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Gonzalez S, Swift J, Yaaran A, Xu J, Miller C, Illouz-Eliaz N, Nery JR, Busch W, Zait Y, Ecker JR. Arabidopsis transcriptome responses to low water potential using high-throughput plate assays. eLife 2024; 12:RP84747. [PMID: 38904663 PMCID: PMC11192529 DOI: 10.7554/elife.84747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2024] Open
Abstract
Soil-free assays that induce water stress are routinely used to investigate drought responses in the plant Arabidopsis thaliana. Due to their ease of use, the research community often relies on polyethylene glycol (PEG), mannitol, and salt (NaCl) treatments to reduce the water potential of agar media, and thus induce drought conditions in the laboratory. However, while these types of stress can create phenotypes that resemble those of water deficit experienced by soil-grown plants, it remains unclear how these treatments compare at the transcriptional level. Here, we demonstrate that these different methods of lowering water potential elicit both shared and distinct transcriptional responses in Arabidopsis shoot and root tissue. When we compared these transcriptional responses to those found in Arabidopsis roots subject to vermiculite drying, we discovered many genes induced by vermiculite drying were repressed by low water potential treatments on agar plates (and vice versa). Additionally, we also tested another method for lowering water potential of agar media. By increasing the nutrient content and tensile strength of agar, we show the 'hard agar' (HA) treatment can be leveraged as a high-throughput assay to investigate natural variation in Arabidopsis growth responses to low water potential.
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Affiliation(s)
- Stephen Gonzalez
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph Swift
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Adi Yaaran
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of JerusalemRehovotIsrael
| | - Jiaying Xu
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Charlotte Miller
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Natanella Illouz-Eliaz
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Joseph R Nery
- Genomic Analysis Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Wolfgang Busch
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
| | - Yotam Zait
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food, and Environment, The Hebrew University of JerusalemRehovotIsrael
| | - Joseph R Ecker
- Plant Biology Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
- Genomic Analysis Laboratory, The Salk Institute for Biological StudiesLa JollaUnited States
- Howard Hughes Medical Institute, The Salk Institute for Biological StudiesLa JollaUnited States
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2
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Niu L, Wang W, Li Y, Wu X, Wang W. Maize multi-omics reveal leaf water status controlling of differential transcriptomes, proteomes and hormones as mechanisms of age-dependent osmotic stress response in leaves. STRESS BIOLOGY 2024; 4:19. [PMID: 38498254 PMCID: PMC10948690 DOI: 10.1007/s44154-024-00159-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
Drought-induced osmotic stress severely affects the growth and yield of maize. However, the mechanisms underlying the different responses of young and old maize leaves to osmotic stress remain unclear. To gain a systematic understanding of age-related stress responses, we compared osmotic-stress-induced changes in maize leaves of different ages using multi-omics approaches. After short-term osmotic stress, old leaves suffered more severe water deficits than young leaves. The adjustments of transcriptomes, proteomes, and hormones in response to osmotic stress were more dynamic in old leaves. Metabolic activities, stress signaling pathways, and hormones (especially abscisic acid) responded to osmotic stress in an age-dependent manner. We identified multiple functional clusters of genes and proteins with potential roles in stress adaptation. Old leaves significantly accumulated stress proteins such as dehydrin, aquaporin, and chaperones to cope with osmotic stress, accompanied by senescence-like cellular events, whereas young leaves exhibited an effective water conservation strategy mainly by hydrolyzing transitory starch and increasing proline production. The stress responses of individual leaves are primarily determined by their intracellular water status, resulting in differential transcriptomes, proteomes, and hormones. This study extends our understanding of the mechanisms underlying plant responses to osmotic stress.
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Affiliation(s)
- Liangjie Niu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Wenkang Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yingxue Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China.
| | - Wei Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450046, China.
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3
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Hsiao AS. Protein Disorder in Plant Stress Adaptation: From Late Embryogenesis Abundant to Other Intrinsically Disordered Proteins. Int J Mol Sci 2024; 25:1178. [PMID: 38256256 PMCID: PMC10816898 DOI: 10.3390/ijms25021178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 01/15/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Global climate change has caused severe abiotic and biotic stresses, affecting plant growth and food security. The mechanical understanding of plant stress responses is critical for achieving sustainable agriculture. Intrinsically disordered proteins (IDPs) are a group of proteins without unique three-dimensional structures. The environmental sensitivity and structural flexibility of IDPs contribute to the growth and developmental plasticity for sessile plants to deal with environmental challenges. This article discusses the roles of various disordered proteins in plant stress tolerance and resistance, describes the current mechanistic insights into unstructured proteins such as the disorder-to-order transition for adopting secondary structures to interact with specific partners (i.e., cellular membranes, membrane proteins, metal ions, and DNA), and elucidates the roles of liquid-liquid phase separation driven by protein disorder in stress responses. By comparing IDP studies in animal systems, this article provides conceptual principles of plant protein disorder in stress adaptation, reveals the current research gaps, and advises on the future research direction. The highlighting of relevant unanswered questions in plant protein disorder research aims to encourage more studies on these emerging topics to understand the mechanisms of action behind their stress resistance phenotypes.
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Affiliation(s)
- An-Shan Hsiao
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
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4
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CPR5-mediated nucleo-cytoplasmic localization of IAA12 and IAA19 controls lateral root development during abiotic stress. Proc Natl Acad Sci U S A 2023; 120:e2209781120. [PMID: 36623191 PMCID: PMC9934060 DOI: 10.1073/pnas.2209781120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Plasticity of the root system architecture (RSA) is essential in enabling plants to cope with various environmental stresses and is mainly controlled by the phytohormone auxin. Lateral root development is a major determinant of RSA. Abiotic stresses reduce auxin signaling output, inhibiting lateral root development; however, how abiotic stress translates into a lower auxin signaling output is not fully understood. Here, we show that the nucleo-cytoplasmic distribution of the negative regulators of auxin signaling AUXIN/INDOLE-3-ACETIC ACID INDUCIBLE 12 (AUX/IAA12 or IAA12) and IAA19 determines lateral root development under various abiotic stress conditions. The cytoplasmic localization of IAA12 and IAA19 in the root elongation zone enforces auxin signaling output, allowing lateral root development. Among components of the nuclear pore complex, we show that CONSTITUTIVE EXPRESSOR OF PATHOGENESIS-RELATED GENES 5 (CPR5) selectively mediates the cytoplasmic translocation of IAA12/19. Under abiotic stress conditions, CPR5 expression is strongly decreased, resulting in the accumulation of nucleus-localized IAA12/19 in the root elongation zone and the suppression of lateral root development, which is reiterated in the cpr5 mutant. This study reveals a regulatory mechanism for auxin signaling whereby the spatial distribution of AUX/IAA regulators is critical for lateral root development, especially in fluctuating environmental conditions.
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5
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Cha OK, Yang S, Lee H. Transcriptomics Using the Enriched Arabidopsis Shoot Apex Reveals Developmental Priming Genes Involved in Plastic Plant Growth under Salt Stress Conditions. PLANTS 2022; 11:plants11192546. [PMID: 36235412 PMCID: PMC9570865 DOI: 10.3390/plants11192546] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
In the shoot apical meristem (SAM), the homeostasis of the stem cell population supplying new cells for organ formation is likely a key mechanism of multicellular plant growth and development. As plants are sessile organisms and constantly encounter environmental abiotic stresses, postembryonic development from the shoot stem cell population must be considered with surrounding abiotic stresses for plant adaptation. However, the underlying molecular mechanisms for plant adaptation remain unclear. Previous studies found that the stem-cell-related mutant clv3-2 has the property of salt tolerance without the differential response of typical stress-responsive genes compared to those in WT Ler. Based on these facts, we hypothesized that shoot meristems contain developmental priming genes having comprehensively converged functions involved in abiotic stress response and development. To better understand the biological process of developmental priming genes in the SAM, we performed RNA sequencing (RNA-seq) and transcriptome analysis through comparing genome-wide gene expression profiles between enriched shoot apex and leaf tissues. As a result, 121 putative developmental priming genes differentially expressed in the shoot apex compared to the leaf were identified under normal and salt stress conditions. RNA-seq experiments also revealed the shoot apex-specific responsive genes for salt stress conditions. Based on combinatorial comparisons, 19 developmental priming genes were finally identified, including developmental genes related to cell division and abiotic/biotic-stress-responsive genes. Moreover, some priming genes showed CLV3-dependent responses under salt stress conditions in the clv3-2. These results presumably provide insight into how shoot meristem tissues have relatively high viability against stressful environmental conditions for the developmental plasticity of plants.
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Affiliation(s)
| | | | - Horim Lee
- Correspondence: ; Tel.: +82-10-3762-6331
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Liu Y, Cao D, Ma L, Jin X. Upregulation of protein N-glycosylation plays crucial roles in the response of Camellia sinensis leaves to fluoride. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 183:138-150. [PMID: 35597102 DOI: 10.1016/j.plaphy.2022.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 05/06/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The tea plant (Camellia sinensis) is one of the three major beverage crops in the world with its leaves consumption as tea. However, it can hyperaccumulate fluoride with about 98% fluoride deposition in the leaves. Our previously studies found that cell wall proteins (CWPs) might play a central role in fluoride accumulation/detoxification in C. sinensis. CWP is known to be glycosylated, however the response of CWP N-glycosylation to fluoride remains unknown in C. sinensis. In this study, a comparative N-glycoproteomic analysis was performed through HILIC enrichment coupled with UPLC-MS/MS based on TMT-labeling approach in C. sinensis leaves. Totally, 237 N-glycoproteins containing 326 unique N-glycosites were identified. 73.4%, 18.6%, 6.3% and 1.7% of these proteins possess 1, 2, 3, and ≥4 modification site, respectively. 93.2% of these proteins were predicted to be localized in the secretory pathway and 78.9% of them were targeted to the cell wall and the plasma membrane. 133 differentially accumulated N-glycosites (DNGSs) on 100 N-glycoproteins (DNGPs) were detected and 85.0% of them exhibited upregulated expression after fluoride treatment. 78.0% DNGPs were extracellular DNGPs, which belonged to CWPs, and 53.0% of them were grouped into protein acting on cell wall polysaccharides, proteases and oxido-reductases, whereas the majority of the remaining DNGPs were mainly related to N-glycoprotein biosynthesis, trafficking and quality control. Our study shed new light on the N-glycoproteome study, and revealed that increased N-glycosylation abundance of CWPs might contribute to fluoride accumulation/detoxification in C. sinensis leave.
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Affiliation(s)
- Yanli Liu
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
| | - Dan Cao
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Linlong Ma
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Xiaofang Jin
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China.
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7
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Nakamichi R, Kitada S, Kishino H. Exploratory analysis of multi‐trait coadaptations in light of population history. Ecol Evol 2022; 12:e8755. [PMID: 35342584 PMCID: PMC8933610 DOI: 10.1002/ece3.8755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/18/2022] [Indexed: 11/15/2022] Open
Abstract
During the process of range expansion, populations encounter a variety of environments. They respond to the local environments by modifying their mutually interacting traits. Common approaches of landscape analysis include first focusing on the genes that undergo diversifying selection or directional selection in response to environmental variation. To understand the whole history of populations, it is ideal to capture the history of their range expansion with reference to the series of surrounding environments and to infer the multitrait coadaptation. To this end, we propose a complementary approach; it is an exploratory analysis using up‐to‐date methods that integrate population genetic features and features of selection on multiple traits. First, we conduct correspondence analysis of site frequency spectra, traits, and environments with auxiliary information of population‐specific fixation index (FST). This visualizes the structure and the ages of populations and helps infer the history of range expansion, encountered environmental changes, and selection on multiple traits. Next, we further investigate the inferred history using an admixture graph that describes the population split and admixture. Finally, principal component analysis of the selection on edge‐by‐trait (SET) matrix identifies multitrait coadaptation and the associated edges of the admixture graph. We introduce a newly defined factor loadings of environmental variables in order to identify the environmental factors that caused the coadaptation. A numerical simulation of one‐dimensional stepping‐stone population expansion showed that the exploratory analysis reconstructed the pattern of the environmental selection that was missed by analysis of individual traits. Analysis of a public dataset of natural populations of black cottonwood in northwestern America identified the first principal component (PC) coadaptation of photosynthesis‐ vs growth‐related traits responding to the geographical clines of temperature and day length. The second PC coadaptation of volume‐related traits suggested that soil condition was a limiting factor for aboveground environmental selection.
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Affiliation(s)
| | - Shuichi Kitada
- Tokyo University of Marine Science and Technology Tokyo Japan
| | - Hirohisa Kishino
- Graduate School of Agriculture and Life Sciences The University of Tokyo Tokyo Japan
- The Research Institute of Evolutionary Biology Tokyo Japan
- AI/Data Science Social Implementation Laboratory Chuo University Tokyo Japan
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8
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Jaballi A, Missihoun TD. The phytohormone abscisic acid modulates protein carbonylation in Arabidopsis thaliana. PHYSIOLOGIA PLANTARUM 2022; 174:e13658. [PMID: 35243640 DOI: 10.1111/ppl.13658] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/20/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Protein carbonylation is a post-translational modification associated with the reactive oxygen species. It results from the direct oxidation of the side chains of Lys, Arg, Pro, and Thr residues by hydroxyl radical HO• or the addition of reactive carbonyl species including α,β-unsaturated aldehydes and oxylipins to the side chain of Cys, His, and Lys. Recent findings indicated that the phytohormone abscisic acid (ABA) induces the production of α,β-unsaturated aldehydes that modulate the effect of ABA on stomatal closure. This indicated that α,β-unsaturated aldehydes might mediate ABA signaling. In this study, we investigated the ABA-induced protein carbonylation events by profiling the carbonylated proteome extracted from Arabidopsis thaliana leaves after ABA treatment. The carbonylated proteins were enriched by affinity chromatography and subjected to liquid chromatography-tandem mass spectrometry. We identified 180 carbonylated proteins. Of these, 26 proteins became carbonylated upon ABA treatment, whereas 163 proteins that were carbonylated in untreated samples were no longer detected in the ABA-treated samples, which points to dynamic control of protein carbonylation by ABA in A. thaliana. A few regulatory stress-related proteins and enzymes involved in the biosynthesis of the aspartate family of amino acids were overrepresented in the list of proteins, which the carbonylation status changed between untreated and ABA-treated samples. These results indicated that ABA triggers a change in the pattern of protein carbonylation in A. thaliana. This change is independent of the commonly seen increased levels of carbonylated proteins in the plants subjected to deadly stress conditions.
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Affiliation(s)
- Amal Jaballi
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
| | - Tagnon D Missihoun
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, Trois-Rivières, Québec, Canada
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9
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Subba P, Prasad TSK. Plant Phosphoproteomics: Known Knowns, Known Unknowns, and Unknown Unknowns of an Emerging Systems Science Frontier. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:750-769. [PMID: 34882020 DOI: 10.1089/omi.2021.0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plant systems science research depends on the dynamic functional maps of the biological substrates of plant phenotypes and host/environment interactions in diverse ecologies. In this context, high-resolution mass spectrometry platforms offer comprehensive insights into the molecular pathways regulated by protein phosphorylation. Reversible protein phosphorylation is a ubiquitous reaction in signal transduction mechanisms in biological systems. In contrast to human and animal biology research, a plethora of experimental options for functional mapping and regulation of plant biology are, however, not currently available. Plant phosphoproteomics is an emerging field of research that aims at addressing this gap in systems science and plant omics, and thus has a large scope to empower fundamental discoveries. To date, large-scale data-intensive identification of phosphorylation events in plants remained technically challenging. In this expert review, we present a critical analysis and overview of phosphoproteomic studies performed in the model plant Arabidopsis thaliana. We discuss the technical strategies used for the enrichment of phosphopeptides and methods used for their quantitative assessment. Various types of mass spectrometry data acquisition and fragmentation methods are also discussed. The insights gathered here can allow plant biology and systems science researchers to design high-throughput function-oriented experimental workflows that elucidate the regulatory signaling mechanisms impacting plant physiology and plant diseases.
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Affiliation(s)
- Pratigya Subba
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
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10
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Li L, Verstraeten I, Roosjen M, Takahashi K, Rodriguez L, Merrin J, Chen J, Shabala L, Smet W, Ren H, Vanneste S, Shabala S, De Rybel B, Weijers D, Kinoshita T, Gray WM, Friml J. Cell surface and intracellular auxin signalling for H + fluxes in root growth. Nature 2021; 599:273-277. [PMID: 34707283 PMCID: PMC7612300 DOI: 10.1038/s41586-021-04037-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 09/17/2021] [Indexed: 11/09/2022]
Abstract
Growth regulation tailors development in plants to their environment. A prominent example of this is the response to gravity, in which shoots bend up and roots bend down1. This paradox is based on opposite effects of the phytohormone auxin, which promotes cell expansion in shoots while inhibiting it in roots via a yet unknown cellular mechanism2. Here, by combining microfluidics, live imaging, genetic engineering and phosphoproteomics in Arabidopsis thaliana, we advance understanding of how auxin inhibits root growth. We show that auxin activates two distinct, antagonistically acting signalling pathways that converge on rapid regulation of apoplastic pH, a causative determinant of growth. Cell surface-based TRANSMEMBRANE KINASE1 (TMK1) interacts with and mediates phosphorylation and activation of plasma membrane H+-ATPases for apoplast acidification, while intracellular canonical auxin signalling promotes net cellular H+ influx, causing apoplast alkalinization. Simultaneous activation of these two counteracting mechanisms poises roots for rapid, fine-tuned growth modulation in navigating complex soil environments.
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Affiliation(s)
- Lanxin Li
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Inge Verstraeten
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Mark Roosjen
- Laboratory of Biochemistry, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, the Netherlands
| | - Koji Takahashi
- Institute of Transformative Bio-Molecules, Division of Biological Science, Nagoya University Chikusa, Nagoya, Japan
- Graduate School of Science, Nagoya University Chikusa, Nagoya, Japan
| | - Lesia Rodriguez
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Jack Merrin
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria
| | - Jian Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lana Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
| | - Wouter Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hong Ren
- Department of Plant & Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Incheon, Republic of Korea
- Department of Plants and Crops, HortiCell, Ghent University, Ghent, Belgium
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Hobart, Tasmania, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dolf Weijers
- Laboratory of Biochemistry, Department of Agrotechnology and Food Sciences, Wageningen University, Wageningen, the Netherlands
| | - Toshinori Kinoshita
- Institute of Transformative Bio-Molecules, Division of Biological Science, Nagoya University Chikusa, Nagoya, Japan
- Graduate School of Science, Nagoya University Chikusa, Nagoya, Japan
| | - William M Gray
- Department of Plant & Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, Klosterneuburg, Austria.
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11
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The Arabidopsis Root Tip (Phospho)Proteomes at Growth-Promoting versus Growth-Repressing Conditions Reveal Novel Root Growth Regulators. Cells 2021; 10:cells10071665. [PMID: 34359847 PMCID: PMC8303113 DOI: 10.3390/cells10071665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/20/2022] Open
Abstract
Auxin plays a dual role in growth regulation and, depending on the tissue and concentration of the hormone, it can either promote or inhibit division and expansion processes in plants. Recent studies have revealed that, beyond transcriptional reprogramming, alternative auxin-controlled mechanisms regulate root growth. Here, we explored the impact of different concentrations of the synthetic auxin NAA that establish growth-promoting and -repressing conditions on the root tip proteome and phosphoproteome, generating a unique resource. From the phosphoproteome data, we pinpointed (novel) growth regulators, such as the RALF34-THE1 module. Our results, together with previously published studies, suggest that auxin, H+-ATPases, cell wall modifications and cell wall sensing receptor-like kinases are tightly embedded in a pathway regulating cell elongation. Furthermore, our study assigned a novel role to MKK2 as a regulator of primary root growth and a (potential) regulator of auxin biosynthesis and signalling, and suggests the importance of the MKK2 Thr31 phosphorylation site for growth regulation in the Arabidopsis root tip.
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12
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Gouguet P, Gronnier J, Legrand A, Perraki A, Jolivet MD, Deroubaix AF, German-Retana S, Boudsocq M, Habenstein B, Mongrand S, Germain V. Connecting the dots: from nanodomains to physiological functions of REMORINs. PLANT PHYSIOLOGY 2021; 185:632-649. [PMID: 33793872 PMCID: PMC8133660 DOI: 10.1093/plphys/kiaa063] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/31/2020] [Indexed: 05/11/2023]
Abstract
REMORINs (REMs) are a plant-specific protein family, proposed regulators of membrane-associated molecular assemblies and well-established markers of plasma membrane nanodomains. REMs play a diverse set of functions in plant interactions with pathogens and symbionts, responses to abiotic stresses, hormone signaling and cell-to-cell communication. In this review, we highlight the established and more putative roles of REMs throughout the literature. We discuss the physiological functions of REMs, the mechanisms underlying their nanodomain-organization and their putative role as regulators of nanodomain-associated molecular assemblies. Furthermore, we discuss how REM phosphorylation may regulate their functional versatility. Overall, through data-mining and comparative analysis of the literature, we suggest how to further study the molecular mechanisms underpinning the functions of REMs.
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Affiliation(s)
- Paul Gouguet
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
- ZMBP, Universität Tübingen, Auf der Morgenstelle 32 72076 Tübingen, Germany
| | - Julien Gronnier
- Department of Plant and Microbial Biology University of Zürich, Zollikerstrasse, Zürich, Switzerland
| | - Anthony Legrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, A11, Geoffroy Saint-Hilaire, Pessac, France
| | - Artemis Perraki
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, UK
- Present address: Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology – Hellas, Heraklion, Crete, Greece
| | - Marie-Dominique Jolivet
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
| | - Anne-Flore Deroubaix
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
| | - Sylvie German-Retana
- Equipe de Virologie, Institut Scientifique de Recherche Agronomique and Université de Bordeaux, BP81, 33883 Villenave d’Ornon, France
| | - Marie Boudsocq
- Université Paris-Saclay, CNRS, INRAE, Université d’Evry, Institute of Plant Sciences Paris Saclay (IPS2), Université de Paris, Orsay, France
| | - Birgit Habenstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), IECB, CNRS, Université de Bordeaux, Institut Polytechnique de Bordeaux, A11, Geoffroy Saint-Hilaire, Pessac, France
| | - Sébastien Mongrand
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
- Author for communication: (S.M.)
| | - Véronique Germain
- Laboratoire de Biogenèse Membranaire (LBM), Unité Mixte de Recherche UMR 5200, CNRS, Université de Bordeaux, Villenave d’Ornon, France
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13
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Pan J, Li Z, Wang Q, Guan Y, Li X, Huangfu Y, Meng F, Li J, Dai S, Liu W. Phosphoproteomic Profiling Reveals Early Salt-Responsive Mechanisms in Two Foxtail Millet Cultivars. FRONTIERS IN PLANT SCIENCE 2021; 12:712257. [PMID: 34616412 PMCID: PMC8488109 DOI: 10.3389/fpls.2021.712257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 08/16/2021] [Indexed: 05/03/2023]
Abstract
Excess soluble salts in saline soils are harmful to most plants. Understanding the biochemical responses to salts in plants and studying the salt tolerance-associated genetic resources in nature will contribute to the improvement of salt tolerance in crops. As an emerging model crop, foxtail millet (Setaria italica L.) has been regarded as a novel species for stress resistance investigation. Here, the dynamic proteomic and phosphoproteomic profiling of two foxtail millet varieties of An04 and Yugu2 with contrasting salt tolerance characteristics were investigated under salt stress. In total, 10,366 sites representing to 2,862 proteins were detected and quantified. There were 759 and 990 sites corresponding to 484 and 633 proteins identified under salinity in An04 and Yugu2, respectively, and 1,264 and 1,131 phosphorylation sites corresponding to 789 and 731 proteins were identified between these two varieties before and after salt stress, respectively. The differentially-regulated phosphoproteins (DRPPs) were mainly involved in signal transduction, regulation of gene expression, translation, ion transport, and metabolism processes. Yugu2 possessed signal perception and transduction capabilities more rapidly and had a more intense response compared with An04 upon salinity. The sucrose metabolism pathway, in particularly, might play a vital role in salt response in foxtail millet, which not only provides UDP-glucose for the cellulose synthesis and energy production, but also promotes flavonoid related synthesis to enhance the salt tolerance ability. Over-expressing the phospho-mimic sucrose synthase (SuS) (SuS S10D ) in soybean roots enhanced salt tolerance compared with over-expressing SuS lines. The knowledge of this research will shed light on elucidating the mechanisms of salt response, and pave the way for crop varieties innovation and cultivation under salinity and stresses.
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Affiliation(s)
- Jiaowen Pan
- Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Zhen Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qingguo Wang
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yanan Guan
- Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xiaobo Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yongguan Huangfu
- Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin, China
| | - Fanhua Meng
- Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jinling Li
- Shandong Academy of Agricultural Sciences, Jinan, China
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Shaojun Dai
- Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
- *Correspondence: Shaojun Dai,
| | - Wei Liu
- Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
- Wei Liu,
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14
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Samarina L, Matskiv A, Simonyan T, Koninskaya N, Malyarovskaya V, Gvasaliya M, Malyukova L, Tsaturyan G, Mytdyeva A, Martinez-Montero ME, Choudhary R, Ryndin A. Biochemical and Genetic Responses of Tea ( Camellia sinensis (L.) Kuntze) Microplants under Mannitol-Induced Osmotic Stress In Vitro. PLANTS 2020; 9:plants9121795. [PMID: 33348920 PMCID: PMC7766420 DOI: 10.3390/plants9121795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
Abstract
Osmotic stress is a major factor reducing the growth and yield of many horticultural crops worldwide. To reveal reliable markers of tolerant genotypes, we need a comprehensive understanding of the responsive mechanisms in crops. In vitro stress induction can be an efficient tool to study the mechanisms of responses in plants to help gain a better understanding of the physiological and genetic responses of plant tissues against each stress factor. In the present study, the osmotic stress was induced by addition of mannitol into the culture media to reveal biochemical and genetic responses of tea microplants. The contents of proline, threonine, epigallocatechin, and epigallocatechin gallate were increased in leaves during mannitol treatment. The expression level of several genes, namely DHN2, LOX1, LOX6, BAM, SUS1, TPS11, RS1, RS2, and SnRK1.3, was elevated by 2–10 times under mannitol-induced osmotic stress, while the expression of many other stress-related genes was not changed significantly. Surprisingly, down-regulation of the following genes, viz. bHLH12, bHLH7, bHLH21, bHLH43, CBF1, WRKY2, SWEET1, SWEET2, SWEET3, INV5, and LOX7, was observed. During this study, two major groups of highly correlated genes were observed. The first group included seven genes, namely CBF1, DHN3, HXK2,SnRK1.1, SPS, SWEET3, and SWEET1. The second group comprised eight genes, viz. DHN2, SnRK1.3, HXK3, RS1, RS2,LOX6, SUS4, and BAM5. A high level of correlation indicates the high strength connection of the genes which can be co-expressed or can be linked to the joint regulons. The present study demonstrates that tea plants develop several adaptations to cope under osmotic stress in vitro; however, some important stress-related genes were silent or downregulated in microplants.
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Affiliation(s)
- Lidiia Samarina
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
- Correspondence: ; Tel.: +79-66-7709038
| | - Alexandra Matskiv
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Taisiya Simonyan
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Natalia Koninskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Valentina Malyarovskaya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Maya Gvasaliya
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Lyudmila Malyukova
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Gregory Tsaturyan
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Alfiya Mytdyeva
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
| | - Marcos Edel Martinez-Montero
- Department of Plant Breeding and Plant Conservation, Bioplantas Center, University of Ciego de Avila, Ciego de Avila 65200, Cuba;
| | - Ravish Choudhary
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Alexey Ryndin
- Federal Research Centre the Subtropical Scientific Centre of the Russian Academy of Sciences, Sochi 354002, Russia; (A.M.); (T.S.); (N.K.); (V.M.); (M.G.); (L.M.); (G.T.); (A.M.); (A.R.)
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Allagulova C, Avalbaev A, Fedorova K, Shakirova F. Methyl jasmonate alleviates water stress-induced damages by promoting dehydrins accumulation in wheat plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 155:676-682. [PMID: 32861034 DOI: 10.1016/j.plaphy.2020.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 05/25/2023]
Abstract
The investigation of dehydrins participation in MeJA-induced protection of wheat plants (Triticum aestivum L.) from drought stress was performed. The dehydration was designed by the presence of mannitol in increasing concentration (3, 4, and 5%) in the growth medium of wheat seedlings. Pre-treatment of 3-days-old seedlings with 0.1 μM MeJA reduced the level of drought-induced growth retardation as well as membrane structures lesions. Exogenous MeJA enhanced accumulation of the TADHN dehydrin transcripts and dehydrin proteins with Mw 28 and 55 kDa in wheat seedlings under normal conditions and additionally increased their expression during dehydration. The obtained data may indicate the dehydrins involvement in MeJA protective effect on wheat plants from the damages caused by water deficit.
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Affiliation(s)
- Chulpan Allagulova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054, Ufa, Russia.
| | - Azamat Avalbaev
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054, Ufa, Russia
| | - Kristina Fedorova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054, Ufa, Russia
| | - Farida Shakirova
- Institute of Biochemistry and Genetics - Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences, 450054, Ufa, Russia
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Smith S, Zhu S, Joos L, Roberts I, Nikonorova N, Vu LD, Stes E, Cho H, Larrieu A, Xuan W, Goodall B, van de Cotte B, Waite JM, Rigal A, Ramans Harborough S, Persiau G, Vanneste S, Kirschner GK, Vandermarliere E, Martens L, Stahl Y, Audenaert D, Friml J, Felix G, Simon R, Bennett MJ, Bishopp A, De Jaeger G, Ljung K, Kepinski S, Robert S, Nemhauser J, Hwang I, Gevaert K, Beeckman T, De Smet I. The CEP5 Peptide Promotes Abiotic Stress Tolerance, As Revealed by Quantitative Proteomics, and Attenuates the AUX/IAA Equilibrium in Arabidopsis. Mol Cell Proteomics 2020; 19:1248-1262. [PMID: 32404488 PMCID: PMC8011570 DOI: 10.1074/mcp.ra119.001826] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/02/2020] [Indexed: 01/20/2023] Open
Abstract
Peptides derived from non-functional precursors play important roles in various developmental processes, but also in (a)biotic stress signaling. Our (phospho)proteome-wide analyses of C-TERMINALLY ENCODED PEPTIDE 5 (CEP5)-mediated changes revealed an impact on abiotic stress-related processes. Drought has a dramatic impact on plant growth, development and reproduction, and the plant hormone auxin plays a role in drought responses. Our genetic, physiological, biochemical, and pharmacological results demonstrated that CEP5-mediated signaling is relevant for osmotic and drought stress tolerance in Arabidopsis, and that CEP5 specifically counteracts auxin effects. Specifically, we found that CEP5 signaling stabilizes AUX/IAA transcriptional repressors, suggesting the existence of a novel peptide-dependent control mechanism that tunes auxin signaling. These observations align with the recently described role of AUX/IAAs in stress tolerance and provide a novel role for CEP5 in osmotic and drought stress tolerance.
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Affiliation(s)
- Stephanie Smith
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom
| | - Shanshuo Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lisa Joos
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ianto Roberts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Natalia Nikonorova
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Hyunwoo Cho
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Antoine Larrieu
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Wei Xuan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Benjamin Goodall
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Brigitte van de Cotte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jessic Marie Waite
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Adeline Rigal
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sigurd Ramans Harborough
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Geert Persiau
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Gwendolyn K Kirschner
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Elien Vandermarliere
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Dominique Audenaert
- Screening Core, Gent, Belgium; Expertise Centre for Bioassay Development and Screening (C-BIOS), Ghent University, Ghent, Belgium
| | - Jirí Friml
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology (CEITEC), Masaryk University (MU), Brno, Czech Republic; Institute of Science and Technology Austria (IST Austria), Klosterneuburg, Austria
| | - Georg Felix
- Zentrum für Molekularbiologie der Pflanzen, Plant Biochemistry, University Tübingen, Tübingen, Germany
| | - Rüdiger Simon
- Institute for Developmental Genetics, Heinrich-Heine University, Düsseldorf, Germany
| | - Malcolm J Bennett
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom; Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Anthony Bishopp
- Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Karin Ljung
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Stefan Kepinski
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Stephanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Jennifer Nemhauser
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Ildoo Hwang
- Department of Life Sciences, POSTECH Biotech Center, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough, United Kingdom; Department of Plant Biotechnology and Bioinformatics, Ghent University, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium; Centre for Plant Integrative Biology, University of Nottingham, Loughborough, United Kingdom.
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17
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Dubois M, Inzé D. Plant growth under suboptimal water conditions: early responses and methods to study them. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:1706-1722. [PMID: 31967643 DOI: 10.1093/jxb/eraa037] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/20/2020] [Indexed: 05/03/2023]
Abstract
Drought stress forms a major environmental constraint during the life cycle of plants, often decreasing plant yield and in extreme cases threatening survival. The molecular and physiological responses induced by drought have been the topic of extensive research during the past decades. Because soil-based approaches to studying drought responses are often challenging due to low throughput and insufficient control of the conditions, osmotic stress assays in plates were developed to mimic drought. Addition of compounds such as polyethylene glycol, mannitol, sorbitol, or NaCl to controlled growth media has become increasingly popular since it offers the advantage of accurate control of stress level and onset. These osmotic stress assays enabled the discovery of very early stress responses, occurring within seconds or minutes following osmotic stress exposure. In this review, we construct a detailed timeline of early responses to osmotic stress, with a focus on how they initiate plant growth arrest. We further discuss the specific responses triggered by different types and severities of osmotic stress. Finally, we compare short-term plant responses under osmotic stress versus in-soil drought and discuss the advantages, disadvantages, and future of these plate-based proxies for drought.
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Affiliation(s)
- Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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18
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Grison MS, Kirk P, Brault ML, Wu XN, Schulze WX, Benitez-Alfonso Y, Immel F, Bayer EM. Plasma Membrane-Associated Receptor-like Kinases Relocalize to Plasmodesmata in Response to Osmotic Stress. PLANT PHYSIOLOGY 2019; 181:142-160. [PMID: 31300470 PMCID: PMC6716232 DOI: 10.1104/pp.19.00473] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/02/2019] [Indexed: 05/17/2023]
Abstract
Plasmodesmata act as key elements in intercellular communication, coordinating processes related to plant growth, development, and responses to environmental stresses. While many of the developmental, biotic, and abiotic signals are primarily perceived at the plasma membrane (PM) by receptor proteins, plasmodesmata also cluster receptor-like activities; whether these two pathways interact is currently unknown. Here, we show that specific PM-located Leu-rich-repeat receptor-like-kinases, Qiān Shŏu kinase (QSK1) and inflorescence meristem kinase2, which under optimal growth conditions are absent from plasmodesmata, rapidly relocate and cluster to the pores in response to osmotic stress. This process is remarkably fast, is not a general feature of PM-associated proteins, and is independent of sterol and sphingolipid membrane composition. Focusing on QSK1, previously reported to be involved in stress responses, we show that relocalization in response to mannitol depends on QSK1 phosphorylation. Loss-of-function mutation in QSK1 results in delayed lateral root (LR) development, and the mutant is affected in the root response to mannitol stress. Callose-mediated plasmodesmata regulation is known to regulate LR development. We found that callose levels are reduced in the qsk1 mutant background with a root phenotype resembling ectopic expression of PdBG1, an enzyme that degrades callose at the pores. Both the LR and callose phenotypes can be complemented by expression of wild-type and phosphomimic QSK1 variants, but not by phosphodead QSK1 mutant, which fails to relocalize at plasmodesmata. Together, the data indicate that reorganization of receptor-like-kinases to plasmodesmata is important for the regulation of callose and LR development as part of the plant response to osmotic stress.
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Affiliation(s)
- Magali S Grison
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
| | - Philip Kirk
- Centre for Plant Science, School of Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Marie L Brault
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
| | - Xu Na Wu
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, 70593 Stuttgart, Germany
| | - Yoselin Benitez-Alfonso
- Centre for Plant Science, School of Biology, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Françoise Immel
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
| | - Emmanuelle M Bayer
- Laboratoire de Biogenèse Membranaire, UMR5200 Centre National de la Recherche Scientifique, Université de Bordeaux, 71 Avenue Edouard Bourlaux, 33883 Villenave d'Ornon cedex, France
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19
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Kumar RR, Singh K, Ahuja S, Tasleem M, Singh I, Kumar S, Grover M, Mishra D, Rai GK, Goswami S, Singh GP, Chinnusamy V, Rai A, Praveen S. Quantitative proteomic analysis reveals novel stress-associated active proteins (SAAPs) and pathways involved in modulating tolerance of wheat under terminal heat. Funct Integr Genomics 2018; 19:329-348. [PMID: 30465139 DOI: 10.1007/s10142-018-0648-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/14/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
Abstract
Terminal heat stress has detrimental effect on the growth and yield of wheat. Very limited information is available on heat stress-associated active proteins (SAAPs) in wheat. Here, we have identified 159 protein groups with 4271 SAAPs in control (22 ± 3 °C) and HS-treated (38 °C, 2 h) wheat cvs. HD2985 and HD2329 using iTRAQ. We identified 3600 proteins to be upregulated and 5825 proteins to be downregulated in both the wheat cvs. under HS. We observed 60.3% of the common SAAPs showing upregulation in HD2985 (thermotolerant) and downregulation in HD2329 (thermosusceptible) under HS. GO analysis showed proton transport (molecular), photosynthesis (biological), and ATP binding (cellular) to be most altered under HS. Most of the SAAPs identified were observed to be chloroplast localized and involved in photosynthesis. Carboxylase enzyme was observed most abundant active enzymes in wheat under HS. An increase in the degradative isoenzymes (α/β-amylases) was observed, as compared to biosynthesis enzymes (ADP-glucophosphorylase, soluble starch synthase, etc.) under HS. Transcript profiling showed very high relative fold expression of HSP17, CDPK, Cu/Zn SOD, whereas downregulation of AGPase, SSS under HS. The identified SAAPs can be used for targeted protein-based precision wheat-breeding program for the development of 'climate-smart' wheat.
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Affiliation(s)
- Ranjeet R Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Khushboo Singh
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sumedha Ahuja
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mohd Tasleem
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Indra Singh
- CABin, Indian Agricultural Statistical Research Institute (IASRI), Pusa, New Delhi, 110012, India
| | - Sanjeev Kumar
- CABin, Indian Agricultural Statistical Research Institute (IASRI), Pusa, New Delhi, 110012, India
| | - Monendra Grover
- CABin, Indian Agricultural Statistical Research Institute (IASRI), Pusa, New Delhi, 110012, India
| | - Dwijesh Mishra
- CABin, Indian Agricultural Statistical Research Institute (IASRI), Pusa, New Delhi, 110012, India
| | - Gyanendra K Rai
- Sher-E-Kashmir University of Agriculture Science and Technology, Chatta, Jammu and Kashmir, 180009, India
| | - Suneha Goswami
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gyanendra P Singh
- Indian Institute of Wheat and Barley Research, Karnal, Haryana, 132001, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anil Rai
- CABin, Indian Agricultural Statistical Research Institute (IASRI), Pusa, New Delhi, 110012, India
| | - Shelly Praveen
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India.
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Spoel SH. Orchestrating the proteome with post-translational modifications. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4499-4503. [PMID: 30169870 PMCID: PMC6117579 DOI: 10.1093/jxb/ery295] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Affiliation(s)
- Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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Nikonorova N, Van den Broeck L, Zhu S, van de Cotte B, Dubois M, Gevaert K, Inzé D, De Smet I. Early mannitol-triggered changes in the Arabidopsis leaf (phospho)proteome reveal growth regulators. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4591-4607. [PMID: 30010984 PMCID: PMC6117580 DOI: 10.1093/jxb/ery261] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 07/04/2018] [Indexed: 05/03/2023]
Abstract
Leaf growth is a complex, quantitative trait, controlled by a plethora of regulatory mechanisms. Diverse environmental stimuli inhibit leaf growth to cope with the perceived stress. In plant research, mannitol is often used to impose osmotic stress and study the underlying growth-repressing mechanisms. In growing leaf tissue of plants briefly exposed to mannitol-induced stress, a highly interconnected gene regulatory network is induced. However, early signalling and associated protein phosphorylation events that probably precede part of these transcriptional changes and that potentially act at the onset of mannitol-induced leaf size reduction are largely unknown. Here, we performed a proteome and phosphoproteome analysis on growing leaf tissue of Arabidopsis thaliana plants exposed to mild mannitol-induced stress and captured the fast (within the first half hour) events associated with this stress. Based on this in-depth data analysis, 167 and 172 differentially regulated proteins and phosphorylated sites were found. We provide these data sets as a community resource and we flag differentially phosphorylated proteins with described growth-regulatory functions, but we also illustrate potential novel regulators of shoot growth.
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Affiliation(s)
- Natalia Nikonorova
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lisa Van den Broeck
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Shanshuo Zhu
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Ghent University, Department of Biochemistry, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Brigitte van de Cotte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Gevaert
- Ghent University, Department of Biochemistry, Ghent, Belgium
- VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Correspondence:
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