Nat Rev Mol Cell Biol , IF:94.444 , 2022 May doi: 10.1038/s41580-022-00479-6
Plant hormone regulation of abiotic stress responses.
Institute of Technology, University of Tartu, Tartu, Estonia.; Institut fur Biologie und Biotechnologie der Pflanzen, Westfalische Wilhelms-Universitat Munster, Munster, Germany.; Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.; Graduate School of Environmental and Life Science, Okayama University, Tsushima-Naka, Okayama, Japan.; Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA. jischroeder@ucsd.edu.
Plant hormones are signalling compounds that regulate crucial aspects of growth, development and environmental stress responses. Abiotic stresses, such as drought, salinity, heat, cold and flooding, have profound effects on plant growth and survival. Adaptation and tolerance to such stresses require sophisticated sensing, signalling and stress response mechanisms. In this Review, we discuss recent advances in understanding how diverse plant hormones control abiotic stress responses in plants and highlight points of hormonal crosstalk during abiotic stress signalling. Control mechanisms and stress responses mediated by plant hormones including abscisic acid, auxin, brassinosteroids, cytokinins, ethylene and gibberellins are discussed. We discuss new insights into osmotic stress sensing and signalling mechanisms, hormonal control of gene regulation and plant development during stress, hormone-regulated submergence tolerance and stomatal movements. We further explore how innovative imaging approaches are providing insights into single-cell and tissue hormone dynamics. Understanding stress tolerance mechanisms opens new opportunities for agricultural applications.
PMID: 35513717
Trends Biotechnol , IF:19.536 , 2022 Jun doi: 10.1016/j.tibtech.2022.06.005
Dynamically regulating metabolic fluxes with synthetic metabolons.
Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany. Electronic address: YOZhang@mpimp-golm.mpg.de.; Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria; Max-Planck-Institute of Molecular Plant Physiology, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany. Electronic address: fernie@mpimp-golm.mpg.de.
Enzyme-enzyme assemblies commonly occur naturally, yet the factors that lead to their transient nature are not fully understood. Mitkas et al. have shown how clustered regularly interspaced short palindromic repeats (CRISPR) enzymes and RNA scaffolds allow synthetic enzyme complexes to be formed and disassembled as needed, providing powerful new tools for metabolic engineering.
PMID: 35753889
Trends Plant Sci , IF:18.313 , 2022 Jun , V27 (6) : P588-600 doi: 10.1016/j.tplants.2021.12.011
Tripartite hormonal regulation of plasma membrane H(+)-ATPase activity.
College of Life Sciences, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China. Electronic address: ruimiao@fafu.edu.cn.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Center for Plant Systems Biology, VIB, Ghent, Belgium.; Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas, Universidad Politecnica de Valencia, ES-46022, Valencia, Spain. Electronic address: prodriguez@ibmcp.upv.es.
The enzyme activity of the plasma membrane (PM) proton pump, well known as arabidopsis PM H(+)-ATPase (AHA) in the model plant arabidopsis (Arabidopsis thaliana), is controlled by phosphorylation. Three different classes of phytohormones, brassinosteroids (BRs), abscisic acid (ABA), and auxin regulate plant growth and responses to environmental stimuli, at least in part by modulating the activity of the pump through phosphorylation of the penultimate Thr residue in its carboxyl terminus. Here, we review the current knowledge regarding this tripartite hormonal AHA regulation and highlight mechanisms of activation and deactivation, as well as the significance of hormonal crosstalk. Understanding the complexity of PM H(+)-ATPase regulation in plants might provide new strategies for sustainable agriculture.
PMID: 35034860
Sci Adv , IF:14.136 , 2022 Jun , V8 (25) : Peabm8791 doi: 10.1126/sciadv.abm8791
Phased small RNA-mediated systemic signaling in plants.
Department of Plant Pathology, University of Kentucky, Lexington, KY 40546, USA.; College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing 400715, China.; Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA.
Systemic acquired resistance (SAR) involves the generation of systemically transported signal that arms distal plant parts against secondary infections. We show that two phased 21-nucleotide (nt) trans-acting small interfering RNA3a RNAs (tasi-RNA) derived from TAS3a and synthesized within 3 hours of pathogen infection are the early mobile signal in SAR. TAS3a undergoes alternate polyadenylation, resulting in the generation of 555- and 367-nt transcripts. The 555-nt transcripts likely serves as the sole precursor for tasi-RNAs D7 and D8, which cleave Auxin response factors (ARF) 2, 3, and 4 to induce SAR. Conversely, increased expression of ARF3 represses SAR. Knockout mutations in TAS3a or RNA silencing components required for tasi-RNA biogenesis compromise SAR without altering levels of known SAR-inducing chemicals. Both tasi-ARFs and the 367-nt transcripts are mobile and transported via plasmodesmata. Together, we show that tasi-ARFs are the early mobile signal in SAR.
PMID: 35749505
Sci Adv , IF:14.136 , 2022 Jun , V8 (23) : Peabn0368 doi: 10.1126/sciadv.abn0368
Coactivation of antagonistic genes stabilizes polarity patterning during shoot organogenesis.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.; Beijing International Center for Mathematical Research, Center for Quantitative Biology, Peking University, Beijing 100871, China.; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences, Center for Quantitative Biology, Peking University, Beijing 100871, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
Spatiotemporal patterns of gene expression are instrumental to morphogenesis. A stable pattern interface, often between reciprocal-inhibiting morphogens, must be robustly maintained after initial patterning cues diminish, organ growth, or organ geometry changes. In plants, floral and leaf primordia obtain the adaxial-abaxial pattern at the shoot apical meristem periphery. However, it is unknown how the pattern is maintained after primordia have left the shoot apex. Here, through a combination of computational simulations, time-lapse imaging, and genetic analysis, we propose a model in which auxin simultaneously promotes both adaxial and abaxial domains of expression. Furthermore, we identified multilevel feedback regulation of auxin signaling to refine the spatiotemporal patterns. Our results demonstrate that coactivation by auxin determines and stabilizes antagonistic adaxial-abaxial patterning during aerial organ formation.
PMID: 35675392
Mol Plant , IF:13.164 , 2022 Jun , V15 (6) : P973-990 doi: 10.1016/j.molp.2022.04.009
Coordination of plant growth and abiotic stress responses by tryptophan synthase beta subunit 1 through modulation of tryptophan and ABA homeostasis in Arabidopsis.
State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.; State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China.; State Key Laboratory of Hybrid Rice, College of Life Sciences, Renmin Hospital of Wuhan University, Wuhan University, Wuhan 430072, China. Electronic address: yingtlu@whu.edu.cn.
To adapt to changing environments, plants have evolved elaborate regulatory mechanisms balancing their growth with stress responses. It is currently unclear whether and how the tryptophan (Trp), the growth-related hormone auxin, and the stress hormone abscisic acid (ABA) are coordinated in this trade-off. Here, we show that tryptophan synthase beta subunit 1 (TSB1) is involved in the coordination of Trp and ABA, thereby affecting plant growth and abiotic stress responses. Plants experiencing high salinity or drought display reduced TSB1 expression, resulting in decreased Trp and auxin accumulation and thus reduced growth. In comparison with the wild type, amiR-TSB1 lines and TSB1 mutants exhibited repressed growth under non-stress conditions but had enhanced ABA accumulation and stress tolerance when subjected to salt or drought stress. Furthermore, we found that TSB1 interacts with and inhibits beta-glucosidase 1 (BG1), which hydrolyses glucose-conjugated ABA into active ABA. Mutation of BG1 in the amiR-TSB1 lines compromised their increased ABA accumulation and enhanced stress tolerance. Moreover, stress-induced H2O2 disrupted the interaction between TSB1 and BG1 by sulfenylating cysteine-308 of TSB1, relieving the TSB1-mediated inhibition of BG1 activity. Taken together, we revealed that TSB1 serves as a key coordinator of plant growth and stress responses by balancing Trp and ABA homeostasis.
PMID: 35488429
Dev Cell , IF:12.27 , 2022 May , V57 (9) : P1177-1192.e6 doi: 10.1016/j.devcel.2022.04.013
Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice.
Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina.; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA.; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy.; Department of Biology, Emory University, Atlanta, GA 30322, USA.; Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA.; Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA.; Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands. Electronic address: serres@ucr.edu.
Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
PMID: 35504287
Plant Cell , IF:11.277 , 2022 Jun doi: 10.1093/plcell/koac179
On the trail of auxin: reporters and sensors.
CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
The phytohormone auxin is a master regulator of plant growth and development in response to many endogenous and environmental signals. The underlying coordination of growth is mediated by the formation of auxin maxima and concentration gradients. The visualization of auxin dynamics and distribution can therefore provide essential information to increase our understanding of the mechanisms by which auxin orchestrates these growth and developmental processes. Several auxin reporters have been developed to better perceive the auxin distribution and signaling machinery in vivo. This review focuses on different types of auxin reporters and biosensors used to monitor auxin distribution and its dynamics, as well as auxin signaling, at the cellular and tissue levels in different plant species. We provide a brief history of each reporter and biosensor group and explain their principles and utilities.
PMID: 35708654
Plant Cell , IF:11.277 , 2022 Jun doi: 10.1093/plcell/koac177
The retrograde signalling regulator ANAC017 recruits the MKK9-MPK3/6, ethylene, and auxin signalling pathways to balance mitochondrial dysfunction with growth.
Department of Animal, Plant and Soil Science, La Trobe University, Bundoora, Victoria 3086, Australia.; ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora, Victoria 3086, Australia.
In plant cells, mitochondria are ideally positioned to sense and balance changes in energy metabolism in response to changing environmental conditions. Retrograde signalling from mitochondria to the nucleus is crucial for adjusting the required transcriptional responses. We show that ANAC017, the master regulator of mitochondrial stress, directly recruits a signalling cascade involving the plant hormones ethylene and auxin as well as the MAP KINASE KINASE (MKK) 9 - MAP KINASE (MPK) 3/6 pathway in Arabidopsis thaliana. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) and overexpression demonstrated that ANAC017 directly regulates several genes of the ethylene and auxin pathways, including MKK9, 1-AMINO-CYCLOPROPANE-1-CARBOXYLATE SYNTHASE 2 and YUCCA 5, in addition to genes encoding transcription factors regulating plant growth and stress responses such as BASIC REGION/LEUCINE ZIPPER MOTIF (bZIP) 60, bZIP53, ANAC081/ATAF2 and RADICAL-INDUCED CELL DEATH1. A time-resolved RNA-seq experiment established that ethylene signalling precedes the stimulation of auxin signalling in the mitochondrial stress response, with a large part of the transcriptional regulation dependent on ETHYLENE INSENSITIVE 3. These results were confirmed by mutant analyses. Our findings identify the molecular components controlled by ANAC017, which integrates the primary stress responses to mitochondrial dysfunction with whole plant growth via the activation of regulatory and partly antagonistic feedback loops.
PMID: 35708648
Plant Cell , IF:11.277 , 2022 May doi: 10.1093/plcell/koac146
A molecular framework of ethylene-mediated fruit growth and ripening processes in tomato.
Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology (SUSTech), 518055 Shenzhen, Guangdong, China.; Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Southern University of Science and Technology (SUSTech), 518055 Shenzhen, Guangdong, China.; Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, 401331 Chongqing, China.; Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology (SUSTech), 518055 Shenzhen, Guangdong, China.
Although the role of ethylene in tomato (Solanum lycopersicum) fruit ripening has been intensively studied, its role in tomato fruit growth remains poorly understood. In addition, the relationship between ethylene and the developmental factors NON-RIPENING (NOR) and RIPENING INHIBITOR (RIN) during ripening is under debate. Here, we carried out comprehensive genetic analyses of genome-edited mutants of tomato ETHYLENE INSENSITIVE 2 (SlEIN2), four EIN3-like genes (SlEIL1-4), and three EIN3 BINDING F-box protein genes (SlEBF1-3). Both slein2-1 and the high-order sleil mutant (sleil1 sleil2 sleil3/SlEIL3 sleil4) showed reduced fruit size, mainly due to decreased auxin biosynthesis. During fruit maturation, slein2 mutants displayed the complete cessation of ripening, which was partially rescued by slebf1 but not slebf2 or slebf3. We also discovered that ethylene directly activates the expression of the developmental genes NOR, RIN, and FRUITFULL1 (FUL1) via SlEIL proteins. Indeed, overexpressing these genes partially rescued the ripening defects of slein2-1. Finally, the signal intensity of the ethylene burst during fruit maturation was intimately connected with the progression of full ripeness. Collectively, our work uncovers a critical role of ethylene in fruit growth and supports a molecular framework of ripening control in which the developmental factors NOR, RIN, and FUL1 act downstream of ethylene signaling.
PMID: 35604102
Plant Cell , IF:11.277 , 2022 May , V34 (6) : P2114-2115 doi: 10.1093/plcell/koac087
The sum is greater than the parts: Co-dependent auxin efflux is mediated by ABCBs and PINs.
Assistant Features Editor, The Plant Cell, American Society of Plant Biologists, USA.; Department of Biology, Duke University, Durham, North Carolina, USA.
PMID: 35394537
Plant Cell , IF:11.277 , 2022 May , V34 (6) : P2309-2327 doi: 10.1093/plcell/koac086
Systems approaches reveal that ABCB and PIN proteins mediate co-dependent auxin efflux.
Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, UK.; Department of Biology, University of Fribourg, Fribourg CH-1700, Switzerland.; Centre for Mathematical Medicine and Biology, School of Mathematical Sciences, University of Nottingham, Nottingham NG7 2RD, UK.
Members of the B family of membrane-bound ATP-binding cassette (ABC) transporters represent key components of the auxin efflux machinery in plants. Over the last two decades, experimental studies have shown that modifying ATP-binding cassette sub-family B (ABCB) expression affects auxin distribution and plant phenotypes. However, precisely how ABCB proteins transport auxin in conjunction with the more widely studied family of PIN-formed (PIN) auxin efflux transporters is unclear, and studies using heterologous systems have produced conflicting results. Here, we integrate ABCB localization data into a multicellular model of auxin transport in the Arabidopsis thaliana root tip to predict how ABCB-mediated auxin transport impacts organ-scale auxin distribution. We use our model to test five potential ABCB-PIN regulatory interactions, simulating the auxin dynamics for each interaction and quantitatively comparing the predictions with experimental images of the DII-VENUS auxin reporter in wild-type and abcb single and double loss-of-function mutants. Only specific ABCB-PIN regulatory interactions result in predictions that recreate the experimentally observed DII-VENUS distributions and long-distance auxin transport. Our results suggest that ABCBs enable auxin efflux independently of PINs; however, PIN-mediated auxin efflux is predominantly through a co-dependent efflux where co-localized with ABCBs.
PMID: 35302640
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Jul , V119 (27) : Pe2202669119 doi: 10.1073/pnas.2202669119
The calcium signaling module CaM-IQM destabilizes IAA-ARF interaction to regulate callus and lateral root formation.
Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; National Center for Plant Gene Research, Beijing 100093, China.
Induction of a pluripotent cell mass, called callus, from detached organs is an initial step in in vitro plant regeneration, during which phytohormone auxin-induced ectopic activation of a root developmental program has been shown to be required for subsequent de novo regeneration of shoots and roots. However, whether other signals are involved in governing callus formation, and thus plant regeneration capability, remains largely unclear. Here, we report that the Arabidopsis calcium (Ca(2+)) signaling module CALMODULIN IQ-MOTIF CONTAINING PROTEIN (CaM-IQM) interacts with auxin signaling to regulate callus and lateral root formation. We show that disruption of IQMs or CaMs retards auxin-induced callus and lateral root formation by dampening auxin responsiveness, and that CaM-IQM complexes physically interact with the auxin signaling repressors INDOLE-3-ACETIC ACID INDUCIBLE (IAA) proteins in a Ca(2+)-dependent manner. We further provide evidence that the physical interaction of CaM6 with IAA19 destabilizes the repressive interaction of IAA19 with AUXIN RESPONSE FACTOR 7 (ARF7), and thus regulates auxin-induced callus formation. These findings not only define a critical role of CaM-IQM-mediated Ca(2+) signaling in callus and lateral root formation, but also provide insight into the interplay of Ca(2+) signaling and auxin actions during plant regeneration and development.
PMID: 35763576
Proc Natl Acad Sci U S A , IF:11.205 , 2022 Jun , V119 (25) : Pe2203633119 doi: 10.1073/pnas.2203633119
Indole-3-pyruvic acid regulates TAA1 activity, which plays a key role in coordinating the two steps of auxin biosynthesis.
Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa 244-0813, Japan.; Western Region Agricultural Research Center (WARC), National Agriculture and Food Research Organization (NARO), Kagawa 765-8508, Japan.
Auxin biosynthesis involves two types of enzymes: the Trp aminotransferases (TAA/TARs) and the flavin monooxygenases (YUCCAs). This two-step pathway is highly conserved throughout the plant kingdom and is essential for almost all of the major developmental processes. Despite their importance, it is unclear how these enzymes are regulated and how their activities are coordinated. Here, we show that TAA1/TARs are regulated by their product indole-3-pyruvic acid (IPyA) (or its mimic KOK2099) via negative feedback regulation in Arabidopsis thaliana. This regulatory system also functions in rice and tomato. This negative feedback regulation appears to be achieved by both the reversibility of Trp aminotransferase activity and the competitive inhibition of TAA1 activity by IPyA. The Km value of IPyA is 0.7 microM, and that of Trp is 43.6 microM; this allows IPyA to be maintained at low levels and prevents unfavorable nonenzymatic indole-3-acetic acid (IAA) formation from IPyA in vivo. Thus, IPyA levels are maintained by the push (by TAA1/TARs) and pull (by YUCCAs) of the two biosynthetic enzymes, in which TAA1 plays a key role in preventing the over- or under-accumulation of IPyA. TAA1 prefer Ala among various amino acid substrates in the reverse reaction of auxin biosynthesis, allowing TAA1 to show specificity for converting Trp and pyruvate to IPyA and Ala, and the reverse reaction.
PMID: 35696560
Curr Biol , IF:10.834 , 2022 May , V32 (9) : P1974-1985.e3 doi: 10.1016/j.cub.2022.03.019
Cytokinin promotes growth cessation in the Arabidopsis root.
Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany.; Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany; Physics Department, Technical University Munich, James-Franck-Str. 1/I, 85748 Garching b. Munich, Germany.; Dipartimento di Biologia e Biotecnologie, Laboratory of Functional Genomics and Proteomics of Model Systems, Universita di Roma, Sapienza, via dei Sardi, 70, 00185 Rome, Italy.; Department of Plant-Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany.; Institute for Cell and Interaction Biology, Heinrich-Heine Universitat Dusseldorf, Universitatsstrasse 1, 40225 Dusseldorf, Germany.; Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany; Department of Computational and Systems Biology, John Innes Centre, Norwich NR4 7UH, UK.; Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne Weg 10, 50829 Cologne, Germany. Electronic address: tsiantis@mpipz.mpg.de.
The Arabidopsis root offers good opportunities to investigate how regulated cellular growth shapes different tissues and organs, a key question in developmental biology. Along the root's longitudinal axis, cells sequentially occupy different developmental states. Proliferative meristematic cells give rise to differentiating cells, which rapidly elongate in the elongation zone, then mature and stop growing in the differentiation zone. The phytohormone cytokinin contributes to this zonation by positioning the boundary between the meristem and the elongation zone, called the transition zone. However, the cellular growth profile underlying root zonation is not well understood, and the cellular mechanisms that mediate growth cessation remain unclear. By using time-lapse imaging, genetics, and computational analysis, we analyze the effect of cytokinin on root zonation and cellular growth. We found that cytokinin promotes growth cessation in the distal (shootward) elongation zone in conjunction with accelerating the transition from elongation to differentiation. We estimated cell-wall stiffness by using osmotic treatment experiments and found that cytokinin-mediated growth cessation is associated with cell-wall stiffening and requires the action of an auxin influx carrier, AUX1. Our measurement of growth and cell-wall mechanical properties at a cellular resolution reveal mechanisms via which cytokinin influences cell behavior to shape tissue patterns.
PMID: 35354067
Curr Biol , IF:10.834 , 2022 May , V32 (9) : P1883-1894.e7 doi: 10.1016/j.cub.2022.02.069
Cell-wall damage activates DOF transcription factors to promote wound healing and tissue regeneration in Arabidopsis thaliana.
Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas alle 5, 756 51, Uppsala, Sweden.; Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan.; Independent Junior Research Group - Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany.; The Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.; Independent Junior Research Group - Designer Glycans, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany; Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA.; Department of Biosciences, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan; Advanced Instrumental Analysis Center, Teikyo University, 1-1 Toyosatodai, Utsunomiya 320-8551, Japan.; Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, Almas alle 5, 756 51, Uppsala, Sweden. Electronic address: charles.melnyk@slu.se.
Wound healing is a fundamental property of plants and animals that requires recognition of cellular damage to initiate regeneration. In plants, wounding activates a defense response via the production of jasmonic acid and a regeneration response via the hormone auxin and several ethylene response factor (ERF) and NAC domain-containing protein (ANAC) transcription factors. To better understand how plants recognize damage and initiate healing, we searched for factors upregulated during the horticulturally relevant process of plant grafting and found four related DNA binding with one finger (DOF) transcription factors, HIGH CAMBIAL ACTIVITY2 (HCA2), TARGET OF MONOPTEROS6 (TMO6), DOF2.1, and DOF6, whose expression rapidly activated at the Arabidopsis graft junction. Grafting or wounding a quadruple hca2, tmo6, dof2.1, dof6 mutant inhibited vascular and cell-wall-related gene expression. Furthermore, the quadruple dof mutant reduced callus formation, tissue attachment, vascular regeneration, and pectin methylesterification in response to wounding. We also found that activation of DOF gene expression after wounding required auxin, but hormone treatment alone was insufficient for their induction. However, modifying cell walls by enzymatic digestion of cellulose or pectin greatly enhanced TMO6 and HCA2 expression, whereas genetic modifications to the pectin or cellulose matrix using the PECTIN METHYLESTERASE INHIBITOR5 overexpression line or korrigan1 mutant altered TMO6 and HCA2 expression. Changes to the cellulose or pectin matrix were also sufficient to activate the wound-associated ERF115 and ANAC096 transcription factors, suggesting that cell-wall damage represents a common mechanism for wound perception and the promotion of tissue regeneration.
PMID: 35320706
New Phytol , IF:10.151 , 2022 Jun doi: 10.1111/nph.18317
miR169o and ZmNF-YA13 act in concert to coordinate the expression of ZmYUC1 that determines seed size and weight in maize kernels.
Biotechnology Research Institute, CAAS/Key Laboratory of Agricultural Genomics (Beijing), Ministry of Agriculture, 100081, Beijing, China.; National Nanfan Research Institute (Sanya), 572022, Hainan, China.; National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, China.; College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, 100039, Beijing, China.
* MicroRNAs play key regulatory roles in seed development and emerge as new key targets for engineering grain size and yield. Zma-miRNA169 family is highly expressed during maize seed development, but its functional roles in seed development remain elusive. * Here, we generated zma-miR169o and ZmNF-YA13 transgenic plants. Phenotypic and genetic analyses were performed on these lines. Seed development and auxins contents were investigated. * Overexpression of maize miRNA zma-miR169o increases seed size and weight, whereas the opposite is true when its expression is suppressed. Further studies revealed that zma-miR169 acts by negatively regulating its target gene, a transcription factor ZmNF-YA13 that also plays a key role in determining seed size. We demonstrate that ZmNF-YA13 regulates the expression of the auxin biosynthetic gene ZmYUC1, which modulates auxin levels in the early developing seeds and determines the number of endosperm cells, thereby governing maize seed size and ultimately yield. * Overall, our present study has identified zma-miR169o and ZmNF-YA13 that form a functional module regulating auxin accumulation in maize seeds and playing an important role in determining maize seed size and yield, providing a set of novel molecular tools for yield improvement in molecular breeding and genetic engineering.
PMID: 35713356
New Phytol , IF:10.151 , 2022 Aug , V235 (3) : P1287-1301 doi: 10.1111/nph.18200
Broad-range metalloprotease profiling in plants uncovers immunity provided by defence-related metalloenzyme.
The Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.; Department of Chemistry and the Ineos Oxford Institute for Antimcrobial Research, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.; The Plant Chemetics Laboratory, Max Planck Institute for Plant Breeding Research, Cologne, 50829, Germany.; Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.; Department of Chemistry, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA.
Plants encode > 100 metalloproteases representing > 19 different protein families. Tools to study this large and diverse class of proteases have not yet been introduced into plant research. We describe the use of hydroxamate-based photoaffinity probes to explore plant proteomes for metalloproteases. We detected labelling of 23 metalloproteases in leaf extracts of the model plant Arabidopsis thaliana that belong to nine different metalloprotease families and localize to different subcellular compartments. The probes identified several chloroplastic FtsH proteases, vacuolar aspartyl aminopeptidase DAP1, peroxisomal metalloprotease PMX16, extracellular matrix metalloproteases and many cytosolic metalloproteases. We also identified nonproteolytic metallohydrolases involved in the release of auxin and in the urea cycle. Studies on tobacco plants (Nicotiana benthamiana) infected with the bacterial plant pathogen Pseudomonas syringae uncovered the induced labelling of PRp27, a secreted protein with implicated metalloprotease activity. PRp27 overexpression increases resistance, and PRp27 mutants lacking metal binding site are no longer labelled, but still show increased immunity. Collectively, these studies reveal the power of broad-range metalloprotease profiling in plants using hydroxamate-based probes.
PMID: 35510806
New Phytol , IF:10.151 , 2022 Jul , V235 (2) : P402-419 doi: 10.1111/nph.18159
Auxin response factors are keys to the many auxin doors.
Univ. Grenoble Alpes, CNRS, CEA, INRAE, IRIG-DBSCI-LPCV, 38000, Grenoble, France.; Laboratoire de Reproduction et Developpement des Plantes, ENS de Lyon, UCB Lyon 1, CNRS, INRA, Univ. Lyon, Lyon, France.
In plants, most developmental programs depend on the action of auxin. The best described model of the auxin signaling pathway, which explains most, but not all, of the auxin transcriptional responses, relies on a de-repression mechanism. The auxin/indole-3-acetic acid repressors (Aux/IAAs) interact with the auxin response factors (ARFs), the transcription factors of the auxin signaling pathway, leading to repression of the ARF-controlled genes. Auxin induces Aux/IAA degradation, releases ARFs and activates transcription. However, this elegant model is not suitable for all ARFs. Indeed, in Arabidopsis, which has 22 ARFs, only five of them fit into the model since they are the ones able to interact with Aux/IAAs. The remaining 17 have a limited capacity to interact with the repressors, and their mechanisms of action are still unclear. The differential interactions between ARF and Aux/IAA proteins constitute one of many examples of the biochemical and structural diversification of ARFs that affect their action and therefore affect auxin transcriptional responses. A deeper understanding of the structural properties of ARFs is fundamental to obtaining a better explanation of the action of auxin in plants.
PMID: 35434800
New Phytol , IF:10.151 , 2022 Jun , V234 (5) : P1735-1752 doi: 10.1111/nph.18079
SAV4 is required for ethylene-induced root hair growth through stabilizing PIN2 auxin transporter in Arabidopsis.
School of Life Sciences, Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiang'an South Road, Xiamen, Fujian Province, 361102, China.
Root hair development is regulated by hormonal and environmental cues, such as ethylene and low phosphate. Auxin efflux carrier PIN2 (PIN-FORMED 2) plays an important role in establishing a proper auxin gradient in root tips, which is required for root hair development. Ethylene promotes root hair development through increasing PIN2 abundance in root tips, which subsequently leads to enhanced expression of auxin reporter genes. However, how PIN2 is regulated remains obscure. Here, we report that Arabidopsis thaliana sav4 (shade avoidance 4) mutant exhibits defects in ethylene-induced root hair development and in establishing a proper auxin gradient in root tips. Ethylene treatment increased SAV4 abundance in root tips. SAV4 and PIN2 co-localize to the shootward plasma membrane (PM) of root tip epidermal cells. SAV4 directly interacts with the PIN2 hydrophilic region (PIN2HL) and regulates PIN2 abundance on the PM. Vacuolar degradation of PIN2 is suppressed by ethylene, which was weakened in sav4 mutant. Furthermore, SAV4 affects the formation of PIN2 clusters and its lateral diffusion on the PM. In summary, we identified SAV4 as a novel regulator of PIN2 that enhances PIN2 membrane clustering and stability through direct protein-protein interactions. Our study revealed a new layer of regulation on PIN2 dynamics.
PMID: 35274300
New Phytol , IF:10.151 , 2022 Jun , V234 (5) : P1832-1847 doi: 10.1111/nph.18078
Comparative transcriptomics of fungal endophytes in co-culture with their moss host Dicranum scoparium reveals fungal trophic lability and moss unchanged to slightly increased growth rates.
Department of Biology, Duke University, 130 Science Drive, Durham, NC, 27708, USA.; North Florida Research and Education Center, University of Florida, 155 Research Road, Quincy, FL, 32351, USA.; Biodiversity Research Center, Academia Sinica, 128 Academia Road, Section 2, Taipei, 11529, Taiwan.; Soil and Water Sciences Department, University of Florida, 1692 McCarty Drive, Gainesville, FL, 32611, USA.; School of Plant Sciences and Department of Ecology and Evolutionary Biology, University of Arizona, 1140 E. South Campus Drive, Tucson, AZ, 85721, USA.; Department of Ecology and Evolutionary Biology, University of Tennessee, 1416 Circle Drive, Knoxville, TN, 37996, USA.; Department of Agronomy, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan.
Mosses harbor fungi whose interactions within their hosts remain largely unexplored. Trophic ranges of fungal endophytes from the moss Dicranum scoparium were hypothesized to encompass saprotrophism. This moss is an ideal host to study fungal trophic lability because of its natural senescence gradient, and because it can be grown axenically. Dicranum scoparium was co-cultured with each of eight endophytic fungi isolated from naturally occurring D. scoparium. Moss growth rates, and gene expression levels (RNA sequencing) of fungi and D. scoparium, were compared between axenic and co-culture treatments. Functional lability of two fungal endophytes was tested by comparing their RNA expression levels when colonizing living vs dead gametophytes. Growth rates of D. scoparium were unchanged, or increased, when in co-culture. One fungal isolate (Hyaloscyphaceae sp.) that promoted moss growth was associated with differential expression of auxin-related genes. When grown with living vs dead gametophytes, Coniochaeta sp. switched from having upregulated carbohydrate transporter activity to upregulated oxidation-based degradation, suggesting an endophytism to saprotrophism transition. However, no such transition was detected for Hyaloscyphaceae sp. Individually, fungal endophytes did not negatively impact growth rates of D. scoparium. Our results support the long-standing hypothesis that some fungal endophytes can switch to saprotrophism.
PMID: 35263447
Cold Spring Harb Perspect Biol , IF:10.005 , 2022 May , V14 (5) doi: 10.1101/cshperspect.a039859
Fourteen Stations of Auxin.
Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria.
Auxin has always been at the forefront of research in plant physiology and development. Since the earliest contemplations by Julius von Sachs and Charles Darwin, more than a century-long struggle has been waged to understand its function. This largely reflects the failures, successes, and inevitable progress in the entire field of plant signaling and development. Here I present 14 stations on our long and sometimes mystical journey to understand auxin. These highlights were selected to give a flavor of the field and to show the scope and limits of our current knowledge. A special focus is put on features that make auxin unique among phytohormones, such as its dynamic, directional transport network, which integrates external and internal signals, including self-organizing feedback. Accented are persistent mysteries and controversies. The unexpected discoveries related to rapid auxin responses and growth regulation recently disturbed our contentment regarding understanding of the auxin signaling mechanism. These new revelations, along with advances in technology, usher us into a new, exciting era in auxin research.
PMID: 34400554
Cold Spring Harb Perspect Biol , IF:10.005 , 2022 May , V14 (4) doi: 10.1101/cshperspect.a039933
Auxin in Root Development.
Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom.
Root system architecture is an important determinant of below-ground resource capture and hence overall plant fitness. The plant hormone auxin plays a central role in almost every facet of root development from the cellular to the whole-root-system level. Here, using Arabidopsis as a model, we review the multiple gene signaling networks regulated by auxin biosynthesis, conjugation, and transport that underpin primary and lateral root development. We describe the role of auxin in establishing the root apical meristem and discuss how the tight spatiotemporal regulation of auxin distribution controls transitions between cell division, cell growth, and differentiation. This includes the localized reestablishment of mitotic activity required to elaborate the root system via the production of lateral roots. We also summarize recent discoveries on the effects of auxin and auxin signaling and transport on the control of lateral root gravitropic setpoint angle (GSA), a critical determinant of the overall shape of the root system. Finally, we discuss how environmental conditions influence root developmental plasticity by modulation of auxin biosynthesis, transport, and the canonical auxin signaling pathway.
PMID: 34312248
Plant Biotechnol J , IF:9.803 , 2022 May doi: 10.1111/pbi.13861
The upregulated LsKN1 gene transforms pinnately to palmately lobed leaves through auxin, gibberellin, and leaf dorsiventrality pathways in lettuce.
Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.; Genome Center and Department of Plant Sciences, University of California, Davis, California, 95616, USA.
Leaf shape represents a vital agronomic trait for leafy vegetables such as lettuce. Some lettuce cultivars produce lobed leaves, varying from pinnately to palmately lobed, but the genetic mechanisms remain unclear. In this study, we cloned one major quantitative trait locus (QTL) controlling palmately lobed leaves. The candidate gene, LsKN1, encodes a homeobox transcription factor, and has been shown previously to be critical for the development of leafy heads in lettuce. The LsKN1 allele that is upregulated by the insertion of a transposon promotes the development of palmately lobed leaves. We demonstrated that LsKN1 upregulated LsCUC2 and LsCUC3 through different mechanisms, and their upregulation was critical for the development of palmately lobed leaves. LsKN1 binds the promoter of LsPID to promote auxin biosynthesis, which positively contributes to the development of palmately lobed leaves. In contrast, LsKN1 suppresses GA biosynthesis to promote palmately lobed leaves. LsKN1 also binds to the promoter of LsAS1, a dorsiventrality gene, to downregulate its expression. Overexpression of the LsAS1 gene compromised the effects of the LsKN1 gene changing palmately to pinnately lobed leaves. Our study illustrated that the upregulated LsKN1 gene led to palmately lobed leaves in lettuce by integrating several downstream pathways, including auxin, gibberellin, and leaf dorsiventrality pathways.
PMID: 35634731
Plant Physiol , IF:8.34 , 2022 Jun doi: 10.1093/plphys/kiac288
Initiation of aboveground organ primordia depends on combined action of auxin, ERECTA family genes, and PINOID.
Department of Biochemistry, Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.; UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, Tennessee, USA.
Leaves and flowers are produced by the shoot apical meristem (SAM) at a certain distance from its center, a process that requires the hormone auxin. The amount of auxin and the pattern of its distribution in the initiation zone determine the size and spatial arrangement of organ primordia. Auxin gradients in the SAM are formed by PIN-FORMED (PIN) auxin efflux carriers whose polar localization in the plasma membrane depends on the protein kinase PINOID (PID). Previous work determined that ERECTA (ER) family genes (ERfs) control initiation of leaves. ERfs are plasma membrane receptors that enable cell-to-cell communication by sensing extracellular small proteins from the EPIDERMAL PATTERNING FACTOR/EPF-LIKE (EPF/EPFL) family. Here, we investigated whether ERfs regulate initiation of organs by altering auxin distribution or signaling in Arabidopsis (Arabidopsis thaliana). Genetic and pharmacological data suggested that ERfs do not regulate organogenesis through PINs while transcriptomics data showed ERfs do not alter primary transcriptional responses to auxin. Our results indicated that in the absence of ERf signaling the peripheral zone cells inefficiently initiate leaves in response to auxin signals and that increased accumulation of auxin in the er erecta-like1 (erl1) erl2 SAM can partially rescue organ initiation defects. We propose that both auxin and ERfs are essential for leaf initiation and that they have common downstream targets. Genetic data also indicated that the role of PID in initiation of cotyledons and leaves cannot be attributed solely to regulation of PIN polarity, and PID is likely to have other functions in addition to regulation of auxin distribution.
PMID: 35703946
Plant Physiol , IF:8.34 , 2022 Jun doi: 10.1093/plphys/kiac266
The Brassicaceae Genome Resource (TBGR): a comprehensive genome platform for Brassicaceae plants.
School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei 063210, China.; Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.; School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.; Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE 68588, USA.
The Brassicaceae is an important plant family. We built a user-friendly, web-based, comparative, and functional genomic database, The Brassicaceae Genome Resource (TBGR, http://www.tbgr.org.cn), based on 82 released genomes from 27 Brassicaceae species. The TBGR database contains a large number of important functional genes, including 4,096 glucosinolate genes, 6,625 auxin genes, 13,805 flowering genes, 36,632 resistance genes, 1,939 anthocyanin genes, and 1,231 m6A genes. A total of 1,174,049 specific guide sequences for CRISPR and 5,856,479 transposable elements were detected in Brassicaceae. TBGR also provides information on synteny, duplication, and orthologs for 27 Brassicaceae species. The TBGR database contains 1,183,851 gene annotations obtained using the TrEMBL, Swiss-Prot, Nr, GO, and Pfam databases. The BLAST, Synteny, Primer Design, Seq_fetch, and JBrowse tools are provided to help users perform comparative genomic analyses. All the genome assemblies, gene models, annotations, and bioinformatics results can be easily downloaded from the TBGR database. We plan to improve and continuously update the database with newly assembled genomes and comparative genomic studies. We expect the TBGR database to become a key resource for the study of the Brassicaceae.
PMID: 35670735
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac245
Ethylene augments root hypoxia tolerance via growth cessation and reactive oxygen species amelioration.
Plant-Environment Signaling, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.; Department of Botany and Plant Biology, University of Geneva, 1211 Geneva, Switzerland.; Plant Environmental Signalling and Development, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany.; CIBSS - Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.; Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, AL5 2JQ, UK.; Botany and Plant Sciences Department and Center for Plant Cell Biology, University of California, Riverside, CA, 92521, USA.; Intelligent Data Ecosystems, Rothamsted Research, Harpenden, AL5 2JQ, UK.
Flooded plants experience impaired gas diffusion underwater, leading to oxygen deprivation (hypoxia). The volatile plant hormone ethylene is rapidly trapped in submerged plant cells and is instrumental for enhanced hypoxia acclimation. However, the precise mechanisms underpinning ethylene-enhanced hypoxia survival remain unclear. We studied the effect of ethylene pre-treatment on hypoxia survival of Arabidopsis (Arabidopsis thaliana) primary root tips. Both hypoxia itself and re-oxygenation following hypoxia are highly damaging to root tip cells, and ethylene pre-treatments reduced this damage. Ethylene pre-treatment alone altered the abundance of transcripts and proteins involved in hypoxia responses, root growth, translation, and reactive oxygen species (ROS) homeostasis. Through imaging and manipulating ROS abundance in planta, we demonstrated that ethylene limited excessive ROS formation during hypoxia and subsequent re-oxygenation and improved oxidative stress survival in a PHYTOGLOBIN1-dependent manner. In addition, we showed that root growth cessation via ethylene and auxin occurred rapidly and that this quiescence behavior contributed to enhanced hypoxia tolerance. Collectively, our results show that the early flooding signal ethylene modulates a variety of processes that all contribute to hypoxia survival.
PMID: 35640551
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac251
Auxin-driven ecophysiological diversification of leaves in domesticated tomato.
Departamento de Biologia Vegetal, Universidade Federal de Vicosa, 36570-900, Vicosa, MG, Brazil.; Departamento de Botanica, Instituto de Biociencias, Universidade de Sao Paulo, 05508-090, Sao Paulo, SP, Brazil.; Departamento de Botanica, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, 31270-901, Belo Horizonte, MG, Brazil.; Centro de Energia Nuclear na Agricultura, Universidade de Sao Paulo, 13400-970, Piracicaba, Sao Paulo, Brazil.; Bioinformatics Multidisciplinary Environment, Instituto Metropole Digital, Universidade Federal Do Rio Grande Do Norte, Natal, RN, Brazil.; Laboratory of Hormonal Control of Plant Development. Departamento de Ciencias Biologicas (LCB), Escola Superior de Agricultura "Luiz de Queiroz", Universidade de Sao Paulo, CP 09, 13418-900, Piracicaba, SP, Brazil.
Heterobaric leaves have bundle sheath extensions (BSEs) that compartmentalize the sub-stomatal cavity, whereas homobaric leaves do not. In tomato (Solanum lycopersicum), BSE development is controlled by the OBSCURAVENOSA (OBV) locus. The obv mutant lacks BSEs, whereas leaves carrying the wild-type allele have BSEs. Here, we identify the obv gene and the causative mutation, a non-synonymous amino acid change. This mutation exists as a rare polymorphism in the natural range of wild tomatoes but has increased in frequency in domesticated tomatoes, suggesting that the latter diversified into heterobaric and homobaric leaf types. The mutation disrupts a C2H2 zinc finger motif in the OBV protein, resulting in the absence of BSEs in leaves and alterations to leaf function: Photosynthetic assimilation rate and leaf hydraulic conductance are both reduced in obv. Here, we show that both of these and other pleiotropic effects, including changes in leaf insertion angle, leaf margin serration, minor vein density, and fruit shape, are controlled by OBV via changes in auxin signalling. Loss of function of the transcriptional regulator AUXIN RESPONSE FACTOR 4 (ARF4) also results in defective BSE development, revealing an additional component of a genetic module controlling aspects of leaf development important for ecological adaptation and for breeding selection.
PMID: 35639975
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac239
Mycorrhizal symbiosis reprograms ion fluxes and fatty acid metabolism in wild jujube during salt stress.
Key Laboratory of National Forestry and Grassland Administration on Silviculture in Loess Plateau, College of Forestry, Northwest A&F University, Yangling, 712100, China.; Farmland Irrigation Research Institute of Chinese Academy of Agricultural Sciences, China.; Department of Biosystems and Technology, Swedish University of Agricultural Sciences, Alnarp, Sweden.
Chinese jujube (Ziziphus jujuba) is an important fruit tree in China, and soil salinity is the main constraint affecting jujube production. It is unclear how arbuscular mycorrhizal (AM) symbiosis supports jujube adaptation to salt stress. Herein, we performed comparative physiological, ion flux, fatty acid (FA) metabolomic, and transcriptomic analyses to examine the mechanism of AM jujube responding to salt stress. AM seedlings showed better performance during salt stress. AM symbiosis altered phytohormonal levels: IAA and ABA contents were significantly increased in AM roots and reduced by salt stress. Mycorrhizal colonization enhanced root H+ efflux and K+ influx, while inducing expression of plasma membrane-type ATPase 7 (ZjAHA7) and high-affinity K+ transporter 2 (ZjHAK2) in roots. High K+/Na+ homeostasis was maintained throughout salt exposure. FA content was elevated in AM leaves as well as roots, especially for palmitic acid, oleic acid, trans oleic acid, and linoleic acid, and similar effects were also observed in AM poplar (P. alba x P. glandulosa cv. 84K) and Medicago truncatula, indicating AM symbiosis elevating FA levels could be a conserved physiological effect. Gene co-expression network analyses uncovered a core gene set including 267 genes in roots associated with AM symbiosis and conserved transcriptional responses, e.g., FA metabolism, phytohormone signal transduction, SNARE interaction in vesicular transport, and biotin metabolism. In contrast to widely up-regulated genes related to FA metabolism in AM roots, limited genes were affected in leaves. We propose a model of AM symbiosis-linked reprogramming of FA metabolism and provide a comprehensive insight into AM symbiosis with a woody species adaptation to salt stress.
PMID: 35604107
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac220
MEDIATOR SUBUNIT17 integrates jasmonate and auxin signaling pathways to regulate thermomorphogenesis.
Plant Mediator Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.; Signalling Lab, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.; Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology,Masaryk University, Brno, Czech Republic.; Plant Transcription Regulation Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
Plant adjustment to environmental changes involves complex crosstalk between extrinsic and intrinsic cues. In the past two decades, extensive research has elucidated the key roles of PHYTOCHROME INTERACTING FACTOR4 (PIF4) and the phytohormone auxin in thermomorphogenesis. In this study, we identified a previously unexplored role of jasmonate (JA) signaling components, the Mediator complex, and their integration with auxin signaling during thermomorphogenesis in Arabidopsis (Arabidopsis thaliana). Warm temperature induces expression of JA signaling genes including MYC2, but, surprisingly, this transcriptional activation is not JA dependent. Warm temperature also promotes accumulation of the JA-signaling receptor CORONATINE INSENSITIVE1 (COI1) and degradation of the JA-signaling repressor JASMONATE-ZIM-DOMAIN PROTEIN9 (JAZ9), which probably leads to de-repression of MYC2, enabling it to contribute to the expression of MEDIATOR SUBUNIT17 (MED17). In response to warm temperature, MED17 occupies the promoters of thermosensory genes including PIF4, YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE19 (IAA19), and IAA29. Moreover, MED17 facilitates enrichment of H3K4me3 on the promoters of PIF4, YUC8, IAA19, and IAA29 genes. Interestingly, both occupancy of MED17 and enrichment of H3K4me3 on these thermomorphogenesis-related promoters are dependent on PIF4 (or PIFs). Altered accumulation of COI1 under warm temperature in the med17 mutant suggests the possibility of a feedback mechanism. Overall, this study reveals the role of the Mediator complex as an integrator of JA and auxin signaling pathways during thermomorphogenesis.
PMID: 35567489
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac215
A PLETHORA/PIN-FORMED/auxin network mediates prehaustorium formation in the parasitic plant Striga hermonthica.
BESE Division, Plant Cell and Developmental Biology, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.; BESE Division, The BioActives Lab, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.; Institute of Cytology and Genetics, Lavrentyeva Avenue 10, Novosibirsk, 630090, Russian Federation.; Novosibirsk State University, 2 Pirogova Street, Novosibirsk, 630090, Russian Federation.; Plant Systems Physiology, Radboud University, Heyendaalseweg 135, 6500 AJ Nijmegen, NL.
The parasitic plant Striga (Striga hermonthica) invades the host root through the formation of a haustorium and has detrimental impacts on cereal crops. The haustorium results from the prehaustorium, which is derived directly from the differentiation of the Striga radicle. The molecular mechanisms leading to radicle differentiation shortly after germination remain unclear. In this study, we determined the developmental programs that regulate terminal prehaustorium formation in S. hermonthica at cellular resolution. We showed that shortly after germination, cells in the root meristem undergo multiplanar divisions. During growth, the meristematic activity declines and associates with reduced expression of the stem cell regulator PLETHORA1 and the cell cycle genes CYCLINB1 and HISTONE H4. We also observed a basal localization of the PIN-FORMED (PIN) proteins and a decrease in auxin levels in the meristem. Using the structural layout of the root meristem and the polarity of outer-membrane PIN proteins, we constructed a mathematical model of auxin transport that explains the auxin distribution patterns observed during S. hermonthica root growth. Our results reveal a fundamental molecular and cellular framework governing the switch of S. hermonthica roots to form the invasive prehaustoria.
PMID: 35543497
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac212
The HD-Zip transcription factor SlHB15A regulates abscission by modulating jasmonoyl-isoleucine biosynthesis.
College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866, People's Republic of China.; Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, Liaoning Province, China.; Department of Plant Sciences, University of California at Davis, CA 95616, USA.; Crops Pathology and Genetic Research Unit, USDA-ARS, Davis, CA 95616, USA.
Plant organ abscission, a process that is important for development and reproductive success, is inhibited by the phytohormone auxin and promoted by another phytohormone, jasmonic acid (JA). However, the molecular mechanisms underlying the antagonistic effects of auxin and JA in organ abscission are unknown. We identified a tomato (Solanum lycopersicum) class III homeodomain-leucine zipper transcription factor, HOMEOBOX15A (SlHB15A), which was highly expressed in the flower pedicel abscission zone and induced by auxin. Knocking out SlHB15A using clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 technology significantly accelerated abscission. In contrast, overexpression of microRNA166-resistant SlHB15A (mSlHB15A) delayed abscission. RNA sequencing and reverse transcription quantitative PCR analyses showed that knocking out SlHB15A altered the expression of genes related to JA biosynthesis and signaling. Furthermore, functional analysis indicated that SlHB15A regulates abscission by depressing JA-isoleucine (JA-Ile) levels through inhabiting the expression of JASMONATE-RESISTANT1 (SlJAR1), a gene involved in JA-Ile biosynthesis, which could induce abscission-dependent and -independent ethylene signaling. SlHB15A bound directly to the SlJAR1 promoter to silence SlJAR1, thus delaying abscission. We also found that flower removal enhanced JA-Ile content and that application of JA-Ile severely impaired the inhibitory effects of auxin on abscission. These results indicated that SlHB15A mediates the antagonistic effect of auxin and JA-Ile during tomato pedicel abscission, while auxin inhibits abscission through the SlHB15A-SlJAR1 module.
PMID: 35522030
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac213
High temperature induces male sterility via MYB66-MYB4-Casein kinase I signaling in cotton.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.; College of Life Sciences, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, Guangdong, China.
High temperature (HT) causes male sterility and decreases crop yields. Our previous works have demonstrated that sugar and auxin signaling pathways, Gossypium hirsutum Casein kinase I (GhCKI), and DNA methylation are all involved in HT-induced male sterility in cotton. However, the signaling mechanisms leading to distinct GhCKI expression patterns induced by HT between HT-tolerant and HT-sensitive cotton anthers remain largely unknown. Here, we identified a GhCKI promoter (ProGhCKI) region that functions in response to HT in anthers and found the transcription factor GhMYB4 binds to this region to act as an upstream positive regulator of GhCKI. In the tapetum of early-stage cotton anthers, upregulated expression of GhMYB4 under HT and overexpressed GhMYB4 under normal temperature both led to severe male sterility phenotypes, coupled with enhanced expression of GhCKI. We also found that GhMYB4 interacts with GhMYB66 to form a heterodimer to enhance its binding to ProGhCKI. However, GhMYB66 showed an expression pattern similar to GhMYB4 under HT but did not directly bind to ProGhCKI. Furthermore, HT reduced siRNA-mediated CHH DNA methylations in the GhMYB4 promoter, which enhanced the expression of GhMYB4 in tetrad stage anthers and promoted the formation of the GhMYB4/GhMYB66 heterodimer, which in turn elevated the transcription of GhCKI in the tapetum, leading to male sterility. Overall, we shed light on the GhMYB66-GhMYB4-GhCKI regulatory pathway in response to HT in cotton anthers.
PMID: 35522025
Plant Physiol , IF:8.34 , 2022 May doi: 10.1093/plphys/kiac194
SAUR15 interaction with BRI1 activates plasma membrane H+-ATPase to promote organ development of Arabidopsis.
State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China.; Department of Biology, Institute of Biochemistry, Carleton University, Ottawa, Ontario, K1S 5B6, Canada.; Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, People's Republic of China.; School of Life Sciences, Guangzhou University, Guangzhou 510006, People's Republic of China.
Brassinosteroids (BRs) are an important group of plant steroid hormones that regulate growth and development. Several members of the SMALL AUXIN UP RNA (SAUR) family have roles in BR-regulated hypocotyl elongation and root growth. However, the mechanisms are unclear. Here, we show in Arabidopsis (Arabidopsis thaliana) that SAUR15 interacts with cell surface receptor-like kinase BRASSINOSTEROID-INSENSITIVE 1 (BRI1) in BR-treated plants, resulting in enhanced BRI1 phosphorylation status and recruitment of the co-receptor BRI1-ASSOCIATED RECEPTOR KINASE 1 (BAK1). Genetic and phenotypic assays indicated that the SAUR15 effect on BRI1 can be uncoupled from BRASSINOSTEROID INSENSITIVE 2 (BIN2) activity. Instead, we show that SAUR15 promotes BRI1 direct activation of plasma membrane H+-ATPase (PM H+-ATPase) via phosphorylation. Consequently, SAUR15-BRI1-PM H+-ATPase acts as a direct, PM-based mode of BR signaling that drives cell expansion to promote the growth and development of various organs. These data define an alternate mode of BR signaling in plants.
PMID: 35511168
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1553-1569 doi: 10.1093/plphys/kiac158
SPATULA and ALCATRAZ confer female sterility and fruit cavity via mediating pistil development in cucumber.
Department of Vegetable Sciences, State Key Laboratories of Agrobiotechnology, Joint International Research Laboratory of Crop Molecular Breeding, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, China Agricultural University, Beijing 100193, China.; College of Horticulture Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China.
Fruits and seeds play essential roles in plant sexual reproduction and the human diet. Successful fertilization involves delivery of sperm in the pollen tube to the egg cell within the ovary along the transmitting tract (TT). Fruit cavity is an undesirable trait directly affecting cucumber (Cucumis sativus) commercial value. However, the regulatory genes underlying fruit cavity formation and female fertility determination remain unknown in crops. Here, we characterized a basic Helix-Loop-Helix (bHLH) gene C. sativus SPATULA (CsSPT) and its redundant and divergent function with ALCATRAZ (CsALC) in cucumber. CsSPT transcripts were enriched in reproductive organs. Mutation of CsSPT resulted in 60% reduction in female fertility, with seed produced only in the upper portion of fruits. Csspt Csalc mutants displayed complete loss of female fertility and fruit cavity due to carpel separation. Further examination showed that stigmas in the double mutant turned outward with defective papillae identity, and extracellular matrix contents in the abnormal TT were dramatically reduced, which resulted in no path for pollen tube extension and no ovules fertilized. Biochemical and transcriptome analysis showed that CsSPT and CsALC act in homodimers and heterodimers to confer fruit cavity and female sterility by mediating genes involved in TT development, auxin-mediated signaling, and cell wall organization in cucumber.
PMID: 35389464
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1757-1773 doi: 10.1093/plphys/kiac157
The interplay of auxin and brassinosteroid signaling tunes root growth under low and different nitrogen forms.
National Institute of Plant Genome Research, New Delhi, 110067, India.
The coordinated signaling activity of auxin and brassinosteroids (BRs) is critical for optimal plant growth and development. Nutrient-derived signals regulate root growth by modulating the levels and spatial distribution of growth hormones to optimize nutrient uptake and assimilation. However, the effect of the interaction of these two hormones and their signaling on root plasticity during low and differential availability of nitrogen (N) forms (NH4+/NO3-) remains elusive. We demonstrate that root elongation under low N (LN) is an outcome of the interdependent activity of auxin and BR signaling pathways in Arabidopsis (Arabidopsis thaliana). LN promotes root elongation by increasing BR-induced auxin transport activity in the roots. Increased nuclear auxin signaling and its transport efficiency have a distinct impact on root elongation under LN conditions. High auxin levels reversibly inhibit BR signaling via BRI1 KINASE INHIBITOR1. Using the tissue-specific approach, we show that BR signaling from root vasculature (stele) tissues is sufficient to promote cell elongation and, hence, root growth under LN condition. Further, we show that N form-defined root growth attenuation or enhancement depends on the fine balance of BR and auxin signaling activity. NH4+ as a sole N source represses BR signaling and response, which in turn inhibits auxin response and transport, whereas NO3- promotes root elongation in a BR signaling-dependent manner. In this study, we demonstrate the interplay of auxin and BR-derived signals, which are critical for root growth in a heterogeneous N environment and appear essential for root N foraging response and adaptation.
PMID: 35377445
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1728-1740 doi: 10.1093/plphys/kiac150
APYRASE1/2 mediate red light-induced de-etiolation growth in Arabidopsis seedlings.
Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA.
In etiolated seedlings, red light (R) activates phytochrome and initiates signals that generate major changes at molecular and physiological levels. These changes include inhibition of hypocotyl growth and promotion of the growth of primary roots, apical hooks, and cotyledons. An earlier report showed that the sharp decrease in hypocotyl growth rapidly induced by R was accompanied by an equally rapid decrease in the transcript and protein levels of two closely related apyrases (APYs; nucleoside triphosphate-diphosphohydrolases) in Arabidopsis (Arabidopsis thaliana), APY1 and APY2, enzymes whose expression alters auxin transport and growth in seedlings. Here, we report that single knockouts of either APY inhibit R-induced promotion of the growth of primary roots, apical hooks, and cotyledons, and RNAi-induced suppression of APY1 expression in the background of apy2 inhibits R-induced apical hook opening. When R-irradiated primary roots and apical hook-cotyledons began to show a gradual increase in their growth relative to dark controls, they concurrently showed increased levels of APY protein, but in hook-cotyledon tissue, this occurred without parallel increases in their transcripts. In wild-type seedlings whose root growth is suppressed by the photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethylurea, the R-induced increased APY expression in roots was also inhibited. In unirradiated plants, the constitutive expression of APY2 promoted both hook opening and changes in the transcript abundance of Small Auxin Upregulated RNA (SAUR), SAUR17 and SAUR50 that help mediate de-etiolation. These results provide evidence that the expression of APY1/APY2 is regulated by R and that APY1/APY2 participate in the signaling pathway by which phytochrome induces differential growth changes in different tissues of etiolated seedlings.
PMID: 35357495
Plant Physiol , IF:8.34 , 2022 Jun , V189 (3) : P1397-1415 doi: 10.1093/plphys/kiac138
MicroRNA858a, its encoded peptide, and phytosulfokine regulate Arabidopsis growth and development.
CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Lucknow 226001, India.; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.; Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Lucknow, India.
Small molecules, such as peptides and miRNAs, are crucial regulators of plant growth. Here, we show the importance of cross-talk between miPEP858a (microRNA858a-encoded peptide)/miR858a and phytosulfokine (PSK4) in regulating plant growth and development in Arabidopsis (Arabidopsis thaliana). Genome-wide expression analysis suggested modulated expression of PSK4 in miR858a mutants and miR858a-overexpressing (miR858aOX) plants. The silencing of PSK4 in miR858aOX plants compromised growth, whereas overexpression of PSK4 in the miR858a mutant rescued the developmental defects. The exogenous application of synthetic PSK4 further complemented the plant development in mutant plants. Exogenous treatment of synthetic miPEP858a in the PSK4 mutant led to clathrin-mediated internalization of the peptide; however, it did not enhance growth as is the case in wild-type plants. We also demonstrated that MYB3 is an important molecular component participating in the miPEP858a/miR858a-PSK4 module. Finally, our work highlights the signaling between miR858a/miPEP858a-MYB3-PSK4 in modulating the expression of key elements involved in auxin responses, leading to the regulation of growth.
PMID: 35325214
Plant Physiol , IF:8.34 , 2022 Jun , V189 (2) : P527-540 doi: 10.1093/plphys/kiac133
Pivotal roles of ELONGATED HYPOCOTYL5 in regulation of plant development and fruit metabolism in tomato.
Shanghai Collaborative Innovation Center of Agri-Seeds/School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; Key Laboratory of Urban Agriculture Ministry of Agriculture, Shanghai Jiao Tong University, Shanghai 200240, China.; Joint Center for Single Cell Biology, Shanghai Jiao Tong University, Shanghai 200240, China.; Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai 200240, China.
The transcription factor ELONGATED HYPOCOTYL5 (HY5) plays critical roles in plant photomorphogenesis. Previous studies on HY5 have mainly focused on the seedling stage in Arabidopsis (Arabidopsis thaliana), and its functions in other plant species have not been well characterized, particularly at adult stages of development. In this report, we investigated the functions of tomato (Solanum lycopersicum) HY5 (SlHY5) from seedlings to adult plants with a focus on fruits. Genome-edited slhy5 mutants exhibited typical compromised photomorphogenesis in response to various light conditions. The slhy5 mutants showed reduced primary root length and secondary root number, which is associated with altered auxin signaling. SlHY5 promoted chlorophyll biosynthesis from seedling to adult stages. Notably, the promotive role of SlHY5 on chlorophyll accumulation was more pronounced on the illuminated side of green fruits than on their shaded side. Consistent with this light-dependent effect, we determined that SlHY5 protein is stabilized by light. Transcriptome and metabolome analyses in fruits revealed that SlHY5 has major functions in the regulation of metabolism, including the biosynthesis of phenylpropanoids and steroidal glycoalkaloids. These data demonstrate that SlHY5 performs both shared and distinct functions in relation to its Arabidopsis counterpart. The manipulation of SlHY5 represents a powerful tool to influence the two vital agricultural traits of seedling fitness and fruit quality in tomato.
PMID: 35312008
Plant Physiol , IF:8.34 , 2022 Jun , V189 (2) : P1065-1082 doi: 10.1093/plphys/kiac099
Maize miR167-ARF3/30-polyamine oxidase 1 module-regulated H2O2 production confers resistance to maize chlorotic mottle virus.
State Key Laboratory for Agro-Biotechnology and Department of Plant Pathology, China Agricultural University, Beijing 100193, China.; International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, Gigiri, Nairobi, Kenya.; College of Agronomy, China Agricultural University, Beijing 100193, China.; Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Taian 271018, China.; College of Agronomy, Yunnan Agricultural University, Kunming 650201, China.
Maize chlorotic mottle virus (MCMV) is the key pathogen causing maize lethal necrosis (MLN). Due to the sharply increased incidence of MLN in many countries, there is an urgent need to identify resistant lines and uncover the underlying resistance mechanism. Here, we showed that the abundance of maize (Zea mays) microR167 (Zma-miR167) positively modulates the degree of resistance to MCMV. Zma-miR167 directly targets Auxin Response Factor3 (ZmARF3) and ZmARF30, both of which negatively regulate resistance to MCMV. RNA-sequencing coupled with gene expression assays revealed that both ZmARF3 and ZmARF30 directly bind the promoter of Polyamine Oxidase 1 (ZmPAO1) and activate its expression. Knockdown or inhibition of enzymatic activity of ZmPAO1 suppressed MCMV infection. Nevertheless, MCMV-encoded p31 protein directly targets ZmPAO1 and enhances the enzyme activity to counteract Zma-miR167-mediated defense to some degree. We uncovered a role of the Zma-miR167-ZmARF3/30 module for restricting MCMV infection by regulating ZmPAO1 expression, while MCMV employs p31 to counteract this defense.
PMID: 35298645
Plant Physiol , IF:8.34 , 2022 Jun , V189 (2) : P715-734 doi: 10.1093/plphys/kiac115
Pleiotropic and nonredundant effects of an auxin importer in Setaria and maize.
Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA.; Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Oklahoma 74078, USA.; Division of Biological Sciences, Interdisciplinary Plant Group, and Missouri Maize Center, University of Missouri, Columbia, Missouri 65211, USA.
Directional transport of auxin is critical for inflorescence and floral development in flowering plants, but the role of auxin influx carriers (AUX1 proteins) has been largely overlooked. Taking advantage of available AUX1 mutants in green millet (Setaria viridis) and maize (Zea mays), we uncover previously unreported aspects of plant development that are affected by auxin influx, including higher order branches in the inflorescence, stigma branch number, glume (floral bract) development, and plant fertility. However, disruption of auxin flux does not affect all parts of the plant, with little obvious effect on inflorescence meristem size, time to flowering, and anther morphology. In double mutant studies in maize, disruptions of ZmAUX1 also affect vegetative development. A green fluorescent protein (GFP)-tagged construct of the Setaria AUX1 protein Sparse Panicle1 (SPP1) under its native promoter showed that SPP1 localizes to the plasma membrane of outer tissue layers in both roots and inflorescences, and accumulates specifically in inflorescence branch meristems, consistent with the mutant phenotype and expected auxin maxima. RNA-seq analysis indicated that most gene expression modules are conserved between mutant and wild-type plants, with only a few hundred genes differentially expressed in spp1 inflorescences. Using clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology, we disrupted SPP1 and the other four AUX1 homologs in S. viridis. SPP1 has a larger effect on inflorescence development than the others, although all contribute to plant height, tiller formation, and leaf and root development. The AUX1 importers are thus not fully redundant in S. viridis. Our detailed phenotypic characterization plus a stable GFP-tagged line offer tools for future dissection of the function of auxin influx proteins.
PMID: 35285930
Plant Physiol , IF:8.34 , 2022 Jun , V189 (2) : P1005-1020 doi: 10.1093/plphys/kiac084
The BTB protein MdBT2 recruits auxin signaling components to regulate adventitious root formation in apple.
State Key Laboratory of Crop Biology, Shandong Collaborative Innovation Center of Fruit and Vegetable Quality and Efficient Production, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China.; Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China.
Ubiquitination is an important post-translational protein modification. Although BROAD-COMPLEX, TRAMTRACK AND BRIC A BRAC and TRANSCRIPTION ADAPTOR PUTATIVE ZINC FINGER domain protein 2 (BT2) is involved in many biological processes, its role in apple (Malus domestic) root formation remains unclear. Here, we revealed that MdBT2 inhibits adventitious root (AR) formation through interacting with AUXIN RESPONSE FACTOR8 (MdARF8) and INDOLE-3-ACETIC ACID INDUCIBLE3 (MdIAA3). MdBT2 facilitated MdARF8 ubiquitination and degradation through the 26S proteasome pathway and negatively regulated GRETCHEN HAGEN 3.1 (MdGH3.1) and MdGH3.6 expression. MdARF8 regulates AR formation through inducing transcription of MdGH3s (MdGH3.1, MdGH3.2, MdGH3.5, and MdGH3.6). In addition, MdBT2 facilitated MdIAA3 stability and slightly promoted its interaction with MdARF8. MdIAA3 inhibited AR formation by forming heterodimers with MdARF8 as well as other MdARFs (MdARF5, MdARF6, MdARF7, and MdARF19). Our findings reveal that MdBT2 acts as a negative regulator of AR formation in apple.
PMID: 35218363
Plant Physiol , IF:8.34 , 2022 May , V189 (1) : P285-300 doi: 10.1093/plphys/kiac046
The CCCH zinc finger protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid signaling.
College of Resources and Environment, Qingdao Agricultural University, Qingdao 266109, China.; Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China.; Academy of Dongying Efficient Agricultural Technology and Industry on Saline and Alkaline Land in Collaboration with Qingdao Agricultural University, Dongying 257000, China.; State Key Laboratory of Wheat and Maize Crop Science and College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China.; College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China.; Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China.; Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Sciences, Shandong University, Jinan 250100, China.; College of Grassland Science, Qingdao Agricultural University, Qingdao 266109, China.
Plant CCCH proteins participate in the control of multiple developmental and adaptive processes, but the regulatory mechanisms underlying these processes are not well known. In this study, we showed that the Arabidopsis (Arabidopsis thaliana) CCCH protein C3H15 negatively regulates cell elongation by inhibiting brassinosteroid (BR) signaling. Genetic and biochemical evidence showed that C3H15 functions downstream of the receptor BR INSENSITIVE 1 (BRI1) as a negative regulator in the BR pathway. C3H15 is phosphorylated by the GLYCOGEN SYNTHASE KINASE 3 -like kinase BR-INSENSITIVE 2 (BIN2) at Ser111 in the cytoplasm in the absence of BRs. Upon BR perception, C3H15 transcription is enhanced, and the phosphorylation of C3H15 by BIN2 is reduced. The dephosphorylated C3H15 protein accumulates in the nucleus, where C3H15 regulates transcription via G-rich elements (typically GGGAGA). C3H15 and BRASSINAZOLE RESISTANT 1 (BZR1)/BRI1-EMS-SUPPRESSOR 1 (BES1), two central transcriptional regulators of BR signaling, directly suppress each other and share a number of BR-responsive target genes. Moreover, C3H15 antagonizes BZR1 and BES1 to regulate the expression of their shared cell elongation-associated target gene, SMALL AUXIN-UP RNA 15 (SAUR15). This study demonstrates that C3H15-mediated BR signaling may be parallel to, or even attenuate, the dominant BZR1 and BES1 signaling pathways to control cell elongation. This finding expands our understanding of the regulatory mechanisms underlying BR-induced cell elongation in plants.
PMID: 35139225
Plant Physiol , IF:8.34 , 2022 May , V189 (1) : P264-284 doi: 10.1093/plphys/kiac041
lncRNA7 and lncRNA2 modulate cell wall defense genes to regulate cotton resistance to Verticillium wilt.
State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Henan University, Kaifeng 475001, China.; College of life science and agricultural engineering, Nanyang Normal University, Nanyang 473000, China.; Chongqing Key Laboratory of Big Data for Bio Intelligence, College of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China.; Southern Plains Agricultural Research Center, Agricultural Research Service, USDA, College Station, Texas 77845, USA.; Kaifeng Academy of Agriculture and Forestry, Kaifeng 475000, China.; State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
In plants, long noncoding RNAs (lncRNAs) regulate disease resistance against fungi and other pathogens. However, the specific mechanism behind this regulation remains unclear. In this study, we identified disease resistance-related lncRNAs as well as their regulating genes and assessed their functions by infection of cotton (Gossypium) chromosome segment substitution lines with Verticillium dahliae. Our results demonstrated that lncRNA7 and its regulating gene Pectin methylesterase inhibitor 13 (GbPMEI13) positively regulated disease resistance via the silencing approach, while ectopic overexpression of GbPMEI13 in Arabidopsis (Arabidopsis thaliana) promoted growth and enhanced resistance to V. dahliae. In contrast, lncRNA2 and its regulating gene Polygalacturonase 12 (GbPG12) negatively regulated resistance to V. dahliae. We further found that fungal disease-related agents, including the pectin-derived oligogalacturonide (OG), could downregulate the expression of lncRNA2 and GbPG12, leading to pectin accumulation. Conversely, OG upregulated the expression of lncRNA7, which encodes a plant peptide phytosulfokine (PSK-alpha), which was confirmed by lncRNA7 overexpression and Ultra Performance Liquid Chromatography Tandem Mass Spectrometry (UPLC-MS) experiments. We showed that PSK-alpha promoted 3-Indoleacetic acid (IAA) accumulation and activated GbPMEI13 expression through Auxin Response Factor 5. Since it is an inhibitor of pectin methylesterase (PME), GbPMEI13 promotes pectin methylation and therefore increases the resistance to V. dahliae. Consistently, we also demonstrated that GbPMEI13 inhibits the mycelial growth and spore germination of V. dahliae in vitro. In this study, we demonstrated that lncRNA7, lncRNA2, and their regulating genes modulate cell wall defense against V. dahliae via auxin-mediated signaling, providing a strategy for cotton breeding.
PMID: 35134243
Plant Physiol , IF:8.34 , 2022 Jun , V189 (2) : P858-873 doi: 10.1093/plphys/kiac015
The histone deacetylase 1/GSK3/SHAGGY-like kinase 2/BRASSINAZOLE-RESISTANT 1 module controls lateral root formation in rice.
State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China.
Lateral roots (LRs) are a main component of the root system of rice (Oryza sativa) that increases root surface area, enabling efficient absorption of water and nutrients. However, the molecular mechanism regulating LR formation in rice remains largely unknown. Here, we report that histone deacetylase 1 (OsHDAC1) positively regulates LR formation in rice. Rice OsHDAC1 RNAi plants produced fewer LRs than wild-type plants, whereas plants overexpressing OsHDAC1 exhibited increased LR proliferation by promoting LR primordia formation. Brassinosteroid treatment increased the LR number, as did mutation of GSK3/SHAGGY-like kinase 2 (OsGSK2), whereas overexpression of OsGSK2 decreased the LR number. Importantly, OsHDAC1 could directly interact with and deacetylate OsGSK2, inhibiting its activity. OsGSK2 deacetylation attenuated the interaction between OsGSK2 and BRASSINAZOLE-RESISTANT 1 (OsBZR1), leading to accumulation of OsBZR1. The overexpression of OsBZR1 increased LR formation by regulating Auxin/IAA signaling genes. Taken together, the results indicate that OsHDAC1 regulates LR formation in rice by deactivating OsGSK2, thereby preventing degradation of OsBZR1, a positive regulator of LR primordia formation. Our findings suggest that OsHDAC1 is a breeding target in rice that can improve resource capture.
PMID: 35078247
Plant Physiol , IF:8.34 , 2022 May , V189 (1) : P248-263 doi: 10.1093/plphys/kiab589
TARGET OF RAPAMYCIN is essential for asexual vegetative reproduction in Kalanchoe.
School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PT, UK.
The unique mechanism by which leaf margin cells regain potency and then form a plantlet in Kalanchoe spp. remains elusive but involves organogenesis and embryogenesis in response to age, day length, nutrient availability, and drought stress. In light of this, we investigated whether TARGET OF RAPAMYCIN (TOR), a conserved protein kinase in eukaryotes that controls cell growth and metabolism in response to nutrient and energy availability, may regulate plantlet formation. Kalanchoe daigremontiana TOR (KdTOR) was expressed in the leaf margin at the site of plantlet initiation, in the early plantlet cotyledons, and in the root tip of the developed plantlet. Both chemical and genetic inhibition of TOR Kinase activity in Kalanchoe daigremontiana leaves disrupted plantlet formation. Furthermore, downregulation of KdTOR in transgenic plants led to wide-ranging transcriptional changes, including decreased K. daigremontiana SHOOTMERISTEMLESS and K. daigremontiana LEAFYCOTYLEDON1 expression, whereas auxin treatments induced KdTOR expression in the plantlet roots. These results suggest that the KdTOR pathway controls plantlet development in cooperation with auxin, organogenesis, and embryogenesis pathways. The ancient and highly conserved TOR Kinase therefore controls diverse and unique developmental pathways, such as asexual reproduction within the land plant lineage.
PMID: 34935983
Sci Total Environ , IF:7.963 , 2022 Jun , V841 : P156486 doi: 10.1016/j.scitotenv.2022.156486
Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India.
Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.; Environmental Microbiology and Genomics Laboratory, Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India. Electronic address: psar@bt.iitkgp.ac.in.
Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 x 10(7) gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO4(3-), SO4(2-) and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO4(2-) and NO3(-) reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO4(3-) and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO3(-) reduction to ammonium), and S (assimilatory SO4(2-) reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.
PMID: 35667424
Plant Cell Environ , IF:7.228 , 2022 May doi: 10.1111/pce.14366
The co-chaperone HOP participates in TIR1 stabilisation and in auxin response in plants.
Centro de Biotecnologia y Genomica de Plantas. Universidad Politecnica de Madrid (UPM) - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC (INIA/CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcon, Madrid, Spain.; Departamento de Botanica, Ecologia y Fisiologia Vegetal, Universidad de Cordoba, Campus de Rabanales, Cordoba, Spain.; Fundacion Instituto Leloir and Instituto de Investigaciones Bioquimicas de Buenos Aires (IIBA, CONICET), Buenos Aires, Argentina.
HOP (HSP70-HSP90 organising protein) is a conserved family of co-chaperones well known in mammals for its role in the folding of signalling proteins associated with development. In plants, HOP proteins have been involved in the response to multiple stresses, but their role in plant development remains elusive. Herein, we describe that the members of the HOP family participate in different aspects of plant development as well as in the response to warm temperatures through the regulation of auxin signalling. Arabidopsis hop1 hop2 hop3 triple mutant shows different auxin-related phenotypes and a reduced auxin sensitivity. HOP interacts with TIR1 auxin coreceptor in vivo. Furthermore, TIR1 accumulation and auxin transcriptional response are reduced in the hop1 hop2 hop3 triple mutant, suggesting that HOP's function in auxin signalling is related, at least, to TIR1 interaction and stabilisation. Interestingly, HOP proteins form part of the same complexes as SGT1b (a different HSP90 co-chaperone) and these co-chaperones synergistically cooperate in auxin signalling. This study provides relevant data about the role of HOP in auxin regulation in plants and uncovers that both co-chaperones, SGT1b and HOP, cooperate in the stabilisation of common targets involved in plant development.
PMID: 35610185
Plant Cell Environ , IF:7.228 , 2022 Jun , V45 (6) : P1796-1812 doi: 10.1111/pce.14316
A novel calmodulin-interacting Domain of Unknown Function 506 protein represses root hair elongation in Arabidopsis.
Noble Research Institute LLC, Ardmore, Oklahoma, USA.
Domain of Unknown Function 506 proteins are ubiquitous in plants. The phosphorus (P) stress-inducible REPRESSOR OF EXCESSIVE ROOT HAIR GROWTH1 (AtRXR1) gene encodes the first characterized DUF506. AtRXR1 inhibits root hair elongation by interacting with RabD2c GTPase. However, functions of other P-responsive DUF506 genes are still missing. Here, we selected two additional P-inducible DUF506 genes for further investigation. The expression of both genes was induced by auxin. Under P-stress, At3g07350 gene expressed ubiquitously in seedlings, whereas At1g62420 (AtRXR3) expression was strongest in roots. AtRXR3 overexpressors and knockouts had shorter and longer root hairs, respectively. A functional AtRXR3-green fluorescent protein fusion localized to root epidermal cells. Chromatin immunoprecipitation and quantitative reverse-transcriptase-polymerase chain reaction revealed that AtRXR3 was transcriptionally activated by RSL4. Bimolecular fluorescence complementation and calmodulin (CaM)-binding assays showed that AtRXR3 interacted with CaM in the presence of Ca(2+) . Moreover, cytosolic Ca(2+) ([Ca(2+) ]cyt ) oscillations in root hairs of rxr3 mutants exhibited elevated frequencies and dampened amplitudes compared to those of wild type. Thus, AtRXR3 is another DUF506 protein that attenuates P-limitation-induced root hair growth through mechanisms that involve RSL4 and interaction with CaM to modulate tip-focused [Ca(2+) ]cyt oscillations.
PMID: 35312071
Chemosphere , IF:7.086 , 2022 Jun , V296 : P134044 doi: 10.1016/j.chemosphere.2022.134044
Increasing atmospheric CO2 differentially supports arsenite stress mitigating impact of arbuscular mycorrhizal fungi in wheat and soybean plants.
Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium; Department of Botany and Microbiology, Faculty of Science, Beni-Suef University, 62521, Beni-Suef, Egypt.; Department of Agricultural Microbiology, Faculty of Agriculture, Mansoura University, Mansoura, 35516, Egypt.; Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia. Electronic address: afamohammed@pnu.edu.sa.; Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh, 11671, Saudi Arabia.; Department of Biological Sciences, College of Science, King Faisal University, Al-Ahsa, 31982, Saudi Arabia; Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, 12613, Egypt.; Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka 72341, Saudi Arabia.; Department of Botany and Microbiology, Faculty of Science, Cairo University, Giza, 12613, Egypt.; Laboratory for Integrated Molecular Plant Physiology Research (IMPRES), Department of Biology, University of Antwerp, Antwerp, Belgium.; Department of Agronomy, Faculty of Agriculture, Mansoura University, Mansoura, 35516, Egypt. Electronic address: salahco_2010@mans.edu.eg.
Arbuscular mycorrhizal fungi (AMF) are beneficial for the plant growth under heavy metal stress. Such beneficial effect is improved by elevated CO2 (eCO2). However, the mechanisms by which eCO2 improves AMF symbiotic associations under arsenite (As(III)) toxicity are hardly studied. Herein, we compared these regulatory mechanisms in species from two agronomical important plant families - grasses (wheat) and legumes (soybean). As(III) decreased plant growth (i.e., 53.75 and 60.29% of wheat and soybean, respectively) and photosynthesis. It also increased photorespiration and oxidative injury in both species, but soybean was more sensitive to oxidative stress as indicated by higher H2O2 accumulation and oxidation of protein and lipid. eCO2 significantly improved AMF colonization by increasing auxin levels, which induced high carotenoid cleavage dioxygenase (CCDs) activity, particularly in soybean roots. The improved sugar metabolism in plant shoots by co-application of eCO2 and As(III) allocated more sugars to roots sequentially. Sugar accumulation in plant roots is further induced by AMF, resulting in more C skeletons to produce organic acids, which are effectively exudated into the soil to reduce As(III) uptake. Exposure to eCO2 reduced oxidative damage and this mitigation was stronger in soybean. This could be attributed to a greater reduction in photorespiration as well as a stronger antioxidant and detoxification defence systems. The grass/legume-specificity was supported by principal component analysis, which revealed that soybean was more affected by As(III) stress and more responsive to AMF and eCO2. This study provided a mechanistic understanding of the impact of AMF, eCO2 and their interaction on As-stressed grass and legume plants, allowing better practical strategies to mitigate As(III) phytotoxicity.
PMID: 35202662
J Integr Plant Biol , IF:7.061 , 2022 Jun , V64 (6) : P1229-1245 doi: 10.1111/jipb.13256
Testing the polar auxin transport model with a selective plasma membrane H(+) -ATPase inhibitor.
State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.; Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.; Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.; Department of Dermatology, Peking University First Hospital, Beijing, 100034, China.; Iomics Biosciences Inc., Beijing, 100102, China.; College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
Auxin is unique among plant hormones in that its function requires polarized transport across plant cells. A chemiosmotic model was proposed to explain how polar auxin transport is derived by the H(+) gradient across the plasma membrane (PM) established by PM H(+) -adenosine triphosphatases (ATPases). However, a classical genetic approach by mutations in PM H(+) -ATPase members did not result in the ablation of polar auxin distribution, possibly due to functional redundancy in this gene family. To confirm the crucial role of PM H(+) -ATPases in the polar auxin transport model, we employed a chemical genetic approach. Through a chemical screen, we identified protonstatin-1 (PS-1), a selective small-molecule inhibitor of PM H(+) -ATPase activity that inhibits auxin transport. Assays with transgenic plants and yeast strains showed that the activity of PM H(+) -ATPases affects auxin uptake as well as acropetal and basipetal polar auxin transport. We propose that PS-1 can be used as a tool to interrogate the function of PM H(+) -ATPases. Our results support the chemiosmotic model in which PM H(+) -ATPase itself plays a fundamental role in polar auxin transport.
PMID: 35352470
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac280
Actin isovariant ACT7 controls root meristem development in Arabidopsis through modulating auxin and ethylene responses.
Department of Plant Bio Sciences, Faculty of Agriculture, Iwate University, Morioka, Japan.; The United Graduate School of Agricultural Sciences, Iwate University, Morioka, Japan.; Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada.
Meristem is the most functionally dynamic part in a plant body. The shaping of the meristem requires constant cell division and cell elongation, which are influenced by hormones and cell cytoskeletal component, actin. Although the roles of hormones in modulating meristem development have been extensively studied, the role of actin in this process is still elusive. Using the single and double mutants of the vegetative class actin, we demonstrate that actin isovariant ACT7 plays an important role in root meristem development. In absence of ACT7, but not ACT8 and ACT2, depolymerization of actin was observed. Consistently, act7 mutant showed reduced cell division, cell elongation, and meristem length. Intracellular distribution and trafficking of auxin transport proteins in the actin mutants revealed that ACT7 specifically functions in root meristem to facilitate the trafficking of auxin efflux carriers PIN1 and PIN2, and consequently the transport of auxin. Compared with act7, act7act8 double mutant shows slightly enhanced phenotypic response and altered intracellular trafficking. The altered distribution of auxin in act7 and act7act8 affects the response of the roots to ethylene but not to cytokinin. Collectively, our results suggest that ACT7 dependent auxin-ethylene response plays a key role in controlling Arabidopsis root meristem development.
PMID: 35749807
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P3828-3830 doi: 10.1093/jxb/erac175
Prohibitin 3 gives birth to a new lateral root primordium.
MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
PMID: 35749693
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P3831-3835 doi: 10.1093/jxb/erac237
Auxins in the right space and time regulate pea fruit development.
Technische Universitat Dresden, Faculty of Biology, D-01062 Dresden, Germany.
PMID: 35749692
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac281
MAX2-dependent competence for callus formation and shoot regeneration from Arabidopsis thaliana root explants.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Gent, Belgium.; Center for Plant Systems Biology, VIB, Technologiepark, Gent, Belgium.; Laboratory of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, Yeonsu-Gu, Incheon, Korea.; Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, UPR2301, Universite Paris-Sud, Universite Paris-Saclay, 1 Avenue de la Terrasse, Gif-sur-Yvette, France.; Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Valentin Vaerwyckweg, Ghent, Belgium.
Although the division of the pericycle cells initiates both the lateral root development and the root-derived callus formation, these developmental processes are affected differently in the strigolactone (SL) and karrikin (KAR)/KAI2 ligand (KL) signalling mutant, more axillary growth 2 (max2). Whereas max2 produces more lateral roots than the wild type, it is defective in the regeneration of shoots from root explants. We suggest that the decreased shoot regeneration of max2 originates from a delayed callus primordium formation, yielding less callus material to regenerate shoots. Indeed, when incubated on callus-inducing medium, the pericycle cell division was reduced in max2 and the early gene expression varied when compared to the wild type, as determined by a transcriptomics analysis. Furthermore, the expression of the LATERAL ORGAN BOUNDARIES DOMAIN genes and of callus induction genes was modified in correlation with the max2 phenotype, suggesting a role for MAX2 in the regulation of the interplay between cytokinin, auxin, and light signalling in callus initiation. Additionally, we found that the in vitro shoot regeneration phenotype of max2 might be caused by a defect in KAI2, rather than D14, signalling. Nevertheless, the shoot regeneration assays revealed that also the SL biosynthesis mutants max3 and max4 play a minor role.
PMID: 35738874
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac253
Stress-induced higher vein density in C3-C4 intermediate Moricandia suffruticosa under drought and heat stress.
Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, Hubei, People's Republic of China.; Hubei Hongshan Laboratory, Wuhan, China.
C4 evolution involves multiple anatomical and physiological modifications, yet our knowledge of its genetic regulation remains elusive. In this study, systematic analyses were conducted between C3-C4 intermediate Moricandia suffruticosa and its C3 relative Brassica napus. We found that M. suffruticosa leaves had significantly higher vein density than those of B. napus, and the vein density was further increased in M. suffruticosa under drought and heat stress. Moreover, the bundle sheath distance decreased and the number of centripetal chloroplasts in bundle sheath cells was found to be altered in M. suffruticosa leaves under drought and heat treatments. These results suggest that abiotic stress can induce a change in an intermediate C3-C4 anatomy towards a C4-like anatomy in land plants. By integrating drought and heat factors, co-expression network and comparative transcriptome analyses between M. suffruticosa and B. napus effectively revealed that inducible auxin signaling regulated vascular development and autophagy-related vesicle trafficking process were associated with this stress-induced anatomy change. Overexpressing three candidate genes, MsERF02, MsSCL01 and MsDOF01, increased leaf vein density and/or also enhanced photosynthetic assimilation and drought adaptability in the transgenic lines. The findings of this study may improve our understanding of the genetic regulation and evolution of C4 anatomy.
PMID: 35675763
J Exp Bot , IF:6.992 , 2022 Jun doi: 10.1093/jxb/erac251
Jasmonate action and crosstalk in flower development and fertility.
Plant Science and Technology College, Beijing University of Agriculture, Beijing, 102206, China.; Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Sciences, Capital Normal University, Beijing, 100048, China.; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.; School of Life Sciences, Tsinghua University, Beijing 100084, China.
Flower development and fertility are coordinately regulated by endogenous developmental signals, including the phytohormones jasmonates (JAs), auxin, and gibberellin, and environmental cues. JAs regulate stamen development and fertility at basal conditions, affect root growth and trichome formation under stress conditions, and control defense responses against insect herbivores and pathogens. Since 1990s, an increasing number of studies have revealed the essential roles of JA biosynthesis, signaling, and crosstalk in regulation of flower development and fertility. Here, we summarize and present an updated overview of JA pathway and crosstalk in modulating flower/sexual organ development and fertility in Arabidopsis, tomato, rice, maize, and sorghum.
PMID: 35670512
J Exp Bot , IF:6.992 , 2022 May doi: 10.1093/jxb/erac228
In vitro functional characterization predicts the impact of bacterial root endophytes on plant growth.
Department of Botany and Plant Pathology, Center for Plant Biology, Purdue University, West Lafayette IN.
Utilizing beneficial microbes for crop improvement is one strategy to achieve sustainable agriculture. However, identifying microbial isolates that promote crop growth is challenging, in part because using bacterial taxonomy to predict an isolate's effect on plant growth may not be reliable. The overall aim of this work was to determine whether in vitro functional traits of bacteria were predictive of their in planta impact. We isolated 183 bacterial endophytes from field-grown roots of two tomato species, Solanum lycopersicum and S. pimpinellifolium. Sixty isolates were screened for six in vitro functional traits: auxin production, siderophore production, phosphate solubilization, antagonism to a soilborne pathogen, and the presence of two antimicrobial metabolite synthesis genes. Hierarchical clustering of the isolates based on the in vitro functional traits identified several groups of isolates sharing similar traits. We called these groups 'functional groups'. To understand how in vitro functional traits of bacteria relate to their impact on plants, we inoculated three isolates from each of the functional groups on tomato seedlings. Isolates within the same functional group promoted plant growth at similar levels, regardless of their host origin or taxonomy. Together, our results demonstrate the importance of examining root endophyte functions for improving crop production.
PMID: 35596672
J Exp Bot , IF:6.992 , 2022 May doi: 10.1093/jxb/erac188
ROOT PENETRATION INDEX 3, a major quantitative trait locus (QTL) associated with root system penetrability in Arabidopsis.
Unidad de Genomica Avanzada/LANGEBIO, Centro de Investigacion y de Estudios Avanzados, Irapuato, Mexico.; Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA.; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX 79409, USA.
Soil mechanical impedance precludes root penetration, confining root system development to shallow soil horizons where mobile nutrients are scarce. Using a two-phase-agar system, we characterized Arabidopsis thaliana responses to low and high mechanical impedance at three root penetration stages. We found that seedlings whose roots fail to penetrate agar barriers show a significant reduction in leaf area, root length and elongation zone and an increment in root diameter, while those capable of penetrating show only minor morphological effects. Analyses using different auxin-responsive reporter lines, exogenous auxins and inhibitor treatments suggest that auxin responsiveness and PIN-mediated auxin distribution play an important role in regulating root responses to mechanical impedance. The assessment of 21 Arabidopsis accessions revealed that primary root penetrability (PRP) varies widely among accessions. To search for quantitative trait loci (QTLs) associated to root system penetrability, we evaluated a recombinant inbred population (RIL) derived from Landsberg erecta (Ler-0, with a high PRP) and Shahdara (Sha, with a low PRP) accessions. QTL analysis revealed a major-effect QTL localized in chromosome 3 (q-RPI3), which accounted for 29.98% (LOD = 8.82) of the total phenotypic variation. Employing an introgression line (IL-321), with a homozygous q-RPI3 region from Sha in the Ler-0 genetic background, we demonstrated that q-RPI3 plays a crucial role in root penetrability. This multiscale study revels new insights into root plasticity during the penetration process in hard agar layers, natural variation and genetic architecture behind primary root penetrability in Arabidopsis.
PMID: 35512438
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4094-4112 doi: 10.1093/jxb/erac152
Auxin receptors as integrators of developmental and hormonal signals during reproductive development in pea.
Plant BioSystems, Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, T6G 2P5, Canada.
Auxins regulate many aspects of plant growth and development. In pea, three of the five TIR1/AFB members (PsTIR1a, PsTIR1b, and PsAFB2) have been implicated in auxin-related responses during fruit/seed development; however, the roles of PsAFB4 and PsAFB6 in these processes are unknown. Using yeast two-hybrid assays, we found that all five pea TIR1/AFB receptor proteins interacted with the pea AUX/IAAs PsIAA6 and/or PsIAA7 in an auxin-dependent manner, a requirement for functional auxin receptors. All five auxin receptors are expressed in young ovaries (pericarps) and rapidly developing seeds, with overlapping and unique developmental and hormone-regulated gene expression patterns. Pericarp PsAFB6 expression was suppressed by seeds and increased in response to deseeding, and exogenous hormone treatments suggest that seed-derived auxin and deseeding-induced ethylene are involved in these responses, respectively. Ethylene-induced elevation of pericarp PsAFB6 expression was associated with 4-Cl-IAA-specific reduction in ethylene responsiveness. In developing seeds, expression of PsTAR2 and PsYUC10 auxin biosynthesis genes was associated with high auxin levels in seed coat and cotyledon tissues, and PsAFB2 dominated the seed tissue transcript pool. Overall, auxin receptors had overlapping and unique developmental and hormone-regulated gene expression patterns during fruit/seed development, suggesting mediation of diverse responses to auxin, with PsAFB6 linking auxin and ethylene signaling.
PMID: 35395070
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4113-4128 doi: 10.1093/jxb/erac143
Reduced auxin signalling through the cyclophilin gene DIAGEOTROPICA impacts tomato fruit development and metabolism during ripening.
Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, Minas Gerais, Brazil.; Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.; Departmento de Ciencias Biologicas, Escola Superior de Agricultura Luiz de Queiroz, Universidade de Sao Paulo, Piracicaba, Brazil.; Central Metabolism Group, Max Planck Institute of Molecular Plant Physiology, D-14476 Potsdam-Golm, Germany.
Auxin is an important hormone playing crucial roles during fruit growth and ripening; however, the metabolic impact of changes in auxin signalling during tomato (Solanum lycopersicum L.) ripening remains unclear. Here, we investigated the significance of changes in auxin signalling during different stages of fruit development by analysing changes in tomato fruit quality and primary metabolism using mutants with either lower or higher auxin sensitivity [diageotropica (dgt) and entire mutants, respectively]. Altered auxin sensitivity modifies metabolism, through direct impacts on fruit respiration and fruit growth. We verified that the dgt mutant plants exhibit reductions in fruit set, total fruit dry weight, fruit size, number of seeds per fruit, and fresh weight loss during post-harvest. Sugar accumulation was associated with delayed fruit ripening in dgt, probably connected with reduced ethylene levels and respiration, coupled with a lower rate of starch degradation. In contrast, despite exhibiting parthenocarpy, increased auxin perception (entire) did not alter fruit ripening, leading to only minor changes in primary metabolism. By performing a comprehensive analysis, our results connect auxin signalling and metabolic changes during tomato fruit development, indicating that reduced auxin signalling led to extensive changes in sugar concentration and starch metabolism during tomato fruit ripening.
PMID: 35383842
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4147-4156 doi: 10.1093/jxb/erac119
Impaired auxin signaling increases vein and stomatal density but reduces hydraulic efficiency and ultimately net photosynthesis.
Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, MG, 36570-900, Brazil.; Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
Auxins are known to regulate xylem development in plants, but their effects on water transport efficiency are poorly known. Here we used tomato plants with the diageotropica mutation (dgt), which has impaired function of a cyclophilin 1 cis-trans isomerase involved in auxin signaling, and the corresponding wild type (WT) to explore the mutation's effects on plant hydraulics and leaf gas exchange. The xylem of the dgt mutant showed a reduced hydraulically weighted vessel diameter (Dh) (24-43%) and conduit number (25-58%) in petioles and stems, resulting in lower theoretical hydraulic conductivities (Kt); on the other hand, no changes in root Dh and Kt were observed. The measured stem and leaf hydraulic conductances of the dgt mutant were lower (up to 81%), in agreement with the Kt values; however, despite dgt and WT plants showing similar root Dh and Kt, the measured root hydraulic conductance of the dgt mutant was 75% lower. The dgt mutation increased the vein and stomatal density, which could potentially increase photosynthesis. Nevertheless, even though it had the same photosynthetic capacity as WT plants, the dgt mutant showed a photosynthetic rate c. 25% lower, coupled with a stomatal conductance reduction of 52%. These results clearly demonstrate that increases in minor vein and stomatal density only result in higher leaf gas exchange when accompanied by higher hydraulic efficiency.
PMID: 35312771
J Exp Bot , IF:6.992 , 2022 Jun , V73 (12) : P4034-4045 doi: 10.1093/jxb/erac115
PHB3 regulates lateral root primordia formation via NO-mediated degradation of AUXIN/INDOLE-3-ACETIC ACID proteins.
State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong, China.; College of Food Science and Engineering, Shandong Agricultural University, Tai'an, Shandong, China.; College of Agriculture Science and Technology, Shandong Agriculture and Engineering University, Jinan Shandong, China.; Section of Cell and Developmental Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, USA.
We have previously shown that Arabidopsis thaliana Prohibitin 3 (PHB3) controls auxin-stimulated lateral root (LR) formation; however, the underlying molecular mechanism is unknown. Here, we demonstrate that PHB3 regulates lateral root (LR) development mainly through influencing lateral root primordia (LRP) initiation, via affecting nitric oxide (NO) accumulation. The reduced LRP in phb3 mutant was largely rescued by treatment with a NO donor. The decreased NO accumulation in phb3 caused a lower expression of GATA TRANSCRIPTION FACTOR 23 (GATA23) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) through inhibiting the degradation of INDOLE-3-ACETIC ACID INDUCIBLE 14/28 (IAA14/28). Overexpression of either GATA23 or LBD16 in phb3 mutant background recovered the reduced density of LRP. These results indicate that PHB3 regulates LRP initiation via NO-mediated auxin signalling, by modulating the degradation of IAA14/28.
PMID: 35303089
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3552-3568 doi: 10.1093/jxb/erac088
Cytokinin oxidase/dehydrogenase family genes exhibit functional divergence and overlap in rice growth and development, especially in control of tillering.
College of Agriculture, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.; Key Laboratory of Crop Physiology Ecology and Production Management, Ministry of Agriculture, Nanjing 210095, People's Republic of China.; Collaborative Innovation Center for Modern Crop Production co-sponsored by Province and Ministry, Nanjing 210095, People's Republic of China.
Cytokinins play key roles in plant growth and development, and hence their biosynthesis and degradation have been extensively studied. Cytokinin oxidase/dehydrogenases (CKXs) are a group of enzymes that regulate oxidative cleavage to maintain cytokinin homeostasis. In rice, 11 CKX genes have been identified to date; however, most of their functions remain unknown. In this study, we comprehensively examined the expression patterns and functions of the CKXs in rice by using CRISPR/Cas9 technology to construct mutants of all 11 genes. The results revealed that the ckx single-mutants and higher-order ckx4 ckx9 mutant lines showed functional overlaps and sub-functionalization. Notably, the ckx1 ckx2 and ckx4 ckx9 double-mutants displayed contrasting phenotypic changes in tiller number and panicle size compared to the wild-type. In addition, we identified several genes with significantly altered expression in both the ckx4 and ckx9 single-mutant and double-mutant plants. Many of the differentially expressed genes were found to be associated with auxin and cytokinin pathways, and cytokinins in the ckx4 ckx9 double-mutant were increased compared to the wild-type. Taken together, our findings provide new insights into the functions of CKX genes in rice growth and may provide the foundations for future studies aimed at improving rice yield.
PMID: 35247044
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3511-3530 doi: 10.1093/jxb/erac083
Nitrate-dependent regulation of miR444-OsMADS27 signalling cascade controls root development in rice.
National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India.; Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Universite Paris- Saclay, Versailles, France.; SASTRA University, Thirumalaisamudram, Thanjavur, India.; Department of Biological Sciences, North Dakota State University, Fargo, ND, USA.
Nitrate is an important nutrient and a key signalling molecule for plant development. A number of transcription factors involved in the response to nitrate and their regulatory mechanisms have been identified. However, little is known about the transcription factors involved in nitrate sensing and their regulatory mechanisms among crop plants. In this study, we identified functions of a nitrate-responsive miR444:MADS-box transcription factor OsMADS27 module and its downstream targets mediating rice root growth and stress responses. Transgenic rice plants expressing miR444 target mimic improved rice root growth. Although miR444 has the potential to target multiple genes, we identified OsMADS27 as the major miR444 target that regulates the expression of nitrate transporters, as well as several key genes including expansins, and those associated with auxin signalling, to promote root growth. In agreement with this, overexpression of miRNA-resistant OsMADS27 improved root development and tolerance to abiotic stresses, while its silencing suppressed root growth. OsMADS27 mediated robust stress tolerance in plants through its ability to bind to the promoters of specific stress regulators, as observed in ChIP-seq analysis. Our results provide evidence of a nitrate-dependent miR444-OsMADS27 signalling cascade involved in the regulation of rice root growth, as well as its surprising role in stress responses.
PMID: 35243491
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3496-3510 doi: 10.1093/jxb/erac079
PUCHI represses early meristem formation in developing lateral roots of Arabidopsis thaliana.
DIADE, Univ Montpellier, IRD, Montpellier, France.; Univ Montpellier, CNRS, INSERM, Montpellier, France.; Montpellier GenomiX, France Genomique, Montpellier, France.
Lateral root organogenesis is a key process in the development of a plant's root system and its adaptation to the environment. During lateral root formation, an early phase of cell proliferation first produces a four-cell-layered primordium, and only from this stage onwards is a root meristem-like structure, expressing root stem cell niche marker genes, being established in the developing organ. Previous studies reported that the gene regulatory network controlling lateral root formation is organized into two subnetworks whose mutual inhibition may contribute to organ patterning. PUCHI encodes an AP2/ERF transcription factor expressed early during lateral root primordium development and required for correct lateral root formation. To dissect the molecular events occurring during this early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 mutants and wild types. Transcriptomic and reporter analyses revealed that meristem-related genes were expressed ectopically at early stages of lateral root formation in puchi-1 mutants. We conclude that, consistent with the inhibition of genetic modules contributing to lateral root development, PUCHI represses ectopic establishment of meristematic cell identities at early stages of organ development. These findings shed light on gene network properties that orchestrate correct timing and patterning during lateral root formation.
PMID: 35224628
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3711-3725 doi: 10.1093/jxb/erac074
Serratia marcescens PLR enhances lateral root formation through supplying PLR-derived auxin and enhancing auxin biosynthesis in Arabidopsis.
The Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, China.; Peking University Institute of Advanced Agricultural Sciences, Weifang, China.; Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China.; State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China.; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
Plant growth promoting rhizobacteria (PGPR) refer to bacteria that colonize the rhizosphere and contribute to plant growth or stress tolerance. To further understand the molecular mechanism by which PGPR exhibit symbiosis with plants, we performed a high-throughput single colony screening from the rhizosphere, and uncovered a bacterium (named promoting lateral root, PLR) that significantly promotes Arabidopsis lateral root formation. By 16S rDNA sequencing, PLR was identified as a novel sub-species of Serratia marcescens. RNA-seq analysis of Arabidopsis integrated with phenotypic verification of auxin signalling mutants demonstrated that the promoting effect of PLR on lateral root formation is dependent on auxin signalling. Furthermore, PLR enhanced tryptophan-dependent indole-3-acetic acid (IAA) synthesis by inducing multiple auxin biosynthesis genes in Arabidopsis. Genome-wide sequencing of PLR integrated with the identification of IAA and its precursors in PLR exudates showed that tryptophan treatment significantly enhanced the ability of PLR to produce IAA and its precursors. Interestingly, PLR induced the expression of multiple nutrient (N, P, K, S) transporter genes in Arabidopsis in an auxin-independent manner. This study provides evidence of how PLR enhances plant growth through fine-tuning auxin biosynthesis and signalling in Arabidopsis, implying a potential application of PLR in crop yield improvement through accelerating root development.
PMID: 35196372
J Exp Bot , IF:6.992 , 2022 Jun , V73 (11) : P3671-3685 doi: 10.1093/jxb/erac059
Ammonium transporters cooperatively regulate rice crown root formation responding to ammonium nitrogen.
MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
Crown roots (CRs) are major components of the rice root system. They form at the basal node of the shoot, and their development is greatly influenced by environmental factors. Ammonium nitrogen is known to impact plant root development through ammonium transporters (AMTs), but it remains unclear whether ammonium and AMTs play roles in rice CR formation. In this study, we revealed a significant role of ammonium, rather than nitrate, in regulating rice CR development. High ammonium supply increases CR formation but inhibits CR elongation. Genetic evidence showed that ammonium regulation of CR development relies on ammonium uptake mediated jointly by ammonium transporters OsAMT1;1, OsAMT1;2; OsAMT1;3, and OsAMT2;1, but not on root acidification which was the result of ammonium uptake. OsAMTs are also needed for glutamine-induced CR formation. Furthermore, we showed that polar auxin transport dependent on the PIN auxin efflux carriers acts downstream of ammonium uptake and assimilation to activate local auxin signaling at CR primordia, in turn promoting CR formation. Taken together, our results highlight a critical role for OsAMTs in cooperatively regulating CR formation through regulating auxin transport under nitrogen-rich conditions.
PMID: 35176162
Int J Biol Macromol , IF:6.953 , 2022 May , V208 : P844-857 doi: 10.1016/j.ijbiomac.2022.03.179
Genomic & structural diversity and functional role of potassium (K(+)) transport proteins in plants.
National Institute of Plant Genome Research, New Delhi 110067, India.; National Institute of Plant Genome Research, New Delhi 110067, India. Electronic address: amarjeet.singh@nipgr.ac.in.
Potassium (K(+)) is an essential macronutrient for plant growth and productivity. It is the most abundant cation in plants and is involved in various cellular processes. Variable K(+) availability is sensed by plant roots, consequently K(+) transport proteins are activated to optimize K(+) uptake. In addition to K(+) uptake and translocation these proteins are involved in other important physiological processes like transmembrane voltage regulation, polar auxin transport, maintenance of Na(+)/K(+) ratio and stomata movement during abiotic stress responses. K(+) transport proteins display tremendous genomic and structural diversity in plants. Their key structural features, such as transmembrane domains, N-terminal domains, C-terminal domains and loops determine their ability of K(+) uptake and transport and thus, provide functional diversity. Most K(+) transporters are regulated at transcriptional and post-translational levels. Genetic manipulation of key K(+) transporters/channels could be a prominent strategy for improving K(+) utilization efficiency (KUE) in plants. This review discusses the genomic and structural diversity of various K(+) transport proteins in plants. Also, an update on the function of K(+) transport proteins and their regulatory mechanism in response to variable K(+) availability, in improving KUE, biotic and abiotic stresses is provided.
PMID: 35367275
Development , IF:6.868 , 2022 Jun , V149 (12) doi: 10.1242/dev.200403
A genetic framework for proximal secondary vein branching in the Arabidopsis thaliana embryo.
Group of Plant Vascular Development, Swiss Federal Institute of Technology (ETH) Zurich, CH-8092 Zurich, Switzerland.; Group of RNA Biology, Swiss Federal Institute of Technology (ETH) Zurich, CH-8092 Zurich, Switzerland.; Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas (CSIC)-Universitat Politecnica de Valencia (UPV), 46022 Valencia, Spain.
Over time, plants have evolved flexible self-organizing patterning mechanisms to adapt tissue functionality for continuous organ growth. An example of this process is the multicellular organization of cells into a vascular network in foliar organs. An important, yet poorly understood component of this process is secondary vein branching, a mechanism employed to extend vascular tissues throughout the cotyledon surface. Here, we uncover two distinct branching mechanisms during embryogenesis by analyzing the discontinuous vein network of the double mutant cotyledon vascular pattern 2 (cvp2) cvp2-like 1 (cvl1). Similar to wild-type embryos, distal veins in cvp2 cvl1 embryos arise from the bifurcation of cell files contained in the midvein, whereas proximal branching is absent in this mutant. Restoration of this process can be achieved by increasing OCTOPUS dosage as well as by silencing RECEPTOR-LIKE PROTEIN KINASE 2 (RPK2) expression. Although RPK2-dependent rescue of cvp2 cvl1 is auxin- and CLE peptide-independent, distal branching involves polar auxin transport and follows a distinct regulatory mechanism. Our work defines a genetic network that confers plasticity to Arabidopsis embryos to spatially adapt vascular tissues to organ growth.
PMID: 35723181
Development , IF:6.868 , 2022 May , V149 (10) doi: 10.1242/dev.200362
Phytochrome-interacting factors orchestrate hypocotyl adventitious root initiation in Arabidopsis.
National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; School of Life Science, Henan University, Kaifeng 457000, China.; Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
Adventitious roots (ARs) are an important type of plant root and display high phenotypic plasticity in response to different environmental stimuli. It is known that photoreceptors inhibit darkness-induced hypocotyl adventitious root (HAR) formation by directly stabilizing Aux/IAA proteins. In this study, we further report that phytochrome-interacting factors (PIFs) plays a central role in HAR initiation by simultaneously inducing the expression of genes involved in auxin biosynthesis, auxin transport and the transcriptional control of root primordium initiation. We found that, on the basis of their activity downstream of phytochrome, PIFs are required for darkness-induced HAR formation. Specifically, PIFs directly bind to the promoters of some genes involved in root formation, including auxin biosynthesis genes YUCCA2 (YUC2) and YUC6, the auxin influx carrier genes AUX1 and LAX3, and the transcription factors WOX5/7 and LBD16/29, to activate their expression. These findings reveal a previously uncharacterized transcriptional regulatory network underlying HAR formation.
PMID: 35502748
Development , IF:6.868 , 2022 May , V149 (9) doi: 10.1242/dev.200381
Species-specific function of conserved regulators in orchestrating rice root architecture.
Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Uttarakhand 247667, India.; School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.; School of Biology, Indian Institute of Science Education and Research, Thiruvananthapuram 695001, Kerala, India.; School of Biology, Indian Institute of Science Education and Research, Pune 411007, Maharashtra, India.; Laboratory of Plant-Microbe Interactions, Regional Center for Biotechnology, Faridabad, Haryana 110076, India.
Shoot-borne adventitious/crown roots form a highly derived fibrous root system in grasses. The molecular mechanisms controlling their development remain largely unknown. Here, we provide a genome-wide landscape of transcriptional signatures - tightly regulated auxin response and in-depth spatio-temporal expression patterns of potential epigenetic modifiers - and transcription factors during priming and outgrowth of rice (Oryza sativa) crown root primordia. Functional analyses of rice transcription factors from WUSCHEL-RELATED HOMEOBOX and PLETHORA gene families reveal their non-redundant and species-specific roles in determining the root architecture. WOX10 and PLT1 regulate both shoot-borne crown roots and root-borne lateral roots, but PLT2 specifically controls lateral root development. PLT1 activates local auxin biosynthesis genes to promote crown root development. Interestingly, O. sativa PLT genes rescue lateral root primordia outgrowth defects of Arabidopsis plt mutants, demonstrating their conserved role in root primordia outgrowth irrespective of their developmental origin. Together, our findings unveil a molecular framework of tissue transdifferentiation during root primordia establishment, leading to the culmination of robust fibrous root architecture. This also suggests that conserved factors have evolved their transcription regulation to acquire species-specific function.
PMID: 35394032
Plant J , IF:6.417 , 2022 Jun doi: 10.1111/tpj.15884
OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice.
State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, 430062, China.; Huazhong Agricultural University, Wuhan, 430070, China.; Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, 430062, China.; State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 311400, China.
As a multigenic trait, rice tillering can optimize plant architecture for the maximum agronomic yield. SQUAMOSA PROMOTER BINDING PROTEIN-LIKE14 (OsSPL14) has been demonstrated to be necessary and sufficient to inhibit rice branching, but the underlying mechanism remains largely unclear. Here, we demonstrated that OsSPL14, which is cleaved by miR529 and miR156, inhibits tillering by fine-tuning auxin transport in rice. RNA interference of OsSPL14 (OsSPL14 RNAi) or miR529 and miR156 overexpression significantly increased the tiller number, whereas OsSPL14 overexpression obviously decreased the tiller number. Histological analysis revealed that the OsSPL14-overexpressing line had normal initiation of axillary buds but inhibited outgrowth of tillers. Moreover, OsSPL14 was found to be responsive to indole-acetic acid (IAA) and 1-naphthylphthalamic acid (NPA), and OsSPL14 RNAi reduced polar auxin transport (PAT) and increased NPA sensitivity of rice plants. Further analysis revealed that OsSPL14 directly binds to the promoter of PIN-FORMED 1b (OsPIN1b) and PIN-LIKE6b (PILS6b) to positively regulate their expression. OsPIN1b and PILS6b were highly expressed in axillary buds and proved to be involved in bud outgrowth. Loss of function of OsPIN1b or PILS6b increased the tiller number of rice. Taken together, our findings suggested that OsSPL14 can control axillary bud outgrowth and tiller number by activating the expression of OsPIN1b and PILS6b to fine-tune auxin transport in rice.
PMID: 35765202
Plant J , IF:6.417 , 2022 Jun doi: 10.1111/tpj.15868
H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple.
Graduate School of Agriculture, Kyoto University, Japan.; Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, China.; School of Engineering, Utsunomiya University, Japan.; National Institute for Basic Biology, Japan.; The Graduate University for Advanced Studies, SOKENDAI, Japan.; Faculty of Agriculture, Shinshu University, Japan.; Agricultural Experimental Station, Ishikawa Prefectural University, Japan.
Bud dormancy helps woody perennials survive winter and activate robust plant development in the spring. For apple (Malus x domestica), short-term chilling induces bud dormancy in autumn, then prolonged chilling leads to dormancy release and a shift to a quiescent state in winter, with subsequent warm periods promoting bud break in spring. Epigenetic regulation contributes to seasonal responses such as vernalization. However, how histone modifications integrate seasonal cues and internal signals during bud dormancy in woody perennials remains largely unknown. Here, we show that H3K4me3 plays a key role in establishing permissive chromatin states during bud dormancy and bud break in apple. The global changes in gene expression strongly correlated with changes in H3K4me3, but not H3K27me3. High expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes, key regulators of dormancy, in autumn was associated with high H3K4me3 levels. In addition, known DAM/SHORT VEGETATIVE PHASE (SVP) target genes significantly overlapped with H3K4me3-modified genes as bud dormancy progressed. These data suggest that H3K4me3 contributes to the central dormancy circuit, consisting of DAM/SVP and abscisic acid (ABA), in autumn. In winter, the lower expression and H3K4me3 levels at DAMs and gibberellin metabolism genes control chilling-induced release of dormancy. Warming conditions in spring facilitate the expression of genes related to phytohormones, the cell cycle, and cell wall modification by increasing H3K4me3 toward bud break. Our study also revealed that activation of auxin and repression of ABA sensitivity in spring are conditioned at least partly through temperature-mediated epigenetic regulation in winter.
PMID: 35699670
Plant J , IF:6.417 , 2022 Jun , V110 (6) : P1717-1730 doi: 10.1111/tpj.15766
Control of OsARF3a by OsKANADI1 contributes to lemma development in rice.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.; University of Chinese Academy of Sciences, Beijing, 100039, China.; Southern University of Science and Technology, Shenzhen, 518055, China.; CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101, China.; Innovative Academy of Seed Design (INASEED), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
In rice (Oryza sativa), the lemma and palea protect the internal organs of the floretprovide nutrients for seed development, and determine grain size. We previously revealed that a trans-acting small interfering RNA targeting AUXIN RESPONSE FACTORS (tasiR-ARF) regulates lemma polarity establishment via post-transcriptional repression of AUXIN RESPONSE FACTORS (ARFs) in rice. TasiR-ARF formation requires RNA-DEPENDENT RNA POLYMERASE 6 (RDR6). However, the underlying molecular mechanism of the tasiR-ARF-ARF regulon in lemma development remains unclear. Here, by genetic screening for suppressors of the thermosensitive mutant osrdr6-1, we identified three suppressors, huifu 1 (hf1), hf9, and hf17. Mapping-by-sequencing revealed that HF1 encodes a MYB transcription factor belonging to the KANADI1 family. The hf1 mutation partially rescued the osrdr6-1 lemma defect but not the defect in tasiR-ARF levels. DNA affinity purification sequencing analysis identified 17 725 OsKANADI1-associated sites, most of which contain the SPBP-box binding motif (RGAATAWW) and are located in the promoter, protein-coding, intron, and intergenic regions. Moreover, we found that OsKANADI1 could directly bind to the intron of OsARF3a in vitro and in vivo and promote OsARF3a expression at the transcriptional level. In addition, hf9 and hf17 are intragenic suppressors containing mutations in OsRDR6 that partially rescue tasiR-ARF levels by restoring OsRDR6 protein levels. Collectively, our results demonstrate that OsKANADI1 and tasiR-ARFs synergistically maintain the proper expression of OsARF3a and thus contribute to rice lemma development.
PMID: 35403315
Plant J , IF:6.417 , 2022 Jun , V110 (5) : P1237-1254 doi: 10.1111/tpj.15759
The GATA factor HANABA TARANU promotes runner formation by regulating axillary bud initiation and outgrowth in cultivated strawberry.
Department of Fruit Science, College of Horticulture, China Agricultural University, Beijing, 100193, China.; Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Latokartanonkaari 7, 00790, Helsinki, Finland.; Key Laboratory of Landscaping Agriculture, Ministry of Agriculture and Rural Affairs, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.; NIAB EMR, Kent, ME19 6BJ, UK.
A runner, as an elongated branch, develops from the axillary bud (AXB) in the leaf axil and is crucial for the clonal propagation of cultivated strawberry (Fragaria x ananassa Duch.). Runner formation occurs in at least two steps: AXB initiation and AXB outgrowth. HANABA TARANU (HAN ) encodes a GATA transcription factor that affects AXB initiation in Arabidopsis and promotes branching in grass species, but the underlying mechanism is largely unknown. Here, the function of a strawberry HAN homolog FaHAN in runner formation was characterized. FaHAN transcripts can be detected in the leaf axils. Overexpression (OE) of FaHAN increased the number of runners, mainly by enhancing AXB outgrowth, in strawberry. The expression of the strawberry homolog of BRANCHED1 , a key inhibitor of AXB outgrowth in many plant species, was significantly downregulated in the AXBs of FaHAN -OE lines, whereas the expression of the strawberry homolog of SHOOT MERISTEMLESS, a marker gene for AXB initiation in Arabidopsis, was upregulated. Moreover, several genes of gibberellin biosynthesis and cytokinin signaling pathways were activated, whereas the auxin response pathway genes were repressed. Further assays indicated that FaHAN could be directly activated by FaNAC2, the overexpression of which in strawberry also increased the number of runners. The silencing of FaNAC2 or FaHAN inhibited AXB initiation and led to a higher proportion of dormant AXBs, confirming their roles in the control of runner formation. Taken together, our results revealed a FaNAC2-FaHAN pathway in the control of runner formation and have provided a means to enhance the vegetative propagation of cultivated strawberry.
PMID: 35384101
Plant J , IF:6.417 , 2022 Jun , V110 (5) : P1433-1446 doi: 10.1111/tpj.15748
Gypsy retrotransposon-derived maize lncRNA GARR2 modulates gibberellin response.
Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, 225009, China.; Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China.
Long non-coding RNAs (lncRNAs) mediate diverse biological events mainly through the modulation of transcriptional hierarchy. The phytohormone gibberellin (GA) is essential for various aspects of plant growth and development. However, the roles of lncRNAs in the regulation of the GA response remain largely unknown. Through sequencing multiple strand-specific and ribosomal-depleted RNA libraries, we delineated the landscape of lncRNAs in maize (Zea mays). Out of identified lncRNAs, 445 GIBBERELLIN-RESPONSIVE lncRNAs (GARRs) were differentially expressed upon GA application. By the intersection of GARRs from normal-height and dwarf plants from an advanced backcross population, four shared GARRs (GARR1 to GARR4) were identified. Out of these four shared GARRs, GARR2 was derived from a Gypsy LTR retrotransposon. GA-responsive element P-boxes were identified upstream of GARR2. GARR2-edited lines exhibited a GA-induced phenotype. Editing of GARR2 resulted in changes in the transcriptional abundance of GA pathway components and endogenous GA contents. Besides GA, GARR2 affected the primary auxin response. An RNA pull-down assay revealed the HECT ubiquitin-protein ligase family member ZmUPL1 as a potential interaction target of GARR2. GARR2 influenced the abundance of ZmUPL1 in the GA response. Our study uncovers lncRNA players involved in the modulation of the GA response and guides the development of plant height ideotype driven by knowledge of the phytohormone GA.
PMID: 35368126
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126841
Arabidopsis ERF012 Is a Versatile Regulator of Plant Growth, Development and Abiotic Stress Responses.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.; Microelement Research Center, College of Resources & Environment, Huazhong Agricultural University, Wuhan 430070, China.; State Key Laboratory of Crop Stress Adaptation and Improvement, Henan University, Kaifeng 475001, China.
The AP2/ERF transcription factors are widely involved in the regulation of plant growth, development and stress responses. Arabidopsis ERF012 is differentially responsive to various stresses; however, its potential regulatory role remains elusive. Here, we show that ERF012 is predominantly expressed in the vascular bundles, lateral root primordium and vein branch points. ERF012 overexpression inhibits root growth, whereas it promotes root hair development and leaf senescence. In particular, ERF012 may downregulate its target genes AtC4H and At4CL1, key players in phenylpropanoid metabolism and cell wall formation, to hinder auxin accumulation and thereby impacting root growth and leaf senescence. Consistent with this, exogenous IAA application effectively relieves the effect of ERF012 overexpression on root growth and leaf senescence. Meanwhile, ERF012 presumably activates ethylene biosynthesis to promote root hair development, considering that the ERF012-mediated root hair development can be suppressed by the ethylene biosynthetic inhibitor. In addition, ERF012 overexpression displays positive and negative effects on low- and high-temperature responses, respectively, while conferring plant resistance to drought, salinity and heavy metal stresses. Taken together, this study provides a comprehensive evaluation of the functional versatility of ERF012 in plant growth, development and abiotic stress responses.
PMID: 35743283
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126784
BIG Modulates Stem Cell Niche and Meristem Development via SCR/SHR Pathway in Arabidopsis Roots.
State Key Laboratory of Hybrid Rice, Department of Plant Sciences, College of Life Sciences, Wuhan University, Wuhan 430072, China.; Hubei Hongshan Laboratory, Wuhan 430070, China.; State Key Laboratory of Hybrid Rice, The Institute for Advanced Studies, Wuhan University, Wuhan 430072, China.
BIG, a regulator of polar auxin transport, is necessary to regulate the growth and development of Arabidopsis. Although mutations in the BIG gene cause severe root developmental defects, the exact mechanism remains unclear. Here, we report that disruption of the BIG gene resulted in decreased quiescent center (QC) activity and columella cell numbers, which was accompanied by the downregulation of WUSCHEL-RELATED HOMEOBOX5 (WOX5) gene expression. BIG affected auxin distribution by regulating the expression of PIN-FORMED proteins (PINs), but the root morphological defects of big mutants could not be rescued solely by increasing auxin transport. Although the loss of BIG gene function resulted in decreased expression of the PLT1 and PLT2 genes, genetic interaction assays indicate that this is not the main reason for the root morphological defects of big mutants. Furthermore, genetic interaction assays suggest that BIG affects the stem cell niche (SCN) activity through the SCRSCARECROW (SCR)/SHORT ROOT (SHR) pathway and BIG disruption reduces the expression of SCR and SHR genes. In conclusion, our findings reveal that the BIG gene maintains root meristem activity and SCN integrity mainly through the SCR/SHR pathway.
PMID: 35743225
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126754
Systematic Identification and Expression Analysis of the Auxin Response Factor (ARF) Gene Family in Ginkgo biloba L.
College of Forestry, Nanjing Forestry University, Nanjing 210037, China.; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China.
Auxin participates in various physiological and molecular response-related developmental processes and is a pivotal hormone that regulates phenotypic formation in plants. Auxin response factors (ARFs) are vital transcription factors that mediate downstream auxin signaling by explicitly binding to auxin-responsive genes' promoters. Here, to investigate the possible developmental regulatory functions of ARFs in Ginkgo biloba, through employing comprehensive bioinformatics, we recognized 15 putative GbARF members. Conserved domains and motifs, gene and protein structure, gene duplication, GO enrichment, transcriptome expression profiles, and qRT-PCR all showed that Group I and III members were highly conserved. Among them, GbARF10b and GbARF10a were revealed as transcriptional activators in the auxin response for the development of Ginkgo male flowers through sequences alignment, cis-elements analysis and GO annotation; the results were corroborated for the treatment of exogenous SA. Moreover, the GbARFs expansion occurred predominantly by segmental duplication, and most GbARFs have undergone purifying selection. The Ka/Ks ratio test identified the functional consistence of GbARF2a and GbARF2c, GbARF10b, and GbARF10a in tissue expression profiles and male flower development. In summary, our study established a new research basis for exploring Ginkgo GbARF members' roles in floral organ development and hormone response.
PMID: 35743196
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126570
Genome-Wide Analysis of Genes Involved in the GA Signal Transduction Pathway in 'duli' Pear (Pyrus betulifolia Bunge).
College of Horticulture, Hebei Agricultural University, Baoding 071000, China.; School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool L3 3AF, UK.
Gibberellic acid (GA) is an important phytohormone that regulates every aspect of plant growth and development. While elements involved in GA signaling have been identified and, hence, their functions have been well studied in model plants, such as Arabidopsis and rice, very little is known in pear. We, therefore, analyzed the genes related to GA signaling from the recently sequenced genome of the wildtype 'duli' pear (Pyrus betulifolia Bunge), a widely used rootstock for grafting in pear cultivation in China due to its vigorous growth and resistance to abiotic and biotic stress. In total, 15 genes were identified, including five GA receptors PbGID1s (GA-INSENSTIVE DWARF 1), six GA negative regulators, PbDELLAs, and four GA positive regulators, PbSLYs. Exogenous application of GA could promote the expression of PbGID1s but inhibit that of PbDELLAs and PbSLYs in tissue culture 'duli' pear seedlings. The expression profiles of these genes in field-grown trees under normal growth conditions, as well as in tissue-cultured seedlings treated with auxin (IAA), GA, paclobutrazol (PAC), abscisic acid (ABA), and sodium chloride (NaCl), were also studied, providing further evidence of the involvement of these genes in GA signaling in 'duli' pear plants. The preliminary results obtained in this report lay a good foundation for future research into GA signaling pathways in pear. Importantly, the identification and preliminary functional verification of these genes could guide molecular breeding in order to obtain the highly desired dwarf pear rootstocks for high-density plantation to aid easy orchard management and high yielding of pear fruits.
PMID: 35743013
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (12) doi: 10.3390/ijms23126390
Transcriptome and Metabolome Analysis Provide New Insights into the Process of Tuberization of Sechium edule Roots.
College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.; Institute for Processing and Storage of Agricultural Products, Chengdu Academy of Agricultural and Forest Sciences, Chengdu 611130, China.
Chayote (Sechium edule) produces edible tubers with high starch content after 1 year of growth but the mechanism of chayote tuberization remains unknown. 'Tuershao', a chayote cultivar lacking edible fruits but showing higher tuber yield than traditional chayote cultivars, was used to study tuber formation through integrative analysis of the metabolome and transcriptome profiles at three tuber-growth stages. Starch biosynthesis- and galactose metabolism-related genes and metabolites were significantly upregulated during tuber bulking, whereas genes encoding sugars will eventually be exported transporter (SWEET) and sugar transporter (SUT) were highly expressed during tuber formation. Auxin precursor (indole-3-acetamide) and ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, were upregulated, suggesting that both hormones play pivotal roles in tuber development and maturation. Our data revealed a similar tuber-formation signaling pathway in chayote as in potatoes, including complexes BEL1/KNOX and SP6A/14-3-3/FDL. Down-regulation of the BEL1/KNOX complex and upregulation of 14-3-3 protein implied that these two complexes might have distinct functions in tuber formation. Finally, gene expression and microscopic analysis indicated active cell division during the initial stages of tuber formation. Altogether, the integration of transcriptome and metabolome analyses unraveled an overall molecular network of chayote tuberization that might facilitate its utilization.
PMID: 35742832
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (11) doi: 10.3390/ijms23116352
The Hydrophilic Loop of Arabidopsis PIN1 Auxin Efflux Carrier Harbors Hallmarks of an Intrinsically Disordered Protein.
Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic.; Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.; VIB-UGent Center for Plant Systems, Technologiepark 71, 9052 Ghent, Belgium.; Department of Applied Genetics and Cell Biology (DAGZ), Institute of Molecular Plant Biology (IMPB), University of Natural Resources and Life Sciences (BOKU), Muthgasse 18, 1190 Vienna, Austria.; Institute of Science and Technology (IST), 3400 Klosterneuburg, Austria.
Much of plant development depends on cell-to-cell redistribution of the plant hormone auxin, which is facilitated by the plasma membrane (PM) localized PIN FORMED (PIN) proteins. Auxin export activity, developmental roles, subcellular trafficking, and polarity of PINs have been well studied, but their structure remains elusive besides a rough outline that they contain two groups of 5 alpha-helices connected by a large hydrophilic loop (HL). Here, we focus on the PIN1 HL as we could produce it in sufficient quantities for biochemical investigations to provide insights into its secondary structure. Circular dichroism (CD) studies revealed its nature as an intrinsically disordered protein (IDP), manifested by the increase of structure content upon thermal melting. Consistent with IDPs serving as interaction platforms, PIN1 loops homodimerize. PIN1 HL cytoplasmic overexpression in Arabidopsis disrupts early endocytic trafficking of PIN1 and PIN2 and causes defects in the cotyledon vasculature formation. In summary, we demonstrate that PIN1 HL has an intrinsically disordered nature, which must be considered to gain further structural insights. Some secondary structures may form transiently during pairing with known and yet-to-be-discovered interactors.
PMID: 35683031
Int J Mol Sci , IF:5.923 , 2022 Jun , V23 (11) doi: 10.3390/ijms23116219
Genome-Wide Identification and Functional Characterization of Auxin Response Factor (ARF) Genes in Eggplant.
State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China.; Scientific Observing and Experimental Station of Facility Agricultural Engineering (Huang-Huai-Hai Region), Ministry of Agriculture and Rural Affairs, Tai'an 271018, China.; Shandong Collaborative Innovation Center for Fruit and Vegetable Production with High Quality and Efficiency, Tai'an 271018, China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crop (Huang-Huai Region), Ministry of Agriculture and Rural Affairs, Tai'an 271018, China.
Auxin response factors (ARFs) are important plant transcription factors that are differentially expressed in response to auxin and various abiotic stresses. ARFs play important roles in mediating plant growth and stress responses; however, these factors have not been studied in eggplants. In this study, genome-wide identification and the functional analysis of the ARF gene family in eggplants (Solanum melongena L.) were performed. A total of 20 ARF (SmARF) genes were identified and phylogenetically classified into three groups. Our analysis revealed four functional domains and 10 motifs in these proteins. Subcellular localization showed that the SmARFs localized in the nucleus. To investigate the biological functions of the SmARFs under 2,4-D and salt stress treatments, quantitative real-time RT-PCR (qRT-PCR) was conducted. Most SmARF genes exhibited changes in expression in response to 2,4-D treatments in the flowers, especially SmARF4 and 7B. All SmARF genes quickly responded to salt stress, except SmARF17 and 19 in leaves, SmARF1A and 7B in roots, and SmARF2A, SmARF7B, and SmARF16B in stems. These results helped to elucidate the role of ARFs in auxin signaling under 2,4-D and salt stress in eggplants.
PMID: 35682898
Int J Mol Sci , IF:5.923 , 2022 May , V23 (11) doi: 10.3390/ijms23116203
Local and Systemic Response to Heterogeneous Sulfate Resupply after Sulfur Deficiency in Rice.
State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.
Sulfur (S) is an essential mineral nutrient required for plant growth and development. Plants usually face temporal and spatial variation in sulfur availability, including the heterogeneous sulfate content in soils. As sessile organisms, plants have evolved sophisticated mechanisms to modify their gene expression and physiological processes in order to optimize S acquisition and usage. Such plasticity relies on a complicated network to locally sense S availability and systemically respond to S status, which remains poorly understood. Here, we took advantage of a split-root system and performed transcriptome-wide gene expression analysis on rice plants in S deficiency followed by sulfate resupply. S deficiency altered the expressions of 6749 and 1589 genes in roots and shoots, respectively, accounting for 18.07% and 4.28% of total transcripts detected. Homogeneous sulfate resupply in both split-root halves recovered the expression of 27.06% of S-deficiency-responsive genes in shoots, while 20.76% of S-deficiency-responsive genes were recovered by heterogeneous sulfate resupply with only one split-root half being resupplied with sulfate. The local sulfate resupply response genes with expressions only recovered in the split-root half resupplied with sulfate but not in the other half remained in S deficiency were identified in roots, which were mainly enriched in cellular amino acid metabolic process and root growth and development. Several systemic response genes were also identified in roots, whose expressions remained unchanged in the split-root half resupplied with sulfate but were recovered in the other split-root half without sulfate resupply. The systemic response genes were mainly related to calcium signaling and auxin and ABA signaling. In addition, a large number of S-deficiency-responsive genes exhibited simultaneous local and systemic responses to sulfate resupply, such as the sulfate transporter gene OsSULTR1;1 and the O-acetylserine (thiol) lyase gene, highlighting the existence of a systemic regulation of sulfate uptake and assimilation in S deficiency plants followed by sulfate resupply. Our studies provided a comprehensive transcriptome-wide picture of a local and systemic response to heterogeneous sulfate resupply, which will facilitate an understanding of the systemic regulation of S homeostasis in rice.
PMID: 35682882
Int J Mol Sci , IF:5.923 , 2022 May , V23 (11) doi: 10.3390/ijms23115902
CkREV Enhances the Drought Resistance of Caragana korshinskii through Regulating the Expression of Auxin Synthetase Gene CkYUC5.
College of Horticulture, Northwest A&F University, Xianyang 712100, China.; College of Life Sciences, Northwest A&F University, Xianyang 712100, China.
As a common abiotic stress, drought severely impairs the growth, development, and even survival of plants. Here we report a transcription factor, Caragana korshinskii REVOLUTA(CkREV), which can bidirectionally regulate the expression of the critical enzyme gene CkYUC5 in auxin synthesis according to external environment changes, so as to control the biosynthesis of auxin and further enhance the drought resistance of plants. Quantitative analysis reveals that the expression level of both CkYUC5 and AtYUC5 is down-regulated after C. korshinskii and Arabidopsis thaliana are exposed to drought. Functional verification of CkREV reveals that CkREV up-regulates the expression of AtYUC5 in transgenic A. thaliana under common conditions, while down-regulating it under drought conditions. Meanwhile, the expression of CkYUC5 is also down-regulated in C. korshinskii leaves instantaneously overexpressing CkREV. We apply a dual-luciferase reporter system to discover that CkREV can bind to the promoter of CkYUC5 to regulate its expression, which is further proved by EMSA and Y1H esxperiments. Functional verification of CkREV in C. korshinskii and transgenic A. thaliana shows that CkREV can regulate the expression of CkYUC5 and AtYUC5 in a contrary way, maintaining the equilibrium of plants between growth and drought resisting. CkREV can positively regulate the expression of CkYUC5 to promote auxin synthesis in favor of growth under normal development. However, CkREV can also respond to external signals and negatively regulate the expression of CkYUC5, which inhibits auxin synthesis in order to reduce growth rate, lower water demands, and eventually improve the drought resistance of plants.
PMID: 35682582
Int J Mol Sci , IF:5.923 , 2022 May , V23 (10) doi: 10.3390/ijms23105309
Genome-Wide Identification of Auxin Response Factors in Peanut (Arachis hypogaea L.) and Functional Analysis in Root Morphology.
Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao 266237, China.; State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.; State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Life Science, Shandong Agricultural University, Tai'an 271018, China.
Auxin response factors (ARFs) play important roles in plant growth and development; however, research in peanut (Arachis hypogaea L.) is still lacking. Here, 63, 30, and 30 AhARF genes were identified from an allotetraploid peanut cultivar and two diploid ancestors (A. duranensis and A. ipaensis). Phylogenetic tree and gene structure analysis showed that most AhARFs were highly similar to those in the ancestors. By scanning the whole-genome for ARF-recognized cis-elements, we obtained a potential target gene pool of AhARFs, and the further cluster analysis and comparative analysis showed that numerous members were closely related to root development. Furthermore, we comprehensively analyzed the relationship between the root morphology and the expression levels of AhARFs in 11 peanut varieties. The results showed that the expression levels of AhARF14/26/45 were positively correlated with root length, root surface area, and root tip number, suggesting an important regulatory role of these genes in root architecture and potential application values in peanut breeding.
PMID: 35628135
Int J Mol Sci , IF:5.923 , 2022 May , V23 (10) doi: 10.3390/ijms23105301
Genetic Dissection of Light-Regulated Adventitious Root Induction in Arabidopsis thaliana Hypocotyls.
Department Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.; Biotechnology Research and Development Institute, Can Tho University, Can Tho City 900000, Vietnam.; Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Technologiepark 71, 9052 Ghent, Belgium.; VIB Center for Plant SystemsBiology, VIB, Technologiepark 71, 9052 Ghent, Belgium.; Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon 21985, Korea.
Photomorphogenic responses of etiolated seedlings include the inhibition of hypocotyl elongation and opening of the apical hook. In addition, dark-grown seedlings respond to light by the formation of adventitious roots (AR) on the hypocotyl. How light signaling controls adventitious rooting is less well understood. Hereto, we analyzed adventitious rooting under different light conditions in wild type and photomorphogenesis mutants in Arabidopsis thaliana. Etiolation was not essential for AR formation but raised the competence to form AR under white and blue light. The blue light receptors CRY1 and PHOT1/PHOT2 are key elements contributing to the induction of AR formation in response to light. Furthermore, etiolation-controlled competence for AR formation depended on the COP9 signalosome, E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC (COP1), the COP1 interacting SUPPRESSOR OF PHYA-105 (SPA) kinase family members (SPA1,2 and 3) and Phytochrome-Interacting Factors (PIF). In contrast, ELONGATED HYPOCOTYL5 (HY5), suppressed AR formation. These findings provide a genetic framework that explains the high and low AR competence of Arabidopsis thaliana hypocotyls that were treated with dark, and light, respectively. We propose that light-induced auxin signal dissipation generates a transient auxin maximum that explains AR induction by a dark to light switch.
PMID: 35628112
Int J Mol Sci , IF:5.923 , 2022 May , V23 (9) doi: 10.3390/ijms23095284
Beyond Photoprotection: The Multifarious Roles of Flavonoids in Plant Terrestrialization.
Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, 50019 Sesto Fiorentino, Florence, Italy.; Institute for Sustainable Plant Protection (IPSP), National Research Council of Italy, 50019 Sesto Fiorentino, Florence, Italy.
Plants evolved an impressive arsenal of multifunctional specialized metabolites to cope with the novel environmental pressures imposed by the terrestrial habitat when moving from water. Here we examine the multifarious roles of flavonoids in plant terrestrialization. We reason on the environmental drivers, other than the increase in UV-B radiation, that were mostly responsible for the rise of flavonoid metabolism and how flavonoids helped plants in land conquest. We are reasonably based on a nutrient-deficiency hypothesis for the replacement of mycosporine-like amino acids, typical of streptophytic algae, with the flavonoid metabolism during the water-to-land transition. We suggest that flavonoids modulated auxin transport and signaling and promoted the symbiosis between plants and fungi (e.g., arbuscular mycorrhizal, AM), a central event for the conquest of land by plants. AM improved the ability of early plants to take up nutrients and water from highly impoverished soils. We offer evidence that flavonoids equipped early land plants with highly versatile "defense compounds", essential for the new set of abiotic and biotic stressors imposed by the terrestrial environment. We conclude that flavonoids have been multifunctional since the appearance of plants on land, not only acting as UV filters but especially improving both nutrient acquisition and biotic stress defense.
PMID: 35563675
Int J Mol Sci , IF:5.923 , 2022 May , V23 (9) doi: 10.3390/ijms23095192
Identification of a Major QTL and Validation of Related Genes for Tiller Angle in Rice Based on QTL Analysis.
Department of Applied Biosciences, Graduate School, Kyungpook National University, Daegu 41566, Korea.; Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju 55365, Korea.; Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea.; Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Korea.
An ideal plant architecture is an important condition to achieve high crop yields. The tiller angle is an important and complex polygenic trait of rice (Oryza sativa L.) plant architecture. Therefore, the discovery and identification of tiller angle-related genes can aid in the improvement of crop architecture and yield. In the present study, 222 SSR markers were used to establish a high-density genetic map of rice doubled haploid population, and a total of 8 quantitative trait loci (QTLs) were detected based on the phenotypic data of the tiller angle and tiller crown width over 2 years. Among them, four QTLs (qTA9, qCW9, qTA9-1, and qCW9-1) were overlapped at marker interval RM6235-RM24288 on chromosome 9 with a large effect value regarded as a stable major QTL. The selected promising related genes were further identified by relative gene expression analysis, which gives us a basis for the future cloning of these genes. Finally, OsSAURq9, which belongs to the SMALL AUXIN UP RNA (SAUR), an auxin-responsive protein family, was selected as a target gene. Overall, this work will help broaden our knowledge of the genetic control of tiller angle and tiller crown width, and this study provides both a good theoretical basis and a new genetic resource for the breeding of ideal-type rice.
PMID: 35563584
Int J Mol Sci , IF:5.923 , 2022 May , V23 (9) doi: 10.3390/ijms23095068
Overexpression of EgrIAA20 from Eucalyptus grandis, a Non-Canonical Aux/IAA Gene, Specifically Decouples Lignification of the Different Cell-Types in Arabidopsis Secondary Xylem.
Laboratoire de Recherche en Sciences Vegetales, Universite de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France.; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China.; Arrhenius Laboratories, Department of Ecology, Environment and Plant Sciences (DEEP), Stockholm University, Svante Arrhenius vag 20A, 106 91 Stockholm, Sweden.
Wood (secondary xylem) formation is regulated by auxin, which plays a pivotal role as an integrator of developmental and environmental cues. However, our current knowledge of auxin-signaling during wood formation is incomplete. Our previous genome-wide analysis of Aux/IAAs in Eucalyptus grandis showed the presence of the non-canonical paralog member EgrIAA20 that is preferentially expressed in cambium. We analyzed its cellular localization using a GFP fusion protein and its transcriptional activity using transactivation assays, and demonstrated its nuclear localization and strong auxin response repressor activity. In addition, we functionally tested the role of EgrIAA20 by constitutive overexpression in Arabidopsis to investigate for phenotypic changes in secondary xylem formation. Transgenic Arabidopsis plants overexpressing EgrIAA20 were smaller and displayed impaired development of secondary fibers, but not of other wood cell types. The inhibition in fiber development specifically affected their cell wall lignification. We performed yeast-two-hybrid assays to identify EgrIAA20 protein partners during wood formation in Eucalyptus, and identified EgrIAA9A, whose ortholog PtoIAA9 in poplar is also known to be involved in wood formation. Altogether, we showed that EgrIAA20 is an important auxin signaling component specifically involved in controlling the lignification of wood fibers.
PMID: 35563457
Front Plant Sci , IF:5.753 , 2022 , V13 : P902694 doi: 10.3389/fpls.2022.902694
Melatonin-Induced Protection Against Plant Abiotic Stress: Mechanisms and Prospects.
Research Center on Ecological Sciences, Jiangxi Agricultural University, Nanchang, China.; Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan.; Department of Agronomy, Sub-Campus Depalpur, Okara, University of Agriculture Faisalabad, Faisalabad, Pakistan.; Biology Department, Collage of Science, Jouf University, Sakaka, Saudi Arabia.; Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Prague, Czechia.; Department of Plant Physiology, Slovak University of Agriculture, Nitra, Slovakia.; Department of Agriculture, Guru Nanak Dev University, Amritsar, India.; Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, Egypt.; Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt, Turkey.; Department of Biology, Al-Jumum University College, Umm Al-Qura University, Makkah, Saudi Arabia.
Global warming in this century increases incidences of various abiotic stresses restricting plant growth and productivity and posing a severe threat to global food production and security. The plant produces different osmolytes and hormones to combat the harmful effects of these abiotic stresses. Melatonin (MT) is a plant hormone that possesses excellent properties to improve plant performance under different abiotic stresses. It is associated with improved physiological and molecular processes linked with seed germination, growth and development, photosynthesis, carbon fixation, and plant defence against other abiotic stresses. In parallel, MT also increased the accumulation of multiple osmolytes, sugars and endogenous hormones (auxin, gibberellic acid, and cytokinins) to mediate resistance to stress. Stress condition in plants often produces reactive oxygen species. MT has excellent antioxidant properties and substantially scavenges reactive oxygen species by increasing the activity of enzymatic and non-enzymatic antioxidants under stress conditions. Moreover, the upregulation of stress-responsive and antioxidant enzyme genes makes it an excellent stress-inducing molecule. However, MT produced in plants is not sufficient to induce stress tolerance. Therefore, the development of transgenic plants with improved MT biosynthesis could be a promising approach to enhancing stress tolerance. This review, therefore, focuses on the possible role of MT in the induction of various abiotic stresses in plants. We further discussed MT biosynthesis and the critical role of MT as a potential antioxidant for improving abiotic stress tolerance. In addition, we also addressed MT biosynthesis and shed light on future research directions. Therefore, this review would help readers learn more about MT in a changing environment and provide new suggestions on how this knowledge could be used to develop stress tolerance.
PMID: 35755707
Front Plant Sci , IF:5.753 , 2022 , V13 : P918112 doi: 10.3389/fpls.2022.918112
The Adaxial/Abaxial Patterning of Auxin and Auxin Gene in Leaf Veins Functions in Leafy Head Formation of Chinese Cabbage.
Beijing Vegetable Research Center (BVRC), Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China.; National Engineering Research Center for Vegetables, Beijing, China.; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, China.; Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China.; Key Laboratory of the Vegetable Postharvest Treatment of Ministry of Agriculture, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Institute of Agri-Food Processing and Nutrition (IAPN), Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Leaf curling is an essential prerequisite for the formation of leafy heads in Chinese cabbage. However, the part or tissue that determines leaf curvature remains largely unclear. In this study, we first introduced the auxin-responsive marker DR5::GUS into the Chinese cabbage genome and visualized its expression during the farming season. We demonstrated that auxin response is adaxially/abaxially distributed in leaf veins. Together with the fact that leaf veins occupy considerable proportions of the Chinese cabbage leaf, we propose that leaf veins play a crucial supporting role as a framework for heading. Then, by combining analyses of QTL mapping and a time-course transcriptome from heading Chinese cabbage and non-heading pak choi during the farming season, we identified the auxin-related gene BrPIN5 as a strong candidate for leafy head formation. PIN5 displays an adaxial/abaxial expression pattern in leaf veins, similar to that of DR5::GUS, revealing an involvement of BrPIN5 in leafy head development. The association of BrPIN5 function with heading was further confirmed by its haplo-specificity to heading individuals in both a natural population and two segregating populations. We thus conclude that the adaxial/abaxial patterning of auxin and auxin genes in leaf veins functions in the formation of the leafy head in Chinese cabbage.
PMID: 35755702
Front Plant Sci , IF:5.753 , 2022 , V13 : P924490 doi: 10.3389/fpls.2022.924490
Integrated Transcriptomic and Proteomic Analyses Uncover the Regulatory Mechanisms of Myricaria laxiflora Under Flooding Stress.
Rare Plants Research Institute of Yangtze River, China Three Gorges Corporation, Yichang, China.; National Engineering Research Center of Eco-Environment Protection for Yangtze River Economic Belt, Beijing, China.; Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, China.; College of Horticulture and Forestry, Huazhong Agricultural University, Wuhan, China.
Flooding is one of the major environmental stresses that severely influence plant survival and development. However, the regulatory mechanisms underlying flooding stress remain largely unknown in Myricaria laxiflora, an endangered plant mainly distributed in the flood zone of the Yangtze River, China. In this work, transcriptome and proteome were performed in parallel in roots of M. laxiflora during nine time-points under the flooding and post-flooding recovery treatments. Overall, highly dynamic and stage-specific expression profiles of genes/proteins were observed during flooding and post-flooding recovery treatment. Genes related to auxin, cell wall, calcium signaling, and MAP kinase signaling were greatly down-regulated exclusively at the transcriptomic level during the early stages of flooding. Glycolysis and major CHO metabolism genes, which were regulated at the transcriptomic and/or proteomic levels with low expression correlations, mainly functioned during the late stages of flooding. Genes involved in reactive oxygen species (ROS) scavenging, mitochondrial metabolism, and development were also regulated exclusively at the transcriptomic level, but their expression levels were highly up-regulated upon post-flooding recovery. Moreover, the comprehensive expression profiles of genes/proteins related to redox, hormones, and transcriptional factors were also investigated. Finally, the regulatory networks of M. laxiflora in response to flooding and post-flooding recovery were discussed. The findings deepen our understanding of the molecular mechanisms of flooding stress and shed light on the genes and pathways for the preservation of M. laxiflora and other endangered plants in the flood zone.
PMID: 35755690
Front Plant Sci , IF:5.753 , 2022 , V13 : P902902 doi: 10.3389/fpls.2022.902902
Design, Synthesis, and Action Mechanism of 1,3-Benzodioxole Derivatives as Potent Auxin Receptor Agonists and Root Growth Promoters.
College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.; College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou, China.; School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, China.
Deeper and longer roots allow crops to survive and flourish, but our understanding of the plant growth regulators promoting root system establishment is limited. Here, we report that, a novel auxin receptor agonist, named K-10, had a remarkable promotive effect on root growth in both Arabidopsis thaliana and Oryza sativa through the enhancement of root-related signaling responses. Using computer-aided drug discovery approaches, we developed potent lead compound by screening artificial chemicals on the basis of the auxin receptor TIR1 (Transport Inhibitor Response 1), and a series of N-(benzo[d] [1,3] dioxol-5-yl)-2-(one-benzylthio) acetamides, K-1 to K-22, were designed and synthesized. The results of bioassay showed that K-10 exhibited an excellent root growth-promoting activity far exceeding that of NAA (1-naphthylacetic acid). A further morphological investigation of the auxin related mutants (yucQ, tir1) revealed that K-10 had auxin-like physiological functions and was recognized by TIR1, and K-10 significantly enhanced auxin response reporter's (DR5:GUS) transcriptional activity. Consistently, transcriptome analysis showed that K-10 induced a common transcriptional response with auxin and down-regulated the expression of root growth-inhibiting genes. Further molecular docking analysis revealed that K-10 had a stronger binding ability with TIR1 than NAA. These results indicated that this class of derivatives could be a promising scaffold for the discovery and development of novel auxin receptor agonists, and the employment of K-10 may be effective for enhancing root growth and crop production.
PMID: 35755644
Front Plant Sci , IF:5.753 , 2022 , V13 : P898786 doi: 10.3389/fpls.2022.898786
Integrative Analysis of the GRAS Genes From Chinese White Pear (Pyrus bretschneideri): A Critical Role in Leaf Regeneration.
School of Life Sciences, Anhui Agricultural University, Hefei, China.; Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia.
GRAS is a transcription regulator factor, which plays an important role in plant growth and development. Previous analyses found that several GRAS functions have been identified, such as axillary bud meristem formation, radial root elongation, gibberellin signaling, light signaling, and abiotic stress. The GRAS family has been comprehensively evaluated in several species. However, little finding is on the GRAS transcription factors (TFs) in Chinese white pear. In this study, 99 PbGRAS were systemically characterized and renamed PbGRAS1 to PbGRAS99 according to their chromosomal localizations. Phylogenetic analysis and structural features revealed that could be classified into eight subfamilies (LISCL, Ls, SHR, HAM, SCL, PAT, SCR, and DELLA). Further analysis of introns/exons and conserved motifs revealed that they are diverse and functionally differentiated in number and structure. Synteny analysis among Pyrus bretschenedri, Prunus mume, Prunus avium, Fragaria vesca, and Prunus persica showed that GRAS duplicated regions were more conserved. Dispersed duplication events are the most common mechanism and may play a crucial role in the expansion of the GRAS gene family. In addition, cis-acting elements of the PbGRAS gene were found in promoter regions associated with hormone and environmental stress responses. Notably, the expression pattern detected by qRT-PCR indicated that PbGRAS genes were differentially expressed under gibberellin (GA), abscisic acid (ABA), and auxin (IAA) conditions, which are responsive to abiotic stress. PbGRAS89 and PbGRAS99 were highly expressed at different stages of hormone treatment and may play important role in leaf development. Therefore, we selected PbGRAS89 and PbGRAS99 to clone and construct pCAMBIA1301-PbGRAS89, 99 and transferred them into Arabidopsis thaliana. Finally, we observed and compared the changes of overexpressed plants and wild-type plants during regeneration. This method was used to analyze their roles in leaf regeneration of Chinese white pear. In addition, we also constructed pCAMBIA1305-PbGRAS89, 99, and transferred them into onion cells to determine the subcellular localization. Subcellular localization experiments showed that PbGRAS89 and PbGRAS99 were localized in the nucleus. In summary, the results of this study indicate that PbGRAS89 and PbGRAS99 are mainly responsible for leaf regeneration of Chinese white pear, which plays a positive role in callus formation and provides rich resources for studying GRAS gene functions.
PMID: 35734253
Front Plant Sci , IF:5.753 , 2022 , V13 : P888939 doi: 10.3389/fpls.2022.888939
Deciphering the Molecular Signatures Associated With Resistance to Botrytis cinerea in Strawberry Flower by Comparative and Dynamic Transcriptome Analysis.
Hubei Key Laboratory of Vegetable Germplasm Enhancement and Genetic Improvement, Institute of Industrial Crops, Hubei Academy of Agricultural Sciences, Wuhan, China.
Gray mold caused by Botrytis cinerea, which is considered to be the second most destructive necrotrophic fungus, leads to major economic losses in strawberry (Fragaria x ananassa) production. B. cinerea preferentially infects strawberry flowers and fruits, leading to flower blight and fruit rot. Compared with those of the fruit, the mechanisms of flower defense against B. cinerea remain largely unexplored. Therefore, in this study, we aimed to unveil the resistance mechanisms of strawberry flower through dynamic and comparative transcriptome analysis with resistant and susceptible strawberry cultivars. Our experimental data suggest that resistance to B. cinerea in the strawberry flower is probably regulated at the transcriptome level during the early stages of infection and strawberry flower has highly complex and dynamic regulatory networks controlling a multi-layered defense response to B. cinerea. First of all, the higher expression of disease-resistance genes but lower expression of cell wall degrading enzymes and peroxidases leads to higher resistance to B. cinerea in the resistant cultivar. Interestingly, CPKs, RBOHDs, CNGCs, and CMLs comprised a calcium signaling pathway especially play a crucial role in enhancing resistance by increasing their expression. Besides, six types of phytohormones forming a complex regulatory network mediated flower resistance, especially JA and auxin. Finally, the genes involved in the phenylpropanoid and amino acids biosynthesis pathways were gene sets specially expressed or different expression genes, both of them contribute to the flower resistance to B. cinerea. These data provide the foundation for a better understanding of strawberry gray mold, along with detailed genetic information and resistant materials to enable genetic improvement of strawberry plant resistance to gray mold.
PMID: 35720571
Front Plant Sci , IF:5.753 , 2022 , V13 : P917354 doi: 10.3389/fpls.2022.917354
Growth-Defense Trade-Offs Induced by Long-term Overgrazing Could Act as a Stress Memory.
School of Ecology and Environment, Inner Mongolia University, Hohhot, China.; Department of Biology, Edge Hill University, Ormskirk, United Kingdom.; Inner Mongolia Mongolian Grass Seed Industry Science and Technology Research Institute Co., Ltd., Hohhot, China.
Long-term overgrazing (OG) is one of the key drivers of global grassland degradation with severe loss of productivity and ecosystem functions, which may result in stress memory such as smaller stature of grassland plants. However, how the OG-induced stress memory could be regulated by phytohormones is unknown. In this study, we investigated the changes of four phytohormones of cloned offspring of Leymus chinensis that were developed from no-grazing (NG) plants and OG plants with a grazing history of 30 years. The concentrations of auxin (IAA) and gibberellic acid (GA) in OG plant leaves were 45% and 20% lower than control, respectively. Meanwhile, the level of abscisic acid (ABA) in OG leaves nearly doubled compared with that in NG leaves. The situation was quite similar in roots. Unexpectedly, no significant changes in the jasmonic acid (JA) level were observed between OG and NG plants. The changes in gene expression patterns between OG and NG plants were also investigated by transcriptomic analysis. In total, 302 differentially expressed genes (DEGs) were identified between OG and NG plants, which were mainly classified into the functions of synthesis, receptor, and signal transduction processes of phytohormones. The expression of 24 key genes related to the biosynthesis and signal transduction of IAA and GA was downregulated in OG plants. Among them, OASA1 and AO1 (regulating the biosynthesis of IAA and ABA, respectively) were reduced significantly by 88 and 92%, respectively. In addition, the content of secondary metabolites related to plant defense such as flavonoids and phenols was also increased in leaves. Taken together, the decrease of positive plant growth-related hormones (IAA and GA) together with the increase of plant stress-related hormones or factors (ABA, flavonoids, and phenols) induced the growth-defense trade-offs for L. chinensis adaptation to long-term OG stress. The findings reported in this study shed new light on the mechanism of plant-animal interaction in the grassland ecosystem and provide a deeper insight into optimizing grazing management and sustainable utilization of grassland.
PMID: 35720531
Front Plant Sci , IF:5.753 , 2022 , V13 : P841693 doi: 10.3389/fpls.2022.841693
Identification of Genetic Loci for Sugarcane Leaf Angle at Different Developmental Stages by Genome-Wide Association Study.
Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou, China.; College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, China.
Sugarcane (Saccharum spp.) is an efficient crop mainly used for sugar and bioethanol production. High yield and high sucrose of sugarcane are always the fundamental demands in sugarcane growth worldwide. Leaf angle and size of sugarcane can be attributed to planting density, which was associated with yield. In this study, we performed genome-wide association studies (GWAS) with a panel of 216 sugarcane core parents and their derived lines (natural population) to determine the genetic basis of leaf angle and key candidate genes with +2, +3, and +4 leaf at the seedling, elongation, and mature stages. A total of 288 significantly associated loci of sugarcane leaf angle at different developmental stages (eight phenotypes) were identified by GWAS with 4,027,298 high-quality SNP markers. Among them, one key locus and 11 loci were identified in all three stages and two stages, respectively. An InDel marker (SNP Ss6A_102766953) linked to narrow leaf angle was obtained. Overall, 4,089 genes were located in the confidence interval of significant loci, among which 3,892 genes were functionally annotated. Finally, 13 core parents and their derivatives tagged with SNPs were selected for marker-assisted selection (MAS). These candidate genes are mainly related to MYB transcription factors, auxin response factors, serine/threonine protein kinases, etc. They are directly or indirectly associated with leaf angle in sugarcane. This research provided a large number of novel genetic resources for the improvement of leaf angles and simultaneously to high yield and high bioethanol production.
PMID: 35693186
Front Plant Sci , IF:5.753 , 2022 , V13 : P878558 doi: 10.3389/fpls.2022.878558
Fine Mapping and Cloning of a Major QTL qph12, Which Simultaneously Affects the Plant Height, Panicle Length, Spikelet Number and Yield in Rice (Oryza sativa L.).
Rice Research Institute, Fujian High Quality Rice Research and Development Center, Fujian Academy of Agricultural Sciences, Fuzhou, China.; College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.; Faculty of Agriculture, Department of Agronomy, Assiut University, Assiut, Egypt.
Plant height is one of the most important agronomical traits in rice (Oryza sativa L.). Introducing the semidwarf rice in the 1960s significantly enhanced the rice yield potential in Asia. Implementing near-isogenic lines (NILs) is the most powerful tool for the identification and fine mapping of quantitative trait loci (QTLs). In this study, 176 NILs were produced from the crossing and back-crossing of two rice cultivars. Specifically, the indica rice cultivar Jiafuzhan served as a recipient, and the restorer japonica cultivar Hui1586 served as a donor. Using the 176 NILs, we identified a novel major QTL for reduced plant height in the NIL36 line. The qph12 QTL was mapped to a 31 kb genomic region between the indel markers Indel12-29 and Indel12-31. The rice genome annotation indicated the presence of three candidate genes in this genomic region. Through gene prediction and cDNA sequencing, we confirmed that LOC_Os12g40890 (qPH12) is the target gene in the NIL36 line. Further analysis showed that the qph12 QTL is caused by a 1 bp deletion in the first exon that resulted in premature termination of the qPH12. Knockout experiments showed that the qph12 QTL is responsible for the reduced plant height phenotype of the NIL36 line. Although the qph12 gene from the NIL36 line showed a shorter panicle length, fewer spikelets per panicle and a lower plant grain yield, the plant also exhibited a lower plant height. Taken together, our results revealed that the qph12 have good specific application prospects in future rice breeding.
PMID: 35693171
Front Plant Sci , IF:5.753 , 2022 , V13 : P884572 doi: 10.3389/fpls.2022.884572
gamma-Aminobutyrate Improves the Postharvest Marketability of Horticultural Commodities: Advances and Prospects.
Department of Horticultural Science, Imam Khomeini International University, Qazvin, Iran.; Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.
Postharvest deterioration can result in qualitative and quantitative changes in the marketability of horticultural commodities, as well as considerable economic loss to the industry. Low temperature and controlled atmosphere conditions (low O2 and elevated CO2) are extensively employed to prolong the postharvest life of these commodities. Nevertheless, they may suffer from chilling injury and other physiological disorders, as well as excessive water loss and bacterial/fungal decay. Research on the postharvest physiological, biochemical, and molecular responses of horticultural commodities indicates that low temperature/controlled atmosphere storage is associated with the promotion of gamma-aminobutyrate (GABA) pathway activity, with or without the accumulation of GABA, delaying senescence, preserving quality and ameliorating chilling injury. Regardless of whether apple fruits are stored under low temperature/controlled atmosphere conditions or room temperature, elevated endogenous GABA or exogenous GABA maintains their quality by stimulating the activity of the GABA shunt (glutamate GABA succinic semialdehyde succinate) and the synthesis of malate, and delaying fruit ripening. This outcome is associated with changes in the genetic and biochemical regulation of key GABA pathway reactions. Flux estimates suggest that the GABA pool is derived primarily from glutamate, rather than polyamines, and that succinic semialdehyde is converted mainly to succinate, rather than gamma-hydroxybutyrate. Exogenous GABA is a promising strategy for promoting the level of endogenous GABA and the activity of the GABA shunt in both intact and fresh-cut commodities, which increases carbon flux through respiratory pathways, restores or partially restores redox and energy levels, and improves postharvest marketability. The precise mechanisms whereby GABA interacts with other signaling molecules such as Ca(2+), H2O2, polyamines, salicylic acid, nitric oxide and melatonin, or with phytohormones such as ethylene, abscisic acid and auxin remain unknown. The occurrence of the aluminum-activated malate transporter and the glutamate/aspartate/GABA exchanger in the tonoplast, respectively, offers prospects for reducing transpirational water in cut flowers and immature green fruit, and for altering the development, flavor and biotic resistance of apple fruits.
PMID: 35693167
Front Plant Sci , IF:5.753 , 2022 , V13 : P904162 doi: 10.3389/fpls.2022.904162
Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress.
Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Science, Weifang, China.; School of Advanced Agricultural Sciences, Peking University, Beijing, China.
Peanut is an oil crop with important economic value that is widely cultivated around the world. It blooms on the ground but bears fruit underground. When the peg penetrates the ground, it enters a dark environment, is subjected to mechanical stress from the soil, and develops into a normal pod. When a newly developed pod emerges from the soil, it turns green and stops growing. It has been reported that both darkness and mechanical stress are necessary for normal pod development. In this study, we investigated changes in gene expression during the reverse process of peg penetration: developmental arrest caused by pod (Pattee 3 pods) excavation. Bagging the aerial pods was used to simulate loss of mechanical pressure, while direct exposure of the aerial pods was used to simulate loss of both mechanical pressure and darkness. After the loss of mechanical stress and darkness, the DEGs were significantly enriched in photosynthesis, photosynthesis-antenna proteins, plant-pathogen interaction, DNA replication, and circadian rhythm pathways. The DNA replication pathway was enriched by down-regulated genes, and the other four pathways were enriched by upregulated genes. Upregulated genes were also significantly enriched in protein ubiquitination and calmodulin-related genes, highlighting the important role of ubiquitination and calcium signaling in pod development. Further analysis of DEGs showed that phytochrome A (Phy A), auxin response factor 9 (IAA9), and mechanosensitive ion channel protein played important roles in geocarpy. The expression of these two genes increased in subterranean pods but decreased in aerial pods. Based on a large number of chloroplast-related genes, calmodulin, kinases, and ubiquitin-related proteins identified in this study, we propose two possible signal transduction pathways involved in peanut geocarpy, namely, one begins in chloroplasts and signals down through phosphorylation, and the other begins during abiotic stress and signals down through calcium signaling, phosphorylation, and ubiquitination. Our study provides valuable information about putative regulatory genes for peanut pod development and contributes to a better understanding of the biological phenomenon of geocarpy.
PMID: 35693161
Front Plant Sci , IF:5.753 , 2022 , V13 : P886700 doi: 10.3389/fpls.2022.886700
The Root Clock as a Signal Integrator System: Ensuring Balance for Survival.
Centro de Biotecnologia y Genomica de Plantas (Universidad Politecnica de Madrid - Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria), Madrid, Spain.
The root system is essential for the survival of terrestrial plants, plant development, and adaptation to changing environments. The development of the root system relies on post-embryonic organogenesis and more specifically on the formation and growth of lateral roots (LR). The spacing of LR along the main root is underpinned by a precise prepatterning mechanism called the Root Clock. In Arabidopsis, the primary output of this mechanism involves the generation of periodic gene expression oscillations in a zone close to the root tip called the Oscillation Zone (OZ). Because of these oscillations, pre-branch sites (PBS) are established in the positions from which LR will emerge, although the oscillations can also possibly regulate the root wavy pattern and growth. Furthermore, we show that the Root Clock is present in LR. In this review, we describe the recent advances unraveling the inner machinery of Root Clock as well as the new tools to track the Root Clock activity. Moreover, we discuss the basis of how Arabidopsis can balance the creation of a repetitive pattern while integrating both endogenous and exogenous signals to adapt to changing environmental conditions. These signals can work as entrainment signals, but in occasions they also affect the periodicity and amplitude of the oscillatory dynamics in gene expression. Finally, we identify similarities with the Segmentation Clock of vertebrates and postulate the existence of a determination front delimiting the end of the oscillations in gene expression and initiating LR organogenesis through the activation of PBS in an ARF7 dependent-manner.
PMID: 35665188
Front Plant Sci , IF:5.753 , 2022 , V13 : P889460 doi: 10.3389/fpls.2022.889460
Nitrilases NIT1/2/3 Positively Regulate Flowering by Inhibiting MAF4 Expression in Arabidopsis.
Department of Biological Sciences, College of Life Sciences, Northeast Agricultural University, Harbin, China.
Three of the nitrilases (NITs), NIT1, NIT2, and NIT3, are ubiquitously existing in plant kingdom, which catalyze indole-3-acetonitrile into the most important auxin indole-3-acetic acid. Auxin is an indispensable hormone, which plays the important roles in almost all processes of plant growth and development. However, there are few reports on the regulation of flowering-time mediated by auxin. Here, we found that in Arabidopsis, nit1/2/3 showed a late flowering phenotype in short days. To explore the molecular mechanism by which NIT1/2/3 regulate flowering time, we performed transcriptome sequencing of nit1/2/3. The results showed that the expression of a MADS-box transcription factor gene MADS AFFECTING FLOWERING4 (MAF4) was dramatically increased in nit1/2/3 comparing to wild type (WT). MAF4 is one of the paralogs of the potent flowering inhibitor FLOWERING LOCUS C (FLC). There are four other paralogs in FLC clade in Arabidopsis, including FLOWERING LOCUS M (FLM/MAF1), MAF2, MAF3, and MAF5. The late flowering phenotype of nit1/2/3 could not be observed in the maf4 background, indicating that the phenotype was specifically dependent on MAF4 rather than other FLC clade members. Interestingly, the expression of a lncRNA gene MAS, which is transcribed in the opposite direction of MAF4, was found significantly increased in nit1/2/3. Also, MAS has been reported to activate MAF4 transcription by promoting histone 3 lysine 4 trimethylation (H3K4me3). As expected, H3K4me3 deposition at MAF4 locus in nit1/2/3 was highly enriched and significantly higher than that of WT. In summary, we show that NITs, NIT1/2/3, positively regulate flowering by repressing MAF4 through manipulating H3K4me3 modification. Further study needs to be performed to explore the largely unknown mechanisms behind it.
PMID: 35665187
Front Plant Sci , IF:5.753 , 2022 , V13 : P899206 doi: 10.3389/fpls.2022.899206
Parental Genome Imbalance Causes Hybrid Seed Lethality as Well as Ovary Abscission in Interspecific and Interploidy Crosses in Nicotiana.
Laboratory of Plant Breeding and Propagation, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, Japan.; Laboratory of Breeding and Genetics, Graduate School of Agriculture, Osaka Metropolitan University, Sakai, Japan.; Education and Research Field, School of Agriculture, Osaka Metropolitan University, Sakai, Japan.; Bioeconomy Research Institute, Research Center for the 21st Century, Osaka Metropolitan University, Sakai, Japan.
Enhanced ovary abscission after pollination and hybrid seed lethality result in post-zygotic reproductive isolation in plant interspecific crosses. However, the connection between these barriers remains unclear. Here, we report that an imbalance in parental genomes or endosperm balance number (EBN) causes hybrid seed lethality and ovary abscission in both interspecific and intraspecific-interploidy crosses in the genus Nicotiana. Auxin treatment suppressed ovary abscission, but not hybrid seed lethality, in an interspecific cross between Nicotiana suaveolens and N. tabacum, suggesting that ovary abscission-related genes are located downstream of those involved in hybrid seed lethality. We performed interploidy crosses among N. suaveolens tetraploids, octoploids, and neopolyploids and revealed hybrid seed lethality and ovary abscission in interploid crosses. Furthermore, a higher maternal EBN than paternal EBN caused these barriers, as previously observed in N. suaveolens x N. tabacum crosses. Altogether, these results suggest that maternal excess of EBN causes hybrid seed lethality, which in turn leads to ovary abscission through the same mechanism in both interspecific and interploidy crosses.
PMID: 35665169
Front Plant Sci , IF:5.753 , 2022 , V13 : P866322 doi: 10.3389/fpls.2022.866322
Full-Length Transcriptional Analysis of the Same Soybean Genotype With Compatible and Incompatible Reactions to Heterodera glycines Reveals Nematode Infection Activating Plant Defense Response.
Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China.; Heilongjiang Academy of Agricultural Sciences, Daqing, China.
Full-length transcriptome sequencing with long reads is a powerful tool to analyze transcriptional and post-transcriptional events; however, it has not been applied on soybean (Glycine max). Here, a comparative full-length transcriptome analysis was performed on soybean genotype 09-138 infected with soybean cyst nematode (SCN, Heterodera glycines) race 4 (SCN4, incompatible reaction) and race 5 (SCN5, compatible reaction) using Oxford Nanopore Technology. Each of 9 full-length samples collected 8 days post inoculation with/without nematodes generated an average of 6.1 GB of clean data and a total of 65,038 transcript sequences. After redundant transcripts were removed, 1,117 novel genes and 41,096 novel transcripts were identified. By analyzing the sequence structure of the novel transcripts, a total of 28,759 complete open reading frame (ORF) sequences, 5,337 transcription factors, 288 long non-coding RNAs, and 40,090 novel transcripts with function annotation were predicted. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of differentially expressed genes (DEGs) revealed that growth hormone, auxin-activated signaling pathway and multidimensional cell growth, and phenylpropanoid biosynthesis pathway were enriched by infection with both nematode races. More DEGs associated with stress response elements, plant-hormone signaling transduction pathway, and plant-pathogen interaction pathway with more upregulation were found in the incompatible reaction with SCN4 infection, and more DEGs with more upregulation involved in cell wall modification and carbohydrate bioprocess were detected in the compatible reaction with SCN5 infection when compared with each other. Among them, overlapping DEGs with a quantitative difference was triggered. The combination of protein-protein interaction with DEGs for the first time indicated that nematode infection activated the interactions between transcription factor WRKY and VQ (valine-glutamine motif) to contribute to soybean defense. The knowledge of the SCN-soybean interaction mechanism as a model will present more understanding of other plant-nematode interactions.
PMID: 35665156
Front Plant Sci , IF:5.753 , 2022 , V13 : P882587 doi: 10.3389/fpls.2022.882587
The hexokinase Gene Family in Cotton: Genome-Wide Characterization and Bioinformatics Analysis.
School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, China.; College of Life Sciences, Shaanxi Normal University, Xi'an, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
Hexokinase (HXK) is involved in hexose phosphorylation, sugar sensing, and signal transduction, all of which regulate plant growth and adaptation to stresses. Gossypium hirsutum L. is one of the most important fiber crops in the world, however, little is known about the HXKs gene family in G. hirsutum L. We identified 17 GhHXKs from the allotetraploid G. hirsutum L. genome (AADD). G. raimondii (DD) and G. arboreum (AA) are the diploid progenitors of G. hirsutum L. and contributed equally to the At_genome and Dt_genome GhHXKs genes. The chromosomal locations and exon-intron structures of GhHXK genes among cotton species are conservative. Phylogenetic analysis grouped the HXK proteins into four and three groups based on whether they were monocotyledons and dicotyledons, respectively. Duplication event analysis demonstrated that HXKs in G. hirsutum L. primarily originated from segmental duplication, which prior to diploid hybridization. Experiments of qRT-PCR, transcriptome and promoter cis-elements demonstrated that GhHXKs' promoters have auxin and GA responsive elements that are highly expressed in the fiber initiation and elongation stages, while the promoters contain ABA-, MeJA-, and SA-responsive elements that are highly expressed during the synthesis of the secondary cell wall. We performed a comprehensive analysis of the GhHXK gene family is a vital fiber crop, which lays the foundation for future studies assessing its role in fiber development.
PMID: 35651774
Front Plant Sci , IF:5.753 , 2022 , V13 : P888425 doi: 10.3389/fpls.2022.888425
Molecular Determinants of in vitro Plant Regeneration: Prospects for Enhanced Manipulation of Lettuce (Lactuca sativa L.).
The Genome Center, University of California, Davis, Davis, CA, United States.; Graduate Group in Horticulture and Agronomy, University of California, Davis, Davis, CA, United States.; Department of Plant Sciences, University of California, Davis, Davis, CA, United States.
In vitro plant regeneration involves dedifferentiation and molecular reprogramming of cells in order to regenerate whole organs. Plant regeneration can occur via two pathways, de novo organogenesis and somatic embryogenesis. Both pathways involve intricate molecular mechanisms and crosstalk between auxin and cytokinin signaling. Molecular determinants of both pathways have been studied in detail in model species, but little is known about the molecular mechanisms controlling de novo shoot organogenesis in lettuce. This review provides a synopsis of our current knowledge on molecular determinants of de novo organogenesis and somatic embryogenesis with an emphasis on the former as well as provides insights into applying this information for enhanced in vitro regeneration in non-model species such as lettuce (Lactuca sativa L.).
PMID: 35615120
Front Plant Sci , IF:5.753 , 2022 , V13 : P855243 doi: 10.3389/fpls.2022.855243
Transcriptomic and Metabolomic Response to High Light in the Charophyte Alga Klebsormidium nitens.
Microalgae Systems Biology and Biotechnology Research Group, Institute for Plant Biochemistry and Photosynthesis, Universidad de Sevilla - Consejo Superior de Investigaciones Cientificas, Seville, Spain.; Department of Computer Science and Artificial Intelligence, Universidad de Sevilla, Seville, Spain.
The characterization of the molecular mechanisms, such as high light irradiance resistance, that allowed plant terrestralization is a cornerstone in evolutionary studies since the conquest of land by plants played a pivotal role in life evolution on Earth. Viridiplantae or the green lineage is divided into two clades, Chlorophyta and Streptophyta, that in turn splits into Embryophyta or land plants and Charophyta. Charophyta are used in evolutionary studies on plant terrestralization since they are generally accepted as the extant algal species most closely related to current land plants. In this study, we have chosen the facultative terrestrial early charophyte alga Klebsormidium nitens to perform an integrative transcriptomic and metabolomic analysis under high light in order to unveil key mechanisms involved in the early steps of plants terrestralization. We found a fast chloroplast retrograde signaling possibly mediated by reactive oxygen species and the inositol polyphosphate 1-phosphatase (SAL1) and 3'-phosphoadenosine-5'-phosphate (PAP) pathways inducing gene expression and accumulation of specific metabolites. Systems used by both Chlorophyta and Embryophyta were activated such as the xanthophyll cycle with an accumulation of zeaxanthin and protein folding and repair mechanisms constituted by NADPH-dependent thioredoxin reductases, thioredoxin-disulfide reductases, and peroxiredoxins. Similarly, cyclic electron flow, specifically the pathway dependent on proton gradient regulation 5, was strongly activated under high light. We detected a simultaneous co-activation of the non-photochemical quenching mechanisms based on LHC-like stress related (LHCSR) protein and the photosystem II subunit S that are specific to Chlorophyta and Embryophyta, respectively. Exclusive Embryophyta systems for the synthesis, sensing, and response to the phytohormone auxin were also activated under high light in K. nitens leading to an increase in auxin content with the concomitant accumulation of amino acids such as tryptophan, histidine, and phenylalanine.
PMID: 35599877
Front Plant Sci , IF:5.753 , 2022 , V13 : P888703 doi: 10.3389/fpls.2022.888703
Cotton miR393-TIR1 Module Regulates Plant Defense Against Verticillium dahliae via Auxin Perception and Signaling.
Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China.; The State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
Plant auxin is essential in plant growth and development. However, the molecular mechanisms of auxin involvement in plant immunity are unclear. Here, we addressed the function of the cotton (Gossypium hirsutum) miR393-TIR1 module in plant defense against Verticillium dahliae infection via auxin perception and signaling. GhTIR1 was directedly cleaved by ghr-miR393 according to mRNA degradome data, 5'-RACE analysis, and a GUS reporter assay. Ghr-miR393 knockdown significantly increased plant susceptibility to V. dahliae compared to the control, while ghr-miR393 overexpression and GhTIR1 knockdown significantly increased plant resistance. External indole-3-acetic acid (IAA) application significantly enhanced susceptibility to V. dahliae in ghr-miR393 knockdown and control plants compared to mock treatment, and only slightly increased susceptibility in overexpressing ghr-miR393 and GhTIR1-silenced plants. Application of external PEO-IAA (an auxin antagonist) had a contrary trend with IAA application. Based on yeast two-hybrid and bimolecular fluorescence complementation assays, GhTIR1 interacted with GhIAA14 in the nucleus, and GhIAA14 knockdown reduced plant resistance to V. dahliae infection. The results suggested that the ghr-miR393-GhTIR1 module regulates plant defense via auxin perception and signaling. Additionally, simultaneous knockdown of GhTIR1 and GhICS1 significantly increased plant susceptibility to V. dahliae compared to the control, indicating that salicylic acid (SA) accumulation is vital for the ghr-miR393-GhTIR1 module to regulates plant resistance. Transcriptome data also demonstrated that GhTIR1 knockdown significantly downregulated expression of auxin-related genes and upregulated expression of SA-related genes. Overall, the ghr-miR393-GhTIR1 module participates in plant response to V. dahliae infection via IAA perception and signaling partially depending on the SA defense pathway.
PMID: 35592575
Front Plant Sci , IF:5.753 , 2022 , V13 : P858686 doi: 10.3389/fpls.2022.858686
New Insights Into the Local Auxin Biosynthesis and Its Effects on the Rapid Growth of Moso Bamboo (Phyllostachys edulis).
Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, International Center for Bamboo and Rattan, Beijing, China.
Auxin plays a crucial regulatory role in higher plants, but systematic studies on the location of auxin local biosynthesis are rare in bamboo and other graminaceous plants. We studied moso bamboo (Phyllostachys edulis), which can grow up to 1 m/day and serves as a reference species for bamboo and other fast-growing species. We selected young tissues such as root tips, shoot tips, young culm sheaths, sheath blades, and internode divisions for local auxin biosynthesis site analysis. IAA immunofluorescence localization revealed that auxin was similarly distributed in different stages of 50-cm and 300-cm bamboo shoots. Shoot tips had the highest auxin content, and it may be the main site of auxin biosynthesis in the early stage of rapid growth. A total of 22 key genes in the YUCCA family for auxin biosynthesis were identified by genome-wide identification, and these had obvious tissue-specific and spatio-temporal expression patterns. In situ hybridization analysis revealed that the localization of YUCCA genes was highly consistent with the distribution of auxin. Six major auxin synthesis genes, PheYUC3-1, PheYUC6-1, PheYUC6-3, PheYUC9-1, PheYUC9-2, and PheYUC7-3, were obtained that may have regulatory roles in auxin accumulation during moso bamboo growth. Culm sheaths were found to serve as the main local sites of auxin biosynthesis and the auxin required for internode elongation may be achieved mainly by auxin transport.
PMID: 35592571
Front Plant Sci , IF:5.753 , 2022 , V13 : P862171 doi: 10.3389/fpls.2022.862171
The Root Hair Development of Pectin Polygalacturonase PGX2 Activation Tagging Line in Response to Phosphate Deficiency.
Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Pectin, cellulose, and hemicellulose constitute the primary cell wall in eudicots and function in multiple developmental processes in plants. Root hairs are outgrowths of specialized epidermal cells that absorb water and nutrients from the soil. Cell wall architecture influences root hair development, but how cell wall remodeling might enable enhanced root hair formation in response to phosphate (P) deficiency remains relatively unclear. Here, we found that POLYGALACTURONASE INVOLVED IN EXPANSION 2 (PGX2) functions in conditional root hair development. Under low P conditions, a PGX2 activation tagged line (PGX2(AT) ) displays bubble-like root hairs and abnormal callose deposition and superoxide accumulation in roots. We found that the polar localization and trafficking of PIN2 are altered in PGX2(AT) roots in response to P deficiency. We also found that actin filaments were less compact but more stable in PGX2(AT) root hair cells and that actin filament skewness in PGX2(AT) root hairs was recovered by treatment with 1-N-naphthylphthalamic acid (NPA), an auxin transport inhibitor. These results demonstrate that activation tagging of PGX2 affects cell wall remodeling, auxin signaling, and actin microfilament orientation, which may cooperatively regulate root hair development in response to P starvation.
PMID: 35586221
Mol Plant Pathol , IF:5.663 , 2022 Jun doi: 10.1111/mpp.13234
A novel strategy for improving watermelon resistance to cucumber green mottle mosaic virus by exogenous boron application.
Liaoning Key Laboratory of Plant Pathology, College of Plant Protection, Shenyang Agricultural University, Shenyang, China.; Centre for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China.; Xinmin City Agricultural Technology Extension Centre, Shenyang, China.
The molecular mode controlling cucumber green mottle mosaic virus (CGMMV)-induced watermelon blood flesh disease (WBFD) is largely unknown. In this study, we have found that application of exogenous boron suppressed CGMMV infection in watermelon fruit and alleviated WBFD symptoms. Our transcriptome analysis showed that the most up-regulated differentially expressed genes (DEGs) were associated with polyamine and auxin biosynthesis, abscisic acid catabolism, defence-related pathways, cell wall modification, and energy and secondary metabolism, while the down-regulated DEGs were mostly involved in ethylene biosynthesis, cell wall catabolism, and plasma membrane functions. Our virus-induced gene silencing results showed that silencing of SPDS expression in watermelon resulted in a higher putrescine content and an inhibited CGMMV infection correlating with no WBFD symptoms. SBT and TUBB1 were also required for CGMMV infection. In contrast, silencing of XTH23 and PE/PEI7 (low-level lignin, cellulose and pectin) and ATPS1 (low-level glutathione) promoted CGMMV accumulation. Furthermore, RAP2-3, MYB6, WRKY12, H2A, and DnaJ11 are likely to participate in host antiviral resistance. In addition, a higher (spermidine + spermine):putrescine ratio, malondialdehyde content, and lactic acid content were responsible for fruit decay and acidification. Our results provide new knowledge on the roles of boron in watermelon resistance to CGMMV-induced WBFD. This new knowledge can be used to design better control methods for CGMMV in the field and to breed CGMMV resistant watermelon and other cucurbit crops.
PMID: 35671152
Front Microbiol , IF:5.64 , 2022 , V13 : P898356 doi: 10.3389/fmicb.2022.898356
Comparative Transcriptomics Suggests Early Modifications by Vintec((R)) in Grapevine Trunk of Hormonal Signaling and Secondary Metabolism Biosynthesis in Response to Phaeomoniella chlamydospora and Phaeoacremonium minimum.
Unite de Recherche Physiologie, Pathologie, et Genetique Vegetales (PPGV), INP PURPAN, Universite de Toulouse, Toulouse, France.; Laboratoire de Recherche en Sciences Vegetales, CNRS, UPS, Toulouse INP, Universite de Toulouse, Toulouse, France.; Metatoul-AgromiX Platform, MetaboHUB, National Infrastructure for Metabolomics and Fluxomics, LRSV, CNRS, UPS, Toulouse INP, Universite de Toulouse, Toulouse, France.; MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France.
Given their well-known antifungal abilities, species of the genus Trichoderma are of significant interest in modern agriculture. Recent studies have shown that Trichoderma species can induce plant resistance against different phytopathogens. To further extend this line of investigation, we investigate herein the transcriptomic response of grapevine trunk to Vintec((R)), which is a Trichoderma atroviride SC1-based commercial formulation for biological control of grapevine trunk diseases and which reduces wood colonization. The aim of the study is to understand whether the biocontrol agent Vintec((R)) modifies the trunk response to Phaeoacremonium minimum and Phaeomoniella chlamydospora, which are two esca-associated fungal pathogens. An analysis of transcriptional regulation identifies clusters of co-regulated genes whose transcriptomic reprogramming in response to infection depends on the absence or presence of Vintec((R)). On one hand, the results show that Vintec((R)) differentially modulates the expression of putative genes involved in hormonal signaling, especially those involved in auxin signaling. On the other hand, most significant gene expression modifications occur among secondary-metabolism-related genes, especially regarding phenylpropanoid metabolism and stilbene biosynthesis. Taken together, these results suggest that the biocontrol agent Vintec((R)) induces wood responses that counteract disease development.
PMID: 35655993
iScience , IF:5.458 , 2022 May , V25 (5) : P104298 doi: 10.1016/j.isci.2022.104298
MNSs-mediated N-glycan processing is essential for auxin homeostasis in Arabidopsis roots during alkaline response.
Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop and College of Resource and Environment, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China.; Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
Early steps in the endoplasmic reticulum (ER) lumen and cis-Golgi comprise trimming of N-glycans by class I alpha-mannosidases (MNSs) play crucial roles in root growth and stress response. Herein, we found that the root growth inhibition in the mns1 mns2 mns3 mutant was partially rescued under alkaline condition, and inhibitor treatment to disrupt auxin transport counteracted this alkaline-maintained root growth. Further study showed that indole-3-acetic acid (IAA) levels were undetectable in mns1 mns2 mns3 at normal condition and recovered at alkaline condition, which corroborate our N-glycopeptide profiling, from which N-glycopeptides related with IAA biosynthesis, amino acid conjugates hydrolysis, and response showed differential abundance between normal and alkaline conditions in mns1 mns2 mns3. Overall, our results linked the need for MNSs-mediated N-glycan processing in the ER and cis-Golgi with maintenance of auxin homeostasis and transport in Arabidopsis roots during the response to alkaline stress.
PMID: 35602943
iScience , IF:5.458 , 2022 May , V25 (5) : P104238 doi: 10.1016/j.isci.2022.104238
Plasma membrane H(+)-ATPases promote TORC1 activation in plant suspension cells.
Molecular Physiology of the Cell, Universite Libre de Bruxelles (ULB), Biopark, B-6041 Gosselies, Belgium.; Louvain Institute of Biomolecular Science and Technology, UCLouvain, B-1348 Louvain-la-Neuve, Belgium.
The TORC1 (Target of Rapamycin Complex 1) kinase complex plays a pivotal role in controlling cell growth in probably all eukaryotic species. The signals and mechanisms regulating TORC1 have been intensely studied in mammals but those of fungi and plants are much less known. We have previously reported that the yeast plasma membrane H(+)-ATPase Pma1 promotes TORC1 activation when stimulated by cytosolic acidification or nutrient-uptake-coupled H(+) influx. Furthermore, a homologous plant H(+)-ATPase can substitute for yeast Pma1 to promote this H(+)-elicited TORC1 activation. We here report that TORC1 activity in Nicotiana tabacum BY-2 cells is also strongly influenced by the activity of plasma membrane H(+)-ATPases. In particular, stimulation of H(+)-ATPases by fusicoccin activates TORC1, and this response is also observed in cells transferred to a nutrient-free and auxin-free medium. Our results suggest that plant H(+)-ATPases, known to be regulated by practically all factors controlling cell growth, contribute to TOR signaling.
PMID: 35494253
Nanomaterials (Basel) , IF:5.076 , 2022 Jun , V12 (12) doi: 10.3390/nano12122099
Potassium Chloroaurate-Mediated In Vitro Synthesis of Gold Nanoparticles Improved Root Growth by Crosstalk with Sucrose and Nutrient-Dependent Auxin Homeostasis in Arabidopsis thaliana.
National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India.; ICAR-Indian Institute of Rice Research, Hyderabad 500030, India.; Department of Bioresources Engineering, Sejong University, Seoul 05006, Korea.; Aerosol and Air Quality Research Laboratory, Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA.; Department of Biology, University City Campus, Saint Joseph's University, 600 S. 43rd St., Philadelphia, PA 19104, USA.; School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India.; Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur 303002, India.
In a hydroponic system, potassium chloroaurate (KAuCl4) triggers the in vitro sucrose (Suc)-dependent formation of gold nanoparticles (AuNPs). AuNPs stimulate the growth of the root system, but their molecular mechanism has not been deciphered. The root system of Arabidopsis (Arabidopsis thaliana) exhibits developmental plasticity in response to the availability of various nutrients, Suc, and auxin. Here, we showed the roles of Suc, phosphorus (P), and nitrogen (N) in facilitating a AuNPs-mediated increase in root growth. Furthermore, the recuperating effects of KAuCl4 on the natural (IAA) auxin-mediated perturbation of the root system were demonstrated. Arabidopsis seedlings harboring the cell division marker CycB1;1::CDB-GUS provided evidence of the restoration efficacy of KAuCl4 on the IAA-mediated inhibitory effect on meristematic cell proliferation of the primary and lateral roots. Arabidopsis harboring synthetic auxin DR5rev::GFP exhibited a reinstating effect of KAuCl4 on IAA-mediated aberration in auxin subcellular localization in the root. KAuCl4 also exerted significant and differential recuperating effects on the IAA-mediated altered expression of the genes involved in auxin signaling and biosynthetic pathways in roots. Our results highlight the crosstalk between KAuCl4-mediated improved root growth and Suc and nutrient-dependent auxin homeostasis in Arabidopsis.
PMID: 35745438
Plant Cell Physiol , IF:4.927 , 2022 Jun doi: 10.1093/pcp/pcac084
Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize.
Department of Biosciences and Bioengineering, Indian Institute of Technology, Roorkee-247667, Uttarakhand, India.
The evolution of the root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, thus becoming a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus displaying species-specific diversity in the adventitious root types. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics, and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of action and interaction of crucial genetic and hormonal regulators. In this review, we provide a comprehensive state-of-the-art on the key regulators involved during different stages of AR development in two important crop plants, rice, and maize. We have reviewed the role of major phytohormones, microRNAs, transcription factors, and their crosstalk during adventitious root development in these cereal crops.
PMID: 35713294
Plant Cell Physiol , IF:4.927 , 2022 Jun doi: 10.1093/pcp/pcac078
Root Cap at Soil Interface: A Driving Force Towards Plant Adaptation and Development.
Indian Institute of Science Education and Research (IISER) Tirupati, Biology Division, Tirupati, 517507, Andhra Pradesh, India.
Land plants have developed robust roots to grow in diverse soil ecosystems. The distal end of the root tip has specialized organ called the "root cap." The root cap assists the roots in penetrating the ground, absorbing water & minerals, avoiding heavy metals, and regulating the rhizosphere microbiota. Furthermore, root cap derived auxin governs the lateral roots patterning and directs root growth under varying soil conditions. The root cap formation is hypothesized as one of the key innovations during root evolution. Morphologically diversified root caps in early land plant lineage and later in angiosperms aids in improving the adaptation of roots and, thereby, plants in diverse soil environments. This review article presents a retrospective view of the root cap's important morphology and physiology characteristics for the root-soil interaction and their response towards various abiotic and biotic stimuli. Recent single-cell RNAseq data shed light on root cap cell-type enriched genes. We complied root cap cell-type enriched genes from Arabidopsis, rice, maize and tomato and analyzed their transcription factor binding site enrichment. Further, the putative gene regulatory networks derived from root cap enriched genes and their transcription factor regulators highlight the species-specific biological functions of root cap genes across the four plant species.
PMID: 35662353
Plant Cell Physiol , IF:4.927 , 2022 May doi: 10.1093/pcp/pcac069
Seed Dormancy and Longevity: A Mutual Dependence or a Trade-Off?
School of Environment and Ecology, Northwestern Polytechnical University, Xi'an 710129, China.; Research & Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, 518057, China.
Seed dormancy is an important agronomic trait in cereals and leguminous crops as low levels of seed dormancy during harvest season, coupled with high humidity, can cause pre-harvest sprouting. Seed longevity is another critical trait for commercial crop propagation and production, directly influencing seed germination and early seedling establishment. Both traits are precisely regulated by the integration of genetic and environmental cues. Despite the significance of these two traits in crop production, the relationship between them at the molecular level is still elusive, even with contradictory conclusions being reported. Some studies have proposed a positive correlation between seed dormancy and longevity in association with differences in seed coat permeability or seed reserve accumulation, whereas an increasing number of studies have highlighted a negative relationship, largely with respect to phytohormone-dependent pathways. In this review paper, we try to provide some insights into the interactions between regulatory mechanisms of genetic and environmental cues which result in positive or negative relationships between seed dormancy and longevity. Finally, we conclude that further dissection of the molecular mechanism responsible for this apparently contradictory relationship between them is needed.
PMID: 35594901
Plant Cell Physiol , IF:4.927 , 2022 May , V63 (5) : P618-634 doi: 10.1093/pcp/pcac017
Warm Temperature Promotes Shoot Regeneration in Arabidopsis thaliana.
RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.; Department of Biological Sciences, Faculty of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.; Institut de Biologie Moleculaire des Plantes, Universite de Strasbourg, 12 rue du General Zimmer, Strasbourg 67084, France.; Department of Biology, Faculty of Science, Niigata University, Ikarashi, Niigata 950-2181, Japan.; College of Bioscience and Biotechnology, Chubu University, 1200 Matsumoto-cho, Kasugai, Aichi 487-8501, Japan.; UMR5004 Biochimie et Physiologie Moleculaire des Plantes, Universite de Montpellier, CNRS, INRAE, Institut Agro, 2 place Pierre Viala, Montpellier 34060, France.; Leibniz-Institut fur Gemuse- und Zierpflanzenbau (IGZ) e.V., Theodor-Echtermeyer-Weg 1, Grossbeeren 14979, Germany.
Many plants are able to regenerate upon cutting, and this process can be enhanced in vitro by incubating explants on hormone-supplemented media. While such protocols have been used for decades, little is known about the molecular details of how incubation conditions influence their efficiency. In this study, we find that warm temperature promotes both callus formation and shoot regeneration in Arabidopsis thaliana. We show that such an increase in shoot regenerative capacity at higher temperatures correlates with the enhanced expression of several regeneration-associated genes, such as CUP-SHAPED COTYLEDON 1 (CUC1) encoding a transcription factor involved in shoot meristem formation and YUCCAs (YUCs) encoding auxin biosynthesis enzymes. ChIP-sequencing analyses further reveal that histone variant H2A.Z is enriched on these loci at 17 degrees C, while its occupancy is reduced by an increase in ambient temperature to 27 degrees C. Moreover, we provide genetic evidence to demonstrate that H2A.Z acts as a repressor of de novo shoot organogenesis since H2A.Z-depleted mutants display enhanced shoot regeneration. This study thus uncovers a new chromatin-based mechanism that influences hormone-induced regeneration and additionally highlights incubation temperature as a key parameter for optimizing in vitro tissue culture.
PMID: 35157760
Biomolecules , IF:4.879 , 2022 Jun , V12 (6) doi: 10.3390/biom12060811
Hormonal Crosstalk and Root Suberization for Drought Stress Tolerance in Plants.
Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Korea.; Department of Biology, Chungbuk National University, Cheong-ju 28644, Korea.; Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheong-ju 28644, Korea.
Higher plants in terrestrial environments face to numerous unpredictable environmental challenges, which lead to a significant impact on plant growth and development. In particular, the climate change caused by global warming is causing drought stress and rapid desertification in agricultural fields. Many scientific advances have been achieved to solve these problems for agricultural and plant ecosystems. In this review, we handled recent advances in our understanding of the physiological changes and strategies for plants undergoing drought stress. The activation of ABA synthesis and signaling pathways by drought stress regulates root development via the formation of complicated signaling networks with auxin, cytokinin, and ethylene signaling. An abundance of intrinsic soluble sugar, especially trehalose-6-phosphate, promotes the SnRK-mediated stress-resistance mechanism. Suberin deposition in the root endodermis is a physical barrier that regulates the influx/efflux of water and nutrients through complex hormonal and metabolic networks, and suberization is essential for drought-stressed plants to survive. It is highly anticipated that this work will contribute to the reproduction and productivity improvements of drought-resistant crops in the future.
PMID: 35740936
Pest Manag Sci , IF:4.845 , 2022 Jul , V78 (7) : P2759-2766 doi: 10.1002/ps.6863
Soybean dose-response to 2,4-D and dicamba at vegetative and reproductive growth stages.
Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, USA.; Department of Agronomy and Horticulture, West Central Research and Extension Center, University of Nebraska-Lincoln, North Platte, NE, USA.; Corteva Agriscience, Wilmington, DE, USA.; Department of Crop, Soil and Environmental Sciences, University of Arkansas, Lonoke, AR, USA.
BACKGROUND: Field experiments were conducted across multiple sites in 2012 and 2013 to describe sensitivity of soybean to 2,4-D (six doses) and dicamba (seven doses) at V3 and R1 growth stages. Further experiments were conducted under greenhouse conditions in 2017 and 2018 to compare soybean response to several dicamba herbicides across a broader range of doses than those tested in the field. RESULTS: Soybean yield loss was 6.1-fold greater from 2,4-D exposure at V3 compared to R1 and 1.4 times greater from dicamba exposure at R1 than at V3. In V3 exposures, soybean was 15.4 times more sensitive to dicamba than 2,4-D and 134.4-fold more sensitive to dicamba when exposed at R1. Plant injury and height correlations to grain yield resulted in coefficients ranging from 0.65 to 0.91. In greenhouse experiments, five dicamba products were tested at up to 19 doses and as low as 0.002 g ae ha(-1) (3.6 x 10(-6) % of maximum single use-rate); however, no differences were observed among formulations used in dicamba-resistant crops versus traditional formulations. A no observable effects dose was not identified due to responses observed even at the lowest doses tested, although hormesis effects were observed in plant height. CONCLUSION: These data suggest that the sensitivity of soybean to dicamba is much greater than what has previously been reported. However, as has been indicated by previous work, that injury does not always result in yield loss. (c) 2022 Society of Chemical Industry.
PMID: 35254733
Plant Sci , IF:4.729 , 2022 Jun , V322 : P111349 doi: 10.1016/j.plantsci.2022.111349
The carbohydrate elicitor Riclinoctaose facilitates defense and growth of potato roots by inducing changes in transcriptional and metabolic profiles.
Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China.; Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China.; Center for Molecular Metabolism, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China; School of Environmental and Biological Engineering, Nanjing University of Science and Technology, 200 Xiaolingwei Street, Nanjing 210094, China. Electronic address: jingli.seb@njust.edu.cn.
Promoting both root growth and defense is conducive to the production of potatoes (Solanum tuberosum L.), while the role of elicitors in this topic hasn't been fully understood. To investigate the effect of Riclinoctaose (RiOc) on root growth and defense, potato tissue cuttings were cultivated with different concentration of RiOc (0, 50, 200 mg/L) for 5 weeks and changes in root morphology, transcription, enzymatic and metabolomic profiles were monitored over time. The results indicated that RiOc triggered the salicylic acid (SA)-mediated defense response and facilitated the growth of adventitious and lateral roots in a dose- and time-dependent manner. MPK3/MPK6, SA- and auxin-signaling pathways and transcription factors such as WUS, SCR and GRAS4/GRAS9 participated in this process. Moreover, the (1)H NMR based metabolome profiling demonstrated that potato roots altered the primary metabolism to respond to the RiOc elicitation and efficiency in production and allocation of defense and growth-related metabolites was improved. After 5-week treatment, the level of glucose, N-acetylglucosamine, glutamine, asparagine, isoleucine, valine, 3-hydroxyisovalerate and ferulate increased, while acetate, acetoacetate, fucose, and 2-hydroxyphenylacetate declined. In conclusion, RiOc played dual roles in activating the SA-mediated defense response and in promoting growth of potato roots by inducing changes in root transcription and metabolism.
PMID: 35709981
Plant Sci , IF:4.729 , 2022 Aug , V321 : P111340 doi: 10.1016/j.plantsci.2022.111340
Modeling-based age-dependent analysis reveals the net patterns of ethylene-dependent and -independent aerenchyma formation in rice and maize roots.
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan. Electronic address: atkyama@agr.nagoya-u.ac.jp.; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan; School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia.
Plants require oxygen for the functioning of roots, and thus the establishment of a long-distance diffusion path from above-water tissues to the submerged roots is essential to survive flooding. Rice (Oryza sativa) constitutively forms aerenchyma (gas spaces) under aerobic conditions, and induces its formation in response to low-oxygen conditions. Constitutive aerenchyma formation in rice roots is regulated by the phytohormone auxin, whereas ethylene stimulates inducible aerenchyma formation. However, the net patterns of the ethylene-dependent and -independent (auxin-dependent) aerenchyma formation remain unclear. In the present study, we used a modeling approach to determine age-dependent aerenchyma formation in the wild-type rice and reduced culm number 1 mutant, in which ethylene production is reduced, to reveal the net patterns of ethylene-dependent and -independent aerenchyma formation. Subsequent comparison of age-dependent aerenchyma formation between rice and maize roots suggested that more rapid induction of ethylene-dependent aerenchyma formation and more aerenchyma in rice roots are essential to achieve efficient oxygen diffusion under low-oxygen conditions. Moreover, rice roots showed rapid increase in the expression levels of ethylene biosynthesis and responsive genes, suggesting that the local ethylene production at an early time point after root-cell emergence contributes to the rapid induction of the ethylene-dependent aerenchyma formation in rice. DATA AVAILABILITY: All data included in this study are available upon request by contact with the corresponding author.
PMID: 35696932
Plant Sci , IF:4.729 , 2022 Aug , V321 : P111326 doi: 10.1016/j.plantsci.2022.111326
Metabolic changes in cucumber leaves are enhanced by blue light but differentially affected by UV interactions with light signalling pathways in the visible spectrum.
Aarhus University, Plant Food and Climate, Department of Food Science, Agrofoodpark 48, DK-8200 Aarhus, Denmark.; School of Science and Technology, Man-Technology-Environment Research Centre (MTM), Orebro University, SE-70182 Orebro, Sweden.; School of Science and Technology, Orebro Life Science Centre, Orebro University, SE-70182 Orebro, Sweden.; Section of Crop Sciences, Institute of Plant and Environmental Sciences, University of Copenhagen, Hojbakkegard Alle 9, DK-2630 Tastrup, Denmark.; School of Science and Technology, Orebro Life Science Centre, Orebro University, SE-70182 Orebro, Sweden. Electronic address: ake.strid@oru.se.
Ultraviolet radiation (UV, 280-400 nm) as an environmental signal triggers metabolic acclimatory responses. However, how different light qualities affect UV acclimation during growth is poorly understood. Here, cucumber plants (Cucumis sativus) were grown under blue, green, red, or white light in combination with UV. Their effects on leaf metabolites were determined using untargeted metabolomics. Blue and white growth light triggered increased levels of compounds related to primary and secondary metabolism, including amino acids, phenolics, hormones, and compounds related to sugar metabolism and the TCA cycle. In contrast, supplementary UV in a blue or white light background decreased leaf content of amino acids, phenolics, sugars, and TCA-related compounds, without affecting abscisic acid, auxin, zeatin, or jasmonic acid levels. However, in plants grown under green light, UV induced increased levels of phenolics, hormones (auxin, zeatin, dihydrozeatin-7-N-dihydrozeatin, jasmonic acid), amino acids, sugars, and TCA cycle-related compounds. Plants grown under red light with UV mainly showed decreased sugar content. These findings highlight the importance of the blue light component for metabolite accumulation. Also, data on interactions of UV with green light on the one hand, and blue or white light on the other, further contributes to our understanding of light quality regulation of plant metabolism.
PMID: 35696926
Plant Sci , IF:4.729 , 2022 Aug , V321 : P111324 doi: 10.1016/j.plantsci.2022.111324
BSISTER transcription factors directly binds to the promoter of IAA19 and IAA29 genes to up-regulate gene expression and promote the root development.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China. Electronic address: tangyujin@nwafu.edu.cn.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China. Electronic address: wangling0922@nwafu.edu.cn.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China. Electronic address: 444807610@qq.com.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China. Electronic address: 1300904734@qq.com.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China. Electronic address: zhaoting@nwafu.edu.cn.; College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China. Electronic address: liyan@nwsuaf.edu.cn.; State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A&F University, Yangling 712100, Shaanxi, China; Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northwest Region), Ministry of Agriculture, Yangling 712100, Shaanxi, China. Electronic address: zhangchaohong@nwsuaf.edu.cn.
Roots play an important role in the growth and development of plants and auxin participates in regulating plant root development. Some studies have shown that BS (BSISTER) gene (the closest gene of class B gene) is involved in plant root development, but whether BS regulates root development via auxin signaling still not clear. To explore VviBS1 and VviBS2 roles in root development, VviBS1 and VviBS2 were overexpressedin Arabidopsis tt16 mutant and we found that they could restore the phenotype of shorter PR (primary roots) and high density of LR (lateral root) of tt16 compared with the wild type Ws Arabidopsis seedlings. However, the addition of exogenous NAA (naphthalene acetic acid) could not significantly promote the PR length of tt16 Arabidopsis, and the auxin signal transduction of tt16 may be blocked. The expression levels of auxin signal transduction pathway genes in Ws, tt16, p35s:VviBS1 in tt16 and p35s:VviBS2 in tt16 seedlings were detected. It was found that the expression of AtARF2, AtARF12, AtARF14, AtARF15, AtARF20, AtGH3, AtGH3-2 and AtSAUR51 genes in tt16 seedlings was higher than that in Ws, while the expression of AtIAA19 and AtIAA29 in Ws seedlings was higher than that of tt16. More importantly, BS may up regulate AtIAA19 and AtIAA29 expression directly by binding to their promoter. In addition, VviBS1 and VviBS2 also affect seed germination and may regulate leaf yellowing by regulating ethylene synthase. Therefore, our findings reveal a molecular mechanism that BS may modulate root system development via Aux/IAA-based auxin signaling, and provide insight into the BS function in regulation of leaf yellowing.
PMID: 35696924
Plant Sci , IF:4.729 , 2022 Aug , V321 : P111307 doi: 10.1016/j.plantsci.2022.111307
Overexpression of HANABA TARANU in cultivated strawberry delays flowering and leads to defective flower and fruit development.
College of Horticulture, China Agricultural University, Beijing 100193, PR China.; College of Horticulture, Nanjing Agricultural University, Nanjing 210095, PR China.; College of Horticulture, China Agricultural University, Beijing 100193, PR China. Electronic address: wanghq@cau.edu.cn.
Cultivated strawberry is one of the most important horticultural crops in the world, and the fruit yields and economic benefits are largely dependent on the quality of floral initiation and floral organ development. However, the underlying regulatory mechanisms controlling these processes in strawberry are largely unknown. In this study, the function of a GATA transcription factor gene, HANABA TARANU (HAN), in floral initiation and floral organ development was characterized in strawberry. FaHAN is expressed in four whorls of the floral organs. Overexpression (OE) of FaHAN in the strawberry cultivar 'Benihoppe' delayed flowering by at least one week by affecting key genes, such as TERMINAL FLOWER 1, APETALA 1...and increased the number of runners. FaHAN-OE plants also showed malformed floral organs, especially the deformed stigmas with disordered arrangement. Several key genes for pistil apical development such as STYLISH, YUCCA 1, and auxin-related genes such as GH3.5, PIN-FORMED 1, which play important roles in pistil primordium development in many plant species, were all down-regulated in FaHAN-OE plants. Further observations showed that the fruit deformity rate was nearly 4-fold higher than in control plants. Together, this study provides a new approach for exploring floral initiation and floral organ development in strawberry.
PMID: 35696907
Plant Sci , IF:4.729 , 2022 Jun , V319 : P111254 doi: 10.1016/j.plantsci.2022.111254
Epigenetic mechanisms affect the curled leaf phenotype in the hypomethylated ddc mutant of Arabidopsis thaliana.
Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium. Electronic address: ivanoforgione@gmail.com.; Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy. Electronic address: antonella.muto@unical.it.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Genetics, Faculty of Biology and Animal Sciences, Wroclaw University of Environmental and Life Sciences, ul. Kozuchowska 7, 51-631 Wroclaw, Poland. Electronic address: magdalena.woloszynska@upwr.edu.pl.; Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy. Electronic address: adriana.chiappetta@unical.it.; Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy. Electronic address: michele.ferrari@unical.it.; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Center Plant Systems Biology, VIB, 9052 Ghent, Belgium. Electronic address: mieke.vanlijsebettens@psb.vib-ugent.be.; Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy. Electronic address: maria_beatrice.bitonti@unical.it.; Department of Biology, Ecology and Earth Science, University of Calabria, Ponte P. Bucci, Arcavacata di Rende, 87036 Cosenza, Italy. Electronic address: leonardo.bruno@unical.it.
The ddc mutant of Arabidopsis thaliana is characterized by pleiotropic phenotypic alterations including a curl-shaped leaf, previously explained by disturbed auxin metabolism and transport. The present study was aimed at further explore the molecular bases underlying the abnormal phenotype of the ddc leaf. We demonstrated that genes specifically related to leaf fate commitment and morphogenesis were misexpressed on developing ddc leaves, such as upregulation of CURLY LEAF (CLF) and downregulation of ASYMMETRIC LEAVES2 (AS2), KNOTTED-like gene from A. thaliana (KNAT6), TEOSINTE-LIKE1 CYCLOIDEA and PROLIFERATING CELL FACTOR 2 (TCP2) and others. The CLF gene, encoding a component of Polycomb repressive complex 2 (PRC2) which adds trimethylation marks at Lys27 of histone H3, was overexpressed in the ddc mutant and concomitantly was correlated with DNA methylation-dependent repression of its negative regulator UCL1. KNAT6, encoding a class 1 KNOX homeotic gene, had increased H3K27me3 trimethylation levels, suggesting it is a target gene of the CLF containing PRC2 complex in the ddc mutant. We postulate that different epigenetic mechanisms modulate expression of genes related to auxin pathways as well as gene targets of Polycomb repressive action, during leaf morphogenesis.
PMID: 35487663
Plant Cell Rep , IF:4.57 , 2022 Jun doi: 10.1007/s00299-022-02882-x
Transcriptome analysis reveals the effects of strigolactone on shoot regeneration of apple.
State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China.; State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China. liwei0522898@163.com.; State Key Laboratory of Agrobiotechnology, College of Horticulture, China Agricultural University, Beijing, 100193, China. rschan@cau.edu.cn.
KEY MESSAGE: We have demonstrated that strigolactone inhibitor, Tis108, could be used to improve shoot regeneration of apple, and provided insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Lack of an efficient transformation system largely stagnated the application of transgenic and CRISPR technology in apple rootstock. High shoot regeneration ability is an important basis for establishing an effective transformation system. In this study, we first demonstrated the inhibitory effects of strigolactones on the adventitious shoot formation of apple rootstock M26. Next, we successfully verified that strigolactone-biosynthesis inhibitor, Tis108, could be used to improve the shoot regeneration of woody plants. Our results also suggest strigolactone-biosynthesis gene, MdCCD7, can be a target gene for biotechnological improvements of shoot regeneration capacity. Furthermore, we have employed transcriptome analysis to reveal the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation. Differentially expressed genes associated with photosynthesis, secondary growth, and organ development were identified. WGCNA suggests SLs might affect shoot regeneration through interaction with other hormones, especially, auxin, cytokinin, and ethylene. We were able to identify important candidate genes mediating the cross-talk between strigolactone and other hormones during the process of adventitious shoot formation. Overall, our findings not only propose a useful chemical for improving shoot regeneration in practice but also provide insights into the molecular mechanism of strigolactone-mediated inhibition of adventitious shoot formation.
PMID: 35680714
Physiol Plant , IF:4.5 , 2022 Jun : Pe13728 doi: 10.1111/ppl.13728
De novo transcriptome sequencing of Capsicum frutescens. L and comprehensive analysis of salt stress alleviating mechanism by Bacillus atrophaeus WU-9.
School of Chemistry and Chemical Engineering, Shihezi University, Shihezi, PR China.; School of Environmental and Chemical Engineering, Xi'an Polytechnic University, Xi'an, PR China.
Salt stress, as one of the most severe environmental stresses, can cause a series of changes in plants. However, the explanation of plant salt stress alleviating mechanism of plant growth-promoting rhizobacteria (PGPR) was hindered by the limited availability of transcriptomic information for salt stress-treated plants grown in a microorganism-controled environment. Our previous reports have selected Bacillus atrophaeus WU-9 as PGPR significantly alleviating pepper (Capsicum frutescens. L) salt stress. In this work, the RNA-seq analysis of salt stress-treated and untreated plants, grown with and without WU-9 in a microorganism-controled environment, was used to reveal the plant salt stress alleviating mechanisms of WU-9. Twelve sequencing libraries, prepared by treating with WU-9 and salt (150 mM NaCl for 36 h), were constructed by RNA-Seq technique. Non-inoculated seedlings mainly respond to salt stress through regulation of signal transduction, such as ethylene-activated signaling pathway, signaling and cell communication, etc. And ethylene signal participated in salt stress response in pepper through regulating defense responses, fruit ripening and senescence. WU-9 inoculation under salt stress mainly improves salt tolerance and plant growth by regulating salt stress-responding ethylene and auxin signal transduction, utilization of proline, photosynthesis, antioxidant enzyme activities and cell enlargement. Furthermore, 86 differentially expressed genes (DEGs) and 20 transcription factors were identified as associated with salt stress response and tolerance. Thus, this innovative transcriptomic study identified the salt stress response and alleviation in C. frutescens. L with PGPR inoculation. This result provided novel insights into the salinity alleviation in pepper regulated by PGPR. This article is protected by copyright. All rights reserved.
PMID: 35675473
Sci Rep , IF:4.379 , 2022 Jun , V12 (1) : P10883 doi: 10.1038/s41598-022-14631-x
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information.
Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA.; Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.; Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA. decook@ksu.edu.; Ming Hsieh Department of Electrical and Computer Engineering, University of Southern California, Los Angeles, CA, 90089, USA. pbogdan@usc.edu.
Cellular biological networks represent the molecular interactions that shape function of living cells. Uncovering the organization of a biological network requires efficient and accurate algorithms to determine the components, termed communities, underlying specific processes. Detecting functional communities is challenging because reconstructed biological networks are always incomplete due to technical bias and biological complexity, and the evaluation of putative communities is further complicated by a lack of known ground truth. To address these challenges, we developed a geometric-based detection framework based on Ollivier-Ricci curvature to exploit information about network topology to perform community detection from partially observed biological networks. We further improved this approach by integrating knowledge of gene function, termed side information, into the Ollivier-Ricci curvature algorithm to aid in community detection. This approach identified essential conserved and varied biological communities from partially observed Arabidopsis protein interaction datasets better than the previously used methods. We show that Ollivier-Ricci curvature with side information identified an expanded auxin community to include an important protein stability complex, the Cop9 signalosome, consistent with previous reported links to auxin response and root development. The results show that community detection based on Ollivier-Ricci curvature with side information can uncover novel components and novel communities in biological networks, providing novel insight into the organization and function of complex networks.
PMID: 35760826
Sci Rep , IF:4.379 , 2022 Jun , V12 (1) : P10453 doi: 10.1038/s41598-022-14568-1
Single trait versus principal component based association analysis for flowering related traits in pigeonpea.
ICAR-National Institute for Plant Biotechnology, New Delhi, India.; ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India.; ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.; Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India.; ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, Jharkhand, India.; ICAR-National Institute for Plant Biotechnology, New Delhi, India. kish2012@gmail.com.
Pigeonpea, a tropical photosensitive crop, harbors significant diversity for days to flowering, but little is known about the genes that govern these differences. Our goal in the current study was to use genome wide association strategy to discover the loci that regulate days to flowering in pigeonpea. A single trait as well as a principal component based association study was conducted on a diverse collection of 142 pigeonpea lines for days to first and fifty percent of flowering over 3 years, besides plant height and number of seeds per pod. The analysis used seven association mapping models (GLM, MLM, MLMM, CMLM, EMLM, FarmCPU and SUPER) and further comparison revealed that FarmCPU is more robust in controlling both false positives and negatives as it incorporates multiple markers as covariates to eliminate confounding between testing marker and kinship. Cumulatively, a set of 22 SNPs were found to be associated with either days to first flowering (DOF), days to fifty percent flowering (DFF) or both, of which 15 were unique to trait based, 4 to PC based GWAS while 3 were shared by both. Because PC1 represents DOF, DFF and plant height (PH), four SNPs found associated to PC1 can be inferred as pleiotropic. A window of +/- 2 kb of associated SNPs was aligned with available transcriptome data generated for transition from vegetative to reproductive phase in pigeonpea. Annotation analysis of these regions revealed presence of genes which might be involved in floral induction like Cytochrome p450 like Tata box binding protein, Auxin response factors, Pin like genes, F box protein, U box domain protein, chromatin remodelling complex protein, RNA methyltransferase. In summary, it appears that auxin responsive genes could be involved in regulating DOF and DFF as majority of the associated loci contained genes which are component of auxin signaling pathways in their vicinity. Overall, our findings indicates that the use of principal component analysis in GWAS is statistically more robust in terms of identifying genes and FarmCPU is a better choice compared to the other aforementioned models in dealing with both false positive and negative associations and thus can be used for traits with complex inheritance.
PMID: 35729192
Sci Rep , IF:4.379 , 2022 May , V12 (1) : P7951 doi: 10.1038/s41598-022-12026-6
Bacillus velezensis strain B26 modulates the inflorescence and root architecture of Brachypodium distachyon via hormone homeostasis.
Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada.; Department of Plant Science, Macdonald Campus of McGill University, 21,111 Lakeshore Rd., Ste-Anne de Bellevue, QC, H9X 3V9, Canada. suha.jabaji@mcgill.ca.
Plant growth-promoting rhizobacteria (PGPR) influence plant health. However, the genotypic variations in host organisms affect their response to PGPR. To understand the genotypic effect, we screened four diverse B. distachyon genotypes at varying growth stages for their ability to be colonized by B. velezensis strain B26. We reasoned that B26 may have an impact on the phenological growth stages of B. distachyon genotypes. Phenotypic data suggested the role of B26 in increasing the number of awns and root weight in wild type genotypes and overexpressing transgenic lines. Thus, we characterized the expression patterns of flowering pathway genes in inoculated plants and found that strain B26 modulates the transcript abundance of flowering genes. An increased root volume of inoculated plants was estimated by CT-scanning which suggests the role of B26 in altering the root architecture. B26 also modulated plant hormone homeostasis. A differential response was observed in the transcript abundance of auxin and gibberellins biosynthesis genes in inoculated roots. Our results reveal that B. distachyon plant genotype is an essential determinant of whether a PGPR provides benefit or harm to the host and shed new insight into the involvement of B. velezensis in the expression of flowering genes.
PMID: 35562386
Sci Rep , IF:4.379 , 2022 May , V12 (1) : P7609 doi: 10.1038/s41598-022-11801-9
Integrated transcriptome and endogenous hormone analysis provides new insights into callus proliferation in Osmanthus fragrans.
Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China.; College of Landscape Architecture, Nanjing Forestry University, Nanjing, China.; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China.; Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China. yueyuanzheng@njfu.edu.cn.; College of Landscape Architecture, Nanjing Forestry University, Nanjing, China. yueyuanzheng@njfu.edu.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China. yueyuanzheng@njfu.edu.cn.; Key Laboratory of Landscape Architecture, Nanjing Forestry University, Nanjing, Jiangsu, China. wlg@njfu.com.cn.; College of Landscape Architecture, Nanjing Forestry University, Nanjing, China. wlg@njfu.com.cn.; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China. wlg@njfu.com.cn.
Osmanthus fragrans is an important evergreen species with both medicinal and ornamental value in China. Given the low efficiency of callus proliferation and the difficulty of adventitious bud differentiation, tissue culture and regeneration systems have not been successfully established for this species. To understand the mechanism of callus proliferation, transcriptome sequencing and endogenous hormone content determination were performed from the initial growth stages to the early stages of senescence on O. fragrans calli. In total, 47,340 genes were identified by transcriptome sequencing, including 1798 previously unidentified genes specifically involved in callus development. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes (DEGs) was significantly enriched in plant hormone signal transduction pathways. Furthermore, our results from the orthogonal projections to latent structures discrimination analysis (OPLS-DA) of six typical hormones in five development stages of O. fragrans calli showed jasmonic acid (JA) could play important role in the initial stages of calli growth, whereas JA and auxin (IAA) were dominant in the early stages of calli senescence. Based on the weighted gene co-expression network analysis, OfSRC2, OfPP2CD5 and OfARR1, OfPYL3, OfEIL3b were selected as hub genes from the modules with the significant relevance to JA and IAA respectively. The gene regulation network and quantitative real-time PCR implied that during the initial stages of callus growth, the transcription factors (TFs) OfERF4 and OfMYC2a could down-regulate the expression of hub genes OfSRC2 and OfPP2CD5, resulting in decreased JA content and rapid callus growth; during the late stage of callus growth, the TFs OfERF4, OfMYC2a and OfTGA21c, OfHSFA1 could positively regulate the expression of hub genes OfSRC2, OfPP2CD5 and OfARR1, OfPYL3, OfEIL3b, respectively, leading to increased JA and IAA contents and inducing the senescence of O. fragrans calli. Hopefully, our results could provide new insights into the molecular mechanism of the proliferation of O. fragrans calli.
PMID: 35534621
Sci Rep , IF:4.379 , 2022 May , V12 (1) : P7481 doi: 10.1038/s41598-022-11689-5
Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).
Department of Plant Breeding, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS), CSIC, P.O. Box 164, 30100, Espinardo, Spain. pjmartinez@cebas.csic.es.; Department of Plant Breeding, Centro de Edafologia y Biologia Aplicada del Segura (CEBAS), CSIC, P.O. Box 164, 30100, Espinardo, Spain.; Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.; Department of Neurodegenerative Disease, University College London, London, WC1N 3BG, UK.; Departamento de Ingenieria de la Informacion y las Comunicaciones, Universidad de Murcia, 30100, Murcia, Spain.
Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.
PMID: 35523985
Plant Physiol Biochem , IF:4.27 , 2022 Jun , V185 : P260-267 doi: 10.1016/j.plaphy.2022.06.013
Mechanism of pod shattering in the forage legume Medicago ruthenica.
Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China.; Grassland and Resources Environment Institute, Inner Mongolia Agriculture University, Hohhot, China.; Grassland Supervision Office, Chahar Right Back Banner, Ulanqab, China.; Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China. Electronic address: zhiyongli1216@126.com.; Grassland Research Institute, Chinese Academy of Agricultural Sciences, Hohhot, China; Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, China. Electronic address: lijun1538@126.com.
Pod shattering is a seed dispersal strategy and an important agronomical trait in domesticated crops. The relationship between pod shattering and pod morphology in the genus Medicago is well known; however, the detailed mechanism underlying pod dehiscence in Medicago ruthenica, a perennial legume used for forage production, is unknown. Here, the pod ventral sutures of shatter-resistant and shatter-susceptible M. ruthenica genotypes were examined at 8, 12, 16, and 20 d after flowering. The mechanism of pod shattering was analyzed through microscopic observations, polygalacturonase (PG) and cellulase (CE) activity analyses, and RNA-sequencing (RNA-Seq), and the results were verified via reverse transcriptase-quantitative polymerase chain reaction. Pod shattering at the ventral suture in M. ruthenica occurs via a combination of two mechanisms: degradation of the middle lamella at the abscission layers (ALs) and detachment of lignified cells on either side of the ALs triggered by physical forces. Increased PG and CE activities in the pod ventral suture are essential for AL cell-autolysis in the shatter-susceptible genotype. RNA-Seq revealed that 11 genes encoding PG and CE were highly expressed in the ventral sutures of the shatter-susceptible genotype. The expression levels of auxin biosynthesis-related genes decreased in the AL cells and they were negatively associated with pod dehiscence. These results enhance our understanding of the pod shattering mechanism not only in M. ruthenica but also in other leguminous plants.
PMID: 35717734
Plant Physiol Biochem , IF:4.27 , 2022 Jun , V185 : P244-259 doi: 10.1016/j.plaphy.2022.06.006
Auxin regulates growth, photosynthetic efficiency and mitigates copper induced toxicity via modulation of nutrient status, sugar metabolism and antioxidant potential in Brassica juncea.
Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India.; Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, 11942, Saudi Arabia.; Department of Botany, Plant Physiology Section, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, India. Electronic address: hayat_68@yahoo.co.in.
The involvement of auxin (IAA) in growth and development of plants is well known, but its role in the mitigation of metal stress, especially copper (Cu), is not fully understood; therefore, it is time to explore its involvement in minimizing the stress. A pot experiment was conducted to assess the protective function of IAA, applied to the foliage, on photosynthetic machinery, carbohydrate metabolism, and growth of Brassica juncea, grown with Cu (30 or 60 mg kg(-1) of soil). Among the different concentrations (10(-10), 10(-8), or 10(-6) M), 10(-8) M of IAA alone enhanced the photosynthetic characteristics, sugar accumulation and vegetative growth with minimal cellular oxidative stress level. Moreover, the same concentration of auxin was most effective in decreasing the stress levels generated by Cu and maintained it nearly to that of the control in terms of photosynthetic attributes, gas exchange parameters, PSII activity, electron transport rate, and growth attributes. Auxin also maintained the membrane stability and ultrastructure of chloroplast, stomatal morphology with a reduction in malondialdehyde (MDA), electrolyte leakage (EL) and cell death in test plants even under Cu stress. IAA also improved the translocation of Cu from root to the aerial parts, thus enhanced the Cu-reclamation in metal contaminated soils. Our findings suggest that the application of 10(-8) M of IAA maintains the overall growth of plants and may be used as an effective agent to improve growth, photosynthesis and phyto-remediation potential of B. juncea in Cu contaminated soil.
PMID: 35717733
Plant Physiol Biochem , IF:4.27 , 2022 Aug , V184 : P98-111 doi: 10.1016/j.plaphy.2022.05.019
Characterization of 24-epibrassinolide-mediated modulation of the drought stress responses: Morphophysiology, antioxidant metabolism and hormones in grapevine (Vitis vinifera L.).
College of Enology, Northwest A&F University, Yangling, Shaanxi, 712100, China.; College of Enology, Northwest A&F University, Yangling, Shaanxi, 712100, China; Shaanxi Engineering Research Center for Viti-Viniculture, Yangling, Shaanxi, 712100, China. Electronic address: xizhumei@nwafu.edu.cn.
Drought stress is one of the major abiotic stresses that limit grape growth and yield. Brassinosteroids (BRs) are a class of phytohormones essential for plant growth, development, and adaptation to environmental stress. This study aimed to reveal the physiological and biochemical mechanisms of exogenous BRs in alleviating the drought stress in grapevines. Two-year-old grape seedlings (Vitis vinifera L.) were sprayed with 24-epibrassinolide (EBR), a synthetic analog of BRs, and then subjected to drought treatment. The results showed that exogenous EBR significantly mitigated the reduction of photosynthetic pigment contents and photosystem II efficiency and decreased the damage to chloroplasts when grape seedlings were subjected to drought stress. Drought stress resulted in the accumulation of reactive oxidative species (ROS) and an increase in lipid peroxidation. A reduction in oxidative damage was observed in EBR-pretreated plants, which was probably due to the elevated antioxidant system. Exogenous EBR improved the activities of superoxide dismutase (14%), catalase (18%), peroxidase (17%), and ascorbate peroxidase (9%), and promoted the accumulation of ascorbic acid (10%) and glutathione (7%) under drought stress. EBR pretreatment also promoted autophagic activity, which contributed to the degradation of damaged chloroplasts. Moreover, EBR pretreatment increased the concentrations of abscisic acid, jasmonic acid, auxin, and gibberellic acid. Taken together, exogenous EBR could ameliorate the deleterious effects of drought stress by up-regulating photosynthetic capacity, antioxidant system, autophagic activity, and hormone concentrations.
PMID: 35636336
Plant Physiol Biochem , IF:4.27 , 2022 Jul , V183 : P46-55 doi: 10.1016/j.plaphy.2022.05.003
Probing into the unique relationship between a soil bacterium, Pseudomonas putida AKMP7 and Arabidopsis thaliana: A case of "conditional pathogenesis".
Department of Biological Sciences, Birla Institute of Technology and Science (Pilani), Hyderabad Campus, India.; Department of Biological Sciences, Birla Institute of Technology and Science (Pilani), Hyderabad Campus, India. Electronic address: sridev.mohapatra@hyderabad.bits-pilani.ac.in.
Plant growth-promoting rhizobacteria (PGPR) are beneficial soil bacteria that colonise the rhizosphere and help plants in growth, development, and stress tolerance. While there is a significant body of research elucidating their benefits to plants, studies on the "abnormal" or "unexpected" behavior of these bacteria are almost non-existent. One such study from our laboratory has previously reported a unique situation in which a certain strain of drought and thermo-tolerant PGPR, namely, Pseudomonas putida AKMP7, becomes pathogenic towards Arabidopsis thaliana under drought conditions, but not under normal (well-watered) conditions. In this study, we have probed deeper into this phenomenon of "conditional pathogenesis". We found that, AKMP7 imparts an enhancement in plant growth under well-watered conditions, while, causing a deterioration in plant health under drought conditions. In an attempt to understand the underlying reasons for this phenomenon, we analysed the phytohormones released by Pseudomonas putida AKMP7 using LC-ESI-MS/MS technique. We identified that AKMP7 releases zeatin (a cytokinin), the auxin derivative -indole acetamide and amino acid-conjugates of auxin (indole-3-acetyl-L-alanine, indole-3-acetyl-L-phenylalanine and indole-3-acetyl-L-aspartate) in the growth medium. By treating the plants with commercially obtained forms of these phytohormones, individually or in combination with AKMP7, we identified that zeatin and auxin derivative indole acetamide can play a crucial role in the conditional pathogenesis exhibited by this bacterium on A. thaliana under drought conditions. Our work lays a foundation for further understanding the precise molecular mechanisms involved in this unique phenomenon of conditional/opportunistic pathogenesis.
PMID: 35567874
Plant Physiol Biochem , IF:4.27 , 2022 May , V179 : P179-190 doi: 10.1016/j.plaphy.2022.03.027
Identification of genes and metabolic pathways involved in wounding-induced kiwifruit ripening.
Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece.; Department of Biology, National and Kapodistrian University of Athens, GR-15784, Athens, Greece.; Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece; Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece.; Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece; Institute of Soil and Water Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece.; Institute of Plant Breeding and Genetic Resources, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece; Joint Laboratory of Horticulture, ELGO-DIMITRA, Thessaloniki-Thermi, 57001, Greece; Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, 50829, Cologne, Germany.; Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, 57001, Greece. Electronic address: amolasio@agro.auth.gr.
Fruit is constantly challenged by wounding events, inducing accelerated ripening and irreversible metabolic changes. However, cognate mechanisms that regulate this process are little known. To expand our knowledge of ripening metabolism induced by wounding, an artificial-wound global transcriptome investigation combined with metabolite profiling study was conducted in postharvest kiwifruit (Actinidia chinensis var. deliciosa (A. Chev.) A. Chev. 'Hayward'). Wounding treatment promoted fruit ripening, as demonstrated by changes in fruit firmness, ethylene production and respiration activity determined periodically during a ripening period of 8 d at room temperature. Calcium imaging using fluorescent probe Fluo-3 AM revealed spatial dynamics of Ca(2+) signaling in the wounding area following 8d ripening. Several sugars including fructose, glucose, and sucrose as well as organic acids such as citric, succinic and galacturonic acid were increased by wounding. Changes of various amino acids in wounded-treated fruit, especially 5-oxoproline and valine along with alternations of soluble alcohols, like myo-inositol were detected. Gene expression analysis of the wounded fruit showed increased expression of genes that are mainly involved in defense response (e.g., AdTLP.1-3, AdPP2C.1-2, AdMALD1), calcium ion binding (e.g., AdCbEFh, AdCLR, AdANX), TCA cycle (e.g., AdMDH.1, AdMDH.2, AdCS), sugars (e.g., AdSUSA.1, AdSPS4, AdABFr), secondary metabolism (e.g., AdPAL.1-3, AdCCR, AdHCT.1-2), lipid processing (e.g., AdGELP.1-4, AdGELP) and pectin degradation (e.g., AdPE.1-2, AdPAE.1-2, AdPG.1-2) as well as in ethylene (AdERF7, AdERF1B, AdACO.1-4) and auxin (AdICE, AdAEFc, AdASII) synthesis and perception. Moreover, genes related to aquaporins, such as AdAQP2, AdAQP4 and AdAQP7 were down-regulated in fruit exposed to wounding. These results demonstrate multiple metabolic points of wounding regulatory control during kiwifruit ripening and provide insights into the molecular basis of wounding-mediated ripening.
PMID: 35358868
Plant Physiol Biochem , IF:4.27 , 2022 May , V179 : P78-89 doi: 10.1016/j.plaphy.2022.03.022
Ultrastructural and hormonal changes related to harmaline-induced treatment in Arabidopsis thaliana (L.) Heynh. root meristem.
Departamento de Bioloxia Vexetal e Ciencias do Solo, Facultade de Bioloxia, Universidade de Vigo, Campus Lagoas-Marcosende s/n, 36310, Vigo, Spain.; Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Universita Statale di Milano, Via Celoria n masculine2, 20133, Milano, Italy.; Departamento de Bioloxia Vexetal e Ciencias do Solo, Facultade de Bioloxia, Universidade de Vigo, Campus Lagoas-Marcosende s/n, 36310, Vigo, Spain. Electronic address: adela@uvigo.es.
Harmaline is an indole alkaloid with demonstrated phytotoxicity and recognized pharmacological applications. However, no information is available concerning its mode of action on plant metabolism. Therefore, the present work evaluated bioherbicide mode of action of harmaline on plant metabolism of Arabidopsis thaliana (L.) Heynh. Harmaline induced a strong inhibitory activity on root growth of treated seedlings, reaching IC50 and IC80 values of 14 and 29 muM, respectively. Treated roots were shorter and thicker than control and were characterized by a shorter root meristem size and an increase of root hairs production. Harmaline induced ultrastructural changes such as increment of cell wall thickness, higher density and condensation of mitochondria and vacuolization, appearance of cell wall deposits, increment of Golgi secretory activity and higher percentage of aberrant nuclei. The ethylene inhibitor AgNO3 reversed high root hair appearance and increment of root thickness, and pTCSn::GFP transgenic line showed fluorescence cytokinin signal in stele zone after harmaline treatment that was absent in control, whereas the auxin signal in the transgenic line DR5 was significantly reduced by the treatment. All these results suggest that the mode of action of harmaline could be involving auxin, ethylene and cytokinin synergic/antagonistic action.
PMID: 35325658
BMC Plant Biol , IF:4.215 , 2022 Jun , V22 (1) : P282 doi: 10.1186/s12870-022-03652-3
Transcriptome analysis reveals multiple effects of nitrogen accumulation and metabolism in the roots, shoots, and leaves of potato (Solanum tuberosum L.).
Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016, Qinghai, China.; Qinghai University/Qinghai Academy of Agriculture and Forestry Sciences/Northwest potato Engineering Research Center of Ministry of Education/Key Laboratory of Qinghai-Tibetan Plateau Biotechnology of Ministry of Education, Xining, 810016, Qinghai, China. jianwang2197@163.com.
BACKGROUND: Nitrogen (N) is a major element and fundamental constituent of grain yield. N fertilizer plays an essential role in the roots, shoots, and leaves of crop plants. Here, we obtained two N-sensitive potato cultivars. RESULTS: The plants were cultivated in the pots using N-deficient and N-sufficient conditions. Crop height, leaf chlorophyll content, dry matter, and N-accumulation significantly decreased under N-deficient conditions. Furthermore, we performed a comprehensive analysis of the phenotype and transcriptome, GO terms, and KEGG pathways. We used WGCNA of co-expressed genes, and 116 differentially expressed hub genes involved in photosynthesis, nitrogen metabolism, and secondary metabolites to generate 23 modules. Among those modules, six NRT gene families, four pigment genes, two auxin-related genes, and two energy-related genes were selected for qRT-PCR validation. CONCLUSIONS: Overall, our study demonstrates the co-expressed genes and potential pathways associated with N transport and accumulation in potato cultivars' roots, shoots, and leaves under N-deficient conditions. Therefore, this study provides new ideas to conduct further research on improving nitrogen use efficiency in potatoes.
PMID: 35676629
BMC Plant Biol , IF:4.215 , 2022 May , V22 (1) : P250 doi: 10.1186/s12870-022-03594-w
Combined use of specific length amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) for rapid identification of genes influencing fiber content of hemp (Cannabis sativa L.).
Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China.; Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Heilongjiang, China.; Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China. wxn_fern@163.com.
Hemp (Cannabis sativa L.), an ancient crop, is a significant source of high-quality fiber that primarily caters to the textile industry worldwide. Fiber content is a crucial quantitative trait for evaluating fiber yield in hemp. Understanding the genetic mechanisms involved in hemp breeding is essential for improving yield. In this study, we developed 660 F1 plants from a cross between Jindao-15 (high fiber content fiber-use variety) and Fire No.1 (low fiber content fiber-use variety), and thirty plants each with high and low fiber content were selected from 305 monoecious plants of this population according to 5%-10% of population size for quantitative traits. The DNA from these plants was extracted to establish two bulk DNA pools and then subjected to the restriction digestion by the enzymes RsaI and HaeIII to obtain 314-364 bp digestion fragments and subjected to sequencing using specific length amplified fragment sequencing (SLAF-seq). Finally, we successfully developed 368,404 SLAF tags, which led to the detection of 25,133 high-quality SNPs. Combing with the resequencing results of parents, the SNPs of mixed pools were then subjected to the SNP-Index correlation algorithm, which revealed four candidate regions related to fiber content traits on Chromosome 1, with a length of 8.68 Mb and containing 389 annotated genes. The annotation information and the comparison results identified 15 genes that were highly likely to modulate the fiber content of hemp. Further, qPCR validation identified six genes (LOC115705530, LOC115705875, LOC115704794, LOC115705371, LOC115705688 and LOC115707511) that were highly positively correlated with influencing the hemp fiber content. These genes were involved in the transcription regulation, auxin and water transportion, one carbon and sugar metabolism. And non-synnoumous mutation SNPs which may play vital role in influencing the fiber content were detected in LOC115705875, LOC115704794, LOC115705688 and LOC115707511. Thus, our study highlights the importance of the combined use of SLAF-Seq and Bulked Segregant analysis (BSA) to locate genes related to hemp fiber content rapidly. Hence, our study provides novel mechanistic inputs for the fast identification of genes related to important agronomic traits of hemp and other crops catering to the textile industry.
PMID: 35596150
Tree Physiol , IF:4.196 , 2022 May , V42 (5) : P1059-1069 doi: 10.1093/treephys/tpab155
The mycorrhizal-induced growth promotion and insect resistance reduction in Populus alba x P. berolinensis seedlings: a multi-omics study.
Department of Forestry School of Forestry, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China.; College of Forestry Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China.; Department of Economics College of Economics and Management, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R.China.; Department of Landscape Architecture College of Landscape Architecture, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, P. R. China.
Arbuscular mycorrhizal (AM) fungi are an alternative to chemical insecticides or fertilizers, and there is an urgent need to extend the application of AM fungi to woody plants. This study aims to investigate the growth and resistance against the gypsy moth larvae (Lymantria dispar) in Glomus intraradices-colonized Populus alba x P. berolinensis seedlings, and to unravel the transcriptome and metabolome phenotypes recruited by AM fungus colonization that affect plant growth and insect resistance. Our results showed a positive mycorrhizal growth response, i.e., growth and biomass of mycorrhizal seedlings were enhanced. However, AM fungus inoculation reduced the resistance of poplar to gypsy moth larvae, as evidenced by the decreased carbon/nitrogen ratio in leaves, as well as the increased larval growth and shortened larval developmental duration. Transcriptome analysis revealed that in both auxin and gibberellin signaling transductions, all nodes were responsive to AM symbiosis and most differentially expressed genes belonging to effectors were up-regulated in mycorrhizal seedlings. Furthermore, the two key enzymes (4-coumarate-CoA ligase and trans-cinnamate 4-monooxygenase) involved in the synthesis of p-Coumaroyl-CoA, an initial metabolite in flavonoid biosynthesis and the first rate-limiting enzyme (chalcone synthase) in flavonoid biosynthesis, were down-regulated at the transcriptional level. Consistent with the transcriptome results, metabolome analysis found that the amounts of all differentially accumulated flavonoid compounds (e.g., catechin and quercetin) identified in mycorrhizal seedlings were decreased. Taken together, these findings highlight the diverse outcomes of AM fungi-host plant-insect interaction and reveal the regulatory network of the positive mycorrhizal growth response and mycorrhizal-induced reduction of insect resistance in poplar.
PMID: 35022794
Tree Physiol , IF:4.196 , 2022 May , V42 (5) : P971-988 doi: 10.1093/treephys/tpab165
Comparable and adaptable strategies to waterlogging stress regulated by adventitious roots between two contrasting species.
School of Ecological and Environmental Sciences, Hainan University, No. 58 Renmin Road, Meilan District, Haikou 570228, China.; Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, No. 58 Renmin Road, Meilan District, Haikou 570228, China.; School of Life Sciences, Hainan University, No. 58 Renmin Road, Meilan District, Haikou 570228, China.; School of Plant Protection, Hainan University, No. 58 Renmin Road, Meilan District, Haikou 570228, China.; Center for Eco-Environmental Restoration Engineering of Hainan Province, No. 58 Renmin Road, Meilan District, Haikou 570228, China.
Cleistocalyx operculatus and Syzygium cumini possess a certain waterlogging tolerance. However, the comparable and adaptable strategies to waterlogging stress between these two species on the basis of waterlogging adventitious root (AR) regulation were still unclear. In this study, the plant performance in response to AR regulation based on AR removal (AR-R) and exogenous hormone application was investigated in terms of plant morphology, physiology, photosynthesis and AR traits. Results showed that C. operculatus possesses stronger waterlogging tolerance than S. cumini based on waterlogging tolerance coefficient, which is mainly due to the higher root biomass, root porosity and length, and activity of ARs, and shorter emergence time of ARs in C. operculatus than in S. cumini. The AR-R treatment increased activity and porosity of primary root, and induced a large amount of up-vertical ARs from the primary root systems in C. operculatus, while similar adaptive morphological changes in roots did not occur in AR-R-treated S. cumini. Exogenous abscisic acid (ABA) application had better effects on alleviating waterlogging damages than exogenous auxin (IAA) in balancing endogenous hormones (ABA and zeatin riboside), promoting AR development (porosity and activity, and the ratio of cortex area to stele area), improving the photosynthesis process and the antioxidant system (soluble protein, free proline and peroxidase). Moreover, under waterlogging conditions, exogenous ABA application induced greater increases in net photosynthesis rate, stomatal conductance, chlorophyll b and carotenoid in S. cumini than in C. operculatus, which suggested that S. cumini responded more positively and efficiently to exogenous ABA application than C. operculatus under waterlogging conditions. Thus, the findings provided new insights into the waterlogging adaptable strategies in waterlogging tolerant woody species on the basis of ARs and could provide scientific guidance for the application of these two species during revegetation activities in wetlands. Cleistocalyx operculatus could alternatively form a majority of up-vertical adventitious roots (ARs) from the primary roots after removing the normal ARs, but Syzygium cumini could not.Cleistocalyx operculatus possessed positive strategies to waterlogging stress, while S. cumini used traditional passive strategies.Exogenous abscisic acid (ABA) application had better effects on alleviating waterlogging damages in both species than exogenous auxin application.Syzygium cumini could more positively and efficiently respond to exogenous ABA application than C. operculatus.Waterlogging tolerance coefficient was significantly controlled by the chlorophyll contents and AR factors in C. operculatus and the AR factors and O2- in S. cumini.The best development of the AR number (ARN) and AR length (ARL) in exogenous ABA-treated C. operculatus may be closely related with positive zeatin riboside accumulation.The development of ARN and ARL was more important to waterlogging tolerance than that of AR porosity under waterlogging conditions.
PMID: 34875093
Mol Plant Microbe Interact , IF:4.171 , 2022 Jun doi: 10.1094/MPMI-05-22-0113-TA
Berberine Bridge Enzyme-Like Oligosaccharide Oxidases Act as Enzymatic Transducers Between Microbial Glycoside Hydrolases and Plant Peroxidases.
University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; anna.scortica@guest.univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; moira.giovannoni@univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; valentina.scafati@guest.univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; francesco.angelucci@univaq.it.; University of Rome La Sapienza Department of Biology and Biotechnology Charles Darwin, 125566, Roma, Lazio, Italy; felice.cervone@uniroma1.it.; University of Rome La Sapienza Department of Biology and Biotechnology Charles Darwin, 125566, Roma, Lazio, Italy; giulia.delorenzo@uniroma1.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; manuel.benedetti@univaq.it.; University of L'Aquila Department of Clinical Medicine Life Health and Environmental Sciences, 367958, L'Aquila, Abruzzo, Italy; mariabenedetta.mattei@univaq.it.
OG-oxidase 1 (OGOX1) and CD-oxidase (CELLOX) are plant berberine bridge enzyme-like oligosaccharide oxidases that oxidize oligogalacturonides (OGs) and cellodextrins (CDs), cell wall fragments with nature of damage-associated molecular patterns (DAMPs). The oxidation of OGs and CDs attenuates their elicitor activity and concomitantly releases H2O2. By using a multiple enzyme-based assay, we demonstrate that the H2O2 generated downstream of the combined action between a fungal polygalacturonase and OGOX1 or an endoglucanase and CELLOX can be directed by plant peroxidases (PODs) either towards a reaction possibly involved in plant defence such as the oxidation of monolignol or a reaction possibly involved in a developmental event such as the oxidation of auxin (IAA), pointing to OGOX1 and CELLOX as enzymatic transducers between microbial glycoside hydrolases and plant PODs.
PMID: 35704684
Planta , IF:4.116 , 2022 Jun , V256 (1) : P6 doi: 10.1007/s00425-022-03916-0
The genome of a mangrove plant, Avicennia marina, provides insights into adaptation to coastal intertidal habitats.
Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.; Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China. zhenghl@xmu.edu.cn.
MAIN CONCLUSION: Whole-genome duplication, gene family and lineage-specific genes analysis based on high-quality genome reveal the adaptation mechanisms of Avicennia marina to coastal intertidal habitats. Mangrove plants grow in a complex habitat of coastal intertidal zones with high salinity, hypoxia, etc. Therefore, it is an interesting question how mangroves adapt to the unique intertidal environment. Here, we present a chromosome-level genome of the Avicennia marina, a typical true mangrove with a size of 480.43 Mb, contig N50 of 11.33 Mb and 30,956 annotated protein-coding genes. We identified 621 Avicennia-specific genes that are mainly related to flavonoid and lignin biosynthesis, auxin homeostasis and response to abiotic stimulus. We found that A. marina underwent a novel specific whole-genome duplication, which is in line with a brief era of global warming that occurred during the paleocene-eocene maximum. Comparative genomic and transcriptomic analyses outline the distinct evolution and sophisticated regulations of A. marina adaptation to the intertidal environments, including expansion of photosynthesis and oxidative phosphorylation gene families, unique genes and pathways for antibacterial, detoxifying antioxidant and reactive oxygen species scavenging. In addition, we also analyzed salt gland secretion-related genes, and those involved in the red bark-related flavonoid biosynthesis, while significant expansions of key genes such as NHX, 4CL, CHS and CHI. High-quality genomes in future investigations will facilitate the understand of evolution of mangrove and improve breeding.
PMID: 35678934
Planta , IF:4.116 , 2022 May , V255 (6) : P123 doi: 10.1007/s00425-022-03908-0
Genome-wide characterization and expression analysis of SAUR gene family in Melon (Cucumis melo L.).
Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.; Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China. chegen@imu.edu.cn.; Key Laboratory of Herbage and Endemic Crop Biotechnology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China. lshasi@imu.edu.cn.
MAIN CONCLUSION: We identified 66 melon SAUR genes by bioinformatic analyses. CmSAUR19, 38, 58, 62 genes are specifically expressed in different stages of fruit growth, suggesting their participation in regulating fruit development. Auxin plays a crucial role in plant growth by regulating the multiple auxin response genes. However, in melon (Cucumis melo L.), the functions of the auxin early response gene family SAUR (Small auxin up RNA) genes in fruit development are still poorly understood. Through genome-wide characterization of CmSAUR family in melon, we identified a total of 66 CmSAUR genes. The open reading frames of the CmSAUR genes ranged from 234 to 525 bp, containing only one exon and lacking introns. Chromosomal position and phylogenetic tree analyses found that the two gene clusters in the melon chromosome are highly homologous in the Cucurbitaceae plants. Among the four conserved motifs in CmSAUR proteins, motif 1, motif 2, and motif 3 located in most of the family protein sequences, and motif 4 showed a close correlation with the two gene clusters. The CmSAUR28 and CmSAUR58 genes have auxin response elements located in the promoters, suggesting they may be involved in the auxin signaling pathway to regulate fruit development. Through transcriptomic profiling in the four developmental stages of fruit and different lateral organs, we selected 16 differentially-expressed SAUR genes for performing further expression analyses. qRT-PCR results showed that five SAUR genes are specifically expressed in flower organs and ovaries. CmSAUR19 and CmSAUR58 were significantly accumulated in the early developmental stage of the fruit. CmSAUR38 and CmAUR62 showed high expression in the climacteric and post-climacteric stages, suggesting their specific role in controlling fruit ripening. This work provides a foundation for further exploring the function of the SAUR gene in fruit development.
PMID: 35552537
Genes (Basel) , IF:4.096 , 2022 Jun , V13 (6) doi: 10.3390/genes13061041
An Aux/IAA Family Member, RhIAA14, Involved in Ethylene-Inhibited Petal Expansion in Rose (Rosa hybrida).
Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing 100193, China.; Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China.
Flower size, a primary agronomic trait in breeding of ornamental plants, is largely determined by petal expansion. Generally, ethylene acts as an inhibitor of petal expansion, but its effect is restricted by unknown developmental cues. In this study, we found that the critical node of ethylene-inhibited petal expansion is between stages 1 and 2 of rose flower opening. To uncover the underlying regulatory mechanism, we carried out a comparative RNA-seq analysis. Differentially expressed genes (DEGs) involved in auxin-signaling pathways were enriched. Therefore, we identified an auxin/indole-3-acetic acid (Aux/IAA) family gene, RhIAA14, whose expression was development-specifically repressed by ethylene. The silencing of RhIAA14 reduced cell expansion, resulting in diminished petal expansion and flower size. In addition, the expressions of cell-expansion-related genes, including RhXTH6, RhCesA2, RhPIP2;1, and RhEXPA8, were significantly downregulated following RhIAA14 silencing. Our results reveal an Aux/IAA that serves as a key player in orchestrating petal expansion and ultimately contributes to flower size, which provides new insights into ethylene-modulated flower opening and the function of the Aux/IAA transcription regulator.
PMID: 35741802
Genes (Basel) , IF:4.096 , 2022 May , V13 (5) doi: 10.3390/genes13050853
Overexpression of LT, an Oncoprotein Derived from the Polyomavirus SV40, Promotes Somatic Embryogenesis in Cotton.
Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Zhongguancun, Nandajie No. 12, Haidian District, Beijing 100081, China.; College of Life Sciences, Inner Mongolia University, University West Street No. 235, Saihan District, Hohhot 010000, China.
Although genetic transformation has opened up a new era for cotton molecular breeding, it still suffers from the limitation problem of long transformation periods, which slows down the generation of new cotton germplasms. In this study, LT gene (SV40 large T antigen), which promotes the transformation efficiency of animal cells, was codon-optimized. Its overexpression vector was transformed into cotton. It was observed that EC (embryogenic callus) formation period was 33% shorter and transformation efficiency was slightly higher in the LT T0 generation than that of control. RNA-seq data of NEC (non-embryonic callus) and EC from LT and control revealed that more DEGs (differential expression genes) in NEC were identified than that of EC, indicating LT mainly functioned in NEC. Further KEGG, GO, and transcription factor analyses showed that DEGs were significantly enriched in brassinosteroid biosynthesis pathways and that bHLH, MYB, and AP2/ERF were the top three gene families, which are involved in EC formation. In addition, the key genes related to the auxin pathway were differentially expressed only in LT overexpression NEC, which caused early response, biosynthesis, and transportation of the hormone, resulting in EC earlier formation. In summary, the results demonstrated that LT can promote somatic embryogenesis in cotton, which provides a new strategy for improving cotton transformation and shortening EC formation time.
PMID: 35627238
Genes (Basel) , IF:4.096 , 2022 May , V13 (5) doi: 10.3390/genes13050817
Novel Role of AaMYBC1 in Regulating Actinidia arguta Vine Architecture by Elongating Internode Based on Multi-Omics Analysis of Transgenic Tobacco.
Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China.; Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China.; Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China.
The internode length affects the status of fruiting branches and shapes the vine architecture. MYB TFs (transcription factors) have been widely studied and reported to control many biological processes including secondary metabolism, abiotic stresses, growth and development, etc. However, the roles of MYB TFs in regulating internode length remain poorly understood. Here, we demonstrated that a secondary metabolism-related R2R3-MYB TF AaMYBC1 from Actinidia arguta was involved in the regulation of internode length by combined analysis of transcriptome and metabolome of transgenic tobacco plants. The metabolome analysis of OE (over-expressed tobacco) and WT (wild-typed tobacco) showed that there were a total of 1000 metabolites, 176 of which had significant differences. A key metabolite pme1651 annotated as indole 3-acetic acid belonged to phytohormone that was involved in internode length regulation. The RNA-seq analysis presented 446 differentially expressed genes (DEGs) between OE and WT, 14 of which were common DEGs in KEGG and GO enrichment. Through the combined analysis of metabolome and transcriptome in transgenic and wild-type tobacco, three key genes including two SAUR and a GH3 gene were possibly involved in internode elongation. Finally, a regulatory module was deduced to show the role of AaMYBC1 in internode elongation. Our results proposed a molecular mechanism of AaMYBC1 regulating internode length by mediated auxin signaling, implying the potential role in regulating the vine architecture.
PMID: 35627204
Plant Genome , IF:4.089 , 2022 Jun , V15 (2) : Pe20199 doi: 10.1002/tpg2.20199
Differential gene expression in tall fescue tissues in response to water deficit.
Dep. of Plant and Soil Sciences, Univ. of Kentucky, Lexington, KY, 40546-0312, USA.; Dep. of Plant Pathology, Univ. of Kentucky, Lexington, KY, 40546-0312, USA.; USDA-ARS, Forage-Animal Production Research Unit, Lexington, KY, 40546-0091, USA.
Tall fescue (Festuca arundinacea Schreb.) is a popular pasture and turf grass particularly known for drought resistance, allowing for its persistence in locations that are unfavorable for other cool-season grasses. Also, its seed-borne fungal symbiont (endophyte) Epichloe coenophiala, which resides in the crown and pseudostem, can be a contributing factor in its drought tolerance. Because it contains the apical meristems, crown survival under drought stress is critical to plant survival as well as the endophyte. In this study, we subjected tall fescue plants with their endophyte to water-deficit stress or, as controls with normal watering, then compared plant transcriptome responses in four vegetative tissues: leaf blades, pseudostem, crown, and roots. A transcript was designated a differentially expressed gene (DEG) if it exhibited at least a twofold expression difference between stress and control samples with an adjusted p value of .001. Pathway analysis of the DEGs across all tissue types included photosynthesis, carbohydrate metabolism, phytohormone biosynthesis and signaling, cellular organization, and a transcriptional regulation. While no specific pathway was observed to be differentially expressed in the crown, genes encoding auxin response factors, nuclear pore anchors, structural maintenance of chromosomes, and class XI myosin proteins were more highly differentially expressed in crown than in the other vegetative tissues, suggesting that regulation in expression of these genes in the crown may aid in survival of the meristems in the crown.
PMID: 35322562
Plant Mol Biol , IF:4.076 , 2022 Jun doi: 10.1007/s11103-022-01289-2
The interaction between exogenous IBA with sucrose, light and ventilation alters the expression of ARFs and Aux/IAA genes in Carica papaya plantlets.
Centro de Investigacion Cientifica de Yucatan A.C., Calle 43 No. 130, Colonia Chuburna de Hidalgo, C.P. 97205, Merida, Yucatan, Mexico. estrella.humberto@inifap.gob.mx.; Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias (INIFAP), Campo Experimental Ixtacuaco, Km 4.5 Carretera Martinez de la Torre-Tlapacoyan, C.P. 93600, Tlapacoyan, Veracruz, Mexico. estrella.humberto@inifap.gob.mx.; Centro de Investigacion Cientifica de Yucatan A.C., Calle 43 No. 130, Colonia Chuburna de Hidalgo, C.P. 97205, Merida, Yucatan, Mexico.; Independent Researcher, Calle 6a 279 a, Jardines de Vista Alegre, Merida, Yucatan, Mexico.; Institute of Nutrition and Functional Foods (INAF), Laval University, 2440 Boulevard Hochelaga, Quebec City, QC, G1V 0A6, Canada.; Centro de Investigacion Cientifica de Yucatan A.C., Calle 43 No. 130, Colonia Chuburna de Hidalgo, C.P. 97205, Merida, Yucatan, Mexico. jorgesm@cicy.mx.
KEY MESSAGE: The interaction between exogenous IBA with sucrose, light and ventilation, alters the expression of ARFs and Aux/IAA genes in in vitro grown Carica papaya plantlets. In vitro papaya plantlets normally show low rooting percentages during their ex vitro establishment that eventually leads to high mortality when transferred to field conditions. Indole-3-butyric acid (IBA) auxin is normally added to culture medium, to achieve adventitious root formation on in vitro papaya plantlets. However, the molecular mechanisms occurring when IBA is added to the medium under varying external conditions of sugar, light and ventilation have not been studied. Auxin response factors (ARF) are auxin-transcription activators, while auxin/indole-3-acetic acid (Aux/IAA) are auxin-transcription repressors, that modulate key components involved in auxin signaling in plants. In the present study, we identified 12 CpARF and 18 CpAux/IAA sequences in the papaya genome. The cis-acting regulatory elements associated to those CpARFs and CpAux/IAA gene families were associated with stress and hormone responses. Furthermore, a comprehensive characterization and expression profiling analysis was performed on 6 genes involved in rhizogenesis formation (CpARF5, 6, 7 and CpAux/IAA11, 13, 14) from in vitro papaya plantlets exposed to different rhizogenesis-inducing treatments. In general, intact in vitro plantlets were not able to produce adventitious roots, when IBA (2 mg L(-1)) was added to the culture medium; they became capable to produce roots and increased their ex-vitro survival. However, the best rooting and survival % were obtained when IBA was added in combination with adequate sucrose supply (20 g L(-1)), increased light intensity (750 micromol photon m(-2) s(-1)) and ventilation systems within the culture vessel. Interestingly, it was precisely under those conditions that promoted high rooting and survival %, where the highest expression of CpARFs, but the lowest expression of CpAux/IAAs occurred. One interesting case occurred when in vitro plantlets were exposed to high levels of light in the absence of added IBA, as high rooting and survival occurred, even though no exogenous auxin was added. In fact, plantlets from this treatment showed the right expression profile between auxin activators/repressors genes, in both stem base and root tissues.
PMID: 35725838
Plant Mol Biol , IF:4.076 , 2022 May doi: 10.1007/s11103-022-01268-7
Generalist endophyte Phomopsis liquidambaris colonization of Oryza sativa L. promotes plant growth under nitrogen starvation.
Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.; Centre for Novel Agricultural Products, Department of Biology, University of York, YO10 5DD, York, United Kingdom.; Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, Jiangsu Key Laboratory for Microbes and Functional Genomics, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China. daichuanchao@njnu.edu.cn.
Fungal endophytes establish symbiotic relationships with host plants, which results in a mutual growth benefit. However, little is known about the plant genetic response underpinning endophyte colonization. Phomopsis liquidambaris usually lives as an endophyte in a wide range of asymptomatic hosts and promotes biotic and abiotic stress resistance. In this study, we show that under low nitrogen conditions P. liquidambaris promotes rice growth in a hydroponic system, which is free of other microorganisms. In order to gain insights into the mechanisms of plant colonization by P. liquidambaris under low nitrogen conditions, we compared root and shoot transcriptome profiles of root-inoculated rice at different colonization stages. We determined that genes related to plant growth promotion, such as gibberellin and auxin related genes, were up-regulated at all developmental stages both locally and systemically. The largest group of up-regulated genes (in both roots and shoots) were related to flavonoid biosynthesis, which is involved in plant growth as well as antimicrobial compounds. Furthermore, genes encoding plant defense-related endopeptidase inhibitors were strongly up-regulated at the early stage of colonization. Together, these results provide new insights into the molecular mechanisms of plant-microbe mutualism and the promotion of plant growth by a fungal endophyte under nitrogen-deficient conditions.
PMID: 35522401
Plant Mol Biol , IF:4.076 , 2022 Jun , V109 (3) : P249-269 doi: 10.1007/s11103-020-01033-8
Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava.
RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. yoshinori.utsumi@riken.jp.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.; RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.; Faculty of Agriculture, Yamagata University, Tsuruoka, Japan.; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan.; Graduate School of Pharmaceutical Sciences, Chiba University, Chiba, Chiba, 260-8675, Japan.; Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan.; Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. motoaki.seki@riken.jp.; RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan. motoaki.seki@riken.jp.; Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan. motoaki.seki@riken.jp.
KEY MESSAGE: Integrative omics approaches revealed a crosstalk among phytohormones during tuberous root development in cassava. Tuberous root formation is a complex process consisting of phase changes as well as cell division and elongation for radial growth. We performed an integrated analysis to clarify the relationships among metabolites, phytohormones, and gene transcription during tuberous root formation in cassava (Manihot esculenta Crantz). We also confirmed the effects of the auxin (AUX), cytokinin (CK), abscisic acid (ABA), jasmonic acid (JA), gibberellin (GA), brassinosteroid (BR), salicylic acid, and indole-3-acetic acid conjugated with aspartic acid on tuberous root development. An integrated analysis of metabolites and gene expression indicated the expression levels of several genes encoding enzymes involved in starch biosynthesis and sucrose metabolism are up-regulated during tuberous root development, which is consistent with the accumulation of starch, sugar phosphates, and nucleotides. An integrated analysis of phytohormones and gene transcripts revealed a relationship among AUX signaling, CK signaling, and BR signaling, with AUX, CK, and BR inducing tuberous root development. In contrast, ABA and JA inhibited tuberous root development. These phenomena might represent the differences between stem tubers (e.g., potato) and root tubers (e.g., cassava). On the basis of these results, a phytohormonal regulatory model for tuberous root development was constructed. This model may be useful for future phytohormonal studies involving cassava.
PMID: 32757126
Phytochemistry , IF:4.072 , 2022 Aug , V200 : P113219 doi: 10.1016/j.phytochem.2022.113219
Complexity of the auxin biosynthetic network in Arabidopsis hypocotyls is revealed by multiple stable-labeled precursors.
Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Alderman Hall, 1970 Folwell Ave, St. Paul, Minnesota, 55108, USA. Electronic address: mkreiser@umn.edu.; Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Alderman Hall, 1970 Folwell Ave, St. Paul, Minnesota, 55108, USA. Electronic address: tangx575@umn.edu.; Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Alderman Hall, 1970 Folwell Ave, St. Paul, Minnesota, 55108, USA. Electronic address: ggardner@umn.edu.; Department of Horticultural Science and Microbial and Plant Genomics Institute, University of Minnesota, Alderman Hall, 1970 Folwell Ave, St. Paul, Minnesota, 55108, USA. Electronic address: cohen047@umn.edu.
Auxin is a key regulator of plant development and in Arabidopsis thaliana can be synthesized through multiple pathways; however, the contributions of various biosynthetic pathways to specific developmental processes are largely unknown. To trace the involvement of various biosynthetic routes to indole-3-acetic acid (IAA) under conditions that induce adventitious root formation in Arabidopsis hypocotyls, we treated seedlings with three different stable isotope-labeled precursors ([(13)C6]anthranilate, [(15)N1]indole, and [(13)C3]serine) and monitored label incorporation into a number of proposed biosynthesis intermediates as well as IAA. We also employed inhibitors targeting tryptophan aminotransferases and flavin monooxygenases of the IPyA pathway, and treatment with these inhibitors differentially altered the labeling patterns from all three precursors into intermediate compounds and IAA. [(13)C3]Serine was used to trace utilization of tryptophan (Trp) and downstream intermediates by monitoring (13)C incorporation into Trp, indole-3-pyruvic acid (IPyA), and IAA; most (13)C incorporation into IAA was eliminated with inhibitor treatments, suggesting Trp-dependent IAA biosynthesis through the IPyA pathway is a dominant contributor to the auxin pool in de-etiolating hypocotyls that can be effectively blocked using chemical inhibitors. Labeling treatment with both [(13)C6]anthranilate and [(15)N1]indole simultaneously resulted in higher label incorporation into IAA through [(15)N1]indole than through [(13)C6]anthranilate; however, this trend was reversed in the proposed precursors that were monitored, with the majority of isotope label originating from [(13)C6]anthranilate. An even greater proportion of IAA became [(15)N1]-labeled compared to [(13)C6]-labeled in seedlings treated with IPyA pathway inhibitors, suggesting that, when the IPyA pathway is blocked, IAA biosynthesis from labeled indole may also come from an origin independent of the measured pool of Trp in these tissues.
PMID: 35523282
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (12) doi: 10.3390/plants11121618
UVB Irradiation-Induced Transcriptional Changes in Lignin- and Flavonoid Biosynthesis and Indole/Tryptophan-Auxin-Responsive Genes in Rice Seedlings.
Department of Crop Science, Chungbuk National University, Cheongju 28644, Korea.
Global warming accelerates the destruction of the ozone layer, increasing the amount of UVB reaching the Earth's surface, which in turn alters plant growth and development. The effects of UVB-induced alterations of plant secondary and cell wall metabolism were previously documented; however, there is little knowledge of its effects on rice seedlings during the developmental phase of leaves. In this study, we examined secondary metabolic responses to UVB stress using a transcriptomic approach, focusing on the biosynthetic pathways for lignin, flavonoid, and indole/tryptophan-auxin responses. As new leaves emerged, they were irradiated with UVB for 5 days (for 3 h/day(-1)). The genes encoding the enzymes related to lignin (4CL, CAD, and POD) and flavonoid biosynthesis (CHS, CHI, and FLS) were highly expressed on day 1 (younger leaves) and day 5 (older leaves) after UVB irradiation. The expression of the genes encoding the enzymes related to tryptophan biosynthesis (AS, PRT, PRAI, IGPS, and TS) increased on day 3 of UVB irradiation, and the level of tryptophan increased and showed the same temporal pattern of occurrence as the expression of the cognate gene. Interestingly, the genes encoding BBX4 and BBX11, negative regulators of UVB signaling, and SAUR27 and SAUR55, auxin response enzymes, were downregulated on day 3 of UVB irradiation. When these results are taken together, they suggest that secondary metabolic pathways in rice seedlings are influenced by the interaction between UVB irradiation and the leaf developmental stage. Thus, the strategies of protection against, adaptation to, and mitigation of UVB might be delicately regulated, and, in this context, our data provide valuable information to understand UVB-induced secondary metabolism in rice seedlings.
PMID: 35736769
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (12) doi: 10.3390/plants11121601
The Mutation of Rice MEDIATOR25, OsMED25, Induces Rice Bacterial Blight Resistance through Altering Jasmonate- and Auxin-Signaling.
Faculty of Agriculture, Kagawa University, Miki 761-0795, Japan.; Philippine Rice Research Institute, Central Experiment Station, Science City of Munoz 3119, Philippines.; International Center for Research and Education in Agriculture, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
Rice bacterial blight disease caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most severe diseases of rice. However, the regulatory mechanisms of rice defense against Xoo remain poorly understood. The rice MEDIATOR25, OsMED25-a subunit of the mediator multiprotein complex that acts as a universal adaptor between transcription factors (TFs) and RNA polymerase II-plays an important role in jasmonic acid (JA)-mediated lateral root development in rice. In this study, we found that OsMED25 also plays an important role in JA- and auxin-mediated resistance responses against rice bacterial blight. The osmed25 loss-of-function mutant exhibited high resistance to Xoo. The expression of JA-responsive defense-related genes regulated by OsMYC2, which is a positive TF in JA signaling, was downregulated in osmed25 mutants. Conversely, expression of some OsMYC2-independent JA-responsive defense-related genes was upregulated in osmed25 mutants. Furthermore, OsMED25 interacted with some AUXIN RESPONSE FACTORS (OsARFs) that regulate auxin signaling, whereas the mutated osmed25 protein did not interact with the OsARFs. The expression of auxin-responsive genes was downregulated in osmed25 mutants, and auxin-induced susceptibility to Xoo was not observed in osmed25 mutants. These results indicate that OsMED25 plays an important role in the stable regulation of JA- and auxin-mediated signaling in rice defense response.
PMID: 35736751
Plants (Basel) , IF:3.935 , 2022 Jun , V11 (12) doi: 10.3390/plants11121580
A Small Gtp-Binding Protein GhROP3 Interacts with GhGGB Protein and Negatively Regulates Drought Tolerance in Cotton (Gossypium hirsutum L.).
College of Life Science, Xinjiang Agricultural University, Nongda East Road, Urumqi 830001, China.; College of Agronomy, Laboratory of Agricultural Biotechnology, Xinjiang Agricultural University, Nongda East Road, Urumqi 830001, China.; Research Center of Cotton Engineering, Ministry of Education, Xinjiang Agricultural University, Nongda East Road, Urumqi 830001, China.
As a plant-specific Rho-like small G protein, the ROP (Rho-related GTPase of plants) protein regulates the growth and development of plants and various stress responses in the form of molecular switches. Drought is a major abiotic stress that limits cotton yield and fiber quality. In this study, virus-induced gene silencing (VIGS) technology was used to analyze the biological function of GhROP3 in cotton drought stress tolerance. Meanwhile, we used yeast two-hybrid and bimolecular fluorescence complementation assays to examine the interaction between GhROP3 and GhGGB. GhROP3 has a high expression level in cotton true leaves and roots, and responds to drought, high salt, cold, heat stress, and exogenous abscisic acid (ABA) and auxin (IAA) treatments. Silencing GhROP3 improved the drought tolerance of cotton. The water loss rates (WLR) of detached leaves significantly reduced in silenced plants. Also, the relative water content (RWC) and total contents of chlorophyll (Chl) and proline (Pro) of leaves after drought stress and the activities of three antioxidant enzymes catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) significantly increased, whereas the contents of hydrogen peroxide (H2O2) and malondialdehyde (MDA) significantly reduced. In the leaves of silenced plants, the expression of genes related to ABA synthesis and its related pathway was significantly upregulated, and the expression of decomposition-related GhCYP707A gene and genes related to IAA synthesis and its related pathways was significantly downregulated. It indicated that GhROP3 was a negative regulator of cotton response to drought by participating in the negative regulation of the ABA signaling pathway and the positive regulation of the IAA signaling pathway. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhROP3 protein interacted with the GhGGB protein in vivo and in vitro. This study provided a theoretical basis for the in-depth investigation of the drought resistance-related molecular mechanism of the GhROP3 gene and the biological function of the GhGGB gene.
PMID: 35736735
Plants (Basel) , IF:3.935 , 2022 May , V11 (11) doi: 10.3390/plants11111472
The Auxin-Response Repressor IAA30 Is Down-Regulated in Reproductive Tissues of Apomictic Paspalum notatum.
Laboratorio de Biologia Molecular, Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR) CONICET-UNR, Facultad de Ciencias Agrarias, Campo Experimental Villarino, Universidad Nacional de Rosario, Zavalla S2125ZAA, Santa Fe, Argentina.; DIADE, Universite de Montpellier, IRD, CIRAD, 34394 Montpellier, France.
The capacity for apomixis in Paspalum notatum is controlled by a single-dominant genomic region, which shows strong synteny to a portion of rice chromosome 12 long arm. The locus LOC_Os12g40890, encoding the Auxin/Indole-3-Acetic Acid (Aux/IAA) family member OsIAA30, is located in this rice genomic segment. The objectives of this work were to identify transcripts coding for Aux/IAA proteins expressed in reproductive tissues of P. notatum, detect the OsIAA30 putative ortholog and analyze its temporal and spatial expression pattern in reproductive organs of sexual and apomictic plants. Thirty-three transcripts coding for AUX/IAA proteins were identified. Predicted protein alignment and phylogenetic analysis detected a highly similar sequence to OsIAA30 (named as PnIAA30) present in both sexual and apomictic samples. The expression assays of PnIAA30 showed a significant down-regulation in apomictic spikelets compared to sexual ones at the stages of anthesis and post-anthesis, representation levels negatively correlated with apospory expressivity and different localizations in sexual and apomictic ovules. Several PnIAA30 predicted interactors also appeared differentially regulated in the sexual and apomictic floral transcriptomes. Our results showed that an auxin-response repressor similar to OsIAA30 is down-regulated in apomictic spikelets of P. notatum and suggests a contrasting regulation of auxin signaling during sexual and asexual seed formation.
PMID: 35684245
Plants (Basel) , IF:3.935 , 2022 May , V11 (11) doi: 10.3390/plants11111457
An Improved Procedure for Agrobacterium-Mediated Transformation of 'Carrizo' Citrange.
Department of Plant Science, University of Connecticut, Storrs, CT 06269, USA.; Horticulture and Landscape College, Hunan Agricultural University, Changsha 410128, China.; Appalachian Fruit Research Station, Agricultural Research Service, U.S. Department of Agriculture, Kearneysville, WV 25430, USA.; Mid-Florida Research and Education Center, Department of Environmental Horticulture, Institute of Food and Agricultural Sciences, University of Florida, Apopka, FL 32703, USA.; Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China.
Although several protocols for genetic transformation of citrus have been published, it is highly desirable to further improve its efficiency. Here we report treatments of Agrobacterium cells and citrus explants prior to and during co-cultivation process to enhance transformation efficiency using a commercially used rootstock 'Carrizo' citrange [Citrus sinensis (L.) Osb. x Poncirius trifoliata (L.) Raf.] as a model plant. We found explants from light-grown seedlings exhibited higher transformation efficiency than those from etiolated seedlings. We pre-cultured Agrobacterium cells in a 1/10 MS, 0.5 g/L 2-(N-morpholino) ethanesulfonic acid (MES) and 100 microM acetosyringone liquid medium for 6 h at 25 degrees C before used to infect citrus explants. We incubated epicotyl segments in an MS liquid medium containing 13.2 microM 6-BA, 4.5 microM 2,4-D, 0.5 microM NAA for 3 h at 25 degrees C prior to Agrobacterium infection. In the co-cultivation medium, we added 30 microM paclobutrazol and 10 microM lipoic acid. Each of these treatments significantly increased the efficiencies of transformation up to 30.4% (treating Agrobacterium with acetosyringone), 31.8% (treating explants with cytokinin and auxin), 34.9% (paclobutrazol) and 38.6% (lipoic acid), respectively. When the three treatments were combined, we observed that the transformation efficiency was enhanced from 11.5% to 52.3%. The improvement of genetic transformation efficiency mediated by these three simple treatments may facilitate more efficient applications of transgenic and gene editing technologies for functional characterization of citrus genes and for genetic improvement of citrus cultivars.
PMID: 35684233
Plants (Basel) , IF:3.935 , 2022 May , V11 (11) doi: 10.3390/plants11111447
Enhanced Cd-Accumulation in Typha latifolia by Interaction with Pseudomonas rhodesiae GRC140 under Axenic Hydroponic Conditions.
Facultad de Ciencias Quimicas, Universidad Autonoma de San Luis Potosi, San Luis Potosi 78210, Mexico.; Facultad de Estudios Profesionales Zona Huasteca, Universidad Autonoma de San Luis Potosi, Ciudad Valles, San Luis Potosi 79060, Mexico.; Secretaria de Investigacion y Posgrado, Centro Nayarita de Innovacion y Transferencia de Tecnologia (CENITT), Universidad Autonoma de Nayarit, Tepic, Nayarit 63173, Mexico.; Colegio de Postgraduados Campus Campeche, Campeche 24450, Mexico.
The Typha genus comprises plant species extensively studied for phytoremediation processes. Recently, Pseudomonas rhodesiae GRC140, an IAA-producing bacterium, was isolated from Typha latifolia roots. This bacterium stimulates the emergence of lateral roots of Arabidopsis thaliana in the presence and absence of cadmium. However, the bacterial influence on cadmium accumulation by the plant has not been determined. Moreover, the P. rhodesiae GRC140 effect in Cd phytoextraction by T. latifolia remains poorly understood. In this work, an axenic hydroponic culture of T. latifolia was established. The plants were used to evaluate the effects of cadmium stress in axenic plants and determine the effects of P. rhodesiae GRC140 and exogenous indole acetic acid (IAA) on Cd tolerance and Cd uptake by T. latifolia. Biomass production, total chlorophyll content, root electrolyte leakage, catalase activity, total glutathione, and Cd content were determined. The results showed that Cd reduces shoot biomass and increases total glutathione and Cd content in a dose-dependent manner in root tissues. Furthermore, P. rhodesiae GRC140 increased Cd translocation to the shoots, while IAA increased the Cd accumulation in plant roots, indicating that both treatments increase Cd removal by T. latifolia plants. These results indicate that axenic plants in hydroponic systems are adequate to evaluate the Cd effects in plants and suggest that T. latifolia phytoextraction abilities could be improved by P. rhodesiae GRC140 and exogenous IAA application.
PMID: 35684220
Plants (Basel) , IF:3.935 , 2022 May , V11 (11) doi: 10.3390/plants11111440
Biochemical and Physiological Changes during Early Adventitious Root Formation in Chrysanthemum indicum Linne Cuttings.
Department of Crop Science, College of Sanghuh Life Science, Konkuk University, Seoul 05029, Korea.; Bioherb Research Institute, Kangwon National University, Chuncheon 24341, Korea.
Chrysanthemum indicum is an important ornamental and medicinal plant that is often difficult to propagate commercially because of its poor germination and low seed viability. This plant is mostly propagated by cutting, but the rooting is slow and non-uniform. The present investigation evaluated the regeneration capacity of stem cutting by examining the influence of auxins, growth medium, temperature, and explant type on adventitious root formation in C. indicum. The auxin-treated cuttings were planted in different growth substrates under greenhouse conditions. Among the different auxins tested, indole-3-butyric acid (IBA) more effectively induced roots. The cutting position of stock plants influenced rooting capacity. Cutting the stock plants from the apical region enhanced root number and length in the explants. Among the different explant types, apical stem cuts with 2000 ppm IBA produced a significantly higher number of adventitious roots when grown in vermiculite and perlite (V + P) at a ratio of 1:1 at 25 degrees C. High-performance liquid chromatography (HPLC) analysis revealed that protocatechuic acid, gentisic acid, chlorogenic acid, biochanin A, salicylic acid, caffeic acid, glycitein, and luteolin were the most dominant phenolic compounds present in C. indicum. These results indicate that IBA treatment promoted the synthesis and accumulation of phenolic compounds in C. indicum stem cuttings at the time of root formation. The present results demonstrate that applying auxins is essential for early root initiation and higher rooting success and thus may be beneficial for vegetative C. indicum propagation.
PMID: 35684213
Plants (Basel) , IF:3.935 , 2022 May , V11 (10) doi: 10.3390/plants11101347
Induction of Somatic Embryogenesis in Tamarillo (Solanum betaceum Cav.) Involves Increases in the Endogenous Auxin Indole-3-Acetic Acid.
Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal.
Somatic embryogenesis (SE) is a complex biological process regulated by several factors, such as the action of plant growth regulators, namely auxins, of which the most physiologically relevant is indole-3-acetic acid (IAA). In tamarillo, an optimized system for induction of SE creates, after an induction process, embryogenic (EC) and non-embryogenic callus (NEC). In this work the endogenous levels of auxin along the induction phase and in the calli samples were investigated using chemical quantifications by colorimetric reactions and HPLC as well as immunohistochemistry approaches. Differential gene expression (IAA 11, IAA 14, IAA 17, TIR 1, and AFB3) analysis during the induction phase was also carried out. The results showed that the endogenous IAA content is considerably higher in embryogenic than in non-embryogenic calli, with a tendency to increase as the dedifferentiation of the original explant (leaf segments) evolves. Furthermore, the degradation rates of IAA seem to be related to these levels, as non-embryogenic tissue presents a higher degradation rate. The immunohistochemical results support the quantifications made, with higher observable labeling on embryogenic tissue that tends to increase along the induction phase. Differential gene expression also suggests a distinct molecular response between EC and NEC.
PMID: 35631771
Plants (Basel) , IF:3.935 , 2022 May , V11 (10) doi: 10.3390/plants11101335
ADA2b and GCN5 Affect Cytokinin Signaling by Modulating Histone Acetylation and Gene Expression during Root Growth of Arabidopsis thaliana.
Department of Botany, School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.; Postgraduate Program Studies "Applications of Biology-Biotechnology, Molecular and Microbial Analysis of Food and Products", School of Biology, Faculty of Science, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece.; Natural Products Research Centre of Excellence (NatPro-AUTh), Center of Interdisciplinary Research and Innovation of Aristotle University of Thessaloniki (CIRI-AUTh), 57001 Thessaloniki, Greece.
In Arabidopsis thaliana, the histone acetyltransferase GCN5 and the associated coactivator ADA2b regulate root growth and affect gene expression. The cytokinin signaling reporter TCS::GFP was introduced into gcn5-1, ada2b-1, and ada2a-2, as well as the ada2a-2ada2b-1 mutants. The early root growth (4 to 7 days post-germination) was analyzed using cellular and molecular approaches. TCS signal accumulated from the fourth to seventh days of root growth in the wild-type columella cells. In contrast, ada2b-1 and gcn5-1 and ada2a-2ada2b-1 double mutants displayed reduced TCS expression relative to wild type. Gene expression analysis showed that genes associated with cytokinin homeostasis were downregulated in the roots of gcn5-1 and ada2b-1 mutants compared to wild-type plants. H3K14 acetylation was affected in the promoters of cytokinin synthesis and catabolism genes during root growth of Arabidopsis. Therefore, GCN5 and ADA2b are positive regulators of cytokinin signaling during root growth by modulating histone acetylation and the expression of genes involved in cytokinin synthesis and catabolism. Auxin application in the roots of wild-type seedlings increased TCS::GFP expression. In contrast, ada2b and ada2ada2b mutant plants do not show the auxin-induced TCS signal, suggesting that GCN5 and ADA2b are required for the auxin-induced cytokinin signaling in early root growth.
PMID: 35631760
Plants (Basel) , IF:3.935 , 2022 May , V11 (10) doi: 10.3390/plants11101304
Tryptophan Levels as a Marker of Auxins and Nitric Oxide Signaling.
Institute for Multidisciplinary Research in Applied Biology (IMAB), Department of Sciences, Agrobiotechnology Building, Public University of Navarre (UPNA), Avda. de Pamplona 123, E-31192 Mutilva, Spain.; Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.; Institute for Advanced Materials and Mathematics (INAMAT2), Department of Sciences, Public University of Navarre (UPNA), Ed. 'Los Acebos', Campus de Arrosadia, E-31006 Pamplona, Spain.
The aromatic amino acid tryptophan is the main precursor for indole-3-acetic acid (IAA), which involves various parallel routes in plants, with indole-3-acetaldoxime (IAOx) being one of the most common intermediates. Auxin signaling is well known to interact with free radical nitric oxide (NO) to perform a more complex effect, including the regulation of root organogenesis and nitrogen nutrition. To fathom the link between IAA and NO, we use a metabolomic approach to analyze the contents of low-molecular-mass molecules in cultured cells of Arabidopsis thaliana after the application of S-nitrosoglutathione (GSNO), an NO donor or IAOx. We separated the crude extracts of the plant cells through ion-exchange columns, and subsequent fractions were analyzed by gas chromatography-mass spectrometry (GC-MS), thus identifying 26 compounds. A principal component analysis (PCA) was performed on N-metabolism-related compounds, as classified by the Kyoto Encyclopedia of Genes and Genomes (KEGG). The differences observed between controls and treatments are mainly explained by the differences in Trp contents, which are much higher in controls. Thus, the Trp is a shared response in both auxin- and NO-mediated signaling, evidencing some common signaling mechanism to both GSNO and IAOx. The differences in the low-molecular-mass-identified compounds between GSNO- and IAOx-treated cells are mainly explained by their concentrations in benzenepropanoic acid, which is highly associated with IAA levels, and salicylic acid, which is related to glutathione. These results show that the contents in Trp can be a marker for the study of auxin and NO signaling.
PMID: 35631729
Plants (Basel) , IF:3.935 , 2022 May , V11 (9) doi: 10.3390/plants11091273
Genome-Wide Characterization, Evolutionary Analysis of ARF Gene Family, and the Role of SaARF4 in Cd Accumulation of Sedum alfredii Hance.
Key Laboratory of Three Gorges Regional Plant Genetic & Germplasm Enhancement (CTGU), Biotechnology Research Center, China Three Gorges University, Yichang 443000, China.; State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China.; Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical of Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.; Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
Auxin response factors (ARFs) play important roles in plant development and environmental adaption. However, the function of ARFs in cadmium (Cd) accumulation are still unknown. Here, 23 SaARFs were detected in the genome of hyperaccumulating ecotype of Sedum alfredii Hance (HE), and they were not evenly distributed on the chromosomes. Their protein domains remained highly conservative. SaARFs in the phylogenetic tree can be divided into three groups. Genes in the group contained three introns at most. However, over ten introns were found in other two groups. Collinearity relationships were exhibited among ten SaARFs. The reasons for generating SaARFs may be segmental duplication and rearrangements. Collinearity analysis among different species revealed that more collinear genes of SaARFs can be found in the species with close relationships of HE. A total of eight elements in SaARFs promoters were related with abiotic stress. The qRT-PCR results indicated that four SaARFs can respond to Cd stress. Moreover, that there may be functional redundancy among six SaARFs. The adaptive selection and functional divergence analysis indicated that SaARF4 may undergo positive selection pressure and an adaptive-evolution process. Overexpressing SaARF4 effectively declined Cd accumulation. Eleven single nucleotide polymorphism (SNP) sites relevant to Cd accumulation can be detected in SaARF4. Among them, only one SNP site can alter the sequence of the SaARF4 protein, but the SaARF4 mutant of this site did not cause a significant difference in cadmium content, compared with wild-type plants. SaARFs may be involved in Cd-stress responses, and SaARF4 may be applied for decreasing Cd accumulation of plants.
PMID: 35567274
Life (Basel) , IF:3.817 , 2022 Jun , V12 (6) doi: 10.3390/life12060921
Transcriptome and Metabolome Analysis of Upland Cotton (Gossypium hirsutum) Seed Pretreatment with MgSO4 in Response to Salinity Stress.
State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China.; Fukang Station of Desert Ecology, Chinese Academy of Sciences, Fukang 831505, China.; College of Agriculture, Xinjiang Agricultural University, Urumqi 830052, China.
Upland cotton (Gossypium hirsutum) is a salt-tolerant crop that can withstand high salinity levels without showing signs of harm to the plant. However, the plant is more prone to salinity stress at the germination stage and a poor germination as well as poor crop stand lead to a weak productivity. It is possible to obtain a comprehensive picture of the cotton seedling germination and establishment against salt stress by examining dynamic changes in the transcriptomic and metabolomic profiles. The reported study employed a pretreatment of cotton seeds by soaking them in 0.2% Magnesium Sulphate (MgSO4) solution at room temperature for 4, 8, and 12 h. The analysis of variance based on the studied traits emergence rate, above and underground plant parts' fresh weight measured, displayed significant differences of the three treatments compared with the control. A total of 28,801 and 264 differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were discovered to code for biological processes such as response to salt stress, cellular response to salt stress, abscisic acid receptor PYR/PYL, regulation of seed growth and germination, and auxin-activated signaling pathways. A large amount of ethylene-responsive transcription factors (ERF) was identified (1235) as differentially expressed, followed by bHLH (252), WRKY (96), MYB (202), GATA (81), RABA (64), DIVARICATA (28), and MADs-box (26) in treated seedling samples. Functional enrichment analysis revealed the significant roles in the hormones and signal transduction, carbohydrates metabolism, and biosynthesis of amino acids, promoting salt stress tolerance. Our results indicated positive effects of MgSO4 at 4 h treatment on seedling germination and growth, seemingly by activating certain growth-regulating enzymes (auxins, gibberellins, jasmonates, abscisic acid, and salicylic acid) and metabolites (phenolic acids, flavonoids, and akaloids). Such pretreatment of MgSO4 on seeds would be beneficial in future cotton management under saline conditions to enhance good crop stand and productivity.
PMID: 35743952
Biol Lett , IF:3.703 , 2022 May , V18 (5) : P20210629 doi: 10.1098/rsbl.2021.0629
Aerial (+)-borneol modulates root morphology, auxin signalling and meristematic activity in Arabidopsis roots.
Center for Ecological Research, Kyoto University, Otsu 520-2113, Japan.; Department of Agrobiological Resources, Faculty of Agriculture, Meijo University, Nagoya 468-8502, Japan.; Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan.; Graduate School of Agricultural Science, Kobe University, Kobe 657-8501, Japan.; Faculty of Science and Engineering, Konan University, Kobe 658-8501, Japan.; Graduate School of Sciences and Technology for Innovation (Faculty of Agriculture), Yamaguchi University, Yamaguchi 753-8515, Japan.; Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba 305-8572, Japan.; Agro-Biotechnology Research Center (AgTech), Graduate School of Agricultural and Life Sciences (GSALS), University of Tokyo, Tokyo 113-8657, Japan.; Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8604, Japan.; Research Institute for Sustainable Humanosphere, Kyoto University, Uji 611-0011, Japan.; National Institute for Environmental Studies, Tsukuba 305-8506, Japan.
One of the characteristic aspects of odour sensing in humans is the activation of olfactory receptors in a slightly different manner in response to different enantiomers. Here, we focused on whether plants showed enantiomer-specific response similar to that in humans. We exposed Arabidopsis seedlings to methanol (control) and (+)- or (-)-borneol, and found that only (+)-borneol reduced the root length. Furthermore, the root-tip width was more increased upon (+)-borneol exposure than upon (-)-borneol exposure. In addition, root-hair formation was observed near the root tip in response to (+)-borneol. Auxin signalling was strongly reduced in the root tip following exposure to (+)-borneol, but was detected following exposure to (-)-borneol and methanol. Similarly, in the root tip, the activity of cyclin B1:1 was detected on exposure to (-)-borneol and methanol, but not on exposure to (+)-borneol, indicating that (+)-borneol inhibits the meristematic activity in the root. These results partially explain the (+)-borneol-specific reduction in the root length of Arabidopsis. Our results indicate the presence of a sensing system specific for (+)-borneol in Arabidopsis.
PMID: 35506238
Gene , IF:3.688 , 2022 Jun : P146692 doi: 10.1016/j.gene.2022.146692
SAUR8, a small auxin-up RNA Gene in poplar, confers drought tolerance to transgenic Arabidopsis plants.
Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 2291204194@qq.com.; Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 2393916926@qq.com.; Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 1240916771@qq.com.; Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 1802094551@qq.com.; Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: 250983262@qq.com.; Laboratory of Modern Biotechnology, School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei, 230036, China. Electronic address: xiangyanahau@sina.com.
SAUR (small auxin-up RNA) is an early auxin-responsive gene. In this study, a novel SAUR gene PtSAUR8 was cloned from poplar (Populus trichocarpa), and subcellular location analysis showed that it is targeted to the nuclear membrane. In addition, PtSAUR8 overexpression in Arabidopsis improved the plant resistance to drought stress. Meanwhile, the loss of function mutant saur53 showed more drought sensitivity compared to the WT. PtSAUR8 conferred drought tolerance in transgenic Arabidopsis, as determined through phenotypic and stress-associated physiological indicator analyses, namely, root length, germination rate, relative water content, proline content, CAT content, POD content, malondialdehyde content, hydrogen peroxide content, and relative conductivity. In addition, after the 1 muM abscisic acid (ABA) treatment, the PtSAUR8-OE lines promoted stomata closure. Quantitative fluorescence analysis of related genes induced by drought mutant stress further confirmed that overexpression of PtSAUR8 can improve drought resistance in transgenic Arabidopsis lines. Therefore, PtSAUR8 may play a role in plant drought resistance through ABA-mediated pathways; thus, providing new research materials for molecular breeding of poplar resistance.
PMID: 35760288
Gene , IF:3.688 , 2022 Jul , V833 : P146592 doi: 10.1016/j.gene.2022.146592
Comparative transcriptome profiling of sweetpotato storage roots during curing-mediated wound healing.
Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea; R&D Center, Genolution Inc., 63, Magokjungang 8-ro 3-gil, Gangseo-gu, Seoul 07793, Republic of Korea.; Department of Biology Education, IALS, Gyeongsang National University, Jinju 52828, Republic of Korea.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea.; Bioenergy Crop Research Institute, National Institute of Crop Science, Rural Development Administration, 199 Muan-ro, Muan-gun 58545, Republic of Korea.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea; Department of Environmental Biotechnology, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Daejeon 34113, Republic of Korea. Electronic address: sskwak@kribb.re.kr.; Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Daejeon 34141, Republic of Korea. Electronic address: hskim@kribb.re.kr.
Sweetpotato (Ipomoea batatas L. Lam) is an economically important crop that is cultivated for its storage roots. Storage roots provide a source of valuable nutrients, processed foods, animal feeds, and pigments. Sweetpotato storage roots spoil during post-harvest handling because of wounding, which makes them more susceptible to disease-causing microorganisms. Curing to promote wound healing is a common method to control microbial spoilage during post-harvest storage. However, molecular mechanisms underlying the process of curing in sweetpotato storage roots are unknown. To better understand the biology behind curing, the transcriptome of the sweetpotato cultivar, Pungwonmi, was studied using RNA-seq. Storage roots of sweetpotato were treated at 33 degrees C (Curing) and 13 degrees C (Control) for 3 days. RNA-seq data identified 78,781 unigenes and 3,366 differentially expressed genes by over log2 fold change (FC) > 2 and <-2. During curing, DEGs encoded genes related to drought/salt stress responses, phyto-hormones (e.g., auxin, ethylene and jasmonic acid), and proteolysis, were up-regulated, whereas those related to redox state, phyto-hormones (e.g., salicylic acid and brassinosteroids), and lignin and flavonoid biosynthesis were down-regulated. Additionally, among the candidate genes, DEGs encoded genes related to proteolysis and pathogen defense, such as protease inhibitors and lipid transfer proteins, were highly up-regulated during curing and storage. This study provides a valuable resource to further understand the molecular basis of curing-mediated wound healing in sweetpotato storage roots. Moreover, genes revealed in this work could present targets for the development of sweetpotato varieties with improved post-harvest storage characteristics.
PMID: 35605748
Gene , IF:3.688 , 2022 Jun , V829 : P146494 doi: 10.1016/j.gene.2022.146494
Whole genome duplication and dispersed duplication characterize the evolution of the plant PINOID gene family across plant species.
State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China.; Department of Biology, California State University East Bay, Hayward, CA, United States of America.; State Key Laboratory of Pharmaceutical Biotechnology, Department of Biotechnology and Pharmaceutical Sciences, School of Life Sciences, Nanjing University, Nanjing, China.; State Key Laboratory of Grassland Agro-Ecosystem, School of Life Sciences, Lanzhou University, Lanzhou, China. Electronic address: ligt18@lzu.edu.cn.
PINOID is a kinase belonging to the AGCVIII family, which regulates the polar distribution of PIN proteins and plays an important role in plant geotropism. However, the origin and evolutionary history of this gene family is not fully known. In this study, we identified 79 similar sequences across 17 plant species genomes (PINOID, D6PK, PINOID2, "hypothetical kinase"). Our results show that the AGCVIII kinase family may have originated from related "Hypothetical Kinases" that come out sister to the rest of the gene family members. These kinases differentiated their functions are found in different plant classes: D6PK in moss and PINOID and PINOID2 evolving in angiosperms including the pioneer plant Amborella trichopoda. Our study investigates the evolution of PINOID kinases from a phylogenetic perspective giving us insight into how this important plant signal transduction network switch evolved to play a fundamental and important function in plant growth and development. We highlight the importance of whole genome duplications and dispersed duplications as opposed to tandem duplications in the evolution of this gene family.
PMID: 35447241
Gene , IF:3.688 , 2022 May , V823 : P146320 doi: 10.1016/j.gene.2022.146320
Tomato zonate spot virus induced hypersensitive resistance via an auxin-related pathway in pepper.
Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Yunnan ProvincialKey Laboratory of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resource and GermplasmInnovation, Ministry of Agriculture, KunmingYunnan 650204, China.; Kunming Institute of Botany, Chinese Academy of Science, Kunming Yunnan 650201, China.; Institute of Biotechnology and Germplasm Resources, Yunnan Academy of Agricultural Sciences, Yunnan ProvincialKey Laboratory of Agricultural Biotechnology, Key Lab of Southwestern Crop Gene Resource and GermplasmInnovation, Ministry of Agriculture, KunmingYunnan 650204, China; Life Science College, Southwest Forestry University, Kunming Yunnan 650224, China.; Life Science College, Southwest Forestry University, Kunming Yunnan 650224, China.; Yunnan University of Chinese Medicine, Kunming Yunnan 650500, China.
Tomato zonate spotvirus (TZSV) often incurs significant losses in many food and ornamental crops in Yunnan province, China, and the surrounding areas. The pepper (Capsicum chinensePI152225)can develop hypersensitive resistance following infection with TZSV, through an as yet unknown mechanism. The transcriptome dataset showed a total of 45.81 GB of clean data were obtained from six libraries, and the average percentage of the reads mapped to the pepper genome was over 90.00 %. A total of 1403 differentially expressed genes (DEGs) were obtained after TZSV infection, including 825significantly up-regulated genes and 578 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that most up-regulated DEGs were involved in basal defenses. RT-qPCR, and virus induced gene silencing (VIGS) were used preliminarily to identifyBBC_22506 and BBC_18917, among total of 71 differentially expressed genes (DEGs), that play a key role in mediating the auxin-induced signaling pathway that might take part in hypersensitive response (HR) conferred resistance to viral infection in pepper (PI152225) byTZSV. This is the first study on the mechanism of auxin resistance, involved in defense responses of pepper against viral diseases, which lay the foundation for further study on the pathogenic mechanism of TZSV, as well as the mechanism of resistance to TZSV, in peppers.
PMID: 35218893
J Plant Physiol , IF:3.549 , 2022 May , V275 : P153738 doi: 10.1016/j.jplph.2022.153738
Bacterial cyclodipeptides elicit Arabidopsis thaliana immune responses reducing the pathogenic effects of Pseudomonas aeruginosa PAO1 strains on plant development.
Laboratorio de Biotecnologia Molecular de Plantas, Instituto de Investigaciones Quimico Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, 58030, Morelia, Michoacan, Mexico.; Laboratorio de Biologia del Desarrollo Vegetal, Instituto de Investigaciones Quimico Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, 58030, Morelia, Michoacan, Mexico.; Instituto de Biotecnologia, Universidad Nacional Autonoma de Mexico, 62250, Cuernavaca, Morelos, Mexico.; Laboratorio de Bioquimica y Biologia Molecular de Plantas, Instituto de Investigaciones Quimico Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, 58030, Morelia, Michoacan, Mexico.; Laboratorio de Interaccion Suelo Planta Microorganismo, Instituto de Investigaciones Quimico Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, 58030, Morelia, Michoacan, Mexico.; Laboratorio de Biotecnologia Microbiana, Instituto de Investigaciones Quimico Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, 58030, Morelia, Michoacan, Mexico. Electronic address: jesus.campos@umich.mx.; Laboratorio de Biotecnologia Molecular de Plantas, Instituto de Investigaciones Quimico Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, 58030, Morelia, Michoacan, Mexico. Electronic address: homero.reyes@umich.mx.
Plants being sessile organisms are exposed to various biotic and abiotic factors, thus causing stress. The Pseudomonas aeruginosa bacterium is an opportunistic pathogen for animals, insects, and plants. Direct exposure of Arabidopsis thaliana to the P. aeruginosa PAO1 strain induces plant death by producing a wide variety of virulence factors, which are regulated mainly by quorum sensing systems. Besides virulence factors, P. aeruginosa PAO1 also produces cyclodipeptides (CDPs), which possess auxin-like activity and promote plant growth through activation of the target of the rapamycin (AtTOR) pathway. On the other hand, plant defense mechanisms are regulated through the production of phytohormones, such as salicylic acid (SA) and jasmonic acid (JA), which are induced in response to pathogen-associated molecular patterns (PAMPs), activating defense genes associated with SA and JA such as PATHOGENESIS-RELATED-1 (PR-1) and LIPOXYGENASE2 (LOX2), respectively. PR proteins are suggested to play critical roles in coordinating the Systemic Acquired Resistance (SAR). In contrast, LOX proteins (LOX2, LOX3, and LOX4) have been associated with the production of JA by producing its precursors, oxylipins. The activation of defense mechanisms involves signaling cascades such as Mitogen-Activated Protein Kinases (MAPKs) or the TOR pathway as a switch for re-directing energy towards defense or growth. In this work, we challenged A. thaliana (wild type, mpk6 or mpk3 mutants, and overexpressing TOR) seedlings with P. aeruginosa PAO1 strains to identify the role of bacterial CDPs in the plant immune response. Results showed that the pre-exposure of these Arabidopsis seedlings to CDPs significantly reduced plant infection of the pathogenic P. aeruginosa PAO1 strains, indicating that plants that over-express AtTOR or lack MPK3/MPK6 protein-kinases are more susceptible to the pathogenic effects. In addition, CDPs induced the GUS activity only in the LOX2::GUS plants, indicative of JA-signaling activation. Our findings indicate that the CDPs are molecules that trigger SA-independent and JA-dependent defense responses in A. thaliana; hence, bacterial CDPs may be considered elicitors of the Arabidopsis immune response to pathogens.
PMID: 35690030
Phytochem Anal , IF:3.373 , 2022 Jun doi: 10.1002/pca.3135
Development of approach for flavonoid profiling of biotechnological raw materials Iris sibirica L. by HPLC with high-resolution tandem mass spectrometry.
Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia.; Saint Petersburg Scientific Research Institute of Vaccines and Serums and the Enterprise for the Production of Bacterial Preparations, Saint Petersburg, Russia.
INTRODUCTION: Iris L. are promising in medicine due to the biological activity of extracts. Iris sibirica L. is spread in Russia but its phytochemical composition has not been studied in detail though it is included in the Red Book. For this reason, I. sibirica L. biotechnology is in high demand. One of the key points in biotechnology is the regulation of plant metabolism using phytohormones. Obtaining of chromatographic metabolite profiles allows to control this process. OBJECTIVE: The aim of this study was to develop an approach for effective control of biotechnological raw materials of I. sibirica L. by flavonoid profiles using high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and to investigate the influence of phytohormones in nutrient media on content of flavonoids. METHODOLOGY: Iris sibirica L. regenerated plants were grown on Murashige-Skoog media with 6-benzylaminopurine (6-BAP) and alpha-naphtylacetic acid (NAA) additives. To optimise extraction conditions, the design of the experiment was used. Profiles of polyphenols were obtained by HPLC-MS/MS in the positive and negative ionisation modes. RESULTS: The process for efficient extraction from leaves of I. sibirica L. were developed. The factors influencing the extraction efficiency of flavonoids have been determined. A total of 36 compounds were identified by HPLC-MS/MS. Among them isoflavones and their glycosides are the main classes. Addition of an auxin-like hormone increased the non-polar flavonoid levels, but decreased the polar ones. The variation in concentration of cytokinin (6-BAP) affected almost all of the analytes. CONCLUSION: The methodology for effective control of I. sibirica L. raw plant material biotechnology was developed by analysing obtained chromatographic polyphenol profiles.
PMID: 35680077
Protoplasma , IF:3.356 , 2022 May doi: 10.1007/s00709-022-01773-y
Genome-wide identification of Aux/IAA and ARF gene families in bread wheat (Triticum aestivum L.).
Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.; Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India. param@genomeindia.org.
Wheat (Triticum aestivum L.) is one of the most important food crops in the world. Somatic embryogenesis is an event that is triggered by the presence of auxin hormone for the induction of somatic cells to get converted to embryonic cells. Somatic embryogenesis represents the most important process of totipotency of plants. The role of auxins is widely understood during various stages of embryogenesis including polarity establishment, de-differentiation, re-differentiations, and morphogenesis. Many of the Aux/IAAs and ARFs which are part of auxin signaling components have been identified to play various roles during embryogenesis. In this analysis, the Aux/IAAs and ARFs of T. aestivum have been analyzed at the genome-scale; their structure, function, and evolutionary relatedness were determined. Several Aux/IAAs and ARFs components of T. aestivum have been found to exclusively regulate axis formation, meristem commitment, and other re-differentiation processes by differential expression studies.
PMID: 35606614
PLoS One , IF:3.24 , 2022 , V17 (6) : Pe0269984 doi: 10.1371/journal.pone.0269984
PIF-independent regulation of growth by an evening complex in the liverwort Marchantia polymorpha.
Plant Ecology and Evolution, Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden.; Department of Plant Biology, Swedish University of Agricultural Sciences, The Linnean Centre of Plant Biology in Uppsala, Uppsala, Sweden.; Physiological Botany, Department of Organismal Biology, Uppsala University, The Linnean Centre for Plant Biology in Uppsala, Uppsala, Sweden.
Previous studies in the liverwort Marchantia polymorpha have shown that the putative evening complex (EC) genes LUX ARRHYTHMO (LUX) and ELF4-LIKE (EFL) have a function in the liverwort circadian clock. Here, we studied the growth phenotypes of MpLUX and MpEFL loss-of-function mutants, to establish if PHYTOCHROME-INTERACTING FACTOR (PIF) and auxin act downstream of the M. polymorpha EC in a growth-related pathway similar to the one described for the flowering plant Arabidopsis. We examined growth rates and cell properties of loss-of-function mutants, analyzed protein-protein interactions and performed gene expression studies using reporter genes. Obtained data indicate that an EC can form in M. polymorpha and that this EC regulates growth of the thallus. Altered auxin levels in Mplux mutants could explain some of the phenotypes related to an increased thallus surface area. However, because MpPIF is not regulated by the EC, and because Mppif mutants do not show reduced growth, the growth phenotype of EC-mutants is likely not mediated via MpPIF. In Arabidopsis, the circadian clock regulates elongation growth via PIF and auxin, but this is likely not an evolutionarily conserved growth mechanism in land plants. Previous inventories of orthologs to Arabidopsis clock genes in various plant lineages showed that there is high levels of structural differences between clocks of different plant lineages. Here, we conclude that there is also variation in the output pathways used by the different plant clocks to control growth and development.
PMID: 35709169
G3 (Bethesda) , IF:3.154 , 2022 May , V12 (5) doi: 10.1093/g3journal/jkac057
Genome-wide analysis of AAAG and ACGT cis-elements in Arabidopsis thaliana reveals their involvement with genes downregulated under jasmonic acid response in an orientation independent manner.
Department of Biological Sciences, Birla Institute of Technology and Science-Pilani, Zuarinagar, Goa 403726, India.; Department of Biological Sciences, Birla Institute of Technology and Science-Pilani, Pilani, Jhunjhunu, Rajasthan 333031, India.; Department of Computer Science and Information Systems, Birla Institute of Technology and Science-Pilani, Zuarinagar, Sancoale, Goa 403726, India.; Faculty of Bioscience, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh 225003, India.
Cis-regulatory elements are regions of noncoding DNA that regulate the transcription of neighboring genes. The study of cis-element architecture that functions in transcription regulation are essential. AAAG and ACGT are a class of cis-regulatory elements, known to interact with Dof and bZIP transcription factors respectively, and are known to regulate the expression of auxin response, gibberellin response, floral development, light response, seed storage proteins genes, biotic and abiotic stress genes in plants. Analysis of the frequency of occurrence of AAAG and ACGT motifs from varying spacer lengths (0-30 base pair) between these 2 motifs in both possible orientations-AAAG (N) ACGT and ACGT (N) AAAG, in the promoters and genome of Arabidopsis thaliana which indicated preferred orientation of AAAG (N) ACGT over ACGT (N) AAAG across the genome and in promoters. Further, microarray analysis revealed the involvement of these motifs in the genes downregulated under jasmonic acid response in an orientation-independent manner. These results were further confirmed by the transient expression studies with promoter-reporter cassettes carrying AAAG and ACGT motifs in both orientations. Furthermore, cluster analysis on genes with AAAG (N) ACGT and ACGT (N) AAAG motifs orientations revealed clusters of genes to be involved in ABA signaling, transcriptional regulation, DNA binding, and metal ion binding. These findings can be utilized in designing synthetic promoters for the development of stress-tolerant transgenic plants and also provides an insight into the roles of these motifs in transcriptional regulation.
PMID: 35302624
Funct Plant Biol , IF:3.101 , 2022 May doi: 10.1071/FP21315
DELAY OF GERMINATION 1 (DOG1) regulates dormancy in dimorphic seeds of Xanthium strumarium.
Seed dormancy ensures plant survival but many mechanisms remain unclear. A high-throughput RNA-seq analysis investigated the mechanisms involved in the establishment of dormancy in dimorphic seeds of Xanthium strumarium (L.) developing in one single burr. Results showed that DOG1, the main dormancy gene in Arabidopsis thaliana L., was over-represented in the dormant seed leading to the formation of two seeds with different cell wall properties. Less expression of DME/EMB1649, UBP26, EMF2, MOM, SNL2, and AGO4 in the non-dormant seed was observed, which function in the chromatin remodelling of dormancy-associated genes through DNA methylation. However, higher levels of ATXR7/SDG25, ELF6, and JMJ16/PKDM7D in the non-dormant seed that act at the level of histone demethylation and activate germination were found. Dramatically lower expression in the splicing factors SUA, PWI, and FY in non-dormant seed may indicate that variation in RNA splicing for ABA sensitivity and transcriptional elongation control of DOG1 is of importance for inducing seed dormancy. Seed size and germination may be influenced by respiratory factors, and alterations in ABA content and auxin distribution and responses. TOR (a serine/threonine-protein kinase) is likely at the centre of a regulatory hub controlling seed metabolism, maturation, and germination. Over-representation of the respiration-associated genes (ACO3, PEPC3, and D2HGDH) was detected in non-dormant seed, suggesting differential energy supplies in the two seeds. Degradation of ABA biosynthesis and/or proper auxin signalling in the large seed may control germinability, and suppression of endoreduplication in the small seed may be a mechanism for cell differentiation and cell size determination.
PMID: 35569923
Plant Biol (Stuttg) , IF:3.081 , 2022 Jun , V24 (4) : P559-568 doi: 10.1111/plb.13417
Hydrogen sulphide (H2 S) in the hidden half: Role in root growth, stress signalling and rhizospheric interactions.
Microbiology Laboratory, Department of Botany, University of North Bengal, Darjeeling, India.; Plant Biochemistry Laboratory, Department of Botany, University of North Bengal, Darjeeling, India.; Department of Biology, Faculty of Science, College of Haql, University of Tabuk, Tabuk, Saudi Arabia.; Department of Botany, Jangipur College, University of Kalyani, Jangipur, India.
Apart from nitric oxide (NO) and carbon monoxide (CO), hydrogen sulphide (H2 S) has emerged as a potential gasotransmitter that has regulatory roles in root differentiation, proliferation and stress signalling. H2 S metabolism in plants exhibits spatio-temporal differences that are intimately associated with sulphide signalling in the cytosol and other subcellular components, e.g. chloroplast and mitochondria. H2 S biosynthesis in plant organs uses both enzymatic and non-enzymatic pathways. H2 S generation in roots and aerial organs is modulated by developmental phase and changes in environmental stimuli. H2 S has an influential role in root development and in the nodulation process. Studies have revealed that H2 S is a part of the auxin and NO signalling pathways in roots, which induce lateral root formation. At the molecular level, exogenous application of H2 S regulates expression of several transcription factors, viz. LBD (Lateral organ Boundaries Domain), MYB (myeloblastosis) and AP2/ERF (Apetala 2/ Ethylene Response Factor), which stimulate upregulation of PpLBD16 (Lateral organ boundaries domain 16), thereby significantly increasing the number of lateral roots. Concomitantly, H2 S acts as a crucial signalling molecule in roots during various abiotic stresses, e.g. drought, salinity heavy metals (HMs), etc., and augments stress tolerance in plants. Interestingly, extensive crosstalk exists between H2 S, NO, ABA, calcium and ethylene during stress, which escalate plant defence and regulate plant growth and productivity. Hence, the present review will elaborate the role of H2 S in root development, stress alleviation, legume-Rhizobium symbiosis and rhizosphere signalling. The review also examines the mechanism of H2 S-mediated abiotic stress mitigation and cross-talk with other signaling molecules.
PMID: 35334141
Plant Biol (Stuttg) , IF:3.081 , 2022 Jun , V24 (4) : P532-539 doi: 10.1111/plb.13376
Hydrogen sulphide: an emerging regulator of plant defence signalling.
Department of Botany, University of Delhi, New Delhi, India.; Department of Biotechnology, TERI School of Advanced Studies, Vasant Kunj, New Delhi, India.; Department of Botany, Dyal Singh College, New Delhi, India.; College of General Education, Kookmin University, Seoul, South Korea.
Hydrogen sulphide (H2 S), a gaseous signalling molecule in plants, has gained considerable attention in recent years because of its emerging roles in the regulation of plant growth and development and responses to abiotic stressors. Although the involvement of H2 S in biotic stress is not well documented in the literature, a growing body of evidence indicates its potential role in plant defence, particularly against bacterial and fungal pathogens. Recent reports have suggested that H2 S participates in plant defence signalling potentially by (1) regulating glutathione metabolism, (2) inducing expression of pathogenesis-related (PR) and other defence-related genes, (3) modulating enzyme activity through post-translational modifications, and (4) interacting with phytohormones such as jasmonic acid, ethylene and auxin. In this review, we discuss the biosynthesis, metabolism and interaction of H2 S with phytohormones, and highlight evidence gathered so far to support the emerging roles of H2 S in plant defence against invading pathogens.
PMID: 34904345
PeerJ , IF:2.984 , 2022 , V10 : Pe13438 doi: 10.7717/peerj.13438
The Microphenotron: a novel method for screening plant growth-promoting rhizobacteria.
Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Punjab, Pakistan.; Department of Microbiology, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS) Quetta, Quetta, Balochistan, Pakistan.
Background: The 'Microphenotron' is an automated screening platform that uses 96-well microtiter plates to test the response of seedlings to natural products. This system allows monitoring the phenotypic effect of a large number of small molecules. Here, this model system was used to study the effect of phytohormones produced by plant growth-promoting rhizobacteria (PGPR) on the growth of wild-type and mutant lines of Arabidopsis thaliana. Methods: In the present study, high-throughput screening based on 'Microphenotron' was used to screen PGPRs. Rhizobacteria were isolated from the rhizosphere of Acacia Arabica, which was growing in saline habitats. The phylogeny of these rhizobacteria was determined by 16S rRNA gene sequencing. Strains were screened for plant growth-promoting traits such as auxin production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and phosphate solubilization. Ultra-Performance Liquid Chromatography (UPLC) was used to detect the presence of different indolic compounds. Finally, PGPR were evaluated to enhance the growth of A. thaliana in the 'Microphenotron' system and pot trials. Results: Selected rhizobacteria strains showed positive results for multiple plant-growth promoting traits. For instance, strain (S-6) of Bacillus endophyticus exhibited the highest ACC-deaminase activity. UPLC analysis indicated the presence of different indolic compounds in bacterial extracts that included indole lactic acid (ILA), indole carboxylic acid (ICA), and indole-3-acetic acid (IAA). Two strains (S-7 and S-11) of Psychrobacter alimentarius produced the most IAA, ICA and ILA. A screening bioassay through 96-well microtiter plates with wild-type Col. N6000 showed an increase in root growth and proliferation. The highest twofold increase was recorded in root growth with B. thuringiensis S-26 and B. thuringiensis S-50. In pot trials, mutant lines of A. thaliana impaired for auxin signaling showed that B. endophyticus S-6, Psy. alimenterius S-11, Enterobacter asburiae S-24 and B. thuringiensis S-26 used auxin signaling for plant growth promotion. Similarly, for ethylene insensitive mutant lines (ein2.5 and etr1), Prolinoborus fasciculus S-3, B. endophyticus S-6, Psy. alimenterius S-7, E. asburiae S-24, and B. thuringiensis S-26 showed the involvement of ethylene signaling. However, the growth promotion pattern for most of the strains indicated the involvement of other mechanisms in enhancing plant growth. The result of Microphenotron assays generally agreed with pot trials with mutant and wild type A. thaliana varieties. Bacterial strains that induced the highest growth response by these cultivars in the 'Microphenotron' promoted plant growth in pot trials. This suggests that Microphenotron can accelerate the evaluation of PGPR for agricultural applications.
PMID: 35586133
J Struct Biol , IF:2.867 , 2022 Jun , V214 (2) : P107857 doi: 10.1016/j.jsb.2022.107857
Structural and biochemical basis for the substrate specificity of Pad-1, an indole-3-pyruvic acid aminotransferase in auxin homeostasis.
Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea.; Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea; Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea. Electronic address: srheesnu@snu.ac.kr.
Phytohormone indole-3-acetic acid (IAA) plays a vital role in regulating plant growth and development. Tryptophan-dependent IAA biosynthesis participates in IAA homeostasis by producing IAA via two sequential reactions, which involve a conversion of tryptophan to indole-3-pyruvic acid (IPyA) by tryptophan aminotransferase (TAA1) followed by the irreversible formation of IAA in the second reaction. Pad-1 from Solanaceae plants regulates IAA levels by catalyzing a reverse reaction of the first step of IAA biosynthesis. Pad-1 is a pyridoxal phosphate (PLP)-dependent aminotransferase, with IPyA as the amino acceptor and l-glutamine as the amino donor. Currently, the structural and functional basis for the substrate specificity of Pad-1 remains poorly understood. In this study, we carried out structural and kinetic analyses of Pad-1 from Solanum melongena. Pad-1 is a homodimeric enzyme, with coenzyme PLP present between a central large alpha/beta domain and a protruding small domain. The active site of Pad-1 includes a vacancy near the phosphate group (P-side) and the 3'-O (O-side) of PLP. These features are distinct from those of TAA1, which is homologous in an overall structure with Pad-1 but includes only the P-side region in the active site. Kinetic analysis suggests that P-side residues constitute a binding pocket for l-glutamine, and O-side residues of Phe124 and Ile350 are involved in the binding of IPyA. These studies illuminate distinct differences in the active site between Pad-1 and TAA1, and provide structural and functional insights into the substrate specificity of Pad-1.
PMID: 35395410
Transgenic Res , IF:2.788 , 2022 Jun , V31 (3) : P325-340 doi: 10.1007/s11248-022-00303-z
Development of a facile genetic transformation system for the Spanish elite rice paella genotype Bomba.
Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain.; ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.; Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain. teresa.capell@udl.cat.
We report the development of an efficient and reproducible genetic transformation system for the recalcitrant Spanish elite rice paella genotype, Bomba. Preconditioned embryos derived from dry seeds were bombarded with gold particles carrying a plasmid containing a screenable and a selectable marker. We confirmed integration and expression of hpt and gusA in the rice genome. Transformation frequency was ca: 10% in several independent experiments. We show Mendelian inheritance of the input transgenes and zygosity determination of the transgenic lines in the T1 generation. A unique and critical step for the regeneration of plants from transformed tissue was shading during the early stages of regeneration, combined with a specific cytokinin:auxin ration at the onset of shifting callus to regeneration media.
PMID: 35416603
Arch Microbiol , IF:2.552 , 2022 May , V204 (6) : P316 doi: 10.1007/s00203-022-02909-7
Exploring plant growth-promoting rhizobacteria as stress alleviators: a methodological insight.
Departamento de Biodiversidad y Biologia Experimental, Facultad de Ciencias Exactas y Naturales. Instituto de Micologia y Botanica, Consejo Nacional de Investigaciones Cientificas y Tecnologicas (INMIBO-CONICET), Universidad de Buenos Aires (UBA), Lab. 69, 4 Piso, Pabellon II, Ciudad Universitaria, Intendente Guiraldes 2160, 1428, Buenos Aires, Argentina. ifdellamonica@gmail.com.; Division Agroalimentaria, Universidad Tecnologica de la Selva, Ocosingo, 29950, Chiapas, Mexico.; Departamento de Biodiversidad y Biologia Experimental, Facultad de Ciencias Exactas y Naturales. Instituto de Micologia y Botanica, Consejo Nacional de Investigaciones Cientificas y Tecnologicas (INMIBO-CONICET), Universidad de Buenos Aires (UBA), Lab. 69, 4 Piso, Pabellon II, Ciudad Universitaria, Intendente Guiraldes 2160, 1428, Buenos Aires, Argentina.; Laboratorio de Edafologia y Ambiente, Facultad de Ciencias, Universidad Autonoma del Estado de Mexico, 50000, Toluca, Estado de Mexico, Mexico.; Laboratorio de Edafologia y Ambiente, Facultad de Ciencias, Universidad Autonoma del Estado de Mexico, 50000, Toluca, Estado de Mexico, Mexico. gyanezo@uaemex.mx.
Rhizospheric and root-endophyte bacteria can stimulate plant growth through diverse biochemical mechanisms and pathways, particularly under biotic and abiotic stresses. For this reason, biotechnological trends on plant growth-promoting rhizobacteria (PGPR) application as biofertilizers, bioremediators, and stress alleviators are gaining increasing interest as ecofriendly strategies for sustainable agriculture management and soil restoration. The first steps needed to implement these technologies are isolation, screening, and characterization of PGPR that can be potentially applied as bioinoculants to alleviate biotic and/or abiotic stresses. Therefore, a complete and accurate methodological study and laboratory techniques are required to warrant the correct achievement of these steps. This review compiles and details the fundamentals, methods, and procedures of key protocols used in isolation and characterization of PGPR for plant stress alleviation.
PMID: 35556177
Biointerphases , IF:2.456 , 2022 Jun , V17 (3) : P031006 doi: 10.1116/6.0001949
Mass spectral imaging showing the plant growth-promoting rhizobacteria's effect on the Brachypodium awn.
State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China.; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354.; Environmental Molecular Science Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354.; Earth and Biological Science Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354.; Materials Science and Technology Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830.
The plant growth-promoting rhizobacteria (PGPR) on the host plant surface play a key role in biological control and pathogenic response in plant functions and growth. However, it is difficult to elucidate the PGPR effect on plants. Such information is important in biomass production and conversion. Brachypodium distachyon (Brachypodium), a genomics model for bioenergy and native grasses, was selected as a C3 plant model; and the Gram-negative Pseudomonas fluorescens SBW25 (P.) and Gram-positive Arthrobacter chlorophenolicus A6 (A.) were chosen as representative PGPR strains. The PGPRs were introduced to the Brachypodium seed's awn prior to germination, and their possible effects on the seeding and growth were studied using different modes of time-of-flight secondary ion mass spectrometry (ToF-SIMS) measurements, including a high mass-resolution spectral collection and delayed image extraction. We observed key plant metabolic products and biomarkers, such as flavonoids, phenolic compounds, fatty acids, and auxin indole-3-acetic acid in the Brachypodium awns. Furthermore, principal component analysis and two-dimensional imaging analysis reveal that the Brachypodium awns are sensitive to the PGPR, leading to chemical composition and morphology changes on the awn surface. Our results show that ToF-SIMS can be an effective tool to probe cell-to-cell interactions at the biointerface. This work provides a new approach to studying the PGPR effects on awn and shows its potential for the research of plant growth in the future.
PMID: 35738921
J Nat Med , IF:2.343 , 2022 Jun doi: 10.1007/s11418-022-01631-4
The ability of callus tissues induced from three Allium plants to accumulate health-beneficial natural products, S-alk(en)ylcysteine sulfoxides.
Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan. naokoy@faculty.chiba-u.jp.; Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan. naokoy@faculty.chiba-u.jp.; School of Pharmacy, Iwate Medical University, 1-1-1 Idaidori, Yahaba, Iwate, 028-3694, Japan.; Graduate School of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan.; Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8675, Japan.; RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, 230-0045, Japan.
S-Alk(en)ylcysteine sulfoxides (CSOs), such as methiin, alliin, and isoalliin, are health-beneficial natural products biosynthesized in the genus Allium. Here, we report the induction of multiple callus tissue lines from three Allium vegetables, onion (A. cepa), Welsh onion (A. fistulosum), and Chinese chive (A. tuberosum), and their ability to accumulate CSOs. Callus tissues were initiated and maintained in the presence of picloram and 2-isopentenyladenine as auxin and cytokinin, respectively. For all plant species tested, the callus tissues almost exclusively accumulated methiin as CSO, while the intact plants contained a substantial amount of isoalliin together with methiin. These results suggest that the cellular developmental conditions and the regulatory mechanisms required for the biosynthesis of methiin are different from those of alliin and isoalliin. The methiin content in the callus tissues of onion and Welsh onion was much higher compared to that in the intact plants, and its cellular concentration could be estimated as 1.9-21.7 mM. The activity of alliinase that degrades CSOs in the callus tissues was much lower than that of the intact plants for onion and Welsh onion, but at similar levels as in the intact plants for Chinese chive. Our findings that the callus tissues of onion and Welsh onion showed high methiin content and low alliinase activity highlighted their potential as a plant-based system for methiin production.
PMID: 35691991
Mol Biol Rep , IF:2.316 , 2022 May doi: 10.1007/s11033-022-07548-1
Overexpression of TaLAX3-1B alters the stomatal aperture and improves the salt stress resistance of tobacco.
College of Agriculture, Guizhou University, Guiyang, 550025, China.; Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China.; College of Agriculture, Guizhou University, Guiyang, 550025, China. xrhgz@163.com.; Guizhou Sub-Center of National Wheat Improvement Center, Guiyang, 550025, China. xrhgz@163.com.
BACKGROUND: Stomata, which play important roles in both optimizing photosynthesis efficiency and adapting to stress, are closely related to IAA and ABA. In plants, the auxin influx carrier LAX3 has been found to play roles in development and stress tolerance. However, the function of LAX3 in stomata and in response to salt stress remains largely unknown. METHODS AND RESULTS: Here, we show that overexpression of wheat TaLAX3-1B in tobacco results in a decrease in stomatal aperture and a relatively closed state of the stomata. In addition, the stomatal movement of the OxTaLAX3-1B lines was less sensitive to ABA than that of the WT. Consistently, compared with the WT, the OxTaLAX3-1B lines showed significantly higher expression of stomate-, IAA- and ABA-related genes and endogenous IAA and ABA contents. Furthermore, compared with the WT, the OxTaLAX3-1B lines exhibited higher proline content, salt stress-related gene expression and ROS antioxidant enzyme activity but lower MDA content and ROS accumulation after salt treatment. CONCLUSIONS: The present results suggest that TaLAX3-1B plays a positive role in regulating stomatal closure and enhancing salt stress tolerance.
PMID: 35624389
Antonie Van Leeuwenhoek , IF:2.271 , 2022 Jul , V115 (7) : P921-932 doi: 10.1007/s10482-022-01745-5
Potential role of rhizobia to enhance chickpea-growth and yield in low fertility-soils of Tunisia.
Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), BP.901, 2050, Hammam-Lif, Tunisia. samir_benromdhane@yahoo.com.; LSTM, UMR 113 IRD/CIRAD/SupAgro/Universite de Montpellier, Campus International de Baillarguet, Montpellier, France.; Department of Plant and Soil Sciences, University of Delaware, Newark, USA.; Laboratory of Legumes, Center of Biotechnology of Borj-Cedria (CBBC), BP.901, 2050, Hammam-Lif, Tunisia.
Plant growth-promoting rhizobacteria are bacteria that improve plant growth and reduce plant pathogen damages. In this study, 100 nodule bacteria were isolated from chickpea, screened for their plant growth-promoting (PGP) traits and then characterised by PCR-RFLP of 16 S rDNA. Results showed that most of the slow-growing isolates fixed nitrogen but those exhibiting fast-growth did not. Fourteen isolates solubilized inorganic phosphorus, 16 strains produced siderophores, and 17 strains produced indole acetic acid. Co-culture experiments identified three strains having an inhibitory effect against Fusarium oxysporum, the primary pathogenic fungus for chickpea in Tunisia. Rhizobia with PGP traits were assigned to Mesorhizobium ciceri, Mesorhizobium mediterraneum, Sinorhizobium meliloti and Agrobacterium tumefaciens. We noted that PGP activities were differentially distributed between M. ciceri and M. mediterraneum. The region of Mateur in northern Tunisia, with clay-silty soil, was the origin of 53% of PGP isolates. Interestingly, we found that S. meliloti and A. tumefaciens strains did not behave as parasitic nodule-bacteria but as PGP rhizobacteria useful for chickpea nutrition and health. In fact, S. meliloti strains could solubilize phosphorus, produce siderophore and auxin. The A. tumefaciens strains could perform the previous PGP traits and inhibit pathogen growth also. Finally, one candidate strain of M. ciceri (LL10)-selected for its highest symbiotic nitrogen fixation and phosphorus solubilization-was used for field experiment. The LL10 inoculation increased grain yield more than three-fold. These finding showed the potential role of rhizobia to be used as biofertilizers and biopesticides, representing low-cost and environment-friendly inputs for sustainable agriculture.
PMID: 35639296
Plant Signal Behav , IF:2.247 , 2022 Jun : P2081397 doi: 10.1080/15592324.2022.2081397
Genetic regulation of lateral root development.
State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Hebei Province for Plant Physiology and Molecular Pathology, College of Life Sciences, Hebei Agricultural University, Baoding, Hebei, China.; Pear Engineering and Technology Research Center of Hebei, College of Horticulture, Hebei Agricultural University, Baoding, Hebei, China.; Ministry of Education, Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, China.; College of Life Sciences, Hengshui University, Hengshui, Hebei, China.; College of Plant Protection, Hebei Agricultural University, Baoding, Hebei, China.; College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China.
Lateral roots (LRs) are an important part of plant root systems. In dicots, for example, after plants adapted from aquatic to terrestrial environments, filamentous pseudorhizae evolved to allow nutrient absorption. A typical plant root system comprises a primary root, LRs, root hairs, and a root cap. Classical plant roots exhibit geotropism (the tendency to grow downward into the ground) and can synthesize plant hormones and other essential substances. Root vascular bundles and complex spatial structures enable plants to absorb water and nutrients to meet their nutrient quotas and grow. The primary root carries out most functions during early growth stages but is later overtaken by LRs, underscoring the importance of LR development water and mineral uptake and the soil fixation capacity of the root. LR development is modulated by endogenous plant hormones and external environmental factors, and its underlying mechanisms have been dissected in great detail in Arabidopsis, thanks to its simple root anatomy and the ease of obtaining mutants. This review comprehensively and systematically summarizes past research (largely in Arabidopsis) on LR basic structure, development stages, and molecular mechanisms regulated by different factors, as well as future prospects in LR research, to provide broad background knowledge for root researchers.
PMID: 35642513
Biosci Biotechnol Biochem , IF:2.043 , 2022 Jun , V86 (7) : P824-831 doi: 10.1093/bbb/zbac070
Facilitation of auxin biosynthesis and metabolism by salt stress in rice plants.
Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto, Japan.
To investigate the effects of salt stress on the auxin in rice plants, we analyzed indole-3-acetic acid (IAA) and its metabolites in hydroponically grown rice plant seedlings (Oryza sativa cv. Nipponbare) and in the culture medium using LC-ESI/MS/MS. We found that the IAA level in the culture medium was increased 39-fold due to salt stress treatment, while those in the shoots and roots were increased by less than 2-fold. The culture medium also contained high amounts of oxidized metabolites such as OxIAA, DiOxIAA, DiOxIAA-Glu, and DiOxIAA-Asp. The total amount of IAA and its metabolites in the shoots, roots, and culture medium was significantly increased with salt treatment. A salt stress-responsive increase in the IAA metabolites was observed in 9 tested cultivars of rice. The results indicate that salt stress facilitates the metabolic turnover of IAA in rice plants and may open new insight into the role of auxin.
PMID: 35580591
Evol Bioinform Online , IF:1.625 , 2022 , V18 : P11769343221106795 doi: 10.1177/11769343221106795
In Silico Identification and Characterization of B12D Family Proteins in Viridiplantae.
Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam bin Abdulaziz University, Al-kharj, Saudi Arabia.
B12D family proteins are transmembrane proteins that contain the B12D domain involved in membrane trafficking. Plants comprise several members of the B12D family, but these members' numbers and specific functions are not determined. This study aims to identify and characterize the members of B12D protein family in plants. Phytozome database was retrieved for B12D proteins from 14 species. The total 66 B12D proteins were analyzed in silico for gene structure, motifs, gene expression, duplication events, and phylogenetics. In general, B12D proteins are between 86 and 98 aa in length, have 2 or 3 exons, and comprise a single transmembrane helix. Motif prediction and multiple sequence alignment show strong conservation among B12D proteins of 11 flowering plants species. Despite that, the phylogenetic tree revealed a distinct cluster of 16 B12D proteins that have high conservation across flowering plants. Motif prediction revealed 41 aa motif conserved in 58 of the analyzed B12D proteins similar to the bZIP motif, confirming that in the predicted biological process and molecular function, B12D proteins are DNA-binding proteins. Cis-regulatory elements screening in putative B12D promoters found various responsive elements for light, abscisic acid, methyl jasmonate, cytokinin, drought, and heat. Despite that, there is specific elements for cold stress, cell cycle, circadian, auxin, salicylic acid, and gibberellic acid in the promoter of a few B12D genes indicating for functional diversification for B12D family members. The digital expression shows that B12D genes of Glycine max have similar expression patterns consistent with their clustering in the phylogenetic tree. However, the expression of B12D genes of Hordeum vulgure appears inconsistent with their clustering in the tree. Despite the strong conservation of the B12D proteins of Viridiplantae, gene association analysis, promoter analysis, and digital expression indicate different roles for the members of the B12D family during plant developmental stages.
PMID: 35721582
Plant Commun , 2022 Jun : P100351 doi: 10.1016/j.xplc.2022.100351
Natural variation in the transcription factor Replumless contributes to both disease resistance and plant growth in Arabidopsis.
School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China.; School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China. Electronic address: deng@pku.edu.cn.
When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, which frequently incurs growth penalties. This phenomenon is known as growth-defense tradeoff, which is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes need further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly up-regulated in the rpl mutants, which led to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. On the other hand, RPL repressed flavonol synthesis through directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.
PMID: 35752937
Heliyon , 2022 May , V8 (5) : Pe09532 doi: 10.1016/j.heliyon.2022.e09532
UHPLC-MS/MS and QRT-PCR profiling of PGP agents and Rhizobium spp. of induced phytohormones for growth promotion in mungbean (var. Co4).
Department of Plant Molecular Biology and Biotechnology, Navsari Agricultural University, Navsari, 396450, Gujarat, India.; Food Quality Testing Laboratory, N. M. College of Agriculture, Navsari Agricultural University, Navsari, 396450, Gujarat, India.; ASPEE Shakilam Biotechnology Institute, Navsari Agricultural University, Surat, 395007, Gujarat, India.; Department of Basic Science and Humanities, ACHF, Navsari Agricultural University, Navsari, 396450, Gujarat, India.; Main Cotton Research Station, Navsari Agricultural University, Surat, 395007, Gujarat, India.
In present study, five potential strains with different plant growth promotion (PGP) characteristics were used. By considering various PGP properties of different bacterial strains, several treatments based on various combinations were developed and studied on mungbean (var. Co4). The quantification of the phytohormones was performed on ultrahigh-performance liquid chromatograph coupled to heated electrospray ionization tandem mass spectrometry (UHPLC/HESI-MS/MS). Indole 3-acetic acid (IAA) and Indole 3-butyric acid (IBA) were quantified in positive ionization mode while Gibberellic acid (GA3) and salicylic acid (SA) were quantified in negative ionization mode. Among all the treatments two penta combinations of consortia 1 (Rhizobium + Azospirillum + Pseudomonas + Bacillus spp. + Bacillus licheniformis) and consortia 2 (Rhizobium + Azotobacter + Pseudomonas + Bacillus spp. + Bacillus licheniformis) were found most effective. Higher amount of IAA (1.043 mug g(-1)), IBA (0.036 mug g(-1)), GA3 (1.999 mug g(-1)) and SA (0.098 mug g(-1)) Fresh weight (FW) were found in treated adolescent root tissues of consortia 2 as compared to consortia 1. Moreover, transcriptional level of the plant hormones were 2-4 fold higher in the relative gene expression study of three genes: ARF (Auxin responsive factors), ERF-IF (Ethylene-responsive Initiation Factors) and GAI (Gibberellic-Acid Insensitive) in consortia 2, on the 15(th), 30(th) and 45(th) day using quantitative real time-Polymerase chain reaction (qRT-PCR). Furthermore, Yield attributing characters like, the number of nodules plant(-1), number of pods plant(-1), weight of nodule and seed yield plant(-1) were also increased as compared to the control. As a result, the current research elucidated that penta combinations consortium of Rhizobium sp. and rhizobacteria can be developed as a single delivery system biofertilizer for enhancing mungbean productivity.
PMID: 35663748
Biotechnol Biofuels Bioprod , 2022 May , V15 (1) : P55 doi: 10.1186/s13068-022-02155-5
Physiological and comparative transcriptome analyses reveal the mechanisms underlying waterlogging tolerance in a rapeseed anthocyanin-more mutant.
School of Life Sciences, Jiangsu University, Zhenjiang, China.; School of Life Sciences, Jiangsu University, Zhenjiang, China. xltan@ujs.edu.cn.
BACKGROUND: Rapeseed (Brassica napus) is the second largest oil crop worldwide. It is widely used in food, energy production and the chemical industry, as well as being an ornamental. Consequently, it has a large economic value and developmental potential. Waterlogging is an important abiotic stress that restricts plant growth and development. However, little is known about the molecular mechanisms underlying waterlogging tolerance in B. napus. RESULTS: In the present study, the physiological changes and transcriptomes of germination-stage rapeseed in response to waterlogging stress were investigated in the B. napus cultivar 'Zhongshuang 11' (ZS11) and its anthocyanin-more (am) mutant, which was identified in our previous study. The mutant showed stronger waterlogging tolerance compared with ZS11, and waterlogging stress significantly increased anthocyanin, soluble sugar and malondialdehyde contents and decreased chlorophyll contents in the mutant after 12 days of waterlogging. An RNA-seq analysis identified 1370 and 2336 differently expressed genes (DEGs) responding to waterlogging stress in ZS11 and am, respectively. An enrichment analysis revealed that the DEGs in ZS11 were predominately involved in carbohydrate metabolism, whereas those in the am mutant were particularly enriched in plant hormone signal transduction and response to endogenous stimulation. In total, 299 DEGs were identified as anthocyanin biosynthesis-related structural genes (24) and regulatory genes encoding transcription factors (275), which may explain the increased anthocyanin content in the am mutant. A total of 110 genes clustered in the plant hormone signal transduction pathway were also identified as DEGs, including 70 involved in auxin and ethylene signal transduction that were significantly changed in the mutant. Furthermore, the expression levels of 16 DEGs with putative roles in anthocyanin accumulation and biotic/abiotic stress responses were validated by quantitative real-time PCR as being consistent with the transcriptome profiles. CONCLUSION: This study provides new insights into the molecular mechanisms of increased anthocyanin contents in rapeseed in response to waterlogging stress, which should be useful for reducing the damage caused by waterlogging stress and for further breeding new rapeseed varieties with high waterlogging tolerance.
PMID: 35596185