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

BMC Genomics. 2010 Jul 16;11:435. doi: 10.1186/1471-2164-11-435.


Background: Protein 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.

Results: In 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.

Conclusions: Exploration 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain
  • Chromosomes, Plant / genetics
  • Gene Duplication
  • Gene Expression Profiling*
  • Genome, Plant / genetics*
  • Oryza / enzymology*
  • Oryza / genetics*
  • Oryza / growth & development
  • Oryza / physiology
  • Phosphoprotein Phosphatases / chemistry
  • Phosphoprotein Phosphatases / classification
  • Phosphoprotein Phosphatases / genetics*
  • Phylogeny
  • Proteome / chemistry
  • Proteome / classification
  • Proteome / genetics*
  • Reproduction
  • Stress, Physiological / genetics*


  • Proteome
  • Phosphoprotein Phosphatases