Cell , IF:38.637 , 2019 Jul , V178 (2) : P400-412.e16 doi: 10.1016/j.cell.2019.06.021
Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport.
Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.; Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria.; Plant Molecular and Cellular Biology Laboratory, and Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Gregor Mendel Institute (GMI), Austrian Academy of Sciences, Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria. Electronic address: wbusch@salk.edu.
Root system architecture (RSA), the distribution of roots in soil, plays a major role in plant survival. RSA is shaped by multiple developmental processes that are largely governed by the phytohormone auxin, suggesting that auxin regulates responses of roots that are important for local adaptation. However, auxin has a central role in numerous processes, and it is unclear which molecular mechanisms contribute to the variation in RSA for environmental adaptation. Using natural variation in Arabidopsis, we identify EXOCYST70A3 as a modulator of the auxin system that causes variation in RSA by acting on PIN4 protein distribution. Allelic variation and genetic perturbation of EXOCYST70A3 lead to alteration of root gravitropic responses, resulting in a different RSA depth profile and drought resistance. Overall our findings suggest that the local modulation of the pleiotropic auxin pathway can gives rise to distinct RSAs that can be adaptive in specific environments.
PMID: 31299202
Cell , IF:38.637 , 2019 Jul , V178 (2) : P269-271 doi: 10.1016/j.cell.2019.06.018
A New Angle on How Roots Acclimate to Sporadic Rainfall.
Plant and Crop Sciences, School of Biosciences, University of Nottingham, UK.; Plant and Crop Sciences, School of Biosciences, University of Nottingham, UK. Electronic address: malcolm.bennett@nottingham.ac.uk.
Root architecture critically influences a plant's ability to forage for nutrients and water in soil. In this issue of Cell, Ogura et al. (2019) report a new regulatory gene and elegant molecular mechanism that links auxin-dependent root-angle regulation with improved plant fitness under variable rainfall conditions.
PMID: 31299198
Trends Plant Sci , IF:14.416 , 2019 Jul , V24 (7) : P602-610 doi: 10.1016/j.tplants.2019.04.002
The BAP Module: A Multisignal Integrator Orchestrating Growth.
Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universite Paris-Saclay, 78000 Versailles, France; Universite Paris-Sud, Universite Paris-Saclay, 91405 Orsay, France.; Department of Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.; Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universite Paris-Saclay, 78000 Versailles, France. Electronic address: nicolas.arnaud@inra.fr.
Coordination of cell proliferation, cell expansion, and differentiation underpins plant growth. To maximise reproductive success, growth needs to be fine-tuned in response to endogenous and environmental cues. This developmental plasticity relies on a cellular machinery that integrates diverse signals and coordinates the downstream responses. In arabidopsis, the BAP regulatory module, which includes the BRASSINAZOLE RESISTANT 1 (BZR1), AUXIN RESPONSE FACTOR 6 (ARF6), and PHYTOCHROME INTERACTING FACTOR 4 (PIF4) transcription factors (TFs), has been shown to coordinate growth in response to multiple growth-regulating signals. In this Opinion article, we provide an integrative view on the BAP module control of cell expansion and discuss whether its function is conserved or diversified, thus providing new insights into the molecular control of growth.
PMID: 31076166
Nat Commun , IF:12.121 , 2019 Jul , V10 (1) : P2904 doi: 10.1038/s41467-019-10867-w
Orthogonal regulation of phytochrome B abundance by stress-specific plastidial retrograde signaling metabolite.
Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.; Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA. kdehesh@ucr.edu.
Plant survival necessitates constant monitoring of fluctuating light and balancing growth demands with adaptive responses, tasks mediated via interconnected sensing and signaling networks. Photoreceptor phytochrome B (phyB) and plastidial retrograde signaling metabolite methylerythritol cyclodiphosphate (MEcPP) are evolutionarily conserved sensing and signaling components eliciting responses through unknown connection(s). Here, via a suppressor screen, we identify two phyB mutant alleles that revert the dwarf and high salicylic acid phenotypes of the high MEcPP containing mutant ceh1. Biochemical analyses show high phyB protein levels in MEcPP-accumulating plants resulting from reduced expression of phyB antagonists and decreased auxin levels. We show that auxin treatment negatively regulates phyB abundance. Additional studies identify CAMTA3, a MEcPP-activated calcium-dependent transcriptional regulator, as critical for maintaining phyB abundance. These studies provide insights into biological organization fundamentals whereby a signal from a single plastidial metabolite is transduced into an ensemble of regulatory networks controlling the abundance of phyB, positioning plastids at the information apex directing adaptive responses.
PMID: 31266952
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Jul , V116 (28) : P14325-14330 doi: 10.1073/pnas.1906300116
PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation.
Unite Mixte de Recherche (UMR) Diversite Adaptation et Developpement des Plantes, Institut de Recherche pour le Developpement, Universite de Montpellier, 34394 Montpellier Cedex 5, France.; Department of Pharmacological, Medical and Agronomical Biotechnology, University of Science and Technology of Hanoi, Cau Giay District, Hanoi, Vietnam.; University of Nottingham, Sutton Bonington, Loughborough LE12 5RD, United Kingdom.; Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan.; Laboratoire de Biogenese Membranaire, UMR 5200, CNRS, Universite de Bordeaux, 33882 Villenave d'Ornon Cedex, France.; Institut Jean-Pierre Bourgin, UMR 1318, Institut National de la Recherche Agronomique, AgroParisTech, CNRS, Universite Paris-Saclay, 78026 Versailles Cedex, France.; Department of Biology, Graduate School of Science, Kobe University, Kobe 657-8501, Japan.; Unite Mixte de Recherche (UMR) Diversite Adaptation et Developpement des Plantes, Institut de Recherche pour le Developpement, Universite de Montpellier, 34394 Montpellier Cedex 5, France; laurent.laplaze@ird.fr soazig.guyomarch@ird.fr.
Lateral root organogenesis plays an essential role in elaborating plant root system architecture. In Arabidopsis, the AP2 family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify potential targets of PUCHI, we analyzed a time course transcriptomic dataset of lateral root formation. We report that multiple genes coding for very long chain fatty acid (VLCFA) biosynthesis enzymes are induced during lateral root development in a PUCHI-dependent manner. Significantly, several mutants perturbed in VLCFA biosynthesis show similar lateral root developmental defects as puchi-1 Moreover, puchi-1 roots display the same disorganized callus formation phenotype as VLCFA biosynthesis-deficient mutants when grown on auxin-rich callus-inducing medium. Lipidomic profiling of puchi-1 roots revealed reduced VLCFA content compared with WT. We conclude that PUCHI-regulated VLCFA biosynthesis is part of a pathway controlling cell proliferation during lateral root and callus formation.
PMID: 31235573
Proc Natl Acad Sci U S A , IF:9.412 , 2019 Jul , V116 (27) : P13299-13304 doi: 10.1073/pnas.1900711116
Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants.
Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.; Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN 46268.; Department of Chemistry, The Pennsylvania State University, University Park, PA 16802.; Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802.; Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; snair@illinois.edu.; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.
The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and alpha-ketoglutarate (Fe/alphaKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from Bradyrhizobium diazoefficiens USDA 110 as a catalyst to degrade (S)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (R)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (S)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.
PMID: 31209034
PLoS Biol , IF:7.076 , 2019 Jul , V17 (7) : Pe3000085 doi: 10.1371/journal.pbio.3000085
A novel Ca2+-binding protein that can rapidly transduce auxin responses during root growth.
School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.; Institute of Biology and Biotechnology of Plants, University of Munster, Munster, Germany.; Department of Biology, University of Indiana, Bloomington, Indiana, United States of America.; Howard Hughes Medical Institute and Division of Biology, University of California, San Diego, La Jolla, California, United States of America.; Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, Israel.
Signaling cross talks between auxin, a regulator of plant development, and Ca2+, a universal second messenger, have been proposed to modulate developmental plasticity in plants. However, the underlying molecular mechanisms are largely unknown. Here, we report that in Arabidopsis roots, auxin elicits specific Ca2+ signaling patterns that spatially coincide with the expression pattern of auxin-regulated genes. We have identified the single EF-hand Ca2+-binding protein Ca2+-dependent modulator of ICR1 (CMI1) as an interactor of the Rho of plants (ROP) effector interactor of constitutively active ROP (ICR1). CMI1 expression is directly up-regulated by auxin, whereas the loss of function of CMI1 associates with the repression of auxin-induced Ca2+ increases in the lateral root cap and vasculature, indicating that CMI1 represses early auxin responses. In agreement, cmi1 mutants display an increased auxin response including shorter primary roots, longer root hairs, longer hypocotyls, and altered lateral root formation. Binding to ICR1 affects subcellular localization of CMI1 and its function. The interaction between CMI1 and ICR1 is Ca2+-dependent and involves a conserved hydrophobic pocket in CMI1 and calmodulin binding-like domain in ICR1. Remarkably, CMI1 is monomeric in solution and in vitro changes its secondary structure at cellular resting Ca2+ concentrations ranging between 10-9 and 10-8 M. Hence, CMI1 is a Ca2+-dependent transducer of auxin-regulated gene expression, which can function in a cell-specific fashion at steady-state as well as at elevated cellular Ca2+ levels to regulate auxin responses.
PMID: 31295257
Plant Physiol , IF:6.902 , 2019 Jul , V180 (3) : P1647-1659 doi: 10.1104/pp.18.01576
Cell Death Triggered by the YUCCA-like Bs3 Protein Coincides with Accumulation of Salicylic Acid and Pipecolic Acid But Not of Indole-3-Acetic Acid.
Center for Plant Molecular Biology, Eberhard-Karls-University Tuebingen, Tuebingen 72076, Germany.; Integrated Plant Genetics, Inc., Gainesville, Florida 32653.; Genetics, Faculty of Biology, Ludwig-Maximilians-University, D-82152 Munich Martinsried, Germany.; Center for Plant Molecular Biology, Eberhard-Karls-University Tuebingen, Tuebingen 72076, Germany thomas.lahaye@zmbp.uni-tuebingen.de.
The pepper (Capsicum annuum) resistance gene bacterial spot3 (Bs3) is transcriptionally activated by the matching Xanthomonas euvesicatoria transcription-activator-like effector (TALE) AvrBs3. AvrBs3-induced Bs3 expression triggers a rapid and local cell death reaction, the hypersensitive response (HR). Bs3 is most closely related to plant flavin monooxygenases of the YUCCA (YUC) family, which catalyze the final step in auxin biosynthesis. Targeted mutagenesis of predicted NADPH- and FAD-cofactor sites resulted in Bs3 derivatives that no longer trigger HR, thereby suggesting that the enzymatic activity of Bs3 is crucial to Bs3-triggered HR. Domain swap experiments between pepper Bs3 and Arabidopsis (Arabidopsis thaliana) YUC8 uncovered functionally exchangeable and functionally distinct regions in both proteins, which is in agreement with a model whereby Bs3 evolved from an ancestral YUC gene. Mass spectrometric measurements revealed that expression of YUCs, but not expression of Bs3, coincides with an increase in auxin levels, suggesting that Bs3 and YUCs, despite their sequence similarity, catalyze distinct enzymatic reactions. Finally, we found that expression of Bs3 coincides with increased levels of the salicylic acid and pipecolic acid, two compounds that are involved in systemic acquired resistance.
PMID: 31068387
Plant Physiol , IF:6.902 , 2019 Jul , V180 (3) : P1450-1466 doi: 10.1104/pp.19.00055
HY5 Interacts with the Histone Deacetylase HDA15 to Repress Hypocotyl Cell Elongation in Photomorphogenesis.
Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.; State Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an 271018, China.; University of Chinese Academy of Sciences, Beijing 100049, China.; Institute of Plant Biology, National Taiwan University, Taipei 106, Taiwan.; Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, and Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China xunchengliu@scbg.ac.cn.
Photomorphogenesis is a critical plant developmental process that involves light-mediated transcriptome and histone modification changes. The transcription factor ELONGATED HYPOCOTYL5 (HY5) acts downstream of multiple families of photoreceptors to promote photomorphogenesis by regulating the expression of light-responsive genes. However, the molecular mechanism for HY5-mediated transcriptional regulation remains largely unclear. Here, we demonstrated that HY5 directly interacts with a Reduced Potassium Dependence3/Histone Deacetylase1 (HDA1)-type histone deacetylase, HDA15, both in vitro and in vivo. Phenotypic analysis revealed that HDA15 is a negative regulator of hypocotyl cell elongation under both red and far-red light conditions in Arabidopsis (Arabidopsis thaliana) seedlings. The enzymatic activity of HDA15 is required for inhibition of hypocotyl elongation. Furthermore, HDA15 and HY5 act interdependently in the repression of hypocotyl cell elongation in photomorphogenesis. Genome-wide transcriptome analysis revealed that HDA15 and HY5 corepress the transcription of a subset of cell wall organization and auxin signaling-related genes. In addition, HDA15 is required for the function of HY5 in the repression of genes related to hypocotyl cell elongation in Arabidopsis seedlings. Moreover, HY5 recruits HDA15 to the promoters of target genes and represses gene expression by decreasing the levels of histone H4 acetylation in a light-dependent manner. Our study revealed a key transcription regulatory node in which HY5 interacts with HDA15 involved in repressing hypocotyl cell elongation to promote photomorphogenesis.
PMID: 31061103
Plant Physiol , IF:6.902 , 2019 Jul , V180 (3) : P1725-1739 doi: 10.1104/pp.19.00130
Salicylic Acid Affects Root Meristem Patterning via Auxin Distribution in a Concentration-Dependent Manner.
Institute for Biology II, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany.; State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'An 271018, China.; Institute of Cytology and Genetics, Novosibirsk 630090, Russia.; Novosibirsk State University, Novosibirsk 630090, Russia.; Institute for Biology II, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany victoria.v.mironova@gmail.com.; BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany.; Center for Biosystems Analysis, Albert-Ludwigs-University Freiburg, D-79104 Freiburg, Germany.; Institute of Cytology and Genetics, Novosibirsk 630090, Russia victoria.v.mironova@gmail.com.
The phytohormone salicylic acid (SA) is well known for its induction of pathogenesis-related proteins and systemic acquired resistance; SA also has specific effects on plant growth and development. Here we analyzed the effect of SA on Arabidopsis (Arabidopsis thaliana) root development. We show that exogenous SA treatment at low (below 50 microM) and high (greater than 50 microM) concentrations affect root meristem development in two different PR1-independent ways. Low-concentration SA promoted adventitious roots and altered architecture of the root apical meristem, whereas high-concentration SA inhibited all growth processes in the root. All exposures to exogenous SA led to changes in auxin synthesis and transport. A wide range of SA treatment concentrations activated auxin synthesis, but the effect of SA on auxin transport was dose dependent. Mathematical modeling of auxin synthesis and transport predicted auxin accumulation or depletion in the root tip following low- or high-concentration SA treatments, respectively. SA-induced auxin accumulation led to the formation of more layers of columella initials, an additional cortical cell layer (middle cortex), and extra files of epidermis, cortex, and endodermis cells. Suppression of SHORT ROOT and activation of CYCLIN D6;1 mediated the changes in radial architecture of the root. We propose that low-concentration SA plays an important role in shaping root meristem structure and root system architecture.
PMID: 31036755
Genomics , IF:6.205 , 2019 Jul , V111 (4) : P700-709 doi: 10.1016/j.ygeno.2018.04.007
Transcriptome sequencing of active buds from Populus deltoides CL. and Populusxzhaiguanheibaiyang reveals phytohormones involved in branching.
Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China.; Key Laboratory of Agricultural Ecology and Environment, College of Forestry, Shandong Agricultural University, Tai'an, Shandong 271018, PR China; Silviculture Key Lab of Shandong Province Forestry, College of Shandong Agricultural University, Tai'an, Shandong 271018, PR China. Electronic address: jhli@sdau.edu.cn.; Key Laboratory of Tree Breeding of Zhejiang Province, The Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, PR China. Electronic address: hanxj@caf.ac.cn.
Branching in woody plants affects their ecological benefits and impacts wood formation. To obtain genome-wide insights into the transcriptome changes and regulatory mechanisms associated with branching, we performed high-throughput RNA sequencing to characterize cDNA libraries generated from active buds of Populus deltoides CL. 'zhonglin2025' (BC) and Populusxzhaiguanheibaiyang (NC). NC has more branches than BC and rapid growth. We obtained a total of 198.2 million high-quality clean reads from the NC and BC libraries. We detected 3543 differentially expressed genes (DEGs) between the NC and BC libraries; 1418 were down-regulated and 2125 were up-regulated. Gene ontology functional classification of the DEGs indicated that they included 89 genes that encoded proteins related to hormone biosynthesis, 364 genes related to hormone signaling transduction, and 104 related to the auxin efflux transmembrane transporter. We validated the expression profiles of 16 degrees by real-time quantitative PCR and found that their expression patterns were similar to those obtained from the high-throughput RNA sequencing data. We also measured the hormone content in young buds of BC and NC by high-pressure liquid chromatography. In this study, we identified global hormone regulatory patterns and differences in gene expression between NC and BC, and constructed a hormone regulatory network to explain branching in Populus buds. In addition, candidate genes that may be useful for molecular breeding of particular plant types were identified. Our results will provide a starting point for future investigations into the molecular mechanisms of branching in Populus.
PMID: 29660475
J Exp Bot , IF:5.908 , 2019 Jul , V70 (14) : P3467-3494 doi: 10.1093/jxb/erz278
Posture control in land plants: growth, position sensing, proprioception, balance, and elasticity.
Universite Clermont Auvergne, INRA, PIAF, Clermont-Ferrand, France.; Department of Collective Behaviour, Max Planck Institute for Ornithology and Department of Biology, University of Konstanz, Konstanz, Germany.; Aix-Marseille Universite, CNRS, IUSTI, Marseille, France.
The colonization of the atmosphere by land plants was a major evolutionary step. The mechanisms that allow for vertical growth through air and the establishment and control of a stable erect habit are just starting to be understood. A key mechanism was found to be continuous posture control to counterbalance the mechanical and developmental challenges of maintaining a growing upright structure. An interdisciplinary systems biology approach was invaluable in understanding the underlying principles and in designing pertinent experiments. Since this discovery previously held views of gravitropic perception had to be reexamined and this has led to the description of proprioception in plants. In this review, we take a purposefully pedagogical approach to present the dynamics involved from the cellular to whole-plant level. We show how the textbook model of how plants sense gravitational force has been replaced by a model of position sensing, a clinometer mechanism that involves both passive avalanches and active motion of statoliths, granular starch-filled plastids, in statocytes. Moreover, there is a transmission of information between statocytes and other specialized cells that sense the degree of organ curvature and reset asymmetric growth to straighten and realign the structure. We give an overview of how plants have used the interplay of active posture control and elastic sagging to generate a whole range of spatial displays during their life cycles. Finally, a position-integrating mechanism has been discovered that prevents directional plant growth from being disrupted by wind-induced oscillations.
PMID: 31305901
J Exp Bot , IF:5.908 , 2019 Jul , V70 (13) : P3401-3414 doi: 10.1093/jxb/erz272
Jasmonate and auxin perception: how plants keep F-boxes in check.
Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.; VIB Center for Plant Systems Biology, Ghent, Belgium.; Centre for Plant Biotechnology and Genomics, Parque Cientifico y Tecnologico, UPM Campus de Montegancedo, Madrid, Spain.
Phytohormones regulate the plasticity of plant growth and development, and responses to biotic and abiotic stresses. Many hormone signal transduction cascades involve ubiquitination and subsequent degradation of proteins by the 26S proteasome. The conjugation of ubiquitin to a substrate is facilitated by the E1 activating, E2 conjugating, and the substrate-specifying E3 ligating enzymes. The most prevalent type of E3 ligase in plants is the Cullin-RING ligase (CRL)-type, with F-box proteins (FBPs) as the substrate recognition component. The activity of these SKP-Cullin-F-box (SCF) complexes needs to be tightly regulated in time and place. Here, we review the regulation of SCF function in plants on multiple levels, with a focus on the auxin and jasmonate SCF-type receptor complexes. We discuss in particular the relevance of protein-protein interactions and post-translational modifications as mechanisms to keep SCF functioning under control. Additionally, we highlight the unique property of SCFTIR1/AFB and SCFCOI1 to recognize substrates by forming co-receptor complexes. Finally, we explore how engineered selective agonists can be used to study and uncouple the outcomes of the complex auxin and jasmonate signaling networks that are governed by these FBPs.
PMID: 31173086
J Exp Bot , IF:5.908 , 2019 Jul , V70 (14) : P3495-3506 doi: 10.1093/jxb/erz158
Gravity sensing and signal conversion in plant gravitropism.
Division of Plant Environmental Responses, National Institute for Basic Biology, Okazaki, Japan.; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan.
Plant organs control their growth orientation in response to gravity. Within gravity-sensing cells, the input (gravity sensing) and signal conversion (gravity signalling) progress sequentially. The cells contain a number of high-density, starch-accumulating amyloplasts, which sense gravity when they reposition themselves by sedimentation to the bottom of the cell when the plant organ is re-orientated. This triggers the next step of gravity signalling, when the physical signal generated by the sedimentation of the amyloplasts is converted into a biochemical signal, which redirects auxin transport towards the lower flank of the plant organ. This review focuses on recent advances in our knowledge of the regulatory mechanisms that underlie amyloplast sedimentation and the system by which this is perceived, and on recent progress in characterising the factors that play significant roles in gravity signalling by which the sedimentation is linked to the regulation of directional auxin transport. Finally, we discuss the contribution of gravity signalling factors to the mechanisms that control the gravitropic set-point angle.
PMID: 30976802
Development , IF:5.611 , 2019 Jul , V146 (14) doi: 10.1242/dev.174375
miR167 limits anther growth to potentiate anther dehiscence.
Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.; College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China.; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA jreed@email.unc.edu.; Laboratoire de Reproduction et Developpement des Plantes, Ecole Normale Superieure de Lyon, 69342 Lyon, France.
In flowering plants, anther dehiscence and pollen release are essential for sexual reproduction. Anthers dehisce after cell wall degradation weakens stomium cell junctions in each anther locule, and desiccation creates mechanical forces that open the locules. Either effect or both together may break stomium cell junctions. The microRNA miR167 negatively regulates ARF6 and ARF8, which encode auxin response transcription factors. Arabidopsis mARF6 or mARF8 plants with mutated miR167 target sites have defective anther dehiscence and ovule development. Null mir167a mutations recapitulated mARF6 and mARF8 anther and ovule phenotypes, indicating that MIR167a is the main miR167 precursor gene that delimits ARF6 and ARF8 expression in these organs. Anthers of mir167a or mARF6/8 plants overexpressed genes encoding cell wall loosening functions associated with cell expansion, and grew larger than wild-type anthers did starting at flower stage 11. Experimental desiccation enabled dehiscence of miR167-deficient anthers, indicating competence to dehisce. Conversely, high humidity conditions delayed anther dehiscence in wild-type flowers. These results support a model in which miR167-mediated anther growth arrest permits anther dehiscence. Without miR167 regulation, excess anther growth delays dehiscence by prolonging desiccation.
PMID: 31262724
Ecotoxicol Environ Saf , IF:4.872 , 2019 Jul , V176 : P95-107 doi: 10.1016/j.ecoenv.2019.03.054
Nitric oxide alters nitrogen metabolism and PIN gene expressions by playing protective role in arsenic challenged Brassica juncea L.
Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 25, India.; National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 67, India.; Ecotoxicogenomics Lab, Department of Biotechnology, Jamia Millia Islamia, New Delhi, 25, India. Electronic address: meetu_gpt@yahoo.com.
Plants have ability to adapt themselves through altering their growth process. In the present study, we examined exogenous application of nitric oxide (NO) on nitrogen metabolism and auxin (PIN) gene expression, and its possible role in alleviation of arsenic (As) toxicity in Brassica juncea seedlings. Seven days old hydroponically grown B. juncea seedlings were exposed to As(III) (150muM), Sodium nitroprusside (NO donor, 100muM), As(III) + SNP and control (without metal)for 48 h. Experimental results revealed that As(III) stress: enhanced the level of nitrite, NiR activity, NO3(-) and NH4(+)content as well as NADH-GOGAT activity; but GDH level decreased; enhanced content of amino acids; upregulated gene expression level of N metabolism and downregulated polar auxin transporter genes (PIN); inhibited plant growth and morphological parameters; increased MDA, H2O2, cysteine, proline content, enzymatic antioxidants (SOD, CAT, APX; GSH, TT, NPT); and decreased nutrient content. As(III) + SNP combination reduced the accumulation of As; improved growth; chlorophyll, protein and mineral nutrient content by scavenging ROS generation; maintained amino acids content; downregulated expression of N metabolism genes and upregulated expression of auxin transporter (PIN) genes . Additional biochemical data depicts reduction in the level of nitrogen related enzymatic activities, and other stress related parameters. Overall, this study provides an integrated view that exogenous SNP (NO donor) supplementation alleviated the inhibitory role of As(III) in B. juncea seedlings by altering nutrients, amino acids and auxin redistribution via expression of nitrogen and PIN gene profiling.
PMID: 30925332
Int J Mol Sci , IF:4.556 , 2019 Jul , V20 (15) doi: 10.3390/ijms20153707
Physiological and Transcriptomic Changes during the Early Phases of Adventitious Root Formation in Mulberry Stem Hardwood Cuttings.
College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China.; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China.; College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China. 201600000016@just.edu.cn.; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China. 201600000016@just.edu.cn.; College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212003, China. 198900001874@just.edu.cn.; Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Areas, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang 212018, China. 198900001874@just.edu.cn.
The initiation and induction of root primordia are of great importance for adventitious root (AR) formation in cutting propagation of horticultural and forestry crops. However, the underlying mechanisms orchestrating these early phases of AR formation remain largely unexplored. Here, we investigated the physiological and transcriptomic changes during the early AR phases in mulberry stem hardwood cuttings. The results showed that the concentrations of soluble proteins increased, whereas concentrations of soluble sugars and starch were decreased. Indole-3-acetic acid (IAA) and zeatin had a rapid transit peak at 6 h after planting (hAP) and declined thereafter. The activities of peroxidase and catalase persistently increased and indole-3-acetic acid oxidase was maintained at a higher stable level from 0 hAP, while the activities of polyphenol oxidase fluctuated with soluble phenolics and IAA levels. The comparative transcriptome identified 4276 common genes that were differentially regulated at -6, 0 and 54 hAP. They were separated into five clusters with distinct biological functions such as defense response and photosynthesis. Considerable common genes were assigned to pathways of sugar metabolism, mitogen-activated protein kinase, and circadian rhythm. The gene co-expression network analysis revealed three major co-expressed modules involved in stress responses, hormone signaling, energy metabolism, starch metabolism, and circadian rhythm. These findings demonstrate the positive effect of auxin on AR induction, and uncovered the crucial roles of stress responses, hormone signaling and circadian rhythm in coordinating the physiological changes during the early phases of AR formation in mulberry stem hardwood cuttings.
PMID: 31362363
Int J Mol Sci , IF:4.556 , 2019 Jul , V20 (14) doi: 10.3390/ijms20143432
AtCRK5 Protein Kinase Exhibits a Regulatory Role in Hypocotyl Hook Development during Skotomorphogenesis.
Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary.; Doctoral School in Biology, Faculty of Science and Informatics, University of Szeged, 6720 Szeged, Hungary.; Agricultural Biotechnology Institute, Szent-Gyorgyi Albert u. 4, H-2100 Godollo, Hungary.; Developmental and Cell Biology of Plants, CEITEC Masaryk University, 62500 Brno, Czech Republic.; Department of Plant Biology, University of Szeged, 52. Kozep fasor, H-6726 Szeged, Hungary.; Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary. rigo.gabor@brc.mta.hu.; Department of Plant Biology, University of Szeged, 52. Kozep fasor, H-6726 Szeged, Hungary. rigo.gabor@brc.mta.hu.; Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, 6726 Szeged, Hungary. cseplo.agnes@brc.mta.hu.
Seedling establishment following germination requires the fine tuning of plant hormone levels including that of auxin. Directional movement of auxin has a central role in the associated processes, among others, in hypocotyl hook development. Regulated auxin transport is ensured by several transporters (PINs, AUX1, ABCB) and their tight cooperation. Here we describe the regulatory role of the Arabidopsis thaliana CRK5 protein kinase during hypocotyl hook formation/opening influencing auxin transport and the auxin-ethylene-GA hormonal crosstalk. It was found that the Atcrk5-1 mutant exhibits an impaired hypocotyl hook establishment phenotype resulting only in limited bending in the dark. The Atcrk5-1 mutant proved to be deficient in the maintenance of local auxin accumulation at the concave side of the hypocotyl hook as demonstrated by decreased fluorescence of the auxin sensor DR5::GFP. Abundance of the polar auxin transport (PAT) proteins PIN3, PIN7, and AUX1 were also decreased in the Atcrk5-1 hypocotyl hook. The AtCRK5 protein kinase was reported to regulate PIN2 protein activity by phosphorylation during the root gravitropic response. Here it is shown that AtCRK5 can also phosphorylate in vitro the hydrophilic loops of PIN3. We propose that AtCRK5 may regulate hypocotyl hook formation in Arabidopsis thaliana through the phosphorylation of polar auxin transport (PAT) proteins, the fine tuning of auxin transport, and consequently the coordination of auxin-ethylene-GA levels.
PMID: 31336871
Int J Mol Sci , IF:4.556 , 2019 Jul , V20 (13) doi: 10.3390/ijms20133337
Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.
Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria.; Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria. jiri.friml@ist.ac.at.
Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation.
PMID: 31284661
Int J Mol Sci , IF:4.556 , 2019 Jul , V20 (13) doi: 10.3390/ijms20133270
Comparative Analysis of the PIN Auxin Transporter Gene Family in Different Plant Species: A Focus on Structural and Expression Profiling of PINs in Solanum tuberosum.
State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China.; School of Stomatology, Wuhan University, Wuhan 430072, China. mahaoli@nwsuaf.edu.cn.; College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China. chenpeter2289@nwafu.edu.cn.
Plant growth and morphogenesis largely benefit from cell elongation and expansion and are normally regulated by environmental stimuli and endogenous hormones. Auxin, as one of the most significant plant growth regulators, controls various phases of plant growth and development. The PIN-FORMED (PIN) gene family of trans-membrane proteins considered as auxin efflux carriers plays a pivotal role in polar auxin transport and then mediates the growth of different plant tissues. In this study, the phylogenetic relationship and structural compositions of the PIN gene family in 19 plant species covering plant major lineages from algae to angiosperms were identified and analyzed by employing multiple bioinformatics methods. A total of 155 PIN genes were identified in these species and found that representative of the PIN gene family in algae came into existence and rapidly expanded in angiosperms (seed plants). The phylogenetic analysis indicated that the PIN proteins could be divided into 14 distinct clades, and the origin of PIN proteins could be traced back to the common ancestor of green algae. The structural analysis revealed that two putative types (canonical and noncanonical PINs) existed among the PIN proteins according to the length and the composition of the hydrophilic domain of the protein. The expression analysis of the PIN genes exhibited inordinate responsiveness to auxin (IAA) and ABA both in shoots and roots of Solanum tuberosum. While the majority of the StPINs were up-regulated in shoot and down-regulated in root by the two hormones. The majority of PIN genes had one or more putative auxin responses and ABA-inducible response elements in their promoter regions, respectively, implying that these phytohormones regulated the expression of StPIN genes. Our study emphasized the origin and expansion of the PIN gene family and aimed at providing useful insights for further structural and functional exploration of the PIN gene family in the future.
PMID: 31277248
Int J Mol Sci , IF:4.556 , 2019 Jul , V20 (13) doi: 10.3390/ijms20133235
Genome-Wide Analysis and Characterization of the Aux/IAA Family Genes Related to Floral Scent Formation in Hedychium coronarium.
The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.; College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.; The Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China. fanyanping@scau.edu.cn.; Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University, Guangzhou 510642, China. fanyanping@scau.edu.cn.
Auxin plays a key role in different plant growth and development processes, including flower opening and development. The perception and signaling of auxin depend on the cooperative action of various components, among which auxin/indole-3-acetic acid (Aux/IAA) proteins play an imperative role. In a recent study, the entire Aux/IAA gene family was identified and comprehensively analyzed in Hedychium coronarium, a scented species used as an ornamental plant for cut flowers. Phylogenetic analysis showed that the Aux/IAA gene family in H. coronarium is slightly contracted compared to Arabidopsis, with low levels of non-canonical proteins. Sequence analysis of promoters showed numerous cis-regulatory elements related to various phytohormones. HcIAA genes showed distinct expression patterns in different tissues and flower developmental stages, and some HcIAA genes showed significant responses to auxin and ethylene, indicating that Aux/IAAs may play an important role in linking hormone signaling pathways. Based on the expression profiles, HcIAA2, HcIAA4, HcIAA6 and HcIAA12, were selected as candidate genes and HcIAA2 and HcIAA4 were screened for further characterization. Downregulation of HcIAA2 and HcIAA4 by virus-induced gene silencing in H. coronarium flowers modified the total volatile compound content, suggesting that HcIAA2 and HcIAA4 play important roles in H. coronarium floral scent formation. The results presented here will provide insights into the putative roles of HcIAA genes and will assist the elucidation of their precise roles during floral scent formation.
PMID: 31266179
iScience , IF:4.447 , 2019 Jul , V17 : P144-154 doi: 10.1016/j.isci.2019.06.024
Strigolactones Play an Important Role in Shaping Exodermal Morphology via a KAI2-Dependent Pathway.
Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland.; Laboratoire Reproduction et Developpement des Plantes, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRA, 69342 Lyon, France.; Department of Reproduction and Plant Development, CNRS/INRA/ENS, 69634 Lyon, France.; Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland. Electronic address: enrico.martinoia@uzh.ch.; Department of Plant and Microbial Biology, University of Zurich, 8008 Zurich, Switzerland. Electronic address: lorenzo.borghi@uzh.zh.
The majority of land plants have two suberized root barriers: the endodermis and the hypodermis (exodermis). Both barriers bear non-suberized passage cells that are thought to regulate water and nutrient exchange between the root and the soil. We learned a lot about endodermal passage cells, whereas our knowledge on hypodermal passage cells (HPCs) is still very scarce. Here we report on factors regulating the HPC number in Petunia roots. Strigolactones exhibit a positive effect, whereas supply of abscisic acid (ABA), ethylene, and auxin result in a strong reduction of the HPC number. Unexpectedly the strigolactone signaling mutant d14/dad2 showed significantly higher HPC numbers than the wild-type. In contrast, its mutant counterpart max2 of the heterodimeric receptor DAD2/MAX2 displayed a significant decrease in HPC number. A mutation in the Petunia karrikin sensor KAI2 exhibits drastically decreased HPC amounts, supporting the hypothesis that the dimeric KAI2/MAX2 receptor is central in determining the HPC number.
PMID: 31276958
J Agric Food Chem , IF:4.192 , 2019 Jul , V67 (29) : P8186-8190 doi: 10.1021/acs.jafc.9b02048
De Novo Biosynthesis of Indole-3-acetic Acid in Engineered Escherichia coli.
Key Laboratory of Organo-Pharmaceutical Chemistry , Jiangxi Province Gannan Normal University , Ganzhou 341000 , China.
Indole-3-acetic acid (IAA) is considered the most common and important naturally occurring auxin in plants and a major regulator of plant growth and development. In this study, an aldehyde dehydrogenase AldH from Escherichia coli was found to convert indole-3-acetylaldehyde into IAA. Then we established an artificial pathway in engineered E. coli for microbial production of IAA from glucose. The overall pathway includes the upstream pathway from glucose to L-tryptophan and the downstream pathway from L-tryptophan to IAA. To our knowledge, this is the first report on the biosynthesis of IAA directly from a renewable carbon source. The study described here shows the way for the development of a beneficial microbe for biosynthesis of auxin and promoting plant growth in the future.
PMID: 31272146
J Agric Food Chem , IF:4.192 , 2019 Jul , V67 (26) : P7223-7231 doi: 10.1021/acs.jafc.8b05567
3-Chloro-5-trifluoromethylpyridine-2-carboxylic acid, a Metabolite of the Fungicide Fluopyram, Causes Growth Disorder in Vitis vinifera.
Laimburg Research Centre , Laimburg 6 , Pfatten (Vadena), IT-39040 Auer (Ora), South Tyrol , Italy.; South Tyrolean Extension Service for Fruit- and Winegrowing , Via Andreas Hofer 9/1 , IT-39011 Lana , South Tyrol , Italy.
The aim of this study was to investigate the effect of 3-chloro-5-trifluoromethylpyridine-2-carboxylic acid (PCA), a metabolite of the fungicide fluopyram, on grapevine. During spring and summer 2015, grapevine growth disorders were observed in several countries in Europe. An unprecedented herbicide-like damage was diagnosed on leaves and flowers, causing significant loss of harvest. This study proposes PCA as the causing agent of the observed growth disorders. PCA was shown to cause leaf epinasty, impaired berry development that leads to crop loss, and root growth anomalies in Vitis vinifera similar to auxin herbicides in a dose-dependent manner. Using both field trials and greenhouse experiments, the present study provides first evidence for a link between the application of fluopyram in vineyards 2014, the formation of PCA, and the emergence of growth anomalies in 2015. Our data could be useful to optimize dosage, application time point, and other conditions for an application of fluopyram without phytotoxic effects.
PMID: 31180671
Physiol Plant , IF:4.148 , 2019 Jul , V166 (3) : P833-847 doi: 10.1111/ppl.12858
Comprehensive transcriptome profiling and phenotyping of rootstock and scion in a tomato/potato heterografting system.
College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201, China.; Root & Tuber Crops Research Institute, Yunnan Agricultural University, Kunming, 650201, China.
Tomato/potato heterografting-triggered phenotypic variations are well documented, yet the molecular mechanisms underlying grafting-induced phenotypic processes remain unknown. To investigate the phenotypic and transcriptomic responses of grafting parents in heterografting in comparison with self-grafting, tomato (Sl) was grafted onto potato rootstocks (St), and comparative phenotyping and transcriptome profiling were performed. Phenotypic analysis showed that Sl/St heterografting induced few phenotypic changes in the tomato scion. A total of 209 upregulated genes were identified in the tomato scion, some of which appear to be involved in starch and sucrose biosynthesis. Sl/St heterografting induced several modifications in the potato rootstocks (St-R), stolon number, stolon length and tuber number decreased significantly, together with an increase in GA3 content of stolon and tuber, compared with self-grafted potato (St-WT). These results indicate that the tomato scion is less effective at producing substances or signals to induce tuberization but promotes stolon development into aerial stems and sprouting. RNA-Seq data analysis showed that 1529 genes were upregulated and 1329 downregulated between St-WT and St-R; some of these genes are involved in plant hormone signal transduction, with GID1-like gibberellin receptor (StGID1) and DELLA protein (StDELLA) being upregulated. Several genes in auxin, abscisic acid and ethylene pathways were differentially expressed as well. Various hormone signals engage in crosstalk to regulate diverse phenotypic events after grafting. This work provides abundant transcriptome profile data and lays a foundation for further research on the molecular mechanisms underlying RNA-based interactions between rootstocks and scions after tomato/potato heterografting.
PMID: 30357855
Physiol Plant , IF:4.148 , 2019 Jul , V166 (3) : P794-811 doi: 10.1111/ppl.12839
Nitrate affects transcriptional regulation of UPBEAT1 and ROS localisation in roots of Zea mays L.
Department of Agriculture, Food, Natural Resources, Animals and the Environment, University of Padua, 35020, Legnaro, Padua, Italy.
Nitrogen (N) is an indispensable nutrient for crops but its availability in agricultural soils is subject to considerable fluctuation. Plants have developed plastic responses to external N fluctuations in order to optimise their development. The coordinated action of nitric oxide and auxin seems to allow the cells of the root apex transition zone (TZ) of N-deprived maize to rapidly sense nitrate (NO3 (-) ). Preliminary results support the hypothesis that reactive oxygen species (ROS) signalling might also have a role in this pathway, probably through a putative maize orthologue of UPBEAT1 (UPB1). To expand on this hypothesis and better understand the different roles played by different root portions, we investigated the dynamics of ROS production, and the molecular and biochemical regulation of the main components of ROS production and scavenging in tissues of the meristem, transition zone, elongation zone and maturation zone of maize roots. The results suggest that the inverse regulation of ZmUPB1 and ZmPRX112 transcription observed in cells of the TZ in response to nitrogen depletion or NO3 (-) supply affects the balance between superoxide (O2 (*-) ) and hydrogen peroxide (H2 O2 ) in the root apex and consequently triggers differential root growth. This explanation is supported by additional results on the overall metabolic and transcriptional regulation of ROS homeostasis.
PMID: 30238472
Physiol Plant , IF:4.148 , 2019 Jul , V166 (3) : P812-820 doi: 10.1111/ppl.12835
2,4-D-induced parthenocarpy in pear is mediated by enhancement of GA4 biosynthesis.
College of Horticulture, Northwest A&F University, Yangling, Shaanxi, China.
Parthenocarpy, the productions of seedless fruit without pollination or fertilization, is a potentially desirable trait in many commercially grown fruits, especially in pear, which is self-incompatible. Phytohormones play important roles in fruit set, a process crucial for parthenocarpy. In this study, 2,4-dichlorophenoxyacetic acid (2,4-D), an artificially synthesized plant growth regulator with functions similar to auxin, was found to induce parthenocarpy in pear. Histological observations revealed that 2,4-D promoted cell division and expansion, which increased cortex thickness, but the effect was weakened by paclobutrazol (PAC), a gibberellin (GA) biosynthesis inhibitor. Phenotypic differences in pear may therefore be due to different GA contents. Hormone testing indicated that 2,4-D mainly induced the production of bioactive GA4 , rather than GA3. Three key oxidase genes function in the GA biosynthetic pathway: GA20ox, GA3ox and GA2ox. In a pear group treated with only 2,4-D, PbGA20ox2-like and PbGA3ox-1 were significantly upregulated. When treated with 2,4-D supplemented with PAC, however, expression levels of these genes were significantly downregulated. Additionally, PbGA2ox1-like and PbGA2ox2-like expression levels were significantly downregulated in pear treated with either 2,4-D only or 2,4-D supplemented with PAC. We thus hypothesize that 2,4-D can induce parthenocarpy by enhancing GA4 biosynthesis.
PMID: 30203555
Plant Cell Physiol , IF:4.062 , 2019 Jul , V60 (7) : P1581-1594 doi: 10.1093/pcp/pcz061
CmTCP20 Plays a Key Role in Nitrate and Auxin Signaling-Regulated Lateral Root Development in Chrysanthemum.
Department of Ornamental Horticulture, National Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, Shandong, China.; Department of Plants, College of Life Sciences, Shandong University, Qingdao, Shandong, China.
Lateral root (LR) formation and development play a vital role in plant development by permitting the establishment of branched root systems. It is well known that nutrient availability controls LR development. Moreover, LR development is fine-tuned by a myriad of hormonal signals. Many transcription factors (TFs) participate in LR development. Here, we discuss the TFs involved in the nitrate and auxin signaling pathways and how these function in the regulation of LR formation and development in chrysanthemum. AtTCP20 is a plant-specific TF, which can modulate LR development in response to nitrate. The roles of CmTCP20 in LR development were identified by overexpression in chrysanthemum and heterologous expression in Arabidopsis. Overexpression of CmTCP20 significantly increased the number and average length of LRs compared with the wild type in chrysanthemum and Arabidopsis. We also found that CmTCP20 positively influenced auxin accumulation in the LRs at least partly by improving auxin biosynthesis, transport and response, thereby promoting LR development. Moreover, we found that CmTCP20 interacts with an auxin response factor, CmARF8, which also can be induced by nitrate and combined to proximal sites in the upstream promoter region of CmCYCB1;1 to positively regulate the cell cycle. The CmTCP20-CmARF8 heterodimer links nitrate and auxin signaling and converts cell-cycle signals to regulate LR initiation and growth.
PMID: 31058993
Plant Cell Physiol , IF:4.062 , 2019 Jul , V60 (7) : P1487-1503 doi: 10.1093/pcp/pcz055
Auxin and Cell Wall Crosstalk as Revealed by the Arabidopsis thaliana Cellulose Synthase Mutant Radially Swollen 1.
Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA.; Molecular Plant Sciences Graduate Group, Washington State University, Pullman, WA, USA.
Plant cells sheath themselves in a complex lattice of polysaccharides, proteins and enzymes forming an integral matrix known as the cell wall. Cellulose microfibrils, the primary component of cell walls, are synthesized at the plasma membrane by CELLULOSE SYNTHASE A (CESA) proteins throughout cellular growth and are responsible for turgor-driven anisotropic expansion. Associations between hormone signaling and cell wall biosynthesis have long been suggested, but recently direct links have been found revealing hormones play key regulatory roles in cellulose biosynthesis. The radially swollen 1 (rsw1) allele of Arabidopsis thaliana CESA1 harbors a single amino acid change that renders the protein unstable at high temperatures. We used the conditional nature of rsw1 to investigate how auxin contributes to isotropic growth. We found that exogenous auxin treatment reduces isotropic swelling in rsw1 roots at the restrictive temperature of 30i inverted question mark(1/2)C. We also discovered decreases in auxin influx between rsw1 and wild-type roots via confocal imaging of AUX1-YFP, even at the permissive temperature of 19i inverted question mark(1/2)C. Moreover, rsw1 displayed mis-expression of auxin-responsive and CESA genes. Additionally, we found altered auxin maxima in rsw1 mutant roots at the onset of swelling using DII-VENUS and DR5:vYFP auxin reporters. Overall, we conclude disrupted cell wall biosynthesis perturbs auxin transport leading to altered auxin homeostasis impacting both anisotropic and isotropic growth that affects overall root morphology.
PMID: 31004494
Sci Rep , IF:3.998 , 2019 Jul , V9 (1) : P10177 doi: 10.1038/s41598-019-46684-w
Transcriptome analysis of rice (Oryza sativa L.) shoots responsive to cadmium stress.
Institute of ECO-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.; Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai, 201403, China.; Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai, 201403, China.; Shanghai Engineering Research Centre of Low-carbon Agriculture (SERLA), Shanghai, 201403, China.; Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, 201403, China.; College of Resources and Environmental Sciences, Nanjing Agricultural University, No. 1, Weigang, Xuanwu District, Nanjing, 210095, China.; Institute of ECO-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China. qinqin19870987@126.com.; Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai, 201403, China. qinqin19870987@126.com.; Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai, 201403, China. qinqin19870987@126.com.; Shanghai Engineering Research Centre of Low-carbon Agriculture (SERLA), Shanghai, 201403, China. qinqin19870987@126.com.; Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, 201403, China. qinqin19870987@126.com.; Institute of ECO-Environment and Plant Protection, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China. exueyong@163.com.; Shanghai Scientific Observation and Experimental Station for Agricultural Environment and Land Conservation, Shanghai, 201403, China. exueyong@163.com.; Shanghai Environmental Protection Monitoring Station of Agriculture, Shanghai, 201403, China. exueyong@163.com.; Shanghai Engineering Research Centre of Low-carbon Agriculture (SERLA), Shanghai, 201403, China. exueyong@163.com.; Shanghai Key Laboratory of Protected Horticultural Technology, Shanghai, 201403, China. exueyong@163.com.
Cadmium (Cd) is highly toxic to living organisms. This study aimed to elucidate the regulation of gene expression in rice shoots under Cd stress. Rice plants were exposed to 0, 50, 75, 100 mumol/L CdCl2 in hydroponic culture for 7 d. Transcriptional changes in rice shoots were examined by transcriptome sequencing techniques. A total of 2197 DEGs (987 up-regulated and 1210 down-regulated) were detected in rice shoots under the exposure of 75 mumol/L CdCl2. GO and KEGG enrichment analyses showed that genes encoding auxin-responsive protein IAA and peroxidase were up-regulated, while genes encoding proteins involved in signal transduction, including TIFY family, ERF and bZIP were down-regulated. Abundant ROS related terms were also identified and grouped into significantly differentially expressed GO terms, including oxidoreductase activity, catalytic activity, oxidation-reduction process, confirming the enhanced oxidative stress of Cd. Genes encoding photosystem I reaction center subunit and photosynthetic NDH subunit of luminal location were up-regulated in pathway of energy metabolism, suggesting an interference of photosynthesis by Cd stress. Our results improve the understanding of the complex molecular responsive mechanisms of rice shoots under Cd stress.
PMID: 31308454
Sci Rep , IF:3.998 , 2019 Jul , V9 (1) : P9846 doi: 10.1038/s41598-019-46327-0
Phosphorylation of p23-1 cochaperone by protein kinase CK2 affects root development in Arabidopsis.
Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131, Padova, Italy.; Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, I-35131, Padova, Italy.; Department of Biology, University of Padova, Via U. Bassi 58/B, I-35131, Padova, Italy. michela.zottini@unipd.it.; Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/B, I-35131, Padova, Italy. maria.ruzzene@unipd.it.
Root growth is a fundamental process in plants and assures nutrient and water uptake required for efficient photosynthesis and metabolism. Postembryonic development of roots is controlled by the functionality of the meristem. Several hormones and signaling molecules regulate the size of the meristem, and among them, auxins play a major role. Protein kinase CK2, along with the chaperone protein HSP90, has been found to be involved in the regulation of auxin transport. Here, we show that p23-1, a cochaperone of HSP90, is phosphorylated by CK2 in Arabidopsis. We identified Ser201 as the major CK2 target site in p23-1 and demonstrated that phosphorylation of this site is necessary for normal root development. Moreover, we shed light on the nature of CK2 in Arabidopsis, showing that the three catalytic isoforms, CK2 alphaA, alphaB and alphaC, are proteins of approximately 40 kDa. Our results increase knowledge of the connection among HSP90, p23-1 and CK2 in Arabidopsis, suggesting the existence of a possible common root development mechanism controlled by these signaling molecules.
PMID: 31285503
Rice (N Y) , IF:3.912 , 2019 Jul , V12 (1) : P53 doi: 10.1186/s12284-019-0313-y
The heterotrimeric G protein beta subunit RGB1 is required for seedling formation in rice.
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, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College, Yangzhou University, Yangzhou, 225009, China.; 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, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College, Yangzhou University, Yangzhou, 225009, China. ricegb@yzu.edu.cn.
BACKGROUND: The heterotrimeric G protein beta subunit RGB1 plays an important role in plant growth and development. However, the molecular mechanisms underlying the regulation of rice growth by RGB1 remain elusive. RESULTS: Here, the rgb1 mutants rgb1-1 (+ 1 bp), rgb1-2 (- 1 bp), and rgb1-3 (- 11 bp) were isolated using the CRISPR/Cas9 system, and they were arrested at 1 day after germination and ultimately exhibited seedling lethality. The dynamic anatomical characteristics of the embryos of the rgb1 seedlings and WT during early postgermination and according to TUNEL assays showed that the suppressed growth of the rgb1 mutants was caused by cell death. In addition to the limited shoot and root development, the development of the embryo shoot-root axis was suppressed in the rgb1 mutants. RGB1 was expressed mainly in the root epidermal and vascular tissues of the embryo. Moreover, transcript profiling analysis revealed that the expression of a large number of auxin-, cytokinin-, and brassinosteroid-inducible genes was upregulated or downregulated in the rgb1 mutant compared to the wild type during seedling development. CONCLUSIONS: Overall, the rgb1 mutants provide an ideal material for exploring the molecular mechanism underlying rice seedling formation during early postgermination development by G proteins. SIGNIFICANCE STATEMENT: The heterotrimeric G protein beta subunit RGB1 acts as a crucial factor in promoting early postgermination seedling development in rice.
PMID: 31321558
Methods , IF:3.812 , 2019 Jul , V164-165 : P73-80 doi: 10.1016/j.ymeth.2019.04.010
Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole.
Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan.; Department of Biochemistry, Okayama University of Science, Okayama 700-0005, Japan.; Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka 411-8540, Japan; Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka 411-8540, Japan. Electronic address: mkanemak@nig.ac.jp.
Controlling protein expression using a degron is advantageous because the protein of interest can be rapidly depleted in a reversible manner. We pioneered the development of the auxin-inducible degron (AID) technology by transplanting a plant-specific degradation pathway to non-plant cells. In human cells expressing an E3 ligase component, OsTIR1, it is possible to degrade a degron-fused protein with a half-life of 15-45min in the presence of the phytohormone auxin. We reported previously the generation of human HCT116 mutants in which the C terminus of endogenous proteins was fused with the degron by CRISPR-Cas9-based knock-in. Here, we show new plasmids for N-terminal tagging and describe a detailed protocol for the generation of AID mutants of human HCT116 and DLD1 cells. Moreover, we report the use of an OsTIR1 inhibitor, auxinole, to suppress leaky degradation of degron-fused proteins. The addition of auxinole is also useful for rapid re-expression after depletion of degron-fused proteins. These improvements enhance the utility of AID technology for studying protein function in living human cells.
PMID: 31026591
Genes (Basel) , IF:3.759 , 2019 Jul , V10 (7) doi: 10.3390/genes10070555
Identification and Expression of SAUR Genes in the CAM Plant Agave.
School of Agriculture, Yunnan University, Kunming 650504, China.; Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China. hxalong@gmail.com.; College of Forestry, Hainan University, Haikou 570228, China.; Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China.; College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA.; Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China. yikexian@126.com.
Agave species are important crassulacean acid metabolism (CAM) plants and widely cultivated in tropical areas for producing tequila spirit and fiber. The hybrid H11648 of Agave ((A. amaniensis x A. angustifolia) x A. amaniensis) is the main cultivar for fiber production in Brazil, China, and African countries. Small Auxin Up-regulated RNA (SAUR) genes have broad effect on auxin signaling-regulated plant growth and development, while only few SAUR genes have been reported in Agave species. In this study, we identified 43, 60, 24, and 21 SAUR genes with full-length coding regions in A. deserti, A. tequilana, A. H11648, and A. americana, respectively. Although phylogenetic analysis revealed that rice contained a species-specific expansion pattern of SAUR gene, no similar phenomena were observed in Agave species. The in silico expression indicated that SAUR genes had a distinct expression pattern in A. H11648 compared with other Agave species; and four SAUR genes were differentially expressed during CAM diel cycle in A. americana. Additionally, an expression analysis was conducted to estimate SAUR gene expression during different leaf developmental stages, abiotic and biotic stresses in A. H11648. Together, we first characterized the SAUR genes of Agave based on previously published transcriptome datasets and emphasized the potential functions of SAUR genes in Agave's leaf development and stress responses. The identification of which further expands our understanding on auxin signaling-regulated plant growth and development in Agave species.
PMID: 31340544
Plant Physiol Biochem , IF:3.72 , 2019 Jul , V140 : P18-26 doi: 10.1016/j.plaphy.2019.05.004
Arabidopsis mutant dnd2 exhibits increased auxin and abscisic acid content and reduced stomatal conductance.
Faculty of Biology, University of Latvia, 1 Jelgavas Street, Riga, LV-1004, Latvia.; Faculty of Chemistry, University of Latvia, 1 Jelgavas Street, Riga, LV-1004, Latvia.; Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia.; Institute of Technology, University of Tartu, Nooruse 1, Tartu, 50411, Estonia; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.; Faculty of Biology, University of Latvia, 1 Jelgavas Street, Riga, LV-1004, Latvia. Electronic address: nils.rostoks@lu.lv.
Arabidopsis thaliana cyclic nucleotide-gated ion channel gene 4 (AtCNGC4) loss-of-function mutant dnd2 exhibits elevated accumulation of salicylic acid (SA), dwarfed morphology, reduced hypersensitive response (HR), altered disease resistance and spontaneous lesions on plant leaves. An orthologous barley mutant, nec1, has been reported to over-accumulate indole-3-acetic acid (IAA) and to exhibit changes in stomatal regulation in response to exogenous auxin. Here we show that the Arabidopsis dnd2 over-accumulates both IAA and abscisic acid (ABA) and displays related phenotypic and physiological changes, such as, reduced stomatal size, higher stomatal density and stomatal index. dnd2 showed increased salt tolerance in root growth assay and significantly reduced stomatal conductance, while maintaining near wt reaction in stomatal conductance upon external application of ABA, and probably consequently increased drought stress tolerance. Introduction of both sid2-1 and fmo1 into dnd2 background resulting in removal of SA did not alter stomatal conductance. Hence, the closed stomata of dnd2 is probably a result of increased ABA levels and not increased SA levels. The triple dnd2sid2abi1-1 mutant exhibited intermediate stomatal conductance compared to dnd2 and abi1-1 (ABA insensitive, open stomata), while the response to external ABA was as in abi1-1 suggesting that reduced stomatal conductance in dnd2 is not due to impaired ABA signaling. In conclusion, Arabidopsis dnd2 mutant exhibited ABA overaccumulation and stomatal phenotypes, which may contribute to the observed improvement in drought stress resistance. Thus, Arabidopsis dnd2 mutant may serve as a model for studying crosstalk between biotic and abiotic stress and hormonal response in plants.
PMID: 31078052
Mol Plant Microbe Interact , IF:3.696 , 2019 Jul , V32 (7) : P813-827 doi: 10.1094/MPMI-10-18-0268-R
Deep Sequencing Reveals Early Reprogramming of Arabidopsis Root Transcriptomes Upon Ralstonia solanacearum Infection.
1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.; 2 National Wolfberry Engineering Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia 750002, China.; 3 Genetics section, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain.; 4 Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, 08193 Barcelona, Catalonia, Spain.
Bacterial wilt caused by the bacterial pathogen Ralstonia solanacearum is one of the most devastating crop diseases worldwide. The molecular mechanisms controlling the early stage of R. solanacearum colonization in the root remain unknown. Aiming to better understand the mechanism of the establishment of R. solanacearum infection in root, we established four stages in the early interaction of the pathogen with Arabidopsis roots and determined the transcriptional profiles of these stages of infection. A total 2,698 genes were identified as differentially expressed genes during the initial 96 h after infection, with the majority of changes in gene expression occurring after pathogen-triggered root-hair development observed. Further analysis of differentially expressed genes indicated sequential activation of multiple hormone signaling cascades, including abscisic acid (ABA), auxin, jasmonic acid, and ethylene. Simultaneous impairment of ABA receptor genes promoted plant wilting symptoms after R. solanacearum infection but did not affect primary root growth inhibition or root-hair and lateral root formation caused by R. solanacearum. This indicated that ABA signaling positively regulates root defense to R. solanacearum. Moreover, transcriptional changes of genes involved in primary root, lateral root, and root-hair formation exhibited high temporal dynamics upon infection. Taken together, our results suggest that successful infection of R. solanacearum on roots is a highly programmed process involving in hormone crosstalk.
PMID: 31140930
BMC Genomics , IF:3.594 , 2019 Jul , V20 (1) : P610 doi: 10.1186/s12864-019-5947-z
Small RNA discovery in the interaction between barley and the powdery mildew pathogen.
Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA.; Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA.; Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA.; Department of Statistics, Iowa State University, Ames, Iowa, 50011, USA.; Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA.; Donald Danforth Plant Science Center, St. Louis, MO, 63132, USA.; Division of Plant Sciences, University of Missouri - Columbia, 52 Agriculture Lab, Columbia, MO, 65211, USA.; Interdepartmental Genetics & Genomics, Iowa State University, Ames, Iowa, 50011, USA. roger.wise@ars.usda.gov.; Department of Plant Pathology & Microbiology, Iowa State University, Ames, Iowa, 50011, USA. roger.wise@ars.usda.gov.; Interdepartmental Bioinformatics & Computational Biology, Iowa State University, Ames, Iowa, 50011, USA. roger.wise@ars.usda.gov.; Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service, Iowa State University, Ames, Iowa, 50011, USA. roger.wise@ars.usda.gov.
BACKGROUND: Plants encounter pathogenic and non-pathogenic microorganisms on a nearly constant basis. Small RNAs such as siRNAs and miRNAs/milRNAs influence pathogen virulence and host defense responses. We exploited the biotrophic interaction between the powdery mildew fungus, Blumeria graminis f. sp. hordei (Bgh), and its diploid host plant, barley (Hordeum vulgare) to explore fungal and plant sRNAs expressed during Bgh infection of barley leaf epidermal cells. RESULTS: RNA was isolated from four fast-neutron immune-signaling mutants and their progenitor over a time course representing key stages of Bgh infection, including appressorium formation, penetration of epidermal cells, and development of haustorial feeding structures. The Cereal Introduction (CI) 16151 progenitor carries the resistance allele Mla6, while Bgh isolate 5874 harbors the AVRa6 avirulence effector, resulting in an incompatible interaction. Parallel Analysis of RNA Ends (PARE) was used to verify sRNAs with likely transcript targets in both barley and Bgh. Bgh sRNAs are predicted to regulate effectors, metabolic genes, and translation-related genes. Barley sRNAs are predicted to influence the accumulation of transcripts that encode auxin response factors, NAC transcription factors, homeodomain transcription factors, and several splicing factors. We also identified phasing small interfering RNAs (phasiRNAs) in barley that overlap transcripts that encode receptor-like kinases (RLKs) and nucleotide-binding, leucine-rich domain proteins (NLRs). CONCLUSIONS: These data suggest that Bgh sRNAs regulate gene expression in metabolism, translation-related, and pathogen effectors. PARE-validated targets of predicted Bgh milRNAs include both EKA (effectors homologous to AVRk1 and AVRa10) and CSEP (candidate secreted effector protein) families. We also identified barley phasiRNAs and miRNAs in response to Bgh infection. These include phasiRNA loci that overlap with a significant proportion of receptor-like kinases, suggesting an additional sRNA control mechanism may be active in barley leaves as opposed to predominant R-gene phasiRNA overlap in many eudicots. In addition, we identified conserved miRNAs, novel miRNA candidates, and barley genome mapped sRNAs that have PARE validated transcript targets in barley. The miRNA target transcripts are enriched in transcription factors, signaling-related proteins, and photosynthesis-related proteins. Together these results suggest both barley and Bgh control metabolism and infection-related responses via the specific accumulation and targeting of genes via sRNAs.
PMID: 31345162
BMC Genomics , IF:3.594 , 2019 Jul , V20 (1) : P596 doi: 10.1186/s12864-019-5933-5
Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana.
School of Biological Sciences, National Institute of Science Education and Research (NISER), Homi Bhabha National Institute (HBNI), P.O. Bhimpur- Padanpur, Via Jatni, Dist. Khurda, Odisha, 752050, India.; National Institute of Plant Genome Research (NIPGR), Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi, Delhi, 110067, India.; School of Biological Sciences, National Institute of Science Education and Research (NISER), Homi Bhabha National Institute (HBNI), P.O. Bhimpur- Padanpur, Via Jatni, Dist. Khurda, Odisha, 752050, India. panigrahi@niser.ac.in.
BACKGROUND: Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. Photoreceptors are differentially expressed in both shoot and root cells. The light irradiation to the root affects shoot morphology as well as whole plant development. The current work aims to understand the white light intensity dependent changes in root patterning and correlate that with the global gene expression profile. RESULTS: Different fluence of white light (WL) regulate overall root development via modulating the expression of a specific set of genes. Phytochrome A deficient Arabidopsis thaliana (phyA-211) showed shorter primary root compared to phytochrome B deficient (phyB-9) and wild type (WT) seedlings at a lower light intensity. However, at higher intensity, both mutants showed shorter primary root in comparison to WT. The lateral root number was observed to be lowest in phyA-211 at intensities of 38 and 75 mumol m (- )(2) s (- )(1). The number of adventitious roots was significantly lower in phyA-211 as compared to WT and phyB-9 under all light intensities tested. With the root phenotypic data, microarray was performed for four different intensities of WL light in WT. Here, we identified ~ 5243 differentially expressed genes (DEGs) under all light intensities. Gene ontology-based analysis indicated that different intensities of WL predominantly affect a subset of genes having catalytic activity and localized to the cytoplasm and membrane. Furthermore, when root is irradiated with different intensities of WL, several key genes involved in hormone, light signaling and clock-regulated pathways are differentially expressed. CONCLUSION: Using genome wide microarray-based approach, we have identified candidate genes in Arabidopsis root that responded to the changes in light intensities. Alteration in expression of genes such as PIF4, COL9, EPR1, CIP1, ARF18, ARR6, SAUR9, TOC1 etc. which are involved in light, hormone and clock pathway was validated by qRT-PCR. This indicates their potential role in light intensity mediated root development.
PMID: 31325959
BMC Genomics , IF:3.594 , 2019 Jul , V20 (1) : P591 doi: 10.1186/s12864-019-5952-2
geneHummus: an R package to define gene families and their expression in legumes and beyond.
Department of Genetics ETSIAM, University of Cordoba, Cordoba, Spain.; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA.; Department of Biological Sciences, Texas Tech University, TX, Lubbock, 79409, USA.; National Institute on Drug Abuse, National Institutes of Health, 6001 Executive Blvd, Bethesda, MD, 20892, USA.; Department of Computer Science, University of Ibadan, Ibadan, Nigeria.; National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD, 20894, USA. Ben.Busby@nih.gov.
BACKGROUND: During the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called 'orphan crops') is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. The analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed and many gene families remain to be investigated. Manual identification of gene families is highly time-consuming and laborious, requiring an iterative process of manual and computational analysis to identify members of a given family, typically combining numerous BLAST searches and manually cleaning data. Due to the increasing abundance of genome sequences and the agronomical interest in plant gene families, the field needs a clear, automated annotation tool. RESULTS: Here, we present the geneHummus package, an R-based pipeline for the identification and characterization of plant gene families. The impact of this pipeline comes from a reduction in hands-on annotation time combined with high specificity and sensitivity in extracting only proteins from the RefSeq database and providing the conserved domain architectures based on SPARCLE. As a case study we focused on the auxin receptor factors gene (ARF) family in Cicer arietinum (chickpea) and other legumes. CONCLUSION: We anticipate that our pipeline should be suitable for any taxonomic plant family, and likely other gene families, vastly improving the speed and ease of genomic data processing.
PMID: 31319791
BMC Genomics , IF:3.594 , 2019 Jul , V20 (1) : P542 doi: 10.1186/s12864-019-5842-7
Transcriptional reprogramming caused by the geminivirus Tomato yellow leaf curl virus in local or systemic infections in Nicotiana benthamiana.
Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.; University of the Chinese Academy of Sciences, Beijing, 100049, China.; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China. xfu@sibcb.ac.cn.; Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China. lozano-duran@sibs.ac.cn.
BACKGROUND: Viruses have evolved to create a cellular environment permissive for viral replication in susceptible hosts. Possibly both enabling and resulting from these virus-triggered changes, infected hosts undergo a dramatic transcriptional reprogramming, the analysis of which can shed light on the molecular processes underlying the outcome of virus-host interactions. The study of the transcriptional changes triggered by the plant DNA viruses geminiviruses is potentially hampered by the low representation of infected cells in the total population, a situation that becomes extreme in those cases, like that of Tomato yellow leaf curl virus (TYLCV), in which the virus is restricted to phloem companion cells. RESULTS: In order to gain insight into how different the transcriptional landscapes of TYLCV-infected cells or whole tissues of TYLCV-infected plants might be, here we compare the transcriptional changes in leaf patches infected with TYLCV by agroinfiltration or in systemic leaves of TYLCV-infected plants in Nicotiana benthamiana. Our results show that, in agreement with previous works, infection by TYLCV induces a dramatic transcriptional reprogramming; the detected changes, however, are not equivalent in local and systemic infections, with a much larger number of genes differentially expressed locally, and some genes responding in an opposite manner. Interestingly, a transcriptional repression of the auxin signalling pathway and a transcriptional activation of the ethylene signalling pathway were detected in both local and systemically infected samples. A transcriptional activation of defence was also detectable in both cases. Comparison with the transcriptional changes induced by systemic infection by the geminivirus Tobacco curly shoot virus (TbSV) shows common subsets of up- and down-regulated genes similarly affected by both viral species, unveiling a common transcriptional repression of terpenoid biosynthesis, a process also suppressed by the geminivirus Tomato yellow leaf curl China virus. CONCLUSIONS: Taken together, the results presented here not only offer insight into the transcriptional changes derived from the infection by TYLCV in N. benthamiana, but also demonstrate that the resolution provided by local and systemic infection approaches largely differs, highlighting the urge to come up with a better system to gain an accurate view of the molecular and physiological changes caused by the viral invasion.
PMID: 31272383
Plant Sci , IF:3.591 , 2019 Jul , V284 : P135-142 doi: 10.1016/j.plantsci.2019.04.010
Review: Phytostimulation and root architectural responses to quorum-sensing signals and related molecules from rhizobacteria.
Red de Estudios Moleculares Avanzados, Instituto de Ecologia A. C., Carretera Antigua a Coatepec 351, El Haya, C. P. 91070 Xalapa, Veracruz, Mexico.; Instituto de Investigaciones Quimico-Biologicas, Universidad Michoacana de San Nicolas de Hidalgo, Edificio B3, Ciudad Universitaria, C. P. 58030, Morelia, Michoacan, Mexico. Electronic address: jbucio@umich.mx.
Bacteria rely on chemical communication to sense the environment and to retrieve information on their population densities. Accordingly, a vast repertoire of molecules is released, which synchronizes expression of genes, coordinates behavior through a process termed quorum-sensing (QS), and determines the relationships with eukaryotic species. Already identified QS molecules from Gram negative bacteria can be grouped into two main classes, N-acyl-L-homoserine lactones (AHLs) and cyclodipeptides (CDPs), with roles in biofilm formation, bacterial virulence or symbiotic interactions. Noteworthy, plants detect each of these molecules, change their own gene expression programs, re-configurate root architecture, and activate defense responses, improving in this manner their adaptation to natural and agricultural ecosystems. AHLs may act as alarm signals, pathogen and/or microbe-associated molecular patterns, whereas CDPs function as hormonal mimics for plants via their putative interactions with the auxin receptor Transport Inhibitor Response1 (TIR1). A major challenge is to identify the molecular pathways of QS-mediated crosstalk and the plant receptors and interacting proteins for AHLs, CDPs and related signals.
PMID: 31084866
BMC Plant Biol , IF:3.497 , 2019 Jul , V19 (1) : P329 doi: 10.1186/s12870-019-1932-6
Comprehensive analyses of ZFP gene family and characterization of expression profiles during plant hormone response in cotton.
College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.; Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.; Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.; State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.; Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.; College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China. guanghuix@snnu.edu.cn.; Key Laboratory of the Ministry of Education for Medicinal Plant Resources and Natural Pharmaceutical Chemistry, National Engineering Laboratory for Resource Development of Endangered Crude Drugs in the Northwest of China, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China. guanghuix@snnu.edu.cn.
BACKGROUND: Zinc finger proteins (ZFPs) containing only a single zinc finger domain play important roles in the regulation of plant growth and development, as well as in biotic and abiotic stress responses. To date, the evolutionary history and functions of the ZFP gene family have not been identified in cotton. RESULTS: In this paper, we identified 29 ZFP genes in Gossypium hirsutum. This gene family was divided into seven subfamilies, 22 of which were distributed over 17 chromosomes. Bioinformatic analysis revealed that 20 GhZFP genes originated from whole genome duplications and two originated from dispersed duplication events, indicating that whole genome duplication is the main force in the expansion of the GhZFP gene family. Most GhZFP8 subfamily genes, except for GhZFP8-3, were highly expressed during fiber cell growth, and were induced by brassinosteroids in vitro. Furthermore, we found that a large number of GhZFP genes contained gibberellic acid responsive elements, auxin responsive elements, and E-box elements in their promoter regions. Exogenous application of these hormones significantly stimulated the expression of these genes. CONCLUSIONS: Our findings reveal that GhZFP8 genes are involved in cotton fiber development and widely induced by auxin, gibberellin and BR, which provides a foundation for the identification of more downstream genes with potential roles in phytohormone stimuli, and a basis for breeding better cotton varieties in the future.
PMID: 31337346
BMC Plant Biol , IF:3.497 , 2019 Jul , V19 (1) : P324 doi: 10.1186/s12870-019-1938-0
Fine mapping of an up-curling leaf locus (BnUC1) in Brassica napus.
National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China.; National Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China. guanrzh@njau.edu.cn.
BACKGROUND: Leaf shape development research is important because leaf shapes such as moderate curling can help to improve light energy utilization efficiency. Leaf growth and development includes initiation of the leaf primordia and polar differentiation of the proximal-distal, adaxial-abaxial, and centrolateral axes. Changes in leaf adaxial-abaxial polarity formation, auxin synthesis and signaling pathways, and development of sclerenchyma and cuticle can cause abnormal leaf shapes such as up-curling leaf. Although many genes related to leaf shape development have been reported, the detailed mechanism of leaf development is still unclear. Here, we report an up-curling leaf mutant plant from our Brassica napus germplasm. We studied its inheritance, mapped the up-curling leaf locus BnUC1, built near-isogenic lines for the Bnuc1 mutant, and evaluated the effect of the dominant leaf curl locus on leaf photosynthetic efficiency and agronomic traits. RESULTS: The up-curling trait was controlled by one dominant locus in a progeny population derived from NJAU5734 and Zhongshuang 11 (ZS11). This BnUC1 locus was mapped in an interval of 2732.549 kb on the A05 chromosome of B. napus using Illumina Brassica 60 K Bead Chip Array. To fine map BnUC1, we designed 201 simple sequence repeat (SSR) primers covering the mapping interval. Among them, 16 polymorphic primers that narrowed the mapping interval to 54.8 kb were detected using a BC6F2 family population with 654 individuals. We found six annotated genes in the mapping interval using the B. napus reference genome, including BnaA05g18250D and BnaA05g18290D, which bioinformatics and gene expression analyses predicted may be responsible for leaf up-curling. The up-curling leaf trait had negative effects on the agronomic traits of 30 randomly selected individuals from the BC6F2 population. The near-isogenic line of the up-curling leaf (ZS11-UC1) was constructed to evaluate the effect of BnUC1 on photosynthetic efficiency. The results indicated that the up-curling leaf trait locus was beneficial to improve the photosynthetic efficiency. CONCLUSIONS: An up-curling leaf mutant Bnuc1 was controlled by one dominant locus BnUC1. This locus had positive effects on photosynthetic efficiency, negative effects on some agronomic traits, and may help to increase planting density in B. napus.
PMID: 31324149
BMC Plant Biol , IF:3.497 , 2019 Jul , V19 (1) : P306 doi: 10.1186/s12870-019-1914-8
Transcriptome analysis reveals candidate genes related to phosphorus starvation tolerance in sorghum.
College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.; College of Agriculture, Anhui Science and Technology University, Fengyang, China.; College of Agro-grassland Science, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China. yingjunchi@njau.edu.cn.
BACKGROUND: Phosphorus (P) deficiency in soil is a worldwide issue and a major constraint on the production of sorghum, which is an important staple food, forage and energy crop. The depletion of P reserves and the increasing price of P fertilizer make fertilizer application impractical, especially in developing countries. Therefore, identifying sorghum accessions with low-P tolerance and understanding the underlying molecular basis for this tolerance will facilitate the breeding of P-efficient plants, thereby resolving the P crisis in sorghum farming. However, knowledge in these areas is very limited. RESULTS: The 29 sorghum accessions used in this study demonstrated great variability in their tolerance to low-P stress. The internal P content in the shoot was correlated with P tolerance. A low-P-tolerant accession and a low-P-sensitive accession were chosen for RNA-seq analysis to identify potential underlying molecular mechanisms. A total of 2089 candidate genes related to P starvation tolerance were revealed and found to be enriched in 11 pathways. Gene Ontology (GO) enrichment analyses showed that the candidate genes were associated with oxidoreductase activity. In addition, further study showed that malate affected the length of the primary root and the number of tips in sorghum suffering from low-P stress. CONCLUSIONS: Our results show that acquisition of P from soil contributes to low-P tolerance in different sorghum accessions; however, the underlying molecular mechanism is complicated. Plant hormone (including auxin, ethylene, jasmonic acid, salicylic acid and abscisic acid) signal transduction related genes and many transcriptional factors were found to be involved in low-P tolerance in sorghum. The identified accessions will be useful for breeding new sorghum varieties with enhanced P starvation tolerance.
PMID: 31296169
BMC Plant Biol , IF:3.497 , 2019 Jul , V19 (1) : P289 doi: 10.1186/s12870-019-1855-2
Comparative transcriptomic and metabolic analysis reveals the effect of melatonin on delaying anthracnose incidence upon postharvest banana fruit peel.
Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China.; Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, China. huijun_gao@aliyun.com.; Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China. yunze@scbg.ac.cn.
BACKGROUND: Banana anthracnose, caused by Colletotrichum musae, is one of the most severe postharvest diseases in banana. Melatonin is widely known for its role in enhancing plant stress tolerance. However, little is known about the control of melatonin on anthracnose in postharvest banana fruit. RESULTS: In this study, exogenous melatonin treatment could significantly reduce the incidence of anthracnose in ripe yellow banana fruit and delay fruit senescence. However, melatonin treatment did not affect the growth of Colletotrichum musae in vitro. Transcriptomic analysis of banana peel showed that 339 genes were up-regulated and 241 were down-regulated in the peel after melatonin treatment, compared with the control. Based on GO terms and KEGG pathway, these up-regulated genes were mainly categorized into signal transduction, cell wall formation, secondary metabolism, volatile compounds synthesis and response to stress, which might be related to the anti-anthracnose of banana fruit induced by melatonin treatment. This view was also supported by the increase of volatile compounds, cell wall components and IAA content in the melatonin-treated fruit peel via the metabolomic analysis. After melatonin treatment, auxin, ethylene and mitogen-activated protein kinase (MAPK) signaling pathways were enhanced, which might be involved in the enhanced fruit resistance by regulating physiological characteristics, disease-resistant proteins and metabolites. CONCLUSIONS: Our results provide a better understanding of the molecular processes in melatonin treatment delaying banana fruit senescence and anthracnose incidence.
PMID: 31262259
Planta , IF:3.39 , 2019 Jul , V250 (1) : P333-345 doi: 10.1007/s00425-019-03175-6
Selenium downregulates auxin and ethylene biosynthesis in rice seedlings to modify primary metabolism and root architecture.
Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, Minas Gerais, 36570-900, Brazil.; Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, Minas Gerais, 36570-900, Brazil.; Departamento de Biologia Vegetal, Universidade Federal de Vicosa, Vicosa, Minas Gerais, 36570-900, Brazil. dimas.ribeiro@ufv.br.
MAIN CONCLUSION: Selenium modulates the formation of primary and lateral roots through alterations in auxin and ethylene, leading to new patterns of root architecture in rice seedlings. Selenium (Se) at low concentrations can control root growth through interaction with hormone biosynthesis. Auxin and ethylene have been shown to control the root architecture, with most of the information obtained from the eudicots such Arabidopsis and Nicotiana tabacum. Here, we presented the effects of Se on auxin and ethylene pathways and examined their impact on primary metabolism and root system architecture in rice (Oryza sativa L.) seedlings. Se treatment increased elongation of primary root, but decreased the number and length of lateral roots. Se led to decreased expression of genes associated with the biosynthesis of auxin and ethylene, concomitantly with reduced production of these hormones by the roots. Moreover, Se decreased the abundance of transcripts encoding auxin transport proteins. Indole-3-acetic acid (IAA) treatment overrode the repressive effect of Se on lateral root growth. The ethylene synthesis inhibitor L-alpha-(2-aminoethoxyvinyl)-glycine (AVG) increased elongation of primary root, whereas the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) resulted in the opposite effect. Soluble sugars accumulate in roots of rice seedlings under Se treatment. Thus, Se modulates the formation of primary and lateral roots through alterations in auxin and ethylene, leading to new patterns of root architecture in rice seedlings.
PMID: 31030327
Planta , IF:3.39 , 2019 Jul , V250 (1) : P199-217 doi: 10.1007/s00425-019-03163-w
Comparative proteomics illustrates the complexity of Fe, Mn and Zn deficiency-responsive mechanisms of potato (Solanum tuberosum L.) plants in vitro.
College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China.; College of Horticulture, Gansu Agricultural University, Lanzhou, China.; College of Agronomy, Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, 730070, China. zhangf@gsau.edu.cn.
MAIN CONCLUSION: The present study is the first to integrate physiological and proteomic data providing information on Fe, Mn and Zn deficiency-responsive mechanisms of potato plants in vitro. Micronutrient deficiency is an important limiting factor for potato production that causes substantial tuber yield and quality losses. To under the underlying molecular mechanisms of potato in response to Fe, Mn and Zn deficiency, a comparative proteomic approach was applied. Leaf proteome change of in vitro-propagated potato plantlets subjected to a range of Fe-deficiency treatments (20, 10 and 0 muM Na-Fe-EDTA), Mn-deficiency treatments (1 and 0 muM MnCl2.4H2O) and Zn-deficiency treatment (0 muM ZnCl2) using two-dimensional gel electrophoresis was analyzed. Quantitative image analysis showed a total of 146, 55 and 42 protein spots under Fe, Mn and Zn deficiency with their abundance significantly altered (P < 0.05) more than twofold, respectively. By MALDI-TOF/TOF MS analyses, the differentially abundant proteins were found mainly involved in bioenergy and metabolism, photosynthesis, defence, redox homeostasis and protein biosynthesis/degradation under the metal deficiencies. Signaling, transport, cellular structure and transcription-related proteins were also identified. The hierarchical clustering results revealed that these proteins were involved in a dynamic network in response to Fe, Mn and Zn deficiency. All these metal deficiencies caused cellular metabolic remodeling to improve metal acquisition and distribution in potato plants. The reduced photosynthetic efficiency occurred under each metal deficiency, yet Fe-deficient plants showed a more severe damage of photosynthesis. More defence mechanisms were induced by Fe deficiency than Mn and Zn deficiency, and the antioxidant systems showed different responses to each metal deficiency. Reprogramming of protein biosynthesis/degradation and assembly was more strongly required for acclimation to Fe deficiency. The signaling cascades involving auxin and NDPKs might also play roles in micronutrient stress signaling and pinpoint interesting candidates for future studies. Our results first provide an insight into the complex functional and regulatory networks in potato plants under Fe, Mn and Zn deficiency.
PMID: 30976909
Planta , IF:3.39 , 2019 Jul , V250 (1) : P145-162 doi: 10.1007/s00425-019-03155-w
Transcriptome and hormone analyses provide insights into hormonal regulation in strawberry ripening.
State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. gutingting@njau.edu.cn.; State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.; Laboratory of Plant hormone, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.; State Key Laboratory of Plant Genetics and Germplasm Enhancement and College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China. yi.li@uconn.edu.; Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT, 06269, USA. yi.li@uconn.edu.
MAIN CONCLUSION: The possible molecular mechanisms regulating strawberry fruit ripening were revealed by plant hormone quantification, exogenous hormone application, and RNA-sequencing. Fruit ripening involves a complex interplay among plant hormones. Strawberry is a model for studies on non-climacteric fruit ripening. However, the knowledge on how plant hormones are involved in strawberry ripening is still limited. To understand hormonal actions in the ripening process, we performed genome-wide transcriptome and hormonal analysis for the five major hormones (abscisic acid and catabolites, auxins, cytokinins, gibberellins, and ethylene) in achenes and receptacles (flesh) at different ripening stages of the woodland strawberry Fragaria vesca. Our results demonstrate that the pre-turning stage (a stage with white flesh and red achenes defined in this study) is the transition stage from immature to ripe fruits. The combinatorial analyses of hormone content, transcriptome data, and exogenous hormone treatment indicate that auxin is synthesized predominantly in achenes, while abscisic acid (ABA), bioactive free base cytokinins, gibberellins, and ethylene are mainly produced in receptacles. Furthermore, gibberellin may delay ripening, while ethylene and cytokinin are likely involved at later stages of the ripening process. Our results also provide additional evidence that ABA promotes ripening, while auxin delays it. Although our hormone analysis demonstrates that the total auxin in receptacles remains relatively low and unchanged during ripening, our experimental evidence further indicates that ABA likely enhances expression of the endoplasmic reticulum-localized auxin efflux carrier PIN-LIKES, which may subsequently reduce the auxin level in nucleus. This study provides a global picture for hormonal regulation of non-climacteric strawberry fruit ripening and also evidence for a possible mechanism of ABA and auxin interaction in the ripening process.
PMID: 30949762
Plant Mol Biol , IF:3.302 , 2019 Jul , V100 (4-5) : P467-479 doi: 10.1007/s11103-019-00871-5
Different knockout genotypes of OsIAA23 in rice using CRISPR/Cas9 generating different phenotypes.
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China. sihaiyang@nju.edu.cn.; State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China. xiaohuizhang@nju.edu.cn.
KEY MESSAGE: We have isolated several Osiaa23 rice mutants with different knockout genotypes, resulting in different phenotypes, which suggested that different genetic backgrounds or mutation types influence gene function. The Auxin/Indole-3-Acetic Acid (Aux/IAA) gene family performs critical roles in auxin signal transduction in plants. In rice, the gene OsIAA23 (Os06t0597000) is known to affect development of roots and shoots, but previous knockouts in OsIAA23 have been sterile and difficult for research continuously. Here, we isolate new Osiaa23 mutants using the CRISPR/Cas9 system in japonica (Wuyunjing24) and indica (Kasalath) rice, with extensive genome re-sequencing to confirm the absence of off-target effects. In Kasalath, mutants with a 13-amino acid deletion showed profoundly greater dwarfing, lateral root developmental disorder, and fertility deficiency, relative to mutants with a single amino acid deletion, demonstrating that those 13 amino acids in Kasalath are essential to gene function. In Wuyunjing24, we predicted that mutants with a single base-pair frameshift insertion would experience premature termination and strong phenotypic defects, but instead these lines exhibited negligible phenotypic difference and normal fertility. Through RNA-seq, we show here that new mosaic transcripts of OsIAA23 were produced de novo, which circumvented the premature termination and thereby preserved the wild-type phenotype. This finding is a notable demonstration in plants that mutants can mask loss of function CRISPR/Cas9 editing of the target gene through de novo changes in alternative splicing.
PMID: 31004275
Molecules , IF:3.267 , 2019 Jul , V24 (14) doi: 10.3390/molecules24142615
Identification of Auxin Metabolites in Brassicaceae by Ultra-Performance Liquid Chromatography Coupled with High-Resolution Mass Spectrometry.
Chemical Laboratories, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera odos 75, 11855 Athens, Greece.; Chemical Laboratories, Department of Food Science and Human Nutrition, Agricultural University of Athens, Iera odos 75, 11855 Athens, Greece. vikon@aua.gr.
Auxins are signaling molecules involved in multiple stages of plant growth and development. The levels of the most important auxin, indole-3-acetic acid (IAA), are regulated by the formation of amide and ester conjugates with amino acids and sugars. In this work, IAA and IAA amide conjugates with amino acids bearing a free carboxylic group or a methyl ester group, along with some selected IAA metabolites, were studied in positive and negative electrospray ionization (ESI) modes, utilizing high-resolution mass spectrometry (HRMS) as a tool for their structural analysis. HRMS/MS spectra revealed the fragmentation patterns that enable us to identify IAA metabolites in plant extracts from eight vegetables of the Brassicaceae family using a fast and reliable ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-QToF-MS) method. The accurate m/z (mass to charge) ratio and abundance of the molecular and fragment ions of the studied compounds in plant extracts matched those obtained from commercially available or synthesized compounds and confirmed the presence of IAA metabolites.
PMID: 31323791
Proteomics , IF:3.254 , 2019 Jul , V19 (14) : Pe1900004 doi: 10.1002/pmic.201900004
Label-Free Quantitative Proteomics of Enriched Nuclei from Sugarcane (Saccharum ssp) Stems in Response to Drought Stress.
Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, 13081, Brazil.; W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, 27695, USA.; Escola Superior de Agricultura "Luiz de Queiroz", Universidade de Sao Paulo, Piracicaba, SP, 13418, Brazil.
Drought is considered the major abiotic stress limiting crop productivity. This study seeks to identify proteins involved in the drought response in sugarcane stems submitted to drought stress. The integration of nuclei enrichment sample preparation with the shotgun proteomic approach results in great coverage of the sugarcane stem proteome with 5381 protein groups identified. A total of 1204 differentially accumulated proteins are detected in response to drought, among which 586 and 618 are increased and reduced in abundance, respectively. A total of 115 exclusive proteins are detected, being 41 exclusives of drought-stressed plants and 74 exclusives of control plants. In the control plants, most of these proteins are related to cell wall metabolism, indicating that drought affects negatively the cell wall metabolism. Also, 37 transcription factors (TFs) are identified, which are low abundant nuclear proteins and are differentially accumulated in response to drought stress. These TFs are associated to protein domains such as leucine-rich (bZIP), C2H2, NAC, C3H, LIM, Myb-related, heat shock factor (HSF) and auxin response factor (ARF). Increased abundance of chromatin remodeling and RNA processing proteins are also observed. It is suggested that these variations result from an imbalance of protein synthesis and degradation processes induced by drought.
PMID: 31172662
Funct Integr Genomics , IF:3.058 , 2019 Jul , V19 (4) : P659-672 doi: 10.1007/s10142-019-00671-6
Salinity-associated microRNAs and their potential roles in mediating salt tolerance in rice colonized by the endophytic root fungus Piriformospora indica.
Department of Plant Breeding and Biotechnology (PBB), Faculty of Agriculture, University of Zabol, Zabol, Iran.; Department of Agronomy, Faculty of Agriculture, Malayer University, Malayer, Iran.; Department of Agriculture, Food and Resource Sciences, University of Maryland Eastern Shore, Princess Anne, Maryland, USA.; Department of Soil Science, School of Agriculture, Shiraz University, Shiraz, Iran.; Department of Molecular Sciences, Macquarie University, Sydney, NSW, Australia.; Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran.; Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education, and Extension Organization (AREEO), Karaj, Iran. ghaffari@abrii.ac.ir.
Piriformospora indica (P. indica), an endophytic root fungus, supports the growth and enhanced tolerance of plants to biotic and abiotic stresses. Several recent studies showed the significant role of small RNA (sRNA) molecules including microRNAs (miRNAs) in plant adaption to environmental stress, but little is known concerning the symbiosis-mediated salt stress tolerance regulated at miRNAs level. The overarching goal of this research is to elucidate the impact of miRNAs in regulating the P. indica-mediated salt tolerance in rice. Applying sRNA-seq analysis led to identify a set of 547 differentially abundant miRNAs in response to P. indica inoculation and salt stress. These included 206 rice-specific and 341 previously known miRNAs from other plant species. In silico analysis of miRNAs predictions of the differentially abundant miRNAs led to identifying of 193 putatively target genes, most of which were encoded either genes or transcription factors involved in nutrient uptake, sodium ion transporters, growth regulators, and auxin- responsive proteins. The rice-specific miRNAs targeted the transcription factors involved in the import of potassium ions into the root cells, the export of sodium ions, and plant growth and development. Interestingly, P. indica affected the differential abundance of miRNAs regulated genes and transcription factors linked to salt stress tolerance. Our data helps to understand the molecular basis of salt stress tolerance mediated by symbionts in plant and the potential impact of miRNAs for genetic improvement of rice varieties for tolerance to salt stress.
PMID: 30903405
Funct Integr Genomics , IF:3.058 , 2019 Jul , V19 (4) : P597-615 doi: 10.1007/s10142-019-00668-1
High-throughput sequencing and differential expression analysis of miRNAs in response to Brassinosteroid treatment in Arabidopsis thaliana.
University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, 110078, India. gunjan.roy08@gmail.com.; University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, 110078, India.; University School of Biotechnology, Guru Gobind Singh Indraprastha University, Dwarka, New Delhi, 110078, India. meenukapoor@me.com.
Brassinosteroids are a class of phytohormones that play crucial roles in improving stress tolerance in plants. Many biochemical and physiological changes in response to abiotic stress are related to regulation of gene expression and accumulation of associated proteins. MicroRNAs (miRNAs) are class of small non-coding RNAs that regulate gene expression post-transcriptionally. Roles of these regulatory RNAs in brassinosteroid (BR) signalling have however remained elusive. In this study using high-throughput small RNA sequencing method, we present a comprehensive compilation of BR-induced differentially expressed microRNAs in root and shoots of Arabidopsis thaliana seedlings. We identified 229 known miRNAs belonging to 102 families and 27 novel miRNAs that express in response to exogenous BR treatment. Out of 102 families, miRNAs belonging to known 48 families and out of 27 novel miRNAs, 23 were observed to be differentially expressed in response to BR treatment. Among the conserved miRNAs, all members of miR169 were observed to be downregulated in both shoot and root samples. While, auxin-responsive factors were predicted to be direct targets of some novel miRNAs that are upregulated in shoots and suppressed in roots. The BR-responsive tissue-specific miRNome characterized in this study can be used as a starting point by investigators for functional validation studies that will shed light on the underlying molecular mechanism of BR-mediated stress tolerance at the level of post-transcriptional gene regulation.
PMID: 30783808
FEBS Lett , IF:3.057 , 2019 Jul , V593 (13) : P1415-1430 doi: 10.1002/1873-3468.13499
HSP90 and co-chaperones: a multitaskers' view on plant hormone biology.
Department of Biology, University of Fribourg, Switzerland.
In order to survive under ever-changing conditions plants must be able to adaptively respond to their environment. Plant hormones and the signaling cross-talk among them play a key role in integrating external and internal cues, enabling the plants to acclimate accordingly. HSP90 and several of its co-chaperones are known as pleiotropic factors involved in the signaling pathways of multiple stress responses, including temperature, drought, and pathogen infection. Recently, hormone receptor components for auxin and jasmonic acid, respectively, have been identified as clients of the HSP90 chaperone system, suggesting a direct HSP90-dependent link to hormone signaling. In this review, we give an overview of the multiple roles of HSP90 and its co-chaperones in plant hormone biology and discuss the largely unexplored targets for signal integration that the activity of these apparent multitaskers may suggest.
PMID: 31211865
Gene , IF:2.984 , 2019 Jul , V707 : P65-77 doi: 10.1016/j.gene.2019.04.089
Transcriptome analysis of differentially expressed genes during anther development stages on male sterility and fertility in Cucumis melo L. line.
Shihezi University, Shihezi, Xinjiang Province, China; Department of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, China; Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Daqing, Heilongjiang Province, China.; Department of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, China; Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Daqing, Heilongjiang Province, China.; Hebei Tourism Vocational College, Chengde, Heibei Province, China.; Department of Agriculture, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province, China; Key Laboratory of Modern Agricultural Cultivation and Crop Germplasm Improvement of Heilongjiang Province, Daqing, Heilongjiang Province, China. Electronic address: shengyunyan12345@163.com.; Department of Horticulture, Northeast Agricultural University, Harbin, Heilongjiang Province, China.
The genic male sterility (MS) plays a major role in melon hybrids production, it could reduce the cost of pollination and increase the yield and quality. However, the molecular mechanism underlying genetic male sterility is yet poorly understood. The morphological differences of flower buds of melon were observed showed that the flower buds were tetrad when they were 1mm stage and monocyte microspore when they were 2mm stage. Electron microscopy showed that there was significant difference between MS lines and MF (male fertility) lines. In order to detect the global expression of the genes during the melon anther development and association with MS, 12 DEGs (differentially expressed genes) libraries were constructed from the anther of MS and MF in the bud stage with 1 and 2mm diameter, respectively. A total of 765 DEGs expressed in anther during different developmental stage (MS 1mm vs. MS 2mm), 148 and 309 DEGs were found to be related to MS as compared to MF (MS 1mm vs. MF 1mm, and MS 2mm vs. MF 2mm) at a false discovery rate FDR <0.01. Among these, 10 DEGs were expressed in all the three comparisons, including transcription factor bHLH genes. Among the DEGs in RNA-seq analysis, 28 were validated by qRT-PCR. Of these, a number of genes were involved in ABC transfactor B family, cytochrome-related genes, hormone-related genes (auxin transporter, gibberellin-regulated protein), MADS-box protein genes, F-box protein genes, peroxidase-related, and Zinc finger protein genes. These genes are involved in many biological pathways, including starch and sucrose metabolism, signal transduction mechanisms and transcription factors, etc. Compared to the same developmental stage of MS and MF, the different developmental stages of MS indicated diverse gene regulation pathways involved in the anther development in MS. These results would provide novel insight into the global network to male sterility in melon.
PMID: 31059736
Plants (Basel) , IF:2.762 , 2019 Jul , V8 (7) doi: 10.3390/plants8070243
The Diverse Roles of Auxin in Regulating Leaf Development.
State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.; 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. yljiao@genetics.ac.cn.; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China. yljiao@genetics.ac.cn.
Leaves, the primary plant organs that function in photosynthesis and respiration, have highly organized, flat structures that vary within and among species. In recent years, it has become evident that auxin plays central roles in leaf development, including leaf initiation, blade formation, and compound leaf patterning. In this review, we discuss how auxin maxima form to define leaf primordium formation. We summarize recent progress in understanding of how spatial auxin signaling promotes leaf blade formation. Finally, we discuss how spatial auxin transport and signaling regulate the patterning of compound leaves and leaf serration.
PMID: 31340506
Plants (Basel) , IF:2.762 , 2019 Jul , V8 (7) doi: 10.3390/plants8070242
Identification of Auxin Response Factor-Encoding Genes Expressed in Distinct Phases of Leaf Vein Development and with Overlapping Functions in Leaf Formation.
Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.; Department of Botany, The University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada.; Department of Neurosurgery, Stanford University, 300 Pasteur Dr., Palo Alto, CA 94304, USA.; Department of Biological Sciences, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada. jmattsso@sfu.ca.
Based on mutant phenotypes the MONOPTEROS (MP)/Auxin Response Factor 5 (ARF5) gene acts in several developmental processes including leaf vein development. Since overlapping functions among ARF genes are common, we assessed the related ARF 3-8 and 19 genes for potential overlap in expression during vein development using in-situ hybridization. Like MP/ARF5, ARF3 was expressed in preprocambial and procambial cells. ARF7 was also expressed in procambial cells, close to and during vein differentiation. ARF19 was expressed in differentiating vessel elements. To assess if genes with vein expression have overlapping functions, double mutants were generated. While arf3, 5 and 7 mutants formed leaves normally, double mutant combinations of mp/arf5 with arf3 or arf7 resulted in a breakdown of leaf formation. Instead, novel structures not present in any of the single mutants formed. The results implicate ARF3 and ARF7 in rosette leaf formation and suggest that their functions overlap and act in parallel with MP/ARF5 in this process. The observed vascular expression patterns suggest unique functions (ARF7 and 19) and potentially overlapping functions (ARF3 and 5) in vein development. Since arf3 arf5 double mutants do not form leaves, assessment of their potential combined action in vein development will require the use of conditional mutants.
PMID: 31340490
Plants (Basel) , IF:2.762 , 2019 Jul , V8 (7) doi: 10.3390/plants8070240
What Makes Adventitious Roots?
Universite de Montpellier, IRD, UMR DIADE, 34,394 Montpellier, France.; Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University Olomouc, Slechtitelu 27, 783 71 Olomouc, Czech Republic. veronique.bergougnoux@upol.cz.; Department of Molecular Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Palacky University Olomouc, Slechtitelu 27, 783 71 Olomouc, Czech Republic.
The spermatophyte root system is composed of a primary root that develops from an embryonically formed root meristem, and of different post-embryonic root types: lateral and adventitious roots. Adventitious roots, arising from the stem of the plants, are the main component of the mature root system of many plants. Their development can also be induced in response to adverse environmental conditions or stresses. Here, in this review, we report on the morphological and functional diversity of adventitious roots and their origin. The hormonal and molecular regulation of the constitutive and inducible adventitious root initiation and development is discussed. Recent data confirmed the crucial role of the auxin/cytokinin balance in adventitious rooting. Nevertheless, other hormones must be considered. At the genetic level, adventitious root formation integrates the transduction of external signals, as well as a core auxin-regulated developmental pathway that is shared with lateral root formation. The knowledge acquired from adventitious root development opens new perspectives to improve micropropagation by cutting in recalcitrant species, root system architecture of crops such as cereals, and to understand how plants adapted during evolution to the terrestrial environment by producing different post-embryonic root types.
PMID: 31336687
Plants (Basel) , IF:2.762 , 2019 Jul , V8 (7) doi: 10.3390/plants8070226
Integration of Phenotype and Hormone Data during Adventitious Rooting in Carnation (Dianthus caryophyllus L.) Stem Cuttings.
Instituto de Bioingenieria, Universidad Miguel Hernandez, 03202 Elche, Spain.; Universidad Catolica San Antonio de Murcia, Campus de los Jeronimos, 30107 Guadalupe, Spain.; CEBAS-CSIC, Campus Universitario de Espinardo, 30100 Murcia, Spain.; Departamento de Biologia Vegetal, Universidad de Murcia, 30100 Murcia, Spain.; Dummen Orange, 30890 Puerto Lumbreras, Spain.; Instituto de Bioingenieria, Universidad Miguel Hernandez, 03202 Elche, Spain. jmperez@umh.es.
The rooting of stem cuttings is a highly efficient procedure for the vegetative propagation of ornamental plants. In cultivated carnations, an increased auxin level in the stem cutting base produced by active auxin transport from the leaves triggers adventitious root (AR) formation from the cambium. To provide additional insight into the physiological and genetic basis of this complex trait, we studied AR formation in a collection of 159 F1 lines derived from a cross between two hybrid cultivars (2003 R 8 and 2101-02 MFR) showing contrasting rooting performances. In three different experiments, time-series for several stem and root architectural traits were quantified in detail in a subset of these double-cross hybrid lines displaying extreme rooting phenotypes and their parental genotypes. Our results indicate that the water content and area of the AR system directly contributed to the shoot water content and shoot growth. Moreover, morphometric data and rooting quality parameters were found to be associated with some stress-related metabolites such as 1-aminocyclopropane-1-carboxylic acid (ACC), the ethylene precursor, and the conjugated auxin indol-3-acetic acid-aspartic acid (IAA-Asp).
PMID: 31311180
BMC Genet , IF:2.567 , 2019 Jul , V20 (1) : P62 doi: 10.1186/s12863-019-0756-6
Functional characterization of Gh_A08G1120 (GH3.5) gene reveal their significant role in enhancing drought and salt stress tolerance in cotton.
State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of 15 Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China.; School of Biological and Physical Sciences (SBPS), Jaramogi Oginga Odinga University of Science and Technology (JOOUST), Main Campus, 210-40601, Bondo, Kenya.; Research Base in Anyang Institute of Technology, State Key Laboratory of Cotton Biology/ Anyang Institute of technology, Anyang, 455000, Henan, China.; State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of 15 Agricultural Sciences (ICR, CAAS), Anyang, 455000, Henan, China. liufcri@163.com.
BACKGROUND: Auxins play an important role in plant growth and development; the auxins responsive gene; auxin/indole-3-acetic acid (Aux/IAA), small auxin-up RNAs (SAUR) and Gretchen Hagen3 (GH3) control their mechanisms. The GH3 genes function in homeostasis by the catalytic activities in auxin conjugation and bounding free indole-3-acetic acid (IAA) to amino acids. RESULTS: In our study, we identified the GH3 genes in three cotton species; Gossypium hirsutum, Gossypium arboreum and Gossypium raimondii, analyzed their chromosomal distribution, phylogenetic relationships, cis-regulatory element function and performed virus induced gene silencing of the novel Gh_A08G1120 (GH3.5) gene. The phylogenetic tree showed four clusters of genes with clade 1, 3 and 4 having mainly members of the GH3 of the cotton species while clade 2 was mainly members belonging to Arabidopsis. There were no paralogous genes, and few orthologous genes were observed between Gossypium and other species. All the GO terms were detected, but only 14 genes were found to have described GO terms in upland cotton, more biological functions were detected, as compared to the other functions. The GH3.17 subfamily harbored the highest number of the cis-regulatory elements, most having promoters towards dehydration-responsiveness. The RNA expression analysis revealed that 10 and 8 genes in drought and salinity stress conditions respectively were upregulated in G. hirsutum. All the genes that were upregulated in plants under salt stress conditions were also upregulated in drought stress; moreover, Gh_A08G1120 (GH3.5) exhibited a significant upregulation across the two stress factors. Functional characterization of Gh_A08G1120 (GH3.5) through virus-induced gene silencing (VIGS) revealed that the VIGS plants ability to tolerate drought and salt stresses was significantly reduced compared to the wild types. The chlorophyll content, relative leaf water content (RLWC), and superoxide dismutase (SOD) concentration level were reduced significantly while malondialdehyde concentration and ion leakage as a measure of cell membrane stability (CMS) increased in VIGS plants under drought and salt stress conditions. CONCLUSION: This study revealed the significance of the GH3 genes in enabling the plant's adaptation to drought and salt stress conditions as evidenced by the VIGS results and RT-qPCR analysis.
PMID: 31337336
Braz J Microbiol , IF:2.428 , 2019 Jul , V50 (3) : P603-612 doi: 10.1007/s42770-019-00083-5
Hydrophobin HFBII-4 from Trichoderma asperellum induces antifungal resistance in poplar.
School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China.; School of Forestry, Northeast Forestry University, 26 Hexing Road, Harbin, 150040, China. LZHNEFU@126.com.
Herein, the class II hydrophobin gene HFBII-4 was cloned from the biocontrol agent Trichoderma asperellum ACCC30536 and recombinant rHFBII-4 was expressed in Pichia pastoris GS115. Treatment of Populus davidiana x P. alba var. pyramidalis (PdPap poplar) with rHFBII-4 altered the expression levels of genes in the auxin, salicylic acid (SA), and jasmonic acid (JA) signal transduction pathways. Polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL) enzyme activities were induced with rHFBII-4. Evans Blue and nitro blue tetrazolium (NBT) staining indicated that cell membrane permeability and reactive oxygen species were lower in the leaves of plants treated with rHFBII-4. The chlorophyll content was higher than that of control at 2-5 days after treatment. Furthermore, poplar seedlings were inoculated with Alternaria alternata, disease symptoms were observed. The diseased area was smaller in leaves induced with rHFBII-4 compared with control. In summary, rHFBII-4 enhances resistance to A. alternata.
PMID: 30982213
Plant Biol (Stuttg) , IF:2.167 , 2019 Jul , V21 (4) : P627-633 doi: 10.1111/plb.12981
Photomorphogenesis of the root system in developing sunflower seedlings: a role for sucrose.
Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA.
The domestic sunflower (Helianthus annuus L. cv. 'Giganteus') has been used since the 19th century as a model plant for the study of seedling development in darkness and white light (WL) (scoto- versus photomorphogenesis). However, most pertinent studies have focused on the developmental patterns of the hypocotyl and cotyledons, whereas the root system has been largely ignored. In this study, we analysed entire sunflower seedlings (root and shoot) and quantified organ development in the above- and belowground parts of the organism under natural (non-sterile) conditions. We document that seedlings, raised in moist vermiculite, are covered with methylobacteria, microbes that are known to promote root development in Arabidopsis. Quantitative data revealed that during photomorphogenesis in WL, the root system expands by 90%, whereas stem elongation is inhibited, and hook opening/cotyledon expansion occurs. Root morphogenesis may be mediated via imported sucrose provided by the green, photosynthetically active cotyledons. This hypothesis is supported by the documented effect of sucrose on the induction of lateral root initials in sunflower cuttings. Under these experimental conditions, phytohormones (auxin, cytokinin, brassinolide) exerted little effect on root and cotyledon expansion, and no hormone-induced initiation of lateral roots was observed. It is concluded that sucrose not only acts as an energy source to fuel cell metabolism but is also a shoot-derived signalling molecule that triggers root morphogenesis.
PMID: 30821893
Genome , IF:2.037 , 2019 Jul , V62 (7) : P455-466 doi: 10.1139/gen-2018-0207
Comparative profile analysis reveals differentially expressed microRNAs regulate anther and pollen development in kenaf cytoplasmic male sterility line.
a Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China.; b College of Life Science and Technology, Guangxi University, Nanning, China.
Cytoplasmic male sterility (CMS) is advantageous in extensive crop breeding and represents a perfect model for understanding anther and pollen development research. MicroRNAs (miRNAs) play key roles in regulating various biological processes. However, the miRNA-mediated regulatory network in kenaf CMS occurrence remains largely unknown. In the present study, a comparative deep sequencing approach was used to investigate the miRNAs and their roles in regulating anther and pollen development during CMS occurrence. We identified 283 known and 46 new candidate miRNAs in kenaf anther. A total of 67 differentially expressed miRNAs (DEMs) were discovered between CMS and its maintainer line. Among them, 40 and 27 miRNAs were up- and downregulated, respectively. These 67 DEMs were predicted to target 189 genes. Validation of DEMs and putative target genes were confirmed by using real-time quantitative PCR. In addition, a potential miRNA-mediated regulatory network, which mainly involves the auxin signaling pathway, signal transduction, glycolysis and energy metabolism, gene expression, transmembrane transport, protein modification and metabolism, and floral development, that mediates anther development during CMS occurrence was proposed. Taken together, our findings provide a better understanding of the molecular mechanism of miRNA regulation in pollen development and CMS occurrence in kenaf.
PMID: 31084581
Plant Direct , IF:1.725 , 2019 Jul , V3 (7) : Pe00147 doi: 10.1002/pld3.147
Accelerating structure-function mapping using the ViVa webtool to mine natural variation.
Department of Biology University of Washington Seattle Washington.; Department of Biology Whitman College Walla Walla Washington.; Biological Systems Engineering Virginia Tech Blacksburg Virginia.
Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of these data remain inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family, or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well-studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less-studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project ( http://snp-seek.irri.org/) and human genetic variation ( https://www.ncbi.nlm.nih.gov/clinvar/).
PMID: 31372596
J Vis Exp , IF:1.163 , 2019 Jul (149) doi: 10.3791/59874
Tuning Degradation to Achieve Specific and Efficient Protein Depletion.
Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; david.barrass@ed.ac.uk.; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Department of Plant Sciences, University of Cambridge.; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Sir William Dunn School of Pathology, University of Oxford.; Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh.
The plant auxin binding receptor, TIR1, recognizes proteins containing a specific auxin-inducible degron (AID) motif in the presence of auxin, targeting them for degradation. This system is exploited in many non-plant eukaryotes, such that a target protein, tagged with the AID motif, is degraded upon auxin addition. The level of TIR1 expression is critical; excessive expression leads to degradation of the AID-tagged protein even in the absence of auxin, whereas low expression leads to slow depletion. A beta-estradiol-inducible AID system was created, with expression of TIR1 under the control of a beta-estradiol inducible promoter. The level of TIR1 is tunable by changing the time of incubation with beta-estradiol before auxin addition. This protocol describes how to rapidly deplete a target protein using the AID system. The appropriate beta-estradiol incubation time depends on the abundance of the target protein. Therefore, efficient depletion depends on optimal timing that also minimizes auxin-independent depletion.
PMID: 31380835