Genome-wide investigation and expression analysis of Sodium/Calcium exchanger gene family in rice and Arabidopsis

Abstract

BackgroundThe Na+/Ca2+ Exchanger (NCX) protein family is a member of the Cation/Ca2+ exchanger superfamily and its members play important roles in cellular Ca2+ homeostasis. While the functions of NCX family of proteins is well understood in humans, not much is known about the total complement of Na+/Ca2+ exchangers in plants and their role in various physiological and developmental processes. In the present study, we have identified all the NCX proteins encoded in the genomes of rice and Arabidopsis and studied their phylogeny, domain architecture and expression profiles across different tissues, at various developmental stages and under stress conditions.ResultsThrough whole genome investigation, we identified twenty-two NCX proteins encoded by fifteen genes in rice and sixteen NCX proteins encoded by thirteen genes in Arabidopsis. Based on phylogenetic reconstruction, these could be classified into five clades, members of most of which were found to possess distinct domain architecture. Expression profiling of the identified NCX genes using publicly available MPSS and microarray data showed differential expression patterns under abiotic stresses, and at various development stages. In rice, OsNCX1, OsNCX8, OsNCX9 and OsNCX15 were found to be highly expressed in all the plant parts and various developmental stages. qRT-PCR based expression analysis revealed that OsNCX3, OsNCX10 and OsNCX15 were highly induced by salt and dehydration stress. Besides, expression profiling showed differential regulation of rice NCX genes in response to calcium and EGTA. Interestingly, expression of none of the NCX genes was found to be co-regulated by NaCl and calcium.ConclusionsTogether, our results present insights into the potential role of NCX family of proteins in abiotic stresses and development. Findings of the present investigation should serve as a starting point for future studies aiming functional characterization of plant NCX family proteins.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0054-5) contains supplementary material, which is available to authorized users.

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

“…The identified TaCaCA proteins were classified into 14 TaCAX, 10 TaCCX, 7 TaNCL, and 3 TaMHX proteins on the basis of their close similarity and tight phylogenetic clustering with respective known proteins from various plants (Figure S1; File S1). In other higher plants, a total of 14 (6 AtCAX, 5 AtCCX, 2 AtNCL, and 1 AtMHX), 15 (6 OsCAX, 5 OsCCX, 2 OsNCL, and 2 OsMHX), and 14 (6 ZmCAX, 6 ZmCCX, 1 ZmNCL, and 1 ZmMHX) CaCA protein are reported in Arabidopsis, rice, and maize, respectively (Emery et al, 2012; Singh et al, 2015; Pittman and Hirschi, 2016a). It was earlier established that T. aestivum consisted of higher number of genes in each gene family (Shumayla et al, 2016a,b) due to their large allohexaploid (2n = 6x = 42; AABBDD) nature of genome (Marcussen et al, 2014).…”

“…Occurrence of CaCA genes on various chromosomes has also been reported in Arabidopsis and rice, where these genes are distributed on four out of five, and eight out of twelve chromosomes, respectively. Five genes of Arabidopsis are located on chromosome I, while three genes are reported on each of chromosome II, III and XI of rice (Singh et al, 2015). …”

“…To identify the CaCA superfamily proteins (TaCaCA) in the genome of T. aestivum , BLASTp search ( e -value 0.00001) of known CaCA proteins sequences from rice and Arabidopsis (Emery et al, 2012; Gaash et al, 2013; Singh et al, 2015; Pittman and Hirschi, 2016a) was performed against the protein model sequences of T. aestivum obtained from IWGSC server (Nussbaumer et al, 2013; IWGSC, 2014) (http://www.wheatgenome.org/, http://wheat-urgi.versailles.inra.fr/Seq-Repository/Genes-annotations). A total of 6 CAX, 5 CCX and 1 each MHX and NCL sequences from Arabidopsis, and 6 CAX, 5 CCX, 2 MHX, and 2 NCL sequences from rice were used in BLAST search as described earlier (Pittman and Hirschi, 2016a).…”

“…Modulated expression of these proteins have also been observed in various plants during numerous abiotic stresses, which indicated their role in stress response (Hirschi et al, 1996, 2000; Shaul et al, 1999; Kamiya et al, 2005; Morris et al, 2008; Wang et al, 2012; Singh et al, 2015; Li et al, 2016). Functional characterization of certain CaCA proteins like AtNCL, AtCAX1, OsCAX4, SsCAX1 and others further established their role in various kinds of abiotic stress response (Mei et al, 2007; Han et al, 2012; Wang et al, 2012; Yamada et al, 2014; Li et al, 2016; Pittman and Hirschi, 2016b; Zhang et al, 2016).…”

“…CaCA proteins basically form a composite superfamily, which consists of five different families of exchanger proteins- YRBG, Na + /Ca 2+ exchanger (NCX), Na + /Ca 2+ , K + exchanger (NCKX), cation/Ca 2+ exchanger (CCX), and H + /cation exchanger (CAX), which are classified on the basis of their function and evolutionary relationship (Cai and Lytton, 2004a; Emery et al, 2012; Pittman and Hirschi, 2016a). Recently, Singh et al (2015) proposed the classification of all the CaCA superfamily proteins as NCX family due to the occurrence of Na_Ca_ex (PF01699) domain and tight evolutionary relationship between them. However, Pittman and Hirschi (2016a) by phylogenetic analysis and structure modeling further established that the CaCA superfamily members exhibit diverse structural and functional characteristics, and all of them cannot be classified as NCX proteins.…”