustered the DEGs into clear and distinct expression profiles for each cultivar, with several functional and regulatory genes involved in the cell wall assembly, lignin biosynthetic process and hormone metabolic process being identified in the special clusters related to lodging resistance. Subsequently, integrating metabolome and transcriptome analyses revealed nine key lignin-associated metabolites that showed different expression trends in the three hybrid cultivars, among which L-phenylalanine and p-coumaric acid were regarded as differentially changed metabolites (DCMs). These two DCMs belonged to phenylalanine metabolism and biosynthesis pathways and were also supported by the RNA-Seq data. Furthermore, plant hormone signal transduction pathway-related genes encoding auxin, abscisic acid, jasmonates, and salicylic acid were differentially expressed in the three comparisons of lodging resistance, indicating these DEGs were valuable potential targets for improving maize lodging resistance. Finally, comparative physiological and qRT-PCR analyses results supported our transcriptome-based findings. Our research not only provides a preliminary theoretical basis and experimental ideas for an in-depth study of the regulatory networks involved in maize lodging resistance regulation but also opens up new avenues for molecular maize stalk lodging resistance breeding.
PMID: 36299597
Plant Cell Rep , IF:4.57 , 2022 Oct 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.
KEY MESSAGE: 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 Oct 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.
KEY MESSAGE: 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 Oct , V41 (10) : P2089-2105 doi: 10.1007/s00299-022-02908-4
The strigolactone receptor SlDWARF14 plays a role in photosynthetic pigment accumulation and photosynthesis in tomato.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.; Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China.; Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA.; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. wuhan@njau.edu.cn.
KEY MESSAGE: Tomato DWARF14 regulates the development of roots, shoot branches and leaves, and also plays a role in photosynthetic pigment accumulation and photosynthetic capacity. Strigolactones (SLs) are a novel class of plant hormones. DWARF14 (D14) is the only SL receptor identified to date, but it is not functionally analyzed in tomato (Solanum lycopersicum). In the present study, we identified the potential SL receptor in tomato by bioinformatic analysis, which was designated as SlD14. SlD14 was expressed in roots, stems, flowers and developing fruits, with the highest expression level in leaves. sld14 mutant plants produced by the CRISPR/Cas9 system displayed reduced plant height and root biomass, increased shoot branching and altered leaf shape comparing with WT plants. The cytokinin biosynthetic gene ISOPENTENYLTRANSFERASE 3 (SlIPT3), auxin biosynthetic genes FLOOZY (SlFZY) and TRYPTOPHAN AMINOTRANSFERASE RELATED 1 (SlTAR1) and several auxin transport genes SlPINs, which are involved in branch formation, showed higher expression levels in the sld14 plant stem. In addition, sld14 plants exhibited light-green leaves, reduced chlorophyll and carotenoid contents, abnormal chloroplast structure and reduced photosynthetic capacity. Transcriptomic analysis showed that the transcript levels of six chlorophyll biosynthetic genes, three carotenoid biosynthetic genes and numerous chlorophyll a/b-binding protein genes were decreased in sld14 plants. These results suggest that tomato SL receptor gene SlD14 not only regulates the development of roots, shoot branches and leaves, but also plays a role in regulating photosynthetic pigment accumulation and photosynthetic capacity.
PMID: 35907035
Physiol Plant , IF:4.5 , 2022 Oct : Pe13805 doi: 10.1111/ppl.13805
Transcriptome analysis of perennial ryegrass reveals the regulatory role of Aspergillus aculeatus under salt stress.
Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, Shandong, P.R. China.; CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, China.
Perennial ryegrass (Lolium perenne) is an important turf grass and forage grass with moderately tolerant to salinity stress. A. aculeatus has been documented to involved in salt stress response of perennial ryegrass, while the A. aculeatus-mediated molecular mechanisms are unclear. Therefore, to investigate the molecular mechanisms underlying A. aculeatus-mediated salt tolerance, the comprehensive transcriptome analysis of the perennial ryegrass roots was performed. Twelve cDNA libraries from roots were constructed after 12 h of plant-fungus cocultivation under 300 mM salt stress concentrations. A total of 21,915 differentially expressed genes (DEGs) were identified through pairwise comparisons. Enrichment analysis revealed that potentially important A. aculeatus-induced salt responsive genes belonging to specific categories, such as hormonal metabolism (auxin and salicylic acid metabolism related genes), secondary metabolism (flavonoid's metabolism related genes) and transcription factors (MYB, HSF and AP2/EREBP family). In addition, weighted gene co-expression network analysis (WGCNA) showed that blue and black modules were significantly positively correlated with the peroxidase activity and proline content, then the hub genes within these two modules were further identified. Taken together, we found the categories of A. aculeatus-induced salt responsive genes, revealing underlying fungus-induced molecular mechanisms of salt stress response in perennial ryegrass roots. Besides, fungus-induced salt-tolerant hub genes represent a foundation for further exploring the molecular mechanisms.
PMID: 36270788
Molecules , IF:4.411 , 2022 Sep , V27 (18) doi: 10.3390/molecules27185806
Nitric Oxide Is Essential for Melatonin to Enhance Nitrate Tolerance of Cucumber Seedlings.
College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
Melatonin (MT) and nitric oxide (NO) in plants can function cooperatively to alleviate salt stress, sodic alkaline stress and immune response, as well as adventitious root formation. The interaction of MT and NO on the nitrate stress tolerance of cucumber seedlings are not well understood. We investigated the effects of exogenous MT, NO donor (SNP) and NO scavenger (cPTIO) on the growth; photosynthesis; characteristics of root morphological; accumulation of mineral elements, endogenous NO, MT, IAA and ABA; and related genes expression in cucumber (Cucumis sativus L. "Jin You No. 1") seedlings grown under high nitrate condition (HN). The results showed that MT and NO independently alleviated the inhibition of growth and photosynthesis capacity of cucumber seedlings under nitrate stress. NO was required for MT to enhance the root activity, root length, lateral root number and the accumulation of calcium, magnesium and iron in the roots of cucumber seedlings grown under nitrate stress. Consistently, the expression of adventitious rootless 1 gene (CsARL1) was modulated. Furthermore, exogenous MT induced accumulation of endogenous MT, NO, indole-3-acetic acid (IAA) and abscisic acid (ABA), mainly within 24 h after treatment, in which MT and NO were further increased at 48 h and 96 h, IAA and ABA were further increased at 16 h in the presence of SNP. In contrast, the accumulation of endogenous IAA, MT and ABA slightly decreased within 24 h, NO significantly decreased at 192 h in the presence of cPTIO. Correspondingly, the expression levels of genes involved in nitrogen metabolism (CsNR1 and CsNR2), MT metabolism (CsT5H, CsSNAT2 and Cs2-ODD33), auxin carriers and response factors (CsAUX1, CsGH3.5, CsARF17), ABA synthesis and catabolism (CsNCED1, CsNCED3 and CsCYP707A1) were upregulated by MT, in which CsNR1, CsNR2, CsAUX1, CsNCED3 and CsT5H were further induced in the presence of SNP in roots of cucumber seedlings. These observations indicated that NO act as a crucial factor in MT, alleviating nitrate stress through regulating the mechanism of root growth in cucumber seedlings.
PMID: 36144541
Sci Rep , IF:4.379 , 2022 Sep , V12 (1) : P15027 doi: 10.1038/s41598-022-19399-8
Common and novel metabolic pathways related ESTs were upregulated in three date palm cultivars to ameliorate drought stress.
Department of Arid Land Agriculture, College of Agriculture and Food Sciences, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia.; Date Palm Research Center of Excellence, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia.; Central Laboratories, King Faisal University, PO Box 31982, Al-Ahsa, Saudi Arabia. zafar@kfu.edu.sa.
Date palm is an important staple crop in Saudi Arabia, and about 400 different date palm cultivars grown here, only 50-60 of them are used commercially. The most popular and commercially consumed cultivars of these are Khalas, Reziz, and Sheshi, which are also widely cultivated across the country. Date palm is high water-demanding crop in oasis agriculture, with an inherent ability to tolerate drought stress. However, the mechanisms by which it tolerates drought stress, especially at the transcriptomic level, are still elusive. This study appraised the physiological and molecular response of three commercial date palm cultivars Khalas, Reziz, and Sheshi at two different field capacities (FC; 100% and 25%) levels. At 25% FC (drought stress), leaf relative water content, chlorophyll, photosynthesis, stomatal conductance, and transpiration were significantly reduced. However, leaf intercellular CO2 concentration and water use efficiency increased under drought stress. In comparison to cvs. Khalas and Reziz, date palm cv. Sheshi showed less tolerance to drought stress. A total of 1118 drought-responsive expressed sequence tags (ESTs) were sequenced, 345 from Khalas, 391 from Reziz, and 382 from Sheshi and subjected to functional characterization, gene ontology classification, KEGG pathways elucidation, and enzyme codes dissemination. Three date palm cultivars deployed a multivariate approach to ameliorate drought stress by leveraging common and indigenous molecular, cellular, biological, structural, transcriptional and reproductive mechanisms. Approximately 50% of the annotated ESTs were related to photosynthesis regulation, photosynthetic structure, signal transduction, auxin biosynthesis, osmoregulation, stomatal conductance, protein synthesis/turnover, active transport of solutes, and cell structure modulation. Along with the annotated ESTs, ca. 45% of ESTs were novel. Conclusively, the study provides novel clues and opens the myriads of genetic resources to understand the fine-tuned drought amelioration mechanisms in date palm.
PMID: 36056140
Ann Bot , IF:4.357 , 2022 Oct 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 (ACPs) 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 that in shoots or lower. 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 usually prevailed 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 ACPs indicate an association with different dominant functions of these organs: nutrient uptake by traps vs. 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 , 2022 Nov , V191 : P89-98 doi: 10.1016/j.plaphy.2022.09.022
Advances towards understanding the responses of root cells to acidic stress.
Instituto de Ciencias Biologicas, Departamento de Botanica, Plant Physiology Laboratory, Federal University of Minas Gerais, Antonio Carlos, 6627, Bloco I-2, 316, Belo Horizonte, MG, 31270-901, Brazil. Electronic address: jonathasgracas@gmail.com.; Laboratoire de Recherche en Sciences Vegetales, Universite de Toulouse, CNRS, UPS, Toulouse-INP 24, chemin de Borde Rouge 31320 Auzeville-Tolosane, France. Electronic address: jamet@lrsv.ups-tlse.fr.; Instituto de Ciencias Biologicas, Departamento de Botanica, Plant Physiology Laboratory, Federal University of Minas Gerais, Antonio Carlos, 6627, Bloco I-2, 316, Belo Horizonte, MG, 31270-901, Brazil. Electronic address: jonilima@icb.ufmg.br.
"Acid soil syndrome" is a worldwide phenomenon characterized by low pH (pH < 5.5), scarce nutrient availability (K(+), Ca(2+), Mg(2+), P), and mineral toxicity such as those caused by soluble aluminium (Al) forms. Regardless of the mineral toxicity, the low pH by itself is detrimental to crop development causing striking sensitivity responses such as root growth arrest. However, low pH-induced responses are still poorly understood and underrated. Here, we review and discuss the core evidence about the action of low pH upon specific root zones, distinct cell types, and possible cellular targets (cell wall, plasma membrane, and alternative oxidase). The role of different players in signaling processes leading to low pH-induced responses, such as the STOP transcription factors, the reactive oxygen species (ROS), auxin, ethylene, and components of the antioxidant system, is also addressed. Information at the molecular level is still lacking to link the low pH targets and the subsequent actors that trigger the observed sensitivity responses. Future studies will have to combine genetic tools to identify the signaling processes triggered by low pH, unraveling not only the mechanisms by which low pH affects root cells but also finding new ways to engineer the tolerance of domesticated plants to acidic stress.
PMID: 36195036
BMC Plant Biol , IF:4.215 , 2022 Oct , V22 (1) : P500 doi: 10.1186/s12870-022-03873-6
Comparison of anther transcriptomes in response to cold stress at the reproductive stage between susceptible and resistant Japonica rice varieties.
Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China.; National Engineering Research Center of Plant Space Breeding, South China Agricultural University, 510642, Guangzhou, Guangdong, China.; Jiamusi Branch of Heilongjiang Academy of Agricultural Sciences, 154007, Jiamusi, Heilongjiang, China. cai_lijun@yeah.net.; Crops Research Institute, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China.; Jiamusi Longjing Seed Industry Co., LTD, 154026, Jiamusi, Heilongjiang, China.; Qiqihar Branch of Heilongjiang Academy of Agricultural Sciences, 161006, Qiqihar, Heilongjiang, China.; Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China. zixuanfeng2008@163.com.; Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China. liuchuanxue2007@163.com.; Rice Research Institute of Heilongjiang Academy of Agricultural Sciences, 154026, Jiamusi, Heilongjiang, China. panguojun777@163.com.
BACKGROUND: Rice is one of the most important cereal crops in the world but is susceptible to cold stress (CS). In this study, we carried out parallel transcriptomic analysis at the reproductive stage on the anthers of two Japonica rice varieties with contrasting CS resistance: cold susceptible Longjing11 (LJ11) and cold resistant Longjing25 (LJ25). RESULTS: According to the obtained results, a total of 16,762 differentially expressed genes (DEGs) were identified under CS, including 7,050 and 14,531 DEGs in LJ25 and LJ11, respectively. Examining gene ontology (GO) enrichment identified 35 up- and 39 down-regulated biological process BP GO terms were significantly enriched in the two varieties, with 'response to heat' and 'response to cold' being the most enriched. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 33 significantly enriched pathways. Only the carbon metabolism and amino acid biosynthesis pathways with down-regulated DEGs were enriched considerably in LJ11, while the plant hormone signal transduction pathway (containing 153 DEGs) was dramatically improved. Eight kinds of plant hormones were detected in the pathway, while auxin, abscisic acid (ABA), salicylic acid (SA), and ethylene (ETH) signaling pathways were found to be the top four pathways with the most DEGs. Furthermore, the protein-protein interaction (PPI) network analysis identified ten hub genes (co-expressed gene number >/= 30), including six ABA-related genes. Various DEGs (such as OsDREB1A, OsICE1, OsMYB2, OsABF1, OsbZIP23, OsCATC, and so on) revealed distinct expression patterns among rice types when the DEGs between LJ11 and LJ25 were compared, indicating that they are likely responsible for CS resistance of rice in cold region. CONCLUSION: Collectively, our findings provide comprehensive insights into complex molecular mechanisms of CS response and can aid in CS resistant molecular breeding of rice in cold regions.
PMID: 36284279
BMC Plant Biol , IF:4.215 , 2022 Oct , V22 (1) : P484 doi: 10.1186/s12870-022-03861-w
Functional analysis revealed the involvement of ZmABCB15 in resistance to rice black-streaked dwarf virus infection.
Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China.; Weihai Academy of Agricultural Sciences, Weihai, China.; Henan Academy of Agricultural Sciences Zhengzhou, Zhengzhou, China. tieshaugngui308@126.com.; Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan, China. mengzhd981@126.com.
BACKGROUND: Maize rough dwarf disease (MRDD), caused by rice black-streaked dwarf virus (RBSDV) belonging to the Fijivirus genus, seriously threatens maize production worldwide. Three susceptible varieties (Ye478, Zheng 58, and Zhengdan 958) and two resistant varieties (P138 and Chang7-2) were used in our study. RESULTS: A set of ATP-binding cassette subfamily B (ABCB) transporter genes were screened to evaluate their possible involvements in RBSDV resistance. In the present study, ZmABCB15, an ABCB transporter family member, was cloned and functionally identified. Expression analysis showed that ZmABCB15 was significantly induced in the resistant varieties, not in the susceptible varieties, suggesting its involvement in resistance to the RBSDV infection. ZmABCB15 gene encodes a putative polar auxin transporter containing two trans-membrane domains and two P-loop nucleotide-binding domains. Transient expression analysis indicated that ZmABCB15 is a cell membrance localized protein. Over-expression of ZmABCB15 enhanced the resistance by repressing the RBSDV replication ratio. ZmABCB15 might participate in the RBSDV resistance by affecting the homeostasis of active and inactive auxins in RBSDV infected seedlings. CONCLUSIONS: Polar auxin transport might participate in the RBSDV resistance by affecting the distribution of endogenous auxin among tissues. Our data showed the involvement of polar auxin transport in RBSDV resistance and provided novel mechanism underlying the auxin-mediated disease control technology.
PMID: 36217105
BMC Plant Biol , IF:4.215 , 2022 Sep , V22 (1) : P456 doi: 10.1186/s12870-022-03837-w
Analysis of controlling genes for tiller growth of Psathyrostachys juncea based on transcriptome sequencing technology.
College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China.; College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, 010018, China. yunlan@imau.edu.cn.; Key Laboratory of Grassland Resources of the Ministry of Education and Key Laboratory of Forage Cultivation, Processing and High Efficient Utilization of the Ministry of Agriculture, Hohhot, 010018, China. yunlan@imau.edu.cn.
BACKGROUND: Tillering is a complicated process in plant and is a significant trait that affects biomass and seed yield of bunch grass Psathyrostachys juncea, a typical perennial forage species. To clarify the regulatory mechanisms of tillering in P. juncea and to explore related candidate genes could be helpful to improve the seed and forage yield of perennial gramineous forages. We selected the tiller node tissues of P. juncea for transcriptome sequencing to determine the differentially expressed genes (DEG) between dense and sparse tillering genotypes. The metabolic pathway was studied, candidate genes were screened, and reference genes stability were evaluated. RESULTS: The results showed that approximately 5466 DEGs were identified between the two genotypes with dense and sparse tillers of P. juncea, which significantly differed in tiller number. Tillering regulation pathways analysis suggested that DEGs closely related to the biosynthesis of three plant hormones, namely auxin (IAA), cytokinin (CTK), and strigolactones (SLs), while "biosynthesis of lignin" and "nitrogen metabolism" have remarkable differences between the dense and sparse tillering genotypes. Meanwhile, the reference gene Actin1, having the best stability, was screened from twelve genes with highest expression level and was used in verification of ten tillering related candidate genes. CONCLUSIONS: The tillering mechanism of perennial grass P. juncea was expounded by transcriptome analysis of tiller node tissues. We demonstrated that dense-tillering genotypes may be distinguished by their low expression patterns of genes involved in SL, IAA, and high expression patterns of genes involved in CTK biosynthesis at the tillering stage, and nitrogen metabolism and lignin biosynthesis can also affect the number of tillers. Furthermore, the expression level of ten tillering related candidate genes were verified using Actin1 as reference gene. These candidate genes provide valuable breeding resources for marker assisted selection and yield traits improvement of P. juncea.
PMID: 36151542
BMC Plant Biol , IF:4.215 , 2022 Sep , V22 (1) : P427 doi: 10.1186/s12870-022-03810-7
Hormone biosynthesis and metabolism members of 2OGD superfamily are involved in berry development and respond to MeJA and ABA treatment of Vitis vinifera L.
Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China.; University of Chinese Academy of Sciences, Beijing, 100049, China.; Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.; Beijing Key Laboratory of Grape Science and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China. zl249@ibcas.ac.cn.
BACKGROUND: Hormones play an indispensable role during fruit ripening, nine clades in 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily are responsible for the hormone biosynthesis and metabolism, but less information is known about them. RESULTS: A total of 163 Vv2OGD superfamily members were identified from grape genome, which were mainly expanded by local (tandem and proximal) duplication. Phylogenetic analysis of 2OGD members in grape and Arabidopsis indicates 37 members in Vv2OGD superfamily are related to hormone biosynthesis and metabolism process (Vv2OGD-H), which could be divided into 9 clades, gibberellin (GA) 3-oxidase (GA3ox), GA 20-oxidase (GA20ox), carbon-19 GA 2-oxidase (C19-GA2ox), carbon-20 GA 2-oxidase (C20-GA2ox), 1-aminocyclopropane-1-carboxylic acid oxidase (ACO), dioxygenase for auxin oxidation (DAO), lateral branching oxidoreductas (LBO), downy mildew resistant 6 and DMR6-like oxygenase (DMR6/DLO) and jasmonate-induced oxygenase (JOX). Sixteen of these 37 Vv2OGD-Hs are expressed in grape berry, in which the expression patterns of VvGA2oxs, VvDAOs and VvJOXs shows a correlation with the change patterns of GAs, indole-3-acetic acid (IAA) and jasmonates (JAs), indicating the involvement of these genes in grape berry development by regulating corresponding hormones. Twelve Vv2OGD-Hs respond to methyl JA (MeJA) treatment, of which eight may lead to the inhibition of the ripening process by the crosstalk of JAs-salicylic acids (SAs), JAs-GAs and JAs-JAs, while seven Vv2OGD-Hs respond to ABA treatment may be responsible for the promotion of ripening process by the interplay of abscisic acid (ABA)-strigolactones (SLs), ABA-SAs, ABA-GAs, ABA-JAs. Especially, VvLBO1 reach an expression peak near veraison and up-regulate about four times after ABA treatment, which implies SLs and ABA-SLs crosstalk may be related to the onset of berry ripening in grape. CONCLUSIONS: This study provides valuable clues and new insights for the mechanism research of Vv2OGD-Hs in hormones regulation during the grape berry development.
PMID: 36064347
Mol Plant Microbe Interact , IF:4.171 , 2022 Oct , V35 (10) : P881-886 doi: 10.1094/MPMI-05-22-0113-TA
Berberine Bridge Enzyme-like Oligosaccharide Oxidases Act as Enzymatic Transducers Between Microbial Glycoside Hydrolases and Plant Peroxidases.
Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy.; Department of Biology and Biotechnology "Charles Darwin", Sapienza University of Rome, 00185 Rome, Italy.
Oligogalacturonide (OG)-oxidase 1 (OGOX1) and cellodextrin (CD)-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide oxidases that oxidize OGs and CDs, cell-wall fragments with the nature of damage-associated molecular patterns. The oxidation of OGs and CDs attenuates their elicitor activity and concomitantly releases H2O2. By using a multiple enzyme-based assay, we demonstrate that the H2O2 generated downstream of the combined action between a fungal polygalacturonase and OGOX1 or an endoglucanase and CELLOX can be directed by plant peroxidases (PODs) either towards a reaction possibly involved in plant defense, such as the oxidation of monolignol or a reaction possibly involved in a developmental event, such as the oxidation of auxin (indole-3-acetic acid), pointing to OGOX1 and CELLOX as enzymatic transducers between microbial glycoside hydrolases and plant PODs. [Formula: see text] Copyright (c) 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
PMID: 35704684
Microorganisms , IF:4.128 , 2022 Oct , V10 (10) doi: 10.3390/microorganisms10102047
A Plant Endophytic Bacterium Priestia megaterium StrainBP-R2 Isolated from the Halophyte Bolboschoenus planiculmis Enhances Plant Growth under Salt and Drought Stresses.
Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402, Taiwan.; Institute of Plant and Microbial Biology, Academia Sinica, Taipei 115, Taiwan.; Department of Plant Pathology, National Chung Hsing University, Taichung 402, Taiwan.
Global warming and climate change have contributed to the rise of weather extremes. Severe drought and soil salinization increase because of rising temperatures. Economically important crop production and plant growth and development are hindered when facing various abiotic stresses. Plant endophytic bacteria live inside host plants without causing visible harm and can be isolated from surface-sterilized plant tissues. Using plant endophytic bacteria to stimulate plant growth and increase environmental stress tolerance has become an alternative approach besides using the traditional breeding and genetically modifying approaches to select or create new crop types resistant to different environmental stresses. The plant endophytic bacterium, Priestia megaterium (previously known as Bacillus megaterium) strain BP-R2, was isolated from the surface-sterilized root tissues of the salt marsh halophyte Bolboschoenus planiculmis. The bacteria strain BP-R2 showed high tolerance to different sodium chloride (NaCl) concentrations and produced the auxin plant hormone, indole acetic acid (IAA), under various tested growth conditions. Inoculation of Arabidopsis and pak choi (Brassica rapa L. R. Chinensis Group) plants with the strain BP-R2 greatly enhanced different growth parameters of the host plants under normal and salt and drought stress conditions compared to that of the mock-inoculated plants. Furthermore, the hydrogen peroxide (H2O2) content, electrolyte leakage (EL), and malondialdehyde (MDA) concentration accumulated less in the BP-R2-inoculated plants than in the mock-inoculated control plants under salt and drought stresses. In summary, the plant endophytic bacterium strain BP-R2 increased host plant growth and stress tolerance to salt and drought conditions.
PMID: 36296323
Microorganisms , IF:4.128 , 2022 Sep , V10 (9) doi: 10.3390/microorganisms10091802
The Metabolic Potential of Endophytic Actinobacteria Associated with Medicinal Plant Thymus roseus as a Plant-Growth Stimulator.
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.; Department of Biological, Marine Sciences and Environmental Agriculture, Institute for Post Graduate Environmental Studies, Arish University, Al-Arish 45511, Egypt.; Department of Environmental Protection, Faculty of Environmental Agricultural Sciences, Arish University, Al-Arish 45511, Egypt.; Faculty of Biology, National University of Uzbekistan, Tashkent 100174, Uzbekistan.; Institute of Fundamental and Applied Research, National Research University (TIIAME), Tashkent 100000, Uzbekistan.; Faculty of Organic Agriculture, Heliopolis University, Cairo 2834, Egypt.; State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan 430074, China.; State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
Bio-fertilizer practice considers not only economical but also environmentally friendly, sustainable agriculture. Endophytes can play important beneficiary roles in plant development, directly, indirectly, or synergistically. In this study, the majority of our endophytic actinobacteria were able to possess direct plant growth-promoting (PGP) traits, including auxin (88%), ammonia (96%), siderophore production (94%), and phosphate solubilization (24%), along with cell-wall degrading enzymes such as protease (75%), cellulase (81%), lipase (81%), and chitinase (18%). About 45% of tested strains have an inhibitory effect on the phytopathogen Fusarium oxysporum, followed by 26% for Verticillium dahlia. Overall, our results showed that strains XIEG63 and XIEG55 were the potent strains with various PGP traits that caused a higher significant increase (p
PMID: 36144404
Genes (Basel) , IF:4.096 , 2022 Oct , V13 (10) doi: 10.3390/genes13101903
Comparative Biochemical and Transcriptomic Analyses Provide New Insights into Phytoplasma Infection Responses in Cucumber.
School of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China.; Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China.; Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
Flat stem and witches' broom phytoplasma-like symptoms in the cucumber inbred line C17 were observed in a greenhouse at Yangzhou University, China for three consecutive planting seasons; these symptoms resulted in a decreased yield. To better understand the cause of these symptoms, 16S rRNA PCR, plant hormones, mineral elements, and RNA-seq profiling were performed using symptomatic and normal stem samples. The results showed that the causal agent was classified as the Candidatus phytoplasma asteris strain, a plant pathogenic prokaryote that could not be cultured in vitro. Measurement of plant hormones showed that auxin, salicylic acid, and jasmonic acid contents were significantly increased, whereas that of ethylene's immediate biosynthetic precursor, 1-aminocyclopropane-1-carboxylic acid, was decreased in the phytoplasma-infected stems compared with the healthy stems. Furthermore, measurement of mineral element composition showed that magnesium, calcium, sodium, iron, and zinc concentrations significantly changed in the phytoplasma-infected cucumber stems compared with the uninfected stems. Comparative RNA-seq identified 253 differentially expressed genes, including 179 upregulated and 74 downregulated genes. Further analyses suggested that genes related to phenylpropanoid biosynthesis, phenylalanine metabolism, and plant hormone signal transduction contributed to phytoplasma infection. Taken together, this study presents the first in-depth assessment of disease symptoms and biochemical content of cucumber stems known to be infected with phytoplasma.
PMID: 36292788
Genes (Basel) , IF:4.096 , 2022 Oct , V13 (10) doi: 10.3390/genes13101803
Effects of Exogenous (K(+)) Potassium Application on Plant Hormones in the Roots of Tamarix ramosissima under NaCl Stress.
Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.; Department of Forest Resources Management, Faculty of Science, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Abiotic stresses such as salt stress seriously affect the growth and yield of plants. Tamarix ramosissima Lcdcb (T. ramosissima) is a widely cultivated halophyte in saline-alkali areas of the world. As an essential element for plant growth and development, K(+) plays an irreplaceable role in improving the tolerance of plants to salt stress. However, there are few reports on the mechanism of K(+) in promoting plant hormones to reduce the damage of NaCl stress to T. ramosissima. In this study, we sequenced the transcriptome of the roots of T. ramosissima which were treated with exogenous potassium (K(+)) for 0 h, 48 h and 168 h under NaCl stress, according to the changes in the expression levels of differentially expressed genes (DEGs) in T. ramosissima roots. Key candidate genes and metabolic pathways related to plant hormones were mined for analysis and further verified by quantitative real-time PCR (qRT-PCR). The results showed that under NaCl stress for 48 h and 168 h, there were a large number of DEGs in the roots of T. ramosissima, and the expression levels changed over time. In particular, we found that 56 plant hormone-related genes were annotated to the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and with the increase of time, their expression levels were mainly up-regulated and involved in the related metabolic pathways to resist NaCl stress. It is worth noting that 7 DEGs related to abscisic acid (ABA), 28 DEGs related to auxin, 1 DEG related to ethylene (ET), and 1 DEG related to cytokinin (CK) were added within 168 h of exogenous potassium, and they were involved in alleviating the root damage of T. ramosissima under NaCl stress and played an important role. In addition, we found the plant hormone signal transduction pathway, which plays an important role in resistance to NaCl stress. As a result of this study, the molecular mechanism of plant hormones involved in applying exogenous potassium under NaCl stress is further understood, resulting in a better understanding of how exogenous potassium can alleviate the damage caused by NaCl under stress in T. ramosissima.
PMID: 36292689
Genes (Basel) , IF:4.096 , 2022 Sep , V13 (9) doi: 10.3390/genes13091577
Comprehensive In Silico Characterization and Expression Pro-Filing of DA1/DAR Family Genes in Brassica rapa.
State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
The DA1/DAR family genes have been shown to play important roles in regulating organ size and plant biomass in the model plant Arabidopsis and several crops. However, this family has not been characterized in Brassica rapa (B. rapa). In this study, we identified 17 DA1&DAR genes from B. rapa. Phylogenetic analysis indicated that these genes are classified into four groups. Structural and motif analysis of BrDA1&DARs discovered that the genes within the same group have similar exon-intron structures and share an equal number of conserved motifs except for BrDAR6.3 from group IV, which contains two conserved motifs. Cis-regulatory elements identified four phytohormones (Salicylic acid, Abscisic acid, Gibberellin, and auxin) and three major abiotic (Light, Low temperature, and drought) responsive elements. Further, six br-miRNAs named br-miR164a, br-miR164b, br-miR164c, br-miR164d, br-miRN360, and br-miRN366 were found which target BrDAR6.1, BrDA1.4, and BrDA1.5. BrDA1&DAR genes were highly expressed in stem, root, silique, flower, leaf, and callus tissues. Moreover, qRT-PCR analyses indicated that some of these genes were responsive to abiotic stresses or phytohormone treatments. Our findings provide a foundation for further genetic and physiological studies of BrDA1&DARs in B. rapa.
PMID: 36140744
Plant Mol Biol , IF:4.076 , 2022 Sep 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.
KEY MESSAGE: 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 Oct , V110 (3) : P253-268 doi: 10.1007/s11103-022-01298-1
SlBBX28 positively regulates plant growth and flower number in an auxin-mediated manner in tomato.
Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.; Escola Superior de Agricultura 'Luiz de Queiroz', Universidade de Sao Paulo, Sao Paulo, SP, Brazil.; Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.; Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, Sao Paulo, SP, Brazil. mmrossi@usp.br.
KEY MESSAGE: SlBBX28 is a positive regulator of auxin metabolism and signaling, affecting plant growth and flower number in tomato B-box domain-containing proteins (BBXs) comprise a family of transcription factors that regulate several processes, such as photomorphogenesis, flowering, and stress responses. For this reason, attention is being directed toward the functional characterization of these proteins, although knowledge in species other than Arabidopsis thaliana remains scarce. Particularly in the tomato, Solanum lycopersicum, only three out of 31 SlBBX proteins have been functionally characterized to date. To deepen the understanding of the role of these proteins in tomato plant development and yield, SlBBX28, a light-responsive gene, was constitutively silenced, resulting in plants with smaller leaves and fewer flowers per inflorescence. Moreover, SlBBX28 knockdown reduced hypocotyl elongation in darkness-grown tomato. Analyses of auxin content and responsiveness revealed that SlBBX28 promotes auxin-mediated responses. Altogether, the data revealed that SlBBX28 promotes auxin production and signaling, ultimately leading to proper hypocotyl elongation, leaf expansion, and inflorescence development, which are crucial traits determining tomato yield.
PMID: 35798935
BMC Genomics , IF:3.969 , 2022 Sep , V23 (1) : P655 doi: 10.1186/s12864-022-08870-5
Transcriptome analysis of sweet potato responses to potassium deficiency.
Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China. wangfangsaas@126.com.; Environment-friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China.
BACKGROUND: As one of three essential nutrients, potassium is regarded as a main limiting factor for growth and development in plant. Sweet potato (Ipomoea batatas L.) is one of seven major food crops grown worldwide, and is both a nutrient-rich food and a bioenergy crop. It is a typical 'K-favoring' crop, and the level of potassium ion (K(+)) supplementation directly influences its production. However, little is known about the transcriptional changes in sweet potato genes under low-K(+) conditions. Here, we analyzed the transcriptomic profiles of sweet potato roots in response to K(+) deficiency to determine the effect of low-K(+) stress on this economically important crop. RESULTS: The roots of sweet potato seedlings with or without K(+) treatment were harvested and used for transcriptome analyses. The results showed 559 differently expressed genes (DEGs) in low and high K(+) groups. Among the DEGs, 336 were upregulated and 223 were downregulated. These DEGs were involved in transcriptional regulation, calcium binding, redox-signaling, biosynthesis, transport, and metabolic process. Further analysis revealed previously unknow genes involved in low-K(+) stress, which could be investigated further to improve low K(+) tolerance in plants. Confirmation of RNA-sequencing results using qRT-PCR displayed a high level of consistency between the two experiments. Analysis showed that many auxin-, ethylene- and jasmonic acid-related genes respond to K(+) deficiency, suggesting that these hormones have important roles in K(+) nutrient signaling in sweet potato. CONCLUSIONS: According to the transcriptome data of sweet potato, various DEGs showed transcriptional changes in response to low-K(+) stress. However, the expression level of some kinases, transporters, transcription factors (TFs), hormone-related genes, and plant defense-related genes changed significantly, suggesting that they have important roles during K(+) deficiency. Thus, this study identifies potential genes for genetic improvement of responses to low-K(+) stress and provides valuable insight into the molecular mechanisms regulating low K(+) tolerance in sweet potato. Further research is required to clarify the function of these DEGs under low-K(+) stress.
PMID: 36109727
BMC Genomics , IF:3.969 , 2022 Sep , V23 (1) : P638 doi: 10.1186/s12864-022-08864-3
Identification and characterization of miRNAs and PHAS loci related to the early development of the embryo and endosperm in Fragaria x ananassa.
Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China.; Laboratory of Fruit Crop Biotechnology, College of Horticulture, Nanjing Agricultural University, No. 1 Weigang, Nanjing, Jiangsu, 210095, People's Republic of China. qiaoyushan@njau.edu.cn.
BACKGROUND: The strawberry fleshy fruit is actually enlarged receptacle tissue, and the successful development of the embryo and endosperm is essential for receptacle fruit set. MicroRNAs (miRNAs) and phased small interfering RNAs (phasiRNAs) play indispensable regulatory roles in plant growth and development. However, miRNAs and phasiRNAs participating in the regulation of strawberry embryo and endosperm development have yet to be explored. RESULTS: Here, we performed genome-wide identification of miRNA and phasiRNA-producing loci (PHAS) in strawberry seeds with a focus on those involved in the development of the early embryo and endosperm. We found that embryos and endosperm have different levels of small RNAs. After bioinformatics analysis, the results showed that a total of 404 miRNAs (352 known and 52 novel) and 156 PHAS genes (81 21-nt and 75 24-nt genes) could be found in strawberry seed-related tissues, of which four and nine conserved miRNA families displayed conserved expression in the endosperm and embryo, respectively. Based on refined putative annotation of PHAS loci, some auxin signal-related genes, such as CM3, TAR2, AFB2, ASA1, NAC and TAS3, were found, which demonstrates that IAA biosynthesis is important for endosperm and embryo development during early fruit growth. Additionally, some auxin signal-related conserved (miR390-TAS3) and novel (miR156-ASA1) trigger-PHAS pairs were identified. CONCLUSIONS: Taken together, these results expand our understanding of sRNAs in strawberry embryo and endosperm development and provide a genomic resource for early-stage fruit development.
PMID: 36076187
Pestic Biochem Physiol , IF:3.963 , 2022 Oct , V187 : P105211 doi: 10.1016/j.pestbp.2022.105211
Multiple resistance mechanisms to penoxsulam in Echinochloa crus-galli from China.
Department of Plant Protection, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China.; General Station of Plant Protection, Hubei Province, Wuhan 430070, Hubei, PR China.; General Station of Plant Protection, Hubei Province, Wuhan 430070, Hubei, PR China. Electronic address: 897015023@qq.com.; Department of Plant Protection, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, PR China. Electronic address: mahongju@mail.hzau.edu.cn.
Penoxsulam is an important herbicide for the control of Echinochloa crus-galli (L.) P. Beauv. Two resistant populations 17GA (R1) and 16NXB (R2) showed 17- and 3-fold resistance to penoxsulam, respectively. A known resistance mutation of Trp-574-Leu in ALS gene and enhanced rates of penoxsulam metabolism likely involving GST contribute to penoxsulam resistance in R1 population. This population had resistance to the ALS-inhibitors pyribenzoxim and bispyribacsodium and the auxin herbicide quinclorac, but was susceptible to ACCase-inhibitors quizalofop-p-ethyl and cyhalofop-butyl. No known mutations in the ALS gene conferring target site resistance to ALS-inhibiting herbicides were presented in R2 population. However, penoxsulam metabolism in R2 plants was about 4-fold greater than in susceptible population 14YC (S0) plants. The enzyme inhibitors piperonyl butoxide, malathion and 4-chloro-7-nitrobenzoxadiazole reversed penoxsulam resistance in this population. GST and P450 enzyme activities and the genes of GST1-1, GST1-2, GST1-3, CYP81A18, CYP81A12, CYP81A21 were increased significantly in R2 population. These results indicate that multiple resistance mechanisms had occurred in E. crus-galli populations in central China and resistance needs to be managed effectively by diverse chemical and non-chemical methods.
PMID: 36127055
Plants (Basel) , IF:3.935 , 2022 Oct , V11 (19) doi: 10.3390/plants11192640
The S-Gene YUC6 Pleiotropically Determines Male Mating Type and Pollen Size in Heterostylous Turnera (Passifloraceae): A Novel Neofunctionalization of the YUCCA Gene Family.
School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.; Department of Biology, York University, Toronto, ON M3J 1P3, Canada.
In heterostylous, self-incompatible Turnera species, a member of the YUCCA gene family, YUC6, resides at the S-locus and has been hypothesized to determine the male mating type. YUCCA gene family members synthesize the auxin, indole-3-acetic acid, via a two-step process involving the TAA gene family. Consequently, it has been speculated that differences in auxin concentration in developing anthers are the biochemical basis underlying the male mating type. Here, we provide empirical evidence that supports this hypothesis. Using a transgenic knockdown approach, we show that YUC6 acts pleiotropically to control both the male physiological mating type and pollen size, but not the filament length dimorphism associated with heterostyly in Turnera. Using qPCR to assess YUC6 expression in different transgenic lines, we demonstrate that the level of YUC6 knockdown correlates with the degree of change observed in the male mating type. Further assessment of YUC6 expression through anther development, in the knockdown lines, suggests that the male mating type is irreversibly determined during a specific developmental window prior to microsporogenesis, which is consistent with the genetically sporophytic nature of this self-incompatibility system. These results represent the first gene controlling male mating type to be characterized in any species with heterostyly.
PMID: 36235506
Plants (Basel) , IF:3.935 , 2022 Sep , V11 (19) doi: 10.3390/plants11192483
Identification of a BAHD Acyltransferase Gene Involved in Plant Growth and Secondary Metabolism in Tea Plants.
Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, National Center for Tea Improvement, Tea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS), Hangzhou 310008, China.; Graduate School of Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Plant acyl-CoA dominated acyltransferases (named BAHD) comprise a large appointed protein superfamily and play varied roles in plant secondary metabolism like synthesis of modified anthocyanins, flavonoids, volatile esters, etc. Tea (Camellia sinensis) is an important non-alcoholic medicinal and fragrancy plant synthesizing different secondary metabolites, including flavonoids. In the tea (C.A sinensis) cultivar Longjing 43 (LJ43), eight samples were performed into three groups for transcriptome analysis under three biological replications. Among the BAHD acyltransferase genes in tea cultivars, the expression of TEA031065 was highest in buds and young leaves following the RNA sequencing data, which was coincident with the tissue rich in catechins and other flavonoids. We then transformed this gene into wild-type Arabidopsis as an over-expression (OX) line 1 and line 2 in (1/2) MS media to verify its function. In the wild types (WT), the primary root length, number of secondary roots, and total root weight were significantly higher at 24%, 15%, and 53.92%, respectively, compared to the transgenic lines (OX1 and OX2). By contrast, the leaves displayed larger rosettes (21.58%), with higher total leaf weight (32.64%) in the transgenic lines than in the wild type (WT). This result is consistent with DCR mutant At5g23940 gene in Arabidopsis thaliana. Here, anthocyanin content in transgenic lines was also increased (21.65%) as compared to WT. According to the RNA sequencing data, a total of 22 growth regulatory genes and 31 structural genes with TFs (transcription factors) that are correlative with plant growth and anthocyanin accumulation were identified to be differentially expressed in the transgenic lines. It was found that some key genes involved in IAA (Auxin) and GA (Gibberellin) biosynthesis were downregulated in the transgenic lines, which might be correlated with the phenotype changes in roots. Moreover, the upregulation of plant growth regulation genes, such as UGT73C4 (zeatin), ARR15, GH3.5, ETR2, ERS2, APH4, and SAG113 might be responsible for massive leaf growth. In addition, transgenic lines shown high anthocyanin accumulation due to the upregulation of the (1) 3AT1 and (3) GSTF, particularly, GSTF12 genes in the flavonoid biosynthesis pathway. However, the TFs such as, CCoAMT, bHLH, WRKY, CYP, and other MYBs were also significantly upregulated in transgenic lines, which increased the content of anthocyanins in A. thaliana seedlings. In conclusion, a BAHD acyltransferase (TEA031065) was identified, which might play a vital role in tea growth and secondary metabolites regulation. This study increases our knowledge concerning the combined functionality of the tea BAHD acyltransferase gene (TEA031065).
PMID: 36235354
Plants (Basel) , IF:3.935 , 2022 Sep , V11 (19) doi: 10.3390/plants11192467
Identification of the OsCML4 Gene in Rice Related to Salt Stress Using QTL Analysis.
Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Korea.; Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea.; Natural and Medical Science Research Center, University of Nizwa, Nizwa 616, Oman.; Department of Botany, Garden Campus, Abdul Wali Khan University, Mardan 23200, Pakistan.
Soil salinity is a major abiotic stress that causes disastrous losses in crop yields. To identify favorable alleles that enhance the salinity resistance of rice (Oryza sativa L.) crops, a set of 120 Cheongcheong Nagdong double haploid (CNDH) lines derived from a cross between the Indica variety Cheongcheong and the Japonica variety Nagdong were used. A total of 23 QTLs for 8 different traits related to salinity resistance on chromosomes 1-3 and 5-12 were identified at the seedling stage. A QTL related to the salt injury score (SIS), qSIS-3b, had an LOD score of six within the interval RM3525-RM15904 on chromosome 3, and a phenotypic variation of 31% was further examined for the candidate genes. Among all the CNDH populations, five resistant lines (CNDH 27, CNDH 34-1, CNDH 64, CNDH 78, and CNDH 112), five susceptible lines (CNDH 52-1, CNDH 67, CNDH 69, CNDH 109, and CNDH 110), and the parent lines Cheongcheong and Nagdong were selected for relative gene expression analysis. Among all the genes, two candidate genes were highly upregulated in resistant lines, including the auxin-responsive protein IAA13 (Os03g0742900) and the calmodulin-like protein 4 (Os03g0743500-1). The calmodulin-like protein 4 (Os03g0743500-1) showed a higher expression in all the resistant lines than in the susceptible lines and a high similarity with other species in sequence alignment and phylogenetic tree, and it also showed a protein-protein interaction with other important proteins. The genes identified in our study will provide new genetic resources for improving salt resistance in rice using molecular breeding strategies in the future.
PMID: 36235331
Plants (Basel) , IF:3.935 , 2022 Sep , V11 (19) doi: 10.3390/plants11192457
Jatropha curcas L. as a Plant Model for Studies on Vegetative Propagation of Native Forest Plants.
Programa de Pos-Graduacao em Agronomia, Universidade Tecnologica Federal do Parana, Pato Branco 85503-390, PR, Brazil.; Department of Environmental Management, Mato Grosso do Sul State University, Mundo Novo 79980-000, MS, Brazil.; Department of Plant Protection, Rural Engineering and Soils, School of Engineering, Sao Paulo State University-UNESP-FEIS, Ilha Solteira 15385-000, SP, Brazil.; Agricultural Defense Coordination of Sao Paulo, Presidente Prudente 19013-050, SP, Brazil.; Department of Plant Production, School of Agricultural, Sao Paulo State University-FCA/UNESP, Botucatu 18610-034, SP, Brazil.; Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia.; Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, 2020 Antwerp, Belgium.; Botany and Microbiology Department, Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt.
Even though it is a forest native plant, there are already several studies evaluating the small genome of Jatropha curcas L., which belongs to the Euphorbiaceae family, and may be an excellent representative model for the other plants from the same family. Jatropha curcas L. plant has fast growth, precocity, and great adaptability, facilitating silvicultural studies, allowing important information to be obtained quickly, and reducing labor costs. This information justifies the use of the species as a model plant in studies involving the reproduction of native plants. This study aimed to evaluate the possibility of using Jatropha curcas L. as a model plant for studies involving native forest plants and establish possible recommendations for the vegetative propagation of the species using hardwood cuttings. The information collected can be helpful to other native forest plant species, similar to Jatropha curcas L. To this end, the effects of hardwood cutting length (10, 20, and 30 cm) and the part of the hardwood cuttings (basal, middle, and apex) were evaluated. Moreover, the influence of immersing the hardwood cuttings in solutions containing micronutrients (boron or zinc) or plant regulators (2,4-D, GA3) and a biostimulant composed of kinetin (0.09 g L(-1)), gibberellic acid (0.05 g L(-1)), and 4-indole-3-butyric acid (0.05 g L(-1)). The experiments were carried out in duplicates. In one duplicate, sand was used as the substrate, and rooting evaluations were made 77 days after planting. In another duplicate, a substrate composed of 50% soil, 40% poultry litter, and 10% sand was used, and the evaluations of the saplings were performed 120 days after planting. The GA3 solutions inhibited the roots' and sprouts' emissions, while immersion in 2,4-D solution increased the number of primary roots at 77 days after planting. The hardwood cuttings from the basal part of the branch had the best results for producing saplings.
PMID: 36235323
Plants (Basel) , IF:3.935 , 2022 Sep , V11 (18) doi: 10.3390/plants11182400
Dynamic RNA-Seq Study Reveals the Potential Regulators of Seed Germination in Paris polyphylla var. yunnanensis.
The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou 510642, China.; Guangzhou Key Laboratory for Research and Development of Crop Germplasm Resources, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.; College of Traditional Chinese Medicine, Yunnan University of Chinese Medicine, Kunming 650500, China.
Paris polyphylla var. yunnanensis is an important traditional Chinese medicine, but poor seed germination limits its large-scale artificial cultivation. Thus, it is crucial to understand the regulators of seed germination to obtain clues about how to improve the artificial cultivation of Paris polyphylla. In this study, the seeds at three germination stages, including ungerminated seeds (stage 1), germinated seeds with a 0.5 cm radicel length (stage 2), and germinated seeds with a 2.0 cm radicel length (stage 3) after warm stratification (20 degrees C) for 90 days were used for RNA sequencing. Approximately 220 million clean reads and 447,314 annotated unigenes were obtained during seed germination, of which a total of 4454, 5150, and 1770 differentially expressed genes (DEGs) were identified at stage 1 to stage 2, stage 1 to stage 3, and stage 2 to stage 3, respectively. Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the DEGs were significantly enriched in carbohydrate metabolism, lipid metabolism, signal transduction, and translation. Of them, several genes encoding the glutamate decarboxylase, glutamine synthetase, alpha-galactosidase, auxin-responsive protein IAA30, abscisic-acid-responsive element binding factor, mitogen-activated protein kinase kinase 9/18, and small and large subunit ribosomal proteins were identified as potentially involved in seed germination. The identified genes provide a valuable resource to study the molecular basis of seed germination in Paris polyphylla var. yunnanensis.
PMID: 36145801
Plants (Basel) , IF:3.935 , 2022 Sep , V11 (18) doi: 10.3390/plants11182344
Crosstalk of Cytokinin with Ethylene and Auxin for Cell Elongation Inhibition and Boron Transport in Arabidopsis Primary Root under Boron Deficiency.
Departamento de Fisiologia, Anatomia y Biologia Celular, Universidad Pablo de Olavide, E-41013 Sevilla, Spain.
Several studies have shown the role of phytohormones in the regulation of root growth of Arabidopsis plants under boron (B) deficiency. Ethylene and auxin play an important role in the control of Arabidopsis primary root cell elongation under short-term B deprivation, whereas cytokinins regulate root growth inhibition under B deficiency by controlling meristem cell proliferation. In this work, we study the possible interaction among cytokinin, ethylene, and auxin in the primary root response to B-deprivation treatment, as well as their possible role in B uptake and transport. Wild type (WT) and two mutants related to auxin and ethylene (aux1 and acs11) Arabidopsis plants were grown in control (10 microM B) or B starvation (0 microM B) treatment, in the absence or presence of trans-zeatin, and their primary root growth was analyzed. The possible interaction between these hormones was also studied by analyzing AUX1 gene expression in the acs11 mutant and ACS11 gene expression in the aux1 mutant. The GUS reporter lines ARR5::GUS, IAA2::GUS, and EBS::GUS were used to observe changes in cytokinin, auxin, and ethylene levels in the root, respectively. The results of this work suggest that cytokinin inhibits root cell elongation under B deficiency through two different mechanisms: (i) an ethylene-dependent mechanism through increased expression of the ACS11 gene, which would lead to increased ethylene in the root, and (ii) an ethylene-independent mechanism through decreased expression of the AUX1 gene, which alters auxin signaling in the meristematic and elongation zones and stele. We also report that changes in the expression of several B transporters occur in response to auxin, ethylene, and cytokinin that may affect the plant B content.
PMID: 36145745
Plants (Basel) , IF:3.935 , 2022 Sep , V11 (17) doi: 10.3390/plants11172324
Identification of QTL under Brassinosteroid-Combined Cold Treatment at Seedling Stage in Rice Using Genotyping-by-Sequencing (GBS).
Key Laboratory of Agricultural Biotechnology of Liaoning Province, College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China.; Rice Research Institute, College of Agronomy, Shenyang Agricultural University, Shenyang 110866, China.; Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China.; Department of Agronomy, College of Agriculture, Purdue University, West Lafayette, IN 47907, USA.
Cold stress is a major threat to the sustainability of rice yield. Brassinosteroids (BR) application can enhance cold tolerance in rice. However, the regulatory mechanism related to cold tolerance and the BR signaling pathway in rice has not been clarified. In the current study, the seedling shoot length (SSL), seedling root length (SRL), seedling dry weight (SDW), and seedling wet weight (SWW) were used as the indices for identifying cold tolerance under cold stress and BR-combined cold treatment in a backcross recombinant inbred lines (BRIL) population. According to the phenotypic characterization for cold tolerance and a high-resolution SNP genetic map obtained from the GBS technique, a total of 114 QTLs were identified, of which 27 QTLs were detected under cold stress and 87 QTLs under BR-combined cold treatment. Among them, the intervals of many QTLs were coincident under different treatments, as well as different traits. A total of 13 candidate genes associated with cold tolerance or BR pathway, such as BRASSINAZOLE RESISTANT1 (OsBZR1), OsWRKY77, AP2 domain-containing protein, zinc finger proteins, basic helix-loop-helix (bHLH) protein, and auxin-induced protein, were predicted. Among these, the expression levels of 10 candidate genes were identified under different treatments in the parents and representative BRIL individuals. These results were helpful in understanding the regulation relationship between cold tolerance and BR pathway in rice.
PMID: 36079705
Am J Bot , IF:3.844 , 2022 Sep , V109 (9) : P1360-1381 doi: 10.1002/ajb2.16046
Complex developmental and transcriptional dynamics underlie pollinator-driven evolutionary transitions in nectar spur morphology in Aquilegia (columbine).
Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave., Cambridge, MA, 02138, USA.; Department of Biological Sciences, California State University Sacramento, 6000 J St., Sacramento, CA, 95819, USA.
PREMISE: Determining the developmental programs underlying morphological variation is key to elucidating the evolutionary processes that generated the stunning biodiversity of the angiosperms. Here, we characterized the developmental and transcriptional dynamics of the elaborate petal nectar spur of Aquilegia (columbine) in species with contrasting pollination syndromes and spur morphologies. METHODS: We collected petal epidermal cell number and length data across four Aquilegia species, two with short, curved nectar spurs of the bee-pollination syndrome and two with long, straight spurs of the hummingbird-pollination syndrome. We also performed RNA-seq on A. brevistyla (bee) and A. canadensis (hummingbird) distal and proximal spur compartments at multiple developmental stages. Finally, we intersected these data sets with a previous QTL mapping study on spur length and shape to identify new candidate loci. RESULTS: The differential growth between the proximal and distal surfaces of curved spurs is primarily driven by differential cell division. However, independent transitions to straight spurs in the hummingbird syndrome have evolved by increasing differential cell elongation between spur surfaces. The RNA-seq data reveal these tissues to be transcriptionally distinct and point to auxin signaling as being involved with the differential cell elongation responsible for the evolution of straight spurs. We identify several promising candidate genes for future study. CONCLUSIONS: Our study, taken together with previous work in Aquilegia, reveals the complexity of the developmental mechanisms underlying trait variation in this system. The framework we established here will lead to exciting future work examining candidate genes and processes involved in the rapid radiation of the genus.
PMID: 35971626
Biosci Rep , IF:3.84 , 2022 Sep , V42 (9) doi: 10.1042/BSR20221504
Negative regulation of seed germination by maternal AFB1 and AFB5 in Arabidopsis.
Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, 301 Physical Sciences, Stillwater, OK 74078, U.S.A.
The plant hormone auxin suppresses seed germination, but how auxin does it remains poorly understood. While studying the functions of the AUXIN SIGNALING F-BOX (AFB) auxin co-receptors in Arabidopsis, we consistently isolated AFB1 and AFB5 in reproductive tissues in co-immunoprecipitation experiments using their interacting protein ASK1 as the bait. However, T2 seeds of the AFB1 or AFB5 transgenic lines generated for the co-immunoprecipitation experiments frequently failed to germinate, which led to the studies of seed germination in these plants and afb1 and afb5 mutants, and AFB1 and AFB5 expression in nearly mature fruit and imbibed seeds using AFB1:GUS and AFB5:GUS lines. We found that AFB1 and AFB5 acted in maternal tissues to suppress seed germination and their effects were positively correlated with the plants' sensitivity to indole acetic acid. Conversely, afb1 and afb5 single mutants exhibited faster seed germination than the wild type and the seeds of the afb1-5afb5-5 double mutant germinated even faster than those of the afb1-5 and afb5-5 single mutants. Seed germination of the afb1-5afb5-5 double mutant also exhibited higher sensitivity to gibberellic acid than that of the wild-type and the afb1-3, afb1-5 and afb5-5 single mutants. Both AFB1 and AFB5 were expressed in the funiculus during seed maturation, and AFB1 was also transiently expressed in a small chalazal region surrounding the hilum in the seed coat during seed imbibition. Therefore, AFB1 and AFB5 likely suppress seed germination in the funiculus and AFB1 also briefly suppresses seed germination in the chalaza during seed imbibition.
PMID: 36039862
Life (Basel) , IF:3.817 , 2022 Sep , V12 (10) doi: 10.3390/life12101484
Red Light Enhances Plant Adaptation to Spaceflight and Mars g-Levels.
Centro de Investigaciones Biologicas Margarita Salas-CSIC, 28040 Madrid, Spain.; Department of Biology, University of North Carolina at Greensboro, Greensboro, NC 27402-6170, USA.
Understanding how plants respond and adapt to extraterrestrial conditions is essential for space exploration initiatives. Deleterious effects of the space environment on plant development have been reported, such as the unbalance of cell growth and proliferation in the root meristem, or gene expression reprogramming. However, plants are capable of surviving and completing the seed-to-seed life cycle under microgravity. A key research challenge is to identify environmental cues, such as light, which could compensate the negative effects of microgravity. Understanding the crosstalk between light and gravity sensing in space was the major objective of the NASA-ESA Seedling Growth series of spaceflight experiments (2013-2018). Different g-levels were used, with special attention to micro-g, Mars-g, and Earth-g. In spaceflight seedlings illuminated for 4 days with a white light photoperiod and then photostimulated with red light for 2 days, transcriptomic studies showed, first, that red light partially reverted the gene reprogramming induced by microgravity, and that the combination of microgravity and photoactivation was not recognized by seedlings as stressful. Two mutant lines of the nucleolar protein nucleolin exhibited differential requirements in response to red light photoactivation. This observation opens the way to directed-mutagenesis strategies in crop design to be used in space colonization. Further transcriptomic studies at different g-levels showed elevated plastid and mitochondrial genome expression in microgravity, associated with disturbed nucleus-organelle communication, and the upregulation of genes encoding auxin and cytokinin hormonal pathways. At the Mars g-level, genes of hormone pathways related to stress response were activated, together with some transcription factors specifically related to acclimation, suggesting that seedlings grown in partial-g are able to acclimate by modulating genome expression in routes related to space-environment-associated stress.
PMID: 36294919
Gene , IF:3.688 , 2022 Oct : 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, the People's Republic of China; School of Tropical Crops, Hainan University, Haikou 570228, the People's Republic of China.; College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, the People's Republic of China.; Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou 570228, the 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, the People's Republic of China.; Hainan Key Laboratory for the Sustainable Utilization of Tropical Bioresources, Hainan University, Haikou 570228, the People's Republic of China; School of Tropical Crops, Hainan University, Haikou 570228, the 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, the 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 , 2022 Oct , V277 : P153792 doi: 10.1016/j.jplph.2022.153792
Regulation of pollen tube growth by cellular pH and ions.
MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China. Electronic address: zhouzhg18@lzu.edu.cn.; College of Life Sciences, Northwest Normal University, Lanzhou, Gansu, 730070, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai, 810016, China.; MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China.; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.; MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 73000, China; Academy of Plateau Science and Sustainability, Qinghai Normal University, Xining, Qinghai, 810016, China; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China. Electronic address: qiuqsh@lzu.edu.cn.
Tip growth of the pollen tube is a model system for the study of cell polarity establishment in flowering plants. The tip growth of the pollen tube displays an oscillating pattern corresponding to cellular ion and pH dynamics. Therefore, cellular pH and ions play an important role in pollen growth and development. In this review, we summarized the current advances in understanding the function of cellular pH and ions in regulating pollen tube growth. We analyzed the physiological roles and underlying mechanisms of cellular pH and ions, including Ca(2+), K(+), and Cl(-), in regulating pollen tube growth. We further examined the function of Ca(2+) in regulating cytoskeletons, small G proteins, and cell wall development in relation to pollen tube growth. We also examined the regulatory roles of cellular pH in pollen tube growth as well as pH regulation of ion flow, cell wall development, auxin signaling, and cytoskeleton function in pollen. In addition, we assessed the regulation of pollen tube growth by proton pumps and the maintenance of pH homeostasis in the trans-Golgi network by ion transporters. The interplay of ion homeostasis and pH dynamics was also assessed. We discussed the unanswered questions regarding pollen tube growth that need to be addressed in the future.
PMID: 35973258
Protoplasma , IF:3.356 , 2022 Sep doi: 10.1007/s00709-022-01808-4
Insights of auxin signaling F-box genes in wheat (Triticum aestivum L.) and their dynamic expression during the leaf rust infection.
Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.; Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India. kmukhopadhyay@bitmesra.ac.in.
The TRANSPORT INHIBITOR RESPONSE 1/AUXIN SIGNALING F-BOX (TIR1/AFB) protein serves as auxin receptor and links with Aux/IAA repressor protein leading to its degradation via SKP-Cullin-F box (SCF(TIR1/AFB)) complex in the auxin signaling pathway. Present study revealed 11 TIR1/AFB genes in wheat by genome-wide search using AFB HMM profile. Phylogenetic analysis clustered these genes in two classes. Several phytohormone, abiotic, and biotic stress responsive cis-elements were detected in promoter regions of TIR1/AFB genes. These genes were localized on homoeologous chromosome groups 2, 3, and 5 showing orthologous relation with other monocot plants. Most genes were interrupted by introns and the gene products were localized in cytoplasm, nucleus, and cell organelles. TaAFB3, TaAFB5, and TaAFB8 had nuclear localization signals. The evolutionary constraint suggested paralogous sister pairs and orthologous genes went through strong purifying selection process and are slowly evolving at protein level. Functional annotation revealed all TaAFB genes participated in auxin activated signaling pathway and SCF-mediated ubiquitination process. Furthermore, in silico expression study revealed their diverse expression profiles during various developmental stages in different tissues and organs as well as during biotic and abiotic stress. QRT-PCR based studies suggested distinct expression pattern of TIR1-1, TIR1-3, TaAFB1, TaAFB2, TaAFB3, TaAFB4, TaAFB5, TaAFB7, and TaAFB8 displaying maximum expression at 24 and 48 h post inoculation in both susceptible and resistant near isogenic wheat lines infected with leaf rust pathogen. Importantly, this also reflects coordinated responses in expression patterns of wheat TIR1/AFB genes during progression stages of leaf rust infection.
PMID: 36100728
PLoS One , IF:3.24 , 2022 , V17 (10) : Pe0274740 doi: 10.1371/journal.pone.0274740
Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress.
Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, Canada.; Department of Biology, School of Natural Sciences, Laurentian University, Sudbury, Ontario, Canada.
Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27-45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value /=1 (upregulated) or
PMID: 36227867
PLoS One , IF:3.24 , 2022 , V17 (10) : Pe0275588 doi: 10.1371/journal.pone.0275588
Ecotype-specific blockage of tasiARF production by two different RNA viruses in Arabidopsis.
Department of Plant Biotechnology, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Godollo, Hungary.; Doctoral School of Biology, Institute of Biology, ELTE Eotvos Lorand University, Budapest, Hungary.
Arabidopsis thaliana is one of the most studied model organisms of plant biology with hundreds of geographical variants called ecotypes. One might expect that this enormous genetic variety could result in differential response to pathogens. Indeed, we observed previously that the Bur ecotype develops much more severe symptoms (upward curling leaves and wavy leaf margins) upon infection with two positive-strand RNA viruses of different families (turnip vein-clearing virus, TVCV, and turnip mosaic virus, TuMV). To find the genes potentially responsible for the ecotype-specific response, we performed a differential expression analysis of the mRNA and sRNA pools of TVCV and TuMV-infected Bur and Col plants along with the corresponding mock controls. We focused on the genes and sRNAs that showed an induced or reduced expression selectively in the Bur virus samples in both virus series. We found that the two ecotypes respond to the viral infection differently, yet both viruses selectively block the production of the TAS3-derived small RNA specimen called tasiARF only in the virus-infected Bur plants. The tasiARF normally forms a gradient through the adaxial and abaxial parts of the leaf (being more abundant in the adaxial part) and post-transcriptionally regulates ARF4, a major leaf polarity determinant in plants. The lack of tasiARF-mediated silencing could lead to an ectopically expressed ARF4 in the adaxial part of the leaf where the misregulation of auxin-dependent signaling would result in an irregular growth of the leaf blade manifesting as upward curling leaf and wavy leaf margin. QTL mapping using Recombinant Inbred Lines (RILs) suggests that the observed symptoms are the result of a multigenic interaction that allows the symptoms to develop only in the Bur ecotype. The particular nature of genetic differences leading to the ecotype-specific symptoms remains obscure and needs further study.
PMID: 36197942
PLoS One , IF:3.24 , 2022 , V17 (10) : Pe0275566 doi: 10.1371/journal.pone.0275566
Identification and characterization of miRNAome and target genes in Pseudostellaria heterophylla.
Guizhou University of Traditional Chinese Medicine, Guiyang, China.
miRNAs play a crucial role in the development and growth of plants by inhibiting the function of targeted genes at the post-transcription level. However, no miRNAs in Pseudostellaria heterophylla have been reported and their function in the morphogenesis of organs is still unclear. In this study, a total of 159 conserved miRNAs (belonging to 64 families) and 303 level miRNAs were identified from P. heterophylla. Some of them showed specifically up or down-regulated expression in different tissues and numbers of unigenes involved in Plant-pathogen interaction and MAPK signaling pathway-plant were targeted. The significant negative correlation of expression profiles between 30 miRNAs and their target genes (37 unigenes) was observed, respectively. Further, a large number of genes involved with signal transduction of auxin, zeatin, abscisic acid and, jasmonic acid were targeted. Predicated targets of two miRNAs were validated by 5'RLM-RACE, respectively. A large number of mRNAs from four pathogens were targeted by miRNAs from P. heterophylla and some of them were targeted by miR414. In summary, we reported a population of miRNAs from four different vegetative tissues of P. heterophylla by high throughput sequencing, which was analyzed by combining with the constructed transcriptome. These results may help to explain the function of miRNAs in the morphogenesis of organs and defense of pathogens, and may provide theoretical basis for breeding and genetic improvement of P. heterophylla.
PMID: 36197881
Funct Plant Biol , IF:3.101 , 2022 Sep doi: 10.1071/FP22002
Crucial role of Arabidopsis glutaredoxin S17 in heat stress response revealed by transcriptome analysis.
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 Oct , V6 (10) : Pe456 doi: 10.1002/pld3.456
Phenotypic and transcriptomic analysis reveals early stress responses in transgenic rice expressing Arabidopsis DREB1a.
Department of Crop, Soil, and Environmental Sciences University of Arkansas System Division of Agriculture Fayetteville Arkansas USA.; Present address: Biological and Life Sciences Division, School of Arts and Sciences Ahmedabad University Central Campus Navrangpura Ahmedabad India.; Department of Agriculture Federal University of Lavras Lavras Minas Gerais Brazil.
Overexpression of Arabidopsis dehydration response element binding 1a (DREB1a) is a well-known approach for developing salinity, cold and/or drought stress tolerance. However, understanding of the genetic mechanisms associated with DREB1a expression in rice is generally limited. In this study, DREB1a-associated early responses were investigated in a transgenic rice line harboring cold-inducible DREB1a at a gene stacked locus. Although the function of other genes in the stacked locus was not relevant to stress tolerance, this study demonstrates DREB1a can be co-localized with other genes for multigenic trait enhancement. As expected, the transgenic lines displayed improved tolerance to salinity stress and water withholding as compared with non-transgenic controls. RNA sequencing and transcriptome analysis showed upregulation of complex transcriptional networks and metabolic reprogramming as DREB1a expression led to the upregulation of multiple transcription factor gene families, suppression of photosynthesis, and induction of secondary metabolism. In addition to the detection of previously described mechanisms such as production of protective molecules, potentially novel pathways were also revealed. These include jasmonate, auxin, and ethylene signaling, induction of JAZ and WRKY regulons, trehalose synthesis, and polyamine catabolism. These genes regulate various stress responses and ensure timely attenuation of the stress signal. Furthermore, genes associated with heat stress response were downregulated in DREB1a expressing lines, suggesting antagonism between heat and dehydration stress response pathways. In summary, through a complex transcriptional network, multiple stress signaling pathways are induced by DREB1a that presumably lead to early perception and prompt response toward stress tolerance as well as attenuation of the stress signal to prevent deleterious effects of the runoff response.
PMID: 36267847
PeerJ , IF:2.984 , 2022 , V10 : Pe14236 doi: 10.7717/peerj.14236
Identification and functional analysis of PIN family genes in Gossypium barbadense.
College of Agronomy, Xinjiang Agricultural University, Urumqi, Xinjiang, China.; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China.; Postdoctoral Research Station, Xinjiang Agricultural University, Urumqi, Xinjiang, China.
Background: PIN proteins are an important class of auxin polar transport proteins that play an important regulatory role in plant growth and development. However, their characteristics and functions have not been identified in Gossypium barbadense. Methods: PIN family genes were identified in the cotton species G. barbadense, Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, and detailed bioinformatics analyses were conducted to explore the roles of these genes in G. barbadense using transcriptome data and quantitative reverse-transcription polymerase chain reaction (qRT-PCR) technology. Functional verification of the genes was performed using virus-induced gene silencing (VIGS) technology. Results: A total of 138 PIN family genes were identified in the four cotton species; the genes were divided into seven subgroups. GbPIN gene family members were widely distributed on 20 different chromosomes, and most had repeated duplication events. Transcriptome analysis showed that some genes had differential expression patterns in different stages of fiber development. According to 'PimaS-7' and '5917' transcript component association analysis, the transcription of five genes was directly related to endogenous auxin content in cotton fibers. qRT-PCR analysis showed that the GbPIN7 gene was routinely expressed during fiber development, and there were significant differences among materials. Transient silencing of the GbPIN7 gene by VIGS led to significantly higher cotton plant growth rates and significantly lower endogenous auxin content in leaves and stems. This study provides comprehensive analyses of the roles of PIN family genes in G. barbadense and their expression during cotton fiber development. Our results will form a basis for further PIN auxin transporter research.
PMID: 36275460
3 Biotech , IF:2.406 , 2022 Nov , V12 (11) : P326 doi: 10.1007/s13205-022-03392-z
Identification, characterization, and genome sequencing of Brevibacterium sediminis MG-1 isolate with growth-promoting properties.
Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia.grid.77268.3c0000 0004 0543 9688; Laboratory of Agrobioengineering, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia.grid.77268.3c0000 0004 0543 9688; Department of Molecular Pathobiology, New York University College of Dentistry, New York, USA.grid.137628.90000 0004 1936 8753; Research Center Regulatory Genomics, Institute of Fundamental Medicine and Biology, Kazan (Volga Region), Federal University, Kazan, Russia.grid.77268.3c0000 0004 0543 9688; Department of Breeding and Biotechnology of Potatoes, Tatar Research Institute of Agriculture, Federal Research Center "Kazan Scientific Center of Russian Academy of Sciences", Kazan, Russia.grid.465285.80000 0004 0637 9007
In recent years, plant growth-promoting rhizobacteria (PGPR) have received increased attention due to their prospective use as biofertilizers for the enhancement of crop growth and yields. However, there is a growing need to identify new PGPR isolates with additional beneficial properties. In this paper, we describe the identification of a new strain of a non-sporulating Gram-positive bacterium isolated from the rhizosphere of potato plants, classified as Brevibacterium sediminis MG-1 based on whole-genome sequencing. The bacteria are aerobic; they grow in a pH range of 6.0-10.0 (optimum 6.0), and a temperature range of 20-37 degrees C (optimum 30 degrees C). At 96 h of cultivation, strain MG-1 synthesizes 28.65 microg/ml of indole-3-acetic acid (IAA) when 500 microg/ml of l-tryptophan is added. It is a producer of catechol-type siderophores and ACC deaminase (213 +/- 12.34 ng/ml) and shows halotolerance. Treatment of pea, rye, and wheat seeds with a suspension of MG-1 strain cells resulted in the stimulation of stem and root biomass accumulation by 12-26% and 6-25% (P < 0.05), respectively. Treatment of seeds with bacteria in the presence of high salt concentration reduced the negative effects of salt stress on plant growth by 18-50%. The hypothetical gene lin, encoding the bacteriocin Linocin-M18, RIPP-like proteins, and polyketide synthase type III (T3PKS) loci, gene clusters responsible for iron acquisition and metabolism of siderophores, as well as gene clusters responsible for auxin biosynthesis, were identified in the B. sediminis MG-1 genome. Thus, the rhizosphere-associated strain B. sediminis MG-1 has growth-stimulating properties and can be useful for the treatment of plants grown on soils with high salinity. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-022-03392-z.
PMID: 36276447
3 Biotech , IF:2.406 , 2022 Oct , V12 (10) : P262 doi: 10.1007/s13205-022-03322-z
Phosphate solubilization and indole acetic acid production by rhizosphere yeast Torulaspora globosa: improvement of culture conditions for better performance in vitro.
Pos-Graduacao Em Producao Vegetal E Bioprocessos Associados, Universidade Federal de Sao Carlos, Rod Anhanguera km 174, Araras, Sao Paulo, Brazil.grid.411247.50000 0001 2163 588X; Departamento de Tecnologia Agroindustrial E Socio-Economia Rural, Universidade Federal de Sao Carlos, Rod. Anhanguera km 174, Araras, Sao Paulo, Brazil.grid.411247.50000 0001 2163 588X; Departamento de Recursos Naturais E Protecao Ambiental, Universidade Federal de Sao Carlos, Rod Anhanguera km 174, Araras, Sao Paulo, Brazil.grid.411247.50000 0001 2163 588X
The rhizosphere yeast Torulaspora globosa is known to produce indole acetic acid (IAA) and to solubilize minerals. Due to the prospective use of this yeast as a biostimulant for agricultural applications, this work aimed to optimize the cultural conditions for both IAA production and phosphate solubilization. For phosphate solubilization, the temperature (20, 25 and 30 degrees C), initial medium pH (3.0, 5.0, and 7.0), and shaker speed (without mixing, 100 rpm, 150 rpm, and 200 rpm) were considered using the one-factor-at-a-time (OFAT) design. Temperature of 25 degrees C, initial medium pH 7.0, and static cultures were the conditions of greatest phosphate solubilization, with 40% of the total phosphorus content solubilized from calcium phosphate (419.86 mg L(-1)) after 48 h. By using the response surface methodology, the maximum IAA production (217.73 microg mL(-1)) was obtained with the highest initial pH 7.0, the lowest nitrogen, and glucose concentrations (5 g L(-1) and 10 g L(-1), respectively) and the lowest agitator speed (100 rpm). Further tests indicated that nitrogen affected significantly IAA production and the absence of nitrogen in the medium promoted higher IAA production (457 microg mL(-1)). The results obtained here may contribute to the scaling up for industrial and agricultural applications of a yeast-based product with T. globosa.
PMID: 36091086
J Math Biol , IF:2.259 , 2022 Sep , V85 (4) : P41 doi: 10.1007/s00285-022-01793-5
Scaling relations for auxin waves.
Mathematical Institute, Universiteit Leiden, P.O. Box 9512, 2300 RA, Leiden, The Netherlands.; Department of Mathematics, Kennesaw State University, 850 Polytechnic Lane, MD #9085, Marietta, GA, 30060, USA.; Mathematical Institute, Universiteit Leiden, P.O. Box 9512, 2300 RA, Leiden, The Netherlands. hhupkes@math.leidenuniv.nl.; Mathematical Institute and Institute of Biology Leiden, Universiteit Leiden, P.O. Box 9512, 2300 RA, Leiden, The Netherlands.
We analyze an 'up-the-gradient' model for the formation of transport channels of the phytohormone auxin, through auxin-mediated polarization of the PIN1 auxin transporter. We show that this model admits a family of travelling wave solutions that is parameterized by the height of the auxin-pulse. We uncover scaling relations for the speed and width of these waves and verify these rigorous results with numerical computations. In addition, we provide explicit expressions for the leading-order wave profiles, which allows the influence of the biological parameters in the problem to be readily identified. Our proofs are based on a generalization of the scaling principle developed by Friesecke and Pego to construct pulse solutions to the classic Fermi-Pasta-Ulam-Tsingou model, which describes a one-dimensional chain of coupled nonlinear springs.
PMID: 36163567
Curr Microbiol , IF:2.188 , 2022 Sep , V79 (11) : P331 doi: 10.1007/s00284-022-03031-z
Analysis of Blueberry Plant Rhizosphere Bacterial Diversity and Selection of Plant Growth Promoting Rhizobacteria.
School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China. amy133253@126.com.; School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi, China.; Shaanxi Key Laboratory of Bioresources, Shaanxi University of Technology, Hanzhong, Shaanxi, China.; School of Nutrition and Food Sciences, Louisiana State University, Baton Rouge, LA, USA.
Microbial metabolites in rhizosphere soil are important to plant growth. In this study, microbial diversity in blueberry plant rhizosphere soil was characterized using high-throughput amplicon sequencing technology. There were 11 bacterial phyla and three fungal phyla dominating in the soil. In addition, inorganic-phosphate-solubilizing bacteria (iPSB) in the rhizosphere soil were isolated and evaluated by molybdenum-antimony anti-coloration method. Their silicate solubilizing, auxin production, and nitrogen fixation capabilities were also determined. Eighteen iPSB in the rhizosphere soil strains were isolated and identified as Buttiauxella, Paraburkholderia and Pseudomonas. The higher phosphorus-solubilizing capacity and auxin production in blueberry rhizosphere belonged to genus Buttiauxella sp. The strains belong to genus Paraburkholderia had the same function of dissolving both phosphorus and producing auxin, as well as silicate and nitrogen fixation. The blueberry seeds incubated with the strains had higher germination rates. The results of this study could be helpful in developing the plant growth-promoting rhizobacteria (PGPR) method for enhancing soil nutrients to blueberry plant.
PMID: 36156157
Methods Enzymol , IF:1.6 , 2022 , V676 : P239-278 doi: 10.1016/bs.mie.2022.07.038
Using targeted metabolomics to elucidate the indole auxin network in plants.
Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, United States. Electronic address: cohen047@umn.edu.; Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, United States.; Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, MN, United States; Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, MN, United States.
The plant hormone auxin plays important roles throughout the entire life span of a plant and facilitates its adaptation to a changing environment. Multiple metabolic pathways intersect to control the levels and flux through indole-3-acetic acid (IAA), the primary auxin in most plant species. Measurement of changes in these pathways represents an important objective to understanding core aspects of auxin signal regulation. Such studies have become approachable through the technologies encompassed by targeted metabolomics. By monitoring incorporation of stable isotopes from labeled precursors into proposed intermediates, it is possible to trace pathway utilization and characterize new biosynthetic routes to auxin. Chemical inhibitors that target specific steps or entire pathways related to auxin synthesis aid these techniques. Here we describe methods for obtaining stable isotope labeled pathway intermediates necessary for pathway analysis and quantification of compounds. We describe how to use isotope dilution with methods employing either gas chromatography or high performance liquid chromatography mass spectrometry techniques for sensitive analysis of IAA. Complete biosynthetic pathway analysis in seedlings using multiple stable isotope-labeled precursors and chemical inhibitors coupled with highly sensitive liquid chromatography-mass spectrometry methods are described that allow rapid measurement of isotopic flux into biochemical pools. These methods should prove to be useful to researchers studying aspects of the auxin metabolic network in vivo in a variety of plant tissues and during various environmental conditions.
PMID: 36280352
Plant Commun , 2022 Oct : P100456 doi: 10.1016/j.xplc.2022.100456
A chromosome-level genome assembly for Dracaena cochinchinesis reveals molecular basis of its longevity and formation of dragon's blood.
Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education& National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China.; Novogene Bioinformatics Institute, 100083 Beijing, China.; Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Jinghong 666100, China.; Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China.; Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.; Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education& National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100193, China; Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou 570311, China. Electronic address: wjianh@263.net.
Dracaena, a remarkably long-lived and slowly maturing species of plant, is world famous for its ability to produce dragon's blood, a precious traditional medicine used by different cultures since ancient times. However, there is no detailed and high-quality genome available for this species at present; thus, the molecular mechanisms underlying the important traits of this plant are largely unknown. These factors seriously limit the protection and regeneration of the rare and endangered plant resources. Here, we sequenced and assembled the genome of Dracaena cochinchinensis at the chromosomal level. The D. cochinchinensis genome covered 1.21 Gb with a scaffold N50 of 50.06 Mb and encodes 31,619 predicted protein-coding genes. Analysis showed that D. cochinchinensis has undergone two whole genome duplications (WGDs) and two long terminal repeat (LTR) insertion burst events. The expansion of two genes, cis-zeatin O-glucosyltransferase (cZOGT) and small auxin up-regulated RNA (SAUR), were found to account for its longevity and slow growth. Two transcription factors (bHLH and MYB) were found to be core regulators of the flavonoid biosynthesis pathway and reactive oxygen species (ROS) was identified as the specific signal molecule responsible for the injury-induced formation of dragon's blood. Our study provides high-quality genomic knowledge relating to D. cochinchinensis and significant insight into the molecular mechanisms responsible for longevity and the formation of dragon's blood. These findings will facilitate the resource protection and sustainable utilization of Dracaena.
PMID: 36196059
Curr Protoc , 2022 Oct , V2 (10) : Pe562 doi: 10.1002/cpz1.562
Maize Seedling Growth and Hormone Response Assays Using the Rolled Towel Method.
Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa.; Current address: Corteva Agriscience, 8325 NW 62nd Ave, Johnston, Iowa.
Root system architecture is a critical factor in maize health and stress resilience. Determining the genetic and environmental factors that shape maize root system architecture is an active research area. However, the ability to phenotype juvenile root systems is hindered by the use of field-grown and soil-based systems. An alternative to soil- and field-based growing conditions for maize seedlings is a controlled environment with a soil-free medium, which can facilitate root system phenotyping. Here, we describe how to grow maize under soil-free conditions for up to 12 days to facilitate root phenotyping. Maize seeds are sterilized and planted on specialized seed germination paper to minimize fungal contamination and ensure synchronized seedling growth, followed by imaging at the desired time point. The root images are then analyzed to quantify traits of interest, such as primary root length, lateral root density, seminal root length, and seminal root number. In addition, juvenile shoot traits can be quantified using manual annotation methods. We also outline the steps for performing rigorous hormone response assays for four classical phytohormones: auxin, brassinosteroid, cytokinin, and jasmonic acid. This protocol can be rapidly scaled up and is compatible with genetic screens and sample collection for downstream molecular analyses such as transcriptomics and proteomics. (c) 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Maize seedling rolled towel assay and phenotyping Basic Protocol 2: Maize seedling hormone response assays using the rolled towel assay.
PMID: 36194012
Microbiol Resour Announc , 2022 Sep , V11 (9) : Pe0042522 doi: 10.1128/mra.00425-22
Draft Genome Sequence of Bacillus paralicheniformis Strain GSFE7, a Halotolerant Plant Growth-Promoting Bacterial Endophyte Isolated from Cultivated Saline Areas of the Dead Sea Region.
Department of Land, Water, and Environment, School of Agriculture, The University of Jordan, Amman, Jordan.; Department of Biological Sciences, School of Science, The University of Jordan, Amman, Jordan.; Hamdi Mango Center for Scientific Research, The University of Jordan, Amman, Jordan.
Here, we report the draft genome sequence of Bacillus paralicheniformis strain GSFE7, which was isolated from saline fields near the Dead Sea region. The genome was 4,452,800 bp in size and contained 4,382 coding sequences. Several genes were predicted to be involved in auxin production, nitrogen fixation, phosphate mobilization, and putative production of siderophores and antibiotics such as bacitracin, butirosin, and fengycin.
PMID: 35950866
Plant Commun , 2022 Sep , V3 (5) : P100351 doi: 10.1016/j.xplc.2022.100351
Natural variation in the transcription factor REPLUMLESS contributes to both disease resistance and plant growth in Arabidopsis.
School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: deng@pku.edu.cn.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: heguangming@pku.edu.cn.
When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, frequently incurring growth penalties. This phenomenon is known as the growth-defense tradeoff and is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes require further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly upregulated in rpl mutants, leading to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. RPL also repressed flavonol synthesis by directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.
PMID: 35752937
Plant Commun , 2022 Sep , V3 (5) : P100327 doi: 10.1016/j.xplc.2022.100327
Right time, right place: The dynamic role of hormones in rhizobial infection and nodulation of legumes.
Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia.; Discipline of Biological Sciences, School of Natural Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia. Electronic address: eloise.foo@utas.edu.au.
Many legume plants form beneficial associations with rhizobial bacteria that are hosted in new plant root organs, nodules, in which atmospheric nitrogen is fixed. This association requires the precise coordination of two separate programs, infection in the epidermis and nodule organogenesis in the cortex. There is extensive literature indicating key roles for plant hormones during nodulation, but a detailed analysis of the spatial and temporal roles of plant hormones during the different stages of nodulation is required. This review analyses the current literature on hormone regulation of infection and organogenesis to reveal the differential roles and interactions of auxin, cytokinin, brassinosteroids, ethylene, and gibberellins during epidermal infection and cortical nodule initiation, development, and function. With the exception of auxin, all of these hormones suppress infection events. By contrast, there is evidence that all of these hormones promote nodule organogenesis, except ethylene, which suppresses nodule initiation. This differential role for many of the hormones between the epidermal and cortical programs is striking. Future work is required to fully examine hormone interactions and create a robust model that integrates this knowledge into our understanding of nodulation pathways.
PMID: 35605199