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

Singh AK, Kumar R, Tripathi AK, Gupta BK, Pareek A, Singla-Pareek SL - Rice (N Y) (2015)

Bottom Line: 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.Interestingly, expression of none of the NCX genes was found to be co-regulated by NaCl and calcium.Together, our results present insights into the potential role of NCX family of proteins in abiotic stresses and development.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India, anils13@gmail.com.

ABSTRACT

Background: The Na(+)/Ca(2+) Exchanger (NCX) protein family is a member of the Cation/Ca(2+) exchanger superfamily and its members play important roles in cellular Ca(2+) homeostasis. While the functions of NCX family of proteins is well understood in humans, not much is known about the total complement of Na(+)/Ca(2+) 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.

Results: Through 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.

Conclusions: Together, 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.

No MeSH data available.


Related in: MedlinePlus

Predicted topological structure of each of the NCX family members in Arabidopsis and rice. Here, all the members are divided into clades according to phylogenetic relationship among Arabidopsis and rice NCX families (as shown in Additional file 1: Figure S1 and in Fig. 3). Topological structures were generated using Protter v1.0 (see Methods). For splice variants possessing a similar predicted topological architecture, only a single model for the topology has been provided. Red colored N-terminal regions in a few NCX proteins represent putative signal peptides. Finger-like projections are loops joining N- and C-terminus groups of TMS, these loops may act as EF hand. The box at the top-left is a schematic representation of the plasma membrane (shown as orange bar) with the extra- and the intra-cellular regions specified
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Fig3: Predicted topological structure of each of the NCX family members in Arabidopsis and rice. Here, all the members are divided into clades according to phylogenetic relationship among Arabidopsis and rice NCX families (as shown in Additional file 1: Figure S1 and in Fig. 3). Topological structures were generated using Protter v1.0 (see Methods). For splice variants possessing a similar predicted topological architecture, only a single model for the topology has been provided. Red colored N-terminal regions in a few NCX proteins represent putative signal peptides. Finger-like projections are loops joining N- and C-terminus groups of TMS, these loops may act as EF hand. The box at the top-left is a schematic representation of the plasma membrane (shown as orange bar) with the extra- and the intra-cellular regions specified

Mentions: Topological structures of all the NCX proteins of Arabidopsis and rice (for the longest ORFs among the spliced variants) were predicted using Protter software (Fig. 3). Presence of transmembrane segments (TMSs) indicated that all the NCX proteins are transmembrane proteins. In general, proteins clustered in same clade in phylogenetic tree (Additional file 1: Figure S1) share similar membrane topologies. Thus, topological models were arranged as per the phylogenetic clustering of NCX proteins. The number of TMSs was found to be variable in various NCX proteins and ranged from 5 to 14. In many NCX proteins from both rice and Arabidopsis, a large hydrophilic loop intruding into the cytoplasm apparently separated the TMSs into two groups joined together by the large hydrophilic loop. However, as an exception, in case of OsNCX15, the TMSs were found to be separated by an extracellular loop. It was observed that generally lesser number of TMSs lie towards the N-terminal side of the loop and more were present towards C-terminal side (Fig. 3). This loop comprises sites important for calcium regulation, Na+ dependent inactivation and alternative splicing (Iwamoto et al. 1999; Marshall et al. 2005). Some proteins such as AtNCX2, OsNCX1 and OsNCX4 also have EF hand loop in between two spans of TMS (marked as clade I in Fig. 3). Two spans of TMS have also been reported earlier in case of NCX domain containing calcium/proton exchangers (CAX), calcium/cation exchangers (CCX) and Magnesium/cation exchangers (MHX) in Arabidopsis, but they differ in function with little modification in the N- and C terminal residues of TMS (Kamiya and Maeshima 2004; Shigaki et al. 2006). Based on experimental evidences, NCX proteins are modeled to have nine putative TMSs (Iwamoto et al. 1999; Nicoll et al. 1999) in animals. Five TMSs were reported to be present in the N-terminal domain and 4 in the C-terminal domain. These NCX proteins comprised ~30 residues long signal peptide that is cleaved during initial processing. Interestingly, proteins with signal peptide on their N-terminal were clustered in clade I and clade V (Fig. 3).Fig. 3


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

Singh AK, Kumar R, Tripathi AK, Gupta BK, Pareek A, Singla-Pareek SL - Rice (N Y) (2015)

Predicted topological structure of each of the NCX family members in Arabidopsis and rice. Here, all the members are divided into clades according to phylogenetic relationship among Arabidopsis and rice NCX families (as shown in Additional file 1: Figure S1 and in Fig. 3). Topological structures were generated using Protter v1.0 (see Methods). For splice variants possessing a similar predicted topological architecture, only a single model for the topology has been provided. Red colored N-terminal regions in a few NCX proteins represent putative signal peptides. Finger-like projections are loops joining N- and C-terminus groups of TMS, these loops may act as EF hand. The box at the top-left is a schematic representation of the plasma membrane (shown as orange bar) with the extra- and the intra-cellular regions specified
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4488139&req=5

Fig3: Predicted topological structure of each of the NCX family members in Arabidopsis and rice. Here, all the members are divided into clades according to phylogenetic relationship among Arabidopsis and rice NCX families (as shown in Additional file 1: Figure S1 and in Fig. 3). Topological structures were generated using Protter v1.0 (see Methods). For splice variants possessing a similar predicted topological architecture, only a single model for the topology has been provided. Red colored N-terminal regions in a few NCX proteins represent putative signal peptides. Finger-like projections are loops joining N- and C-terminus groups of TMS, these loops may act as EF hand. The box at the top-left is a schematic representation of the plasma membrane (shown as orange bar) with the extra- and the intra-cellular regions specified
Mentions: Topological structures of all the NCX proteins of Arabidopsis and rice (for the longest ORFs among the spliced variants) were predicted using Protter software (Fig. 3). Presence of transmembrane segments (TMSs) indicated that all the NCX proteins are transmembrane proteins. In general, proteins clustered in same clade in phylogenetic tree (Additional file 1: Figure S1) share similar membrane topologies. Thus, topological models were arranged as per the phylogenetic clustering of NCX proteins. The number of TMSs was found to be variable in various NCX proteins and ranged from 5 to 14. In many NCX proteins from both rice and Arabidopsis, a large hydrophilic loop intruding into the cytoplasm apparently separated the TMSs into two groups joined together by the large hydrophilic loop. However, as an exception, in case of OsNCX15, the TMSs were found to be separated by an extracellular loop. It was observed that generally lesser number of TMSs lie towards the N-terminal side of the loop and more were present towards C-terminal side (Fig. 3). This loop comprises sites important for calcium regulation, Na+ dependent inactivation and alternative splicing (Iwamoto et al. 1999; Marshall et al. 2005). Some proteins such as AtNCX2, OsNCX1 and OsNCX4 also have EF hand loop in between two spans of TMS (marked as clade I in Fig. 3). Two spans of TMS have also been reported earlier in case of NCX domain containing calcium/proton exchangers (CAX), calcium/cation exchangers (CCX) and Magnesium/cation exchangers (MHX) in Arabidopsis, but they differ in function with little modification in the N- and C terminal residues of TMS (Kamiya and Maeshima 2004; Shigaki et al. 2006). Based on experimental evidences, NCX proteins are modeled to have nine putative TMSs (Iwamoto et al. 1999; Nicoll et al. 1999) in animals. Five TMSs were reported to be present in the N-terminal domain and 4 in the C-terminal domain. These NCX proteins comprised ~30 residues long signal peptide that is cleaved during initial processing. Interestingly, proteins with signal peptide on their N-terminal were clustered in clade I and clade V (Fig. 3).Fig. 3

Bottom Line: 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.Interestingly, expression of none of the NCX genes was found to be co-regulated by NaCl and calcium.Together, our results present insights into the potential role of NCX family of proteins in abiotic stresses and development.

View Article: PubMed Central - PubMed

Affiliation: Plant Molecular Biology Group, International Centre for Genetic Engineering & Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi, 110067, India, anils13@gmail.com.

ABSTRACT

Background: The Na(+)/Ca(2+) Exchanger (NCX) protein family is a member of the Cation/Ca(2+) exchanger superfamily and its members play important roles in cellular Ca(2+) homeostasis. While the functions of NCX family of proteins is well understood in humans, not much is known about the total complement of Na(+)/Ca(2+) 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.

Results: Through 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.

Conclusions: Together, 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.

No MeSH data available.


Related in: MedlinePlus