Genome-wide Identification Of Rice (Oryza Sativa. L) Protein Phosphatase, Phylogenetic And Expression Analysis

Protein kinase and protein phosphatase act as key elements in the reversible protein phosphorylation, which takes part in many cardinal signal transduction pathways in cell function in vivo. These refer to various signal transduction pathway in cell process, such as glycogen metabolism, stress signal, mitogenic signaling and pathogen. As soon as the completion of rice whole genome sequence, many kinds of protein families were identified and analysised in recent years. Although both protein kinase and protein phosphatase are essential to organisms, the analysis of protein phosphatase in the genome level was cast few attentions compared to protein kinase. Therefore, based on the completed rice whole genome, we surveyed a systematic analysis to protein phosphatase superfamily of this staple plant. In this study, we first constructed Pfam profiles depending on the well-annotated protein phosphatases sequences from web database and then scanned the rice whole proteome in TIGR using these profiles. At last, we identified 126 putative protein phosphatases including 84 PP2Cs, 19 PPPs, DSPs, 3 TSPs and 1 LWP. Protein phosphatases are stable in the evolution, and they have not undergone the large-scale duplications like protein kinase. In order to analysis these phosphatases in phylogenetics, we first grouped each family according to the sequence similarity and phylogenetic relationship. Then we made a comparison with Arabidopsis thaliana and human. Then we annotated each group based on the known phosphatases in other species. We found that most protein phosphatases in rice and Arabidopsis thaliana are homologous which indicates the conservation of protein phosphatase in monocotyledon and dicotyledon. The annotated groups will be useful to plant scientists for further study of protein phosphatases. Besides, we also surveyed the expression status of rice phosphatases through rice MPSS dataset. As a result, we found that a majority of the 126 phosphatases are well expressed in various tissues and organs under different environments. These expressed phosphatases, compared to rice protein kinases, are superior not only in the percentage, but also in the unit expression value in which the protein phosphatase is one order of magnitude greater than protein kinase. Considering the absolutely dominance of protein kinases in number, we concluded that protein phosphatases and protein kinases establish a balanced relationship in expression and both play key roles in the reversible protein phosphorylation in cell.