Trends Plant Sci , IF:18.313 , 2023 Aug doi: 10.1016/j.tplants.2023.07.001
25 Years of thermomorphogenesis research: milestones and perspectives.
Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany. Electronic address: marcel.quint@landw.uni-halle.de.; Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany.; School of Biological Sciences, Monash University, Clayton Campus, VIC 3800, Australia.; Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, UK.; IFEVA, Universidad de Buenos Aires and CONICET, 1417 Buenos Aires, Argentina; Fundacion Instituto Leloir, C1405 BWE, Buenos Aires, Argentina.; Department of Biology, Wilfrid Laurier University, Waterloo, Ontario N2L 3C5, Canada.; Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.; School of Life Sciences, Peking University, Beijing 100871, China.; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium.; Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland.; University of Bristol, Bristol BS8 1TQ, UK.; Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh 3H9 3BF, UK.; Laboratory of Plant Physiology, Wageningen University & Research, 6708 PB Wageningen, The Netherlands.; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China.; Department of Biological Sciences, Sungkyunkwan University, 16419 Suwon, South Korea.; School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.; Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK.; Department of Pharmaceutical Biology, Julius von Sachs Institute of Biosciences, University of Wurzburg, 97082 Wurzburg, Germany.; Department of Life Sciences, Korea University, 02841 Seoul, Korea.; Department of Chemistry, Seoul National University, 08826 Seoul, Korea; Plant Genomics and Breeding Institute, Seoul National University, 08826 Seoul, Korea.; Department of Crop Genetics, John Innes Centre, Norwich NR4 7UH, UK.; Department of Biosciences, University of Milan, 20133 Milan, Italy.; Department of Plant Responses to Stress, Centre for Research in Agricultural Genomics (CRAG), Campus UAB, 08193 Cerdanyola, Barcelona, Spain.; Institute of Plant Sciences, University of Bern, 3013 Bern, Switzerland.; Leibniz Institut fur Gemuse und Zierpflanzenbau, 14979 Grossbeeren, Germany; Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany.; Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80521, USA.; Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, The Netherlands. Electronic address: m.vanzanten@uu.nl.
In 1998, Bill Gray and colleagues showed that warm temperatures trigger arabidopsis hypocotyl elongation in an auxin-dependent manner. This laid the foundation for a vibrant research discipline. With several active members of the 'thermomorphogenesis' community, we here reflect on 25 years of elevated ambient temperature research and look to the future.
PMID: 37574427
Trends Plant Sci , IF:18.313 , 2023 Aug , V28 (8) : P873-875 doi: 10.1016/j.tplants.2023.05.003
A complex signaling trio in seed germination: Auxin-JA-ABA.
Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland.; Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Jagiellonska 28, 40-032 Katowice, Poland. Electronic address: agata.daszkowska@us.edu.pl.
Recently. Mei et al. discovered the molecular mechanism behind the synergistic action of auxins and jasmonates in enhancing the role of abscisic acid (ABA) in seed germination. They found that JASMONATE-ZIM DOMAIN (JAZ) proteins interact with AUXIN RESPONSE FACTOR (ARF)-16 to mediate auxin-jasmonic acid (JA) crosstalk. Furthermore, they revealed that ARF16 interacts with ABSCISIC ACID INSENSITIVE (ABI)-5 and positively modulates ABA responses at seed germination.
PMID: 37208202
Nucleic Acids Res , IF:16.971 , 2023 Aug , V51 (15) : P7798-7819 doi: 10.1093/nar/gkad521
Spatially resolved transcriptomic analysis of the germinating barley grain.
Department of Animal, Plant and Soil Science, La Trobe Institute for Sustainable Agriculture and Food, School of Agriculture, Biomedical and Environmental Sciences, La Trobe University, Bundoora, Victoria 3086, Australia.; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Building, La Trobe University, Bundoora, VIC 3086, Australia.; Research Centre for Engineering Biology, College of Life Science, Zhejiang University, 718 East Haizhou Road, Haining, Jiaxing, Zhejiang 314400, China.
Seeds are a vital source of calories for humans and a unique stage in the life cycle of flowering plants. During seed germination, the embryo undergoes major developmental transitions to become a seedling. Studying gene expression in individual seed cell types has been challenging due to the lack of spatial information or low throughput of existing methods. To overcome these limitations, a spatial transcriptomics workflow was developed for germinating barley grain. This approach enabled high-throughput analysis of spatial gene expression, revealing specific spatial expression patterns of various functional gene categories at a sub-tissue level. This study revealed over 14 000 genes differentially regulated during the first 24 h after imbibition. Individual genes, such as the aquaporin gene family, starch degradation, cell wall modification, transport processes, ribosomal proteins and transcription factors, were found to have specific spatial expression patterns over time. Using spatial autocorrelation algorithms, we identified auxin transport genes that had increasingly focused expression within subdomains of the embryo over time, suggesting their role in establishing the embryo axis. Overall, our study provides an unprecedented spatially resolved cellular map for barley germination and identifies specific functional genomics targets to better understand cellular restricted processes during germination. The data can be viewed at https://spatial.latrobe.edu.au/.
PMID: 37351575
Nat Plants , IF:15.793 , 2023 Aug doi: 10.1038/s41477-023-01494-x
Plastid-localized amino acid metabolism coordinates rice ammonium tolerance and nitrogen use efficiency.
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.; VIB-UGent Center for Plant Systems Biology, Ghent, Belgium.; Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, China.; Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. Tom.Beeckman@psb.vib-ugent.be.; VIB-UGent Center for Plant Systems Biology, Ghent, Belgium. Tom.Beeckman@psb.vib-ugent.be.; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization and MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Sanya Institute of Nanjing Agricultural University, Nanjing Agricultural University, Nanjing, China. wexua@njau.edu.cn.
Ammonium toxicity affecting plant metabolism and development is a worldwide problem impeding crop production. Remarkably, rice (Oryza sativa L.) favours ammonium as its major nitrogen source in paddy fields. We set up a forward-genetic screen to decipher the molecular mechanisms conferring rice ammonium tolerance and identified rohan showing root hypersensitivity to ammonium due to a missense mutation in an argininosuccinate lyase (ASL)-encoding gene. ASL localizes to plastids and its expression is induced by ammonium. ASL alleviates ammonium-inhibited root elongation by converting the excessive glutamine to arginine. Consequently, arginine leads to auxin accumulation in the root meristem, thereby stimulating root elongation under high ammonium. Furthermore, we identified natural variation in the ASL allele between japonica and indica subspecies explaining their different root sensitivity towards ammonium. Finally, we show that ASL expression positively correlates with root ammonium tolerance and that nitrogen use efficiency and yield can be improved through a gain-of-function approach.
PMID: 37604972
Nat Plants , IF:15.793 , 2023 Aug , V9 (8) : P1306-1317 doi: 10.1038/s41477-023-01485-y
A network of CLAVATA receptors buffers auxin-dependent meristem maintenance.
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.; Department of Biological Sciences, Auburn University, Auburn, AL, USA.; Thermo Fisher Scientific, Raleigh, NC, USA.; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. zackn@email.unc.edu.; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. zackn@email.unc.edu.
Plant body plans are elaborated in response to both environmental and endogenous cues. How these inputs intersect to promote growth and development remains poorly understood. During reproductive development, central zone stem cell proliferation in inflorescence meristems is negatively regulated by the CLAVATA3 (CLV3) peptide signalling pathway. In contrast, floral primordia formation on meristem flanks requires the hormone auxin. Here we show that CLV3 signalling is also necessary for auxin-dependent floral primordia generation and that this function is partially masked by both inflorescence fasciation and heat-induced auxin biosynthesis. Stem cell regulation by CLAVATA signalling is separable from primordia formation but is also sensitized to temperature and auxin levels. In addition, we uncover a novel role for the CLV3 receptor CLAVATA1 in auxin-dependent meristem maintenance in cooler environments. As such, CLV3 signalling buffers multiple auxin-dependent shoot processes across divergent thermal environments, with opposing effects on cell proliferation in different meristem regions.
PMID: 37550370
Trends Biochem Sci , IF:13.807 , 2023 Aug doi: 10.1016/j.tibs.2023.07.006
Substrate recognition and transport mechanism of the PIN-FORMED auxin exporters.
Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.; Plant Systems Biology, School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany.; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, NY 10016, USA.; Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark. Electronic address: bpp@mbg.au.dk.
Auxins are pivotal plant hormones that regulate plant growth and transmembrane polar auxin transport (PAT) direct patterns of development. The PIN-FORMED (PIN) family of membrane transporters mediate auxin export from the plant cell and play crucial roles in PAT. Here we describe the recently solved structures of PIN transporters, PIN1, PIN3, and PIN8, and also their mechanisms of substrate recognition and transport of auxin. We compare structures of PINs in both inward- and outward-facing conformations, as well as PINs with different binding configurations for auxin. By this comparative analysis, a model emerges for an elevator transport mechanism. Central structural elements necessary for function are identified, and we show that these are shared with other distantly related protein families.
PMID: 37574372
Plant Cell , IF:11.277 , 2023 Aug doi: 10.1093/plcell/koad214
The transcription factor ERF108 interacts with AUXIN RESPONSE FACTORs to mediate cotton fiber secondary cell wall biosynthesis.
Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China.; Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China.; College of Biomedicine and Health & College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
Phytohormones play indispensable roles in plant growth and development. However, the molecular mechanisms underlying phytohormone-mediated regulation of fiber secondary cell wall (SCW) formation in cotton (Gossypium hirsutum) remain largely underexplored. Here, we provide mechanistic evidence for functional interplay between the AP2/ERF transcription factor GhERF108 and auxin response factors GhARF7-1 and GhARF7-2 in dictating the ethylene-auxin signaling crosstalk that regulates fiber SCW biosynthesis. Specifically, in vitro cotton ovule culture revealed that ethylene and auxin promote fiber SCW deposition. GhERF108 RNAi cotton displayed remarkably reduced cell wall thickness compared with controls. GhERF108 interacted with GhARF7-1 and GhARF7-2 to enhance the activation of the MYB transcription factor gene GhMYBL1 (MYB domain like protein 1) in fibers. GhARF7-1 and GhARF7-2 respond to auxin signals that promote fiber SCW thickening. GhMYBL1 RNAi and, GhARF7-1 and GhARF7-2 VIGS cotton displayed similar defects in fiber SCW formation as GhERF108 RNAi cotton. Moreover, the ethylene and auxin responses were reduced in GhMYBL1 RNAi plants. GhMYBL1 directly binds to the promoters of GhCesA4-1, GhCesA4-2, and GhCesA8-1 and activates their expression to promote cellulose biosynthesis, thereby boosting fiber SCW formation. Collectively, our findings demonstrate that the collaboration between GhERF108 and GhARF7-1 or GhARF7-2 establishes ethylene-auxin signaling crosstalk to activate GhMYBL1, ultimately leading to the activation of fiber SCW biosynthesis.
PMID: 37542517
Plant Cell , IF:11.277 , 2023 Aug , V35 (8) : P2871-2886 doi: 10.1093/plcell/koad130
The transcriptional hub SHORT INTERNODES1 integrates hormone signals to orchestrate rice growth and development.
State Key Laboratory of Crop Genetics and Germplasm Enhancement and Utilization, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.; State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
Plants have evolved sophisticated mechanisms to coordinate their growth and stress responses via integrating various phytohormone signaling pathways. However, the precise molecular mechanisms orchestrating integration of the phytohormone signaling pathways remain largely obscure. In this study, we found that the rice (Oryza sativa) short internodes1 (shi1) mutant exhibits typical auxin-deficient root development and gravitropic response, brassinosteroid (BR)-deficient plant architecture and grain size as well as enhanced abscisic acid (ABA)-mediated drought tolerance. Additionally, we found that the shi1 mutant is also hyposensitive to auxin and BR treatment but hypersensitive to ABA. Further, we showed that OsSHI1 promotes the biosynthesis of auxin and BR by activating the expression of OsYUCCAs and D11, meanwhile dampens ABA signaling by inducing the expression of OsNAC2, which encodes a repressor of ABA signaling. Furthermore, we demonstrated that 3 classes of transcription factors, AUXIN RESPONSE FACTOR 19 (OsARF19), LEAF AND TILLER ANGLE INCREASED CONTROLLER (LIC), and OsZIP26 and OsZIP86, directly bind to the promoter of OsSHI1 and regulate its expression in response to auxin, BR, and ABA, respectively. Collectively, our results unravel an OsSHI1-centered transcriptional regulatory hub that orchestrates the integration and self-feedback regulation of multiple phytohormone signaling pathways to coordinate plant growth and stress adaptation.
PMID: 37195873
Plant Cell , IF:11.277 , 2023 Aug , V35 (8) : P2848-2870 doi: 10.1093/plcell/koad125
SHORT ROOT and INDETERMINATE DOMAIN family members govern PIN-FORMED expression to regulate minor vein differentiation in rice.
Biotechnology Research Institute (BRI), Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China.; Joint Laboratory for Photosynthesis Enhancement and C4 Rice Development, BRI, CAAS, Beijing 100081, China.; C4 Rice Centre, International Rice Research Institute, Los Banos, Laguna 4030, Philippines.; Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
C3 and C4 grasses directly and indirectly provide the vast majority of calories to the human diet, yet our understanding of the molecular mechanisms driving photosynthetic productivity in grasses is largely unexplored. Ground meristem cells divide to form mesophyll or vascular initial cells early in leaf development in C3 and C4 grasses. Here we define a genetic circuit composed of SHORT ROOT (SHR), INDETERMINATE DOMAIN (IDD), and PIN-FORMED (PIN) family members that specifies vascular identify and ground cell proliferation in leaves of both C3 and C4 grasses. Ectopic expression and loss-of-function mutant studies of SHR paralogs in the C3 plant Oryza sativa (rice) and the C4 plant Setaria viridis (green millet) revealed the roles of these genes in both minor vein formation and ground cell differentiation. Genetic and in vitro studies further suggested that SHR regulates this process through its interactions with IDD12 and 13. We also revealed direct interactions of these IDD proteins with a putative regulatory element within the auxin transporter gene PIN5c. Collectively, these findings indicate that a SHR-IDD regulatory circuit mediates auxin transport by negatively regulating PIN expression to modulate minor vein patterning in the grasses.
PMID: 37154077
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Aug , V120 (35) : Pe2300446120 doi: 10.1073/pnas.2300446120
The transcription factors, STOP1 and TCP20, are required for root system architecture alterations in response to nitrate deficiency.
Global Institute for Food Security, University of Saskatchewan, Saskatoon, Saskatchewan S7N 4J8, Canada.; Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan.; NRGene Canada Inc., Saskatoon, SK S7N 3R3, Canada.; RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan.
Nitrate distribution in soils is often heterogeneous. Plants have adapted to this by modifying their root system architecture (RSA). Previous studies showed that NITRATE-TRANSPORTER1.1 (NRT1.1), which also transports auxin, helps inhibit lateral root primordia (LRP) emergence in nitrate-poor patches, by preferentially transporting auxin away from the LRP. In this study, we identified the regulatory system for this response involving the transcription factor (TF), SENSITIVE-TO-PROTON-RHIZOTOXICITY1 (STOP1), which is accumulated in the nuclei of LRP cells under nitrate deficiency and directly regulates Arabidopsis NRT1.1 expression. Mutations in STOP1 mimic the root phenotype of the loss-of-function NRT1.1 mutant under nitrate deficiency, compared to wild-type plants, including increased LR growth and higher DR5promoter activity (i.e., higher LRP auxin signaling/activity). Nitrate deficiency-induced LR growth inhibition was almost completely reversed when STOP1 and the TF, TEOSINTE-BRANCHED1,-CYCLOIDEA,-PCF-DOMAIN-FAMILY-PROTEIN20 (TCP20), a known activator of NRT1.1 expression, were both mutated. Thus, the STOP1-TCP20 system is required for activation of NRT1.1 expression under nitrate deficiency, leading to reduced LR growth in nitrate-poor regions. We found this STOP1-mediated system is more active as growth media becomes more acidic, which correlates with reductions in soil nitrate as the soil pH becomes more acidic. STOP1 has been shown to be involved in RSA modifications in response to phosphate deficiency and increased potassium uptake, hence, our findings indicate that root growth regulation in response to low availability of the major fertilizer nutrients, nitrogen, phosphorus and potassium, all involve STOP1, which may allow plants to maintain appropriate root growth under the complex and varying soil distribution of nutrients.
PMID: 37611056
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Aug , V120 (31) : Pe2218865120 doi: 10.1073/pnas.2218865120
Endoplasmic reticulum stress controls PIN-LIKES abundance and thereby growth adaptation.
Institute of Biology II, Chair of Molecular Plant Physiology, University of Freiburg, 79104 Freiburg, Germany.; Center for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.; Department of Applied Genetics and Cell Biology, Institute of Molecular Plant Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria.; CNRS-University of Bordeaux, UMR 5200 Membrane Biogenesis Laboratory, National Research Institute for Agriculture, Food and the Environment Bordeaux Aquitaine, 33140 Bordeaux, France.
Extreme environmental conditions eventually limit plant growth [J. R. Dinneny, Annu. Rev. Cell Dev. Biol. 35, 1-19 (2019), N. Gigli-Bisceglia, C. Testerink, Curr. Opin. Plant Biol. 64, 102120 (2021)]. Here, we reveal a mechanism that enables multiple external cues to get integrated into auxin-dependent growth programs in Arabidopsis thaliana. Our forward genetics approach on dark-grown hypocotyls uncovered that an imbalance in membrane lipids enhances the protein abundance of PIN-LIKES (PILS) [E. Barbez et al., Nature 485, 119 (2012)] auxin transport facilitators at the endoplasmic reticulum (ER), which thereby limits nuclear auxin signaling and growth rates. We show that this subcellular response relates to ER stress signaling, which directly impacts PILS protein turnover in a tissue-dependent manner. This mechanism allows PILS proteins to integrate environmental input with phytohormone auxin signaling, contributing to stress-induced growth adaptation in plants.
PMID: 37487064
Curr Biol , IF:10.834 , 2023 Aug , V33 (15) : PR805-R808 doi: 10.1016/j.cub.2023.06.065
Plant signaling: The sugar-coated story of root growth.
Plant-Environment Signaling, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands.; Plant-Environment Signaling, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, the Netherlands. Electronic address: r.pierik@uu.nl.
A new study draws attention to photosynthetically produced sucrose as a major shoot-derived and auxin-dependent regulator of root growth and development in plants.
PMID: 37552945
J Hazard Mater , IF:10.588 , 2023 Aug , V455 : P131637 doi: 10.1016/j.jhazmat.2023.131637
Indole-3-acetic acid and zinc synergistically mitigate positively charged nanoplastic-induced damage in rice.
Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-bioengineering, Guizhou University, Guiyang 550025, PR China.; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, PR China; National Key Laboratory of Rice Biology, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, PR China.; National Key Laboratory of Rice Biology, The Advanced Seed Institute, Zhejiang University, Hangzhou 310058, PR China.; Institute of Nuclear Agricultural Sciences, Zhejiang University, Hangzhou 310058, PR China. Electronic address: zhen.yang@zju.edu.cn.; Hainan Institute, Zhejiang University, Yazhou Bay Science and Technology City, Sanya 572025, PR China. Electronic address: mengjiang@zju.edu.cn.
Recent research has shown that polystyrene nanoplastics (PS-NPs) can inhibit plant growth and the development of crops, such as rice. In this study, we aimed to investigate the effects of PS-NPs of different particle sizes (80 nm, 200 nm, and 2 microm) and charges (negative, neutral, and positive) on rice growth, and to explore the underlying mechanisms and potential strategies for mitigating their impacts. Two-week-old rice plants were planted in a standard (1/2) Murashige-Skoog liquid medium holding 50 mg/L of different particle sizes and/or charged PS-NPs for 10 days, and the liquid medium without PS-NPs was used as control. The results showed that positively charged PS-NPs (80 nm PS-NH(2)) had the greatest impact on plant growth and greatly reduced the dry biomass, root length, and plant height of rice by 41.04%, 46.34%, and 37.45%, respectively. The positively charged NPs with a size of 80 nm significantly decreased the zinc (Zn) and indole-3-acetic acid (IAA, auxin) contents by 29.54% and 48.00% in roots, and 31.15% and 64.30% in leaves, respectively, and down-regulated the relative expression level of rice IAA response and biosynthesis genes. Moreover, Zn and/or IAA supplements significantly alleviated the adverse effects of 80 nm PS-NH(2) on rice plant growth. Exogenous Zn and/or IAA increased seedlings' growth, decreased PS-NPs distribution, maintained redox homeostasis, and improved tetrapyrrole biosynthesis in rice treated with 80 nm PS-NH(2). Our findings suggest that Zn and IAA synergistically alleviate positively charged NP-induced damage in rice.
PMID: 37210880
New Phytol , IF:10.151 , 2023 Aug doi: 10.1111/nph.19157
The YABBY gene SHATTERING1 controls activation rather than patterning of the abscission zone in Setaria viridis.
Donald Danforth Plant Science Center, 975 North Warson Road, St Louis, MO, 63132, USA.; Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, OK, 74078, USA.; College of Biological Sciences, University of Minnesota, St Paul, MN, 55108, USA.
Abscission is predetermined in specialized cell layers called the abscission zone (AZ) and activated by developmental or environmental signals. In the grass family, most identified AZ genes regulate AZ anatomy, which differs among lineages. A YABBY transcription factor, SHATTERING1 (SH1), is a domestication gene regulating abscission in multiple cereals, including rice and Setaria. In rice, SH1 inhibits lignification specifically in the AZ. However, the AZ of Setaria is nonlignified throughout, raising the question of how SH1 functions in species without lignification. Crispr-Cas9 knockout mutants of SH1 were generated in Setaria viridis and characterized with histology, cell wall and auxin immunofluorescence, transmission electron microscopy, hormonal treatment and RNA-Seq analysis. The sh1 mutant lacks shattering, as expected. No differences in cell anatomy or cell wall components including lignin were observed between sh1 and the wild-type (WT) until abscission occurs. Chloroplasts degenerated in the AZ of WT before abscission, but degeneration was suppressed by auxin treatment. Auxin distribution and expression of auxin-related genes differed between WT and sh1, with the signal of an antibody to auxin detected in the sh1 chloroplast. SH1 in Setaria is required for activation of abscission through auxin signaling, which is not reported in other grass species.
PMID: 37533135
New Phytol , IF:10.151 , 2023 Sep , V239 (6) : P2248-2264 doi: 10.1111/nph.19126
Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus.
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.; State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.; Bredesen Center for Interdisciplinary Research, University of Tennessee, Knoxville, TN, 37996, USA.; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.; Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, 30602, USA.; Department of Genetics, University of Georgia, Athens, GA, 30602, USA.; Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.; Department of Academic Education, Central Community College - Hastings, Hastings, NE, 68902, USA.; Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, 80401, USA.; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.; HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA.
Plant establishment requires the formation and development of an extensive root system with architecture modulated by complex genetic networks. Here, we report the identification of the PtrXB38 gene as an expression quantitative trait loci (eQTL) hotspot, mapped using 390 leaf and 444 xylem Populus trichocarpa transcriptomes. Among predicted targets of this trans-eQTL were genes involved in plant hormone responses and root development. Overexpression of PtrXB38 in Populus led to significant increases in callusing and formation of both stem-born roots and base-born adventitious roots. Omics studies revealed that genes and proteins controlling auxin transport and signaling were involved in PtrXB38-mediated adventitious root formation. Protein-protein interaction assays indicated that PtrXB38 interacts with components of endosomal sorting complexes required for transport machinery, implying that PtrXB38-regulated root development may be mediated by regulating endocytosis pathway. Taken together, this work identified a crucial root development regulator and sheds light on the discovery of other plant developmental regulators through combining eQTL mapping and omics approaches.
PMID: 37488708
New Phytol , IF:10.151 , 2023 Aug , V239 (3) : P964-978 doi: 10.1111/nph.19004
Ethylene controls cambium stem cell activity via promoting local auxin biosynthesis.
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China.; College of Horticulture, Qingdao Agricultural University, Qingdao, 266109, Shandong, China.; School of Applied Chemistry and Biotechnology, Shenzhen Polytechnic, Shenzhen, 518055, Guangdong, China.; Core Facilities, College of Life Sciences, Peking University, Beijing, 100871, China.; Faculty of Agriculture, New Valley University, New Valley Governorate, 72511, New Valley, Egypt.; Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, China.; Crop Pathology and Genetic Research Unit, United States Department of Agriculture, Agricultural Research Service, Davis, CA, 95616, USA.; Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA.; Plant Biology Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA.
The vascular cambium is the main secondary meristem in plants that produces secondary phloem (outside) and xylem (inside) on opposing sides of the cambium. The phytohormone ethylene has been implicated in vascular cambium activity, but the regulatory network underlying ethylene-mediated cambial activity remains to be elucidated. Here, we found that PETAL MOVEMENT-RELATED PROTEIN1 (RhPMP1), an ethylene-inducible HOMEODOMAIN-LEUCINE ZIPPER I transcription factor in woody plant rose (Rosa hybrida), regulates local auxin biosynthesis and auxin transport to maintain cambial activity. Knockdown of RhPMP1 resulted in smaller midveins and reduced auxin content, while RhPMP1 overexpression resulted in larger midveins and increased auxin levels compared with the wild-type plants. Furthermore, we revealed that Indole-3-pyruvate monooxygenase YUCCA 10 (RhYUC10) and Auxin transporter-like protein 2 (RhAUX2), encoding an auxin biosynthetic enzyme and an auxin influx carrier, respectively, are direct downstream targets of RhPMP1. In summary, our results suggest that ethylene promotes an auxin maximum in the cambium adjacent to the xylem to maintain cambial activity.
PMID: 37282811
New Phytol , IF:10.151 , 2023 Aug , V239 (3) : P949-963 doi: 10.1111/nph.18988
SlMYB99-mediated auxin and abscisic acid antagonistically regulate ascorbic acids biosynthesis in tomato.
Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 400044, China.
Ascorbic acid (AsA) is a water-soluble antioxidant that plays important roles in plant development and human health. Understanding the regulatory mechanism underlying AsA biosynthesis is imperative to the development of high AsA plants. In this study, we reveal that the auxin response factor SlARF4 transcriptionally inhibits SlMYB99, which subsequently modulates AsA accumulation via transcriptional activation of AsA biosynthesis genes GPP, GLDH, and DHAR. The auxin-dependent transcriptional cascade of SlARF4-SlMYB99-GPP/GLDH/DHAR modulates AsA synthesis, while mitogen-activated protein kinase SlMAPK8 not only phosphorylates SlMYB99, but also activates its transcriptional activity. Both SlMYB99 and SlMYB11 proteins physically interact with each other, thereby synergistically regulating AsA biosynthesis by upregulating the expression of GPP, GLDH, and DHAR genes. Collectively, these results demonstrate that auxin and abscisic acid antagonistically regulate AsA biosynthesis during development and drought tolerance in tomato via the SlMAPK8-SlARF4-SlMYB99/11 module. These findings provide new insights into the mechanism underlying phytohormone regulation of AsA biosynthesis and provide a theoretical basis for the future development of high AsA plants via molecular breeding.
PMID: 37247338
Plant Biotechnol J , IF:9.803 , 2023 Aug doi: 10.1111/pbi.14107
Grain yield improvement by genome editing of TaARF12 that decoupled peduncle and rachis development trajectories via differential regulation of gibberellin signalling in wheat.
National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.; The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
Plant breeding is constrained by trade-offs among different agronomic traits by the pleiotropic nature of many genes. Genes that contribute to two or more favourable traits with no penalty on yield are rarely reported, especially in wheat. Here, we describe the editing of a wheat auxin response factor TaARF12 by using CRISPR/Cas9 that rendered shorter plant height with larger spikes. Changes in plant architecture enhanced grain number per spike up to 14.7% with significantly higher thousand-grain weight and up to 11.1% of yield increase under field trials. Weighted Gene Co-Expression Network Analysis (WGCNA) of spatial-temporal transcriptome profiles revealed two hub genes: RhtL1, a DELLA domain-free Rht-1 paralog, which was up-regulated in peduncle, and TaNGR5, an organ size regulator that was up-regulated in rachis, in taarf12 plants. The up-regulation of RhtL1 in peduncle suggested the repression of GA signalling, whereas up-regulation of TaNGR5 in spike may promote GA response, a working model supported by differential expression patterns of GA biogenesis genes in the two tissues. Thus, TaARF12 complemented plant height reduction with larger spikes that gave higher grain yield. Manipulation of TaARF12 may represent a new strategy in trait pyramiding for yield improvement in wheat.
PMID: 37589238
Cell Rep , IF:9.423 , 2023 Aug , V42 (8) : P112966 doi: 10.1016/j.celrep.2023.112966
WOX-ARF modules initiate different types of roots.
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China. Electronic address: xulin@cemps.ac.cn.
Seed plants have evolved a complex root system consisting of at least three root types, i.e., adventitious roots, lateral roots, and the primary root. Auxin is the key hormone that controls the initiation of different root types. Here, we show that protein complexes with different combinations of intermediate-clade WUSCHEL-RELATED HOMEOBOXs (IC-WOXs) and class-A AUXIN RESPONSE FACTORs (A-ARFs) initiate the three root types in Arabidopsis thaliana. In adventitious root founder cells from detached leaves, the WOX11-ARF6/8 complex activates RGF1 INSENSITIVEs (RGIs) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) to initiate the adventitious root primordium. In lateral root founder cells, ARF7/19 activate RGIs and LBD16 without IC-WOX to initiate the lateral root primordium. In the primary root founder cell (i.e., hypophysis of an embryo), the WOX9-ARF5 complex initiates the primary root by activation of RGIs. Overall, the WOX-ARF modules show a division of labor to initiate different type of roots.
PMID: 37556327
Plant Physiol , IF:8.34 , 2023 Aug doi: 10.1093/plphys/kiad465
Changes in cell wall composition due to a pectin biosynthesis enzyme GAUT10 impact root growth.
Department of Genetics, Development and Cell Biology, Iowa State University.; Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University.; Umea Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden.; Department of Plant Pathology, Entomology, and Microbiology, Iowa State University.
Arabidopsis (Arabidopsis thaliana) root development is regulated by multiple dynamic growth cues that require central metabolism pathways such as beta-oxidation and auxin. Loss of the pectin biosynthesizing enzyme GALACTURONOSYLTRANSFERASE 10 (GAUT10) leads to a short root phenotype under sucrose-limited conditions. The present study focused on determining the specific contributions of GAUT10 to pectin composition in primary roots and the underlying defects associated with gaut10 roots. Using live-cell microscopy, we determined reduced root growth in gaut10 is due to a reduction in both root apical meristem size and epidermal cell elongation. In addition, GAUT10 was required for normal pectin and hemicellulose composition in primary Arabidopsis roots. Specifically, loss of GAUT10 led to a reduction in galacturonic acid and xylose in root cell walls and altered the presence of rhamnogalacturonan I (RG-I) and homogalacturonan (HG) polymers in the root. Transcriptomic analysis of gaut10 roots compared to wild-type uncovered hundreds of genes differentially expressed in the mutant, including genes related to auxin metabolism and peroxisome function. Consistent with these results, both auxin signaling and metabolism were modified in gaut10 roots. The sucrose-dependent short root phenotype in gaut10 was linked to beta-oxidation based on hypersensitivity to indole-3-butyric acid (IBA) and an epistatic interaction with TRANSPORTER OF IBA1 (TOB1). Altogether, these data support a growing body of evidence suggesting that pectin composition may influence auxin pathways and peroxisome activity.
PMID: 37606259
Plant Physiol , IF:8.34 , 2023 Aug doi: 10.1093/plphys/kiad431
LIPID TRANSFER PROTEIN4 regulates cotton ceramide content and activates fiber cell elongation.
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China.; Engineering Research Center of Ministry of Education for Cotton Germplasm Enhancement and Application, Nanjing Agricultural University, Nanjing 210095, China.; The Sanya Institute of Nanjing Agricultural University, Sanya, China.
Cell elongation is a fundamental process for plant growth and development. Studies have shown lipid metabolism plays important roles in cell elongation; however, the related functional mechanisms remain largely unknown. Here, we report that cotton (Gossypium hirsutum) LIPID TRANSFER PROTEIN4 (GhLTP4) promotes fiber cell elongation via elevating ceramides (Cers) content and activating auxin-responsive pathways. GhLTP4 was preferentially expressed in elongating fibers. Over-expression and down-regulation of GhLTP4 led to longer and shorter fiber cells, respectively. Cers were greatly enriched in GhLTP4-overexpressing lines and decreased dramatically in GhLTP4-down-regulating lines. Moreover, auxin content and transcript levels of IAA-responsive genes were significantly increased in GhLTP4-overexpressing cotton fibers. Exogenous application of Cers promoted fiber elongation, while NPA (N-1-naphthalic acid, a polar auxin transport inhibitor) counteracted the promoting effect, suggesting that IAA functions downstream of Cers in regulating fiber elongation. Furthermore, we identified a bHLH transcription factor, GhbHLH105, that binds to the E-box element in the GhLTP4 promoter region and promotes the expression of GhLTP4. Suppression of GhbHLH105 in cotton reduced the transcripts level of GhLTP4, resulting in smaller cotton bolls and decreased fiber length. These results provide insights into the complex interactions between lipids and auxin signaling pathways to promote plant cell elongation.
PMID: 37527491
Plant Physiol , IF:8.34 , 2023 Aug , V193 (1) : P661-676 doi: 10.1093/plphys/kiad345
WUSCHEL controls genotype-dependent shoot regeneration capacity in potato.
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea.; Department of Crop Science, Chungnam National University, Daejeon 34134, South Korea.; Disease Target Structure Research Center, Korea Research Institute of Bioscience & Biotechnology, Daejeon 34141, South Korea.; Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology, Daejeon 34113, South Korea.; Department of Functional Genomics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, South Korea.; Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, South Korea.
Plant cells can reprogram their fate. The combinatorial actions of auxin and cytokinin dedifferentiate somatic cells to regenerate organs, which can develop into individual plants. As transgenic plants can be generated from genetically modified somatic cells through these processes, cell fate transition is an unavoidable step in crop genetic engineering. However, regeneration capacity closely depends on the genotype, and the molecular events underlying these variances remain elusive. In the present study, we demonstrated that WUSCHEL (WUS)-a homeodomain transcription factor-determines regeneration capacity in different potato (Solanum tuberosum) genotypes. Comparative analysis of shoot regeneration efficiency and expression of genes related to cell fate transition revealed that WUS expression coincided with regeneration rate in different potato genotypes. Moreover, in a high-efficiency genotype, WUS silencing suppressed shoot regeneration. Meanwhile, in a low-efficiency genotype, regeneration could be enhanced through the supplementation of a different type of cytokinin that promoted WUS expression. Computational modeling of cytokinin receptor-ligand interactions suggested that the docking pose of cytokinins mediated by hydrogen bonding with the core residues may be pivotal for WUS expression and shoot regeneration in potatoes. Furthermore, our whole-genome sequencing analysis revealed core sequence variations in the WUS promoters that differentiate low- and high-efficiency genotypes. The present study revealed that cytokinin responses, particularly WUS expression, determine shoot regeneration efficiency in different potato genotypes.
PMID: 37348867
Plant Physiol , IF:8.34 , 2023 Aug , V193 (1) : P537-554 doi: 10.1093/plphys/kiad352
Inhibitor AN3661 reveals biological functions of Arabidopsis CLEAVAGE and POLYADENYLATION SPECIFICITY FACTOR 73.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian 361102, China.; Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA 91766, USA.
Cleavage and polyadenylation specificity factor (CPSF) is a protein complex that plays an essential biochemical role in mRNA 3'-end formation, including poly(A) signal recognition and cleavage at the poly(A) site. However, its biological functions at the organismal level are mostly unknown in multicellular eukaryotes. The study of plant CPSF73 has been hampered by the lethality of Arabidopsis (Arabidopsis thaliana) homozygous mutants of AtCPSF73-I and AtCPSF73-II. Here, we used poly(A) tag sequencing to investigate the roles of AtCPSF73-I and AtCPSF73-II in Arabidopsis treated with AN3661, an antimalarial drug with specificity for parasite CPSF73 that is homologous to plant CPSF73. Direct seed germination on an AN3661-containing medium was lethal; however, 7-d-old seedlings treated with AN3661 survived. AN3661 targeted AtCPSF73-I and AtCPSF73-II, inhibiting growth through coordinating gene expression and poly(A) site choice. Functional enrichment analysis revealed that the accumulation of ethylene and auxin jointly inhibited primary root growth. AN3661 affected poly(A) signal recognition, resulted in lower U-rich signal usage, caused transcriptional readthrough, and increased the distal poly(A) site usage. Many microRNA targets were found in the 3' untranslated region lengthened transcripts; these miRNAs may indirectly regulate the expression of these targets. Overall, this work demonstrates that AtCPSF73 plays important part in co-transcriptional regulation, affecting growth, and development in Arabidopsis.
PMID: 37335917
Plant Physiol , IF:8.34 , 2023 Aug , V193 (1) : P112-124 doi: 10.1093/plphys/kiad321
Axes and polarities in leaf vein formation.
Department of Biological Sciences, University of Alberta, CW-405 Biological Sciences Building, Edmonton, AB T6G 2E9, Canada.
For multicellular organisms to develop, cells must grow, divide, and differentiate along preferential or exclusive orientations or directions. Moreover, those orientations, or axes, and directions, or polarities, must be coordinated between cells within and between tissues. Therefore, how axes and polarities are coordinated between cells is a key question in biology. In animals, such coordination mainly depends on cell migration and direct interaction between proteins protruding from the plasma membrane. Both cell movements and direct cell-cell interactions are prevented in plants by cell walls that surround plant cells and keep them apart and in place. Therefore, plants have evolved unique mechanisms to coordinate their cell axes and polarities. Here I will discuss evidence suggesting that understanding how leaf veins form may uncover those unique mechanisms. Indeed, unlike previously thought, the cell-to-cell polar transport of the plant hormone auxin along developing veins cannot account for many features of vein patterning. Instead, those features can be accounted for by models of vein patterning that combine polar auxin transport with auxin diffusion through plasmodesmata along the axis of developing veins. Though it remains unclear whether such a combination of polar transport and axial diffusion of auxin can account for the formation of the variety of vein patterns found in plant leaves, evidence suggests that such a combined mechanism may control plant developmental processes beyond vein patterning.
PMID: 37261944
Plant Physiol , IF:8.34 , 2023 Aug , V193 (1) : P70-82 doi: 10.1093/plphys/kiad309
Cell signaling in the shoot apical meristem.
College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.; State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China.; Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China.
Distinct from animals, plants maintain organogenesis from specialized tissues termed meristems throughout life. In the shoot apex, the shoot apical meristem (SAM) produces all aerial organs, such as leaves, from its periphery. For this, the SAM needs to precisely balance stem cell renewal and differentiation, which is achieved through dynamic zonation of the SAM, and cell signaling within functional domains is key for SAM functions. The WUSCHEL-CLAVATA feedback loop plays a key role in SAM homeostasis, and recent studies have uncovered new components, expanding our understanding of the spatial expression and signaling mechanism. Advances in polar auxin transport and signaling have contributed to knowledge of the multifaceted roles of auxin in the SAM and organogenesis. Finally, single-cell techniques have expanded our understanding of the cellular functions within the shoot apex at single-cell resolution. In this review, we summarize the most up-to-date understanding of cell signaling in the SAM and focus on the multiple levels of regulation of SAM formation and maintenance.
PMID: 37224874
Plant Physiol , IF:8.34 , 2023 Aug , V193 (1) : P775-791 doi: 10.1093/plphys/kiad293
GmGAMYB-BINDING PROTEIN 1 promotes small auxin-up RNA gene transcription to modulate soybean maturity and height.
Key Laboratory of Soybean Biology of Ministry of Education China, Northeast Agricultural University, Harbin 150030, China.
Flowering time, maturity, and plant height are crucial agronomic traits controlled by photoperiod that affect soybean (Glycine max [L.] Merr.) yield and regional adaptability. It is important to cultivate soybean cultivars of earlier maturity that adapt to high latitudes. GAMYB-binding protein 1 (GmGBP1), a member of the SNW/SKIP family of transcriptional coregulators in soybean, is induced by short days and interacts with transcription factor GAMYB (GmGAMYB) during photoperiod control of flowering time and maturity. In the present study, GmGBP1:GmGBP1 soybean showed the phenotypes of earlier maturity and higher plant height. Chromatin immunoprecipitation sequencing (ChIP-seq) assays of GmGBP1-binding sites and RNA sequencing (RNA-seq) of differentially expressed transcripts in GmGBP1:GmGBP1 further identified potential targets of GmGBP1, including small auxin-up RNA (GmSAUR). GmSAUR:GmSAUR soybean also showed earlier maturity and higher plant height. GmGBP1 interacted with GmGAMYB, bound to the promoter of GmSAUR and promoted the expression of FLOWER LOCUS T homologs 2a (GmFT2a) and FLOWERING LOCUS D LIKE 19 (GmFDL19). Flowering repressors such as GmFT4 were negatively regulated, resulting in earlier flowering and maturity. Furthermore, the interaction of GmGBP1 with GmGAMYB increased the gibberellin (GA) signal to promote height and hypocotyl elongation by activating GmSAUR and GmSAUR bound to the promoter of the GA-positive activating regulator gibberellic acid-stimulated Arabidopsis 32 (GmGASA32). These results suggested a photoperiod regulatory pathway in which the interaction of GmGBP1 with GmGAMYB directly activated GmSAUR to promote earlier maturity and plant height in soybean.
PMID: 37204820
Plant Physiol , IF:8.34 , 2023 Aug , V192 (4) : P2838-2854 doi: 10.1093/plphys/kiad289
miR171-targeted SCARECROW-LIKE genes CsSCL2 and CsSCL3 regulate somatic embryogenesis in citrus.
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China.; Hubei Hongshan Laboratory, Wuhan 430070, China.
Somatic embryogenesis (SE) is a key regeneration pathway in various biotechnology approaches to crop improvement, especially for economically important perennial woody crops like citrus. However, maintenance of SE capability has long been a challenge and becomes a bottleneck in biotechnology-facilitated plant improvement. In the embryogenic callus (EC) of citrus, we identified 2 csi-miR171c-targeted SCARECROW-LIKE genes CsSCL2 and CsSCL3 (CsSCL2/3), which exert positive feedback regulation on csi-miR171c expression. Suppression of CsSCL2 expression by RNA interference (RNAi) enhanced SE in citrus callus. A thioredoxin superfamily protein CsClot was identified as an interactive protein of CsSCL2/3. Overexpression of CsClot disturbed reactive oxygen species (ROS) homeostasis in EC and enhanced SE. Chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA-Seq identified 660 genes directly suppressed by CsSCL2 that were enriched in biological processes including development-related processes, auxin signaling pathway, and cell wall organization. CsSCL2/3 bound to the promoters of regeneration-related genes, such as WUSCHEL-RELATED HOMEOBOX 2 (CsWOX2), CsWOX13, and Lateral Organ Boundaries Domain 40 (LBD40), and repressed their expression. Overall, CsSCL2/3 modulate ROS homeostasis through the interactive protein CsClot and directly suppress the expression of regeneration-related genes, thus regulating SE in citrus. We uncovered a regulatory pathway of miR171c-targeted CsSCL2/3 in SE, which shed light on the mechanism of SE and regeneration capability maintenance in citrus.
PMID: 37204807
Plant Physiol , IF:8.34 , 2023 Aug , V193 (1) : P42-53 doi: 10.1093/plphys/kiad264
Computer models of cell polarity establishment in plants.
Centro de Biotecnologia y Genomica de Plantas, Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo, Pozuelo de Alarcon, Madrid, Spain.
Plant development is a complex task, and many processes involve changes in the asymmetric subcellular distribution of cell components that strongly depend on cell polarity. Cell polarity regulates anisotropic growth and polar localization of membrane proteins and helps to identify the cell's position relative to its neighbors within an organ. Cell polarity is critical in a variety of plant developmental processes, including embryogenesis, cell division, and response to external stimuli. The most conspicuous downstream effect of cell polarity is the polar transport of the phytohormone auxin, which is the only known hormone transported in a polar fashion in and out of cells by specialized exporters and importers. The biological processes behind the establishment of cell polarity are still unknown, and researchers have proposed several models that have been tested using computer simulations. The evolution of computer models has progressed in tandem with scientific discoveries, which have highlighted the importance of genetic, chemical, and mechanical input in determining cell polarity and regulating polarity-dependent processes such as anisotropic growth, protein subcellular localization, and the development of organ shapes. The purpose of this review is to provide a comprehensive overview of the current understanding of computer models of cell polarity establishment in plants, focusing on the molecular and cellular mechanisms, the proteins involved, and the current state of the field.
PMID: 37144853
Plant Physiol , IF:8.34 , 2023 Aug , V192 (4) : P3189-3202 doi: 10.1093/plphys/kiad254
Integration of multiple stress signals in plants using synthetic Boolean logic gates.
Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA.; BioDiscovery Institute, University of North Texas, Denton, TX 76203, USA.
As photosynthetic organisms, plants have a potential role in the sustainable production of high-value products such as medicines, biofuels, and chemical feedstocks. With effective engineering using synthetic biology approaches, plant-based platforms could conceivably be designed to minimize the costs and waste of production for materials that would otherwise be uneconomical. Additionally, modern agricultural crops could be engineered to be more productive, resilient, or restorative in different or rapidly changing environments and climates. Information-processing genetic devices and circuits containing multiple interacting parts that behave predictably must be developed to achieve these complex goals. A genetic Boolean AND logic gate is a device that computes the presence or absence of 2 inputs (signals and stimuli) and produces an output (response) only when both inputs are present. We optimized individual genetic components and used synthetic protein heterodimerizing domains to rationally assemble genetic AND logic gates that integrate 2 hormonal inputs in transgenic Arabidopsis thaliana plants. These AND gates produce an output only in the presence of both abscisic acid and auxin but not when either or neither hormone is present. The AND logic gate can also integrate signals resulting from 2 plant stresses, cold temperature and bacterial infection, to produce a response. The design principles used here are generalizable, and, therefore, multiple orthogonal AND gates could be assembled and rationally layered to process complex genetic information in plants. These layered logic gates may be used in genetic circuits to probe fundamental questions in plant biology, such as hormonal crosstalk, in addition to plant engineering for bioproduction.
PMID: 37119276
Plant Physiol , IF:8.34 , 2023 Aug , V192 (4) : P2687-2702 doi: 10.1093/plphys/kiad248
WAVE-DAMPENED2-LIKE4 modulates the hyper-elongation of light-grown hypocotyl cells.
Department of Biology, Indiana University, Bloomington, IN 47405, USA.
Light, temperature, water, and nutrient availability influence how plants grow to maximize access to resources. Axial growth, the linear extension of tissues by coordinated axial cell expansion, plays a central role in these adaptive morphological responses. Using Arabidopsis (Arabidopsis thaliana) hypocotyl cells to explore axial growth control mechanisms, we investigated WAVE-DAMPENED2-LIKE4 (WDL4), an auxin-induced, microtubule-associated protein and member of the larger WDL gene family shown to modulate hypocotyl growth under changing environmental conditions. Loss-of-function wdl4 seedlings exhibited a hyper-elongation phenotype under light conditions, continuing to elongate when wild-type Col-0 hypocotyls arrested and reaching 150% to 200% of wild-type length before shoot emergence. wdl4 seedling hypocotyls showed dramatic hyper-elongation (500%) in response to temperature elevation, indicating an important role in morphological adaptation to environmental cues. WDL4 was associated with microtubules under both light and dark growth conditions, and no evidence was found for altered microtubule array patterning in loss-of-function wdl4 mutants under various conditions. Examination of hormone responses showed altered sensitivity to ethylene and evidence for changes in the spatial distribution of an auxin-dependent transcriptional reporter. Our data provide evidence that WDL4 regulates hypocotyl cell elongation without substantial changes to microtubule array patterning, suggesting an unconventional role in axial growth control.
PMID: 37096683
Curr Opin Plant Biol , IF:7.834 , 2023 Aug , V74 : P102377 doi: 10.1016/j.pbi.2023.102377
How do plants reprogramme the fate of differentiated cells?
RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan. Electronic address: hatsune.morinaka@riken.jp.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehirocho, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo, 113-0033, Japan. Electronic address: keiko.sugimoto@riken.jp.
Being able to change cell fate after differentiation highlights the remarkable developmental plasticity of plant cells. Recent studies show that phytohormones, such as auxin and cytokinin, promote cell cycle reactivation, a critical first step to reprogramme mitotically inactive, differentiated cells into organogenic stem cells. Accumulating evidence suggests that wounding provides an additional cue to convert the identity of differentiated cells by promoting the loss of existing cell fate and/or acquisition of new cell fate. Differentiated cells can also alter cell fate without undergoing cell division and in this case, wounding and phytohormones induce master regulators that can directly assign new cell fate.
PMID: 37167921
Plant Cell Environ , IF:7.228 , 2023 Aug doi: 10.1111/pce.14702
Heat-dependent postpollination limitations on maize pollen tube growth and kernel sterility.
College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.; Department of Agronomy, Kansas State University, Manhattan, Kansas, USA.; College of Agriculture, South China Agricultural University, Guangzhou, China.; Division of Biochemistry, Indian Agricultural Research Institute, Pusa, New Delhi, India.; Institute of Maize and Featured Upland Crops, Zhejiang Academy of Agricultural Sciences, Dongyang, China.; Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas, USA.
Heat stress has a negative impact on pollen development in maize (Zea mays L.) but the postpollination events that determine kernel sterility are less well characterised. The impact of short-term (hours) heat exposure during postpollination was therefore assessed in silks and ovaries. The temperatures inside the kernels housed within the husks was significantly lower than the imposed heat stress. This protected the ovaries and possibly the later phase of pollen tube growth from the adverse effects of heat stress. Failure of maize kernel fertilization was observed within 6 h of heat stress exposure postpollination. This was accompanied by a significant restriction of early pollen tube growth rather than pollen germination. Limitations on early pollen tube growth were therefore a major factor contributing to heat stress-induced kernel sterility. Exposure to heat stress altered the sugar composition of silks, suggesting that hexose supply contributed to the limitations on pollen tube growth. Moreover, the activities of sucrose metabolising enzymes, the expression of sucrose degradation and trehalose biosynthesis genes were decreased following heat stress. Significant increases in reactive oxygen species, abscisic acid and auxin levels accompanied by altered expression of phytohormone-related genes may also be important in the heat-induced suppression of pollen tube growth.
PMID: 37623372
Plant Cell Environ , IF:7.228 , 2023 Aug doi: 10.1111/pce.14680
UV-B responses in the spotlight: Dynamic photoreceptor interplay and cell-type specificity.
Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium.; Department of Agricultural Economics, Ghent University, Coupure Links 653 B-9000, Ghent, Belgium.
Plants are constantly exposed to a multitude of external signals, including light. The information contained within the full spectrum of light is perceived by a battery of photoreceptors, each with specific and shared signalling outputs. Recently, it has become clear that UV-B radiation is a vital component of the electromagnetic spectrum, guiding growth and being crucial for plant fitness. However, given the large overlap between UV-B specific signalling pathways and other photoreceptors, understanding how plants can distinguish UV-B specific signals from other light components deserves more scrutiny. With recent evidence, we propose that UV-B signalling and other light signalling pathways occur within distinct tissues and cell-types and that the contribution of each pathway depends on the type of response and the developmental stage of the plant. Elucidating the precise site(s) of action of each molecular player within these signalling pathways is key to fully understand how plants are able to orchestrate coordinated responses to light within the whole plant body. Focusing our efforts on the molecular study of light signal interactions to understand plant growth in natural environments in a cell-type specific manner will be a next step in the field of photobiology.
PMID: 37554043
Microbiol Spectr , IF:7.171 , 2023 Aug , V11 (4) : Pe0151023 doi: 10.1128/spectrum.01510-23
Volatile Organic Compounds Emitted by the Biocontrol Agent Pythium oligandrum Contribute to Ginger Plant Growth and Disease Resistance.
Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China.; School of Biosciences, University of Birmingham, Birmingham, United Kingdom.; Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes of Ministry of Education, College of Environment, Hohai University, Nanjing, China.; Fungal Genomics Laboratory (FungiG), Jiangsu Provincial Key Lab of Organic Solid Waste Utilization, Nanjing Agricultural University, Nanjing, China.; College of Food and Bioengineering, Henan University of Science and Technology, Luoyang, Henan, China.; Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, China.; Jiangsu Coastal Ecological Science and Technology Development Co., Ltd., Nanjing, China.
The oomycete Pythium oligandrum is a potential biocontrol agent to control a wide range of fungal and oomycete-caused diseases, such as Pythium myriotylum-caused rhizome rot in ginger, leading to reduced yields and compromised quality. Previously, P. oligandrum has been studied for its plant growth-promoting potential by auxin production and induction of disease resistance by elicitors such as oligandrin. Volatile organic compounds (VOCs) play beneficial roles in sustainable agriculture by enhancing plant growth and resistance. We investigated the contribution of P. oligandrum-produced VOCs on plant growth and disease suppression by initially using Nicotiana benthamiana plants for screening. P. oligandrum VOCs significantly enhanced tobacco seedling and plant biomass contents. Screening of the individual VOCs showed that 3-octanone and hexadecane promoted the growth of tobacco seedlings. The total VOCs from P. oligandrum also enhanced the shoot and root growth of ginger plants. Transcriptomic analysis showed a higher expression of genes related to plant growth hormones and stress responses in the leaves of ginger plants exposed to P. oligandrum VOCs. The concentrations of plant growth hormones such as auxin, zeatin, and gibberellic acid were higher in the leaves of ginger plants exposed to P. oligandrum VOCs. In a ginger disease biocontrol assay, the VOC-exposed ginger plants infected with P. myriotylum had lower levels of disease severity. We conclude that this study contributes to understanding the growth-promoting mechanisms of P. oligandrum on ginger and tobacco, priming of ginger plants against various stresses, and the mechanisms of action of P. oligandrum as a biocontrol agent. IMPORTANCE Plant growth promotion plays a vital role in enhancing production of agricultural crops, and Pythium oligandrum is known for its plant growth-promoting potential through production of auxins and induction of resistance by elicitors. This study highlights the significance of P. oligandrum-produced VOCs in plant growth promotion and disease resistance. Transcriptomic analyses of leaves of ginger plants exposed to P. oligandrum VOCs revealed the upregulation of genes involved in plant growth hormone signaling and stress responses. Moreover, the concentration of growth hormones significantly increased in P. oligandrum VOC-exposed ginger plants. Additionally, the disease severity was reduced in P. myriotylum-infected ginger plants exposed to P. oligandrum VOCs. In ginger, P. myriotylum-caused rhizome rot disease results in severe losses, and biocontrol has a role as part of an integrated pest management strategy for rhizome rot disease. Overall, growth enhancement and disease reduction in plants exposed to P. oligandrum-produced VOCs contribute to its role as a biocontrol agent.
PMID: 37534988
Chemosphere , IF:7.086 , 2023 Aug , V340 : P139833 doi: 10.1016/j.chemosphere.2023.139833
Maximizing trace metal phytoextraction through planting methods: Role of rhizosphere fertility and microbial activities.
Lebanese University, Applied Plant Biotechnology Laboratory, Hadath, Lebanon; Universite de Lorraine, INRAE, LSE, F-54000, Nancy, France.; Universite de Lorraine, INRAE, LSE, F-54000, Nancy, France.; Lebanese University, Applied Plant Biotechnology Laboratory, Hadath, Lebanon.; Universite de Lorraine, INRAE, LSE, F-54000, Nancy, France; Centre for Mined Land Rehabilitation, SMI, University of Queensland, St Lucia, QLD, Australia.; Universite de Lorraine, INRAE, LSE, F-54000, Nancy, France. Electronic address: catherine.sirguey@univ-lorraine.fr.
Brownfields are a widespread problem in the world. The poor quality of these soils and the potential presence of contaminants can pose a significant threat to plant establishment and growth. However, it may be possible to improve their establishment with an appropriate agricultural practice. In this paper, the effects of two common planting strategies, seeding and transplanting, on the establishment and growth of the hyperaccumulator species Noccaea caerulescens and on its phytoextraction capacity were investigated. A field experiment was conducted by direct sowing of N. caerulescens seeds on a plot of contaminated Technosols in Jeandelaincourt, France. At the same time, seeds were sown on potting soil under controlled conditions. One month later, the seedlings were transplanted to the field. One year later, the results showed that transplanting improved the establishment and growth of N. caerulescens. This was due to a decrease in soil pH in the rhizosphere, which subsequently increased nutrient availability. This change in rhizosphere properties also appeared to be the key that improved microbial activities in the rhizosphere soil of transplanted plants. The observed improvement in both rhizosphere nutrient availability and microbial activities, in turn, increased auxin concentrations in the rhizosphere and consequently a more developed root system was observed in the transplanted plants. Furthermore, the Cd and Zn phytoextraction yield of transplanted plants is 2.5 and 5 times higher, respectively, than that of sown plants. In conclusion, N. caerulescens transplantation on contaminated sites seems to be an adequate strategy to improve plant growth and enhance trace metal phytoextraction.
PMID: 37595688
J Integr Plant Biol , IF:7.061 , 2023 Aug doi: 10.1111/jipb.13554
The advantages of crosstalk during the evolution of the BZR1-ARF6-PIF4 (BAP) module.
College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
The BAP module, comprising BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), functions as a molecular hub to orchestrate plant growth and development. In Arabidopsis thaliana, components of the BAP module physically interact to form a complex system that integrates light, brassinosteroid (BR), and auxin signals. Little is known about the origin and evolution of the BAP module. Here, we conducted comparative genomic and transcriptomic analyses to investigate the evolution and functional diversification of the BAP module. Our results suggest that the BAP module originated in land plants and that the zeta, epsilon, and gamma whole-genome duplication/triplication events contributed to the expansion of BAP module components in seed plants. Comparative transcriptomic analysis suggested that the prototype BAP module arose in Marchantia polymorpha, experienced stepwise evolution, and became established as a mature regulatory system in seed plants. We developed a formula to calculate the signal transduction productivity of the BAP module and demonstrate that more crosstalk among components enables higher signal transduction efficiency. Our results reveal the evolutionary history of the BAP module and provide insights into the evolution of plant signaling networks and the strategies employed by plants to integrate environmental and endogenous signals. This article is protected by copyright. All rights reserved.
PMID: 37552560
J Exp Bot , IF:6.992 , 2023 Aug doi: 10.1093/jxb/erad325
Auxin and Abiotic Stress Responses.
Department of Biology, Duke University, Durham, NC 27008, USA.
Plants are exposed to a variety of abiotic stresses; these stresses have profound effects on plant growth, survival, and productivity. Tolerance and adaptation to stress require sophisticated stress sensing, signaling, and various regulatory mechanisms. The plant hormone auxin is a key regulator of plant growth and development, playing pivotal roles in the integration of abiotic stress signals and control of downstream stress responses. In this review, we summarize and discuss recent advances in understanding the intersection of auxin and abiotic stress in plants, with a focus on temperature, salt, and drought stresses. We also explore the auxin roles in stress tolerance and arising opportunities for agricultural applications.
PMID: 37591508
J Exp Bot , IF:6.992 , 2023 Aug doi: 10.1093/jxb/erad324
Molecular regulation of apple and grape ripening: exploring common and distinct transcriptional aspects of representative climacteric and non-climacteric fruits.
Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy.; Department of Agricultural, Forest and Food Sciences - University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco, TO, Italy.; Research and Innovation Centre, Fondazione Edmund Mach, Via Mach 1, 39098 San Michele all'Adige (Trento), Italy.; Center Agriculture Food Environment (C3A), University of Trento, Via Mach 1, 39098 San Michele all'Adige (Trento), Italy.
Fleshy fruits of angiosperms are organs specialized for promoting seed dispersal by attracting herbivores and enticing them to consume the organ and the contained seeds. Ripening can be broadly defined as the processes serving as a plant strategy to make the fleshy fruit appealing to animals and leads to a coordinated series of changes in color, texture, aroma and flavor, as result of an intricate interplay of genetically and epigenetically programmed events. The ripening of fruits can be categorized into two types: climacteric, which is characterized by a rapid increase in respiration rate typically accompanied by a burst of ethylene production, and non-climacteric, where this pronounced peak in respiration is absent. Here we review the most current knowledge on transcriptomic changes taking place in apple (climacteric) and grapevine (non-climacteric) fruit during ripening, with the aim to highlight specific and common hormonal and molecular events governing the process in both species. In this perspective, we found that specific NAC transcription factor members participate in the ripening initiation in grape and are involved in the attempt to restore the normal physiological ripening progression in impaired fruit ripening physiology in apple. These elements suggest the existence of a common regulatory mechanism operated by NAC transcription factors and auxin in the two species.
PMID: 37591311
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P3951-3960 doi: 10.1093/jxb/erad213
Flowering also has to end: knowns and unknowns of reproductive arrest in monocarpic plants.
Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas - Universidad Politecnica de Valencia, 46022, Valencia, Spain.
All flowering plants adjust their reproductive period for successful reproduction. Flower initiation is controlled by a myriad of intensively studied factors, so it can occur in the most favorable conditions. However, the end of flowering is also a controlled process, required to optimize the size of the offspring and to maximize resource allocation. Reproductive arrest was described and mainly studied in the last century by physiological approaches, but it is much less understood at the genetic or molecular level. In this review, we present an overview of recent progress in this topic, fueled by highly complementary studies that are beginning to provide an integrated view of how the end of flowering is regulated. In this emerging picture, we also highlight key missing aspects that will guide future research and may provide new biotechnological avenues to improve crop yield in annual plants.
PMID: 37280109
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4377-4383 doi: 10.1093/jxb/erad185
PIN structures shed light on their mechanism of auxin efflux.
School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.; Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
Polar auxin transport is a quintessential feature of higher plant physiology and it has been known for many years that some of the primary drivers of polar auxin transport are the PIN-formed (PIN) auxin efflux proteins. Formative research established many key biochemical features of the transport system and discovered inhibitors such as 1-naphthylphthalamic acid (NPA), but the mechanism of action of PINs has remained elusive. This changed in 2022 with the publication of high-resolution structures of the membrane-spanning domains of three PIN proteins. The atomic structures and associated activity assays reveal that PINs use an elevator mechanism to transport auxin anions out of the cell. NPA was shown to be a competitive inhibitor that traps PINs in their inward-open conformation. The secrets of the hydrophilic cytoplasmic loop of PIN proteins remain to be discovered.
PMID: 37195878
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4503-4519 doi: 10.1093/jxb/erad178
Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis.
State Key Laboratory of Plant Physiology and Biochemistry, Engineering Research Center of Plant Growth Regulator, Ministry of Education & College of Agronomy and Biotechnology, China Agricultural University, No.2 Yuanmingyuan West Road, Haidian, Beijing 100193, China.; North China Key Laboratory for Crop Germplasm Resources, Ministry of Education, State Key Laboratory of North China Crop Improvement and Regulation & College of Agronomy, Hebei Agricultural University, Baoding, Hebei 071001, China.; College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
The lengths of the basal internodes is an important factor for lodging resistance of maize (Zea mays). In this study, foliar application of coronatine (COR) to 10 cultivars at the V8 growth stage had different suppression effects on the length of the eighth internode, with three being categorized as strong-inhibition cultivars (SC), five as moderate (MC), and two as weak (WC). RNA-sequencing of the eighth internode of the cultivars revealed a total of 7895 internode elongation-regulating genes, including 777 transcription factors (TFs). Genes related to the hormones cytokinin, gibberellin, auxin, and ethylene in the SC group were significantly down-regulated compared to WC, and more cell-cycle regulatory factors and cell wall-related genes showed significant changes, which severely inhibited internode elongation. In addition, we used EMSAs to explore the direct regulatory relationship between two important TFs, ZmABI7 and ZmMYB117, which regulate the cell cycle and cell wall modification by directly binding to the promoters of their target genes ZmCYC1, ZmCYC3, ZmCYC7, and ZmCPP1. The transcriptome reported in this study will provide a useful resource for studying maize internode development, with potential use for targeted genetic control of internode length to improve the lodging resistance of maize.
PMID: 37170764
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4489-4502 doi: 10.1093/jxb/erad173
The ARF2-MYB6 module mediates auxin-regulated petal expansion 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.
In cut rose (Rosa hybrida), the flower-opening process is closely associated with vase life. Auxin induces the expression of transcription factor genes that function in petal growth via cell expansion. However, the molecular mechanisms underlying the auxin effect during flower opening are not well understood. Here, we identified the auxin-inducible transcription factor gene RhMYB6, whose expression level is high during the early stages of flower opening. Silencing of RhMYB6 delayed flower opening by controlling petal cell expansion through down-regulation of cell expansion-related genes. Furthermore, we demonstrated that the auxin response factor RhARF2 directly interacts with the promoter of RhMYB6 and represses its transcription. Silencing of RhARF2 resulted in larger petal size and delayed petal movement. We also showed that the expression of genes related to ethylene and petal movement showed substantial differences in RhARF2-silenced petals. Our results indicate that auxin-regulated RhARF2 is a critical player that controls flower opening by governing RhMYB6 expression and mediating the crosstalk between auxin and ethylene signaling.
PMID: 37158672
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4324-4348 doi: 10.1093/jxb/erad168
The phenomenon of autonomous endosperm in sexual and apomictic plants.
Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Gdansk, Poland.; School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
Endosperm is a key nutritive tissue that supports the developing embryo or seedling, and serves as a major nutritional source for human and livestock feed. In sexually-reproducing flowering plants, it generally develops after fertilization. However, autonomous endosperm (AE) formation (i.e. independent of fertilization) is also possible. Recent findings of AE loci/ genes and aberrant imprinting in native apomicts, together with a successful initiation of parthenogenesis in rice and lettuce, have enhanced our understanding of the mechanisms bridging sexual and apomictic seed formation. However, the mechanisms driving AE development are not well understood. This review presents novel aspects related to AE development in sexual and asexual plants underlying stress conditions as the primary trigger for AE. Both application of hormones to unfertilized ovules and mutations that impair epigenetic regulation lead to AE development in sexual Arabidopsis thaliana, which may point to a common pathway for both phenomena. Apomictic-like AE development under experimental conditions can take place due to auxin-dependent gene expression and/or DNA methylation.
PMID: 37155961
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4642-4653 doi: 10.1093/jxb/erad163
Local phytochrome signalling limits root growth in light by repressing auxin biosynthesis.
Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.
In nature, plant shoots are exposed to light whereas the roots grow in relative darkness. Surprisingly, many root studies rely on in vitro systems that leave the roots exposed to light whilst ignoring the possible effects of this light on root development. Here, we investigated how direct root illumination affects root growth and development in Arabidopsis and tomato. Our results show that in light-grown Arabidopsis roots, activation of local phytochrome A and B by far-red or red light inhibits respectively PHYTOCHROME INTERACTING FACTORS 1 or 4, resulting in decreased YUCCA4 and YUCCA6 expression. As a result, auxin levels in the root apex become suboptimal, ultimately resulting in reduced growth of light-grown roots. These findings highlight once more the importance of using in vitro systems where roots are grown in darkness for studies that focus on root system architecture. Moreover, we show that the response and components of this mechanism are conserved in tomato roots, thus indicating its importance for horticulture as well. Our findings open up new research possibilities to investigate the importance of light-induced root growth inhibition for plant development, possibly by exploring putative correlations with responses to other abiotic signals, such as temperature, gravity, touch, or salt stress.
PMID: 37140032
J Exp Bot , IF:6.992 , 2023 Aug , V74 (15) : P4471-4488 doi: 10.1093/jxb/erad159
Cytokinin-inducible response regulator SlRR6 controls plant height through gibberellin and auxin pathways in tomato.
Department of Horticulture, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China.; Institute of Vegetable Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310022, China.; Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agricultural, Zhejiang University, Hangzhou 310058, China.
Plant height is a key agronomic trait regulated by several phytohormones such as gibberellins (GAs) and auxin. However, little is known about how cytokinin (CK) participates in this process. Here, we report that SlRR6, a type-A response regulator in the CK signaling pathway, positively regulates plant height in tomato. SlRR6 was induced by exogenous kinetin and GA3, but inhibited by indole-3-acetic acid (IAA). Knock out of SlRR6 reduced tomato plant height through shortening internode length, while overexpression of SlRR6 caused taller plants due to increased internode number. Cytological observation of longitudinal stems showed that both knock out and overexpression of SlRR6 generated larger cells, but significantly reduced cell numbers in each internode. Further studies demonstrated that overexpression of SlRR6 enhanced GA accumulation and lowered IAA content, along with expression changes in GA- and IAA-related genes. Exogenous paclobutrazol and IAA treatments restored the increased plant height phenotype in SlRR6-overexpressing lines. Yeast two-hybrid, bimolecular fluorescence complementation, and co-immunoprecipitation assays showed that SlRR6 interacts with a small auxin up RNA protein, SlSAUR58. Moreover, SlSAUR58-overexpressing plants were dwarf with decreased internode length. Overall, our findings establish SlRR6 as a vital component in the CK signaling, GA, and IAA regulatory network that controls plant height.
PMID: 37115725
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P4093-4109 doi: 10.1093/jxb/erad152
The transcription factor GhTCP7 suppresses petal expansion by interacting with the WIP-type zinc finger protein GhWIP2 in Gerbera hybrida.
State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan, Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, Yunnan 650091, China.; Key Laboratory of Southern Subtropical Plant Diversity, Fairy Lake Botanical Garden, Shenzhen & Chinese Academy of Sciences, Shenzhen, Guangdong 518004, China.; Department of Plant and Soil Sciences, Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY 40546, USA.; Institute of Biomass Engineering; Key Laboratory of Energy Plants Resource and Utilization, Ministry of Agriculture and Rural Affairs; Guangdong Engineering Technology Research Center of Agricultural and Forestry Biomass, South China Agricultural University, Guangzhou 510642, China.; Provincial Key Lab of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, Guangdong 510631, China.
Petal size is a critical factor in plant reproduction and horticulture, and is largely determined by cell expansion. Gerbera hybrida is an important horticultural plant and serves as a model for studying petal organogenesis. We have previously characterized GhWIP2, a Trp-Ile-Pro (WIP)-type zinc protein, that constrains petal size by suppressing cell expansion. However, the underlying molecular mechanism remains largely unclear. Using yeast two-hybrid screening, bimolecular fluorescence complementation, and co-immunoprecipitation, we identified a TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) family transcription factor, GhTCP7, that interacts with GhWIP2 both in vitro and in vivo. Using reverse genetic approaches, we elucidated the function of the GhTCP7-GhWIP2 complex in controlling petal expansion. GhTCP7 overexpression severely reduced cell expansion and petal size, whereas GhTCP7 silencing resulted in increased cell expansion and petal size. GhTCP7 showed similar expression patterns to GhWIP2 in various types of G. hybrida petals. We further identified GhIAA26, which encodes an auxin signalling regulator, that is activated by the GhTCP7-GhWIP2 complex, leading to the suppression of petal expansion. Our findings reveal a previously unknown transcriptional regulatory mechanism that involves protein-protein interactions between two different transcription factor families to activate a negative regulator of petal organogenesis.
PMID: 37102769
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P3903-3922 doi: 10.1093/jxb/erad137
Lessons from a century of apical dominance research.
ARC Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, QLD 4072, Australia.; School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.; Universite Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
The process of apical dominance by which the apical bud/shoot tip of the plant inhibits the outgrowth of axillary buds located below has been studied for more than a century. Different approaches were used over time, with first the physiology era, the genetic era, and then the multidisciplinary era. During the physiology era, auxin was thought of as the master regulator of apical dominance acting indirectly to inhibit bud outgrowth via unknown secondary messenger(s). Potential candidates were cytokinin (CK) and abscisic acid (ABA). The genetic era with the screening of shoot branching mutants in different species revealed the existence of a novel carotenoid-derived branching inhibitor and led to the significant discovery of strigolactones (SLs) as a novel class of plant hormones. The re-discovery of the major role of sugars in apical dominance emerged from modern physiology experiments and involves ongoing work with genetic material affected in sugar signalling. As crops and natural selection rely on the emergent properties of networks such as this branching network, future work should explore the whole network, the details of which are critical but not individually sufficient to solve the 'wicked problems' of sustainable food supply and climate change.
PMID: 37076257
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P3887-3902 doi: 10.1093/jxb/erad132
A matter of time: auxin signaling dynamics and the regulation of auxin responses during plant development.
Laboratoire Reproduction et Developpement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, F-69342, Lyon, France.
As auxin is a major regulator of plant development, studying the signaling mechanisms by which auxin influences cellular activities is of primary importance. In this review, we describe current knowledge on the different modalities of signaling, from the well-characterized canonical nuclear auxin pathway, to the more recently discovered or re-discovered non-canonical modes of auxin signaling. In particular, we discuss how both the modularity of the nuclear auxin pathway and the dynamic regulation of its core components allow specific transcriptomic responses to be triggered. We highlight the fact that the diversity of modes of auxin signaling allows for a wide range of time scales of auxin responses, from second-scale cytoplasmic responses to minute-/hour-scale modifications of gene expression. Finally, we question the extent to which the temporality of auxin signaling and responses contributes to development in both the shoot and the root meristems. We conclude by stressing the fact that future investigations should allow an integrative view to be built not only of the spatial control, but also of the temporality of auxin-mediated regulation of plant development, from the cell to the whole organism.
PMID: 37042516
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P4158-4168 doi: 10.1093/jxb/erad131
The dynamics of H2A.Z on SMALL AUXIN UP RNAs regulate abscisic acid-auxin signaling crosstalk in Arabidopsis.
Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200032, China.
Extreme environmental changes threaten plant survival and worldwide food production. In response to osmotic stress, the plant hormone abscisic acid (ABA) activates stress responses and restricts plant growth. However, the epigenetic regulation of ABA signaling and crosstalk between ABA and auxin are not well known. Here, we report that the histone variant H2A.Z-knockdown mutant in Arabidopsis Col-0, h2a.z-kd, has altered ABA signaling and stress responses. RNA-sequencing data showed that a majority of stress-related genes are activated in h2a.z-kd. In addition, we found that ABA directly promotes the deposition of H2A.Z on SMALL AUXIN UP RNAs (SAURs), and that this is involved in ABA-repression of SAUR expression. Moreover, we found that ABA represses the transcription of H2A.Z genes through suppressing the ARF7/19-HB22/25 module. Our results shed light on a dynamic and reciprocal regulation hub through H2A.Z deposition on SAURs and ARF7/19-HB22/25-mediated H2A.Z transcription to integrate ABA/auxin signaling and regulate stress responses in Arabidopsis.
PMID: 37022978
J Exp Bot , IF:6.992 , 2023 Aug , V74 (14) : P4031-4049 doi: 10.1093/jxb/erad123
GOLVEN peptides regulate lateral root spacing as part of a negative feedback loop on the establishment of auxin maxima.
Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Ghent 9052, Belgium.; Center for Plant Systems Biology, VIB-UGent, Ghent 9052, Belgium.; Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent 9000, Belgium.; Department of Forest Genetics and Plant Physiology, Umea Plant Science Centre, Swedish University of Agricultural Sciences, 90183 Umea, Sweden.
Lateral root initiation requires the accumulation of auxin in lateral root founder cells, yielding a local auxin maximum. The positioning of auxin maxima along the primary root determines the density and spacing of lateral roots. The GOLVEN6 (GLV6) and GLV10 signaling peptides and their receptors have been established as regulators of lateral root spacing via their inhibitory effect on lateral root initiation in Arabidopsis. However, it was unclear how these GLV peptides interfere with auxin signaling or homeostasis. Here, we show that GLV6/10 signaling regulates the expression of a subset of auxin response genes, downstream of the canonical auxin signaling pathway, while simultaneously inhibiting the establishment of auxin maxima within xylem-pole pericycle cells that neighbor lateral root initiation sites. We present genetic evidence that this inhibitory effect relies on the activity of the PIN3 and PIN7 auxin export proteins. Furthermore, GLV6/10 peptide signaling was found to enhance PIN7 abundance in the plasma membranes of xylem-pole pericycle cells, which likely stimulates auxin efflux from these cells. Based on these findings, we propose a model in which the GLV6/10 signaling pathway serves as a negative feedback mechanism that contributes to the robust patterning of auxin maxima along the primary root.
PMID: 37004244
Int J Biol Macromol , IF:6.953 , 2023 Aug , V247 : P125750 doi: 10.1016/j.ijbiomac.2023.125750
Auxin-responsive protein MaIAA17-like modulates fruit ripening and ripening disorders induced by cold stress in 'Fenjiao' banana.
Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China.; Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China; Key Laboratory of Food Processing Technology and Quality Control in Shandong Province, College of Food Science and Engineering, Shandong Agricultural University, Tai'an, China.; Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center for Postharvest Technology of Horticultural Crops in South China, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, Guangdong 510642, China. Electronic address: xiaoyang_zhu@scau.edu.cn.
Cold stress severely affects the banana fruit softening and de-greening, significantly inhibiting the ripening processes. However, the mechanism of ripening disorder caused by chilling injury (CI) in banana fruit remains largely unknown. Herein, MaIAA17-like, an Auxin/Indole-3-Acetic Acid (Aux/IAA) family member, was found to be highly related to the softening and de-greening in 'Fenjiao' banana. Its expression was rapidly increased with fruit ripening and then gradually decreased under normal ripening conditions (22 degrees C). Notably, cold storage severely repressed MaIAA17-like expression but was rapidly increased following ethephon treatment for ripening in fruits without CI. However, the expression repression was not reverted in fruits with serious CI symptoms after 12 days of storage at 7 degrees C. AtMaIAA17-like bound and regulated the activities of promoters of chlorophyll (MaNOL and MaSGR1), starch (MaBAM6 and MaBAM8), and cell wall (MaSUR14 and MaPL8) degradation-related genes. MaIAA17-like also interacted with ethylene-insensitive 3-binding F-box protein (MaEBF1), further activating the expression of MaNOL, MaBAM8, MaPL8, and MaSUR14. Generally, the transient overexpression of MaIAA17-like promoted fruit ripening by inducing the expression of softening and de-greening related genes. However, silencing MaIAA17-like inhibited fruit ripening by reducing the expression of softening and de-greening related genes. These results imply that MaIAA17-like modulates fruit ripening by transcriptionally upregulating the key genes related to fruit softening and de-greening.
PMID: 37453644
Development , IF:6.868 , 2023 Aug doi: 10.1242/dev.201608
The maize preligule band is subdivided into distinct domains with contrasting cellular properties prior to ligule outgrowth.
Department of Botany and Plant Sciences, Center for Plant Cell Biology, University of California, Riverside, CA 92521, USA.; Department of Molecular Biology, University of Wyoming, Laramie, WY 82071, USA.; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.; California NanoSystems Institute, Los Angeles, CA 90095, USA.
The maize ligule is an epidermis-derived structure that arises from the preligule band (PLB) at a boundary between the blade and sheath. A hinge-like auricle also develops immediately distal to the ligule and contributes to blade angle. Here, we characterize the stages of PLB and early ligule development in terms of topography, cell area, division orientation, cell wall rigidity, and auxin response dynamics. Differential thickening of epidermal cells and localized periclinal divisions contributed to the formation of a ridge within the PLB, which ultimately produces the ligule fringe. Patterns in cell wall rigidity were consistent with the subdivision of the PLB into two regions along a distinct line positioned at the nascent ridge. The proximal region produces the ligule, while the distal region contributes to one epidermal face of the auricles. Whereas the auxin transporter PIN1 accumulated in the PLB, observed differential auxin transcriptional response did not underlie the partitioning of the PLB. Our data demonstrate that two zones with contrasting cellular properties, the preligule and preauricle, are specified within the ligular region prior to ligule outgrowth.
PMID: 37539661
Development , IF:6.868 , 2023 Oct , V150 (20) doi: 10.1242/dev.201762
The class VIII myosin ATM1 is required for root apical meristem function.
Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.; Broad Institute, Cambridge, MA 04212, USA.
Myosins are evolutionarily conserved motor proteins that interact with actin filaments to regulate organelle transport, cytoplasmic streaming and cell growth. Plant-specific class XI myosin proteins direct cell division and root organogenesis. However, the roles of plant-specific class VIII myosin proteins in plant growth and development are less understood. Here, we investigated the function of an auxin-regulated class VIII myosin, Arabidopsis thaliana MYOSIN 1 (ATM1), using genetics, transcriptomics and live cell microscopy. ATM1 is associated with the plasma membrane and plasmodesmata within the root apical meristem (RAM). Loss of ATM1 function results in decreased RAM size and reduced cell proliferation in a sugar-dependent manner. Auxin signaling and transcriptional responses were dampened in atm1-1 roots. Complementation of atm1-1 with a tagged ATM1 driven under the native ATM1 promoter restored root growth and cell cycle progression. Genetic analyses of atm1-1 seedlings with HEXOKINASE 1 (HXK1) and TARGET OF RAPAMYCIN COMPLEX 1 (TORC1) overexpression lines indicate that ATM1 is downstream of TOR. Collectively, these results provide previously unreported evidence that ATM1 functions to influence cell proliferation in primary roots in response to auxin and sugar cues.
PMID: 37306290
Plant J , IF:6.417 , 2023 Aug doi: 10.1111/tpj.16430
Structure-activity relationship of 2,4-D correlates auxinic activity with the induction of somatic embryogenesis in Arabidopsis thaliana.
Plant Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylviusweg 72, 2333 BE, Leiden, Netherlands.; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands.; Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia San Sebastian, Spain.
2,4-dichlorophenoxyacetic acid (2,4-D) is a synthetic analogue of the plant hormone auxin that is commonly used in many in vitro plant regeneration systems, such as somatic embryogenesis (SE). Its effectiveness in inducing SE, compared to the natural auxin indole-3-acetic acid (IAA), has been attributed to the stress triggered by this compound rather than its auxinic activity. However, this hypothesis has never been thoroughly tested. Here we used a library of forty 2,4-D analogues to test the structure-activity relationship with respect to the capacity to induce SE and auxinic activity in Arabidopsis thaliana. Four analogues induced SE as effectively as 2,4-D and 13 analogues induced SE but were less effective. Based on root growth inhibition and auxin response reporter expression, the 2,4-D analogues were classified into different groups, ranging from very active to not active auxin analogues. A halogen at the 4-position of the aromatic ring was important for auxinic activity, whereas a halogen at the 3-position resulted in reduced activity. Moreover, a small substitution at the carboxylate chain was tolerated, as was extending the carboxylate chain with an even number of carbons. The auxinic activity of most 2,4-D analogues was consistent with their simulated TIR1-Aux/IAA coreceptor binding characteristics. A strong correlation was observed between SE induction efficiency and auxinic activity, which is in line with our observation that 2,4-D-induced SE and stress both require TIR1/AFB auxin co-receptor function. Our data indicate that the stress-related effects triggered by 2,4-D and considered important for SE induction are downstream of auxin signalling.
PMID: 37647363
Plant J , IF:6.417 , 2023 Aug doi: 10.1111/tpj.16394
An enhancer trap system to track developmental dynamics in Marchantia polymorpha.
Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK.
A combination of streamlined genetics, experimental tractability and relative morphological simplicity compared to vascular plants makes the liverwort Marchantia polymorpha an ideal model system for studying many aspects of plant biology. Here we describe a transformation vector combining a constitutive fluorescent membrane marker with a nuclear marker that is regulated by nearby enhancer elements and use this to produce a library of enhancer trap lines for Marchantia. Screening gemmae from these lines allowed the identification and characterization of novel marker lines, including markers for rhizoids and oil cells. The library allowed the identification of a margin tissue running around the thallus edge, highlighted during thallus development. The expression of this marker is correlated with auxin levels. We generated multiple markers for the meristematic apical notch region, which have different spatial expression patterns, reappear at different times during meristem regeneration following apical notch excision and have varying responses to auxin supplementation or inhibition. This reveals that there are proximodistal substructures within the apical notch that could not be observed otherwise. We employed our markers to study Marchantia sporeling development, observing meristem emergence as defining the protonema-to-prothallus stage transition, and subsequent production of margin tissue during the prothallus stage. Exogenous auxin treatment stalls meristem emergence at the protonema stage but does not inhibit cell division, resulting in callus-like sporelings with many rhizoids, whereas pharmacologically inhibiting auxin synthesis and transport does not prevent meristem emergence. This enhancer trap system presents a useful resource for the community and will contribute to future Marchantia research.
PMID: 37583263
Plant J , IF:6.417 , 2023 Jul doi: 10.1111/tpj.16410
HISTONE DEACETYLASE 9 promotes hypocotyl-specific auxin response under shade.
Temasek Life Sciences Laboratory, National University of Singapore, 1 Research Link, Singapore, 117604, Singapore.; Department of Biological Sciences, National University of Singapore, Singapore, 117543, Singapore.
Vegetative shade causes an array of morphological changes in plants called shade avoidance syndrome, which includes hypocotyl and petiole elongation, leaf hyponasty, reduced leaf growth, early flowering and rapid senescence. Here, we show that loss-of-function mutations in HISTONE DEACETYLASE 9 (HDA9) attenuated the shade-induced hypocotyl elongation in Arabidopsis. However, the hda9 cotyledons and petioles under shade were not significantly different from those in wild-type, suggesting a specific function of HDA9 in hypocotyl elongation in response to shade. HDA9 expression levels were stable under shade and its protein was ubiquitously detected in cotyledon, hypocotyl and root. Organ-specific transcriptome analysis unraveled that shade induced a set of auxin-responsive genes, such as SMALL AUXIN UPREGULATED RNAs (SAURs) and AUXIN/INDOLE-3-ACETIC ACIDs (AUX/IAAs) and their induction was impaired in hda9-1 hypocotyls. In addition, HDA9 binding to loci of SAUR15/65, IAA5/6/19 and ACS4 was increased under shade. The genetic and organ-specific gene expression analyses further revealed that HDA9 may cooperate with PHYTOCHROME-INTERACTING FACTOR 4/7 in the regulation of shade-induced hypocotyl elongation. Furthermore, HDA9 and PIF7 proteins were found to interact together and thus it is suggested that PIF7 may recruit HDA9 to regulate the shade/auxin responsive genes in response to shade. Overall, our study unravels that HDA9 can work as one component of a hypocotyl-specific transcriptional regulatory machinery that activates the auxin response at the hypocotyl leading to the elongation of this organ under shade.
PMID: 37522556
Plant J , IF:6.417 , 2023 Sep , V115 (5) : P1428-1442 doi: 10.1111/tpj.16333
Auxin biosynthesis gene FveYUC4 is critical for leaf and flower morphogenesis in woodland strawberry.
National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China.; Hubei Hongshan Laboratory, Wuhan, 430070, China.; Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland, 20742, USA.
Auxin plays an essential role in plant growth and development, particularly in fruit development. The YUCCA (YUC) genes encode flavin monooxygenases that catalyze a rate-limiting step in auxin biosynthesis. Mutations that disrupt YUC gene function provide useful tools for dissecting general and specific functions of auxin during plant development. In woodland strawberry (Fragaria vesca), two ethyl methanesulfonate mutants, Y422 and Y1011, have been identified that exhibit severe defects in leaves and flowers. In particular, the width of the leaf blade is greatly reduced, and each leaflet in the mutants has fewer and deeper serrations. In addition, the number and shape of the floral organs are altered, resulting in smaller fruits. Mapping by sequencing revealed that both mutations reside in the FveYUC4 gene, and were therefore renamed as yuc4-1 and yuc4-2. Consistent with a role for FveYUC4 in auxin synthesis, free auxin and its metabolites are significantly reduced in the yuc4 leaves and flowers. This role of FveYUC4 in leaf and flower development is supported by its high and specific expression in young leaves and flower buds using GUS reporters. Furthermore, germline transformation of pYUC4::YUC4, which resulted in elevated expression of FveYUC4 in yuc4 mutants, not only rescued the leaf and flower defects but also produced parthenocarpic fruits. Taken together, our data demonstrate that FveYUC4 is essential for leaf and flower morphogenesis in woodland strawberry by providing auxin hormone at the proper time and in the right tissues.
PMID: 37248638
Plant J , IF:6.417 , 2023 Sep , V115 (5) : P1408-1427 doi: 10.1111/tpj.16330
A very long chain fatty acid responsive transcription factor, MYB93, regulates lateral root development in Arabidopsis.
Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.; Department of Biological Chemistry, College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi, 478-8501, Japan.; Department of Electrical and Electronic Engineering, Faculty of Science and Technology, Meijo University, 1-501 Shiogamaguchi, Tempaku-ku, Nagoya, Aichi, 468-8502, Japan.
Lateral roots (LRs) are critical to root system architecture development in plants. Although the molecular mechanisms by which auxin regulates LR development have been extensively studied, several additional regulatory systems are hypothesized to be involved. Recently, the regulatory role of very long chain fatty acids (VLCFAs) has been shown in LR development. Our analysis showed that LTPG1 and LTPG2, transporters of VLCFAs, are specifically expressed in the developing LR primordium (LRP), while the number of LRs is reduced in the ltpg1/ltpg2 double mutant. Moreover, late LRP development was hindered when the VLCFA levels were reduced by the VLCFA synthesis enzyme mutant, kcs1-5. However, the details of the regulatory mechanisms of LR development controlled by VLCFAs remain unknown. In this study, we propose a novel method to analyze the LRP development stages with high temporal resolution using a deep neural network and identify a VLCFA-responsive transcription factor, MYB93, via transcriptome analysis of kcs1-5. MYB93 showed a carbon chain length-specific expression response following treatment of VLCFAs. Furthermore, myb93 transcriptome analysis suggested that MYB93 regulated the expression of cell wall organization genes. In addition, we also found that LTPG1 and LTPG2 are involved in LR development through the formation of root cap cuticle, which is different from transcriptional regulation by VLCFAs. Our results suggest that VLCFA is a regulator of LRP development through transcription factor-mediated regulation of gene expression and the transportation of VLCFAs is also involved in LR development through root cap cuticle formation.
PMID: 37247130
Plant J , IF:6.417 , 2023 Sep , V115 (5) : P1394-1407 doi: 10.1111/tpj.16328
ELONGATED HYPOCOTYL5 (HY5) and HY5 HOMOLOGUE (HYH) maintain shade avoidance suppression in UV-B.
School of Biological Sciences, Life Sciences Building, University of Bristol, Bristol, BS8 1TQ, UK.; School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
Reductions in red to far-red ratio (R:FR) provide plants with an unambiguous signal of vegetational shade and are monitored by phytochrome photoreceptors. Plants integrate this information with other environmental cues to determine the proximity and density of encroaching vegetation. Shade-sensitive species respond to reductions in R:FR by initiating a suite of developmental adaptations termed shade avoidance. These include the elongation of stems to facilitate light foraging. Hypocotyl elongation is driven by increased auxin biosynthesis promoted by PHYTOCHROME INTERACTING FACTORs (PIF) 4, 5 and 7. UV-B perceived by the UV RESISTANCE LOCUS 8 (UVR8) photoreceptor rapidly inhibits shade avoidance, in part by suppressing PIF4/5 transcript accumulation and destabilising PIF4/5 protein. Here, we show that longer-term inhibition of shade avoidance is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOGUE (HYH), which regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification. HY5 and HYH are elevated in UV-B and suppress the expression of XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE (XTH) genes involved in cell wall loosening. They additionally increase expression GA2-OXIDASE1 (GA2ox1) and GA2ox2, encoding gibberellin catabolism enzymes that act redundantly to stabilise the PIF-inhibiting DELLA proteins. UVR8 therefore regulates temporally distinct signalling pathways to first rapidly inhibit and subsequently maintain suppression of shade avoidance following UV-B exposure.
PMID: 37243898
Plant J , IF:6.417 , 2023 Sep , V115 (5) : P1357-1376 doi: 10.1111/tpj.16324
PIN2/3/4 auxin carriers mediate root growth inhibition under conditions of boron deprivation in Arabidopsis.
International Research Center for Environmental Membrane Biology & Department of Horticulture, Foshan University, Foshan, 528000, China.; National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000, China.; Microelement Research Center/Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China.; Institute of Botany, Plant Science and Biodiversity Center, Slovak Academy of Sciences, Bratislava, Slovakia.; School of Agriculture and Environment & Institute of Agriculture, University of Western Australia, Perth, 6009, Australia.; Tasmanian Institute for Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, 7001, Australia.; School of Biological Sciences, University of Western Australia, Perth, 6009, Australia.; Institute of Cellular and Molecular Botany, University of Bonn, D-53115, Bonn, Germany.; Institute of Soil Science Chinese Academy of Sciences, State Key Laboratory of Soil and Sustainable Agriculture, Nanjing, 210018, China.
The mechanistic basis by which boron (B) deprivation inhibits root growth via the mediation of root apical auxin transport and distribution remains elusive. This study showed that B deprivation repressed root growth of wild-type Arabidopsis seedlings, which was related to higher auxin accumulation (observed with DII-VENUS and DR5-GFP lines) in B-deprived roots. Boron deprivation elevated the auxin content in the root apex, coinciding with upregulation of the expression levels of auxin biosynthesis-related genes (TAA1, YUC3, YUC9, and NIT1) in shoots, but not in root apices. Phenotyping experiments using auxin transport-related mutants revealed that the PIN2/3/4 carriers are involved in root growth inhibition caused by B deprivation. B deprivation not only upregulated the transcriptional levels of PIN2/3/4, but also restrained the endocytosis of PIN2/3/4 carriers (observed with PIN-Dendra2 lines), resulting in elevated protein levels of PIN2/3/4 in the plasma membrane. Overall, these results suggest that B deprivation not only enhances auxin biosynthesis in shoots by elevating the expression levels of auxin biosynthesis-related genes but also promotes the polar auxin transport from shoots to roots by upregulating the gene expression levels of PIN2/3/4, as well as restraining the endocytosis of PIN2/3/4 carriers, ultimately resulting in auxin accumulation in root apices and root growth inhibition.
PMID: 37235684
Ecotoxicol Environ Saf , IF:6.291 , 2023 Aug , V262 : P115315 doi: 10.1016/j.ecoenv.2023.115315
Root system architecture and genomic plasticity to salinity provide insights into salt-tolerant traits in tall fescue.
School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China.; African Sustainable Agriculture Research Institute, Mohammed VI Polytechnic University, Laayoune 70000, Morocco.; Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Science, Wuhan 430061, PR China.; School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China. Electronic address: 38019113@qq.com.; School of Resources and Environmental Engineering, Ludong University, Yantai 264000, PR China. Electronic address: yatingli@ldu.edu.cn.
Salinity is detrimental to soil health, plant growth, and crop productivity. Understanding salt tolerance mechanisms offers the potential to introduce superior crops, especially in coastal regions. Root system architecture (RSA) plasticity is vital for plant salt stress adaptation. Tall fescue is a promising forage grass in saline regions with scarce RSA studies. Here, we used the computer-integrated and -automated programs EZ-Rhizo II and ROOT-Vis II to analyze and identify natural RSA variations and adaptability to high salt stress at physiological and genetic levels in 17 global tall fescue accessions. Total root length rather than the number of lateral roots contribute more to water uptake and could be used to separate salt-tolerant (LS-11) and -sensitive accessions (PI531230). Comparative evaluation of LS-11 and PI531230 demonstrated that the lateral root length rather than the main root contributed more towards the total root length in LS-11. Also, high water uptake was associated with a larger lateral root vector and position while low water intake was associated with an insignificant correlation between root length, vector, and position. To examine candidate gene expression, we performed transcriptome and transcription analyses using high-throughput RNA sequencing and real-time quantitative PCR, respectively of the lateral and main roots. The main root displayed more differentially expressed genes than the lateral root. A Poisson comparison of LS-11 vs PI531230 demonstrated significant upregulation of PLASMA MEMBRANE AQUAPORIN 1 and AUXIN RESPONSE FACTOR 22 in both the main and lateral root, which are associated with transmembrane water transport and the auxin-activated signaling system, respectively. There is also an upregulation of BASIC HELIX-LOOP-HELIX 5 in the main root and a downregulation in the lateral root, which is ascribed to sodium ion transmembrane transport, as well as an upregulation of THE MEDIATOR COMPLEX 1 assigned to water transport in the lateral root and a downregulation in the main root. Gene-protein interaction analysis found that more genes interacting with aquaporins proteins were upregulated in the lateral root than in the main root. We inferred that deeper main roots with longer lateral roots emanating from the bottom of the main root were ideal for tall fescue water uptake and salt tolerance, rather than many shallow roots, and that, while both main lateral roots may play similar roles in salt sensing and water uptake, there are intrinsic genomic differences.
PMID: 37542983
Int J Mol Sci , IF:5.923 , 2023 Aug , V24 (16) doi: 10.3390/ijms241612857
Brassinosteroids Regulate the Water Deficit and Latex Yield of Rubber Trees.
Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture and Rural Affairs, Hainan Key Laboratory for Cultivation & Physiology of Tropical Crops, State Key Laboratory Incubation Base for Cultivation and Physiology of Tropical Crops, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.
Brassinolide (BR) is an important plant hormone that regulates the growth and development of plants and the formation of yield. The yield and quality of latex from Hevea brasiliensis are regulated by phytohormones. The understanding of gene network regulation mechanism of latex formation in rubber trees is still very limited. In this research, the rubber tree variety CATAS73397 was selected to analyze the relationship between BR, water deficit resistance, and latex yield. The results showed that BR improves the vitality of rubber trees under water deficit by increasing the rate of photosynthesis, reducing the seepage of osmotic regulatory substances, increasing the synthesis of energy substances, and improving the antioxidant system. Furthermore, BR increased the yield and quality of latex by reducing the plugging index and elevating the lutoid bursting index without decreasing mercaptan, sucrose, and inorganic phosphorus. This was confirmed by an increased expression of genes related to latex flow. RNA-seq analysis further indicated that DEG encoded proteins were enriched in the MAPK signaling pathway, plant hormone signal transduction and sucrose metabolism. Phytohormone content displayed significant differences, in that trans-Zeatin, ethylene, salicylic acid, kinetin, and cytokinin were induced by BR, whereas auxin, abscisic acid, and gibberellin were not. In summary, the current research lays a foundation for comprehending the molecular mechanism of latex formation in rubber trees and explores the potential candidate genes involved in natural rubber biosynthesis to provide useful information for further research in relevant areas.
PMID: 37629038
Int J Mol Sci , IF:5.923 , 2023 Aug , V24 (16) doi: 10.3390/ijms241612718
Characterization of the Molecular Events Underlying the Establishment of Axillary Meristem Region in Pepper.
Department of Vegetable Science, College of Horticulture, China Agricultural University, Beijing 100193, China.; Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.; Sanya Institute, China Agricultural University, Sanya 572025, China.
Plant architecture is a major motif of plant diversity, and shoot branching patterns primarily determine the aerial architecture of plants. In this study, we identified an inbred pepper line with fewer lateral branches, 20C1734, which was free of lateral branches at the middle and upper nodes of the main stem with smooth and flat leaf axils. Successive leaf axil sections confirmed that in normal pepper plants, for either node n, P(n) (Primordium n) < 1 cm and P(n+1) < 1 cm were the critical periods between the identification of axillary meristems and the establishment of the region, whereas P(n+3) < 1 cm was fully developed and formed a completely new organ. In 20C1734, the normal axillary meristematic tissue region establishment and meristematic cell identity confirmation could not be performed on the axils without axillary buds. Comparative transcriptome analysis revealed that "auxin-activated signaling pathway", "response to auxin", "response to abscisic acid", "auxin biosynthetic process", and the biosynthesis of the terms/pathways, such as "secondary metabolites", were differentially enriched in different types of leaf axils at critical periods of axillary meristem development. The accuracy of RNA-seq was verified using RT-PCR for some genes in the pathway. Several differentially expressed genes (DEGs) related to endogenous phytohormones were targeted, including several genes of the PINs family. The endogenous hormone assay showed extremely high levels of IAA and ABA in leaf axils without axillary buds. ABA content in particular was unusually high. At the same time, there is no regular change in IAA level in this type of leaf axils (normal leaf axils will be accompanied by AM formation and IAA content will be low). Based on this, we speculated that the contents of endogenous hormones IAA and ABA in 20C1734 plant increased sharply, which led to the abnormal expression of genes in related pathways, which affected the formation of Ams in leaf axils in the middle and late vegetative growth period, and finally, nodes without axillary buds and side branches appeared.
PMID: 37628899
Int J Mol Sci , IF:5.923 , 2023 Aug , V24 (16) doi: 10.3390/ijms241612617
NO Is Not the Same as GSNO in the Regulation of Fe Deficiency Responses by Dicot Plants.
Department of Agronomy (DAUCO Maria de Maeztu Unit of Excellence 2021-2023), Campus de Excelencia Internacional Agroalimentario, Universidad de Cordoba, 14071 Cordoba, Spain.; Department of Botany, Ecology and Plant Physiology, Campus de Excelencia Internacional Agroalimentario, Universidad de Cordoba, 14071 Cordoba, Spain.
Iron (Fe) is abundant in soils but with a poor availability for plants, especially in calcareous soils. To favor its acquisition, plants develop morphological and physiological responses, mainly in their roots, known as Fe deficiency responses. In dicot plants, the regulation of these responses is not totally known, but some hormones and signaling molecules, such as auxin, ethylene, glutathione (GSH), nitric oxide (NO) and S-nitrosoglutathione (GSNO), have been involved in their activation. Most of these substances, including auxin, ethylene, GSH and NO, increase their production in Fe-deficient roots while GSNO, derived from GSH and NO, decreases its content. This paradoxical result could be explained with the increased expression and activity in Fe-deficient roots of the GSNO reductase (GSNOR) enzyme, which decomposes GSNO to oxidized glutathione (GSSG) and NH(3). The fact that NO content increases while GSNO decreases in Fe-deficient roots suggests that NO and GSNO do not play the same role in the regulation of Fe deficiency responses. This review is an update of the results supporting a role for NO, GSNO and GSNOR in the regulation of Fe deficiency responses. The possible roles of NO and GSNO are discussed by taking into account their mode of action through post-translational modifications, such as S-nitrosylation, and through their interactions with the hormones auxin and ethylene, directly related to the activation of morphological and physiological responses to Fe deficiency in dicot plants.
PMID: 37628796
Microb Biotechnol , IF:5.813 , 2023 Aug , V16 (8) : P1611-1615 doi: 10.1111/1751-7915.14235
The emerging role of auxins as bacterial signal molecules: Potential biotechnological applications.
Department of Biotechnology and Environmental Protection, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain.; Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain.; Department of Microbiology, Facultad de Farmacia, Universidad de Granada, Granada, Spain.
Microorganisms are exposed in their natural niches to a wide diversity of signal molecules. Specific detection of these signals results in alterations in microbial metabolism and physiology. Auxins like indole-3-acetic acid are key phytohormones that regulate plant growth and development. Nonetheless, auxin biosynthesis is not restricted to plants but is ubiquitous in all kingdoms of life. This wide phylogenetic distribution of auxins production, together with the diversity of regulated cellular processes, have made auxins key intra- and inter-kingdom signal molecules in life modulating, for example microbial physiology, metabolism and virulence. Despite their increasing importance as global signal molecules, the mechanisms by which auxins perform their regulatory functions in microorganisms are largely unknown. In this article, we outline recent research that has advanced our knowledge of the mechanisms of bacterial auxin perception. We also highlight the potential applications of this research in aspects such as antibiotic production, biosensor design, plant microbiome engineering and antivirulence therapies.
PMID: 37466451
Microb Biotechnol , IF:5.813 , 2023 Aug , V16 (8) : P1671-1689 doi: 10.1111/1751-7915.14296
Regulation of indole-3-acetic acid biosynthesis and consequences of auxin production deficiency in Serratia plymuthica.
Department of Biotechnology and Environmental Protection, Estacion Experimental del Zaidin, Consejo Superior de Investigaciones Cientificas, Granada, Spain.
Indole-3-acetic acid (IAA) is emerging as a key intra- and inter-kingdom signal molecule that modulates a wide range of processes of importance during plant-microorganism interaction. However, the mechanisms by which IAA carries out its functions in bacteria as well as the regulatory processes by which bacteria modulate auxin production are largely unknown. Here, we found that IAA synthesis deficiency results in important global transcriptional changes in the broad-range antibiotic-producing rhizobacterium Serratia plymuthica A153. Most pronounced transcriptional changes were observed in various gene clusters for aromatic acid metabolism, including auxin catabolism. To delve into the corresponding molecular mechanisms, different regulatory proteins were biochemically characterized. Among them, a TyrR orthologue was essential for IAA production through the activation of the ipdc gene encoding a key enzyme for IAA biosynthesis. We showed that TyrR specifically recognizes different aromatic amino acids which, in turn, alters the interactions of TyrR with the ipdc promoter. Screening of mutants defective in various transcriptional and post-transcriptional regulators allowed the identification of additional regulators of IAA production, including PigP and quorum sensing-related genes. Advancing our knowledge on the mechanisms that control the IAA biosynthesis in beneficial phytobacteria is of biotechnological interest for improving agricultural productivity and sustainable agricultural development.
PMID: 37345981
Front Plant Sci , IF:5.753 , 2023 , V14 : P1239917 doi: 10.3389/fpls.2023.1239917
Uncovering transcriptional reprogramming during callus development in soybean: insights and implications.
Department of Applied Bioscience, Dong-A University, Busan, Republic of Korea.; Department of Molecular Genetics, Dong-A University, Busan, Republic of Korea.
Callus, a valuable tool in plant genetic engineering, originates from dedifferentiated cells. While transcriptional reprogramming during callus formation has been extensively studied in Arabidopsis thaliana, our knowledge of this process in other species, such as Glycine max, remains limited. To bridge this gap, our study focused on conducting a time-series transcriptome analysis of soybean callus cultured for various durations (0, 1, 7, 14, 28, and 42 days) on a callus induction medium following wounding with the attempt of identifying genes that play key roles during callus formation. As the result, we detected a total of 27,639 alterations in gene expression during callus formation, which could be categorized into eight distinct clusters. Gene ontology analysis revealed that genes associated with hormones, cell wall modification, and cell cycle underwent transcriptional reprogramming throughout callus formation. Furthermore, by scrutinizing the expression patterns of genes related to hormones, cell cycle, cell wall, and transcription factors, we discovered that auxin, cytokinin, and brassinosteroid signaling pathways activate genes involved in both root and shoot meristem development during callus formation. In summary, our transcriptome analysis provides significant insights into the molecular mechanisms governing callus formation in soybean. The information obtained from this study contributes to a deeper understanding of this intricate process and paves the way for further investigation in the field.
PMID: 37600197
Front Plant Sci , IF:5.753 , 2023 , V14 : P1198160 doi: 10.3389/fpls.2023.1198160
Comparative sequence analysis of pPATH pathogenicity plasmids in Pantoea agglomerans gall-forming bacteria.
School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.; The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
Acquisition of the pathogenicity plasmid pPATH that encodes a type III secretion system (T3SS) and effectors (T3Es) has likely led to the transition of a non-pathogenic bacterium into the tumorigenic pathogen Pantoea agglomerans. P. agglomerans pv. gypsophilae (Pag) forms galls on gypsophila (Gypsophila paniculata) and triggers immunity on sugar beet (Beta vulgaris), while P. agglomerans pv. betae (Pab) causes galls on both gypsophila and sugar beet. Draft sequences of the Pag and Pab genomes were previously generated using the MiSeq Illumina technology and used to determine partial T3E inventories of Pab and Pag. Here, we fully assembled the Pab and Pag genomes following sequencing with PacBio technology and carried out a comparative sequence analysis of the Pab and Pag pathogenicity plasmids pPATH(pag) and pPATH(pab). Assembly of Pab and Pag genomes revealed a ~4 Mbp chromosome with a 55% GC content, and three and four plasmids in Pab and Pag, respectively. pPATH(pag) and pPATH(pab) share 97% identity within a 74% coverage, and a similar GC content (51%); they are ~156 kb and ~131 kb in size and consist of 198 and 155 coding sequences (CDSs), respectively. In both plasmids, we confirmed the presence of highly similar gene clusters encoding a T3SS, as well as auxin and cytokinins biosynthetic enzymes. Three putative novel T3Es were identified in Pab and one in Pag. Among T3SS-associated proteins encoded by Pag and Pab, we identified two novel chaperons of the ShcV and CesT families that are present in both pathovars with high similarity. We also identified insertion sequences (ISs) and transposons (Tns) that may have contributed to the evolution of the two pathovars. These include seven shared IS elements, and three ISs and two transposons unique to Pab. Finally, comparative sequence analysis revealed plasmid regions and CDSs that are present only in pPATH(pab) or in pPATH(pag). The high similarity and common features of the pPATH plasmids support the hypothesis that the two strains recently evolved into host-specific pathogens.
PMID: 37583594
Theor Appl Genet , IF:5.699 , 2023 Aug , V136 (9) : P182 doi: 10.1007/s00122-023-04434-7
The genetic architecture of prolificacy in maize revealed by association mapping and bulk segregant analysis.
National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China.; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, People's Republic of China.; Zhucheng Mingjue Tender Company Limited, Weifang, People's Republic of China.; National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China. xuehai85@126.com.; National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China. tangjihua1@163.com.; The Shennong Laboratory, Zhengzhou, People's Republic of China. tangjihua1@163.com.
Here, we revealed maize prolificacy highly correlated with domestication and identified a causal gene ZmEN1 located in one novel QTL qGEN261 that regulating maize prolificacy by using multiple-mapping methods. The development of maize prolificacy (EN) is crucial for enhancing yield and breeding specialty varieties. To achieve this goal, we employed a genome-wide association study (GWAS) to analyze the genetic architecture of EN in maize. Using 492 inbred lines with a wide range of EN variability, our results demonstrated significant differences in genetic, environmental, and interaction effects. The broad-sense heritability (H(2)) of EN was 0.60. Through GWAS, we identified 527 significant single nucleotide polymorphisms (SNPs), involved 290 quantitative trait loci (QTL) and 806 genes. Of these SNPs, 18 and 509 were classified as major effect loci and minor loci, respectively. In addition, we performed a bulk segregant analysis (BSA) in an F(2) population constructed by a few-ears line Zheng58 and a multi-ears line 647. Our BSA results identified one significant QTL, qBEN1. Importantly, combining the GWAS and BSA, four co-located QTL, involving six genes, were identified. Three of them were expressed in vegetative meristem, shoot tip, internode and tip of ear primordium, with ZmEN1, encodes an unknown auxin-like protein, having the highest expression level in these tissues. It suggested that ZmEN1 plays a crucial role in promoting axillary bud and tillering to encourage the formation of prolificacy. Haplotype analysis of ZmEN1 revealed significant differences between different haplotypes, with inbred lines carrying hap6 having more EN. Overall, this is the first report about using GWAS and BSA to dissect the genetic architecture of EN in maize, which can be valuable for breeding specialty maize varieties and improving maize yield.
PMID: 37555969
Biology (Basel) , IF:5.079 , 2023 Aug , V12 (8) doi: 10.3390/biology12081074
Barnyard Grass Stress Triggers Changes in Root Traits and Phytohormone Levels in Allelopathic and Non-Allelopathic Rice.
Longping Branch, College of Biology, Hunan University, Changsha 410125, China.; Hunan Provincial Key Laboratory of Phytohormones, Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Hunan Agricultural University, Changsha 410128, China.; Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China.
Despite the growing knowledge concerning allelopathic interference with barnyard grass, little is understood regarding the competitive physiological mechanisms of the interaction between allelopathic rice and herbicide-resistant barnyard grass. A hydroponic system was employed to investigate the root morphological traits and different phytohormonal changes in allelopathic and non-allelopathic rice cultivars when co-planted with quinclorac-resistant and -susceptible barnyard grass, respectively. The results show that shoot and root biomass were greater in PI. Barnyard grass stress induced an increase in shoot and root biomass in PI at 7 and 14 days of co-culturing rice and barnyard grass. Especially under the stress of quinclorac-resistant barnyard grass, the shoot biomass of PI increased by 23% and 68%, respectively, and the root biomass increased by 37% and 34%, respectively. In terms of root morphology, PI exhibited a significantly higher fine-root length, in root diameters of <0.5 mm, a greater number of root tips, and longer root tips compared to LE. The response to quinclorac-resistant barnyard grass stress was consistent in terms of the SA and JA content. The obvious accumulation of SA and JA was observed in two rice cultivars under quinclorac-resistant barnyard grass stress, with greater amounts of SA and JA in PI. The significant decrease in auxin (IAA) and abscisic acid (ABA) content in rice was detected from 7 to 14 days under co-culture stress. Additionally, highly significant and positive correlations were found between SA and JA content, and the number of root tips and root tip length at root diameters of 0-0.5 mm in rice.
PMID: 37626960
Plant Cell Physiol , IF:4.927 , 2023 Jul doi: 10.1093/pcp/pcad084
Genetic Interaction between Arabidopsis SUR2/CYP83B1 and GNOM Indicates the Importance of Stabilizing Local Auxin Accumulation in Lateral Root Initiation.
Department of Biology, Graduate School of Science, Kobe University, 1-1 Rokkodai, Kobe 657-8501, Japan.; Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0192, Japan.; Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai, Fuchu 183-8509, Japan.; RIKEN Center for Sustainable Resource Science, Riken, Yokohama, Kanagawa 230-0045, Japan.; Graduate School of Integrated Science for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan.; Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.; College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
Lateral root (LR) formation is an important developmental event for the establishment of the root system in most vascular plants. In Arabidopsis thaliana, the fewer roots (fwr) mutation in the GNOM gene, encoding an Arf GTPase guanine nucleotide exchange factor that regulates vesicle trafficking, severely inhibits LR formation. Local accumulation of auxin response for LR initiation is severely affected in fwr. To better understand how local accumulation of auxin response for LR initiation is regulated, we identified a mutation, fewer roots suppressor1 (fsp1), that partially restores LR formation in fwr. The gene responsible for fsp1 was identified as SUPERROOT2 (SUR2), encoding CYP83B1 that positions at the metabolic branch point in the biosynthesis of auxin/indole-3-acetic acid (IAA) and indole glucosinolate. The fsp1 mutation increases both endogenous IAA levels and the number of the sites where auxin response locally accumulates prior to LR formation in fwr. SUR2 is expressed in the pericycle of the differentiation zone and in the apical meristem in roots. Time-lapse imaging of the auxin response revealed that local accumulation of auxin response is more stable in fsp1. These results suggest that SUR2/CYP83B1 affects LR founder cell formation at the xylem pole pericycle cells where auxin accumulates. Analysis of the genetic interaction between SUR2 and GNOM indicates the importance of stabilization of local auxin accumulation sites for LR initiation.
PMID: 37522618
Appl Microbiol Biotechnol , IF:4.813 , 2023 Sep , V107 (18) : P5651-5668 doi: 10.1007/s00253-023-12667-1
Biotechnology of Passiflora edulis: role of Agrobacterium and endophytic microbes.
Department of Botany, Bhairab Ganguly College (West Bengal State University), Feeder Road, Belghoria, Kolkata, 700056, West Bengal, India.; Department of Botany, Dr. Kanailal Bhattacharyya College, Howrah, India.; Department of Life Sciences, Presidency University, Kolkata, West Bengal, India.; Department of Botany, Siddha Clinical Research Unit, Central Council for Research in Siddha, Palayamkottai, 627 002, Tamil Nadu, India.; Department of Botany, DDU Gorakhpur University, Gorakhpur, India.; Division of Pathology, Indian Veterinary Research Institute (IVRI), Izatnagar, 243 122, Bareilly, Uttar Pradesh, India.; Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, 144411, Punjab, India.; Plant Biotechnology Unit, Kanchi Mamunivar Government Institute for Postgraduate Studies and Research, Lawspet, Puducherry, 605 008, India. smahipal3@gmail.com.; Department of Life Sciences, Presidency University, Kolkata, West Bengal, India. abhijit.dbs@presiuniv.ac.in.
Two forms of the genus Passiflora, belonging to the Passifloraceae family, are commonly called yellow and purple passion. These perennial woody climbers are found in the cooler regions at higher altitudes and in lowlands of tropical areas. The presence of alkaloids, terpenes, stilbenes, flavonoids, glycosides, carotenoids, etc. in different parts of the plant provides several pharmacological properties. Because of the various uses in foods and pharmaceuticals, in vitro propagation of this genus has been performed hugely and is of great interest to researchers. From different explants via direct organogenesis under controlled aseptic conditions, callus, root, shoot, and somatic embryos are induced successfully. Different PGRs are augmented in the media for the rapid multiplication or organogenesis, especially, the high ratio of cytokinin and auxin in the basal media efficiently regenerates the shoot and root respectively. The in vitro regenerated plantlets are then acclimatized and hardened properly before transferring to the field conditions. Thus, the present first of its kind review on P. edulis exclusively encompasses the wide applications of biotechnology for this species alongside its organogenesis, embryogenesis, cytology, and endophytic microbes with special emphasis on the role of genetic transformation studies mediated by Agrobacterium sp. KEY POINTS: * Critical assessment on in vitro biotechnology in P. edulis. * Agrobacterium-mediated transformation in P. edulis. * Role of endophytic microbes in P. edulis.
PMID: 37505288
Plant Sci , IF:4.729 , 2023 Oct , V335 : P111823 doi: 10.1016/j.plantsci.2023.111823
Harmonized biochemical modification of cell walls to get permission for entrance of Azospirillum sp. to rice roots.
Laboratory of Plant Physiology, Department Biology, Golestan University, Gorgan, Iran.; Laboratory of Plant Physiology, Department Biology, Golestan University, Gorgan, Iran. Electronic address: Aghdasi1346@gmail.com.; Department of Plant Biology, Faculty of Biological Scuience, Tarbiat Modares University, Tehran, Iran.; Department of Soil and Water Research, Golestan's Agricultural and Natural Resources Research Center, Gorgan, Iran.
Biological nitrogen-fixation is important in increasing crop efficiency. Azospirillum is a nitrogen-fixing microorganism that naturally coexists with grasses roots. The present study was undertaken to clarify the role of rice root cell walls in the acceptance of two Azospirillum species, alone or in combination with indole-3-acetic acid (IAA) and gibberellic acid (GA(3)) treatments. Rice seedlings were grown in Yoshida solution for 21 days and then inoculated with A. brasilense and A. irakens in the presence of 0, 0.57, and 1.14 mM of IAA or 0, 0.29, and 0.58 mM GA(3) or a combination of 1.14 mM of IAA and 0.58 mM of GA(3). The results showed that the amount of hydrogen peroxide, lipid peroxidation, total nitrogen and activity of ferulic acid peroxidase, NADPH oxidase, nitrate reductase, pectin methyl esterase, cellulase, mannanase, xylanase and pectinase were significantly increased in inoculated samples treated with or without phytohormones. The highest activity of these enzymes was observed in A. brasilense- inoculated rice roots in auxin+gibberellin treatment. In the latter, the activity of phenylalanine ammonia lyase and wall ferulic acid peroxidase enzymes, the content of cell wall polysaccharide, lignin, and total phenolic compounds were the least, compared to controls and also with those samples which were inoculated with A. irakens. The results indicate an active role of the wall and its enzymes in allowing bacteria to enter the roots. Understanding this mechanism can improve the methods of inoculating bacteria into plants and increase crop efficiency, which will result in reduced use of chemical fertilizers and their destructive environmental effects.
PMID: 37572965
Plant Sci , IF:4.729 , 2023 Oct , V335 : P111818 doi: 10.1016/j.plantsci.2023.111818
Systems biology of root development in Populus: Review and perspectives.
Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, WA, USA. Electronic address: amir.ahkami@pnnl.gov.
The root system of plants consists of primary, lateral, and adventitious roots (ARs) (aka shoot-born roots). ARs arise from stem- or leaf-derived cells during post-embryonic development. Adventitious root development (ARD) through stem cuttings is the first requirement for successful establishment and growth of planted trees; however, the details of the molecular mechanisms underlying ARD are poorly understood. This knowledge is important to both basic plant biology and because of its necessary role in the successful propagation of superior cultivars of commercial woody bioenergy crops, like poplar. In this review article, the molecular mechanisms that control both endogenous (auxin) and environmentally (nutrients and microbes) regulated ARD and how these systems interact to control the rooting efficiency of poplar trees are described. Then, potential future studies in employing integrated systems biology approaches at cellular resolutions are proposed to more precisely identify the molecular mechanisms that cause AR. Using genetic transformation and genome editing approaches, this information can be used for improving ARD in economically important plants for which clonal propagation is a requirement.
PMID: 37567482
Plant Sci , IF:4.729 , 2023 Oct , V335 : P111816 doi: 10.1016/j.plantsci.2023.111816
Review: Losing JAZ4 for growth and defense.
Department of Plant Sciences, University of California, Davis, CA, USA; Horticulture and Agronomy Graduate Group, University of California, Davis, CA, USA.; Department of Plant Sciences, University of California, Davis, CA, USA.; Department of Plant Sciences, University of California, Davis, CA, USA; Plant Pathology Graduate Group, University of California, Davis, CA, USA.; Department of Plant Sciences, University of California, Davis, CA, USA. Electronic address: melotto@ucdavis.edu.
JAZ proteins are involved in the regulation of the jasmonate signaling pathway, which is responsible for various physiological processes, such as defense response, adaptation to abiotic stress, growth, and development in Arabidopsis. The conserved domains of JAZ proteins can serve as binding sites for a broad array of regulatory proteins and the diversity of these protein-protein pairings result in a variety of functional outcomes. Plant growth and defense are two physiological processes that can conflict with each other, resulting in undesirable plant trade-offs. Recent observations have revealed a distinguishing feature of JAZ4; it acts as negative regulator of both plant immunity and growth and development. We suggest that these complex biological processes can be decoupled at the JAZ4 regulatory node, due to prominent expression of JAZ4 in specific tissues and organs. This spatial separation of actions could explain the increased disease resistance and size of the plant root and shoot in the absence of JAZ4. At the tissue level, JAZ4 could play a role in crosstalk between hormones such as ethylene and auxin to control organ differentiation. Deciphering biding of JAZ4 to specific regulators in different tissues and the downstream responses is key to unraveling molecular mechanisms toward developing new crop improvement strategies.
PMID: 37543224
Plant Sci , IF:4.729 , 2023 Oct , V335 : P111782 doi: 10.1016/j.plantsci.2023.111782
MdGRF11-MdARF19-2 module acts as a positive regulator of drought resistance in apple rootstock.
College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China.; College of Horticulture, China Agricultural University, Beijing 100193, PR China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture and Rural Affairs, Beijing 100193, PR China. Electronic address: wangyi@cau.edu.cn.
14-3-3 proteins play an important role in the response of plants to drought resistance. In this study, 14-3-3 protein MdGRF11 was cloned from Malus xiaojinensis, and its positive regulation of drought resistance was verified using Orin calli and M. xiaojinensis plants. The transcription factor MdARF19-2 was further screened for interaction with this protein in vitro and in vivo. We also conducted experiments using Orin calli and found that the overexpression of MdARF19-2 decreased the level of reactive oxygen species (ROS) and increased the activity of enzymes that scavenge ROS in plant materials. This indicates that MdARF19-2 is a positive regulator in the drought resistance of plants. The drought tolerance was further improved by the overexpression of both MdGRF11 and MdARF19-2 in the calli. In addition, we examined several genes related to ROS scavenging with auxin response factor binding elements in their promoters and found that their level of expression was regulated by the MdGRF11-MdARF19-2 module. In conclusion, the enhancement of plant drought resistance by MdGRF11 could be owing to its accumulation at the protein level in response to drought, which then combined with MdARF19-2, affecting the expression of MdARF19-2 downstream genes. Thus, it scavenges ROS, which ultimately improves the resistance of plant to drought stress.
PMID: 37406680
Life Sci Alliance , IF:4.591 , 2023 Sep , V6 (9) doi: 10.26508/lsa.202302090
The mRNA decapping machinery targets LBD3/ASL9 to mediate apical hook and lateral root development.
Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark.; Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Vienna, Austria.; Laboratory of Molecular Microbiology, School of Agriculture, Nagoya University, Nagoya, Japan.; Crop Genetics Department, John Innes Centre, Norwich Research Park, Norwich, UK.; Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark shutko@bio.ku.dk.
Multicellular organisms perceive and transduce multiple cues to optimize development. Key transcription factors drive developmental changes, but RNA processing also contributes to tissue development. Here, we report that multiple decapping deficient mutants share developmental defects in apical hook, primary and lateral root growth. More specifically, LATERAL ORGAN BOUNDARIES DOMAIN 3 (LBD3)/ASYMMETRIC LEAVES 2-LIKE 9 (ASL9) transcripts accumulate in decapping deficient plants and can be found in complexes with decapping components. Accumulation of ASL9 inhibits apical hook and lateral root formation. Interestingly, exogenous auxin application restores lateral roots formation in both ASL9 over-expressors and mRNA decay-deficient mutants. Likewise, mutations in the cytokinin transcription factors type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs) ARR10 and ARR12 restore the developmental defects caused by over-accumulation of capped ASL9 transcript upon ASL9 overexpression. Most importantly, loss-of-function of asl9 partially restores apical hook and lateral root formation in both dcp5-1 and pat triple decapping deficient mutants. Thus, the mRNA decay machinery directly targets ASL9 transcripts for decay, possibly to interfere with cytokinin/auxin responses, during development.
PMID: 37385753
Plant Cell Rep , IF:4.57 , 2023 Aug , V42 (8) : P1279-1290 doi: 10.1007/s00299-023-03030-9
The SMC5/6 complex subunit MMS21 regulates stem cell proliferation in rice.
College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China.; Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China.; Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China.; College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China. dingcq@njau.edu.cn.; Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing, 210095, China. dingcq@njau.edu.cn.; Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing, 210095, China. dingcq@njau.edu.cn.
SMC5/6 complex subunit OsMMS21 is involved in cell cycle and hormone signaling and required for stem cell proliferation during shoot and root development in rice. The structural maintenance of chromosome (SMC)5/6 complex is required for nucleolar integrity and DNA metabolism. Moreover, METHYL METHANESULFONATE SENSITIVITY GENE 21 (MMS21), a SUMO E3 ligase that is part of the SMC5/6 complex, is essential for the root stem cell niche and cell cycle transition in Arabidopsis. However, its specific role in rice remains unclear. Here, OsSMC5 and OsSMC6 single heterozygous mutants were generated using CRISPR/Cas9 technology to elucidate the function of SMC5/6 subunits, including OsSMC5, OsSMC6, and OsMMS21, in cell proliferation in rice. ossmc5/ + and ossmc6/ + heterozygous single mutants did not yield homozygous mutants in their progeny, indicating that OsSMC5 and OsSMC6 both play necessary roles during embryo formation. Loss of OsMMS21 caused severe defects in both the shoot and roots in rice. Transcriptome analysis showed a significant decrease in the expression of genes involved in auxin signaling in the roots of osmms21 mutants. Moreover, the expression levels of the cycB2-1 and MCM genes, which are involved the cell cycle, were significantly lower in the shoots of the mutants, indicating that OsMMS21 was involved in both hormone signaling pathways and the cell cycle. Overall, these findings indicate that the SUMO E3 ligase OsMMS21 is required for both shoot and root stem cell niches, improving the understanding of the function of the SMC5/6 complex in rice.
PMID: 37178216
Genetics , IF:4.562 , 2023 Aug , V224 (4) doi: 10.1093/genetics/iyad102
How flower development genes were identified using forward genetic screens in Arabidopsis thaliana.
School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia.
In the later part of the 1980s, the time was ripe for identifying genes controlling flower development. In that pregenomic era, the easiest way to do this was to induce random mutations in seeds by chemical mutagens (or irradiation) and to screen thousands of plants for those with phenotypes specifically defective in floral morphogenesis. Here, we discuss the results of premolecular screens for flower development mutants in Arabidopsis thaliana, carried out at Caltech and Monash University, emphasizing the usefulness of saturation mutagenesis, multiple alleles to identify full loss-of-function, conclusions based on multiple mutant analyses, and from screens for enhancer and suppressor modifiers of original mutant phenotypes. One outcome was a series of mutants that led to the ABC floral organ identity model (AP1, AP2, AP3, PI, and AG). In addition, genes controlling flower meristem identity (AP1, CAL, and LFY), floral meristem size (CLV1 and CLV3), development of individual floral organ types (CRC, SPT, and PTL), and inflorescence meristem properties (TFL1, PIN1, and PID) were defined. These occurrences formed targets for cloning that eventually helped lead to an understanding of transcriptional control of the identity of floral organs and flower meristems, signaling within meristems, and the role of auxin in initiating floral organogenesis. These findings in Arabidopsis are now being applied to investigate how orthologous and paralogous genes act in other flowering plants, allowing us to wander in the fertile fields of evo-devo.
PMID: 37294732
Ann Bot , IF:4.357 , 2023 Aug , V131 (7) : P1039-1050 doi: 10.1093/aob/mcad071
Stomatal development and orientation: a phylogenetic and ecophysiological perspective.
Royal Botanic Gardens, Kew, Richmond, UK.
BACKGROUND: Oriented patterning of epidermal cells is achieved primarily by transverse protodermal cell divisions perpendicular to the organ axis, followed by axial cell elongation. In linear leaves with parallel venation, most stomata are regularly aligned with the veins. This longitudinal patterning operates under a strong developmental constraint and has demonstrable physiological benefits, especially in grasses. However, transversely oriented stomata characterize a few groups, among both living angiosperms and extinct Mesozoic seed plants. SCOPE: This review examines comparative and developmental data on stomatal patterning in a broad phylogenetic context, focusing on the evolutionary and ecophysiological significance of guard-cell orientation. It draws from a diverse range of literature to explore the pivotal roles of the plant growth hormone auxin in establishing polarity and chemical gradients that enable cellular differentiation. CONCLUSIONS: Transverse stomata evolved iteratively in a few seed-plant groups during the Mesozoic era, especially among parasitic or xerophytic taxa, such as the hemiparasitic mistletoe genus Viscum and the xerophytic shrub Casuarina, indicating a possible link with ecological factors such as the Cretaceous CO2 decline and changing water availability. The discovery of this feature in some extinct seed-plant taxa known only from fossils could represent a useful phylogenetic marker.
PMID: 37288594
Bioessays , IF:4.345 , 2023 Aug : Pe2300018 doi: 10.1002/bies.202300018
AUXIN RESPONSE FACTOR protein accumulation and function.
Department of Biology, Duke University, Durham, North Carolina, USA.
Auxin is a key regulator of plant developmental processes. Its effects on transcription are mediated by the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. ARFs tightly control specific auxin responses necessary for proper plant growth and development. Recent research has revealed that regulated ARF protein accumulation and ARF nucleo-cytoplasmic partitioning can determine auxin transcriptional outputs. In this review, we explore these recent findings and consider the potential for regulated ARF accumulation in driving auxin responses in plants.
PMID: 37584215
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V202 : P107932 doi: 10.1016/j.plaphy.2023.107932
Auxin-dependent regulation of growth via rolB-induced modulation of the ROS metabolism in the long-term cultivated pRiA4-transformed Rubiacordifolia L. calli.
Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia. Electronic address: gala-vera@mail.ru.; Federal Scientific Center of the East Asia Terrestrial Biodiversity of the Far East Branch of the Russian Academy of Sciences, Vladivostok, 690022, Russia.
Gene transfer from Agrobacterium to plants is the best studied example of horizontal gene transfer (HGT) between prokaryotes and eukaryotes. The rol genes of A. rhizogenes (Rhizobium rhizogenes) provide uncontrolled root growth, or "hairy root" syndrome, the main diagnostic feature. In the present study, we investigated the stable pRiA4-transformed callus culture of Rubia cordifolia L. While untransformed callus cultures need PGRs (plant growth regulators) as an obligatory supplement, pRiA4 calli is able to achieve long-term PGR-free cultivation. For the first time, we described the pRiA4-transformed callus cultures' PGR-dependent ROS status, growth, and specialized metabolism. As we have shown, expression of the rolA and rolB but not the rolC genes is contradictory in a PGR-dependent manner. Moreover, a PGR-free pRiA4 transformed cell line is characterised as more anthraquinone (AQ) productive than an untransformed cell culture. These findings pertain to actual plant biotechnology: it could be the solution to troubles in choosing the best PGR combination for the cultivation of some rare, medicinal, and woody plants; wild-type Ri-plants and tissue cultures may become freed from legal controls on genetically modified organisms in the future. We propose possible PGR-dependent relationships between rolA and rolB as well as ROS signalling targets. The present study highlighted the high importance of the rolA gene in the regulation of combined rol gene effects and the large knowledge gap in rolA action.
PMID: 37557016
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107827 doi: 10.1016/j.plaphy.2023.107827
Mutant IAA21 genes from Dendrocalamus sinicus Chia et J. L. Sun inhibit stem and root growth in transgenic tobacco by interacting with ARF5.
College of Life Science, Xinjiang Normal University, Xinyi Road, Shayibake District, Urumqi, 830054, PR China; Institute of Highland Forest Science, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233, PR China.; Institute of Highland Forest Science, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233, PR China.; College of Life Science, Xinjiang Normal University, Xinyi Road, Shayibake District, Urumqi, 830054, PR China; Xinjiang Key Laboratory of Special Species Conservation and Regulatory Biology, Xinyi Road, Shayibake District, Urumqi, 830054, PR China.; Institute of Highland Forest Science, Chinese Academy of Forestry, Bailongsi, Panlong District, Kunming, 650233, PR China. Electronic address: yanghanqikm@aliyun.com.
Woody bamboos are important resource of industrial fibres. Auxin signaling plays a key role in multiple plant developmental processes, as yet the role of auxin/indole acetic acid (Aux/IAA) in culm development of woody bamboos has not been previously characterized. Dendrocalamus sinicus Chia et J. L. Sun is the largest woody bamboo documented in the world. Here, we identified two alleles of DsIAA21 gene (sIAA21 and bIAA21) from the straight- and bent-culm variants of D. sinicus, respectively, and studied how the domains I, i, and II of DsIAA21 affect the gene transcriptional repression. The results showed that bIAA21 expression was rapidly induced by exogenous auxin in D. sinicus. In transgenic tobacco, sIAA21 and bIAA21 mutated in domains i, and II significantly regulated plant architecture and root development. Stem cross sections revealed that parenchyma cells were smaller in transgenic plants than that in wild type plants. Domain i mutation changed the leucine and proline at position 45 to proline and leucine (siaa21(L45P) and biaa21(P45L)) strongly repressed cell expansion and root elongation by reducing the gravitropic response. Substitution of isoleucine with valine in domain II of the full length DsIAA21 resulted in dwarf stature in transgenic tobacco plants. Furthermore, the DsIAA21 interacted with auxin response factor 5 (ARF5) in transgenic tobacco plants, suggesting that DsIAA21 might inhibit stem and root elongation via interacting with ARF5. Taken together, our data indicated that DsIAA21 was a negative regulator of plant development and suggested that amino acid differences in domain i of sIAA21 versus bIAA21 affected their response to auxin, and might play a key role in the formation of the bent culm variant in D. sinicus. Our results not only shed a light on the morphogenetic mechanism in D. sinicus, but also provided new insights into versatile function of Aux/IAAs in plants.
PMID: 37329689
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107832 doi: 10.1016/j.plaphy.2023.107832
Wheat type one protein phosphatase promotes salt and osmotic stress tolerance in arabidopsis via auxin-mediated remodelling of the root system.
Plant Physiology and Functional Genomics Research Unit, Higher Institute of Biotechnology, University of Sfax, BP "1175", 3038, Sfax, Tunisia.; Plant Physiology and Functional Genomics Research Unit, Higher Institute of Biotechnology, University of Sfax, BP "1175", 3038, Sfax, Tunisia. Electronic address: chantal.ebel@isbs.usf.tn.
The control of optimal root growth and plant stress responses depends largely on a variety of phytohormones among which auxin and brassinosteroids (BRs) are the most influential. We have previously reported that the durum wheat type 1 protein phosphatase TdPP1 participates in the control of root growth by modulating BR signaling. In this study, we pursue our understanding of how TdPP1 fulfills this regulatory function on root growth by evaluating the physiological and molecular responses of Arabidopsis TdPP1 over-expressing lines to abiotic stresses. Our results showed that when exposed to 300 mM Mannitol or 100 mM NaCl, the seedlings of TdPP1 over-expressors exhibit modified root architecture with higher lateral root density, and longer root hairs concomitant with a lower inhibition of the primary root growth. These lines also exhibit faster gravitropic response and a decrease in primary root growth inhibition when exposed to high concentrations of exogenous IAA. On another hand, a cross between TdPP1 overexpressors and DR5:GUS marker line was performed to monitor auxin accumulation in roots. Remarkably, the TdPP1 overexpression resulted in an enhanced auxin gradient under salt stress with a higher accumulation in primary and lateral root tips. Moreover, TdPP1 transgenics exhibit a significant induction of a subset of auxin-responsive genes under salt stress conditions. Therefore, our results reveal a role of PP1 in enhancing auxin signaling to help shape greater root plasticity thus improving plant stress resilience.
PMID: 37327648
Plant Physiol Biochem , IF:4.27 , 2023 Aug , V201 : P107808 doi: 10.1016/j.plaphy.2023.107808
Advances in nanoparticle and organic formulations for prolonged controlled release of auxins.
Southern Federal University, ul. Bolshaya Sadovaya 105/42, Rostov-on-Don, 344006, Russian Federation; Institute of General and Inorganic Chemistry, Bulgarian Academy of Sciences, Sofia, 1113, Bulgaria. Electronic address: vbutova@sfedu.ru.; Southern Federal University, ul. Bolshaya Sadovaya 105/42, Rostov-on-Don, 344006, Russian Federation.
Plant hormones have been well known since Charles Darwin as signaling molecules directing plant metabolism. Their action and transport pathways are at the top of scientific interest and were reviewed in many research articles. Modern agriculture applies phytohormones as supplements to achieve desired physiological plant response. Auxins are a class of plant hormones extensively used for crop management. Auxins stimulate the formation of lateral roots and shoots, seed germination, while extensively high concentrations of these chemicals act as herbicides. Natural auxins are unstable; light or enzyme action leads to their degradation. Moreover, the concentration dependant action of phytohormones denier one-shot injection of these chemicals and require constant slow additive of supplement. It obstructs the direct introduction of auxins. On the other hand, delivery systems can protect phytohormones from degradation and provide a slow release of loaded drugs. Moreover, this release can be managed by external stimuli like pH, enzymes, or temperature. The present review is focused on three auxins: indole-3-acetic, indole-3-butyric, and 1-naphthaleneacetic acids. We collected some examples of inorganic (oxides, Ag, layered double hydroxides) and organic (chitosan, organic formulations) delivery systems. The action of carriers can enhance auxin effects via protection and targeted delivery of loaded molecules. Moreover, nanoparticles can act as nano fertilizers, intensifying the phytohormone effect, providing slow controlled release. So delivery systems for auxins are extremely attractive for modern agriculture opening sustainable management of plant metabolism and morphogenesis.
PMID: 37290135
Environ Sci Pollut Res Int , IF:4.223 , 2023 Aug , V30 (37) : P87102-87117 doi: 10.1007/s11356-023-28029-3
The changes in the maize root cell walls after exogenous application of auxin in the presence of cadmium.
Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38, Bratislava, Slovakia.; Institute of Chemistry, Slovak Academy of Sciences, Dubravska cesta 9, 845 38, Bratislava, Slovakia. zuzana.vivodova@savba.sk.
Cadmium (Cd) is a transition metal and hazardous pollutant that has many toxic effects on plants. This heavy metal poses a health risk for both humans and animals. The cell wall is the first structure of a plant cell that is in contact with Cd; therefore, it can change its composition and/or ratio of wall components accordingly. This paper investigates the changes in the anatomy and cell wall architecture of maize (Zea mays L.) roots grown for 10 days in the presence of auxin indole-3-butyric acid (IBA) and Cd. The application of IBA in the concentration 10(-9) M delayed the development of apoplastic barriers, decreased the content of lignin in the cell wall, increased the content of Ca(2+) and phenols, and influenced the composition of monosaccharides in polysaccharide fractions when compared to the Cd treatment. Application of IBA improved the Cd(2+) fixation to the cell wall and increased the endogenous concentration of auxin depleted by Cd treatment. The proposed scheme from obtained results may explain the possible mechanisms of the exogenously applied IBA and its effects on the changes in the binding of Cd(2+) within the cell wall, and on the stimulation of growth that resulted in the amelioration of Cd stress.
PMID: 37418187
Tree Physiol , IF:4.196 , 2023 Aug , V43 (8) : P1416-1431 doi: 10.1093/treephys/tpad055
Effects of different phosphorus levels on tiller bud development in hydroponic Phyllostachys edulis seedlings.
The State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, 311300 Zhejiang, China.
An appropriate amount of phosphate fertilizer can improve the germination rate of bamboo buds and increase the bamboo shoot output. However, the underlying biological mechanisms of phosphate fertilizer in bamboo shoot development have not been systematically reported. Herein, the effects of low (LP, 1 muM), normal (NP, 50 muM) and high (HP, 1000 muM) phosphorus (P) on the growth and development of moso bamboo (Phyllostachys edulis) tiller buds were first investigated. Phenotypically, the seedling biomass, average number of tiller buds and bud height growth rate under the LP and HP treatments were significantly lower than those under the NP treatment. Next, the microstructure difference of tiller buds in the late development stage (S4) at three P levels was analyzed. The number of internode cells and vascular bundles were significantly lower in the LP treatments than in the NP treatments. The relative expression levels of eight P transport genes, eight hormone-related genes and four bud development genes at the tiller bud developmental stage (S2-S4) and the tiller bud re-tillering stage were analyzed with real-time polymerase chain reaction. The results showed that the expression trends for most P transport genes, hormone-related genes and bud development genes from S2 to S4 were diversified at different P levels, and the expression levels were also different at different P levels. In the tiller bud re-tillering stage, the expression levels of seven P transport genes and six hormone-related genes showed a downward trend with increasing P level. REV expression level decreased under LP and HP conditions. TB1 expression level increased under HP condition. Therefore, we conclude that P deficiency inhibits tiller bud development and re-tillering, and that P depends on the expression of REV and TB1 genes and auxin, cytokinin and strigolactones synthesis and transporter genes to mediate tiller bud development and re-tillering.
PMID: 37099799
Microorganisms , IF:4.128 , 2023 Aug , V11 (8) doi: 10.3390/microorganisms11082077
Biosynthetic Pathways and Functions of Indole-3-Acetic Acid in Microorganisms.
Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou 310018, China.
Indole-3-acetic acid (IAA) belongs to the family of auxin indole derivatives. IAA regulates almost all aspects of plant growth and development, and is one of the most important plant hormones. In microorganisms too, IAA plays an important role in growth, development, and even plant interaction. Therefore, mechanism studies on the biosynthesis and functions of IAA in microorganisms can promote the production and utilization of IAA in agriculture. This mini-review mainly summarizes the biosynthesis pathways that have been reported in microorganisms, including the indole-3-acetamide pathway, indole-3-pyruvate pathway, tryptamine pathway, indole-3-acetonitrile pathway, tryptophan side chain oxidase pathway, and non-tryptophan dependent pathway. Some pathways interact with each other through common key genes to constitute a network of IAA biosynthesis. In addition, functional studies of IAA in microorganisms, divided into three categories, have also been summarized: the effects on microorganisms, the virulence on plants, and the beneficial impacts on plants.
PMID: 37630637
Microorganisms , IF:4.128 , 2023 Aug , V11 (8) doi: 10.3390/microorganisms11082061
Sphingomonas sediminicola Dae20 Is a Highly Promising Beneficial Bacteria for Crop Biostimulation Due to Its Positive Effects on Plant Growth and Development.
Ecologie et Dynamique des Systemes Anthropises (EDYSAN, UMR7058 CNRS), Universite de Picardie Jules Verne (UPJV), 80000 Amiens, France.; Agroecologie, Hydrogeochimie, Milieux et Ressources (AGHYLE, UP2018.C101) UniLaSalle Rouen, SFR NORVEGE FED 4277, 76130 Mont-Saint Aignan, France.; Centre de Ressources Regionales en Biologie Moleculaire (CRRBM), Universite de Picardie Jules Verne (UPJV), 80000 Amiens, France.; AgroStation, 68700 Aspach-le-Bas, France.
Current agricultural practices rely heavily on synthetic fertilizers, which not only consume a lot of energy but also disrupt the ecological balance. The overuse of synthetic fertilizers has led to soil degradation. In a more sustainable approach, alternative methods based on biological interactions, such as plant growth-promoting bacteria (PGPRs), are being explored. PGPRs, which include both symbiotic and free-living bacteria, form mutualistic relationships with plants by enhancing nutrient availability, producing growth regulators, and regulating stress responses. This study investigated the potential of Sphingomonas sediminicola Dae20, an alpha-Proteobacteria species commonly found in the rhizosphere, as a beneficial PGPR. We observed that S. sediminicola Dae20 stimulated the root system and growth of three different plant species in the Brassicaceae family, including Arabidopsis thaliana, mustard, and rapeseed. The bacterium produced auxin, nitric oxide, siderophores and showed ACC deaminase activity. In addition to activating an auxin response in the plant, S. sediminicola Dae20 exhibited the ability to modulate other plant hormones, such as abscisic acid, jasmonic acid and salicylic acid, which are critical for plant development and defense responses. This study highlights the multifunctional properties of S. sediminicola Dae20 as a promising PGPR and underscores the importance of identifying effective and versatile beneficial bacteria to improve plant nutrition and promote sustainable agricultural practices.
PMID: 37630621
Planta , IF:4.116 , 2023 Aug , V258 (3) : P68 doi: 10.1007/s00425-023-04219-8
AUX1, PIN3, and TAA1 collectively maintain fertility in Arabidopsis.
Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, 300071, China.; Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin, 300071, China. shuzhenmen@nankai.edu.cn.
We found that auxin synthesis gene TAA1 and auxin polar transport genes AUX1 and PIN3 collectively maintain fertility and seed size in Arabidopsis. Auxin plays a vital role in plant gametophyte development and embryogenesis. The auxin synthesis gene TAA1 and the auxin polar transport genes AUX1 and PIN3 are expressed during Arabidopsis gametophyte and seed development. However, aux1, pin3, and taa1 single mutants only exhibit mild reproductive defects. We, therefore, generated aux1-T pin3 taa1-k2 and aux1-T pin3-2 taa1-k1 triple mutants by crossing or CRISPR/Cas9 technique. These triple mutants displayed severe reproductive defects with approximately 70% and 77%, respectively, of the siliques failing to elongate after anthesis. Reciprocal crosses and microscopy analyses showed that the development of pollen and ovules in the aux1 pin3 taa1 mutants was normal, whereas the filaments were remarkably short, which might be the cause of the silique sterility. Further analyses indicated that the development and morphology of aux1 pin3 taa1 seeds were normal, but their size was smaller compared with that of the wild type. These results indicate that AUX1, PIN3, and TAA1 act in concert to maintain fertility and seed size in Arabidopsis.
PMID: 37598130
Plant Mol Biol , IF:4.076 , 2023 Aug doi: 10.1007/s11103-023-01373-1
Ethylene response factor ERF022 is involved in regulating Arabidopsis root growth.
School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China. jiangli@ustc.edu.cn.; School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China.
Ethylene response factors (ERFs) are involved in the regulation of plant development processes and stress responses. In this study, we provide evidence for the role of ERF022, a member of the ERF transcription factor group III, in regulating Arabidopsis root growth. We found that ERF022-loss-of-function mutants exhibited increased primary root length and lateral root numbers, and also morphological growth advantages compared to wild-type. Further studies showed that mutants had enhanced cell size in length in the root elongation zones. These results were accompanied by significant increase in the expression of cell elongation and cell wall expansion related genes SAUR10, GASA14, LRX2, XTH19 in mutants. Moreover, ERF022-mediated root growth was associated with the enhanced endogenous auxin and gibberellins levels. Our results suggest that loss-of-function of ERF022 up-regulated the expression of cell elongation and cell wall related genes through auxin and gibberellins signal in the regulation of root growth. Unexpectedly, ERF022 overexpression lines also showed longer primary roots and more lateral roots compared to wild-type, and had longer root apical meristematic zone with increased cell numbers. Overexpression of ERF022 significantly up-regulated cell proliferation, organ growth and auxin biosynthesis genes EXO, HB2, GALK2, LBD26, YUC5, which contribute to enhanced root growth. Altogether, our results provide genetic evidence that ERF022 plays an important role in regulating root growth in Arabidopsis thaliana.
PMID: 37553544
BMC Genomics , IF:3.969 , 2023 Aug , V24 (1) : P498 doi: 10.1186/s12864-023-09610-z
Genome-wide identification and expression analysis of the Auxin-Response factor (ARF) gene family in Medicago sativa under abiotic stress.
College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China.; College of Pratacultural Science, Gansu Agricultural University, Key Laboratory of Grassland Ecosystem, Ministry of Education, Pratacultural Engineering Laboratory of Gansu Province, Sino-U.S. Center for Grazingland Ecosystem Sustainability, Yingmencun, Anning District, Gansu province, Lanzhou, Gansu, 730070, China. mahl@gsau.edu.cn.
BACKGROUND: Alfalfa (Medicago sativa) is the most widely planted legume forage and one of the most economically valuable crops in the world. The periodic changes in its growth and development and abiotic stress determine its yield and economic benefits. Auxin controls many aspects of alfalfa growth by regulating gene expression, including organ differentiation and stress response. Auxin response factors (ARF) are transcription factors that play an essential role in auxin signal transduction and regulate the expression of auxin-responsive genes. However, the function of ARF transcription factors is unclear in autotetraploid-cultivated alfalfa. RESULT: A total of 81 ARF were identified in the alfalfa genome in this study. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, identifying that ARF genes are mainly involved in transcriptional regulation and plant hormone signal transduction pathways. Phylogenetic analysis showed that MsARF was divided into four clades: I, II, III, and IV, each containing 52, 13, 7, and 9 genes, respectively. The promoter region of the MsARF gene contained stress-related elements, such as ABRE, TC-rich repeats, MBS, LTR. Proteins encoded by 50 ARF genes were localized in the nucleus without guide peptides, signal peptides, or transmembrane structures, indicating that most MsARF genes are not secreted or transported but only function in the nucleus. Protein structure analysis revealed that the secondary and tertiary structures of the 81 MsARF genes varied. Chromosomal localization analysis showed 81 MsARF genes were unevenly distributed on 25 chromosomes, with the highest distribution on chromosome 5. Furthermore, 14 segmental duplications and two sets of tandem repeats were identified. Expression analysis indicated that the MsARF was differentially expressed in different tissues and under various abiotic stressors. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression profiles of 23 MsARF genes were specific to abiotic stresses such as drought, salt, high temperature, and low temperature, as well as tissue-specific and closely related to the duration of stress. CONCLUSION: This study identified MsARF in the cultivated alfalfa genome based on the autotetraploid level, which GO, KEGG analysis, phylogenetic analysis, sequence characteristics, and expression pattern analysis further confirmed. Together, these findings provide clues for further investigation of MsARF functional verification and molecular breeding of alfalfa. This study provides a novel approach to systematically identify and characterize ARF transcription factors in autotetraploid cultivated alfalfa, revealing 23 MsARF genes significantly involved in response to various stresses.
PMID: 37644390
Plants (Basel) , IF:3.935 , 2023 Aug , V12 (16) doi: 10.3390/plants12162942
Optimization of Callus Induction and Shoot Regeneration from Tomato Cotyledon Explants.
Instituto de Bioingenieria, Universidad Miguel Hernandez, 03202 Elche, Spain.
Cultivated tomato (Solanum lycopersicum L.) is one of the most important horticultural crops in the world. The optimization of culture media for callus formation and tissue regeneration of different tomato genotypes presents numerous biotechnological applications. In this work, we have analyzed the effect of different concentrations of zeatin and indole-3-acetic acid on the regeneration of cotyledon explants in tomato cultivars M82 and Micro-Tom. We evaluated regeneration parameters such as the percentage of callus formation and the area of callus formed, as well as the initiation percentage and the number of adventitious shoots. The best hormone combination produced shoot-like structures after 2-3 weeks. We observed the formation of leaf primordia from these structures after about 3-4 weeks. Upon transferring the regenerating micro-stems to a defined growth medium, it was possible to obtain whole plantlets between 4 and 6 weeks. This hormone combination was applied to other genotypes of S. lycopersicum, including commercial varieties and ancestral tomato varieties. Our method is suitable for obtaining many plantlets of different tomato genotypes from cotyledon explants in a very short time, with direct applications for plant transformation, use of gene editing techniques, and vegetative propagation of elite cultivars.
PMID: 37631154
Plants (Basel) , IF:3.935 , 2023 Aug , V12 (16) doi: 10.3390/plants12162899
Impact of Susceptibility on Plant Hormonal Composition during Clubroot Disease Development in Canola (Brassica napus).
Plant BioSystems, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada.
Clubroot, caused by Plasmodiophora brassicae, is a soilborne disease of crucifers associated with the formation of large root galls. This root enlargement suggests modulation of plant hormonal networks by the pathogen, stimulating cell division and elongation and influencing host defense. We studied physiological changes in two Brassica napus cultivars, including plant hormone profiles-salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), the auxin indole-3-acetic acid (IAA), and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC)-along with their selected derivatives following inoculation with virulent and avirulent P. brassicae pathotypes. In susceptible plants, water uptake declined from the initial appearance of root galls by 21 days after inoculation, but did not have a significant effect on photosynthetic rate, stomatal conductance, or leaf chlorophyll levels. Nonetheless, a strong increase in ABA levels indicated that hormonal mechanisms were triggered to cope with water stress due to the declining water uptake. The free SA level in the roots increased strongly in resistant interactions, compared with a relatively minor increase during susceptible interactions. The ratio of conjugated SA to free SA was higher in susceptible interactions, indicating that resistant interactions are linked to the plant's ability to maintain higher levels of bioactive free SA. In contrast, JA and its biologically active form JA-Ile declined up to 7-fold in susceptible interactions, while they were maintained during resistant interactions. The ACC level increased in the roots of inoculated plants by 21 days, irrespective of clubroot susceptibility, indicating a role of ethylene in response to pathogen interactions that is independent of disease severity. IAA levels at early and later infection stages were lower only in susceptible plants, suggesting a modulation of auxin homeostasis by the pathogen relative to the host defense system.
PMID: 37631111
Plants (Basel) , IF:3.935 , 2023 Aug , V12 (15) doi: 10.3390/plants12152877
Development of a New Micropropagation Protocol and Transfer of In Vitro Plants to In Vivo Conditions for Cascade Hop.
Department of Agricultural, Food and Forest Sciences, Universita Degli Studi di Palermo, Viale delle Scienze 13, Building 4, 90128 Palermo, Italy.
The vegetative propagation of hops, despite being a reliable method, is not very common due to the unavailability of the plant material. In this study, the technique of in vitro propagation was applied to the Cascade variety of Humulus lupulus L. The plant material was collected from a private field in Sicily; the explants were subjected to sterilization before in vitro culture. Single-node explants were placed in in vitro culture in nine different culture media for multiplication. Thidiazuron (TDZ), Benzyladenine (BAP) and meta-Topoline (mT) were tested for multiplication phase. For the rooting phase, five types of different culture media were evaluated. Binodal cuttings coming from the previous multiplication test were placed in the culture. The rooting media differ from each other in the concentration and ratio of two auxin hormones: Indolo-3-acetic acid (IAA) and Indole-3-butyric acid (IBA). In vitro rooted plants obtained from the rooting phase were transferred to ex vitro conditions in a microbox with agri-perlite and a solution containing Murashige and Skoog (MS) basal medium at half concentration. With a culture medium containing the highest TDZ doses (H6) and combination with cytokinin (H8 and H9), the highest shoot percentage was obtained. After 3 months of in vitro culture, the highest shoot percentage was observed in the culture medium with 2 mL L(-1) of BAP. The highest rooting percentage, roots numbers and root length were found when the culture medium was supplemented with 1 mL L(-1) of IAA. The usage of agri-perlite and MS at half concentration, without PGR, allowed us to obtain a 99.1% survival rate. This micropropagation protocol is useful for obtaining virus-free plants and for the development of the brewery industry.
PMID: 37571031
Plants (Basel) , IF:3.935 , 2023 Aug , V12 (15) doi: 10.3390/plants12152842
GA20ox Family Genes Mediate Gibberellin and Auxin Crosstalk in Moso bamboo (Phyllostachys edulis).
Key Laboratory of National Forestry and Grassland Administration, Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing 100102, China.
Moso bamboo (Phyllostachys edulis) is one of the fastest growing plants. Gibberellin (GA) is a key phytohormone regulating growth, but there are few studies on the growth of Moso bamboo regulated by GA. The gibberellin 20 oxidase (GA20ox) gene family was targeted in this study. Chromosomal distribution and collinearity analysis identified 10 GA20ox genes evenly distributed on chromosomes, and the family genes were relatively conservative in evolution. The genetic relationship of GA20ox genes had been confirmed to be closest in different genera of plants in a phylogenetic and selective pressure analysis between Moso bamboo and rice. About 1/3 GA20ox genes experienced positive selective pressure with segmental duplication being the main driver of gene family expansion. Analysis of expression patterns revealed that only six PheGA20ox genes were expressed in different organs of shoot development and flowers, that there was redundancy in gene function. Underground organs were not the main site of GA synthesis in Moso bamboo, and floral organs are involved in the GA biosynthesis process. The auxin signaling factor PheARF47 was located upstream of PheGA20ox3 and PheGA20ox6 genes, where PheARF47 regulated PheGA20ox3 through cis-P box elements and cis-AuxRR elements, based on the result that promoter analysis combined with yeast one-hybrid and dual luciferase detection analysis identified. Overall, we identified the evolutionary pattern of PheGA20ox genes in Moso bamboo and the possible major synthesis sites of GA, screened for key genes in the crosstalk between auxin and GA, and laid the foundation for further exploration of the synergistic regulation of growth by GA and auxin in Moso bamboo.
PMID: 37570996
J Plant Physiol , IF:3.549 , 2023 Aug , V287 : P154054 doi: 10.1016/j.jplph.2023.154054
Ginkgo biloba GbbZIP08 transcription factor is involved in the regulation of flavonoid biosynthesis.
College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China.; College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China. Electronic address: yejiabao@yangtzeu.edu.cn.; College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, Hubei, China. Electronic address: xufeng@yangtzeu.edu.cn.
Ginkgo biloba is the oldest relict plant on Earth and an economic plant resource derived from China. Flavonoids extracted from G. biloba are beneficial to the prevention and treatment of cardiovascular and cerebrovascular diseases. Basic leucine zipper (bZIP) transcription factors (TFs) have been recognized to play important roles in plant secondary metabolism. In this study, GbbZIP08 was isolated and characterized. It encodes a protein containing 154 amino acids, which belongs to hypocotyl 5 in group H of the bZIP family. Tobacco transient expression assay indicated that GbbZIP08 was localized in the plant nucleus. GbbZIP08 overexpression showed that the contents of total flavonoids, kaempferol, and anthocyanin in transgenic tobacco were significantly higher than those in the wild type. Transcriptome sequencing analysis revealed significant upregulation of structural genes in the flavonoid biosynthesis pathway. In addition, phytohormone signal transduction pathways, such as the abscisic acid, salicylic acid, auxin, and jasmonic acid pathways, were enriched with a large number of differentially expressed genes. TFs such as MYB, AP2, WRKY, NAC, bZIP, and bHLH, were also differentially expressed. The above results indicated that GbbZIP08 overexpression promoted flavonoid accumulation and increased the transcription levels of flavonoid-synthesis-related genes in plants.
PMID: 37487356
J Plant Physiol , IF:3.549 , 2023 Aug , V287 : P154003 doi: 10.1016/j.jplph.2023.154003
Comparison of two contrasting Leymus chinensis accessions reveals the roles of the cell wall and auxin in rhizome development.
Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China.; Grassland Work Station of East Ujimqin Banner of Xilin Gol League of Inner Mongolia, East Ujimqin Banner, 026300, China.; Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China. Electronic address: 111986015@imu.edu.cn.; Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China. Electronic address: kangyan105@imu.edu.cn.; Key Laboratory of Forage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010010, China. Electronic address: qizhi@imu.edu.cn.
Leymus chinensis, a perennial native forage grass, is widely distributed in the steppes of Inner Mongolia as the dominant species. The main reproductive strategy of this grass is clonal propagation, which occurs via the proliferation of subterranean horizontal stems known as rhizomes. To elucidate the mechanism underlying rhizome development in this grass, we collected 60 accessions of L. chinensis and evaluated their rhizome development. One accession, which we named SR-74 (Strong Rhizomes), had significantly better rhizome development capacity than the accession WR-16 (Weak Rhizomes) in terms of rhizome number, total and primary rhizome length, and number of rhizome seedlings. Rhizome elongation was positively correlated with the number of internodes in the rhizome, which affected plant biomass. Compared to WR-16, SR-74 had higher rhizome tip hardness, higher abundance of transcripts participating in the biosynthesis of cell wall components, and higher levels of the metabolites L-phenylalanine, trans-cinnamic acid, 3-coumaric acid, ferulic acid, and coniferin. These metabolites in the phenylpropanoid biosynthesis pathway are precursors of lignin. In addition, SR-74 rhizomes contained higher amounts of auxin and auxin metabolites, including L-Trp, IPA, IBA, IAA and IAA-Asp, as well as upregulated expression of the auxin biosynthesis and signaling genes YUCCA6, YUCCA8, YUCCA10, YUCCA11, PIN1, PIN2, UGT1, UGT2, UGT4, UGT10, GH3, IAA7, IAA23, and IAA30. We propose a network between auxin signaling and the cell wall underlying rhizome development in L. chinensis.
PMID: 37301035
Protoplasma , IF:3.356 , 2023 Sep , V260 (5) : P1389-1405 doi: 10.1007/s00709-023-01855-5
Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.).
Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China.; Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China.; Songyang Institute of Zhejiang Chinese Medical University, Lishui, 323400, China.; State Key Laboratory of Dao-Di Herbs, Beijng, 100700, China.; Key Laboratory of Plant Secondary Metabolism Regulation in Zhejiang Province, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, China. wangdk@zstu.edu.cn.
Auxin response factor (ARF) is an important transcription factor that regulates the expression of auxin-responsive genes by direct binding to their promoters, which play a central role in plant growth, development, and response to abiotic stresses. The availability of the entire Coix (Coix lacryma-jobi L.) genome sequence provides an opportunity to investigate the characteristics and evolutionary history of the ARF gene family in this medicine and food homology plant for the first time. In this study, a total of 27 ClARF genes were identified based on the genome-wide sequence of Coix. Twenty-four of the 27 ClARF genes were unevenly distributed on 8 chromosomes except Chr 4 and 10, and the remaining three genes (ClARF25-27) were not assigned to any chromosome. Most of the ClARF proteins were predicted to be localized to the nucleus, except ClARF24, which was localized to both the plasma membrane and nucleus. Twenty-seven ClARFs were clustered into six subgroups based on the phylogenetic analysis. Duplication analysis showed that segmental duplication, rather than tandem duplications promoting the expansion of the ClARF gene family. Synteny analysis showed that purifying selection might have been a primary driving force in the development of the ARF gene family in Coix and other investigated cereal plants. The prediction of the cis element of the promoter showed that 27 ClARF genes contain several stress response elements, suggesting that ClARFs might be involved in the abiotic stress response. Expression profile analysis shows that 27 ClARF genes were all expressed in the root, shoot, leaf, kernel, glume, and male flower of Coix with varying expression levels. Furthermore, qRT-PCR analyses revealed that the majority of ClARFs members were upregulated or downregulated in response to hormone treatment and abiotic stress. The current study expands our understanding of the functional roles of ClARFs in stress responses and provides basic information for the ClARF genes.
PMID: 37041371
PLoS One , IF:3.24 , 2023 , V18 (8) : Pe0287452 doi: 10.1371/journal.pone.0287452
GWAS of adventitious root formation in roses identifies a putative phosphoinositide phosphatase (SAC9) for marker-assisted selection.
Institute of Horticultural Production Systems, Section Woody Plant and Propagation Physiology, Leibniz Universitat Hannover, Hannover, Germany.; Institute of Plant Genetics, Section Molecular Plant Breeding, Leibniz Universitat Hannover, Hannover, Germany.
Rose propagation by cuttings is limited by substantial genotypic differences in adventitious root formation. To identify possible genetic factors causing these differences and to develop a marker for marker-assisted selection for high rooting ability, we phenotyped 95 cut and 95 garden rose genotypes in a hydroponic rooting system over 6 weeks. Data on rooting percentage after 3 to 6 weeks, root number, and root fresh mass were highly variable among genotypes and used in association mappings performed on genotypic information from the WagRhSNP 68 K Axiom SNP array for roses. GWAS analyses revealed only one significantly associated SNP for rooting percentage after 3 weeks. Nevertheless, prominent genomic regions/peaks were observed and further analysed for rooting percentage after 6 weeks, root number and root fresh mass. Some of the SNPs in these peak regions were associated with large effects on adventitious root formation traits. Very prominent were ten SNPs, which were all located in a putative phosphoinositide phosphatase SAC9 on chromosome 2 and showed very high effects on rooting percentage after 6 weeks of more than 40% difference between nulliplex and quadruplex genotypes. SAC9 was reported to be involved in the regulation of endocytosis and in combination with other members of the SAC gene family to regulate the translocation of auxin-efflux PIN proteins via the dephosphorylation of phosphoinositides. For one SNP within SAC9, a KASP marker was successfully derived and used to select genotypes with a homozygous allele configuration. Phenotyping these homozygous genotypes for adventitious root formation verified the SNP allele dosage effect on rooting. Hence, the presented KASP derived from a SNP located in SAC9 can be used for marker-assisted selection in breeding programs for high rooting ability in the future.
PMID: 37595005
Plant Biol (Stuttg) , IF:3.081 , 2023 Aug doi: 10.1111/plb.13565
Relationship between seasonal variation in isoprene emission and plant hormone profiles in the tropical plant Ficus septica.
The United Graduate School of Agricultural Sciences, Kagoshima University, Kagoshima, Japan.; Department of Biosciences, Teikyo University, Utsunomiya, Tochigi, Japan.; Advanced Instrumental Analysis Center, Teikyo University, Tochigi, Japan.; Tropical Biosphere Research Center, University of the Ryukyus, Okinawa, Japan.; Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang, Jiangsu, China.; Faculty of Agriculture, University of the Ryukyus, Okinawa, Japan.
In Ficus septica, the short-term control of isoprene production and, therefore, isoprene emission has been linked to the hormone balance between auxin (IAA) and jasmonic acid (JA). However, the relationship between long-term changes in isoprene emission and that of plant hormones remains unknown. This study tracked isoprene emissions from F. septica leaves, plant hormone concentrations and signalling gene expression, MEP pathway metabolite concentrations, and related enzyme gene expression for 1 year in the field to better understand the role of plant hormones and their long-term control. Seasonality of isoprenes was mainly driven by temperature- and light-dependent variations in substrate availability through the MEP route, as well as transcriptional and post-transcriptional control of isoprene synthase (IspS). Isoprene emissions are seasonally correlated with plant hormone levels. This was especially evident in the cytokinin profiles, which decreased in summer and increased in winter. Only 4-hydroxy-3-methylbut-2-butenyl-4-diphosphate (HMBDP) exhibited a positive connection with cytokinins among the MEP metabolites examined, suggesting that HMBDP and its biosynthetic enzyme, HMBDP synthase (HDS), play a role in channelling of MEP pathway metabolites to cytokinin production. Thus, it is probable that cytokinins have potential feed-forward regulation of isoprene production. Under long-term natural conditions, the hormonal balance of IAA/JA-Ile was not associated with IspS transcripts or isoprene emissions. This study builds on prior work by revealing differences between short- and long-term hormonal modulation of isoprene emissions in the tropical tree F. septica.
PMID: 37565537
Mol Biotechnol , IF:2.695 , 2023 Sep , V65 (9) : P1414-1420 doi: 10.1007/s12033-023-00653-x
Loss-of-Function Mutation of ACTIN-RELATED PROTEIN 6 (ARP6) Impairs Root Growth in Response to Salinity Stress.
Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, Vietnam.; National Institute of Medicinal Materials, Hanoi, Vietnam.; Faculty of Biotechnology, Ho Chi Minh City Open University, 97 Vo Van Tan Street, District 3, Ho Chi Minh, Vietnam.; Faculty of Biotechnology, Ho Chi Minh City Open University, 97 Vo Van Tan Street, District 3, Ho Chi Minh, Vietnam. nguyen.nhoai@ou.edu.vn.
H2A.Z-containing nucleosomes have been found to function in various developmental programs in Arabidopsis (e.g., floral transition, warm ambient temperature, and drought stress responses). The SWI2/SNF2-Related 1 Chromatin Remodeling (SWR1) complex is known to control the deposition of H2A.Z, and it has been unraveled that ACTIN-RELATED PROTEIN 6 (ARP6) is one component of this SWR1 complex. Previous studies showed that the arp6 mutant exhibited some distinguished phenotypes such as early flowering, leaf serration, elongated hypocotyl, and reduced seed germination rate in response to osmotic stress. In this study, we aimed to investigate the changes of arp6 mutant when the plants were grown in salt stress condition. The phenotypic observation showed that the arp6 mutant was more sensitive to salt stress than the wild type. Upon salt stress condition, this mutant exhibited attenuated root phenotypes such as shorter primary root length and fewer lateral root numbers. The transcript levels of stress-responsive genes, ABA INSENSITIVE 1 (ABI1) and ABI2, were found to be impaired in the arp6 mutant in comparison with wild-type plants in response to salt stress. In addition, a meta-analysis of published data indicated a number of genes involved in auxin response were induced in arp6 mutant grown in non-stress condition. These imply that the loss of H2A.Z balance (in arp6 mutant) may lead to change stress and auxin responses resulting in alternative root morphogenesis upon both normal and salinity stress conditions.
PMID: 36627550
J Plant Res , IF:2.629 , 2023 Sep , V136 (5) : P769-780 doi: 10.1007/s10265-023-01476-2
Rhizosphere frame system enables nondestructive live-imaging of legume-rhizobium interactions in the soil.
Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan.; Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, 3-1-3 Kannondai, Tsukuba, Ibaraki, 305-8604, Japan. onko@affrc.go.jp.
Most plants interact with various soil microorganisms as they grow through the soil. Root nodule symbiosis by legumes and rhizobia is a well-known phenomenon of plant-microbe interactions in the soil. Although microscopic observations are useful for understanding the infection processes of rhizobia, nondestructive observation methods have not been established for monitoring interactions between rhizobia and soil-grown roots. In this study, we constructed Bradyrhizobium diazoefficiens strains that constitutively express different fluorescent proteins, which allows identification of tagged rhizobia by the type of fluorophores. In addition, we constructed a plant cultivation device, Rhizosphere Frame (RhizoFrame), which is a soil-filled container made of transparent acrylic plates that allows observation of roots growing along the acrylic plates. Combining fluorescent rhizobia with RhizoFrame, we established a live imaging system, RhizoFrame system, that enabled us to track the nodulation processes with fluorescence stereomicroscope while retaining spatial information about roots, rhizobia, and soil. Mixed inoculation with different fluorescent rhizobia using RhizoFrame enabled the visualization of mixed infection of a single nodule with two strains. In addition, observation of transgenic Lotus japonicus expressing auxin-responsive reporter genes indicated that RhizoFrame system could be used for a real-time and nondestructive reporter assay. Thus, the use of RhizoFrame system is expected to enhance the study of the spatiotemporal dynamics of plant-microbe interactions in the soil.
PMID: 37402088
3 Biotech , IF:2.406 , 2023 Sep , V13 (9) : P290 doi: 10.1007/s13205-023-03709-6
Recent advances in auxin biosynthesis and homeostasis.
Kalapet, Pondicherry, 605014 India Department of Biotechnology, School of Life Sciences, Pondicherry University. GRID: grid.412517.4. ISNI: 0000 0001 2152 9956; Puducherry, India.
The plant proliferation is linked with auxins which in turn play a pivotal role in the rate of growth. Also, auxin concentrations could provide insights into the age, stress, and events leading to flowering and fruiting in the sessile plant kingdom. The role in rejuvenation and plasticity is now evidenced. Interest in plant auxins spans many decades, information from different plant families for auxin concentrations, transcriptional, and epigenetic evidences for gene regulation is evaluated here, for getting an insight into pattern of auxin biosynthesis. This biosynthesis takes place via an tryptophan-independent and tryptophan-dependent pathway. The independent pathway initiated before the tryptophan (trp) production involves indole as the primary substrate. On the other hand, the trp-dependent IAA pathway passes through the indole pyruvic acid (IPyA), indole-3-acetaldoxime (IAOx), and indole acetamide (IAM) pathways. Investigations on trp-dependent pathways involved mutants, namely yucca (1-11), taa1, nit1, cyp79b and cyp79b2, vt2 and crd, and independent mutants of tryptophan, ins are compiled here. The auxin conjugates of the IAA amide and ester-linked mutant gh3, iar, ilr, ill, iamt1, ugt, and dao are remarkable and could facilitate the assimilation of auxins. Efforts are made herein to provide an up-to-date detailed information about biosynthesis leading to plant sustenance. The vast information about auxin biosynthesis and homeostasis is consolidated in this review with a simplified model of auxin biosynthesis with keys and clues for important missing links since auxins can enable the plants to proliferate and override the environmental influence and needs to be probed for applications in sustainable agriculture. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03709-6.
PMID: 37547917
Mol Biol Rep , IF:2.316 , 2023 Aug doi: 10.1007/s11033-023-08631-x
Transcriptome analysis reveals the mechanism of different fruit appearance between apricot (Armeniaca vulgaris Lam.) and its seedling.
Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, China.; School of Life Science, Ningxia University, Yinchuan, 750021, China.; Ningxia Facility Horticulture Engineering Technology Center, Yinchuan, 750021, China.; Technological Innovation Center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021, China.; Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, China. zhangguangdi333909@sina.com.; Ningxia Facility Horticulture Engineering Technology Center, Yinchuan, 750021, China. zhangguangdi333909@sina.com.; Technological Innovation Center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, 750021, China. zhangguangdi333909@sina.com.; Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, School of Food Science and Engineering, Ningxia University, Yinchuan, 750021, China. fanght@nxu.edu.cn.
BACKGROUND: Apricot fruit has great economic value. In the process of apricot breeding using traditional breeding methods, we obtained a larger seedling (named Us) from the original variety (named U). And Us fruit is larger than U, taste better. Therefore, revealing its mechanism is very important for Apricot breeding. METHODS: In this study, de novo assembly and transcriptome sequencing (RNA-Seq) was used to screen the differently expressed genes (DEGs) between U and Us at three development stages, including young fruits stage, mid-ripening stage and mature fruit stage. RESULTS: The results showed that there were 6,753 DEGs at different sampling time. "Cellulose synthase (UDP-forming) activity" and "cellulose synthase activity" were the key GO terms enriched in GO, of which CESA and CSL family played a key role. "Photosynthesis-antenna proteins" and "Plant hormone signal transduction" were the candidate pathways and lhca, lhcb, Aux/IAA and SAUR were the main regulators. CONCLUSION: The auxin signaling pathway was active in Us, of which Aux/IAAs and SAUR were the key fruit size regulators. The low level of lhca and lhcb in Us could reveal the low demand for exogenous carbon, but they increased at mature stage, which might be due to the role of aux, who was keeping the fruit growing. Aux and photosynthesis maight be the main causes of appearance formation of Us fruits. Interestingly, the higher expression of CESA and CSL proved that Us entered the hardening process earlier than U. The advanced developmental progress might also be due to the role of Aux.
PMID: 37540452
Mol Biol Rep , IF:2.316 , 2023 Aug , V50 (8) : P6691-6701 doi: 10.1007/s11033-023-08563-6
Transcriptome analysis provides insights into the stress response in cultivated peanut (Arachis hypogaea L.) subjected to drought-stress.
Department of Biosciences, Saurashtra University Rajkot, Christ Campus, 360005, Vidya Niketan, Gujarat, India.; Christ Campus, Saurashtra University, 360005, Vidya Niketan, Rajkot, Gujarat, India.; Bionivid Technology Private Limited, Bengaluru, Karnataka, India.; Department of Biotechnology and Biochemistry, Junagadh Agricultural University, 362001, Junagadh, Gujarat, India.; Department of Biotechnology and Biochemistry, Junagadh Agricultural University, 362001, Junagadh, Gujarat, India. rukam@jau.in.
BACKGROUND: Peanut (Arachis hypogaea L.) is one of the valuable oilseed crops grown in drought-prone areas worldwide. Drought severely limits peanut production and productivity significantly. METHOD AND RESULTS: In order to decipher the drought tolerance mechanism in peanut under drought stress, RNA sequencing was performed in TAG - 24 (drought tolerant genotype) and JL-24 (drought susceptible genotype). Approximately 51 million raw reads were generated from four different libraries of two genotypes subjected to drought stress exerted by 20% PEG 6000 stress and control conditions, of which ~ 41 million (80.87%) filtered reads were mapped to the Arachis hypogaea L. reference genome. The transcriptome analysis detected 1,629 differentially expressed genes (DEGs), 186 genes encoding transcription factors (TFs) and 30,199 SSR among the identified DEGs. Among the differentially expressed TF encoding genes, the highest number of genes were WRKY followed by bZIP, C2H2, and MYB during drought stress. The comparative analysis between the two genotypes revealed that TAG-24 exhibits activation of certain key genes and transcriptional factors that are involved in essential biological processes. Specifically, TAG-24 showed activation of genes involved in the plant hormone signaling pathway such as PYL9, Auxin response receptor gene, and ABA. Additionally, genes related to water deprivation such as LEA protein and those involved in combating oxidative damage such as Glutathione reductase were also found to be activated in TAG-24. CONCLUSION: This genome-wide transcription map, therefore, provides a valuable tool for future transcript profiling under drought stress and enriches the genetic resources available for this important oilseed crop.
PMID: 37378750
Antonie Van Leeuwenhoek , IF:2.271 , 2023 Sep , V116 (9) : P855-866 doi: 10.1007/s10482-023-01850-z
Ancylobacter radicis sp. nov., a novel aerobic methylotrophic bacteria associated with plants.
G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Federal Research Center <
The two novel bacterial strains, designated as VT(T) and ML, were isolated from roots of cinquefoil (Potentilla sp.) and leaves of meadow-grass (Poa sp.) on the flooded bank of lake, respectively. These isolates were Gram-negative, non-spore-forming, non-motile, rod-shaped cells, utilized methanol, methylamine, and polycarbon compounds as carbon and energy sources. In the whole-cell fatty acid pattern of strains prevailed C(18:1)omega7c and C(19:0cyc). Based on the phylogenetic analysis of 16S rRNA gene sequences, strains VT(T) and ML were closely related to the representatives of the genus Ancylobacter (98.3-98.5%). The assembled genome of strain VT(T) has a total length of 4.22 Mbp, and a G + C content is 67.3%. The average nucleotide identity (ANI), average amino acid identity (AAI) and digital DNA-DNA hybridization (dDDH) values between strain VT(T) and closely related type strains of genus Ancylobacter were 78.0-80.6%, 73.8-78.3% and 22.1-24.0%, respectively, that clearly lower than proposed thresholds for species. On the basis of the phylogenetic, phenotypic, and chemotaxonomic analysis, isolates VT(T) and ML represent a novel species of the genus Ancylobacter, for which the name Ancylobacter radicis sp. nov. is proposed. The type strain is VT(T) (= VKM B-3255(T) = CCUG 72400(T)). In addition, novel strains were able to dissolve insoluble phosphates, to produce siderophores and plant hormones (auxin biosynthesis). According to genome analysis genes involved in the biosynthesis of siderophores, polyhydroxybutyrate, exopolysaccharides and phosphorus metabolism, as well as the genes involved in the assimilation of C(1)-compounds (natural products of plant metabolism) were found in the genome of type strain VT(T).
PMID: 37270429
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2218670 doi: 10.1080/15592324.2023.2218670
ChIFNalpha regulates adventitious root development in Lotus japonicus via an auxin-mediated pathway.
Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences/Institute of Agro-Bioengineering, Guizhou University, Guiyang, Guizhou Province, China.; Department of Genetics, University of Georgia, Athens, GA, USA.
Adventitious roots (ARs), developing from non-root tissue, play an important role in some plants. Here, the molecular mechanism of AR differentiation in Lotus japonicus L. (L. japonicus) with the transformed chicken interferon alpha gene (ChIFNalpha) encoding cytokine was studied. ChIFNalpha transgenic plants (TP) were identified by GUS staining, PCR, RT-PCR, and ELISA. Up to 0.175 mug/kg rChIFNalpha was detected in TP2 lines. Expressing rChIFNalpha promotes AR development by producing longer roots than controls. We found that the effect was enhanced with the auxin precursor IBA treatment in TP. IAA contents, POD, and PPO activities associated with auxin regulation were higher than wild type (WT) in TP and exogenous ChIFNalpha treatment plants. Transcriptome analysis revealed 48 auxin-related differentially expressed genes (DEGs) (FDR < 0.05), which expression levels were verified by RT-qPCR analysis. GO enrichment analysis of DEGs also highlighted the auxin pathway. Further analysis found that ChIFNalpha significantly enhanced auxin synthesis and signaling mainly with up-regulated genes of ALDH, and GH3. Our study reveals that ChIFNalpha can promote plant AR development by mediating auxin regulation. The findings help explore the role of ChIFNalpha cytokines and expand animal gene sources for the molecular breeding of growth regulation of forage plants.
PMID: 37288791
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2207845 doi: 10.1080/15592324.2023.2207845
Mendel-200: Pea as a model system to analyze hormone-mediated stem elongation.
I- Cultiver, Inc, Manteca, CA 95336 & Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.
In a recent Review Article on Gregor Mendel's (1822-1884) work with pea (Pisum sativum)-plants, it was proposed that this crop species should be re-vitalized as a model organism for the study of cell- and organ growth. Here, we describe the effect of exogenous gibberellic acid (GA(3)) on the growth of the second internode in 4-day-old light-grown pea seedlings (Pisum sativum, large var. "Senator"). lnjection of glucose into the internode caused a growth-promoting effect similar to that of the hormone GA(3). Imbibition of dry pea seeds in GA(3), or water as control, resulted in a drastic enhancement in organ development in this tall variety. Similar results were reported for dwarf peas. These "classical" experimental protocols are suitable to study the elusive effect of gibberellins (which act in coordination with auxin) on the regulation of plant development at the biochemical and molecular levels.
PMID: 37166004
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2163342 doi: 10.1080/15592324.2022.2163342
Cloning and expression study of a high-affinity nitrate transporter gene from Zea mays L.
Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China.; Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, Heilongjiang, China.; Aulin College, Northeast Forestry University, Harbin, Heilongjiang, China.
A nitrate transporter gene, named B46NRT2.1, from salt-tolerant Zea mays L. B46 has been cloned. B46NRT2.1 contained the same domain belonging to the major facilitator superfamily (PLN00028). The results of the phylogenetic tree indicated that B46NRT2.1 exhibits sequence similarity and the closest relationship with those known nitrate transporters of the NRT2 family. Through RT-qPCR, we found that the expression of B46NRT2.1 mainly happens in the root and leaf. Moreover, the treatment with NaCl, Na(2)CO(3), and NaHCO(3) could significantly increase the expression of B46NRT2.1. B46NRT2.1 was located in the plasma membrane. Through the study of yeast and plant salt response brought by B46NRT2.1 overexpression, we have preliminary knowledge that the expression of B46NRT2.1 makes yeast and plants respond to salt shock. There are 10 different kinds of cis-acting regulatory elements (CRES) in the promotor sequences of B46NRT2.1 gene using the PlantCARE web server to analyze. It mainly includes hormone response, abscisic acid, salicylic acid, gibberellin, methyl jasmonate, and auxin. The B46NRT2.1 gene's co-expression network showed that it was co-expressed with a number of other genes in several biological pathways, including regulation of NO(3) long-distance transit, modulation of nitrate sensing and metabolism, nitrate assimilation, and transduction of Jasmonic acid-independent wound signal. The results of this work should serve as a good scientific foundation for further research on the functions of the NRT2 gene family in plants (inbred line B46), and this research adds to our understanding of the molecular mechanisms under salt tolerance.
PMID: 36645908
Genes Genomics , IF:1.839 , 2023 Aug , V45 (8) : P1073-1083 doi: 10.1007/s13258-023-01385-7
Genome-wide identification of auxin-responsive microRNAs in the poplar stem.
College of Life Science, Inner Mongolia Agricultural University, Hohhot, 010018, China.; College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China.; Grass and Science Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China.; Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying, 257000, China.; Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China. baiyue@imau.edu.cn.; Forestry College, Inner Mongolia Agricultural University, Huhhot, 010018, China. chenyan@qau.edu.cn.; College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China. chenyan@qau.edu.cn.
BACKGROUND: Wood (secondary xylem) of forests is a material of great economic importance. Wood development is strictly controlled by both the phytohormone auxin and microRNAs (miRNAs). Currently, the regulatory mechanisms underlying wood formation by auxin-associated miRNAs remain unclear. OBJECTIVE: This report was designed to identify auxin-responsive miRNAs during wood formation. METHODS: Morphological observation of wood development in the poplar stems was performed under the treatment of different concentrations (0 mg/L, CK; 5 mg/L, Low; 10 mg/L, High) of indol-3-butyric acid (IBA). Using a small RNA sequencing strategy, the effect of IBA treatment on miRNAs expression was genome-widely analyzed. RESULTS: In this study, we found that wood development of poplar was promoted by low concentration of IBA treatment but inhibited by high concentration of IBA treatment. Stringent bioinformatic analysis led to identification of 118 known and 134 novel miRNAs candidates. Sixty-nine unique developmental-related miRNAs, corresponding to 269 target genes, exhibited specific expression patterns in response to auxin, as was consistent with the influence of auxin application on wood formation. Three novel miRNAs had the most number (>/= 9) of target genes, belonging to SPL, GRF and ARF gene families. The evolutionary relationships and tissue expression patterns of 41 SPL, GRF and ARF genes in poplar were thus analyzed. Of them, four representative members and corresponding miRNAs were confirmed using RT-qPCR. CONCLUSIONS: Our results may be helpful for a better understanding of auxin-induced regulation of wood formation in tree species.
PMID: 37336805
Scientifica (Cairo) , 2023 , V2023 : P2983812 doi: 10.1155/2023/2983812
The Optimization of Medium Conditions and Auxins in the Induction of Adventitious Roots of Pokeweed (Phytolacca americana L.) and Their Phytochemical Constituents.
Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand.; Department of Pharmacognosy and Toxicology, Faculty of Pharmaceutical Science, Khon Kaen University, Khon Kaen 40002, Thailand.
Pokeweed, Phytolacca americana L., is considered a widely spreading invasive plant, while saponin contents accumulated in the roots have pharmaceutical uses, such as rheumatism treatments and anti-inflammation. Adventitious root cultures are an important source of diverse secondary metabolites, which have significant applications in various fields. This study focused on the optimization of parameters for root induction using different medium states and treatments with auxins on a pokeweed leaf. Semisolid and liquid MS (Murashige and Skoog, 1962) media were supplemented with indole-3-butyric acid (IBA) and 1-naphthylacetic acid (NAA) at 0.5, 1, 2, and 4 mg/L. Root growth parameters, e.g., induction percentage, root numbers, length, and weight, were measured to determine the adventitious root induction efficiency. Total phenolic content, total flavonoid content, total saponin content, and antioxidant activity were recorded. Results showed that adventitious roots induced in semisolid MS medium supplemented with 0.5 mg/L NAA exhibited a high density of lateral roots. Appropriate medium state and auxin for adventitious root induction in pokeweed were determined as semisolid medium supplemented with 2 mg/L NAA. Considering phytochemicals, adventitious roots induced in liquid medium containing 0.5-1 mg/L NAA had the highest yield extract percentage. Additionally, adventitious roots cultivated in a liquid medium enriched with 1 mg/L NAA exhibited the highest phenolic and saponin contents. A principal component analysis (PCA) biplot and hierarchical cluster analysis (HCA) heatmap demonstrated different response patterns between semisolid and liquid media applied with NAA. The results of the semisolid media were grouped together due to high expression levels of the root induction parameters, while elevated phytochemical values were observed in the liquid media treatments. The results suggested two different media that provide the highest adventitious root induction efficiency and the greatest phytochemical contents: semisolid medium with 2 mg/L NAA and liquid medium with 1 mg/L NAA, respectively. These culture media can be applied to optimize adventitious root culture of pokeweed and in vitro phytochemical production.
PMID: 37645570
STAR Protoc , 2023 Aug , V4 (3) : P102514 doi: 10.1016/j.xpro.2023.102514
Hormone immunolabeling in resin-embedded Arabidopsis tissues.
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, Centro de Investigacion y de Estudios Avanzados del Instituto Politecnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato 36824, 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.
Here, we present a protocol for immunolabeling of molecules in Arabidopsis tissues. We describe steps for tissue fixation and embedding in resin of microtome-derived sections, immunolabeling using fluorescent and non-fluorescent secondary antibodies, and visualization of cytokinin and auxin molecules. This protocol is suitable to study reproductive structures such as inflorescences, flowers, fruits, and tissue-culture-derived samples. This protocol is useful for studying the distribution of a wide range of molecules including hormones and cell wall components. For complete details on the use and execution of this protocol, please refer to Herrera-Ubaldo et al. (2019).(1).
PMID: 37573503
Plant Commun , 2023 Jul : P100669 doi: 10.1016/j.xplc.2023.100669
Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution.
Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria.; Graduate Institute of Biotechnology, National Chung Hsing University, No. 145, Xingda Rd., South Dist., Taichung 40227, Taiwan, R.O.C.; College of Life Sciences, Northwest A&F University, Shaanxi, Yangling, China.; Institute of Plant and Microbial Biology, Academia Sinica, 128 Sec. 2, Academia Rd, Nankang, Taipei 11529, Taiwan, R.O.C.; Institute of Science and Technology Austria (ISTA), Am Campus 1, 3400 Klosterneuburg, Austria. Electronic address: jiri.friml@ist.ac.at.
The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and exogenous PINs in two bryophytes, Physcomitrium patens and Marchantia polymorpha, and in the flowering plant Arabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while exogenous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues of individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms.
PMID: 37528584
Mol Breed , 2023 Aug , V43 (8) : P62 doi: 10.1007/s11032-023-01409-w
Small Auxin Up RNA 56 (SAUR56) regulates heading date in rice.
Guangzhou, 510642 People's Republic of China National Plant Space Breeding Engineering Technology Research Center, South China Agricultural University. GRID: grid.20561.30. ISNI: 0000 0000 9546 5767; Guangzhou, 510642 China Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University. GRID: grid.20561.30. ISNI: 0000 0000 9546 5767; Heyuan Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Heyuan, 517000 Guangdong China.
Heading date is a critical agronomic trait that determines crop yield. Although numerous genes associated with heading date have been identified in rice, the mechanisms involving Small Auxin Up RNA (SAUR) family have not been elucidated. In this study, the biological function of several SAUR genes was initially investigated using the CRISPR-Cas9 technology in the Japonica cultivar Zhonghua11 (ZH11) background. Further analysis revealed that the loss-of-function of OsSAUR56 affected heading date in both NLD (natural long-day) and ASD (artificial short-day). OsSAUR56 exhibited predominant expression in the anther, with its protein localized in both the cytoplasm and nucleus. OsSAUR56 regulated flowering time and heading date by modulating the expression of the clock gene OsGI, as well as two repressors Ghd7 and DTH8. Furthermore, haplotype-phenotype association analysis revealed a strong correlation between OsSAUR56 and heading date, suggesting its role in selection during the domestication of rice. In summary, these findings highlights the importance of OsSAUR56 in the regulation of heading date for further potential facilitating genetic engineering for flowering time during rice breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-023-01409-w.
PMID: 37521314