Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development

Abstract

BackgroundProtein phosphatases are the key components of a number of signaling pathways where they modulate various cellular responses. In plants, protein phosphatases constitute a large gene family and are reportedly involved in the regulation of abiotic stress responses and plant development. Recently, the whole complement of protein phosphatases has been identified in Arabidopsis genome. While PP2C class of serine/threonine phosphatases has been explored in rice, the whole complement of this gene family is yet to be reported.ResultsIn silico investigation revealed the presence of 132-protein phosphatase-coding genes in rice genome. Domain analysis and phylogenetic studies of evolutionary relationship categorized these genes into PP2A, PP2C, PTP, DSP and LMWP classes. PP2C class represents a major proportion of this gene family with 90 members. Chromosomal localization revealed their distribution on all the 12 chromosomes, with 42 genes being present on segmentally duplicated regions and 10 genes on tandemly duplicated regions of chromosomes. The expression profiles of 128 genes under salinity, cold and drought stress conditions, 11 reproductive developmental (panicle and seed) stages along with three stages of vegetative development were analyzed using microarray expression data. 46 genes were found to be differentially expressing in 3 abiotic stresses out of which 31 were up-regulated and 15 exhibited down-regulation. A total of 82 genes were found to be differentially expressing in different developmental stages. An overlapping expression pattern was found for abiotic stresses and reproductive development, wherein 8 genes were up-regulated and 7 down-regulated. Expression pattern of the 13 selected genes was validated employing real time PCR, and it was found to be in accordance with the microarray expression data for most of the genes.ConclusionsExploration of protein phosphatase gene family in rice has resulted in the identification of 132 members, which can be further divided into different classes phylogenetically. Expression profiling and analysis indicate the involvement of this large gene family in a number of signaling pathways triggered by abiotic stresses and their possible role in plant development. Our study will provide the platform from where; the expression pattern information can be transformed into molecular, cellular and biochemical characterization of members belonging to this gene family.

Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development

“…Keeping the fact in mind that abiotic stresses and reproductive development are interconnected processes in the plant life cycle, which has also been proven by overlapping expression of genes in these conditions in prior studies, [24][25][26] we attempted to investigate overlapping expression of PLDs involved in stress and development. Interestingly, all seven PLD genes, which were expressed differentially under abiotic stresses, were also found to be expressed significantly during reproductive developmental stages (Fig.…”

Feedback Regulation of ABA Signaling and Biosynthesis by a bZIP Transcription Factor Targets Drought-Resistance-Related Genes

“…In our RNA-seq analysis, 7 out of 10 clade A PP2Cs in rice were up-regulated by drought stress (Supplemental Table S2), which may imply that the induced expression of clade A PP2Cs may be needed to keep a reasonable scale of the ABA signaling in cells. Investigation of the cis-elements within the 1 Kb promoter region of clade A PP2Cs in rice and Arabidopsis suggests that the frequency of ABREs in the promoter region of clade A PP2Cs is much higher than that in the whole genome (Xue et al, 2008;Singh et al, 2010). The high enrichment of ABREs in the promoter region of PP2Cs indicates that AREB bZIP transcription factors may be involved in the regulation of these PP2C genes.…”

“…A genome-wide and expression analysis of clade A PP2Cs in rice and Arabidopsis indicates that most of them were induced by ABA and drought stress or mannitol treatment, and the ABA response-related element (ABRE) motif was significantly enriched in the promoter region of them (Xue et al, 2008;Singh et al, 2010). Overexpression of the rice clade A PP2C gene OsPP2C108 in Arabidopsis enhanced the tolerance to salt, mannitol, and drought stresses, and sensitivity to ABA treatment (Singh et al, 2015).…”

A STRESS-RESPONSIVE NAC1-Regulated Protein Phosphatase Gene RiceProtein Phosphatase18Modulates Drought and Oxidative Stress Tolerance through Abscisic Acid-Independent Reactive Oxygen Species Scavenging in Rice

“…OsPP18 belongs to the group F2 of the PP2C gene family in rice according to Singh et al (2010). There are five PP2Cs from Arabidopsis and seven PP2Cs from rice in the group F2.…”

“…In the Arabidopsis (Arabidopsis thaliana) genome, there are 76 PP2Cs that are clustered into 10 groups (A-J; Schweighofer et al, 2004). In the rice (Oryza sativa) genome, 90 PP2Cs were identified and classified into 11 groups (A-K; Singh et al, 2010). Plant PP2C proteins have been shown to have critical roles in signaling pathways involved in hormone and stress responses, organ formation, and flower development (Luan, 2003;Schweighofer et al, 2004).…”