Abstract
The genome-wide role of heterotrimeric G-proteins in abiotic stress response in rice has not been examined from a functional genomics perspective, despite the availability of mutants and evidences involving individual genes/processes/stresses. Our rice whole transcriptome microarray analysis (GSE 20925 at NCBI GEO) using the G-alpha subunit (RGA1) null mutant (Daikoku 1 or d1) and its corresponding wild type (Oryza sativa Japonica Nipponbare) identified 2270 unique differentially expressed genes (DEGs). Out of them, we mined for all the potentially abiotic stress-responsive genes using Gene Ontology terms, STIFDB2.0 and Rice DB. The first two approaches produced smaller subsets of the 1886 genes found at Rice DB. The GO approach revealed similar regulation of several families of stress-responsive genes in RGA1 mutant. The Genevestigator analysis of the stress-responsive subset of the RGA1-regulated genes from STIFDB revealed cold and drought-responsive clusters. Meta data analysis at Rice DB revealed large stress-response categories such as cold (878 up/810 down), drought (882 up/837 down), heat (913 up/777 down), and salt stress (889 up/841 down). One thousand four hundred ninety-eight of them are common to all the four abiotic stresses, followed by fewer genes common to smaller groups of stresses. The RGA1-regulated genes that uniquely respond to individual stresses include 111 in heat stress, eight each in cold only and drought only stresses, and two genes in salt stress only. The common DEGs (1498) belong to pathways such as the synthesis of polyamine, glycine-betaine, proline, and trehalose. Some of the common DEGs belong to abiotic stress signaling pathways such as calcium-dependent pathway, ABA independent and dependent pathway, and MAP kinase pathway in the RGA1 mutant. Gene ontology of the common stress responsive DEGs revealed 62 unique molecular functions such as transporters, enzyme regulators, transferases, hydrolases, carbon and protein metabolism, binding to nucleotides, carbohydrates, receptors and lipids, morphogenesis, flower development, and cell homeostasis. We also mined 63 miRNAs that bind to the stress responsive transcripts identified in this study, indicating their post-transcriptional regulation. Overall, these results indicate the potentially extensive role of RGA1 in the regulation of multiple abiotic stresses in rice for further validation.
Highlights
Abiotic stress responses in plants are being increasingly addressed on a genome-wide scale to find newer gene targets for protecting crop yields in the era of climate change (Pandey et al, 2015)
There are 21 stress-related differentially regulated genes (DEGs) that are individually regulated in the RGA1 mutant with no other family member, including upregulated genes such as calciumdependent protein kinase (CDPK), MAP kinase kinase 2, DnaJ like protein, and down-regulated genes such as Myb factor, phytochelatin synthetase, and water-stress inducible protein (RAB21)
Our results clearly indicate the potentially crucial role of the G-protein α subunit (RGA1) in regulating the response of the rice plant to multiple abiotic stresses for further experimental validation
Summary
Abiotic stress responses in plants are being increasingly addressed on a genome-wide scale to find newer gene targets for protecting crop yields in the era of climate change (Pandey et al, 2015). There have been many other whole transcriptome microarray studies in rice under different abiotic stress conditions, but they reported only specific gene families that responded to various stresses They include the MADS-box transcription factor family (Arora et al, 2007), F-Box Proteins (Jain et al, 2007), calciumdependent protein kinase (CDPK) gene family (Ray et al, 2007), auxin-responsive genes (Jain and Khurana, 2009), protein phosphatase gene family (Singh et al, 2010), Sulfotransferase (SOT) gene family (Chen et al, 2012), thioredoxin gene family (Nuruzzaman et al, 2012), half-size ABC protein subgroup G (Matsuda et al, 2012), class III aminotransferase gene family (Sun et al, 2013), Ca2+ATPases gene family (Kamrul Huda et al, 2013), Rice RING E3 Ligase Family (Lim et al, 2013) etc
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