A friend in need is a friend indeed

Department of Plant Sciences, Weizmann Institute of Science
Plant signaling & behavior 09/2011; 6(9). DOI: 10.4161/psb.6.9.16567
Source: PubMed


The response of plants to environmental cues, particularly stresses, involves the coordinated induction or repression of gene expression. In a previous study, we developed a bioinformatics approach to analyze the mutual expression pattern of genes encoding transcription factors and metabolic enzymes upon exposure of Arabidopsis plants to abiotic and biotic stresses. The analysis resulted in three gene clusters, each displaying a unique expression pattern. In the present addendum, we address the composition of each of these three clusters in regard to the functional identity of their encoded proteins as enzymes or transcription factors.

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Available from: Tamar Avin-Wittenberg,
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    • "Whereas most of the described effects might be attributed to specific posttranscriptional regulatory processes, there are hints that regulation at the transcriptional level also contributes to remodeling of the plant membrane composition. The most important evidence is the tight coexpression of genes involved in lipid metabolism and in its particular biochemical pathways in response to stress (Obayashi et al., 2007; Loraine, 2009; Avin-Wittenberg et al., 2011). "
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    ABSTRACT: Glycerolipid metabolism of plants responds dynamically to changes in light intensity and temperature, leading to the modification of membrane lipid composition to ensure optimal biochemical and physical properties in the new environment. Although multiple posttranscriptional regulatory mechanisms have been reported to be involved in the process, the contribution of transcriptional regulation remains largely unknown. Here, we present an integrative analysis of transcriptomic and lipidomic data, revealing large-scale coordination between gene expression and changes in glycerolipid levels during the Arabidopsis thaliana response to light and temperature stimuli. Using a multivariate regression technique called O2PLS, we show that the gene expression response is strictly coordinated at the biochemical pathway level and occurs in parallel with changes of specific glycerolipid pools. Five interesting candidate genes were chosen for further analysis from a larger set of candidates identified based on their close association with various groups of glycerolipids. Lipidomic analysis of knockout mutant lines of these five genes showed a significant relationship between the coordination of transcripts and glycerolipid levels in a changing environment and the effects of single gene perturbations.
    The Plant Cell 03/2014; 26(3). DOI:10.1105/tpc.113.118919 · 9.34 Impact Factor
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    • "This is strengthened by the ratio between genes encoding enzymes and TFs in each of the clusters. While in cluster 1 the ratio is almost 1:1, in cluster 3 the ratio between genes encoding enzymes and TFs is 2:1, suggesting that one TF regulates the coordinated transcription of more enzymes in cluster 3 than in cluster 1 (Avin-Wittenberg et al., 2011; Less et al., 2011). In addition, when observing the network of a specific cluster, some pathways displayed higher sub-network density than other pathways, suggesting strong co-regulation of the two pathways (Figure 5). "
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    ABSTRACT: Plants need to continuously adjust their transcriptome in response to various stresses that lead to inhibition of photosynthesis and the deprivation of cellular energy. This adjustment is triggered in part by a coordinated re-programming of the energy-associated transcriptome to slow down photosynthesis and activate other energy-promoting gene networks. Therefore, understanding the stress-related transcriptional networks of genes belonging to energy-associated pathways is of major importance for engineering stress tolerance. In a bioinformatics approach developed by our group, termed 'gene coordination', we previously divided genes encoding for enzymes and transcription factors in Arabidopsis thaliana into three clusters, displaying altered coordinated transcriptional behaviors in response to multiple biotic and abiotic stresses (Plant Cell, 23, 2011, 1264). Enrichment analysis indicated further that genes controlling energy-associated metabolism operate as a compound network in response to stress. In the present paper, we describe in detail the network association of genes belonging to six central energy-associated pathways in each of these three clusters described in our previous paper. Our results expose extensive stress-associated intra- and inter-pathway interactions between genes from these pathways, indicating that genes encoding proteins involved in energy-associated metabolism are expressed in a highly coordinated manner. We also provide examples showing that this approach can be further utilized to elucidate candidate genes for stress tolerance and functions of isozymes.
    The Plant Journal 01/2012; 70(6):954-66. DOI:10.1111/j.1365-313X.2012.04926.x · 5.97 Impact Factor
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    ABSTRACT: Although amino acids primarily serve as the building blocks of proteins, in plants amino acids also serve as important alternative energy substrates, particularly when plants are exposed to stresses that cause energy deprivation. The contribution of amino acids to energy homeostasis in response to stress occurs through their catabolism, which funnels their carbon backbones to the TCA cycle, providing an alternative source of electrons for the mitochondrial electron transport chain. As such, amino acid catabolism, which also includes the association of the amino acid Glu and the γ-aminobutyric acid (GABA) shunt, is becoming recognized as a critical element of energy metabolism in stress and carbon starvation. In the first part of the present review, we focus on recent findings concerning modes of action of amino acids catabolism as alternative source of energy in stress. Secondly, we enlighten how the systems biology approaches, including gene co-expression analysis and transcript and metabolic profiling, led to the discovery of new biological processes associating plant amino acid metabolism with response and adaptation to stress.
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