A comprehensive analysis of protein phosphatases in rice and Arabidopsis

Protein phosphatases play essential roles in many cellular processes through the reversible protein phosphorylation that dictates many signal transduction pathways among organisms. Based on an in silico analysis, we classified 163 and 164 non-redundant protein phosphatases in rice and Arabidopsis, respectively. Protein serine/threonine phosphatases make up 67% of the total in both plants, in contrast to those of human, where this fraction is about 27%. Based on domain organization and intron composition analyses, we found that protein phosphatases in the two plants are highly conserved in structure. Evolutionary analysis suggests that segmental duplications occurring 40-70 million years ago, contributed to the limited expansion of protein phosphatases. Gene expression analysis suggests that most phosphatases have broad expression spectra, with high abundance in four surveyed tissues (root, leaf, inflorescence, and seedling); only 46 and 12 phosphatases expressed in a single tissue of rice and Arabidopsis, respectively, regardless of their expression levels. Promoter analysis among different phosphatase subfamilies demonstrates a variable distribution of the w-box (a cis-element involved in disease resistance) between rice and Arabidopsis.