Research article Genome-wide analysis of plant-type II Ca 2þ ATPases gene family from rice and Arabidopsis: Potential role in abiotic stresses Kazi Md. Kamrul Huda, Sandep Yadav, Mst. Sufara Akhter Banu, Dipesh Kumar Trivedi, Narendra Tuteja * Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India article info Article history: Received 27 December 2012 Accepted 18 January 2013 Available online 30 January 2013 Keywords: Abiotic stress Arabidopsis Phylogenetic analysis Rice Transmembrane domains and motifs Type II Ca 2þ ATPases abstract The Plant Ca 2þ 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 2þ , Mn 2þ and Zn 2þ . Their role in abiotic stress adaptation by activation of different sig- naling pathways is emerging. In Arabidopsis, the P-type Ca 2þ 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 2þ 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 2þ 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 2þ ATPases clustered with Arabidopsis type IIA Ca 2þ ATPases and showed high sequence similarity within the group, whereas rice type IIB Ca 2þ ATPases presented variable sequence similarities with Arabidopsis type IIB members. The protein homology modeling, identification of putative trans- membrane domains and conserved motifs of rice P-type II Ca 2þ ATPases provided information on their functions and structural architecture. The analysis of P-type II Ca 2þ ATPases promoter regions in rice showed multiple stress-induced cis-acting elements. The expression profile analysis indicated vital roles of P-type II Ca 2þ ATPases in stress signaling, plant development and abiotic stress responses. The com- prehensive analysis and expression profiling provided a critical platform for functional characterization of P-type II Ca 2þ ATPase genes that could be applied in engineering crop plants with modified calcium signaling and homeostatic pathways. Ó 2013 Elsevier Masson SAS. All rights reserved. 1. Introduction Ca 2þ acts as a secondary messenger and is involved in regulation of growth, development, reproduction, circadian rhythms, immu- nity, redox status, hormone biosynthesis as well as response to biotic and abiotic stresses by activation of various signaling path- ways [1]. Plant Ca 2þ ATPases are members of P-type ATPase super- family implicated in the restoration and maintenance of ion homeostasis by pumping calcium ions out of the cytosol [2]. Plant P-type Ca 2þ ATPases have been divided into two groups, type IIA and IIB, the latter contains an N-terminal autoinhibitory domain that binds to calmodulin and activates the Ca 2þ pump [3]. Type IIA and IIB Ca 2þ ATPases can be found in either or both plasma mem- brane and endomembrane systems [3]. This distribution is in contrast with animal cells, where type IIA and IIB Ca 2þ ATPases are found exclusively in the inner membranes and plasma membrane (PM), respectively. In Arabidopsis, type IIA Ca 2þ ATPases are extensively localized in the endoplasmic reticulum (ER) and Golgi complex [4]. Unlike the type IIA Ca 2þ ATPases, the type IIB Ca 2þ ATPases have been reported in various subcellular structures. For instance, At-ACA1 and At-ACA2 have been reported in chlor- oplast and ER [4], At-ACA4 and At-ACA11 were localized in vacuole [4,5], while At-ACA7 [6], At-ACA8 [4], At-ACA9 [4] are localized in PM, while At-ACA10 has been predicted to be plasma membrane localized [7]. Their variable localization in different cellular com- partments could indicate the involvement in different Ca 2þ medi- ated signaling pathways. The P-type II Ca 2þ ATPases are characterized by a high homology (50e80%) at amino acid level. The structures obtained from crys- tals of mammalian type IIA Ca 2þ ATPase showed the presence of 10 transmembrane helices [8], while the hydrophobicity analysis in Abbreviations: ACA, autoinhibited Ca 2þ ATPase; ECA, ER-type Ca 2þ ATPase; ER, endoplasmic reticulum; PCA1, Physcomitrella Ca 2þ ATPase; PCD, programmed cell death; qRT-PCR, quantitative reverse transcription PCR; SCA1, Soybean Ca 2þ ATPase; TM, transmembrane. * Corresponding author. Tel.: þ91 11 26742357; fax: þ91 11 26742316. E-mail address: narendra@icgeb.res.in (N. Tuteja). Contents lists available at SciVerse ScienceDirect Plant Physiology and Biochemistry journal homepage: www.elsevier.com/locate/plaphy 0981-9428/$ e see front matter Ó 2013 Elsevier Masson SAS. All rights reserved. http://dx.doi.org/10.1016/j.plaphy.2013.01.002 Plant Physiology and Biochemistry 65 (2013) 32e47