Limits...
Investigation of genes encoding calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum L.).

Meena MK, Ghawana S, Sardar A, Dwivedi V, Khandal H, Roy R, Chattopadhyay D - PLoS ONE (2015)

Bottom Line: Most of the CaCBL genes exhibited high expression in flowers.Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance.These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.

ABSTRACT
Calcium ion (Ca2+) is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants' response process. Calcineurin B-like proteins (CBLs) are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea) genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS) suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL) were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

No MeSH data available.


Comparison of structures of CBL proteins from different species.Protein structure of calcineurin B of Saccharomyces cerevisiae (A) and CBL1 from, Ostreococcus tauri (B), Chlorella variabilis (C), Physcomitrella patens (D), chickpea (E) and Arabidopsis (F) were generated using Phyre2 remote homology modeling server. All five structures from different species were analysed by pyMOL program. All the structures were superimposed (G) to show presence of extra helix (in boxes) in CBL proteins of Chlorella and chickpea.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4390317&req=5

pone.0123640.g003: Comparison of structures of CBL proteins from different species.Protein structure of calcineurin B of Saccharomyces cerevisiae (A) and CBL1 from, Ostreococcus tauri (B), Chlorella variabilis (C), Physcomitrella patens (D), chickpea (E) and Arabidopsis (F) were generated using Phyre2 remote homology modeling server. All five structures from different species were analysed by pyMOL program. All the structures were superimposed (G) to show presence of extra helix (in boxes) in CBL proteins of Chlorella and chickpea.

Mentions: Crystal structure of AtCBL2 [48] was used to derive peptide structures of OtCBL1, CvCBL1, PpCBL1, AtCBL1 and CaCBL1. Although these peptide sequences share 38–81% amino acid identity, they maintain very similar protein structure (Fig 3), suggesting a high conservation of function. Structure of yeast calcineurin B is also presented to show an overall similarity in structure. Structure of CvCBL1 showed some deviation from those of OtCBL1 and other plant CBLs presented in the figure. All the CBL peptides are devoid of beta sheets and composed of helix and loops. Yeast calcineurin B protein and OtCBL1 have 11 helices. All other CBLs in higher organisms are composed of 13–14 helices. The last two helices were broken into four helices in CBL peptides of higher organisms to result in 13 helices. CvCBL1 possesses 14 helices because it has a long N-terminus and the sequence ‘VEVEAKA’ in the N-terminal domain forms an extra helix. CaCBL1, with a small N-terminus, is composed of 14 helices because of a small C-terminal helix composed of a sequence stretch ‘FVFNS’. Although, this sequence stretch is fairly conserved in other CBLs (S2 Fig), it formed loops in those peptides, but a helix in CaCBL1. In the merged peptide structure these two deviations in CaCBL1 and CvCBL1 could be identified.


Investigation of genes encoding calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum L.).

Meena MK, Ghawana S, Sardar A, Dwivedi V, Khandal H, Roy R, Chattopadhyay D - PLoS ONE (2015)

Comparison of structures of CBL proteins from different species.Protein structure of calcineurin B of Saccharomyces cerevisiae (A) and CBL1 from, Ostreococcus tauri (B), Chlorella variabilis (C), Physcomitrella patens (D), chickpea (E) and Arabidopsis (F) were generated using Phyre2 remote homology modeling server. All five structures from different species were analysed by pyMOL program. All the structures were superimposed (G) to show presence of extra helix (in boxes) in CBL proteins of Chlorella and chickpea.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4390317&req=5

pone.0123640.g003: Comparison of structures of CBL proteins from different species.Protein structure of calcineurin B of Saccharomyces cerevisiae (A) and CBL1 from, Ostreococcus tauri (B), Chlorella variabilis (C), Physcomitrella patens (D), chickpea (E) and Arabidopsis (F) were generated using Phyre2 remote homology modeling server. All five structures from different species were analysed by pyMOL program. All the structures were superimposed (G) to show presence of extra helix (in boxes) in CBL proteins of Chlorella and chickpea.
Mentions: Crystal structure of AtCBL2 [48] was used to derive peptide structures of OtCBL1, CvCBL1, PpCBL1, AtCBL1 and CaCBL1. Although these peptide sequences share 38–81% amino acid identity, they maintain very similar protein structure (Fig 3), suggesting a high conservation of function. Structure of yeast calcineurin B is also presented to show an overall similarity in structure. Structure of CvCBL1 showed some deviation from those of OtCBL1 and other plant CBLs presented in the figure. All the CBL peptides are devoid of beta sheets and composed of helix and loops. Yeast calcineurin B protein and OtCBL1 have 11 helices. All other CBLs in higher organisms are composed of 13–14 helices. The last two helices were broken into four helices in CBL peptides of higher organisms to result in 13 helices. CvCBL1 possesses 14 helices because it has a long N-terminus and the sequence ‘VEVEAKA’ in the N-terminal domain forms an extra helix. CaCBL1, with a small N-terminus, is composed of 14 helices because of a small C-terminal helix composed of a sequence stretch ‘FVFNS’. Although, this sequence stretch is fairly conserved in other CBLs (S2 Fig), it formed loops in those peptides, but a helix in CaCBL1. In the merged peptide structure these two deviations in CaCBL1 and CvCBL1 could be identified.

Bottom Line: Most of the CaCBL genes exhibited high expression in flowers.Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance.These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.

ABSTRACT
Calcium ion (Ca2+) is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants' response process. Calcineurin B-like proteins (CBLs) are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea) genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS) suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL) were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

No MeSH data available.