Genome-wide analysis of plant-type II Ca(2+)ATPases gene family from rice and Arabidopsis: potential role in abiotic stresses

Abstract

The Plant Ca(2+)ATPases are members of the P-type ATPase superfamily and play essential roles in pollen tube growth, vegetative development, inflorescence architecture, stomatal opening or closing as well as transport of Ca(2+), Mn(2+) and Zn(2+). Their role in abiotic stress adaptation by activation of different signaling pathways is emerging. In Arabidopsis, the P-type Ca(2+)ATPases can be classified in two distinct groups: type IIA (ECA) and type IIB (ACA). The availability of rice genome sequence allowed performing a genome-wide search for P-type Ca(2+)ATPases proteins, and the comparison of the identified proteins with their homologs in Arabidopsis model plant. In the present study, we identified the P-type II Ca(2+)ATPases from rice by analyzing their phylogenetic relationship, multiple alignment, cis-regulatory elements, protein domains, motifs and homology percentage. The phylogenetic analysis revealed that rice type IIA Ca(2+)ATPases clustered with Arabidopsis type IIA Ca(2+)ATPases and showed high sequence similarity within the group, whereas rice type IIB Ca(2+)ATPases presented variable sequence similarities with Arabidopsis type IIB members. The protein homology modeling, identification of putative transmembrane domains and conserved motifs of rice P-type II Ca(2+)ATPases provided information on their functions and structural architecture. The analysis of P-type II Ca(2+)ATPases promoter regions in rice showed multiple stress-induced cis-acting elements. The expression profile analysis indicated vital roles of P-type II Ca(2+)ATPases in stress signaling, plant development and abiotic stress responses. The comprehensive analysis and expression profiling provided a critical platform for functional characterization of P-type II Ca(2+)ATPase genes that could be applied in engineering crop plants with modified calcium signaling and homeostatic pathways.