Abiotic stress induced “common-alarm signals” in plants
Thus, to interpret the involvement of ROS in stress signalling, the publicly available transcriptome datasets from selected AEM encoding genes of Arabidopsis thaliana including aox1a (mitochondria; (Umbach et al., 2005), cat2 (chloroplast, peroxisome and mitochondria; (Vanderauwera et al., 2005), sal1 (chloroplast and mitochondria; (Wilson et al., 2009), tapx (chloroplast; (Maruta et al., 2012), vtc1 (cytoplasm and nucleus; (Foyer et al., 2012; Pastori et al., 2003) and vtc2 (cytoplasm and nucleus; (Foyer et al., 2012) were utilized for analysis. There are atleast 50% overlap between the differentially expressed genes (DEGs) in Arabidopsis mutants including tapx, cat2, aox1a, vtc1 and vtc2 (Fig. 2A-B). The highest number of up- and down-regulated DEGs was observed in sal1 mutant, indicating it as one of the key regulators of nuclear gene expression. The other mutants follow the order of vtc2>tapx>vtc1>aox1>cat2, as per the total number of DEGs (Fig 2A). The median value indicated that the maximum change in gene expression in cat2, followed by sal1>tapx>vtc2>vtc1>aox1 and sal1>vtc1>vtc2>tapx>aox1 in case of up- and down-regulated genes, respectively (Fig. 2A). Thus, the maximum impact on nuclear gene expression was noticed under sal1 (as per DEGs number) and cat2 (as per expression change), which were incidentally having multiple sub-cellular localization.
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Supplementary Fig S1: Protein-protein interaction network and MCODE components identified in the DEGs. Protein-protein interaction network with MCODE (Molecular Complex Detection) algorithm applied on densely connected network components. Pathway and process enrichment analysis was applied independently to each MCODE modules independently, and the three best-scoring terms by p-value was used as the functional description of the corresponding components. A) Protein-protein interactions for all genes. B) Representative significant genes in each MCODE. (The corresponding functional classification of each MCODE is given below: MCODE 1: response to bacterium, chaperone-mediated protein folding, response to metal ion; MCODE 2: protein processing in endoplasmic reticulum, protein processing in endoplasmic reticulum, protein folding; MCODE 3: flavonoid biosynthesis, flavonoid biosynthesis, flavonoid biosynthetic process; MCODE 4: response to wounding, jasmonic acid mediated signaling pathway, cellular response to jasmonic acid stimulus; MCODE 5: protein localization; MCODE 6: starch and sucrose metabolism, starch and sucrose metabolism, starch metabolic process; MCODE 7: phenylpropanoid biosynthesis, phenylpropanoid biosynthesis, lignin metabolic process; MCODE 8: intracellular signal transduction, positive regulation of translation; MCODE 9: sulfate assimilation, inositol phosphate metabolic process, sulfur metabolism; MCODE 10: mRNA splicing, via spliceosome, RNA splicing, via transesterification reactions, RNA splicing, via transesterification reactions with bulged adenosine as nucleophile; MCODE 11: starch and sucrose metabolism, starch and sucrose metabolism, cellular carbohydrate biosynthetic process; MCODE 12: response to ROS) Supplementary Fig S2: Figure S2: Novel motifs discovered in the DEGs of Redox responsive genes. A) Motif from DEGs of vtc1 mutant with no TF complimentary to the site. B) Motif from DEGs of tapx mutant with 1 TF complimentary to the site with TF binding E-value more than 5. A) Motif from DEGs of abi4 mutant with 1 TF complimentary to the site with TF binding E-value more than 4. A) Motif from DEGs of vtc1 mutant with 2 TFs complimentary to the site with TF binding E-value more than 2. Supplementary Table S1: Differentially expressed genes (DEGs) in the antioxidant enzyme mutants. A list of DGEs of the mutants with respective fold change values. Supplementary Table S2: ROS-responsive Transcription factors. A list of ROS-responsive Primary and Secondary TFs with the number of binding sites in the promoter region of candidate genes Supplementary Table S3: ROS responsive Transcription factor binding site on promoter region of the candidate genes.