Systems Biology: A Promising Tool to Study Abiotic Stress Responses

Chawla, Konika; Barah, Pankaj; Kuiper, Martin; Bones, Atle M.

doi:10.2174/978160805092511101010163

Cited by 14 publications

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“…Most such studies have used Arabidopsis as a model because of its amenability to subsequent forward and reverse genetic analyses (Somerville and Koornneef, 2002). Robust algorithms have been developed for high-throughput microarray data to decipher global biological processes and to generate testable biological hypotheses (Harr and Schlötterer, 2006;Chawla et al, 2011). For example, lists of transcripts differentially responding to different stresses can be generated and ranked by biological criteria (Dudoit et al, 2002;Nielsen et al, 2007).…”

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confidence: 99%

“…Network-based algorithms can successfully deal with some of the complexities of biological and other physical systems (Barabási and Oltvai, 2004). Different methods and algorithms have been developed (Chawla et al, 2011) to construct major types of biological networks, including gene-metabolite, protein-protein interaction, transcriptional regulatory, gene regulatory, and coexpression networks (Yuan et al, 2008). Coexpression or coregulation of genes may implicate them in similar biological processes, such that individual modules of genes can be attributed to specific processes.…”

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Transcriptome Responses to Combinations of Stresses in Arabidopsis

et al. 2013

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Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity have profound effects on crop performance and yields. Thus, delineation of the regulatory networks and metabolic pathways responding to single and multiple concurrent stresses is required for breeding and engineering crop stress tolerance. Many studies have described transcriptome changes in response to single stresses. However, exposure of plants to a combination of stress factors may require agonistic or antagonistic responses or responses potentially unrelated to responses to the corresponding single stresses. To analyze such responses, we initially compared transcriptome changes in 10 Arabidopsis (Arabidopsis thaliana) ecotypes using cold, heat, high-light, salt, and flagellin treatments as single stress factors as well as their double combinations. This revealed that some 61% of the transcriptome changes in response to double stresses were not predictable from the responses to single stress treatments. It also showed that plants prioritized between potentially antagonistic responses for only 5% to 10% of the responding transcripts. This indicates that plants have evolved to cope with combinations of stresses and, therefore, may be bred to endure them. In addition, using a subset of this data from the Columbia and Landsberg erecta ecotypes, we have delineated coexpression network modules responding to single and combined stresses.

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Transcriptome Responses to Combinations of Stresses in Arabidopsis

et al. 2013

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“…Plants have developed several biochemical, physiological and metabolic strategies in order to combat such abiotic stresses. Often it is difficult to predict the complex signaling pathway that are activated or deactivated in response to different abiotic stresses [2]. The attempt to integrate multidimensional biological information in a network and model leads to the development of system biology.…”

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“…Most of the plant system biology approaches relies on four main axes, viz., genomics, proteomics, transcriptomics and metabolomics, which provide us with a detailed knowledge about the topology and dynamic function of a molecular system [3]. The complex molecular regulatory system involved in stress tolerance and adaptation in plants can be easily deciphered with the help of different 'omics' study [2]. Genomics involves study of genome; transcriptomics includes structural and functional analyses of coding and non-coding RNA or transcriptome, proteomics deals with protein and post-translational protein modification along with their regulatory pathway and metabolomics, which provide a powerful tool to analyze about various metabolites when analyzed in an integrated way can be a very powerful tool in identifying the complex network involved in stress tolerance.…”

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Plant Abiotic Stress:‘Omics’ Approach

Gupta¹

2013

J Plant Biochem Physiol

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“…Plants have adopted numerous biochemical, physiological and metabolic strategies in order to combat such abiotic stresses. More frequently, it is difficult to guess the complex signalling pathway that are activated or deactivated in reply to different abiotic stresses (Chawla et al, 2011). Most of the plant system biology methods depend on four main axes are genomics, proteomics, transcriptomics and metabolomics, which provide us with detailed information about the topology and dynamic function of a molecular system (Yuan et al, 2008;Chawla et al, 2011).…”

Section: Environmental Stresses Encountered By Plantsmentioning

confidence: 99%

Advances in detection of stress tolerance in plants through metabolomics approaches

Khan¹,

Ali²,

Shahid³

et al. 2017

Plant Omics

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Heat and drought stresses are presently the principal risk on world's food quantity, limiting yield. Both of these two stresses affect plants metabolism, physiological and morphological processes, which ultimately reduces the productivity. The plant cell develops different stress induced self-defence mechanisms to reduce the effect of stresses. These defence mechanisms are developed by modifying gene expression pattern, which results in qualitative and quantitative deviations in proteins synthesis, leading to the modulation of certain metabolic and defensive pathways. New metabolic profiling technologies offer a great opportunity for biologist to understand defence mechanism of plants under stress conditions. Metabolomics technologies presently enabled the using of different multi-variate analyses, generated from various hyphenated and chromatographic discovery systems, such as gas or liquid chromatography together with mass spectrometry, or nuclear magnetic resonance (NMR) based methods. Investigation and mining of metabolomics data can be done through a blend of different statistical methods, such as independent component analysis and analysis of variance. Metabolomics in combination with gene expression, protein interaction and other different regulatory pathways can be useful to diverse organisms with trivial alterations. In recent time, this technology has been used to investigate drought tolerance in plant crops to find particular stress related patterns in metabolic expression. These studies identified the vital roles of primary and secondary metabolites associated with abiotic stress tolerance.

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Systems Biology: A Promising Tool to Study Abiotic Stress Responses

Cited by 14 publications

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Transcriptome Responses to Combinations of Stresses in Arabidopsis

Transcriptome Responses to Combinations of Stresses in Arabidopsis

Plant Abiotic Stress:‘Omics’ Approach

Advances in detection of stress tolerance in plants through metabolomics approaches

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