Microarray Analysis of Rice d1 (RGA1) Mutant Reveals the Potential Role of G-Protein Alpha Subunit in Regulating Multiple Abiotic Stresses Such as Drought, Salinity, Heat, and Cold

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.

Heterotrimeric G protein are involved in the regulation of multiple agronomic traits and stress tolerance in rice

“…The null mutant of the RGA1 gene exhibits a severe dwarf phenotype in rice [33,34], whereas the down-regulation of the expression of the RGA1 gene causes a semi-dwarf phenotype [19]. Microarray analysis of RGA1 showed that RGA1 might participate in the regulation of multiple abiotic stresses, such as drought, salinity, heat, and cold tolerance [35]. During drought, rga1 mutant plants exhibit greater stomatal conductance than the WT, but both genotypes exhibit the same transpirational water loss per unit leaf area [25].…”

Heterotrimeric G-protein α subunit (LeGPA1) confers cold stress tolerance in Processing tomato plants (Lycopersicon esculentum Mill)

“…The G-protein α subunits also play important roles in the signal transduction pathway of abiotic stress in plants [26]. The full transcriptome microarray analysis of rice revealed that rice RGA1 can regulate low temperature, salt, and drought stress and transmit stress signals to the small phosphorylase GTPase and corresponding effector proteins or molecules, such as ion channels [28]. In the pea, expression of the PsGPA1 gene was significantly changed by NaCl and high temperature [29].…”

“…Studies have shown that GPA1 in Arabidopsis is involved in oxidative stress signal transduction and can positively regulate the abiotic stress factors upstream of reactive oxygen species (ROS) and nicotinamide adenine dinucleotide phosphate (NADPH) [27]. Arabidopsis Gα subunit mutations reduced the sensitivity of the plant to ozone stress [28]. In the pea (Pisum sativum Linn.…”

Mutation ofIDR1enhances drought tolerance by reducing ROS production and activating ROS scavenging in rice

“…DSM1 was required for the normal expression of two ROS-scavenging genes, OsPOX22.3 and OsPOX8.1 (Ning et al, 2010). LEA3-1 was considered as a protectant for desiccation and oxidation stress (Jangam et al, 2016). To see whether idr1-1 mutant has increased expression levels of the ROS-scavenging genes due to mutation of IDR1, we further checked the transcript levels of a dozen or so genes implicated in ROS scavenging.…”

“…Data from other studies revealed that RGA1 regulated expression of an abundant group of genes. For example, in rga1 mutant, there were 626 genes, which separately responded to heat (522), drought (101), salt (37), and cold (15) stresses, found to be changed in gene expression levels (Jangam et al, 2016).…”