Cell , IF:41.582 , 2023 Oct , V186 (22) : P4788-4802.e15 doi: 10.1016/j.cell.2023.09.014
Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants.
Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Key Laboratory of Vegetable Research Center, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.; The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA.; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China. Electronic address: chenhaodong@tsinghua.edu.cn.
Gravity controls directional growth of plants, and the classical starch-statolith hypothesis proposed more than a century ago postulates that amyloplast sedimentation in specialized cells initiates gravity sensing, but the molecular mechanism remains uncharacterized. The LAZY proteins are known as key regulators of gravitropism, and lazy mutants show striking gravitropic defects. Here, we report that gravistimulation by reorientation triggers mitogen-activated protein kinase (MAPK) signaling-mediated phosphorylation of Arabidopsis LAZY proteins basally polarized in root columella cells. Phosphorylation of LAZY increases its interaction with several translocons at the outer envelope membrane of chloroplasts (TOC) proteins on the surface of amyloplasts, facilitating enrichment of LAZY proteins on amyloplasts. Amyloplast sedimentation subsequently guides LAZY to relocate to the new lower side of the plasma membrane in columella cells, where LAZY induces asymmetrical auxin distribution and root differential growth. Together, this study provides a molecular interpretation for the starch-statolith hypothesis: the organelle-movement-triggered molecular polarity formation.
PMID: 37741279
Trends Plant Sci , IF:18.313 , 2023 Oct , V28 (10) : P1098-1100 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
Nat Plants , IF:15.793 , 2023 Oct , V9 (10) : P1578 doi: 10.1038/s41477-023-01549-z
Auxin aids nitrogen foraging.
Nature Plants, . raphael.troesch@nature.com.
PMID: 37814024
Nat Plants , IF:15.793 , 2023 Oct doi: 10.1038/s41477-023-01533-7
Improving rice nitrogen-use efficiency by modulating a novel monouniquitination machinery for optimal root plasticity response to nitrogen.
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China.; Department of Biology, University of Oxford, Oxford, UK.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China. shanli@njau.edu.cn.; Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China. shanli@njau.edu.cn.
Plant nitrogen (N)-use efficiency (NUE) is largely determined by the ability of root to take up external N sources, whose availability and distribution in turn trigger the modification of root system architecture (RSA) for N foraging. Therefore, improving N-responsive reshaping of RSA for optimal N absorption is a major target for developing crops with high NUE. In this study, we identified RNR10 (REGULATOR OF N-RESPONSIVE RSA ON CHROMOSOME 10) as the causal gene that underlies the significantly different root developmental plasticity in response to changes in N level exhibited by the indica (Xian) and japonica (Geng) subspecies of rice. RNR10 encodes an F-box protein that interacts with a negative regulator of auxin biosynthesis, DNR1 (DULL NITROGEN RESPONSE1). Interestingly, RNR10 monoubiquitinates DNR1 and inhibits its degradation, thus antagonizing auxin accumulation, which results in reduced root responsivity to N and nitrate (NO(3)(-)) uptake. Therefore, modulating the RNR10-DNR1-auxin module provides a novel strategy for coordinating a desirable RSA and enhanced N acquisition for future sustainable agriculture.
PMID: 37798338
Trends Biochem Sci , IF:13.807 , 2023 Nov , V48 (11) : P937-948 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
Mol Plant , IF:13.164 , 2023 Oct , V16 (10) : P1678-1694 doi: 10.1016/j.molp.2023.09.007
Rice roots avoid asymmetric heavy metal and salinity stress via an RBOH-ROS-auxin signaling cascade.
State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China. Electronic address: fangjie.zhao@njau.edu.cn.
Root developmental plasticity is crucial for plants to adapt to a changing soil environment, where nutrients and abiotic stress factors are distributed heterogeneously. How plant roots sense and avoid heterogeneous abiotic stress in soil remains unclear. Here, we show that, in response to asymmetric stress of heavy metals (cadmium, copper, or lead) and salt, rice roots rapidly proliferate lateral roots (LRs) in the stress-free area, thereby remodeling root architecture to avoid localized stress. Imaging and quantitative analyses of reactive oxygen species (ROS) showed that asymmetric stress induces a ROS burst in the tips of the exposed roots and simultaneously triggers rapid systemic ROS signaling to the unexposed roots. Addition of a ROS scavenger to either the stressed or stress-free area abolished systemic ROS signaling and LR proliferation induced by asymmetric stress. Asymmetric stress also enhanced cytosolic calcium (Ca(2+)) signaling; blocking Ca(2+)signaling inhibited systemic ROS propagation and LR branching in the stress-free area. We identified two plasma-membrane-localized respiratory burst oxidase homologs, OsRBOHA and OsRBOHI, as key players in systemic ROS signaling under asymmetric stress. Expression of OsRBOHA and OsRBOHI in roots was upregulated by Cd stress, and knockout of either gene reduced systemic ROS signaling and LR proliferation under asymmetric stress. Furthermore, we demonstrated that auxin signaling and cell wall remodeling act downstream of the systemic ROS signaling to promote LR development. Collectively, our study reveals an RBOH-ROS-auxin signaling cascade that enables rice roots to avoid localized stress of heavy metals and salt and provides new insight into root system plasticity in heterogenous soil.
PMID: 37735869
Plant Cell , IF:11.277 , 2023 Oct doi: 10.1093/plcell/koad255
Transcriptional activation by WRKY23 and derepression by removal of bHLH041 coordinately establish callus pluripotency in Arabidopsis regeneration.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, China National Botanical Garden, Beijing 100093, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; National Center for Plant Gene Research, Beijing 100093, China.
Induction of the pluripotent cell mass termed callus from detached organs or tissues is an initial step in typical in vitro plant regeneration, during which auxin-induced ectopic activation of root stem cell factors are required for subsequent de novo shoot regeneration. While Arabidopsis (Arabidopsis thaliana) AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and their downstream transcription factors LATERAL ORGAN BOUNDARIES DOMAIN (LBD) are known to play key roles in directing callus formation, the molecules responsible for activation of root stem cell factors and thus establishment of callus pluripotency are unclear. Here, we identified Arabidopsis WRKY23 and BASIC HELIX-LOOP-HELIX 041 (bHLH041) as a transcriptional activator and repressor, respectively, of root stem cell factors during establishment of auxin-induced callus pluripotency. We show that auxin-induced WRKY23 downstream of ARF7 and ARF19 directly activates the transcription of PLETHORA 3 (PLT3) and PLT7 and thus that of the downstream genes PLT1, PLT2 and WUSCHEL-RELATED HOMEOBOX 5 (WOX5), while LBD-induced removal of bHLH041 derepresses the transcription of PLT1, PLT2 and WOX5. We provide evidence that transcriptional activation by WRKY23 and loss of bHLH041-imposed repression act synergistically in conferring shoot-regenerating capability on callus cells. Our findings thus disclose a transcriptional mechanism underlying auxin-induced cellular reprogramming, which, together with previous studies, outlines the molecular framework of auxin-induced pluripotent callus formation for in vitro plant regeneration programs.
PMID: 37804093
Plant Cell , IF:11.277 , 2023 Oct , V35 (11) : P4133-4154 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.; College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070,China.; 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 APETALA2/ethylene response factor (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 RNA interference (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 virus-induced gene silencing (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
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Oct , V120 (42) : Pe2306263120 doi: 10.1073/pnas.2306263120
Disruption of the rice 4-DEOXYOROBANCHOL HYDROXYLASE unravels specific functions of canonical strigolactones.
The BioActives Lab, Center for Desert Agriculture, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.; The Plant Science Program, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.; Department of Life Sciences and Systems Biology, University of Torino, Torino 10125, Italy.; Biological and Environmental Science and Engineering (BESE) Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
Strigolactones (SLs) regulate many developmental processes, including shoot-branching/tillering, and mediate rhizospheric interactions. SLs originate from carlactone (CL) and are structurally diverse, divided into a canonical and a noncanonical subfamily. Rice contains two canonical SLs, 4-deoxyorobanchol (4DO) and orobanchol (Oro), which are common in different plant species. The cytochrome P450 OsMAX1-900 forms 4DO from CL through repeated oxygenation and ring closure, while the homologous enzyme OsMAX1-1400 hydroxylates 4DO into Oro. To better understand the biological function of 4DO and Oro, we generated CRISPR/Cas9 mutants disrupted in OsMAX1-1400 or in both OsMAX1-900 and OsMAX1-1400. The loss of OsMAX1-1400 activity led to a complete lack of Oro and an accumulation of its precursor 4DO. Moreover, Os1400 mutants showed shorter plant height, panicle and panicle base length, but no tillering phenotype. Hormone quantification and transcriptome analysis of Os1400 mutants revealed elevated auxin levels and changes in the expression of auxin-related, as well as of SL biosynthetic genes. Interestingly, the Os900/1400 double mutant lacking both Oro and 4DO did not show the observed Os1400 architectural phenotypes, indicating their being a result of 4DO accumulation. Treatment of wild-type plants with 4DO confirmed this assumption. A comparison of the Striga seed germinating activity and the mycorrhization of Os900, Os900/1400, and Os1400 loss-of-function mutants demonstrated that the germination activity positively correlates with 4DO content while disrupting OsMAX1-1400 has a negative impact on mycorrhizal symbiosis. Taken together, our paper deciphers the biological function of canonical SLs in rice and reveals their particular contributions to establishing architecture and rhizospheric communications.
PMID: 37819983
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Oct , V120 (42) : Pe2309007120 doi: 10.1073/pnas.2309007120
Dynamic context-dependent regulation of auxin feedback signaling in synthetic gene circuits.
Centro de Biotecnologia y Genomica de Plantas (CBGP), Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion Agraria y Alimentaria (INIA/CSIC), 28223 Madrid, Spain.
Phytohormone auxin plays a key role in regulating plant organogenesis. However, understanding the complex feedback signaling network that involves at least 29 proteins in Arabidopsis in the dynamic context remains a significant challenge. To address this, we transplanted an auxin-responsive feedback circuit responsible for plant organogenesis into yeast. By generating dynamic microfluidic conditions controlling gene expression, protein degradation, and binding affinity of auxin response factors to DNA, we illuminate feedback signal processing principles in hormone-driven gene expression. In particular, we recorded the regulatory mode shift between stimuli counting and rapid signal integration that is context-dependent. Overall, our study offers mechanistic insights into dynamic auxin response interplay trackable by synthetic gene circuits, thereby offering instructions for engineering plant architecture.
PMID: 37812708
Proc Natl Acad Sci U S A , IF:11.205 , 2023 Oct , V120 (40) : Pe2302996120 doi: 10.1073/pnas.2302996120
Trehalose-6-phosphate signaling regulates lateral root formation in Arabidopsis thaliana.
Department of Plant Biotechnology and Bioinformatics Ghent University, Ghent B-9052, Belgium.; Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, Ghent B-9052, Belgium.; Laboratory of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven B3001, Belgium.; Vlaams Instituut voor Biotechnologie-Katholieke Universiteit Leuven Center for Microbiology, Leuven B3001, Belgium.; Department of Organic and Macromolecular Chemistry, Laboratory for Organic and Bio-Organic Synthesis, Ghent University, Ghent B-9000, Belgium.; Department of Sustainable Soils and Crops, Rothamsted Research, Harpenden AL5 2JQ, United Kingdom.; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom.; Next Generation Chemistry, The Rosalind Franklin Institute, Didcot OX1 3TA, United Kingdom.; Department of Pharmacology, University of Oxford, Oxford OX1 3TA, United Kingdom.; Katholieke Universiteit Leuven Plant Institute, Katholieke Universiteit Leuven, Leuven B3001, Belgium.
Plant roots explore the soil for water and nutrients, thereby determining plant fitness and agricultural yield, as well as determining ground substructure, water levels, and global carbon sequestration. The colonization of the soil requires investment of carbon and energy, but how sugar and energy signaling are integrated with root branching is unknown. Here, we show through combined genetic and chemical modulation of signaling pathways that the sugar small-molecule signal, trehalose-6-phosphate (T6P) regulates root branching through master kinases SNF1-related kinase-1 (SnRK1) and Target of Rapamycin (TOR) and with the involvement of the plant hormone auxin. Increase of T6P levels both via genetic targeting in lateral root (LR) founder cells and through light-activated release of the presignaling T6P-precursor reveals that T6P increases root branching through coordinated inhibition of SnRK1 and activation of TOR. Auxin, the master regulator of LR formation, impacts this T6P function by transcriptionally down-regulating the T6P-degrader trehalose phosphate phosphatase B in LR cells. Our results reveal a regulatory energy-balance network for LR formation that links the 'sugar signal' T6P to both SnRK1 and TOR downstream of auxin.
PMID: 37748053
Curr Biol , IF:10.834 , 2023 Oct , V33 (19) : P4085-4097.e5 doi: 10.1016/j.cub.2023.08.061
Genome and transcriptome of Selaginella kraussiana reveal evolution of root apical meristems in vascular plants.
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.; School of Life Sciences, Nantong University, Nantong 226019, China.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.; National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China. Electronic address: xulin@cemps.ac.cn.
The evolution of roots allowed vascular plants to adapt to land environments. Fossil evidence indicates that roots evolved independently in euphyllophytes (ferns and seed plants) and lycophytes, the two lineages of extant vascular plants. Based on a high-quality genome assembly, mRNA sequencing (mRNA-seq) data, and single-cell RNA-seq data for the lycophyte Selaginella kraussiana, we show that the two root origin events in lycophytes and euphyllophytes adopted partially similar molecular modules in the regulation of root apical meristem (RAM) development. In S. kraussiana, the RAM initiates from the rhizophore primordium guided by auxin and duplicates itself by dichotomous branching. The auxin signaling pathway directly upregulates euAINTEGUMENTAb (SkeuANTb), and then SkeuANTb directly promotes the expression of SkeuANTa and the WUSCHEL-RELATED HOMEOBOX13b (SkWOX13b) for RAM maintenance, partially similar to the molecular pathway involving the euANT-branch PLETHORA (AtPLT) genes and AtWOX5 in root initiation in the seed plant Arabidopsis thaliana. Other molecular modules, e.g., SHORT-ROOT and SCARECROW, also have partially similar expression patterns in the RAMs of S. kraussiana and A. thaliana. Overall, our study not only provides genome and transcriptome tools of S. kraussiana but also indicates the employment of some common molecular modules in RAMs during root origins in lycophytes and euphyllophytes.
PMID: 37716350
J Hazard Mater , IF:10.588 , 2024 Jan , V461 : P132541 doi: 10.1016/j.jhazmat.2023.132541
Genome-wide profiling of genetic variations reveals the molecular basis of aluminum stress adaptation in Tibetan wild barley.
Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China.; Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.; Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China.; Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; Plant Biotechnology Laboratory, Center for Viticulture & Small Fruit Research, Florida A&M University, FL 32317, USA.; Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China. Electronic address: wufeibo@zju.edu.cn.
Aluminum (Al) toxicity in acidic soil is a major factor affecting crop productivity. The extensive genetic diversity found in Tibetan wild barley germplasms offers a valuable reservoir of alleles associated with aluminum tolerance. Here, resequencing of two Al-tolerant barley genotypes (Tibetan wild barley accession XZ16 and cultivated barley Dayton) identified a total of 19,826,182 and 16,287,277 single nucleotide polymorphisms (SNPs), 1628,052 and 1386,973 insertions/deletions (InDels), 61,532 and 57,937 structural variations (SVs), 248,768 and 240,723 copy number variations (CNVs) in XZ16 and Dayton, respectively, and uncovered approximately 600 genes highly related to Al tolerance in barley. Comparative genomic analyses unveiled 71 key genes that contain unique genetic variants in XZ16 and are predominantly associated with organic acid exudation, Al sequestration, auxin response, and transcriptional regulation. Manipulation of these key genes at the genetic and transcriptional level is a promising strategy for developing optimal haplotype combinations and new barley cultivars with improved Al tolerance. This study represents the first comprehensive examination of genetic variation in Al-tolerant Tibetan wild barley through genome-wide profiling. The obtained results make the deep insight into the mechanisms underlying barley adaptation to Al toxicity, and identified the candidate genes useful for improvement of Al tolerance in barley.
PMID: 37716271
New Phytol , IF:10.151 , 2023 Oct doi: 10.1111/nph.19303
FASEB: the mechanism of plant development: Saxtons River, Vermont, 24-29 July 2022.
Centro de Biotecnologia y Genomica de Plantas (CBGP), Universidad Politecnica de Madrid (UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria (CNINIA, CSIC), Campus de Montegancedo, Pozuelo de Alarcon, 28223, Madrid, Spain.; Departement de Sciences Biologique, Institut de Recherche en Biologie Vegetale, Universite de Montreal, Montreal, QC, H1X 2B2, Canada.; Laboratory of Biochemistry, Wageningen University, Wageningen, 6708 WE, the Netherlands.; Sainsbury Laboratory, University of Cambridge, CB2 1LR, Cambridge, UK.; Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA.
PMID: 37817389
New Phytol , IF:10.151 , 2023 Oct doi: 10.1111/nph.19292
Chemical induction of hypocotyl rooting reveals extensive conservation of auxin signalling controlling lateral and adventitious root formation.
Horticell, Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, 9000, Ghent, Belgium.; Institute of Food and Biotechnology, Can Tho University, 900000, Can Tho City, Vietnam.; Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.; School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.; Department of Biosciences, University of Milan, via Celoria 26, 20133, Milan, Italy.; Institute of Biophysics, National Research Council of Italy (CNR), 20133, Milan, Italy.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.; VIB Centre for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.; Department of Plant Physiology, Umea Plant Science Centre, Umea University, SE-90736, Umea, Sweden.; Universite Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France.
Upon exposure to light, etiolated Arabidopsis seedlings form adventitious roots (AR) along the hypocotyl. While processes underlying lateral root formation are studied intensively, comparatively little is known about the molecular processes involved in the initiation of hypocotyl AR. AR and LR formation were studied using a small molecule named Hypocotyl Specific Adventitious Root INducer (HYSPARIN) that strongly induces AR but not LR formation. HYSPARIN does not trigger rapid DR5-reporter activation, DII-Venus degradation or Ca(2+) signalling. Transcriptome analysis, auxin signalling reporter lines and mutants show that HYSPARIN AR induction involves nuclear TIR1/AFB and plasma membrane TMK auxin signalling, as well as multiple downstream LR development genes (SHY2/IAA3, PUCHI, MAKR4 and GATA23). Comparison of the AR and LR induction transcriptome identified SAURs, AGC kinases and OFP transcription factors as specifically upregulated by HYSPARIN. Members of the SAUR19 subfamily, OFP4 and AGC2 suppress HYS-induced AR formation. While SAUR19 and OFP subfamily members also mildly modulate LR formation, AGC2 regulates only AR induction. Analysis of HYSPARIN-induced AR formation uncovers an evolutionary conservation of auxin signalling controlling LR and AR induction in Arabidopsis seedlings and identifies SAUR19, OFP4 and AGC2 kinase as novel regulators of AR formation.
PMID: 37787103
New Phytol , IF:10.151 , 2023 Oct , V240 (2) : P846-862 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 Oct , V240 (2) : P489-495 doi: 10.1111/nph.19123
Tale of cAMP as a second messenger in auxin signaling and beyond.
Institute of Science and Technology Austria (ISTA), Klosterneuburg, 3400, Austria.
The 3',5'-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general.
PMID: 37434303
Plant Biotechnol J , IF:9.803 , 2023 Oct , V21 (10) : P1990-2001 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
Plant Physiol , IF:8.34 , 2023 Oct doi: 10.1093/plphys/kiad570
Soybean type-B response regulator GmRR1 mediates phosphorus uptake and yield by modifying root architecture.
National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China.; School of Agriculture, Henan Institute of Science and Technology, Xinxiang 453003, China.; Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China.; Ningxia University, Yinchuan 750021, China.; Northeast Institute of Geography and Agroecology, Key Laboratory of Soybean Molecular Design Breeding, Chinese Academy of Sciences, Harbin150081, China.
Phosphorus (P) plays a pivotal role in plant growth and development. Low P stress can greatly hamper plant growth. Here, we identified a QTL (named QPH-9-1), which is associated with P efficiency across multiple environments through linkage analysis and genome-wide association study (GWAS). Furthermore, we successfully cloned the underlying soybean (Glycine max) gene GmRR1 (a soybean type-B Response Regulator 1) that encodes a type-B response regulator protein. Knockout of GmRR1 resulted in a substantial increase in plant height, biomass, P uptake efficiency, and yield-related traits due to the modification of root structure. In contrast, overexpression of GmRR1 in plants resulted in a decrease in these phenotypes. Further analysis revealed that knockout of GmRR1 substantially increased the levels of auxin and ethylene in roots, thereby promoting root hair formation and growth by promoting the formation of root hair primordium and lengthening the root apical meristem. Yeast two-hybrid, bimolecular fluorescence complementation, and dual-luciferase assays demonstrated an interaction between GmRR1 and Histidine-containing Phosphotransmitter protein 1 (GmHP1). Expression analysis suggested that these proteins co-participated in response to low P stress. Analysis of genomic sequences showed that GmRR1 underwent a selection during soybean domestication. Taken together, this study provides further insights into how plants respond to low P stress by modifying root architecture through phytohormone pathways.
PMID: 37882637
Plant Physiol , IF:8.34 , 2023 Oct doi: 10.1093/plphys/kiad548
Age-dependent analysis dissects the stepwise control of auxin-mediated lateral root development in rice.
Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan.; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.; School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia.; International Center for Research and Education in Agriculture, Nagoya University, Nagoya, 464-8601, Japan.
As root elongation rates are different among each individual root, the distance from the root apices does not always reflect the age of root cells. Thus, methods for correcting variations in elongation rates are needed to accurately evaluate the root developmental process. Here, we show that modeling-based age-dependent analysis is effective for dissecting stepwise lateral root (LR) development in rice (Oryza sativa). First, we measured the increases in LR and LR primordium (LRP) numbers, diameters, and lengths in wild type and an auxin-signaling-defective mutant, which has a faster main (crown) root elongation rate caused by the mutation in the gene encoding AUXIN/INDOLE-3-ACETIC ACID protein 13 (IAA13). The longitudinal patterns of these parameters were fitted by the appropriate models and the age-dependent patterns were identified using the root elongation rates. As a result, we found that LR and LRP numbers and lengths were reduced in iaa13. We also found that the duration of the increases in LR and LRP diameters were prolonged in iaa13. Subsequent age-dependent comparisons with gene expression patterns suggest that AUXIN RESPONSE FACTOR11 (ARF11), the homologue of MONOPTEROS (MP)/ARF5 in Arabidopsis (Arabidopsis thaliana), is involved in the initiation and growth of LR(P). Indeed, the arf11 mutant showed a reduction of LR and LRP numbers and lengths. Our results also suggest that PINOID (PID)-dependent rootward-to-shootward shift of auxin flux contributes to the increase in LR and LRP diameters. Together, we propose that modeling-based age-dependent analysis is useful for root developmental studies by enabling accurate evaluation of root traits' expression.
PMID: 37831077
Plant Physiol , IF:8.34 , 2023 Sep doi: 10.1093/plphys/kiad506
Mechanistic insight into the role of AUXIN RESISTANCE4 in trafficking of AUXIN1 and LIKE AUX1-2.
Division of Plant and Crop Science, School of Biosciences, University of Nottingham, Nottingham, UK.; School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH.; Centre for Plant Integrative Biology, University of Nottingham, Nottingham, UK.
AUXIN RESISTANCE4 (AXR4) regulates trafficking of auxin influx carrier AUXIN1 (AUX1), a plasma-membrane protein that predominantly localises to the endoplasmic reticulum (ER) in the absence of AXR4. In Arabidopsis (Arabidopsis thaliana), AUX1 is a member of a small multigene family comprising four highly conserved genes - AUX1, LIKE-AUX1 (LAX1), LAX2 and LAX3. We report here that LAX2 also requires AXR4 for correct localization to the plasma membrane. AXR4 is a plant-specific protein and contains a weakly conserved alpha/beta hydrolase fold domain that is found in several classes of lipid hydrolases and transferases. We have previously proposed that AXR4 may either act as 1) a post translational modifying enzyme through its alpha/beta hydrolase fold domain or 2) an ER accessory protein, which is a special class of ER protein that regulates targeting of their cognate partner proteins. Here, we show that AXR4 is unlikely to act as a post-translational modifying enzyme as mutations in several highly conserved amino acids in the alpha/beta hydrolase fold domain can be tolerated and active site residues are missing. We also show that AUX1 and AXR4 physically interact with each other and that AXR4 reduces aggregation of AUX1 in a dose-dependent fashion. Our results suggest that AXR4 acts as an ER accessory protein. Better understanding of AXR4 mediated trafficking of auxin transporters in crop plants will be crucial for improving root traits (designer roots) for better acquisition of water and nutrients for sustainable and resilient agriculture.
PMID: 37776522
Plant Physiol , IF:8.34 , 2023 Oct , V193 (3) : P1816-1833 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, Nanjing Agricultural University, Sanya 572000, China.
Cell elongation is a fundamental process for plant growth and development. Studies have shown lipid metabolism plays important role 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 indole-3-acetic acid (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 basic helix-loop-helix 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
Elife , IF:8.14 , 2023 Oct , V12 doi: 10.7554/eLife.83334
The Arabidopsis SHORTROOT network coordinates shoot apical meristem development with auxin dependent lateral organ initiation.
Institute for Developmental Genetics, Heinrich Heine University Dusseldorf, Dusseldorf, Germany.; Genome Dynamics and Function, Centro de Biologia Molecular Severo Ochoa, Madrid, Spain.; Laboratory of Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
Plants produce new organs post-embryonically throughout their entire life cycle. This is due to stem cells present in the shoot and root apical meristems, the SAM and RAM, respectively. In the SAM, stem cells are located in the central zone where they divide slowly. Stem cell daughters are displaced laterally and enter the peripheral zone, where their mitotic activity increases and lateral organ primordia are formed. How the spatial arrangement of these different domains is initiated and controlled during SAM growth and development, and how sites of lateral organ primordia are determined in the peripheral zone is not yet completely understood. We found that the SHORTROOT (SHR) transcription factor together with its target transcription factors SCARECROW (SCR), SCARECROW-LIKE23 (SCL23) and JACKDAW (JKD), promotes formation of lateral organs and controls shoot meristem size. SHR, SCR, SCL23 and JKD are expressed in distinct, but partially overlapping patterns in the SAM. They can physically interact and activate expression of key cell cycle regulators such as CYCLIND6;1 (CYCD6;1) to promote the formation of new cell layers. In the peripheral zone, auxin accumulates at sites of lateral organ primordia initiation and activates SHR expression via the auxin response factor MONOPTEROS (MP) and auxin response elements in the SHR promoter. In the central zone, the SHR-target SCL23 physically interacts with the key stem cell regulator WUSCHEL (WUS) to promote stem cell fate. Both SCL23 and WUS expression are subject to negative feedback regulation from stem cells through the CLAVATA signaling pathway. Together, our findings illustrate how SHR-dependent transcription factor complexes act in different domains of the shoot meristem to mediate cell division and auxin dependent organ initiation in the peripheral zone, and coordinate this activity with stem cell maintenance in the central zone of the SAM.
PMID: 37862096
Sci Total Environ , IF:7.963 , 2023 Nov , V899 : P165676 doi: 10.1016/j.scitotenv.2023.165676
Physiological and transcriptomic analyses reveal that phytohormone pathways and glutathione metabolism are involved in the arsenite toxicity response in tomatoes.
College of Horticulture, Shanxi Agricultural University, Taigu 030801, China.; Center of Experimental Education, Shanxi Agricultural University, Taigu 030801, China.; College of Horticulture, Shanxi Agricultural University, Taigu 030801, China. Electronic address: xujin@sxau.edu.cn.
The main forms of inorganic arsenic (As) in soil are arsenate [As(V)] and arsenite [As(III)]. Both forms inhibit plant growth. Here, we investigate the effects of As(III) toxicity on the growth of tomatoes by integrating physiological and transcriptomic analyses. As(III) toxicity induces oxidative damage, inhibits photosynthetic efficiency, and reduces soluble sugar levels. As(III) toxicity leads to reductions in auxin, cytokinin and jasmonic acid contents by 29 %, 39 % and 55 %, respectively, but leads to increases in the ethylene precursor 1-amino-cyclopropane carboxylic acid, abscisic acid and salicylic acid contents in roots, by 116 %, 79 % and 39 %, respectively, thereby altering phytohormone signalling pathways. The total glutathione, reduced glutathione (GSH) and oxidized glutathione (GSSG) contents are reduced by 59 %, 49 % and 94 % in roots; moreover, a high GSH/GSSG ratio is maintained through increased glutathione reductase activity (increased by 214 %) and decreased glutathione peroxidase activity (decreased by 40 %) in the roots of As(III)-treated tomato seedlings. In addition, As(III) toxicity affects the expression of genes related to the endoplasmic reticulum stress response. The altered expression of aquaporins and ABCC transporters changes the level of As(III) accumulation in plants. A set of hub genes involved in modulating As(III) toxicity responses in tomatoes was identified via a weighted gene coexpression network analysis. Taken together, these results elucidate the physiological and molecular regulatory mechanism underlying As(III) toxicity and provide a theoretical basis for selecting and breeding tomato varieties with low As(III) accumulation. Therefore, these findings are expected to be helpful in improving food safety and to developing sustainable agricultural.
PMID: 37481082
Sci Total Environ , IF:7.963 , 2023 Nov , V899 : P165667 doi: 10.1016/j.scitotenv.2023.165667
Zinc accumulation in Atriplex lentiformis is driven by plant genes and the soil microbiome.
Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA. Electronic address: pkushwaha@arizona.edu.; School of Biological Sciences, Department of Cell and Developmental Biology & Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA.; The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.; Department of Environmental Science, The University of Arizona, Tucson, AZ 85721, USA.
Successful phytoremediation of acidic metal-contaminated mine tailings requires amendments to condition tailings properties prior to plant establishment. This conditioning process is complex and includes multiple changes in tailings bio-physico-chemical properties. The objective of this project is to identify relationships between tailings properties, the soil microbiome, and plant stress response genes during growth of Atriplex lentiformis in compost-amended (10 %, 15 %, 20 % w/w) mine tailings. Analyses include RNA-Seq for plant root gene expression, 16S rRNA amplicon sequencing for bacterial/archaeal communities, metal concentrations in both tailings and plant organs, and phenotypic measures of plant stress. Zn accumulation in A. lentiformis leaves varied with compost levels and was the highest in the intermediate treatment (15 %, TC15). Microbial analysis identified Alicyclobacillus, Hydrotalea, and Pseudolabrys taxa with the highest relative abundance in TC15, and these taxa were strongly associated with Zn accumulation. Furthermore, we identified 190 root genes with significant gene expression changes. These root genes were associated with different pathways including, abscisic acid and auxin signaling, defense responses, ion channels, metal ion binding, oxidative stress, transcription regulation, and transmembrane transport. However, root gene expression changes were not driven by the increasing levels of compost. For example, there were 15 genes that were up-regulated in TC15, whereas 106 genes were down-regulated in TC15. The variables analyzed explained 86 % of the variance in Zn accumulation in A. lentiformis leaves. Importantly, Zn accumulation was driven by Zn shoot concentrations, leaf stress symptoms, plant root genes, and microbial taxa. Therefore, our results suggest there are strong plant-microbiome associations that drive Zn accumulation in A. lentiformis and different plant gene pathways are involved in alleviating varying levels of metal stress. Future work is needed to gain a mechanistic understanding of these plant-microbiome interactions to optimize phytoremediation strategies as they will govern the success or failure of the revegetation process.
PMID: 37478925
Sci Total Environ , IF:7.963 , 2023 Nov , V897 : P165338 doi: 10.1016/j.scitotenv.2023.165338
DNA methylation mediates overgrazing-induced clonal transgenerational plasticity.
School of Ecology and Environment, Inner Mongolia University, Hohhot, China.; School of Ecology and Environment, Inner Mongolia University, Hohhot, China; Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., Ltd., Hohhot 010016, China. Electronic address: rweibo2022@163.com.; Department of Biology, Edge Hill University, Ormskirk, Lancashire L39 4QP, UK.; Industrial Crop Institute, Shanxi Agricultural University, Taiyuan, China.
Overgrazing generally induces dwarfism in grassland plants, and these phenotypic traits could be transmitted to clonal offspring even when overgrazing is excluded. However, the dwarfism-transmitted mechanism remains largely unknown, despite generally thought to be enabled by epigenetic modification. To clarify the potential role of DNA methylation on clonal transgenerational effects, we conducted a greenhouse experiment with Leymus chinensis clonal offspring from different cattle/sheep overgrazing histories via the demethylating agent 5-azacytidine. The results showed that clonal offspring from overgrazed (by cattle or sheep) parents were dwarfed and the auxin content of leaves significantly decreased compared to offspring from no-grazed parents'. The 5-azaC application generally increased the auxin content and promoted the growth of overgrazed offspring while inhibited no-grazed offspring growth. Meanwhile, there were similar trends in the expression level of genes related to auxin-responsive target genes (ARF7, ARF19), and signal transduction gene (AZF2). These results suggest that DNA methylation leads to overgrazing-induced plant transgenerational dwarfism via inhibiting auxin signal pathway.
PMID: 37414175
Curr Opin Plant Biol , IF:7.834 , 2023 Oct , V76 : P102480 doi: 10.1016/j.pbi.2023.102480
Unlocking nature's (sub)cellular symphony: Phase separation in plant meristems.
Institute for Developmental Genetics, Heinrich-Heine University Duesseldorf, Germany.; Institute for Developmental Genetics, Heinrich-Heine University Duesseldorf, Germany; Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich-Heine University Duesseldorf, Germany. Electronic address: Yvonne.Stahl@hhu.de.
Plant development is based on the balance of stem cell maintenance and differentiation in the shoot and root meristems. The necessary cell fate decisions are regulated by intricate networks of proteins and biomolecules within plant cells and require robust and dynamic compartmentalization strategies, including liquid-liquid phase separation (LLPS), which allows the formation of membrane-less compartments. This review summarizes the current knowledge about the emerging field of LLPS in plant development, with a particular focus on the shoot and root meristems. LLPS regulates not only floral transition and flowering time while integrating environmental signals in the shoots but also influences auxin signalling and is putatively involved in maintaining the stem cell niche (SCN) in the roots. Therefore, LLPS has the potential to play a crucial role in the plasticity of plant development, necessitating further research for a comprehensive understanding.
PMID: 37862837
Curr Opin Plant Biol , IF:7.834 , 2023 Oct , V76 : P102479 doi: 10.1016/j.pbi.2023.102479
Tunable recurrent priming of lateral roots in Arabidopsis: More than just a clock?
Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany.; Center for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany. Electronic address: alexis.maizel@cos.uni-heidelberg.de.
Lateral root (LR) formation in Arabidopsis is a continuous, repetitive, post-embryonic process regulated by a series of coordinated events and tuned by the environment. It shapes the root system, enabling plants to efficiently explore soil resources and adapt to changing environmental conditions. Although the auxin-regulated modules responsible for LR morphogenesis and emergence are well documented, less is known about the initial priming. Priming is characterised by recurring peaks of auxin signalling, which, once memorised, earmark cells to form the new LR. We review the recent experimental and modelling approaches to understand the molecular processes underlying the recurring LR formation. We argue that the intermittent priming of LR results from interweaving the pattern of auxin flow and root growth together with an oscillatory auxin-modulated transcriptional mechanism and illustrate its long-range sugar-mediated tuning by light.
PMID: 37857036
Curr Opin Plant Biol , IF:7.834 , 2023 Oct , V76 : P102473 doi: 10.1016/j.pbi.2023.102473
Developing for nutrient uptake: Induced organogenesis in parasitic plants and root nodule symbiosis.
Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.; Nara Institute of Science and Technology, Graduate School of Science and Technology, Ikoma, Nara, Japan.; Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan; Tsukuba Plant-Innovation Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan. Electronic address: suzaki.takuya.fn@u.tsukuba.ac.jp.; Nara Institute of Science and Technology, Graduate School of Science and Technology, Ikoma, Nara, Japan. Electronic address: satokoy@bs.naist.jp.
Plants have evolved diverse strategies to meet their nutritional needs. Parasitic plants employ haustoria, specialized structures that facilitate invasion of host plants and nutrient acquisition. Legumes have adapted to nitrogen-limited conditions by developing nodules that accommodate nitrogen-fixing rhizobia. The formation of both haustoria and nodules is induced by signals originating from the interacting organisms, namely host plants and rhizobial bacteria, respectively. Emerging studies showed that both organogenesis crucially involves plant hormones such as auxin, cytokinins, and ethylene and also integrate nutrient availability, particularly nitrogen. In this review, we discuss recent advances on hormonal and environmental control of haustoria and nodules development with side-by-side comparison. These underscore the remarkable plasticity of plant organogenesis.
PMID: 37826989
Curr Opin Plant Biol , IF:7.834 , 2023 Oct , V75 : P102443 doi: 10.1016/j.pbi.2023.102443
Rapid auxin signaling: Unknowns old and new.
Institute of Science and Technology Austria (ISTA), 3400, Klosterneuburg, Austria.; Institute of Science and Technology Austria (ISTA), 3400, Klosterneuburg, Austria. Electronic address: jiri.friml@ist.ac.at.
To respond to auxin, the chief orchestrator of their multicellularity, plants evolved multiple receptor systems and signal transduction cascades. Despite decades of research, however, we are still lacking a satisfactory synthesis of various auxin signaling mechanisms. The chief discrepancy and historical controversy of the field is that of rapid and slow auxin effects on plant physiology and development. How is it possible that ions begin to trickle across the plasma membrane as soon as auxin enters the cell, even though the best-characterized transcriptional auxin pathway can take effect only after tens of minutes? Recently, unexpected progress has been made in understanding this and other unknowns of auxin signaling. We provide a perspective on these exciting developments and concepts whose general applicability might have ramifications beyond auxin signaling.
PMID: 37666097
Curr Opin Plant Biol , IF:7.834 , 2023 Oct , V75 : P102405 doi: 10.1016/j.pbi.2023.102405
Turning up the volume: How root branching adaptive responses aid water foraging.
Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK. Electronic address: p.mehra@nottingham.ac.uk.; Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK.; Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, LE12 5RD, UK. Electronic address: malcolm.bennett@nottingham.ac.uk.
Access to water is critical for all forms of life. Plants primarily access water through their roots. Root traits such as branching are highly sensitive to water availability, enabling plants to adapt their root architecture to match soil moisture distribution. Lateral root adaptive responses hydropatterning and xerobranching ensure new branches only form when roots are in direct contact with moist soil. Root traits are also strongly influenced by atmospheric humidity, where a rapid drop leads to a promotion of root growth and branching. The plant hormones auxin and/or abscisic acid (ABA) play key roles in regulating these adaptive responses. We discuss how these signals are part of a novel "water-sensing" mechanism that couples hormone movement with hydrodynamics to orchestrate root branching responses.
PMID: 37379661
Curr Opin Plant Biol , IF:7.834 , 2023 Oct , V75 : P102386 doi: 10.1016/j.pbi.2023.102386
Understanding signaling pathways governing the polar development of root hairs in low-temperature, nutrient-deficient environments.
Fundacion Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile.; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile; Centro de Biotecnologia Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile.; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile; Centro de Biotecnologia Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile.; Fundacion Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile; Centro de Biotecnologia Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile. Electronic address: jestevez@leloir.org.ar.
Plants exposed to freezing and above-freezing low temperatures must employ a variety of strategies to minimize fitness loss. There is a considerable knowledge gap regarding how mild low temperatures (around 10 degrees C) affect plant growth and developmental processes, even though the majority of the molecular mechanisms that plants use to adapt to extremely low temperatures are well understood. Root hairs (RH) have become a useful model system for studying how plants regulate their growth in response to both cell-intrinsic cues and environmental inputs. Here, we'll focus on recent advances in the molecular mechanisms underpinning Arabidopsis thaliana RH growth at mild low temperatures and how these discoveries may influence our understanding of nutrient sensing mechanisms by the roots. This highlights how intricately linked mechanisms are necessary for plant development to take place under specific circumstances and to produce a coherent response, even at the level of a single RH cell.
PMID: 37352652
Plant Cell Environ , IF:7.228 , 2023 Oct doi: 10.1111/pce.14746
Natural variation in a K(+) -preferring HKT transporter contributes to wheat shoot K(+) accumulation and salt tolerance.
State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China.; Key Laboratory of Plant Nutrition and Agri-Environment in Northwest China, Ministry of Agriculture and Rural Affairs, College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi, China.; Yangling Seed Industry Innovation Center, Yangling, Shaanxi, China.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China.
Soil salinity can adversely affect crop growth and yield, and an improved understanding of the genetic factors that confer salt tolerance could inform breeding strategies to engineer salt-tolerant crops and improve productivity. Here, a group of K(+) -preferring HKT transporters, TaHKT8, TaHKT9 and TaHKT10, were identified and negatively regulate the wheat shoot K(+) accumulation and salt tolerance. A genome-wide association study (GWAS) and candidate gene association analysis further revealed that TaHKT9-B substantially underlies the natural variation of wheat shoot K(+) accumulation under saline soil conditions. Specifically, an auxin responsive element (ARE) within an 8-bp insertion in the promoter of TaHKT9-B is strongly associated with shoot K(+) content among wheat accessions. This ARE can be directly bound by TaARF4 for transcriptional activation of TaHKT9-B, which subsequently attenuates shoot K(+) accumulation and salt tolerance. Moreover, the tae-miR390/TaTAS3/TaARF4 pathway was identified to regulate the salt-induced root development and salt tolerance in wheat. Taken together, our study describes the genetic basis and accompanying mechanism driving phenotypic variation in wheat shoot K(+) accumulation and salt tolerance. The identified tae-miR390/TaTAS3/TaARF4/TaHKT9-B module is an important regulator in wheat subjected to salt stress, which provides the potentially important genetic resources for breeders to improve wheat salt tolerance.
PMID: 37876337
Plant Cell Environ , IF:7.228 , 2023 Nov , V46 (11) : P3194-3205 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
Plant Cell Environ , IF:7.228 , 2023 Nov , V46 (11) : P3575-3591 doi: 10.1111/pce.14670
The fungal metabolite 4-hydroxyphenylacetic acid from Neofusicoccum parvum modulates defence responses in grapevine.
Department of Molecular Cell Biology, Joseph Gottlieb Kolreuter Institute of Plant Science, Karlsruhe Institute of Technology, Karlsruhe, Germany.; INRAE, SVQV UMR-A 1131, Universite de Strasbourg, Colmar, France.; Institut fur Biotechnologie und Wirkstoff-Forschung gGmbH, Mainz, Germany.; Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Karlsruhe, Germany.; Department of Horticulture, Faculty of Agriculture, Damanhour University, Damanhour, Egypt.
In a consequence of global warming, grapevine trunk diseases (GTDs) have become a pertinent problem to viticulture, because endophytic fungi can turn necrotrophic upon host stress killing the plant. In Neofusicoccum parvum Bt-67, plant-derived ferulic acid makes the fungus release Fusicoccin aglycone triggering plant cell death. Now, we show that the absence of ferulic acid lets the fungus secrete 4-hydroxyphenylacetic acid (4-HPA), mimicking the effect of auxins on grapevine defence and facilitating fungal spread. Using Vitis suspension cells, we dissected the mode of action of 4-HPA during defence triggered by the bacterial cell-death elicitor, harpin. Early responses (cytoskeletal remodelling and calcium influx) are inhibited, as well as the expression of Stilbene Synthase 27 and phytoalexin accumulation. In contrast to other auxins, 4-HPA quells transcripts for the auxin conjugating GRETCHEN HAGEN 3. We suggest that 4-HPA is a key component of the endophytic phase of N. parvum Bt-67 preventing host cell death. Therefore, our study paves the way to understand how GTDs regulate their latent phase for successful colonisation, before turning necrotrophic and killing the vines.
PMID: 37431974
Plant Cell Environ , IF:7.228 , 2023 Oct , V46 (10) : P3158-3169 doi: 10.1111/pce.14645
Genetic control underlying the flowering-drought tolerance trade-off in the Antarctic plant Colobanthus quitensis.
Centro de Ecologia Integrativa, Instituto de Ciencias Biologicas, Universidad de Talca, Talca, Chile.; Instituto de Investigaciones Interdisciplinarias (I3), Universidad de Talca, Talca, Chile.; Departamento de Ciencias Naturales, Laboratorio de Genomica y Biodiversidad (LGB), Universidad del Bio-Bio, Chillan, Chile.; IFEVA (CONICET-Facultad de Agronomia, Universidad de Buenos Aires), Buenos Aires, Argentina.; Centro de Investigacion en Estudios Avanzados del Maule (CIEAM), Universidad Catolica del Maule, Talca, Chile.
Plants inhabiting environments with stressful conditions often exhibit a low number of flowers, which can be attributed to the energetic cost associated with reproduction. One of the most stressful environments for plants is the Antarctic continent, characterized by limited soil water availability and low temperatures. Induction of dehydrins like those from the COR gene family and auxin transcriptional response repressor genes (IAAs), which are involved in floral repression, has been described in response to water stress. Here, we investigated the relationship between the water deficit-induced stress response and the number of flowers in Colobanthus quitensis plants collected from populations along a latitudinal gradient. The expression levels of COR47 and IAA12 genes in response to water deficit were found to be associated with the number of flowers. The relationship was observed both in the field and growth chambers. Watering the plants in the growth chambers alleviated the stress and stimualted flowering, thereby eliminating the trade-off observed in the field. Our study provides a mechanistic understanding of the ecological constraints on plant reproduction along a water availability gradient. However, further experiments are needed to elucidate the primary role of water availability in regulating resource allocation to reproduction in plants inhibiting extreme environments.
PMID: 37309267
Chemosphere , IF:7.086 , 2023 Nov , 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 Exp Bot , IF:6.992 , 2023 Oct doi: 10.1093/jxb/erad419
New molecular components that regulates the transcriptional hub in root hairs: coupling environmental signals to endogenous hormones to coordinate growth.
Fundacion Instituto Leloir and IIBBA-CONICET. Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina.; ANID - Millennium Science Initiative Program - Millennium Nucleus for the DeveIopment of Super Adaptable Plants (MN-SAP), Santiago 8370146, Chile.; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.; ANID - Millennium Science Initiative Program - Millennium Institute for Integrative Biology (iBio), Santiago 8331150, Chile.; Centro de Biotecnologia Vegetal (CBV), Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8370146, Chile.
Root hairs (RH) have become an important model system for studying plant growth and how plants modulate their growth in response to cell-intrinsic and environmental stimuli. Here, we will discuss recent advances in our understanding of the molecular mechanisms underlying the growth of Arabidopsis thaliana RH in the interface between responses to environmental cues (e.g. nutrients such as nitrates, phosphate and microorganism) and hormonal stimuli (e.g. auxin). RH growth is under the control of several transcription factors that are also under strong regulation at different levels. In this review we highlight recent new discoveries along these transcriptional pathways that may increase our capacity to enhance nutrient uptake by the roots in the context of abiotic stresses. We used text-mining capacities of the PlantConnectome database to generate the most updated view of RH growth in these complex biological contexts.
PMID: 37875460
J Exp Bot , IF:6.992 , 2023 Oct doi: 10.1093/jxb/erad394
How do brassinosteroids fit in bud outgrowth models?
Waite Research Institute, School of Agriculture Food & Wine, The University of Adelaide, Adelaide, SA 5064, Australia.; Australian Research Council Training Centre for Future Crops Development, The University of Adelaide, Adelaide, SA 5064, Australia.; Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD 4072, Australia.
PMID: 37846132
J Exp Bot , IF:6.992 , 2023 Oct doi: 10.1093/jxb/erad402
TCP13 promotes shade avoidance syndrome-like responses by directly targeting a subset of shade-responsive gene promoters.
Department of Biological Science, Sookmyung Women's University, Seoul 04310, Korea.; Department of Biological Sciences, KAIST, Daejeon 34141, Korea.; Department of Plant & Environmental New Resources, Kyung Hee University, Yongin 17104, Korea.; Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan.
TCP13 belongs to a TCP subgroup implicated in the shade avoidance syndrome (SAS), but its exact role remains unclear. Here, we show TCP13 promotes the SAS-like response by enhancing hypocotyl elongation and suppressing flavonoid biosynthesis as a part of the incoherent feed-forward loop in light signaling. Shade is known to promote the SAS by activating PIF-auxin signaling in plants, but we found no evidence in a transcriptome analysis that TCP13 activates PIF-auxin signaling. Instead, we found TCP13 mimics shade by activating the expression of a subset of shade-inducible and cell elongation-promoting SAUR genes including SAUR19, via direct targeting of their promoters. We also found TCP13 and PIF4, a molecular proxy for shade, repress the expression of flavonoid biosynthetic genes by directly targeting both shared and distinct sets of biosynthetic gene promoters. Together, our results indicate TCP13 promotes the SAS-like response by directly targeting a subset of shade-responsive genes without activating the PIF-auxin signaling pathway.
PMID: 37824096
J Exp Bot , IF:6.992 , 2023 Oct doi: 10.1093/jxb/erad391
Flavonols have opposite effects on the interrelated glucosinolate and camalexin biosynthetic pathways in Arabidopsis thaliana.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi-110067, India.; Bielefeld University, Faculty of Biology, Genetics and Genomics of Plants, 33615 Bielefeld, Germany.; Plant Science and Agrotechnology Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.
Flavonols are structurally and functionally diverse biomolecules involved in plant biotic and abiotic stress tolerance, pollen development, and inhibition of auxin transport. Despite the ubiquitous nature and multifunctionality of flavonols in land plants, their effects on global gene expression and signaling pathways are unclear. To explore the roles of flavonol metabolites in signaling, we performed comparative transcriptome and targeted metabolite profiling of seedlings from the flavonol-deficient Arabidopsis (Arabidopsis thaliana) loss-of-function mutant flavonol synthase1 (fls1) with and without exogenous supplementation of flavonol derivatives (kaempferol, quercetin, and rutin). Our RNA-seq results indicated that flavanols modulate various biological and metabolic pathways, with significant alteration in camalexin and aliphatic glucosinolate synthesis. Flavonols negatively regulated camalexin biosynthesis but appeared to promote the accumulation of aliphatic glucosinolates via transcription factor-mediated upregulation of biosynthesis genes. Interestingly, upstream amino acid biosynthesis genes involved in methionine and tryptophan synthesis were altered under flavonol deficiency and exogenous supplementation. Quercetin treatment significantly upregulated aliphatic glucosinolate biosynthesis genes compared to kaempferol and rutin. In addition, expression and metabolite analysis of the transparent testa7 mutant, which lacks hydroxylated flavonol derivatives, clarified the role of quercetin in the glucosinolate biosynthesis pathway. This study elucidates the molecular mechanisms by which flavonols interfere with signaling pathways, their molecular targets, and the multiple biological activities of flavonols in plants.
PMID: 37813680
J Exp Bot , IF:6.992 , 2023 Oct , V74 (19) : P6089-6103 doi: 10.1093/jxb/erad244
Spatial regulation of plant hormone action.
Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV), 46022-Valencia, Spain.
Although many plant cell types are capable of producing hormones, and plant hormones can in most cases act in the same cells in which they are produced, they also act as signaling molecules that coordinate physiological responses between different parts of the plant, indicating that their action is subject to spatial regulation. Numerous publications have reported that all levels of plant hormonal pathways, namely metabolism, transport, and perception/signal transduction, can help determine the spatial ranges of hormone action. For example, polar auxin transport or localized auxin biosynthesis contribute to creating a differential hormone accumulation across tissues that is instrumental for specific growth and developmental responses. On the other hand, tissue specificity of cytokinin actions has been proposed to be regulated by mechanisms operating at the signaling stages. Here, we review and discuss current knowledge about the contribution of the three levels mentioned above in providing spatial specificity to plant hormone action. We also explore how new technological developments, such as plant hormone sensors based on FRET (fluorescence resonance energy transfer) or single-cell RNA-seq, can provide an unprecedented level of resolution in defining the spatial domains of plant hormone action and its dynamics.
PMID: 37401809
J Exp Bot , IF:6.992 , 2023 Oct , V74 (19) : P6104-6118 doi: 10.1093/jxb/erac508
Fine-tuned nitric oxide and hormone interface in plant root development and regeneration.
Departamento de Botanica y Fisiologia Vegetal, Instituto de Investigacion en Agrobiotecnologia (CIALE), Facultad de Biologia, Universidad de Salamanca, C/ Rio Duero 12, 37185 Salamanca, Spain.; Universidad Politecnica de Madrid, Madrid, Spain.
Plant root growth and developmental capacities reside in a few stem cells of the root apical meristem (RAM). Maintenance of these stem cells requires regenerative divisions of the initial stem cell niche (SCN) cells, self-maintenance, and proliferative divisions of the daughter cells. This ensures sufficient cell diversity to guarantee the development of complex root tissues in the plant. Damage in the root during growth involves the formation of a new post-embryonic root, a process known as regeneration. Post-embryonic root development and organogenesis processes include primary root development and SCN maintenance, plant regeneration, and the development of adventitious and lateral roots. These developmental processes require a fine-tuned balance between cell proliferation and maintenance. An important regulator during root development and regeneration is the gasotransmitter nitric oxide (NO). In this review we have sought to compile how NO regulates cell rate proliferation, cell differentiation, and quiescence of SCNs, usually through interaction with phytohormones, or other molecular mechanisms involved in cellular redox homeostasis. NO exerts a role on molecular components of the auxin and cytokinin signaling pathways in primary roots that affects cell proliferation and maintenance of the RAM. During root regeneration, a peak of auxin and cytokinin triggers specific molecular programs. Moreover, NO participates in adventitious root formation through its interaction with players of the brassinosteroid and cytokinin signaling cascade. Lately, NO has been implicated in root regeneration under hypoxia conditions by regulating stem cell specification through phytoglobins.
PMID: 36548145
Development , IF:6.868 , 2023 Oct doi: 10.1242/dev.202106
Abscisic acid biosynthesis is necessary for full auxin effects on hypocotyl elongation.
Department of Biology, Washington University, St. Louis, MO 63130, USA.; Center for Biomolecular Condensates, Washington University, St. Louis, MO 63130, USA.; Center for Engineering Mechanobiology, Washington University, St. Louis, MO 63130, USA.; Department of Biology, Duke University, Durham, NC 27708, USA.; Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia.; Department of Cell & Systems Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
In concert with other phytohormones, auxin regulates plant growth and development. However, how auxin and other phytohormones coordinately regulate distinct processes is not fully understood. In this work, we uncover an auxin - abscisic acid (ABA) interaction module that is specific to coordinating activities of these hormones in the hypocotyl. From our forward genetics screen, we determine that ABA biosynthesis is required for the full effects of auxin on hypocotyl elongation. Our data also suggest that ABA biosynthesis is not required for the inhibitory effects of auxin treatment on root elongation. Our transcriptome analysis identified distinct auxin-responsive genes in root and shoot tissues, consistent with differential regulation of the growth in these tissues. Further, our data suggests that many gene targets repressed upon auxin treatment require an intact ABA pathway for full repression. Our results support a model in which auxin stimulates ABA biosynthesis to fully regulate hypocotyl elongation.
PMID: 37846593
Development , IF:6.868 , 2023 Oct , V150 (19) doi: 10.1242/dev.201775
N6-adenosine methylation of mRNA integrates multilevel auxin response and ground tissue development in Arabidopsis.
Laboratory of Hormonal Regulations in Plants, Institute of Experimental Botany, The Czech Academy of Sciences, Rozvojova 263, CZ-160 00 Prague, Czech Republic.; Department of Functional Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 25, Brno CZ-62500, Czech Republic.; Faculty of Science, Charles University, Vinicna 1594/7, CZ-128 00 Prague, Czech Republic.; Laboratory of Growth Regulators, Faculty of Science, Palacky University and Institute of Experimental Botany, The Czech Academy of Sciences, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic.; Department of Genetics, Development and Cell Biology, Iowa State University of Science and Technology, 3011 Advanced Teaching & Research Building, Ames, IA 50011-3220, USA.; Wood Development Group, Institute of Biotechnology, Faculty of Biological and Environmental Sciences, University of Helsinki, 00014 Helsinki, Finland.
N6-methyl adenosine (m6A) is a widespread internal mRNA modification impacting the expression of numerous genes. Here, we characterize auxin-related defects among the pleiotropic phenotypes of hypomorphic Arabidopsis thaliana mutants with impaired m6A status and reveal that they show strong resistance to exogenously applied auxin. By combining major published m6A datasets, we propose that among high-confidence target transcripts emerge those encoding the main components required for auxin signaling, including the TIR1/AFB auxin receptors and ARF transcriptional regulators. We also observe subtle changes in endogenous levels of indole-3-acetic acid metabolites in these hypomorphic lines, which correlate with the methylation status of indole-3-acetic acid amidohydrolase transcripts. In addition, we reveal that reduced m6A levels lead to defects in endodermal patterning in the primary root arising from impaired timing of periclinal cell divisions. These defects can be reverted by inhibition of auxin signaling. Together, our data underline that m6A likely affects auxin-dependent processes at multiple levels.
PMID: 37724502
Development , IF:6.868 , 2023 Nov , V150 (21) 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. Although 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 before 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 Oct doi: 10.1111/tpj.16493
Root Walker: an automated pipeline for large scale quantification of early root growth responses at high spatial and temporal resolution.
Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, California, 92037, USA.
Plants are sessile organisms that constantly adapt to their changing environment. The root is exposed to numerous environmental signals ranging from nutrients and water to microbial molecular patterns. These signals can trigger distinct responses including the rapid increase or decrease of root growth. Consequently, using root growth as a readout for signal perception can help decipher which external cues are perceived by roots, and how these signals are integrated. To date, studies measuring root growth responses using large numbers of roots have been limited by a lack of high-throughput image acquisition, poor scalability of analytical methods, or low spatiotemporal resolution. Here, we developed the Root Walker pipeline, which uses automated microscopes to acquire time-series images of many roots exposed to controlled treatments with high spatiotemporal resolution, in conjunction with fast and automated image analysis software. We demonstrate the power of Root Walker by quantifying root growth rate responses at different time and throughput scales upon treatment with natural auxin and two mitogen-associated protein kinase cascade inhibitors. We find a concentration-dependent root growth response to auxin and reveal the specificity of one MAPK inhibitor. We further demonstrate the ability of Root Walker to conduct genetic screens by performing a genome-wide association study on 260 accessions in under 2 weeks, revealing known and unknown root growth regulators. Root Walker promises to be a useful toolkit for the plant science community, allowing large-scale screening of root growth dynamics for a variety of purposes, including genetic screens for root sensing and root growth response mechanisms.
PMID: 37871136
Plant J , IF:6.417 , 2023 Oct , V116 (2) : P604-628 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 Nov , V116 (3) : P804-822 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 Nov , V116 (3) : P756-772 doi: 10.1111/tpj.16403
AXR1 modulates trichome morphogenesis through mediating ROP2 stability in Arabidopsis.
State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, USA.
Cell differentiation and morphogenesis are crucial for the establishment of diverse cell types and organs in multicellular organisms. Trichome cells offer an excellent paradigm for dissecting the regulatory mechanisms of plant cell differentiation and morphogenesis due to their unique growth characteristics. Here, we report the isolation of an Arabidopsis mutant, aberrantly branched trichome 3-1 (abt3-1), with a reduced trichome branching phenotype. Positional cloning and molecular complementation experiments confirmed that abt3-1 is a new mutant allele of Auxin resistant 1 (AXR1), which encodes the N-terminal half of ubiquitin-activating enzyme E1 and functions in auxin signaling pathway. Meanwhile, we found that transgenic plants expressing constitutively active version of ROP2 (CA-ROP2) caused a reduction of trichome branches, resembling that of abt3-1. ROP2 is a member of Rho GTPase of plants (ROP) family, serving as versatile signaling switches involved in a range of cellular and developmental processes. Our genetic and biochemical analyses showed AXR1 genetically interacted with ROP2 and mediated ROP2 protein stability. The loss of AXR1 aggravated the trichome defects of CA-ROP2 and induced the accumulation of steady-state ROP2. Consistently, elevated AXR1 expression levels suppressed ROP2 expression and partially rescued trichome branching defects in CA-ROP2 plants. Together, our results presented a new mutant allele of AXR1, uncovered the effects of AXR1 and ROP2 during trichome development, and revealed a pathway of ROP2-mediated regulation of plant cell morphogenesis in Arabidopsis.
PMID: 37516999
Open Biol , IF:6.411 , 2023 Oct , V13 (10) : P230111 doi: 10.1098/rsob.230111
Genome-wide identification of ATP-binding cassette transporter B subfamily, focusing on its structure, evolution and rearrangement in ciliates.
Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, Shandong 266003, People's Republic of China.; Key Laboratory of Evolution & Marine Biodiversity (OUC), Ministry of Education, Qingdao 266003, People's Republic of China.; College of Life Sciences, Capital Normal University, Beijing 100048, People's Republic of China.; School of Life Sciences, Ludong University, Yantai, Shandong 264025, People's Republic of China.; Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.; Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, People's Republic of China.
ATP-binding cassette subfamily B (ABCB) has been implicated in various essential functions such as multidrug resistance, auxin transport and heavy metal tolerance in animals and plants. However, the functions, the genomic distribution and the evolutionary history have not been characterized systematically in lower eukaryotes. As a lineage of highly specialized unicellular eukaryotes, ciliates have extremely diverse genomic features including nuclear dimorphism. To further understand the genomic structure and evolutionary history of this gene family, we investigated the ABCB gene subfamily in 11 ciliates. The results demonstrate that there is evidence of substantial gene duplication, which has occurred by different mechanisms in different species. These gene duplicates show consistent purifying selection, suggesting functional constraint, in all but one species, where positive selection may be acting to generate novel function. We also compare the gene structures in the micronuclear and macronuclear genomes and find no gene scrambling during genome rearrangement, despite the abundance of such scrambling in two of our focal species. These results lay the foundation for future analyses of the function of these genes and the mechanisms responsible for their evolution across diverse eukaryotic lineages.
PMID: 37788709
Ecotoxicol Environ Saf , IF:6.291 , 2023 Oct , V264 : P115458 doi: 10.1016/j.ecoenv.2023.115458
An arbuscular mycorrhizal fungus differentially regulates root traits and cadmium uptake in two maize varieties.
College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, Yunnan, China.; College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, Yunnan, China. Electronic address: zfd97@ynau.edu.cn.
Arbuscular mycorrhizal fungi (AMF) are symbiotic fungi that colonize plant roots, and they are more common in Cd-polluted habitats. However, there is limited understanding of the response of root traits and cadmium (Cd) uptake to AMF in different crop varieties. Two maize varieties, Panyu 3 and Ludan 8, with high and low Cd uptake capacities, respectively, were cultivated as host plants in a pot experiment with Cd-polluted soil (17.1 mg/kg Cd). The effects of AMF on the growth, mineral nutrient concentration, root traits, phytohormone concentrations and Cd uptake of the two maize varieties and their comprehensive response to AMF fungal inoculation were investigated. AMF improved growth, mineral nutrient levels and root morphology and increased lignin and phytohormone concentrations in roots and Cd uptake in the two maize varieties. However, the two maize varieties, Panyu 3 and Ludan 8, had different responses to AMF, and their comprehensive response indices were 753.6% and 389.4%, respectively. The root biomass, branch number, abscisic acid concentrations, lignin concentrations and Cd uptake of maize Panyu 3 increased by 151.1%, 28.6%, 139.7%, 99.5% and 84.7%, respectively. The root biomass, average diameter, auxin concentration, lignin concentration and Cd uptake of maize Ludan 8 increased by 168.7%, 31.8%, 31.4%, 41.7% and 136.7%, respectively. Moreover, Cd uptake in roots presented very significant positive correlations with the average root diameter and abscisic acid concentration. A structural equation model indicated that the root abscisic acid concentration and root surface area had positive effects on Cd uptake by the Panyu 3 maize roots; the root abscisic acid concentration and root tip number had positive effects on Cd uptake by the Ludan 8 maize roots. Thus, AMF differentially regulated Cd uptake in the two maize varieties, and the regulatory effect was closely related to root traits and phytohormone concentrations.
PMID: 37690173
Mol Ecol , IF:6.185 , 2023 Oct , V32 (20) : P5575-5589 doi: 10.1111/mec.17134
Uncovering the genetic architecture of parallel evolution.
School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia.; Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, Australia.
Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.
PMID: 37740681
Int J Mol Sci , IF:5.923 , 2023 Oct , V24 (20) doi: 10.3390/ijms242015357
Identification and Evolutionary Analysis of the Auxin Response Factor (ARF) Family Based on Transcriptome Data from Caucasian Clover and Analysis of Expression Responses to Hormones.
College of Animal Science and Technology, Northeast Agricultural University, Harbin 150030, China.
Caucasian clover (Trifolium ambiguum M. Bieb.) is an excellent perennial plant in the legume family Fabaceae, with a well-developed rhizome and strong clonal growth. Auxin is one of the most important phytohormones in plants and plays an important role in plant growth and development. Auxin response factor (ARF) can regulate the expression of auxin-responsive genes, thus participating in multiple pathways of auxin transduction signaling in a synergistic manner. No genomic database has been established for Caucasian clover. In this study, 71 TaARF genes were identified through a transcriptomic database of Caucasian clover rhizome development. Phylogenetic analysis grouped the TaARFs into six (1-6) clades. Thirty TaARFs contained a complete ARF structure, including three relatively conserved regions. Physical and chemical property analysis revealed that TaARFs are unstable and hydrophilic proteins. We also analyzed the expression pattern of TaARFs in different tissues (taproot, horizontal rhizome, swelling of taproot, rhizome bud and rhizome bud tip). Quantitative real-time RT-PCR revealed that all TaARFs were responsive to phytohormones (indole-3-acetic acid, gibberellic acid, abscisic acid and methyl jasmonate) in roots, stems and leaves. These results helped elucidate the role of ARFs in responses to different hormone treatments in Caucasian clover.
PMID: 37895037
Int J Mol Sci , IF:5.923 , 2023 Oct , V24 (20) doi: 10.3390/ijms242015148
Immunolocalization of Jasmonates and Auxins in Pea Roots in Connection with Inhibition of Root Growth under Salinity Conditions.
Ufa Institute of Biology, Ufa Federal Research Centre, Russian Academy of Sciences, Prospekt Oktyabrya 69, 450054 Ufa, Russia.
Inhibition of root elongation is an important growth response to salinity, which is thought to be regulated by the accumulation of jasmonates and auxins in roots. Nevertheless, the mechanisms of the interaction of these hormones in the regulation of the growth response to salinity are still not clear enough. Their better understanding depends on the study of the distribution of jasmonates and auxins between root cells. This was achieved with the help of immunolocalization of auxin (indoleacetic acid) and jasmonates on the root sections of pea plants. Salinity inhibited root elongation and decreased the size of the meristem zone and the length of cells in the elongation zone. Immunofluorescence based on the use of appropriate, specific antibodies that recognize auxins and jasmonates revealed an increased abundance of both hormones in the meristem zone. The obtained data suggests the participation of either auxins or jasmonates in the inhibition of cell division, which leads to a decrease in the size of the meristem zone. The level of only auxin and not jasmonate increased in the elongation zone. However, since some literature evidence argues against inhibition of root cell division by auxins, while jasmonates have been shown to inhibit this process, we came to the conclusion that elevated jasmonate is a more likely candidate for inhibiting root meristem activity under salinity conditions. Data suggests that auxins, not jasmonates, reduce cell size in the elongation zone of salt-stressed plants, a suggestion supported by the known ability of auxins to inhibit root cell elongation.
PMID: 37894828
Int J Mol Sci , IF:5.923 , 2023 Oct , V24 (20) doi: 10.3390/ijms242015122
Comprehensive Analysis of GH3 Gene Family in Potato and Functional Characterization of StGH3.3 under Drought Stress.
State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China.; College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China.
As an important hormone response gene, Gretchen Hagen 3 (GH3) maintains hormonal homeostasis by conjugating excess auxin with amino acids during plant stress-related signaling pathways. GH3 genes have been characterized in many plant species, but they are rarely reported in potato. Here, 19 StGH3 genes were isolated and characterized. Phylogenetic analysis indicated that StGH3s were divided into two categories (group I and group III). Analyses of gene structure and motif composition showed that the members of a specific StGH3 subfamily are relatively conserved. Collinearity analysis of StGH3 genes in potato and other plants laid a foundation for further exploring the evolutionary characteristics of the StGH3 genes. Promoter analysis showed that most StGH3 promoters contained hormone and abiotic stress response elements. Multiple transcriptome studies indicated that some StGH3 genes were responsive to ABA, water deficits, and salt treatments. Moreover, qRT-PCR analysis indicated that StGH3 genes could be induced by phytohormones (ABA, SA, and MeJA) and abiotic stresses (water deficit, high salt, and low temperature), although with different patterns. Furthermore, transgenic tobacco with transient overexpression of the StGH3.3 gene showed positive regulation in response to water deficits by increasing proline accumulation and reducing the leaf water loss rate. These results suggested that StGH3 genes may be involved in the response to abiotic stress through hormonal signal pathways. Overall, this study provides useful insights into the evolution and function of StGH3s and lays a foundation for further study on the molecular mechanisms of StGH3s in the regulation of potato drought resistance.
PMID: 37894803
Int J Mol Sci , IF:5.923 , 2023 Oct , V24 (20) doi: 10.3390/ijms242015034
Integrated Metabolome and Transcriptome Analysis of Petal Anthocyanin Accumulation Mechanism in Gloriosa superba 'Rothschildiana' during Different Flower Development Stages.
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China.; Guangdong Key Lab of Ornamental Plant Germplasm Innovation and Utilization, Environmental Horticulture Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
Flower color is a key ornamental trait in plants. The petals of Gloriosa superba 'Rothschildiana' petals undergo a color transformation from yellow to red during their development, but the molecular mechanism of this process remains unexplored. This study examines the anthocyanin profiles and gene expression patterns of 'Rothschildiana' petals across four developmental stages: bud (S1), initial opening (S2), half opening (S3), and full opening stage (S4). A total of 59 anthocyanins were identified with significant increases in cyanidin-3,5-O-diglucoside, cyanidin-3-O-glucoside, pelargonidin-3-O-glucoside, and pelargonidin-3,5-O-diglucoside levels observed during petal maturation. Transcriptome analysis revealed 46 differentially expressed genes implicated in flavonoid and anthocyanin biosynthesis. Additionally, three gene modules were found to be associated with anthocyanin accumulation throughout flower development. Expression levels of genes associated with auxin, abscisic acid, brassinosteroid signaling, and transcription factors such as NACs and WRKYs underwent significant changes and exhibited strong correlations with several flavonoid and anthocyanin biosynthetic genes in these modules. These findings offer novel insights into the molecular underpinnings of flower color variation and lay the groundwork for the improvement of G. superba.
PMID: 37894715
Int J Mol Sci , IF:5.923 , 2023 Oct , V24 (19) doi: 10.3390/ijms241914889
Stem Cells: Engines of Plant Growth and Development.
Plant Gene Expression Center, United States Department of Agriculture-Agricultural Research Service, Albany, CA 94710, USA.; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
The development of both animals and plants relies on populations of pluripotent stem cells that provide the cellular raw materials for organ and tissue formation. Plant stem cell reservoirs are housed at the shoot and root tips in structures called meristems, with the shoot apical meristem (SAM) continuously producing aerial leaf, stem, and flower organs throughout the life cycle. Thus, the SAM acts as the engine of plant development and has unique structural and molecular features that allow it to balance self-renewal with differentiation and act as a constant source of new cells for organogenesis while simultaneously maintaining a stem cell reservoir for future organ formation. Studies have identified key roles for intercellular regulatory networks that establish and maintain meristem activity, including the KNOX transcription factor pathway and the CLV-WUS stem cell feedback loop. In addition, the plant hormones cytokinin and auxin act through their downstream signaling pathways in the SAM to integrate stem cell activity and organ initiation. This review discusses how the various regulatory pathways collectively orchestrate SAM function and touches on how their manipulation can alter stem cell activity to improve crop yield.
PMID: 37834339
Front Microbiol , IF:5.64 , 2023 , V14 : P1251698 doi: 10.3389/fmicb.2023.1251698
Plant resistance to tomato yellow leaf curl virus is enhanced by Bacillus amyloliquefaciens Ba13 through modulation of RNA interference.
College of Natural Resources and Environment, Northwest A&F University, Xianyang, China.; College of Agriculture, Guizhou University, Guiyang, China.
INTRODUCTION: Tomato yellow leaf curl virus (TYLCV), which is a typical member of the genus Begomovirus, causes severe crop yield losses worldwide. RNA interference (RNAi) is an important antiviral defense mechanism in plants, but whether plant beneficial microbes used as biocontrol agents would modulate RNAi in defense against TYLCV remains unclear. METHODS: Here, we employed whole-transcriptome, bisulfite, and small RNA sequencing to decipher the possible role of Bacillus amyloliquefaciens Ba13 as a bacterial biocontrol agent against TYLCV in RNAi modulation. RESULTS: Potted tomato plants were exposed to whiteflies for natural viral infection 14 days after bacterial inoculation. Compared with non-inoculated controls, the abundance of TYLCV gene in the leaves of inoculated plants decreased by 70.1% at 28 days post-infection, which mirrored the pattern observed for plant disease index. The expression of the ARGONAUTE family genes (e.g., AGO3, AGO4, AGO5, and AGO7) involved in antiviral defense markedly increased by 2.44-6.73-fold following bacterial inoculation. The methylation level at CpG site 228 (in the open reading frame region of the RNA interference suppressing gene AV2) and site 461 (in the open reading frame regions of AV1 and AV2) was 183.1 and 63.0% higher in inoculated plants than in non-inoculated controls, respectively. The abundances of 10 small interfering RNAs matched to the TYLCV genome were all reduced in inoculated plants, accompanied by enhancement of photosystem and auxin response pathways. DISCUSSION: The results indicate that the application of Ba. amyloliquefaciens Ba13 enhances plant resistance to TYLCV through RNAi modulation by upregulating RNAi-related gene expression and enhancing viral genome methylation.
PMID: 37869663
J Biol Chem , IF:5.157 , 2023 Oct , V299 (10) : P105197 doi: 10.1016/j.jbc.2023.105197
Biochemical investigation of the tryptophan biosynthetic enzyme anthranilate phosphoribosyltransferase in plants.
Department of Biology, Williams College, Williamstown, Massachusetts, USA.; Department of Biology, Williams College, Williamstown, Massachusetts, USA. Electronic address: ckh2@williams.edu.
While mammals require the essential amino acid tryptophan (Trp) in their diet, plants and microorganisms synthesize Trp de novo. The five-step Trp pathway starts with the shikimate pathway product, chorismate. Chorismate is converted to the aromatic compound anthranilate, which is then conjugated to a phosphoribosyl sugar in the second step by anthranilate phosphoribosyltransferase (PAT1). As a single-copy gene in plants, all fixed carbon flux to indole and Trp for protein synthesis, specialized metabolism, and auxin hormone biosynthesis proceeds through PAT1. While bacterial PAT1s have been studied extensively, plant PAT1s have escaped biochemical characterization. Using a structure model, we identified putative active site residues that were variable across plants and kinetically characterized six PAT1s (Arabidopsis thaliana (thale cress), Citrus sinensis (sweet orange), Pistacia vera (pistachio), Juglans regia (English walnut), Selaginella moellendorffii (spike moss), and Physcomitrium patens (spreading earth-moss)). We probed the catalytic efficiency, substrate promiscuity, and regulation of these six enzymes and found that the C. sinensis PAT1 is highly specific for its cognate substrate, anthranilate. Investigations of site-directed mutants of the A. thaliana PAT1 uncovered an active site residue that contributes to promiscuity. While Trp inhibits bacterial PAT1 enzymes, the six plant PAT1s that we tested were not modulated by Trp. Instead, the P. patens PAT1 was inhibited by tyrosine, and the S. moellendorffii PAT1 was inhibited by phenylalanine. This structure-informed biochemical examination identified variations in activity, efficiency, specificity, and enzyme-level regulation across PAT1s from evolutionarily diverse plants.
PMID: 37659723
Plant Cell Physiol , IF:4.927 , 2023 Oct doi: 10.1093/pcp/pcad126
BBX21 integrates brassinosteroid biosynthesis and signalling in the inhibition of hypocotyl growth under shade.
IFEVA (CONICET-UBA), Facultad de Agronomia, Universidad de Buenos Aires, Av. San Martin 4453, Ciudad Autonoma de Buenos Aires, C1417DSE, Argentina.; Laboratory of Growth Regulators, Palacky University & Institute of Experimental Botany, The Czech Academy of Sciences, Slechtitelu 27, CZ-78371 Olomouc, Czech Republic.; Fundacion Instituto Leloir, IIBBA-CONICET, Avenida Patricias Argentinas 435, Ciudad Autonoma de Buenos Aires, C1405BWE, Argentina.; Section of Cell and Developmental Biology, Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.; Instituto de Biologia Molecular y Celular de Plantas, CSIC-Universitat Politecnica de Valencia, C/Ingeniero Fausto Elio s/n, Valencia, 46022, Spain.
B-Box-containing zinc finger transcription factors (BBX) are involved in light-mediated growth, affecting processes such as hypocotyl elongation in Arabidopsis thaliana. However, the molecular and hormonal framework that regulates plant growth through BBX proteins is incomplete. Here, we demonstrate that BBX21 inhibits the hypocotyl elongation through the brassinosteroid (BR) pathway. BBX21 reduces the sensitivity to 24-epiBL, a synthetic active BR, principally at very-low concentrations in simulated shade. The biosynthesis profile of BRs showed that two active BR -brassinolide (BL) and 28-homobrassinolide (28-homoBL)- and 8 of 11 intermediates can be repressed by BBX21 under white light (WL) or simulated shade. Furthermore, BBX21 represses the expression of CYTOCHROME P450 90B1 (DWF4/CYP90B1), BRASSINOSTEROID-6-OXIDASE 1 (BR6OX1, CYP85A1) and BR6OX2 (CYP85A2) genes involved in the BR biosynthesis in WL while specifically promoting DWF4 and PHYB ACTIVATION TAGGED SUPPRESSOR 1 (CYP2B1/BAS1) expression in WL supplemented with far-red (WL+FR), a treatment that simulates shade. In addition, BBX21 represses BR signalling genes such as PACLOBUTRAZOL RESISTANCE1 (PRE1), PRE3 and ARABIDOPSIS MYB-LIKE 2 (MYBL2), and auxin-related and expansin genes, such as INDOLE-3-ACETIC ACID INDUCIBLE 1 (IAA1), IAA4 and EXPANSIN 11 (EXP11) in short-term shade. By a genetic approach we found that BBX21 acts genetically upstream of BRASSINAZOLE-RESISTANT 1 (BZR1) for the promotion of DWF4 and BAS1 gene expression in shade. We propose that BBX21 integrates the BR homeostasis and shade-light signalling allowing the fine-tuning of hypocotyl elongation in Arabidopsis.
PMID: 37847120
Plant Cell Physiol , IF:4.927 , 2023 Oct , V64 (10) : P1146-1158 doi: 10.1093/pcp/pcad078
PINOID and PIN-FORMED Paralogous Genes Are Required for Leaf Morphogenesis in Rice.
College of Agriculture, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, People's Republic of China.; Rice Research Institute, Jiangxi Academy of Agricultural Sciences, No. 602 Nanlian Road, Nanchang 330200, People's Republic of China.; Key Laboratory of Crop Physiology, Ecology and Production Management, Ministry of Agriculture, No. 1 Weigang, Nanjing 210095, People's Republic of China.; Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing Agricultural University, No. 1 Weigang, Nanjing 210095, People's Republic of China.
Auxin plays an essential role in modulating leaf development. However, its role in leaf development in rice (Oryza sativa L.) remains largely unknown. In this study, we found that PINOID (OsPID) and two Sister-of-PIN1s, termed PIN-FORMED1c (OsPIN1c) and OsPIN1d, are necessary for rice leaf development. The ospin1c ospin1d null mutant lines presented severe defects in leaf morphogenesis, including drooping and semi-drooping blades, an abnormally thickened sheath and lamina joint, and fused leaves with absent ligules and auricles. Loss-of-function ospid mutants displayed generally similar leaf morphology but lacked leaf fusion. Interestingly, misshaped leaf genesis displayed a preference for being ipsilateral. In addition, OsPIN1c and OsPID were commonly localized in the initiating leaf primordia. Furthermore, accompanied by the more severe organ morphogenesis in the ospin1c ospin1d ospid triple mutant, RNA sequencing analysis revealed that many genes essential for leaf development have an altered expression level. Together, this study furthers our understanding of the role auxin transport plays during leaf development in monocot rice.
PMID: 37540575
Plant Cell Physiol , IF:4.927 , 2023 Oct , V64 (10) : P1178-1188 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, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan.; Graduate School of Integrated Science for Life, Hiroshima University, 1-4-3 Kagamiyama, 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, 1 University Road, Tainan 701, 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 a guanine nucleotide exchange factor of ADP ribosylation 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
Pest Manag Sci , IF:4.845 , 2023 Oct , V79 (10) : P3581-3592 doi: 10.1002/ps.7541
Nontarget-site resistance due to rapid physiological response in 2,4-D resistant Conyza sumatrensis: reduced 2,4-D translocation and auxin-induced gene expression.
Federal Rural University of Rio de Janeiro, Department of Crop, Seropedica, Brazil.; Colorado State University, Department of Agricultural Biology, Fort Collins, Colorado, USA.; Corteva Agriscience, Field Scientist, Sao Paulo, Brazil.
BACKGROUND: Resistance to 2,4-Dichlorophenoxyacetic acid (2,4-D) has been reported in several weed species since the 1950s; however, a biotype of Conyza sumatrensis showing a novel physiology of the rapid response minutes after herbicide application was reported in 2017. The objective of this research was to investigate the mechanisms of resistance and identify transcripts associated with the rapid physiological response of C. sumatrensis to 2,4-D herbicide. RESULTS: Differences were found in 2,4-D absorption between the resistant and susceptible biotypes. Herbicide translocation was reduced in the resistant biotype compared to the susceptible. In resistant plants 98.8% of [(14) C] 2,4-D was found in the treated leaf, whereas approximately 13% translocated to other plant parts in the susceptible biotype at 96 h after treatment. Resistant plants did not metabolize [(14) C] 2,4-D and had only intact [(14) C] 2,4-D at 96 h after application, whereas susceptible plants metabolized [(14) C] 2,4-D into four detected metabolites, consistent with reversible conjugation metabolites found in other 2,4-D sensitive plant species. Pre-treatment with the cytochrome P450 inhibitor malathion did not enhance 2,4-D sensitivity in either biotype. Following treatment with 2,4-D, resistant plants showed increased expression of transcripts within plant defense response and hypersensitivity pathways, whereas both sensitive and resistant plants showed increased expression of auxin-response transcripts. CONCLUSION: Our results demonstrate that reduced 2,4-D translocation contributes to resistance in the C. sumatrensis biotype. The reduction in 2,4-D transport is likely to be a consequence of the rapid physiological response to 2,4-D in resistant C. sumatrensis. Resistant plants had increased expression of auxin-responsive transcripts, indicating that a target-site mechanism is unlikely. (c) 2023 Society of Chemical Industry.
PMID: 37178347
Plant Sci , IF:4.729 , 2023 Oct : P111902 doi: 10.1016/j.plantsci.2023.111902
Modulation in gene expression and enzyme activity suggested the roles of monodehydroascorbate reductase in development and stress response in bread wheat.
Department of Botany, Panjab University, Chandigarh, India-160014.; Department of Biotechnology, Panjab University, Chandigarh, India-160014.; Department of Botany, Panjab University, Chandigarh, India-160014. Electronic address: skupadhyay@pu.ac.in.
Monodehydroascorbate reductase (MDHAR) is a crucial enzymatic antioxidant of the ascorbate-glutathione pathway involved in reactive oxygen species scavenging. Herein, we identified 15 TaMDHAR genes in bread wheat. Phylogenetic analysis revealed their clustering into three groups, which are also related to the subcellular localization in the peroxisome matrix, peroxisome membrane, and chloroplast. Each TaMDHAR protein consisted of two conserved domains; Pyr_redox and Pyr_redox_2 of the pyridine nucleotide disulfide oxidoreductase family. The occurrence of diverse groups of cis-regulatory elements in the promoter region and their interaction with numerous transcription factors suggest assorted functions of TaMDHARs in growth and development and in light, phytohormones, and stress responses. Expression analysis in various tissues further revealed their importance in vegetative and reproductive development. In addition, the differential gene expression and enhanced enzyme activity during drought, heat, and salt treatments exposed their role in abiotic stress response. Interaction of MDHARs with various antioxidant enzymes and biochemicals related to the ascorbate-glutathione cycle exposed their synchronized functioning. Interaction with auxin indicated the probability of cross-talk between antioxidants and auxin signaling. The miR168a, miR169, miR172 and others interaction with various TaMDHARs further directed their association with developmental processes and stress responses. The current study provides extensive information about the importance of TaMDHARs, moreover, the precise role of each gene needs to be established in future studies.
PMID: 37879539
Plant Sci , IF:4.729 , 2023 Oct , V338 : P111869 doi: 10.1016/j.plantsci.2023.111869
The miR156-SPL4/SPL9 module regulates leaf and lateral branch development in Betula platyphylla.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China.; State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150036, China. Electronic address: lihuiyu2017@126.com.
The miR156 gene is known to play an important role in regulating growth and development in plants. This gene is involved in the transition from juvenile to adult stages, leaf morphology, and root development, among other processes. While the function of miR156 is similar in many plants, there are also differences in the function of this gene between herbaceous and native species. We obtained BpmiR156 overexpression transgenic lines in Betula platyphylla, and the transgenic lines exhibited traits such as delayed development, dwarfism, increased leaf epidermal hairs, larger leaf basal angle and altered stem curvature, which were highly consistent with the overexpression miR156 in Arabidopsis, rice and tomato. However, we also observed a lack of apical dominance, increased number of lateral branches and increased diameter of lateral branches in transgenic B. platyphylla, which is different from the effects reported in other plants. Transgenic plants showed changes in the distribution of IAA, GA3, and Zeatin in lateral branches and main stem, and the ratio of the content of the three hormones was significantly higher than in the non-transgenic plants served as control. Additionally, overexpression of BpmiR156 caused down-regulation of BpSPL4 and BpSPL9 expression, as well as differential expression of genes involved in auxin and cytokinin synthesis such as BpARR3, BpARR11 and BpmiR172.
PMID: 37827250
Plant Sci , IF:4.729 , 2023 Oct , V338 : P111892 doi: 10.1016/j.plantsci.2023.111892
Integrating the multiple functions of CHLH into chloroplast-derived signaling fundamental to plant development and adaptation as well as fruit ripening.
College of Horticulture, China Agricultural University, Beijing 100193, China; College of Plant Science and Technology, Beijing University of Agriculture, 7 Beinong Road, Changping District, Beijing 102206, China.; College of Plant Science and Technology, Beijing University of Agriculture, 7 Beinong Road, Changping District, Beijing 102206, China. Electronic address: sflmn@163.com.
Chlorophyll (Chl)-mediated oxygenic photosynthesis sustains life on Earth. Greening leaves play fundamental roles in plant growth and crop yield, correlating with the idea that more Chls lead to better adaptation. However, they face significant challenges from various unfavorable environments. Chl biosynthesis hinges on the first committed step, which involves inserting Mg(2+) into protoporphyrin. This step is facilitated by the H subunit of magnesium chelatase (CHLH) and features a conserved mechanism from cyanobacteria to plants. For better adaptation to fluctuating land environments, especially drought, CHLH evolves multiple biological functions, including Chl biosynthesis, retrograde signaling, and abscisic acid (ABA) responses. Additionally, it integrates into various chloroplast-derived signaling pathways, encompassing both retrograde signaling and hormonal signaling. The former comprises ROS (reactive oxygen species), heme, GUN (genomes uncoupled), MEcPP (methylerythritol cyclodiphosphate), beta-CC (beta-cyclocitral), and PAP (3'-phosphoadenosine-5'-phosphate). The latter involves phytohormones like ABA, ethylene, auxin, cytokinin, gibberellin, strigolactone, brassinolide, salicylic acid, and jasmonic acid. Together, these elements create a coordinated regulatory network tailored to plant development and adaptation. An intriguing example is how drought-mediated improvement of fruit quality provides insights into chloroplast-derived signaling, aiding the shift from vegetative to reproductive growth. In this context, we explore the integration of CHLH's multifaceted roles into chloroplast-derived signaling, which lays the foundation for plant development and adaptation, as well as fruit ripening and quality. In the future, manipulating chloroplast-derived signaling may offer a promising avenue to enhance crop yield and quality through the homeostasis, function, and regulation of Chls.
PMID: 37821024
Plant Sci , IF:4.729 , 2023 Nov , V336 : P111866 doi: 10.1016/j.plantsci.2023.111866
The many faces of lysine acylation in proteins: Phytohormones as unexplored substrates.
Programa de Pos-graduacao em Genetica e Biologia Molecular (PPGBM), Departamento de Genetica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.; Programa de Pos-graduacao em Genetica e Biologia Molecular (PPGBM), Departamento de Genetica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Programa de Pos-graduacao em Biologia Celular e Molecular (PPGBCM), Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Departamento de Biofisica, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil. Electronic address: rogerio.margis@ufrgs.br.
Protein post-translational modification (PTM) is a ubiquitous process that occurs in most proteins. Lysine residues containing an epsilon-amino group are recognized as hotspots for the addition of different chemical groups. Lysine acetylation, extensively studied in histones, serves as an epigenetic hallmark capable of promoting changes in chromatin structure and availability. Acyl groups derived from molecules involved in carbohydrate and lipid metabolisms, such as lactate, succinate and hydroxybutyrate, were identified as lysine modifications of histones and other proteins. Lysine-acyltransferases do not exhibit significant substrate specificity concerning acyl donors. Furthermore, plant hormones harboring acyl groups often form conjugates with free amino acids to regulate their activity and function during plant physiological processes and responses, a process mediated by GH3 enzymes. Besides forming low-molecular weight conjugates, auxins have been shown to covalently modify proteins in bean seeds. Aside from auxins, other phytohormones with acyl groups are unexplored potential substrates for post-translational acylation of proteins. Using MS data searches, we revealed various proteins with lysine residues linked to auxin, abscisic acid, gibberellic acid, jasmonic acid, and salicylic acid. These findings raise compelling questions about the ability of plant hormones harboring carboxyl groups to serve as new candidates for protein acylation and acting in protein PTM and modulation.
PMID: 37714383
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
Plant Cell Rep , IF:4.57 , 2023 Oct doi: 10.1007/s00299-023-03071-0
Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos.
State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.; State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.; Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.; Department of Biosciences, Rajagiri College of Social Sciences (Autonomous), Kalamassery, Kochi, 683104, Kerala, India.; State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, Jiangsu, China.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.; State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration On Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China. weiqiang@njfu.edu.cn.
This review discusses the epigenetic changes during somatic embryo (SE) development, highlights the genes and miRNAs involved in the transition of somatic cells into SEs as a result of epigenetic changes, and draws insights on biotechnological opportunities to study SE development. Somatic embryogenesis from somatic cells occurs in a series of steps. The transition of somatic cells into somatic embryos (SEs) is the most critical step under genetic and epigenetic regulations. Major regulatory genes such as SERK, WUS, BBM, FUS3/FUSA3, AGL15, and PKL, control SE steps and development by turning on and off other regulatory genes. Gene transcription profiles of somatic cells during SE development is the result of epigenetic changes, such as DNA and histone protein modifications, that control and decide the fate of SE formation. Depending on the type of somatic cells and the treatment with plant growth regulators, epigenetic changes take place dynamically. Either hypermethylation or hypomethylation of SE-related genes promotes the transition of somatic cells. For example, the reduced levels of DNA methylation of SERK and WUS promotes SE initiation. Histone modifications also promote SE induction by regulating SE-related genes in somatic cells. In addition, miRNAs contribute to the various stages of SE by regulating the expression of auxin signaling pathway genes (TIR1, AFB2, ARF6, and ARF8), transcription factors (CUC1 and CUC2), and growth-regulating factors (GRFs) involved in SE formation. These epigenetic and miRNA functions are unique and have the potential to regenerate bipolar structures from somatic cells when a pluripotent state is induced. However, an integrated overview of the key regulators involved in SE development and downstream processes is lacking. Therefore, this review discusses epigenetic modifications involved in SE development, SE-related genes and miRNAs associated with epigenetics, and common cis-regulatory elements in the promoters of SE-related genes. Finally, we highlight future biotechnological opportunities to alter epigenetic pathways using the genome editing tool and to study the transition mechanism of somatic cells.
PMID: 37792027
Plant Cell Rep , IF:4.57 , 2023 Nov , V42 (11) : P1705-1719 doi: 10.1007/s00299-023-03053-2
Dose effects of restorer gene modulate pollen fertility in cotton CMS-D2 restorer lines via auxin signaling and flavonoid biosynthesis.
National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China.; National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China. zhangmeng03@caas.cn.; National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China. dr.wujianyong@live.cn.; National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, 38 Huanghe Dadao, Anyang, 455000, Henan, China. chaozhuxing@126.com.
Dose effects of Rf(1) gene regulated retrieval mechanism of pollen fertility for CMS-D2 cotton. Cytoplasmic male sterility conditioned by Gossypium harknessii cytoplasm (CMS-D2) is an economical pollination control system for producing hybrid cotton seeds compared to artificial and chemical emasculation methods. However, the unstable restoring ability of restorer lines is a main barrier in the large-scale application of "three-line" hybrid cotton in China. Our phenotypic investigation determined that the homozygous Rf(1)Rf(1) allelic genotype had a stronger ability to generate fertile pollen than the heterozygous Rf(1)rf(1) allelic genotype. To decipher the genetic mechanisms that control the differential levels of pollen fertility, an integrated metabolomic and transcriptomic analysis was performed at two environments using pollen grains of four cotton genotypes differing in Rf(1) alleles or cytoplasm. Totally 5,391 differential metabolite features were detected, and 369 specific differential metabolites (DMs) were identified between homozygous and heterozygous Rf(1) allelic genotypes with CMS-D2 cytoplasm. In addition, transcriptome analysis identified 2,490 differentially expressed genes (DEGs) and 96 unique hub DEGs with dynamic regulation in this comparative combination. Further integrated analyses revealed that several key DEGs and DMs involved in indole biosynthesis, flavonoid biosynthesis, and sugar metabolism had strong network linkage with fertility restoration. In vitro application of auxin analogue NAA and inhibitor Auxinole confirmed that over-activated auxin signaling might inhibit pollen development, whereas suppressing auxin signaling partially promoted pollen development in CMS-D2 cotton. Our results provide new insight into how the dosage effects of the Rf(1) gene regulate pollen fertility of CMS-D2 cotton.
PMID: 37715064
Bioessays , IF:4.345 , 2023 Nov , V45 (11) : 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 Oct , V204 : P108129 doi: 10.1016/j.plaphy.2023.108129
Roles of abscisic acid and auxin in plants during drought: A molecular point of view.
Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China.; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA. Electronic address: aartgupt@ttu.edu.; State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, School of Life Sciences, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China.; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA.; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China.; Department of Botany, Hindu Girls College, Maharshi Dayanand University, Sonipat, 131001, India.; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79409, USA. Electronic address: son.tran@ttu.edu.
Plant responses to drought are mediated by hormones like ABA (abscisic acid) and auxin. These hormones regulate plant drought responses by modulating various physiological and biological processes via cell signaling. ABA accumulation and signaling are central to plant drought responses. Auxin also regulates plant adaptive responses to drought, especially via signal transduction mediated by the interaction between ABA and auxin. In this review, we explored the interactive roles of ABA and auxin in the modulation of stomatal movement, root traits and accumulation of reactive oxygen species associated with drought tolerance.
PMID: 37897894
Plant Physiol Biochem , IF:4.27 , 2023 Oct , V204 : P108087 doi: 10.1016/j.plaphy.2023.108087
Transcriptome analysis reveals ZmERF055 contributes to waterlogging tolerance in sweetcorn.
Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.; Southern Zhejiang Key Laboratory of Crop Breeding, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, 325006, China. Electronic address: 362840793@qq.com.; Guangdong Key Laboratory of Plant Molecular Breeding, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China. Electronic address: bowang@scau.edu.cn.
Waterlogging is a major disaster damaging crop production. However, most sweetcorn cultivars are not tolerant to waterlogging, which severely threatens their production. In order to understand the genetic mechanisms underlying waterlogging tolerance in sweetcorn, this study conducted a comprehensive investigation of sweetcorn waterlogging tolerance at the levels of physiology, biochemistry, and transcriptome in two sweetcorn CSSLs (chromosome segment substitution lines), D120 and D81. We found that D120 showed increased plant height, root length, root area, adventitious root numbers, antioxidant enzyme activities, and aerenchyma area ratio compared to D81. The transcriptome results showed that 2492 and 2351 differentially expressed genes (DEGs) were obtained at 4 h and 8 h of waterlogging treatment, respectively. Genes involved in reactive oxygen species (ROS) homeostasis, photosynthesis, and alcohol fermentation are sensitive in the waterlogging tolerant genotype D120, resulting in enhanced ROS scavenging ability, adventitious roots, and aerenchyma formation. Additionally, ethylene-, auxin-, and ABA-related genes exhibited different responses to waterlogging stress in sweetcorn. We integrated transcriptome and differential chromosomal fragments data and identified that ZmERF055 on chromosome 9 was directly involved in waterlogging stress. ZmERF055-overexpressing plants consistently exhibited significantly increased waterlogging tolerance and ROS homeostasis in Arabidopsis. These results offer a network of plant hormone signaling, ROS homeostasis, and energy metabolism co-modulating waterlogging tolerance in sweetcorn. Additionally, the findings support ZmERF055 as a potential ideal target gene in crop breeding to improve plant waterlogging tolerance.
PMID: 37847974
Plant Physiol Biochem , IF:4.27 , 2023 Oct , V203 : P108035 doi: 10.1016/j.plaphy.2023.108035
Metabolic pathways modulated by coumarin to inhibit seed germination and early seedling growth in Eleusine indica.
Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, PR China.; Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, PR China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, PR China.; Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, PR China. Electronic address: zhangchun_0726@163.com.
Coumarin is an allelochemical that is widely present in the plant kingdom and has great potential for weed control. However, its mechanisms of action remain largely unknown. This study employed metabolomic and transcriptomic analyses along with evaluations of amino acid profiles and related physiological indicators to investigate how coumarin inhibits the germination and seedling growth of Eleusine indica by modifying metabolic pathways. At 72 h of germination at 50 and 100 mg L(-1) coumarin, E. indica had lower levels of soluble sugar and activities of amylases and higher levels of starch, O(2)(-), H(2)O(2), auxin (IAA) and abscisic acid (ABA) compared to the control. Metabolomic analysis demonstrated that coumarin treatments had a significant impact on the pathways associated with amino acid metabolism and transport and aminoacyl-tRNA biosynthesis. Exposure to coumarin induced significant alterations in the levels of 19 amino acids, with a decrease in 15 of them, including Met, Leu and gamma-aminobutyric acid (GABA). Additionally, transcriptomic analysis showed that coumarin significantly disrupted several essential biological processes, including protein translation, secondary metabolite synthesis, and hormone signal transduction. The decrease in TCA cycle metabolite (cis-aconitate, 2-oxoglutarate, and malate) contents was associated with the suppression of transcription for related enzymes. Our findings indicate that the inhibition of germination and growth in E. indica by coumarin involves the suppression of starch conversion to sugars, modification of the amino acid profile, interference of hormone signalling and the induction of oxidative stress. The TCA cycle appears to be one of the most essential pathways affected by coumarin.
PMID: 37729857
Environ Sci Pollut Res Int , IF:4.223 , 2023 Oct doi: 10.1007/s11356-023-30608-3
Phytotoxicity alleviation of imazethapyr to non-target plant wheat: active regulation between auxin and DIMBOA.
MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China.; Ningbo Key Laboratory of Agricultural Germplasm Resources Mining and Environmental Regulation, College of Science and Technology, Ningbo University, Cixi, 315300, China.; College of Environmental Science and Engineering, Donghua University, Shanghai, 201620, China.; MOE Key Laboratory of Environmental Remediation & Ecosystem Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China. wenyuezhong@zju.edu.cn.
Effectively controlling target organisms while reducing the adverse effects of pesticides on non-target organisms is a crucial scientific inquiry and challenge in pesticide ecotoxicology research. Here, we studied the alleviation of herbicide (R)-imazethapyr [(R)-IM] to non-target plant wheat by active regulation between auxin and secondary metabolite 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazine-3(4H)-one (DIMBOA). We found (R)-IM reduced 32.4% auxin content in wheat leaves and induced 40.7% DIMBOA accumulation compared to the control group, which effortlessly disrupted the balance between wheat growth and defense. Transcriptomic results indicated that restoration of the auxin level in plants promoted the up-regulation of growth-related genes and the accumulation of DIMBOA up-regulated the expression of defense-related genes. Auxin and DIMBOA alleviated herbicide stress primarily through effects in the two directions of wheat growth and defense, respectively. Additionally, as a common precursor of auxin and DIMBOA, indole adopted a combined growth and defense strategy in response to (R)-IM toxicity, i.e., restoring growth development and enhancing the defense system. Future regulation of auxin and DIMBOA levels in plants may be possible through appropriate methods, thus regulating the plant growth-defense balance under herbicide stress. Our insight into the interference mechanism of herbicides to the plant growth-defense system will facilitate the design of improved strategies for herbicide detoxification.
PMID: 37897577
BMC Plant Biol , IF:4.215 , 2023 Oct , V23 (1) : P499 doi: 10.1186/s12870-023-04514-2
Exogenous auxin regulates the growth and development of peach fruit at the expansion stage by mediating multiple-hormone signaling.
College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. ypzhang@szai.edu.cn.; Faculty of Horticultural Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China. ypzhang@szai.edu.cn.; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.; Faculty of Horticultural Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China.; Inner MongoliaAgricultural University, Huhehaote, 010010, China. Liujiecailiu@163.com.; College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China. wangchen@njau.edu.cn.; Faculty of Horticultural Science and Technology, Suzhou Polytechnic Institute of Agriculture, Suzhou, 215008, China. wangchen@njau.edu.cn.
BACKGROUND: Fruit expansion stage is crucial to fruit yield and quality formation, and auxin plays a significant role by mediating multi-hormone signals during fruit expansion. However, till now, it is still unclear of the molecular regulatory network during auxin-mediated peach fruit expansion. RESULTS: Here, exogenous NAA application markedly increased IAA content and drastically decreased ABA content at the fruit expansion stage. Correspondingly, NAA mainly induced the auxin biosynthesis gene (1 PpYUCCA) and early auxin-responsive genes (7PpIAA, 3 PpGH3, and 14 PpSAUR); while NAA down-regulated ABA biosynthesis genes (2 PpNCED, 1 PpABA3, and 1 PpAAO3). In addition, many DEGs involved in other plant hormone biosynthesis and signal transduction were significantly enriched after NAA treatment, including 7 JA, 7 CTK, 6 ETH, and 3 GA. Furthermore, we also found that NAA treatment down-regulated most of genes involved in the growth and development of peach fruit, including the cell wall metabolism-related genes (PpEG), sucrose metabolism-related genes (PpSPS), phenylalanine metabolism-related genes (PpPAL, Pp4CL, and PpHCT), and transcription factors (PpNAC, PpMADS-box, PpDof, PpSBP, and PpHB). CONCLUSION: Overall, NAA treatment at the fruit expansion stage could inhibit some metabolism processes involved in the related genes in the growth and development of peach fruit by regulating multiple-hormone signaling networks. These results help reveal the short-term regulatory mechanism of auxin at the fruit expansion stage and provide new insights into the multi-hormone cascade regulatory network of fruit growth and development.
PMID: 37848815
BMC Plant Biol , IF:4.215 , 2023 Oct , V23 (1) : P488 doi: 10.1186/s12870-023-04495-2
Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.).
Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran. r.hamid@areeo.ac.ir.; Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India.; Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.; Horticultural Science Department, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas, Iran.; Research Group of Agroecology in Dryland Areas, University of Hormozgan, Bandar Abbas, Iran.; Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
BACKGROUND: Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. RESULTS: Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. CONCLUSIONS: These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.
PMID: 37828433
BMC Plant Biol , IF:4.215 , 2023 Oct , V23 (1) : P483 doi: 10.1186/s12870-023-04491-6
Acclimation of circadian rhythms in woodland strawberries (Fragaria vesca L.) to Arctic and mid-latitude photoperiods.
Department of Arctic and Marine Biology, The Arctic University of Norway, Tromso, 9037, Norway. corine.a.faehn@uit.no.; Department of Biochemistry, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.; Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, 07745, Jena, Germany.; Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, 00790, Finland.; NIBIO, Norwegian Institute of Bioeconomy Research, P.O. Box 115, As, 1431, Norway.; Department of Arctic and Marine Biology, The Arctic University of Norway, Tromso, 9037, Norway.
BACKGROUND: Though many abiotic factors are constantly changing, the photoperiod is a predictable factor that enables plants to time many physiological responses. This timing is regulated by the circadian clock, yet little is known about how the clock adapts to the differences in photoperiod between mid-latitudes and high latitudes. The primary objective of this study was to compare how clock gene expression is modified in four woodland strawberry (Fragaria vesca L.) accessions originating from two different populations in Italy (IT1: Tenno, Italy, 45 degrees N, IT4: Salorno, Italy, 46 degrees N) and two in Northern Norway (NOR2: Alta, Norway, 69 degrees N, NOR13: Indre Nordnes, Norway 69 degrees N) when grown under simulated daylength conditions of an Arctic or mid-latitude photoperiod. The second objective was to investigate whether population origin or the difference in photoperiod influenced phytohormone accumulation. RESULTS: The Arctic photoperiod induced lower expression in IT4 and NOR13 for six clock genes (FvLHY, FvRVE8, FvPRR9, FvPRR7, FvPRR5, and FvLUX), in IT1 for three genes (FvLHY, FvPRR9, and FvPRR5) and in NOR2 for one gene (FvPRR9). Free-running rhythms for FvLHY in IT1 and IT4 were higher after the Arctic photoperiod, while the free-running rhythm for FvLUX in IT4 was higher after the mid-latitude photoperiod. IT1 showed significantly higher expression of FvLHY and FvPRR9 than all other accessions, as well as significantly higher expression of the circadian regulated phytohormone, abscisic acid (ABA), but low levels of salicylic acid (SA). NOR13 had significantly higher expression of FvRVE8, FvTOC1, and FvLUX than all other accessions. NOR2 had extremely low levels of auxin (IAA) and high levels of the jasmonate catabolite, hydroxyjasmonic acid (OH-JA). CONCLUSIONS: Our study shows that circadian rhythms in Fragaria vesca are driven by both the experienced photoperiod and genetic factors, while phytohormone levels are primarily determined by specific accessions' genetic factors rather than the experienced photoperiod.
PMID: 37817085
BMC Plant Biol , IF:4.215 , 2023 Oct , V23 (1) : P482 doi: 10.1186/s12870-023-04505-3
Transcriptomic analysis implicates ABA signaling and carbon supply in the differential outgrowth of petunia axillary buds.
The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand.; School of Biological Sciences, University of Auckland, Auckland, New Zealand.; NetValue Limited, Hamilton, New Zealand.; The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand. Kimberley.Snowden@plantandfood.co.nz.
BACKGROUND: Shoot branching of flowering plants exhibits phenotypic plasticity and variability. This plasticity is determined by the activity of axillary meristems, which in turn is influenced by endogenous and exogenous cues such as nutrients and light. In many species, not all buds on the main shoot develop into branches despite favorable growing conditions. In petunia, basal axillary buds (buds 1-3) typically do not grow out to form branches, while more apical axillary buds (buds 6 and 7) are competent to grow. RESULTS: The genetic regulation of buds was explored using transcriptome analyses of petunia axillary buds at different positions on the main stem. To suppress or promote bud outgrowth, we grew the plants in media with differing phosphate (P) levels. Using RNA-seq, we found many (> 5000) differentially expressed genes between bud 6 or 7, and bud 2. In addition, more genes were differentially expressed when we transferred the plants from low P to high P medium, compared with shifting from high P to low P medium. Buds 6 and 7 had increased transcript abundance of cytokinin and auxin-related genes, whereas the basal non-growing buds (bud 2 and to a lesser extent bud 3) had higher expression of strigolactone, abscisic acid, and dormancy-related genes, suggesting the outgrowth of these basal buds was actively suppressed. Consistent with this, the expression of ABA associated genes decreased significantly in apical buds after stimulating growth by switching the medium from low P to high P. Furthermore, comparisons between our data and transcriptome data from other species suggest that the suppression of outgrowth of bud 2 was correlated with a limited supply of carbon to these axillary buds. Candidate genes that might repress bud outgrowth were identified by co-expression analysis. CONCLUSIONS: Plants need to balance growth of axillary buds into branches to fit with available resources while allowing some buds to remain dormant to grow after the loss of plant parts or in response to a change in environmental conditions. Here we demonstrate that different buds on the same plant with different developmental potentials have quite different transcriptome profiles.
PMID: 37814235
BMC Plant Biol , IF:4.215 , 2023 Oct , V23 (1) : P478 doi: 10.1186/s12870-023-04498-z
Effects of PmaIAA27 and PmaARF15 genes on drought stress tolerance in pinus massoniana.
Forest Resources and Environment Research Center, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550001, China.; Institute of Mountain Resources of Guizhou Province, Guiyang, 550001, China.; Forest Resources and Environment Research Center, Key Laboratory of Forest Cultivation in Plateau Mountain of Guizhou Province, College of Forestry, Guizhou University, Guiyang, 550001, China. gjding@gzu.edu.cn.
BACKGROUND: Auxin plays an important role in plant resistance to abiotic stress. The modulation of gene expression by Auxin response factors (ARFs) and the inhibition of auxin/indole-3-acetic acid (Aux/IAA) proteins play crucial regulatory roles in plant auxin signal transduction. However, whether the stress resistance of Masson pine (Pinus massoniana), as a representative pioneer species, is related to Aux/IAA and ARF genes has not been thoroughly studied and explored. RESULTS: The present study provides preliminary evidence for the regulatory role of the PmaIAA27 gene in abiotic stress response in Masson pine. We investigated the effects of drought and hormone treatments on Masson pine by examining the expression patterns of PmaIAA27 and PmaARF15 genes. Subsequently, we conducted gene cloning, functional testing using transgenic tobacco, and explored gene interactions. Exogenous auxin irrigation significantly downregulated the expression of PmaIAA27 while upregulating PmaARF15 in Masson pine seedlings. Moreover, transgenic tobacco with the PmaIAA27 gene exhibited a significant decrease in auxin content compared to control plants, accompanied by an increase in proline content - a known indicator of plant drought resistance. These findings suggest that overexpression of the PmaIAA27 gene may enhance drought resistance in Masson pine. To further investigate the interaction between PmaIAA27 and PmaARF15 genes, we performed bioinformatics analysis and yeast two-hybrid experiments which revealed interactions between PB1 structural region of PmaARF15 and PmaIAA27. CONCLUSION: The present study provides new insights into the regulatory functions of Aux/IAA and ARF genes in Masson pine. Overexpression of PmaIAA gene may have negative effects on the growth of Masson pine, but may improve the drought resistance. Therefore, this study has great application prospects.
PMID: 37807055
BMC Plant Biol , IF:4.215 , 2023 Oct , V23 (1) : P471 doi: 10.1186/s12870-023-04476-5
Characterization and expression profiles of WUSCHEL-related homeobox (WOX) gene family in cultivated alfalfa (Medicago sativa L.).
College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China.; Beijing Agro-Biotechnology Research Center, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, People's Republic of China.; College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, People's Republic of China. huiwang211@cau.edu.cn.
The WUSCHEL-related homeobox (WOX) family members are plant-specific transcriptional factors, which function in meristem maintenance, embryogenesis, lateral organ development, as well as abiotic stress tolerance. In this study, 14 MsWOX transcription factors were identified and comprehensively analyzed in the cultivated alfalfa cv. Zhongmu No.1. Overall, 14 putative MsWOX members containing conserved structural regions were clustered into three clades according to phylogenetic analysis. Specific expression patterns of MsWOXs in different tissues at different levels indicated that the MsWOX genes play various roles in alfalfa. MsWUS, MsWOX3, MsWOX9, and MsWOX13-1 from the three subclades were localized in the nucleus, among which, MsWUS and MsWOX13-1 exhibited strong self-activations in yeast. In addition, various cis-acting elements related to hormone responses, plant growth, and stress responses were identified in the 3.0 kb promoter regions of MsWOXs. Expression detection of separated shoots and roots under hormones including auxin, cytokinin, GA, and ABA, as well as drought and cold stresses, showed that MsWOX genes respond to different hormones and abiotic stress treatments. Furthermore, transcript abundance of MsWOX3, and MsWOX13-2 were significantly increased after rhizobia inoculation. This study presented comprehensive data on MsWOX transcription factors and provided valuable insights into further studies of their roles in developmental processes and abiotic stress responses in alfalfa.
PMID: 37803258
Tree Physiol , IF:4.196 , 2023 Oct , V43 (10) : P1841-1854 doi: 10.1093/treephys/tpad089
Transcriptomic and physiological comparison of Shatangju (Citrus reticulata) and its late-maturing mutant provides insights into auxin regulation of citrus fruit maturation.
Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences/Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs/Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, No. 80, Dafeng No. 2 street, Tianhe District, Guangzhou 510650, Guangdong Province, China.; Department of Plant Sciences, University of California, Davis, One Shields Avenue, Davis, CA 95616, USA.
Previous studies have shown that abscisic acid (ABA) and ethylene are involved in pulp maturation and peel coloration in the nonclimacteric citrus fruits. There are also signs indicating that other plant hormones may play some roles in citrus fruit ripening. In this study, we compared profiles of genome-wide gene expression and changes in hormones and peel pigments between fruits of Shatangju mandarin (Citrus reticulata Blanco, designated WT) and its natural mutant, Yuenongwanju (designated MT). The MT fruit matures ~2 months later than the WT fruit. Significant differences in fruit diameter, total soluble solids, titratable acid content, chlorophylls and carotenoids were detected between the fruits of the two genotypes at the sampled time points. Genome-wide transcriptome profiling showed that many genes involved in auxin and ABA metabolism and/or signaling pathways were differentially expressed between the MT and the WT fruits. Importantly, the expression of CrYUCCA8 was significantly lower and the expression of CrNCED5 was significantly higher in WT than in MT fruits at 230 and 250 DPA, respectively. In addition, the indole-3-acetic acid (IAA) level in the MT fruit was significantly higher than that in the WT counterpart, whereas a significantly lower level of ABA was detected in the mutant. Treatment of the WT fruit with exogenous IAA significantly delayed fruit maturation. Our results provide experimental evidence supporting the notion that auxin is a negative regulator of fruit maturation in citrus.
PMID: 37462512
Tree Physiol , IF:4.196 , 2023 Oct , V43 (10) : P1811-1824 doi: 10.1093/treephys/tpad085
Heritable epigenetic modification of BpPIN1 is associated with leaf shapes in Betula pendula.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, No. 51, Hexing Road, Harbin, Heilongjiang 150040, China.; Citrus Research and Education Center, University of Florida, Lake Alfred, FL 33580, USA.; Department of Plant Pathology, Kansas State University, Throckmorton Center, 116 Ackert Hall, Manhattan, KS 66506-5502, USA.; College of Life Science, Northeast Forestry University, No. 26, Hexing Road, Harbin, Heilongjiang 150040, China.; College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Dr, Houghton, MI 49931, USA.
The new variety Betula pendula 'Dalecarlica', selected from Betula pendula, shows high ornamental value owing to its lobed leaf shape. In this study, to identify the genetic components of leaf shape formation, we performed bulked segregant analysis and molecular marker-based fine mapping to identify the causal gene responsible for lobed leaves in B. pendula 'Dalecarlica'. The most significant variations associated with leaf shape were identified within the gene BpPIN1 encoding a member of the PIN-FORMED family, responsible for the auxin efflux carrier. We further confirmed the hypomethylation at the promoter region promoting the expression level of BpPIN1, which causes stronger and longer veins and lobed leaf shape in B. pendula 'Dalecarlica'. These results indicated that DNA methylation at the BpPIN1 promoter region is associated with leaf shapes in B. pendula. Our findings revealed an epigenetic mechanism of BpPIN1 in the regulation of leaf shape in Betula Linn. (birch), which could help in the molecular breeding of ornamental traits.
PMID: 37406032
FEMS Microbiol Ecol , IF:4.194 , 2023 Oct , V99 (11) doi: 10.1093/femsec/fiad114
Plant growth promoting activities of Pseudomonas sp. and Enterobacter sp. isolated from the rhizosphere of Vachellia gummifera in Morocco.
Equipe de Microbiologie et Biologie Moleculaire, Centre de Biotechnologies vegetales et microbiennes, Biodiversite et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, B.P. 1014 RP, Rabat 10080, Morocco.; Laboratoire de Zoologie et de Biologie Generale, Centre de Biotechnologies vegetales et microbiennes, Biodiversite et Environnement, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, Agdal, B.P. 1014 RP, Rabat 10080, Morocco.; Departamento de Microbiologia del Suelo y Sistemas Simbioticos Estacion Experimental del Zaidin, CSIC, Apartado Postal 419, 18008 Granada, Spain.
The Moroccan endemic Vachellia gummifera grows wild under extreme desert conditions. This plant could be used as an alternative fodder for goats, and camels, in order to protect the Argan forests against overgrazing in Central and Southwestern Moroccan semiarid areas. With the aim to improve the V. gummifera population's density in semiarid areas, we proposed its inoculation with performing plant growth-promoting bacteria. Hence, 500 bacteria were isolated from the plant rhizosphere. From these, 291 isolates were retained for plant growth-promoting (PGP) activities assessment. A total of 44 isolates showed the best phosphates solubilization potential, as well as siderophore and auxin production. The combination of REP-PCR (repetitive extragenic palindromic-polymerase chain reaction) fingerprinting, PGP activities, and phenotypic properties, allowed the selection of three strains for the inoculation experiments. The three selected strains' 16S rRNA sequencing showed that they are members of the Enterobacter and Pseudomonas genera. The inoculation with three strains had diverse effects on V. gummifera growth parameters. All single and combined inoculations improved the plant shoot weight by more than 200%, and the root length by up to 139%, while some combinations further improved protein and chlorophyll content, thereby improving the plant's forage value. The three selected strains constitute an effective inoculum for use in the arid and semiarid zones of southern Morocco.
PMID: 37742210
Anal Bioanal Chem , IF:4.142 , 2023 Oct doi: 10.1007/s00216-023-04996-x
In situ separation and visualization of isomeric auxin derivatives in Arabidopsis by ion mobility mass spectrometry imaging.
Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Faculty of Science, Palacky University, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic. chao.zhang@upol.cz.; Department of Chemical Biology, Faculty of Science, Palacky University, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic.; Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Faculty of Science, Palacky University, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic.; Department of Experimental Biology, Faculty of Science, Palacky University, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic.; Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Faculty of Science, Palacky University, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic. karel.dolezal@upol.cz.; Department of Chemical Biology, Faculty of Science, Palacky University, Slechtitelu 27, CZ-78371, Olomouc, Czech Republic. karel.dolezal@upol.cz.
In situ separation and visualization of synthetic and naturally occurring isomers from heterogeneous plant tissues, especially when they share similar molecular structures, are a challenging task. In this study, we combined the ion mobility separation with desorption electrospray ionization mass spectrometry imaging (DESI-IM-MSI) to achieve a direct separation and visualization of two synthetic auxin derivatives, auxinole and its structural isomer 4pTb-MeIAA, as well as endogenous auxins from Arabidopsis samples. Distinct distribution of these synthetic isomers and endogenous auxins in Arabidopsis primary roots and hypocotyls was achieved in the same imaging analysis from both individually treated and cotreated samples. We also observed putative metabolites of synthetic auxin derivatives, i.e. auxinole amino acid conjugates and hydrolysed 4pTb-MeIAA product - 4pTb-IAA, based on their unique drifting ion intensity patterns. Furthermore, DESI-IM-MSI-revealed abundance of endogenous auxins and synthetic isomers was validated by liquid chromatography-mass spectrometry (LC-MS). Our results demonstrate that DESI-IM-MSI could be used as a robust technique for detecting endogenous and exogenous isomers and provide a spatiotemporal evaluation of hormonomics profiles in plants.
PMID: 37872415
Planta , IF:4.116 , 2023 Oct , V258 (6) : P108 doi: 10.1007/s00425-023-04262-5
Zoom-in to molecular mechanisms underlying root growth and function under heterogeneous soil environment and abiotic stresses.
ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India. Monika.Dalal@icar.gov.in.; ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.; Department of Biosciences, Durham University, Durham, DH1 3LE, UK.; Graduate School of Science and Technology, Nara Institute of Science and Technology, Takayama 8916-5, Ikoma, Nara, 630-0192, Japan.
The review describes tissue-specific and non-cell autonomous molecular responses regulating the root system architecture and function in plants. Phenotypic plasticity of roots relies on specific molecular and tissue specific responses towards local and microscale heterogeneity in edaphic factors. Unlike gravitropism, hydrotropism in Arabidopsis is regulated by MIZU KUSSIE1 (MIZ1)-dependent asymmetric distribution of cytokinin and activation of Arabidopsis response regulators, ARR16 and ARR17 on the lower water potential side of the root leading to higher cell division and root bending. The cortex specific role of Abscisic acid (ABA)-activated SNF1-related protein kinase 2.2 (SnRK2.2) and MIZ1 in elongation zone is emerging for hydrotropic curvature. Halotropism involves clathrin-mediated internalization of PIN FORMED 2 (PIN2) proteins at the side facing higher salt concentration in the root tip, and ABA-activated SnRK2.6 mediated phosphorylation of cortical microtubule-associated protein Spiral2-like (SP2L) in the root transition zone, which results in anisotropic cell expansion and root bending away from higher salt. In hydropatterning, Indole-3-acetic acid 3 (IAA3) interacts with SUMOylated-ARF7 (Auxin response factor 7) and prevents expression of Lateral organ boundaries-domain 16 (LBD16) in air-side of the root, while on wet side of the root, IAA3 cannot repress the non-SUMOylated-ARF7 thereby leading to LBD16 expression and lateral root development. In root vasculature, ABA induces expression of microRNA165/microRNA166 in endodermis, which moves into the stele to target class III Homeodomain leucine zipper protein (HD-ZIP III) mRNA in non-cell autonomous manner. The bidirectional gradient of microRNA165/6 and HD-ZIP III mRNA regulates xylem patterning under stress. Understanding the tissue specific molecular mechanisms regulating the root responses under heterogeneous and stress environments will help in designing climate-resilient crops.
PMID: 37898971
Genes (Basel) , IF:4.096 , 2023 Oct , V14 (10) doi: 10.3390/genes14101929
Manifestation of Triploid Heterosis in the Root System after Crossing Diploid and Autotetraploid Energy Willow Plants.
Institute of Plant Biology, HUN-REN Biological Research Centre, 6726 Szeged, Hungary.; Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Prague, Czech Republic.; Laboratory of Cellular Imaging, HUN-REN Biological Research Centre, 6726 Szeged, Hungary.; Hungarian Centre of Excellence for Molecular Medicine (HCEMM) Nonprofit Ltd., 6728 Szeged, Hungary.
Successful use of woody species in reducing climatic and environmental risks of energy shortage and spreading pollution requires deeper understanding of the physiological functions controlling biomass productivity and phytoremediation efficiency. Targets in the breeding of energy willow include the size and the functionality of the root system. For the combination of polyploidy and heterosis, we have generated triploid hybrids (THs) of energy willow by crossing autotetraploid willow plants with leading cultivars (Tordis and Inger). These novel Salix genotypes (TH3/12, TH17/17, TH21/2) have provided a unique experimental material for characterization of Mid-Parent Heterosis (MPH) in various root traits. Using a root phenotyping platform, we detected heterosis (TH3/12: MPH 43.99%; TH21/2: MPH 26.93%) in the size of the root system in soil. Triploid heterosis was also recorded in the fresh root weights, but it was less pronounced (MPH%: 9.63-19.31). In agreement with root growth characteristics in soil, the TH3/12 hybrids showed considerable heterosis (MPH: 70.08%) under in vitro conditions. Confocal microscopy-based imaging and quantitative analysis of root parenchyma cells at the division-elongation transition zone showed increased average cell diameter as a sign of cellular heterosis in plants from TH17/17 and TH21/2 triploid lines. Analysis of the hormonal background revealed that the auxin level was seven times higher than the total cytokinin contents in root tips of parental Tordis plants. In triploid hybrids, the auxin-cytokinin ratios were considerably reduced in TH3/12 and TH17/17 roots. In particular, the contents of cytokinin precursor, such as isopentenyl adenosine monophosphate, were elevated in all three triploid hybrids. Heterosis was also recorded in the amounts of active gibberellin precursor, GA(19), in roots of TH3/12 plants. The presented experimental findings highlight the physiological basics of triploid heterosis in energy willow roots.
PMID: 37895278
Plant Mol Biol , IF:4.076 , 2023 Oct , V113 (1-3) : P1-17 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
Phytochemistry , IF:4.072 , 2023 Oct , V216 : P113883 doi: 10.1016/j.phytochem.2023.113883
Auxin and light-mediated regulation of growth, morphogenesis, and alkaloid biosynthesis in Crinum x powellii 'Album' callus.
Department of Chemistry, Biochemistry and Physics, Universite du Quebec a Trois-Rivieres, Trois-Rivieres, QC, Canada.; Department of Chemistry, Biochemistry and Physics, Universite du Quebec a Trois-Rivieres, Trois-Rivieres, QC, Canada; Plant Biology Research Group, Trois-Rivieres, Quebec, Canada. Electronic address: Isabel.Desgagne-Penix@uqtr.ca.
Crinum x powellii 'Album' belongs to the Amaryllidaceae medicinal plant family that produces a range of structurally diverse alkaloids with potential therapeutic properties. The optimal conditions for in vitro tissue growth, morphogenesis, and alkaloid biosynthesis remain unclear. Auxin and light play critical roles in regulating plant growth, development, and alkaloid biosynthesis in several Amaryllidaceae plants. Here, we have succeeded in showing, for the first time, that the combination of auxin and light significantly influence C. x powellii "Album" in vitro tissue growth, survival, and morphogenesis compared to individual treatments. Furthermore, this combination also upregulates the expression of alkaloid biosynthetic genes and led to an increase in the content of certain alkaloids, suggesting a positive impact on the defense and therapeutic potential of the calli. Our findings provide insights into the regulation of genes involved in alkaloid biosynthesis in C. x powellii "Album" callus and underline the potential of auxin and light as tools for enhancing their production in plants. This study provides a foundation for further exploration of C. x powellii "Album" calli as a sustainable source of bioactive alkaloids for pharmaceutical and agricultural applications. Furthermore, this study paves the way to the discovery of the biosynthetic pathway of specialized metabolites from C. x powellii "Album", such as cherylline and lycorine.
PMID: 37820888
Phytochemistry , IF:4.072 , 2023 Nov , V215 : P113838 doi: 10.1016/j.phytochem.2023.113838
Allelopathic studies with furanocoumarins isolated from Ducrosia anethifolia. In vitro and in silico investigations to protect legumes, rice and grain crops.
Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/ Republica Saharaui, 7, 11510, Puerto Real (Cadiz), Spain; Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, CCB, Innrain 80/82, 6020, Innsbruck, Austria. Electronic address: Francisco.Rodriguez-Mejias@uibk.ac.at.; Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, CCB, Innrain 80/82, 6020, Innsbruck, Austria; Institute of Pharmacognosy, University of Szeged, Eotvos u. 6, H-6720, Szeged, Hungary; Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SE, 75007, Uppsala, Sweden.; Institute of Pharmacy/Pharmacognosy, Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, CCB, Innrain 80/82, 6020, Innsbruck, Austria.; Institute of Pharmacognosy, University of Szeged, Eotvos u. 6, H-6720, Szeged, Hungary.; Institute of Pharmacognosy, University of Szeged, Eotvos u. 6, H-6720, Szeged, Hungary; Institute of Clinical Pharmacy, University of Szeged, Szikra u. 8, H-6725, Szeged, Hungary.; Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/ Republica Saharaui, 7, 11510, Puerto Real (Cadiz), Spain. Electronic address: rosa.varela@uca.es.; Allelopathy Group, Department of Organic Chemistry, Institute of Biomolecules (INBIO), Campus CEIA3, School of Science, University of Cadiz, C/ Republica Saharaui, 7, 11510, Puerto Real (Cadiz), Spain.
Six different furanocoumarins were isolated from the aerial parts of Ducrosia anethifolia and tested in vitro for plant cell elongation in etiolated wheat coleoptile. They were also tested for their ability to control three different weeds: ribwort plantain, annual ryegrass, and common purslane. These compounds exhibited strong inhibition of plant cell elongation. In the case of (+)-heraclenin, the IC(50) was lower than 20 muM, indicating a better inhibition than the positive control Logran(R). Computational experiments for docking and molecular dynamics revealed for the investigated furanocoumarins bearing an epoxide moiety an improved fitting and stronger interaction with the auxin-like TIR1 ubiquitin ligase. Furthermore, the formed inhibition complex remained also stable during dynamic evaluation. Bidental interaction at the active site, along with an extended hydrogen-bond lifetime, explained the enhanced activity of the epoxides. The in vitro weed bioassay results showed that Plantago lanceolata was the most affected weed for germination, root, and shoot development. In addition, (+)-heraclenin displayed better inhibition values than positive control even at 300 muM concentration.
PMID: 37648046
BMC Genomics , IF:3.969 , 2023 Oct , V24 (1) : P633 doi: 10.1186/s12864-023-09732-4
Genome-wide identification and expression analysis of the NRT genes in Ginkgo biloba under nitrate treatment reveal the potential roles during calluses browning.
State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China.; Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, 210037, China.; State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, Zhejiang, China. 20190024@zafu.edu.cn.
Nitrate is a primary nitrogen source for plant growth, and previous studies have indicated a correlation between nitrogen and browning. Nitrate transporters (NRTs) are crucial in nitrate allocation. Here, we utilized a genome-wide approach to identify and analyze the expression pattern of 74 potential GbNRTs under nitrate treatments during calluses browning in Ginkgo, including 68 NITRATE TRANSPORTER 1 (NRT1)/PEPTIDE TRANSPORTER (PTR) (NPF), 4 NRT2 and 2 NRT3. Conserved domains, motifs, phylogeny, and cis-acting elements (CREs) were analyzed to demonstrate the evolutionary conservation and functional diversity of GbNRTs. Our analysis showed that the NPF family was divided into eight branches, with the GbNPF2 and GbNPF6 subfamilies split into three groups. Each GbNRT contained 108-214 CREs of 19-36 types, especially with binding sites of auxin and transcription factors v-myb avian myeloblastosis viral oncogene homolog (MYB) and basic helix-loop-helix (bHLH). The E(1)X(1)X(2)E(2)R motif had significant variations in GbNPFs, indicating changes in the potential dynamic proton transporting ability. The expression profiles of GbNRTs indicated that they may function in regulating nitrate uptake and modulating the signaling of auxin and polyphenols biosynthesis, thereby affecting browning in Ginkgo callus induction. These findings provide a better understanding of the role of NRTs during NO(3)(-) uptake and utilization in vitro culture, which is crucial to prevent browning and develop an efficient regeneration and suspension production system in Ginkgo.
PMID: 37872493
BMC Genomics , IF:3.969 , 2023 Oct , V24 (1) : P629 doi: 10.1186/s12864-023-09723-5
Genome-wide analysis of PIN genes in cultivated peanuts (Arachis hypogaea L.): identification, subcellular localization, evolution, and expression patterns.
Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China.; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, 261325, China. xiaoqin.liu@pku-iaas.edu.cn.
BACKGROUND: Auxin is an important hormone in plants and the PIN-FORMED (PIN) genes are essential to auxin distribution in growth and developmental processes of plants. Peanut is an influential cash crop, but research into PIN genes in peanuts remains limited. RESULTS: In this study, 16 PIN genes were identified in the genome of cultivated peanut, resolving into four subfamilies. All PIN genes were predicted to be located in the plasma membrane and a subcellular location experiment confirmed this prediction for eight of them. The gene structure, cis-elements in the promoter, and evolutionary relationships were elucidated, facilitating our understanding of peanut PINs and their evolution. In addition, the expression patterns of these PINs in various tissues were analyzed according to a previously published transcriptome dataset and qRT-PCR, which gave us a clear understanding of the temporal and spatial expression of PIN genes in different growth stages and different tissues. The expression trend of homologous genes was similar. AhPIN2A and AhPIN2B exhibited predominant expression in roots. AhPIN1A-1 and AhPIN1B-1 displayed significant upregulation following peg penetration, suggesting a potential close association with peanut pod development. Furthermore, we presented the gene network and gene ontology enrichment of these PINs. Notably, AhABCB19 exhibited a co-expression relationship with AhPIN1A and AhPIN1B-1, with all three genes displaying higher expression levels in peanut pegs and pods. These findings reinforce their potential role in peanut pod development. CONCLUSIONS: This study details a comprehensive analysis of PIN genes in cultivated peanuts and lays the foundation for subsequent studies of peanut gene function and phenotype.
PMID: 37865765
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203647
Gamma-Aminobutyric Acid Supplementation Boosts the Phytohormonal Profile in 'Candidatus Liberibacter asiaticus'-Infected Citrus.
Department of Plant Pathology, Citrus Research and Education Center, University of Florida, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA.; Department of Agricultural Botany, Faculty of Agriculture, Tanta University, Tanta 31527, Egypt.
The devastating citrus disease, Huanglongbing (HLB), is associated with 'Candidatus Liberibacter sp.' and transmitted by citrus psyllids. Unfortunately, HLB has no known sustainable cure yet. Herein, we proposed gamma-aminobutyric acid (GABA) as a potential eco-friendly therapeutic solution to HLB. Herein, we used GC/MS-based targeted metabolomics combined with gene expression to investigate the role of GABA in citrus response against HLB and to better understand its relationship(s) with different phytohormones. GABA supplementation via root drench boosts the accumulation of endogenous GABA in the leaves of both healthy and 'Ca. L. asiaticus'-infected trees. GABA accumulation benefits the activation of a multi-layered defensive system via modulating the phytohormone levels and regulating the expression of their biosynthesis genes and some pathogenesis-related proteins (PRs) in both healthy and 'Ca. L. asiaticus'-infected plants. Moreover, our findings showed that GABA application stimulates auxin biosynthesis in 'Ca. L. asiaticus'-infected plants via the activation of the indole-3-pyruvate (I3PA) pathway, not via the tryptamine (TAM)-dependent pathway, to enhance the growth of HLB-affected trees. Likewise, GABA accumulation was associated with the upregulation of SA biosynthesis genes, particularly the PAL-dependent route, resulting in higher SA levels that activated CsPR1, CsPR2, CsPR5, and CsWRKY70, which are prominent to activation of the SA-mediated pathway. Additionally, higher GABA levels were correlated with an enhanced JA profile and linked with both CsPR3 and CsPR4, which activates the JA-mediated pathway. Collectively, our findings suggest that exogenous GABA application might be a promising alternative and eco-friendly strategy that helps citrus trees battle HLB.
PMID: 37896110
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203638
Hormonal Interplay Leading to Black Knot Disease Establishment and Progression in Plums.
Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada.; Department of Plant Agriculture, University of Guelph, Vineland Station, ON L0R 2E0, Canada.; Faculty of Agricultural and Food Sciences, American University of Beirut, Beirut 1107-2020, Lebanon.
Black Knot (BK) is a deadly disease of European (Prunus domestics) and Japanese (Prunus salicina) plums caused by the hemibiotrophic fungus Apiosporina morbosa. After infection, the appearance of warty black knots indicates a phytohormonal imbalance in infected tissues. Based on this hypothesis, we quantified phytohormones such as indole-3-acetic acid, tryptophan, indoleamines (N-acetylserotonin, serotonin, and melatonin), and cytokinins (zeatin, 6-benzyladenine, and 2-isopentenyladenine) in temporally collected tissues of susceptible and resistant genotypes belonging to European and Japanese plums during of BK progression. The results suggested auxin-cytokinins interplay driven by A. morbosa appears to be vital in disease progression by hampering the plant defense system. Taken together, our results indicate the possibility of using the phytohormone profile as a biomarker for BK resistance in plums.
PMID: 37896101
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203637
The Cytokinins BAP and 2-iP Modulate Different Molecular Mechanisms on Shoot Proliferation and Root Development in Lemongrass (Cymbopogon citratus).
Departamento de Ingenieria Genetica, Cinvestav Irapuato, Km. 9.6 Libramiento Norte Carr. Irapuato-Leon, Irapuato Gto 36824, Mexico.; Red de Estudios Moleculares Avanzados, Unidad de Microscopia Avanzada, Instituto de Ecologia, A.C. INECOL 1975-2023, Carretera antigua a Coatepec 351, Col. El Haya, Xalapa 91073, Mexico.
The known activities of cytokinins (CKs) are promoting shoot multiplication, root growth inhibition, and delaying senescence. 6-Benzylaminopurine (BAP) has been the most effective CK to induce shoot proliferation in cereal and grasses. Previously, we reported that in lemongrass (Cymbopogon citratus) micropropagation, BAP 10 microM induces high shoot proliferation, while the natural CK 6-(gamma,gamma-Dimethylallylamino)purine (2-iP) 10 microM shows less pronounced effects and developed rooting. To understand the molecular mechanisms involved, we perform a protein-protein interaction (PPI) network based on the genes of Brachypodium distachyon involved in shoot proliferation/repression, cell cycle, stem cell maintenance, auxin response factors, and CK signaling to analyze the molecular mechanisms in BAP versus 2-iP plants. A different pattern of gene expression was observed between BAP- versus 2-iP-treated plants. In shoots derived from BAP, we found upregulated genes that have already been demonstrated to be involved in de novo shoot proliferation development in several plant species; CK receptors (AHK3, ARR1), stem cell maintenance (STM, REV and CLV3), cell cycle regulation (CDKA-CYCD3 complex), as well as the auxin response factor (ARF5) and CK metabolism (CKX1). In contrast, in the 2-iP culture medium, there was an upregulation of genes involved in shoot repression (BRC1, MAX3), ARR4, a type A-response regulator (RR), and auxin metabolism (SHY2).
PMID: 37896100
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203628
Unlocking the Multifaceted Mechanisms of Bud Outgrowth: Advances in Understanding Shoot Branching.
National Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an 271018, China.; Plant Sciences, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium.; Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.
Shoot branching is a complex and tightly regulated developmental process that is essential for determining plant architecture and crop yields. The outgrowth of tiller buds is a crucial step in shoot branching, and it is influenced by a variety of internal and external cues. This review provides an extensive overview of the genetic, plant hormonal, and environmental factors that regulate shoot branching in several plant species, including rice, Arabidopsis, tomato, and wheat. We especially highlight the central role of TEOSINTE BRANCHED 1 (TB1), a key gene in orchestrating bud outgrowth. In addition, we discuss how the phytohormones cytokinins, strigolactones, and auxin interact to regulate tillering/branching. We also shed light on the involvement of sugar, an integral component of plant development, which can impact bud outgrowth in both trophic and signaling ways. Finally, we emphasize the substantial influence of environmental factors, such as light, temperature, water availability, biotic stresses, and nutrients, on shoot branching. In summary, this review offers a comprehensive evaluation of the multifaced regulatory mechanisms that underpin shoot branching and highlights the adaptable nature of plants to survive and persist in fluctuating environmental conditions.
PMID: 37896091
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203621
Arabidopsis ASYMMETRIC LEAVES2 and Nucleolar Factors Are Coordinately Involved in the Perinucleolar Patterning of AS2 Bodies and Leaf Development.
Graduate School of Bioscience and Biotechnology, Chubu University, Kasugai 487-8501, Japan.; Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.; Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan.; Department of Biology, Faculty of Agriculture and Life Science, Hirosaki University, Bunkyo-cho, Hirosaki 036-8561, Japan.; Department of Life Sciences, National Cheng Kung University, Tainan City 701, Taiwan.; Division of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan.; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
Arabidopsis ASYMMETRIC LEAVES2 (AS2) plays a key role in the formation of flat symmetric leaves. AS2 represses the expression of the abaxial gene ETTIN/AUXIN RESPONSE FACTOR3 (ETT/ARF3). AS2 interacts in vitro with the CGCCGC sequence in ETT/ARF3 exon 1. In cells of leaf primordia, AS2 localizes at peripheral regions of the nucleolus as two AS2 bodies, which are partially overlapped with chromocenters that contain condensed 45S ribosomal DNA repeats. AS2 contains the AS2/LOB domain, which consists of three sequences conserved in the AS2/LOB family: the zinc finger (ZF) motif, the ICG sequence including the conserved glycine residue, and the LZL motif. AS2 and the genes NUCLEOLIN1 (NUC1), RNA HELICASE10 (RH10), and ROOT INITIATION DEFECTIVE2 (RID2) that encode nucleolar proteins coordinately act as repressors against the expression of ETT/ARF3. Here, we examined the formation and patterning of AS2 bodies made from as2 mutants with amino acid substitutions in the ZF motif and the ICG sequence in cells of cotyledons and leaf primordia. Our results showed that the amino acid residues next to the cysteine residues in the ZF motif were essential for both the formation of AS2 bodies and the interaction with ETT/ARF3 DNA. The conserved glycine residue in the ICG sequence was required for the formation of AS2 bodies, but not for the DNA interaction. We also examined the effects of nuc1, rh10, and rid2 mutations, which alter the metabolism of rRNA intermediates and the morphology of the nucleolus, and showed that more than two AS2 bodies were observed in the nucleolus and at its periphery. These results suggested that the patterning of AS2 bodies is tightly linked to the morphology and functions of the nucleolus and the development of flat symmetric leaves in plants.
PMID: 37896084
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203610
New Insights into the Enhancement of Adventitious Root Formation Using N,N'-Bis(2,3-methylenedioxyphenyl)urea.
Dipartimento di Scienze Chimiche, della Vita e della Sostenibilita Ambientale, Universita di Parma, Parco Area delle Scienze 11/A, 43124 Parma, Italy.; Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Universita di Parma, Parco Area delle Scienze 7/A, 43124 Parma, Italy.; Dipartimento di Scienze degli Alimenti e del Farmaco, Universita di Parma, Parco Area delle Scienze 27/A, 43124 Parma, Italy.; Departamento de Ciencias de la Vida, Universidad de Alcala, 28871 Alcala de Henares, Spain.
Adventitious rooting is a process of postembryonic organogenesis strongly affected by endogenous and exogenous factors. Although adventitious rooting has been exploited in vegetative propagation programs for many plant species, it is a bottleneck for vegetative multiplication of difficult-to-root species, such as many woody species. The purpose of this research was to understand how N,N'-bis-(2,3-methylenedioxyphenyl)urea could exert its already reported adventitious rooting adjuvant activity, starting from the widely accepted knowledge that adventitious rooting is a hormonally tuned progressive process. Here, by using specific in vitro bioassays, histological analyses, molecular docking simulations and in vitro enzymatic bioassays, we have demonstrated that this urea derivative does not interfere with polar auxin transport; it inhibits cytokinin oxidase/dehydrogenase (CKX); and, possibly, it interacts with the apoplastic portion of the auxin receptor ABP1. As a consequence of this dual binding capacity, the lifespan of endogenous cytokinins could be locally increased and, at the same time, auxin signaling could be favored. This combination of effects could lead to a cell fate transition, which, in turn, could result in increased adventitious rooting.
PMID: 37896073
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203586
Influence of Exogenous 24-Epicasterone on the Hormonal Status of Soybean Plants.
VP Kukhar Institute of Bioorganic Chemistry and Petrochemistry, National Academy of Sciences of Ukraine, 02094 Kyiv, Ukraine.; Genie Enzymatique et Cellulaire, UMR CNRS 7025, Universite de Technologie de Compiegne, 60203 Compiegne, France.; Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Kuprevich Str., 5/2, 220141 Minsk, Belarus.; Institute of Experimental Botany, The Czech Academy of Sciences, 16502 Prague, Czech Republic.
Brassinosteroids (BRs) are key phytohormones involved in the regulation of major processes of cell metabolism that guide plant growth. In the past decades, new evidence has made it clear that BRs also play a key role in the orchestration of plant responses to many abiotic and biotic stresses. In the present work, we analyzed the impact of foliar treatment with 24-epicastasterone (ECS) on the endogenous content of major phytohormones (auxins, salicylic acid, jasmonic acid, and abscisic acid) and their intermediates in soybean leaves 7 days following the treatment. Changes in the endogenous content of phytohormones have been identified and quantified by LC/MS. The obtained results point to a clear role of ECS in the upregulation of auxin content (indole-3-acetic acid, IAA) and downregulation of salicylic, jasmonic, and abscisic acid levels. These data confirm that under optimal conditions, ECS in tested concentrations of 0.25 microM and 1 microM might promote growth in soybeans by inducing auxin contents. Benzoic acid (a precursor of salicylic acid (SA)), but not SA itself, has also been highly accumulated under ECS treatment, which indicates an activation of the adaptation strategies of cell metabolism to possible environmental challenges.
PMID: 37896049
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203577
The Effect of Topophysis on the In Vitro Development of Handroanthus guayacan and on Its Metabolism of Meta-Topolin Riboside.
Laboratory for Applied In Vitro Plant Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium.; Integrated Molecular Plant Physiology Research, Dement of Biology, University of Antwerp, Groenenborgerlaan 170, 2020 Antwerp, Belgium.
An important factor affecting the uniformity of in vitro cultures is the topophysical position of the original explant. We investigated this phenomenon in Handroanthus guayacan, a tropical woody tree species. Shoots from a stock culture were separated into upper, middle and basal sections and transferred to a modified MS medium containing meta-topolin-riboside and indole-butyric acid. After 8 weeks, the middle section produced the most shoots, the longest shoots and the highest number of nodes per plant. Shoots derived from the upper section were elongated, but had the shortest internodes, while those from the basal section formed the largest callus. None of the three types of explants rooted during the proliferation phase. The topophysically dependent spatial distribution of endogenous cytokinins and auxins was determined. The topophysical effect observed could not be explained solely by analyzing the endogenous isoprenoid and auxin. However, the metabolism and distribution of the aromatic cytokinin could provide an explanation. The concentration of the meta hydroxy-substituted topolins was highest in shoots derived from the middle section. Aromatic N- and O-glucosides were much more concentrated in the leaves than in the stems. In conclusion, it is recommended to consider the explant's topophysis when developing a multiplication protocol to avoid heterogeneity in an in vitro culture.
PMID: 37896040
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203566
Unraveling the Guardians of Growth: A Comprehensive Analysis of the Aux/IAA and ARF Gene Families in Populus simonii.
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.; Tongliao Forestry and Grassland Science Research Institute, Tongliao 028000, China.; Jilin Provincial Key Laboratory of Tree and Grass Genetics and Breeding, College of Forestry and Grassland Science, Jilin Agricultural University, Changchun 130118, China.; Changling County Front Seven State-Owned Forest Protection Center, Changling 131500, China.
The auxin/indole-3-acetic acid (Aux/IAA) and auxin response factor (ARF) genes are two crucial gene families in the plant auxin signaling pathway. Nonetheless, there is limited knowledge regarding the Aux/IAA and ARF gene families in Populus simonii. In this study, we first identified 33 putative PsIAAs and 35 PsARFs in the Populus simonii genome. Analysis of chromosomal location showed that the PsIAAs and PsARFs were distributed unevenly across 17 chromosomes, with the greatest abundance observed on chromosomes 2. Furthermore, based on the homology of PsIAAs and PsARFs, two phylogenetic trees were constructed, classifying 33 PsIAAs and 35 PsARFs into three subgroups each. Five pairs of PsIAA genes were identified as the outcome of tandem duplication, but no tandem repeat gene pairs were found in the PsARF family. The expression profiling of PsIAAs and PsARFs revealed that several genes exhibited upregulation in different tissues and under various stress conditions, indicating their potential key roles in plant development and stress responses. The variance in expression patterns of specific PsIAAs and PsARFs was corroborated through RT-qPCR analysis. Most importantly, we instituted that the PsIAA7 gene, functioning as a central hub, exhibits interactions with numerous Aux/IAA and ARF proteins. Furthermore, subcellular localization findings indicate that PsIAA7 functions as a protein localized within the nucleus. To conclude, the in-depth analysis provided in this study will contribute significantly to advancing our knowledge of the roles played by PsIAA and PsARF families in both the development of P. simonii tissue and its responses to stress. The insights gained will serve as a valuable asset for further inquiries into the biological functions of these gene families.
PMID: 37896029
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203542
Transcriptome and Proteome Association Analysis to Screen Candidate Genes Related to Salt Tolerance in Reaumuria soongorica Leaves under Salt Stress.
College of Forestry, Gansu Agricultural University, Lanzhou 730070, China.; School of Forestry Engineering, Shandong Agriculture and Engineering University, Jinan 250100, China.
This work aims at studying the molecular mechanisms underlying the response of Reaumuria soongorica to salt stress. We used RNA sequencing (RNA-Seq) and Tandem Mass Tag (TMT) techniques to identify differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in R. soongorica leaves treated with 0, 200, and 500 mM NaCl for 72 h. The results indicated that compared with the 0 mM NaCl treatment group, 2391 and 6400 DEGs were identified in the 200 and 500 mM NaCl treatment groups, respectively, while 47 and 177 DEPs were also identified. Transcriptome and proteome association analysis was further performed on R. soongorica leaves in the 0/500 mM NaCl treatment group, and 32 genes with consistent mRNA and protein expression trends were identified. SYP71, CS, PCC13-62, PASN, ZIFL1, CHS2, and other differential genes are involved in photosynthesis, vesicle transport, auxin transport, and other functions of plants, and might play a key role in the salt tolerance of R. soongorica. In this study, transcriptome and proteome association techniques were used to screen candidate genes associated with salt tolerance in R. soongorica, which provides an important theoretical basis for understanding the molecular mechanism of salt tolerance in R. soongorica and breeding high-quality germplasm resources.
PMID: 37896006
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203525
Simulated Drift of Dicamba and Glyphosate on Coffee Crop.
Institute of Agrarian Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Brazil.
Weed management in areas adjacent to coffee plantations makes herbicide drift a constant concern, especially with the use of nonselective products such as dicamba. The objective of this study was to evaluate the phytotoxic effects of the herbicide dicamba alone and mixed with glyphosate as a result of simulated drift in a coffee-producing area. The study was conducted in duplicate at two different coffee cherry development stages. The study was performed with a randomized block design and a 2 x 5 + 1 factorial scheme with four replications using two herbicide spray solutions (dicamba and dicamba + glyphosate) and five low doses (0.25; 1; 5; 10; and 20%). Additionally, a control treatment without herbicide application was also employed. In this study, we evaluated the phytotoxic damage and biometric and productive parameters. Visual damages were observed with the use of dicamba and dicamba + glyphosate doses reduced by 0.25% to 5% in the first days after application. The main symptoms were new leaf epinasty, changes in the internodal distance, and plagiotropic branch curvature. Low doses led to reduced plant height and branch length. The treatments did not reduce productivity and performance but altered the physical classifications of grains.
PMID: 37895989
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203523
The Developmental Mechanism of the Root System of Cultivated Terrestrial Watercress.
State Key Laboratory of Crop Genetics & Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of China, Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education of China, Nanjing Agricultural University, Nanjing 210095, China.; Anhui Jianghuai Horticulture Seeds Co., Ltd., Hefei 230000, China.; Nanjing Suman Plasma Engineering Research Institute Co., Ltd., Nanjing 211162, China.
A well-developed root system is crucial for the rapid growth, asexual reproduction, and adaptation to the drought environments of the watercress. After analyzing the transcriptome of the watercress root system, we found that a high concentration of auxin is key to its adaptation to dry conditions. For the first time, we obtained DR5::EGFP watercress, which revealed the dynamic distribution of auxin in watercress root development under drought conditions. Via the application of naphthylphthalamic acid (NPA), 4-biphenylboronic acid (BBO), ethylene (ETH), abscisic acid (ABA), and other factors, we confirmed that auxin has a significant impact on the root development of watercress. Finally, we verified the role of auxin in root development using 35S::NoYUC8 watercress and showed that the synthesis of auxin in the root system mainly depends on the tryptophan, phenylalanine, and tyrosine amino acids (TAA) synthesis pathway. After the level of auxin increases, the root system of the watercress develops toward adaptation to dry environments. The formation of root aerenchyma disrupts the concentration gradient of auxin and is a key factor in the differentiation of lateral root primordia and H cells in watercress.
PMID: 37895987
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (20) doi: 10.3390/plants12203521
Total Content of Saponins, Phenols and Flavonoids and Antioxidant and Antimicrobial Activity of In Vitro Culture of Allochrusa gypsophiloides (Regel) Schischk Compared to Wild Plants.
Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan.; Research and Production Center of Microbiology and Virology, Almaty 050010, Kazakhstan.; Faculty of Science, Department of Molecular Biology and Genetics, Mugla University, Mugla 48000, Turkey.; Department of Biology and Ecology, Faculty of Nature and Technology, University of Odlar Yurdu, AZ1072 Baku, Azerbaijan.
Allochrusa gypsophiloides is a rare Central Asian species, a super-producer of triterpene saponins with pharmacological and technical value. In this work, a comparative evaluation of the in vitro culture of adventitious roots (ARs), in vitro adventitious microshoots (ASs), natural roots and aboveground parts of wild plants from Kazakhstan to define the total saponin (TS), phenol (TP) and flavonoid (TF) content, as well as antioxidant (AOA) and antimicrobial activity, is presented for the first time. In the AR culture, growth index (GI), TS, TP and TF were evaluated on days 25, 45 and 60 of cultivation on (1/2) MS medium without (control) and with auxin application. It was found out that TS and TF were higher in the in vitro AR culture. The amount of TP and TF are higher in the aerial part of vegetative plants with maximum AOA. The concentration of the extract required to inhibit 50% of 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical formation (ICO(50)) in extracts from natural material negatively correlated with TS, TP, TF and in the in vitro AR culture with TF. Control extracts from the in vitro AR culture with high TS levels showed growth-inhibitory activity against S. thermophillus, S. cerevisiae and C. albicans. The influence shares of medium composition factor, cultivation duration factor and their interaction with GI, TS, TP and TF were determined. The in vitro AR culture is promising for obtaining triterpene saponins TSR with high antibacterial and antifungal activity, and the in vitro ASs culture-for shoot multiplication with antioxidant properties.
PMID: 37895985
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (19) doi: 10.3390/plants12193475
Advances in Roles of Salicylic Acid in Plant Tolerance Responses to Biotic and Abiotic Stresses.
School of Biology and Food, Shangqiu Normal University, Shangqiu 476000, China.; Key Laboratory on Agricultural Microorganism Resources Development of Shangqiu, Shangqiu 476000, China.; Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Yancheng Teachers University, Yancheng 224002, China.; Salt-Soil Agricultural Center, Institute of Agricultural Resources and Environment, Jiangsu Academy of Agriculture Sciences (JAAS), Nanjing 210014, China.
A multitude of biotic and abiotic stress factors do harm to plants by bringing about diseases and inhibiting normal growth and development. As a pivotal signaling molecule, salicylic acid (SA) plays crucial roles in plant tolerance responses to both biotic and abiotic stresses, thereby maintaining plant normal growth and improving yields under stress. In view of this, this paper mainly discusses the role of SA in both biotic and abiotic stresses of plants. SA regulates the expression of genes involved in defense signaling pathways, thus enhancing plant immunity. In addition, SA mitigates the negative effects of abiotic stresses, and acts as a signaling molecule to induce the expression of stress-responsive genes and the synthesis of stress-related proteins. In addition, SA also improves certain yield-related photosynthetic indexes, thereby enhancing crop yield under stress. On the other hand, SA acts with other signaling molecules, such as jasmonic acid (JA), auxin, ethylene (ETH), and so on, in regulating plant growth and improving tolerance under stress. This paper reviews recent advances in SA's roles in plant stress tolerance, so as to provide theoretical references for further studies concerning the decryption of molecular mechanisms for SA's roles and the improvement of crop management under stress.
PMID: 37836215
Plants (Basel) , IF:3.935 , 2023 Oct , V12 (19) doi: 10.3390/plants12193470
Genetic Polymorphism in the Amaranthaceae Species in the Context of Stress Tolerance.
Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Al-Farabi 71, Almaty 050040, Kazakhstan.; Institute of Genetic and Physiology, Al-Farabi 93, Almaty 050040, Kazakhstan.; National Center for Biotechnology, Qorghalzhyn 13, Astana 010000, Kazakhstan.
The adaptive potential and biochemical properties of the Amaranthaceae species make them promising for introduction into agriculture and markets, particularly in arid conditions. Molecular genetic polymorphism analysis is the most powerful tool for studying plant resources; therefore, the current study aimed to investigate the polymorphisms of allelic variations in the ARF and SOD gene families, as well as the genetic diversity of six Amaranthaceae species, using retrotransposon-based fingerprinting with the multi-locus EPIC-PCR profiling approach. Additionally, the iPBS PCR amplification was employed for genome profiling, revealing variations in genetic diversity among the studied Amaranthaceae samples. The observed genetic diversity in Amaranthaceae species contributes to their enhanced tolerance to adverse environmental conditions. The knowledge about the genetic diversity of genes crucial in plant development and stress resistance can be useful for the genetic improvement of cultivated Amaranthaceae species.
PMID: 37836210
IUBMB Life , IF:3.885 , 2023 Oct , V75 (10) : P880-892 doi: 10.1002/iub.2761
The long intergenic noncoding RNA ARES modulates root architecture in Arabidopsis.
Institute of Plant Sciences Paris Saclay IPS2, CNRS, INRA, Universite Evry, Universite Paris-Saclay, Gif-sur-Yvette, France.; Institute of Plant Sciences Paris-Saclay IPS2, Universite de Paris, Gif-sur-Yvette, France.; Instituto de Agrobiotecnologia del Litoral, CONICET, Universidad Nacional del Litoral, Santa Fe, Argentina.; Institute for Signals, Systems and Computational Intelligence, sinc(i) CONICET-Universidad Nacional del Litoral, Santa Fe, Argentina.
Long noncoding RNAs (lncRNAs) have emerged as important regulators of gene expression in plants. They have been linked to a wide range of molecular mechanisms, including epigenetics, miRNA activity, RNA processing and translation, and protein localization or stability. In Arabidopsis, characterized lncRNAs have been implicated in several physiological contexts, including plant development and the response to the environment. Here we searched for lncRNA loci located nearby key genes involved in root development and identified the lncRNA ARES (AUXIN REGULATOR ELEMENT DOWNSTREAM SOLITARYROOT) downstream of the lateral root master gene IAA14/SOLITARYROOT (SLR). Although ARES and IAA14 are co-regulated during development, the knockdown and knockout of ARES did not affect IAA14 expression. However, in response to exogenous auxin, ARES knockdown impairs the induction of its other neighboring gene encoding the transcription factor NF-YB3. Furthermore, knockdown/out of ARES results in a root developmental phenotype in control conditions. Accordingly, a transcriptomic analysis revealed that a subset of ARF7-dependent genes is deregulated. Altogether, our results hint at the lncRNA ARES as a novel regulator of the auxin response governing lateral root development, likely by modulating gene expression in trans.
PMID: 37409758
Gene , IF:3.688 , 2023 Dec , V888 : P147758 doi: 10.1016/j.gene.2023.147758
Cloning and functional analysis prohibitins protein-coding gene EuPHB1 in Eucommia ulmoides Oliver.
The 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, China.; Guizhou Plant Conservation Technology Center, Biotechnology Institute of Guizhou, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China. Electronic address: dgzhao@gzu.edu.cn.
As multifunctional proteins, prohibitins(PHBs) participate in many cellular processes and play essential roles in organisms. In this study, using rapid amplification of cDNA end (RACE) technology, EuPHB1 was cloned from Eucommia ulmoides Oliver (E. ulmoides). A subcellular localization assay preliminarily located EuPHB1 in mitochondria. Then EuPHB1 was transformed into tobacco, and phenotype analyses showed that overexpression of EuPHB1 caused leaves to become chlorotic and shrivel. Furthermore, genes related to hormone and auxin signal transduction, auxin binding, and transport, such as ethylene-responsive transcription factor CRF4-like and ABC transporter B family member 11-like, were significantly inhibited in response to EuPHB1 overexpression. Its overexpression disturbs the original signal transduction pathway, thus causing the corresponding phenotypic changes in transgenic tobacco. Indeed, such overexpression caused fading of palisade tissue and an increase in the number of certain mesophyll cells. It also increased adenosine triphosphate (ATP) synthase activity, mitochondrial membrane potential, ATP content, and reactive oxygen species (ROS) levels in cells. Our results suggest that EuPHB1 expression promotes cellular energy metabolism by accelerating the oxidative phosphorylation of the mitochondrial respiratory chain. Elevated levels of EuPHB1 in the mitochondria, which helps supply the extra energy required to support rapid rates of cell division.
PMID: 37661028
J Sci Food Agric , IF:3.638 , 2023 Oct , V103 (13) : P6640-6653 doi: 10.1002/jsfa.12760
Gamma irradiation delays tomato (Solanum lycopersicum) ripening by inducing transcriptional changes.
Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup-si, Republic of Korea.; Department of Food Science and Technology, Graduate School of Chonnam National University, Gwangju, Republic of Korea.; Center for Industrialization of Agricultural and Livestock Microorganisms, Jeongeup-si, Republic of Korea.
BACKGROUND: Tomato (Solanum lycopersicum) has a relatively short shelf life as a result of rapid ripening, limiting its transportability and marketability. Recently, gamma irradiation has emerged as a viable method for delaying tomato fruit ripening. Although few studies have shown that gamma irradiation delays the ripening of tomatoes, the underlying mechanism remains unknown. Therefore, the present study aimed to examine the effects of gamma irradiation on tomato fruit ripening and the underlying mechanisms using transcriptomics. RESULTS: Following gamma irradiation, the total microbial count, weight loss, and decay rate of tomatoes significantly reduced during storage. Furthermore, the redness (a*), color change (∆E), and lycopene content of gamma-irradiated tomatoes decreased in a dose-dependent manner during storage. Moreover, gamma irradiation significantly upregulated the expression levels of genes associated with DNA, chloroplast, and oxidative damage repairs, whereas those of ethylene and auxin signaling-, ripening-, and cell wall metabolism-related, as well as carotenoid genes, were downregulated. CONCLUSION: Gamma irradiation effectively delayed ripening by downregulating the expression of ripening-related genes and inhibiting microbial growth, which prevented decay and prolonged the shelf life of tomatoes. (c) 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
PMID: 37267467
World J Microbiol Biotechnol , IF:3.312 , 2023 Oct , V39 (12) : P351 doi: 10.1007/s11274-023-03809-8
Molecular characterization of vermicompost-derived IAA-releasing bacterial isolates and assessment of their impact on the root improvement of banana during primary hardening.
Division of Agricultural Biotechnology, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India.; Division of Rural Development, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India.; Department of Agricultural Biotechnology, Faculty of Agriculture, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India.; Division of Agricultural Biotechnology, School of Agriculture and Rural Development, Ramakrishna Mission Vivekananda Educational and Research Institute, Ramakrishna Mission Ashrama, Narendrapur, Kolkata, India. syandanssr@gmail.com.
The hardening step of micropropagation is crucial to make the in vitro raised plants mature and further enhancing their survivability in the external environment. Auxin regulates various root physiological parameters in plant systems. Therefore, the present study aimed to assess the impact of three vermicompost-derived IAA-releasing microbial strains, designated S1, S2, and S3, as biofertilizers on in vitro raised banana plantlets during primary hardening. The High-Performance Thin-Layer Chromatography (HPTLC) analysis of these strains revealed a higher IAA content for S1 and S2 than that of S3 after 144 h of incubation. In total, seven different treatments were applied to banana plantlets, and significant variations were observed in all plant growth parameters for all treatments except autoclaved cocopeat (100%) mixed with autoclaved vermicompost (100%) at a 1:1 ratio. Among these treatments, the application of S3 biofertilizer: autoclaved cocopeat (1:1), followed by S2 biofertlizer: autoclaved cocopeat (1:1), was found to be better than other treatments for root numbers per plant, root length per plant, root volume, and chlorophyll content. These findings have confirmed the beneficial effects of microbial strains on plant systems and propose a link between root improvement and bacterial auxin. Further, these strains were identified at the molecular level as Bacillus sp. As per our knowledge, this is the first report of Bacillus strains isolated from vermicompost and applied as biofertilizer along with cocopeat for the primary hardening of banana. This unique approach may be adopted to improve the quality of plants during hardening, which increases their survival under abiotic stresses.
PMID: 37864056
Funct Plant Biol , IF:3.101 , 2023 Oct doi: 10.1071/FP23013
Integrated analysis of transcriptomic and proteomic data reveals novel regulators of soybean (Glycine max) hypocotyl development.
Hypocotyl elongation directly affects the seedling establishment and soil-breaking after germination. In soybean (Glycine max), the molecular mechanisms regulating hypocotyl development remain largely elusive. To decipher the regulatory landscape, we conducted proteome and transcriptome analysis of soybean hypocotyl samples at different development stages. Our results showed that during hypocotyl development, many proteins were with extreme high translation efficiency (TE) and may act as regulators. These potential regulators include multiple peroxidases and cell wall reorganisation related enzymes. Peroxidases may produce ROS including H2O2. Interestingly, exogenous H2O2 application promoted hypocotyl elongation, supporting peroxidases as regulators of hypocotyl development. However, a vast variety of proteins were shown to be with dramatically changed TE during hypocotyl development, including multiple phytochromes, plasma membrane intrinsic proteins (PIPs) and aspartic proteases. Their potential roles in hypocotyl development were confirmed by that ectopic expression of GmPHYA1 and GmPIP1-6 in Arabidopsis thaliana affected hypocotyl elongation. In addition, the promoters of these potential regulatory genes contain multiple light/gibberellin/auxin responsive elements, while the expression of some members in hypocotyls was significantly regulated by light and exogenous auxin/gibberellin. Overall, our results revealed multiple novel regulatory factors of soybean hypocotyl elongation. Further research on these regulators may lead to new approvals to improve soybean hypocotyl traits.
PMID: 37866377
Plant Biol (Stuttg) , IF:3.081 , 2023 Oct , V25 (6) : P981-993 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
Int J Syst Evol Microbiol , IF:2.747 , 2023 Oct , V73 (10) doi: 10.1099/ijsem.0.006119
Pseudomonas hormoni sp. nov., a plant hormone producing bacterium isolated from Arctic grass, Ellesmere Island, Canada.
Department of Environmental Science, Aarhus University, Roskilde, Denmark.; Department of Applied Biology and Food, University of Buenos Aires, Buenos Aires, Argentina.; Biology Department, University of British Columbia, Vancouver, Canada.
Bacterial strain G20-18(T) was previously isolated from the rhizosphere of an Arctic grass on Ellesmere Island, Canada and was characterized and described as Pseudomonas fluorescens. However, new polyphasic analyses coupled with phenotypic, phylogenetic and genomic analyses reported here demonstrate that the affiliation to the species P. fluorescens was incorrect. The strain is Gram-stain-negative, rod-shaped, aerobic and displays growth at 5-25 degrees C (optimum, 20-25 degrees C), at pH 5-9 (optimum, pH 6-7) and with 0-4 % NaCl (optimum, 2 % NaCl). The major fatty acids are C(16 : 0) (35.6 %), C(17 : 0) cyclo omega7c (26.3 %) and summed feature C(18 : 1)/C(18 : 1) omega7c (13.6 %). The respiratory quinones were determined to be Q9 (93.5 %) and Q8 (6.5 %) and the major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Strain G20-18(T) was shown to synthesize cytokinin and auxin plant hormones and to produce 1-aminocyclopropane-1-carboxylate deaminase. The DNA G+C content was determined to be 59.1 mol%. Phylogenetic analysis based on the 16S rRNA gene and multilocus sequence analysis (concatenated 16S rRNA, gyrB, rpoB and rpoD sequences) showed that G20-18(T) was affiliated with the Pseudomonas mandelii subgroup within the genus Pseudomonas. Comparisons of the G20-18(T) genome sequence and related Pseudomonas type strain sequences showed an average nucleotide identity value of
PMID: 37889848
J Plant Res , IF:2.629 , 2023 Nov , V136 (6) : P865-877 doi: 10.1007/s10265-023-01494-0
Plasmodesmata callose binding protein 2 contributes to the regulation of cambium/phloem formation and auxin response during the tissue reunion process in incised Arabidopsis stem.
Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.; Department of Biosciences, Teikyo University, Utsunomiya, Tochigi, 320-8551, Japan.; Advanced Instrumental Analysis Center, Teikyo University, Utsunomiya, Tochigi, 320-8551, Japan.; Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.; Institute of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan. iwai.hiroaki.gb@u.tsukuba.ac.jp.
Plants are exposed to a variety of biotic and abiotic stresses, including wounding at the stem. The healing process (tissue reunion) begins immediately after stem wounding. The plant hormone auxin plays an important role during tissue reunion. In decapitated stems, auxin transport from the shoot apex is reduced and tissue reunion does not occur but is restored by application of indole-3-acetic acid (IAA). In this study, we found that plasmodesmata callose binding protein 2 (PDCB2) affects the expansion of the cambium/phloem region via changes in auxin response during the process of tissue reunion. PDCB2 was expressed in the cortex and endodermis on the incised side of stems 1-3 days after incision. PDCB2-knockout plants showed reduced callose deposition at plasmodesmata and DR5::GUS activity in the endodermis/cortex in the upper region of the incision accompanied by an increase in size of the cambium/phloem region during tissue reunion. In addition, PIN(PIN-FORMED)3, which is involved in lateral auxin transport, was induced by auxin in the cambium/phloem and endodermis/cortex in the upper part of the incision in wild type, but its expression of PIN3 was decreased in pdcb2 mutant. Our results suggest that PDCB2 contributes to the regulation of cambium/phloem development via auxin response.
PMID: 37707645
3 Biotech , IF:2.406 , 2023 Oct , V13 (10) : P336 doi: 10.1007/s13205-023-03751-4
Nanoparticle-mediated amelioration of drought stress in plants: a systematic review.
Department of Plant Sciences, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India. GRID: grid.411639.8. ISNI: 0000 0001 0571 5193; Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India. GRID: grid.411639.8. ISNI: 0000 0001 0571 5193; Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India. GRID: grid.411639.8. ISNI: 0000 0001 0571 5193; Department of Public Health Genomics, Manipal School of Life Sciences, Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India. GRID: grid.411639.8. ISNI: 0000 0001 0571 5193
Drought stress remains one of the most detrimental environmental constraints that hampers plant growth and development resulting in reduced yield and leading to economic losses. Studies have highlighted the beneficial role of carbon-based nanomaterials (NMs) such as multiwalled carbon nanotubes (MWNTs), single-walled carbon nanotubes (SWNTs), graphene, fullerene, and metal-based nanoparticles (NPs) (Ag, Au, Cu, Fe(2)O(3), TiO(2), and ZnO) in plants under unfavorable conditions such as drought. NPs help plants cope with drought by improving plant growth indices and enhancing biomass. It improves water and nutrient uptake and utilization. It helps retain water by altering the cell walls and regulating stomatal closure. The photosynthetic parameters in NP-treated plants reportedly improved with the increase in pigment content and rate of photosynthesis. Due to NP exposure, the activation of enzymatic and nonenzymatic antioxidants has reportedly improved. These antioxidants play a significant role in the defense system against stress. Studies have reported the accumulation of osmolytes and secondary metabolites. Osmolytes scavenge reactive oxygen species, which can cause oxidative stress in plants. Secondary metabolites are involved in the water retention process, thus improving plant coping strategies with stress. The deleterious effects of drought stress are alleviated by reducing malondialdehyde resulting from lipid peroxidation. Reactive oxygen species accumulation is also controlled with NP treatment. Furthermore, NPs have been reported to regulate the expression of drought-responsive genes and the biosynthesis of phytohormones such as abscisic acid, auxin, gibberellin, and cytokinin, which help plants defend against drought stress. This study reviewed 72 journal articles from 192 Google Scholar, ScienceDirect, and PubMed papers. In this review, we have discussed the impact of NP treatment on morphological, physio-biochemical, and molecular responses in monocot and dicot plants under drought conditions with an emphasis on NP uptake, transportation, and localization.
PMID: 37693636
Mol Biol Rep , IF:2.316 , 2023 Oct , V50 (10) : P7995-8003 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
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2270835 doi: 10.1080/15592324.2023.2270835
Quercetin induces pathogen resistance through the increase of salicylic acid biosynthesis in Arabidopsis.
Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Republic of Korea.
Quercetin is a flavonol belonging to the flavonoid group of polyphenols. Quercetin is reported to have a variety of biological functions, including antioxidant, pigment, auxin transport inhibitor and root nodulation factor. Additionally, quercetin is known to be involved in bacterial pathogen resistance in Arabidopsis through the transcriptional increase of pathogenesis-related (PR) genes. However, the molecular mechanisms underlying how quercetin promotes pathogen resistance remain elusive. In this study, we showed that the transcriptional increases of PR genes were achieved by the monomerization and nuclear translocation of nonexpressor of pathogenesis-related proteins 1 (NPR1). Interestingly, salicylic acid (SA) was approximately 2-fold accumulated by the treatment with quercetin. Furthermore, we showed that the increase of SA biosynthesis by quercetin was induced by the transcriptional increases of typical SA biosynthesis-related genes. In conclusion, this study strongly suggests that quercetin induces bacterial pathogen resistance through the increase of SA biosynthesis in Arabidopsis.
PMID: 37902267
Plant Signal Behav , IF:2.247 , 2023 Dec , V18 (1) : P2261744 doi: 10.1080/15592324.2023.2261744
The HOS1-PIF4/5 module controls callus formation in Arabidopsis leaf explants.
Department of Chemistry, Seoul National University, Seoul, Korea.; Research Institute of Basic Sciences, Seoul National University, Seoul, Korea.; Plant Genomics and Breeding Institute, Seoul National University, Seoul, Korea.
A two-step plant regeneration has been widely exploited to genetic manipulation and genome engineering in plants. Despite technical importance, understanding of molecular mechanism underlying in vitro plant regeneration remains to be fully elucidated. Here, we found that the HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 1 (HOS1)-PHYTOCHROME INTERACTING FACTOR 4/5 (PIF4/5) module participates in callus formation. Consistent with the repressive role of HOS1 in PIF transcriptional activation activity, hos1-3 mutant leaf explants exhibited enhanced callus formation, whereas pif4-101 pif5-3 mutant leaf explants showed reduced callus size. The HOS1-PIF4/5 function would be largely dependent on auxin biosynthesis and signaling, which are essential for callus initiation and proliferation. Our findings suggest that the HOS1-PIF4/5 module plays a pivotal role in auxin-dependent callus formation in Arabidopsis.
PMID: 37747842
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
Plant Commun , 2023 Oct : P100738 doi: 10.1016/j.xplc.2023.100738
Enhancing Wheat Regeneration and Genetic Transformation through Overexpression of TaLAX1.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China.; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, Shandong, China. Electronic address: suyh@sdau.edu.cn.
In the realm of genetically transformed crops, the process of plant regeneration holds utmost significance. However, the low regeneration efficiency observed in several wheat varieties currently restricts the application of genetic transformation for gene function analysis and improved crop production. This research delves into the exploration of TaLAX PANICLE1 (TaLAX1) overexpression, which remarkably enhances regeneration efficiency, thereby boosting genetic transformation and genome editing in wheat. Particularly noteworthy is the substantial increase in regeneration efficiency of common wheat varieties, previously regarded as recalcitrant to genetic transformation. Furthermore, our study identifies heightened expression of TaGROWTH-REGULATING FACTOR (TaGRF) genes, alongside their co-factor, TaGRF-INTERACTING FACTOR 1 (TaGIF1), enhanced cytokinin accumulation and auxin response, which may play a pivotal role in the improved regeneration and transformation observed in TaLAX1-overexpressing wheat plants. Remarkably, the overexpression of TaLAX1 homologs also exhibits a significant increase in regeneration efficiency for maize and soybean, suggesting that both monocotyledonous and dicotyledonous crops can benefit from this enhancement. Through our findings, we shed light on a gene that enhances wheat genetic transformation and elucidate molecular mechanisms that potentially underlie wheat regeneration.
PMID: 37897039
Adv Biol (Weinh) , 2023 Oct : Pe2300410 doi: 10.1002/adbi.202300410
A Single-Nucleus Resolution Atlas of Transcriptome and Chromatin Accessibility for Peanut (Arachis Hypogaea L.) Leaves.
Guangdong Provincial Key Laboratory of Crop Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, 510640, China.; Rice Research Institute of Heilongjiang Academy of Agriculture Sciences, Heilongjiang Province, Jiamusi, 154026, China.; USDA-ARS, Crop Genetics and Breeding Research Unit, Department of Plant Pathology, University of Georgia, Tifton, GA, 31793, USA.; State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University (MU), Murdoch, Western Australia, 6150, Australia.; College of Agriculture, South China Agriculture University, Guangzhou, Guangdong Province, 510642, China.
The peanut is an important worldwide cash-crop for edible oil and protein. However, the kinetic mechanisms that determine gene expression and chromatin accessibility during leaf development in peanut represented allotetraploid leguminous crops are poorly understood at single-cell resolution. Here, a single-nucleus atlas of peanut leaves is developed by simultaneously profiling the transcriptome and chromatin accessibility in the same individual-cell using fluorescence-activated sorted single-nuclei. In total, 5930 cells with 50 890 expressed genes are classified into 18 cell-clusters, and 5315 chromatin fragments are enriched with 26 083 target genes in the chromatin accessible landscape. The developmental trajectory analysis reveals the involvement of the ethylene-AP2 module in leaf cell differentiation, and cell-cycle analysis demonstrated that genome replication featured in distinct cell-types with circadian rhythms transcription factors (TFs). Furthermore, dual-omics illustrates that the fatty acid pathway modulates epidermal-guard cells differentiation and providescritical TFs interaction networks for understanding mesophyll development, and the cytokinin module (LHY/LOG) that regulates vascular growth. Additionally, an AT-hook protein AhAHL11 is identified that promotes leaf area expansion by modulating the auxin content increase. In summary, the simultaneous profiling of transcription and chromatin accessibility landscapes using snRNA/ATAC-seq provides novel biological insights into the dynamic processes of peanut leaf cell development at the cellular level.
PMID: 37828417
BMC Res Notes , 2023 Sep , V16 (1) : P242 doi: 10.1186/s13104-023-06510-z
MicroRNAs associated with AGL6 and IAA9 function in tomato fruit set.
Department of Biotechnology, University of Verona, Verona, 37134, Italy.; Department of Biotechnology, University of Verona, Verona, 37134, Italy. tiziana.pandolfini@univr.it.
OBJECTIVE: Fruit set is triggered after ovule fertilization, as a consequence of the downregulation of ovary growth repressors, such as the tomato transcription factors Auxin/indole-3-acetic acid 9 (IAA9) and Agamous-like 6 (AGL6). In a recent work, we developed a method to silence IAA9 and AGL6 in tomato ovaries using exogenous dsRNAs. We also produced small RNA libraries from IAA9- and AGL6-silenced ovaries to confirm the presence of siRNAs, derived from exogenous dsRNA, targeting IAA9 and AGL6. The objective of this work is to exploit these sRNA libraries to identify miRNAs differentially expressed in IAA9- and AGL6-silenced ovaries as compared with unpollinated control ovaries. RESULTS: We identified by RNA sequencing 125 and 104 known and 509 and 516 novel miRNAs from reads mapped to mature or hairpin sequences, respectively. Of the known miRNAs, 7 and 45 were differentially expressed in IAA9- and AGL6-silenced ovaries compared to control ones, respectively. Six miRNAs were common to both datasets, suggesting their importance in the fruit set process. The expression pattern of two of these (miR393 and miR482e-5p) was verified by stem-loop qRT-PCR. The identified miRNAs represent a pool of regulatory sRNAs potentially involved in tomato fruit initiation.
PMID: 37777779