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      Metabolomics and proteomics reveal drought-stress responses of leaf tissues from spring-wheat

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          Abstract

          To reveal the integrative biochemical networks of wheat leaves in response to water deficient conditions, proteomics and metabolomics were applied to two spring-wheat cultivars ( Bahar, drought-susceptible; Kavir, drought-tolerant). Drought stress induced detrimental effects on Bahar leaf proteome, resulting in a severe decrease of total protein content, with impairments mainly in photosynthetic proteins and in enzymes involved in sugar and nitrogen metabolism, as well as in the capacity of detoxifying harmful molecules. On the contrary, only minor perturbations were observed at the protein level in Kavir stressed leaves. Metabolome analysis indicated amino acids, organic acids, and sugars as the main metabolites changed in abundance upon water deficiency. In particular, Bahar cv showed increased levels in proline, methionine, arginine, lysine, aromatic and branched chain amino acids. Tryptophan accumulation via shikimate pathway seems to sustain auxin production (indoleacrylic acid), whereas glutamate reduction is reasonably linked to polyamine (spermine) synthesis. Kavir metabolome was affected by drought stress to a less extent with only two pathways significantly changed, one of them being purine metabolism. These results comprehensively provide a framework for better understanding the mechanisms that govern plant cell response to drought stress, with insights into molecules that can be used for crop improvement projects.

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          Photosynthetic carbon assimilation and associated metabolism in relation to water deficits in higher plants.

          Experimental studies on CO2 assimilation of mesophytic C3 plants in relation to relative water content (RWC) are discussed. Decreasing RWC slows the actual rate of photosynthetic CO2 assimilation (A) and decreases the potential rate (Apot). Generally, as RWC falls from c. 100 to c. 75%, the stomatal conductance (gs) decreases, and with it A. However, there are two general types of relation of Apot to RWC, which are called Type 1 and Type 2. Type 1 has two main phases. As RWC decreases from 100 to c. 75%, Apot is unaffected, but decreasing stomatal conductance (gs) results in smaller A, and lower CO2 concentration inside the leaf (Ci) and in the chloroplast (Cc), the latter falling possibly to the compensation point. Down-regulation of electron transport occurs by energy quenching mechanisms, and changes in carbohydrate and nitrogen metabolism are considered acclimatory, caused by low Ci and reversible by elevated CO2. Below 75% RWC, there is metabolic inhibition of Apot, inhibition of A then being partly (but progressively less) reversible by elevated CO2; gs regulates A progressively less, and Ci and CO2 compensation point, Gamma rise. It is suggested that this is the true stress phase, where the decrease in Apot is caused by decreased ATP synthesis and a consequent decreased synthesis of RuBP. In the Type 2 response, Apot decreases progressively at RWC 100 to 75%, with A being progressively less restored to the unstressed value by elevated CO2. Decreased gs leads to a lower Ci and Cc but they probably do not reach compensation point: gs becomes progressively less important and metabolic limitations more important as RWC falls. The primary effect of low RWC on Apot is most probably caused by limited RuBP synthesis, as a result of decreased ATP synthesis, either through inhibition of Coupling Factor activity or amount due to increased ion concentration. Carbohydrate synthesis and accumulation decrease. Type 2 response is considered equivalent to Type 1 at RWC below c. 75%, with Apot inhibited by limited ATP and RuBP synthesis, respiratory metabolism dominates and Ci and Gamma rise. The importance of inhibited ATP synthesis as a primary cause of decreasing Apot is discussed. Factors determining the Type 1 and Type 2 responses are unknown. Electron transport is maintained (but down-regulated) in Types 1 and 2 over a wide range of RWC, and a large reduced/oxidized adenylate ratio results. Metabolic imbalance results in amino acid accumulation and decreased and altered protein synthesis. These conditions profoundly affect cell functions and ultimately cause cell death. Type 1 and 2 responses may reflect differences in gs and in sensitivity of metabolism to decreasing RWC.
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            MetPA: a web-based metabolomics tool for pathway analysis and visualization.

            MetPA (Metabolomics Pathway Analysis) is a user-friendly, web-based tool dedicated to the analysis and visualization of metabolomic data within the biological context of metabolic pathways. MetPA combines several advanced pathway enrichment analysis procedures along with the analysis of pathway topological characteristics to help identify the most relevant metabolic pathways involved in a given metabolomic study. The results are presented in a Google-map style network visualization system that supports intuitive and interactive data exploration through point-and-click, dragging and lossless zooming. Additional features include a comprehensive compound library for metabolite name conversion, automatic generation of analysis report, as well as the implementation of various univariate statistical procedures that can be accessed when users click on any metabolite node on a pathway map. MetPA currently enables analysis and visualization of 874 metabolic pathways, covering 11 common model organisms. Freely available at http://metpa.metabolomics.ca.
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              Photosynthesis and drought: can we make metabolic connections from available data?

              Photosynthesis is one of the key processes to be affected by water deficits, via decreased CO2 diffusion to the chloroplast and metabolic constraints. The relative impact of those limitations varies with the intensity of the stress, the occurrence (or not) of superimposed stresses, and the species we are dealing with. Total plant carbon uptake is further reduced due to the concomitant or even earlier inhibition of growth. Leaf carbohydrate status, altered directly by water deficits or indirectly (via decreased growth), acts as a metabolic signal although its role is not totally clear. Other relevant signals acting under water deficits comprise: abscisic acid (ABA), with an impact on stomatal aperture and the regulation at the transcription level of a large number of genes related to plant stress response; other hormones that act either concurrently (brassinosteroids, jasmonates, and salycilic acid) or antagonistically (auxin, cytokinin, or ethylene) with ABA; and redox control of the energy balance of photosynthetic cells deprived of CO2 by stomatal closure. In an attempt to systematize current knowledge on the complex network of interactions and regulation of photosynthesis in plants subjected to water deficits, a meta-analysis has been performed covering >450 papers published in the last 15 years. This analysis shows the interplay of sugars, reactive oxygen species (ROS), and hormones with photosynthetic responses to drought, involving many metabolic events. However, more significantly it highlights (i) how fragmented and often non-comparable the results are and (ii) how hard it is to relate molecular events to plant physiological status, namely photosynthetic activity, and to stress intensity. Indeed, the same data set usually does not integrate these different levels of analysis. Considering these limitations, it was hard to find a general trend, particularly concerning molecular responses to drought, with the exception of the genes ABI1 and ABI3. These genes, irrespective of the stress type (acute versus chronic) and intensity, show a similar response to water shortage in the two plant systems analysed (Arabidopsis and barley). Both are associated with ABA-mediated metabolic responses to stress and the regulation of stomatal aperture. Under drought, ABI1 transcription is up-regulated while ABI3 is usually down-regulated. Recently ABI3 has been hypothesized to be essential for successful drought recovery.
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                Author and article information

                Contributors
                zolla@unitus.it
                sara.r@unitus.it
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                9 April 2018
                9 April 2018
                2018
                : 8
                Affiliations
                [1 ]ISNI 0000 0001 2298 9743, GRID grid.12597.38, Department of Ecological and Biological Sciences (DEB), , University of Tuscia, ; Viterbo, Italy
                [2 ]ISNI 0000 0000 8810 3346, GRID grid.412462.7, Department of Agriculture, , Payame Noor University, ; Tehran, Iran
                [3 ]ISNI 0000 0001 1172 3536, GRID grid.412831.d, Department of Biotechnology and Plant Breeding, , University of Tabriz, ; Tabriz, Iran
                [4 ]ISNI 0000 0001 2298 9743, GRID grid.12597.38, Department of Science and Technology for Agriculture, Forestry, Nature and Energy (DAFNE), , University of Tuscia, ; Viterbo, Italy
                Article
                24012
                10.1038/s41598-018-24012-y
                5890255
                29632386
                b2728c2f-d840-4d05-8716-d04cc5263342
                © The Author(s) 2018

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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