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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

Expression profiling of rice NCX genes under different abiotic stresses using qRT-PCR. Bar graphs show fold change in expression of rice NCX genes under various abiotic stresses, viz. a salinity, b dehydration, c heat, d cold, e oxidative (MV), f UV-B, g calcium (calcium chloride) and h calcium chelator EGTA i Heat map generated from the above qRT-PCR data representing the expression profile of rice NCX genes under different abiotic stresses and calcium and EGTA treatment. Color bars at the base represent fold change in expression; green, black and red colors represent downregulated, unaltered and upregulated expression of genes relative to the untreated control, respectively
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Fig8: Expression profiling of rice NCX genes under different abiotic stresses using qRT-PCR. Bar graphs show fold change in expression of rice NCX genes under various abiotic stresses, viz. a salinity, b dehydration, c heat, d cold, e oxidative (MV), f UV-B, g calcium (calcium chloride) and h calcium chelator EGTA i Heat map generated from the above qRT-PCR data representing the expression profile of rice NCX genes under different abiotic stresses and calcium and EGTA treatment. Color bars at the base represent fold change in expression; green, black and red colors represent downregulated, unaltered and upregulated expression of genes relative to the untreated control, respectively

Mentions: Calcium is one of the most important secondary messengers in plant system and its role in various adverse environmental conditions like biotic and abiotic stresses has been well studied. NCX proteins play a pivotal role in Ca2+-homeostasis and hence can potentially participate in the diverse physiological processes involving Ca2+ as the second messenger. To examine the role of rice NCX family members in abiotic stress and calcium homeostasis and to validate the expression profile obtained via analysis of microarray-based expression data, we have carried out expression analysis using quantitative real-time reverse transcription-PCR (qRT-PCR) in rice. The relative transcript abundance of all the OsNCX genes under various abiotic stresses viz. salinity, dehydration, oxidative, heat, cold and UV stress and treatments with calcium and EGTA has been presented as bar graphs and heat maps (Fig. 8a–i). Previous reports have shown that stress related genes are often differentially expressed in rice (Kumari et al. 2009). Expression of OsNCX3, OsNCX9 and OsNCX10 was either upregulated or unaltered under all the stresses imposed in present study which suggests that these NCX proteins might have some important role in response to abiotic stress. In contrast, expression of OsNCX5 was repressed under all the stresses except under UV stress. Interestingly, we found that relative transcript abundance of all the NCX genes was upregulated in response to UV stress. Particularly, OsNCX9, OsNCX10, OsNCX11 and OsNCX12 were highly up regulated by 100, 300, 56 and 50 fold, respectively in response to UV. OsNCX3 seems to be highly responsive to oxidative stress as it showed 122-fold upregulation in response to MV. In response to cold stress transcript level of OsNCX1 was specifically high, suggesting it might have some role in maintaining calcium level during cold stress. The expression of OsNCX3, OsNCX10 and OsNCX15 was predominantly up-regulated in response to salinity and dehydration stress. Transcript levels of OsNCX4 were very low, thus we were not able to detect it under any of the conditions tested in the present study.Fig. 8


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)

Expression profiling of rice NCX genes under different abiotic stresses using qRT-PCR. Bar graphs show fold change in expression of rice NCX genes under various abiotic stresses, viz. a salinity, b dehydration, c heat, d cold, e oxidative (MV), f UV-B, g calcium (calcium chloride) and h calcium chelator EGTA i Heat map generated from the above qRT-PCR data representing the expression profile of rice NCX genes under different abiotic stresses and calcium and EGTA treatment. Color bars at the base represent fold change in expression; green, black and red colors represent downregulated, unaltered and upregulated expression of genes relative to the untreated control, respectively
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig8: Expression profiling of rice NCX genes under different abiotic stresses using qRT-PCR. Bar graphs show fold change in expression of rice NCX genes under various abiotic stresses, viz. a salinity, b dehydration, c heat, d cold, e oxidative (MV), f UV-B, g calcium (calcium chloride) and h calcium chelator EGTA i Heat map generated from the above qRT-PCR data representing the expression profile of rice NCX genes under different abiotic stresses and calcium and EGTA treatment. Color bars at the base represent fold change in expression; green, black and red colors represent downregulated, unaltered and upregulated expression of genes relative to the untreated control, respectively
Mentions: Calcium is one of the most important secondary messengers in plant system and its role in various adverse environmental conditions like biotic and abiotic stresses has been well studied. NCX proteins play a pivotal role in Ca2+-homeostasis and hence can potentially participate in the diverse physiological processes involving Ca2+ as the second messenger. To examine the role of rice NCX family members in abiotic stress and calcium homeostasis and to validate the expression profile obtained via analysis of microarray-based expression data, we have carried out expression analysis using quantitative real-time reverse transcription-PCR (qRT-PCR) in rice. The relative transcript abundance of all the OsNCX genes under various abiotic stresses viz. salinity, dehydration, oxidative, heat, cold and UV stress and treatments with calcium and EGTA has been presented as bar graphs and heat maps (Fig. 8a–i). Previous reports have shown that stress related genes are often differentially expressed in rice (Kumari et al. 2009). Expression of OsNCX3, OsNCX9 and OsNCX10 was either upregulated or unaltered under all the stresses imposed in present study which suggests that these NCX proteins might have some important role in response to abiotic stress. In contrast, expression of OsNCX5 was repressed under all the stresses except under UV stress. Interestingly, we found that relative transcript abundance of all the NCX genes was upregulated in response to UV stress. Particularly, OsNCX9, OsNCX10, OsNCX11 and OsNCX12 were highly up regulated by 100, 300, 56 and 50 fold, respectively in response to UV. OsNCX3 seems to be highly responsive to oxidative stress as it showed 122-fold upregulation in response to MV. In response to cold stress transcript level of OsNCX1 was specifically high, suggesting it might have some role in maintaining calcium level during cold stress. The expression of OsNCX3, OsNCX10 and OsNCX15 was predominantly up-regulated in response to salinity and dehydration stress. Transcript levels of OsNCX4 were very low, thus we were not able to detect it under any of the conditions tested in the present study.Fig. 8

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