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      Effects of abiotic stress on plants: a systems biology perspective

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          Abstract

          The natural environment for plants is composed of a complex set of abiotic stresses and biotic stresses. Plant responses to these stresses are equally complex. Systems biology approaches facilitate a multi-targeted approach by allowing one to identify regulatory hubs in complex networks. Systems biology takes the molecular parts (transcripts, proteins and metabolites) of an organism and attempts to fit them into functional networks or models designed to describe and predict the dynamic activities of that organism in different environments. In this review, research progress in plant responses to abiotic stresses is summarized from the physiological level to the molecular level. New insights obtained from the integration of omics datasets are highlighted. Gaps in our knowledge are identified, providing additional focus areas for crop improvement research in the future.

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          Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins.

          Sang-Youl Park, Pauline Fung, Noriyuki Nishimura … (2009)
          Type 2C protein phosphatases (PP2Cs) are vitally involved in abscisic acid (ABA) signaling. Here, we show that a synthetic growth inhibitor called pyrabactin functions as a selective ABA agonist. Pyrabactin acts through PYRABACTIN RESISTANCE 1 (PYR1), the founding member of a family of START proteins called PYR/PYLs, which are necessary for both pyrabactin and ABA signaling in vivo. We show that ABA binds to PYR1, which in turn binds to and inhibits PP2Cs. We conclude that PYR/PYLs are ABA receptors functioning at the apex of a negative regulatory pathway that controls ABA signaling by inhibiting PP2Cs. Our results illustrate the power of the chemical genetic approach for sidestepping genetic redundancy.
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            Regulators of PP2C phosphatase activity function as abscisic acid sensors.

            Yue Wen Ma, Izabela Szostkiewicz, Arthur Korte … (2009)
            The plant hormone abscisic acid (ABA) acts as a developmental signal and as an integrator of environmental cues such as drought and cold. Key players in ABA signal transduction include the type 2C protein phosphatases (PP2Cs) ABI1 and ABI2, which act by negatively regulating ABA responses. In this study, we identify interactors of ABI1 and ABI2 which we have named regulatory components of ABA receptor (RCARs). In Arabidopsis, RCARs belong to a family with 14 members that share structural similarity with class 10 pathogen-related proteins. RCAR1 was shown to bind ABA, to mediate ABA-dependent inactivation of ABI1 or ABI2 in vitro, and to antagonize PP2C action in planta. Other RCARs also mediated ABA-dependent regulation of ABI1 and ABI2, consistent with a combinatorial assembly of receptor complexes.
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              AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent ABA signaling involved in drought stress tolerance and require ABA for full activation.

              Takuya Yoshida, Yasunari Fujita, Hiroko Sayama … (2010)
              A myriad of drought stress-inducible genes have been reported, and many of these are activated by abscisic acid (ABA). In the promoter regions of such ABA-regulated genes, conserved cis-elements, designated ABA-responsive elements (ABREs), control gene expression via bZIP-type AREB/ABF transcription factors. Although all three members of the AREB/ABF subfamily, AREB1, AREB2, and ABF3, are upregulated by ABA and water stress, it remains unclear whether these are functional homologs. Here, we report that all three AREB/ABF transcription factors require ABA for full activation, can form hetero- or homodimers to function in nuclei, and can interact with SRK2D/SnRK2.2, an SnRK2 protein kinase that was identified as a regulator of AREB1. Along with the tissue-specific expression patterns of these genes and the subcellular localization of their encoded proteins, these findings clearly indicate that AREB1, AREB2, and ABF3 have largely overlapping functions. To elucidate the role of these AREB/ABF transcription factors, we generated an areb1 areb2 abf3 triple mutant. Large-scale transcriptome analysis, which showed that stress-responsive gene expression is remarkably impaired in the triple mutant, revealed novel AREB/ABF downstream genes in response to water stress, including many LEA class and group-Ab PP2C genes and transcription factors. The areb1 areb2 abf3 triple mutant is more resistant to ABA than are the other single and double mutants with respect to primary root growth, and it displays reduced drought tolerance. Thus, these results indicate that AREB1, AREB2, and ABF3 are master transcription factors that cooperatively regulate ABRE-dependent gene expression for ABA signaling under conditions of water stress.
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                Author and article information

                Journal
                Journal ID (nlm-ta): BMC Plant Biol
                Title: BMC Plant Biology
                Publisher: BioMed Central
                ISSN (Electronic): 1471-2229
                Publication date Collection: 2011
                Publication date (Electronic): 17 November 2011
                Volume: 11
                Page: 163
                Affiliations
                [1 ]Department of Biochemistry and Molecular Biology, Mail Stop 330, University of Nevada, Reno, Nevada 89557, USA
                [2 ]Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba 305-0074, Japan
                [3 ]Univ. Bordeaux, ISVV, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33882 Villenave d'Ornon, France
                [4 ]Dipartimento di Biotecnologie, Università di Verona, Strada le Grazie 15, 37134 Verona, Italy
                Article
                Publisher ID: 1471-2229-11-163
                DOI: 10.1186/1471-2229-11-163
                PMC ID: 3252258
                PubMed ID: 22094046
                SO-VID: 6e1a7101-fbac-43b3-89d8-f6f1f5f2ac32
                Copyright © Copyright ©2011 Cramer et al; licensee BioMed Central Ltd.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 5 September 2011
                Date accepted : 17 November 2011
                Categories
                Subject: Review

                ScienceOpen disciplines: Plant science & Botany
                Data availability:
                ScienceOpen disciplines: Plant science & Botany

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