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.


The exon/Intron structure of representative CBL genes from various plant species.Introns and exons are represented by lines and black boxes, respectively. The length of lines and boxes correspond to intron-exon size accordingly. The exon-intron structures of CaCBL genes were determined by aligning their cDNA sequences to the corresponding gene sequences using Gene Structure Display Server 2.0 program. Exon/Intron structures of all the PpCBL and CaCBL genes are shown in S3 Fig.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123640.g002: The exon/Intron structure of representative CBL genes from various plant species.Introns and exons are represented by lines and black boxes, respectively. The length of lines and boxes correspond to intron-exon size accordingly. The exon-intron structures of CaCBL genes were determined by aligning their cDNA sequences to the corresponding gene sequences using Gene Structure Display Server 2.0 program. Exon/Intron structures of all the PpCBL and CaCBL genes are shown in S3 Fig.

Mentions: Comparison of gene and peptide sequences of CBL gene family reveals an evolution of gene structure. 604 base pair (bp)-long calcineurin B gene of yeast encodes a 175 aa-long peptide derived from two coding regions and the protein possesses a motif for N-myristoylation. The only CBL gene of Ostreococcus (Ot16g00900, OtCBL1) is of simple structure without any intron (Fig 2 and S3 Fig) and the protein is devoid of conserved motif for N-myristoylation (S2 Fig). OtCBL1 peptide sequence shows only about 30% amino acid identity with the yeast calcineurin B, indicating that the OtCBL1 might not have been derived from yeast calcineurin B or it has lost myristoylation motif and intron in the evolution. The Chlorella CBL gene (FJ901249.1, CvCBL1) is longer (1617 bp) than those encoding yeast calcineurin B (604 bp) and OtCBL1 (630 bp) and its protein coding sequence (CDS) is distributed in five coding regions showing appearance of complex gene structure with evolution. Increase in intron number is seen as an increase in the probability of differential splicing and ability to absorb mutations. The Chlorella CBL possesses motif for myristoylation. Physcomitrella CBL genes could be divided into two groups according to their gene structure. PpCBL2 (Pp1s4_347V6.1) and PpCBL3 (Pp1s107_63V6.1) are encoded by single coding regions of their ~650 bp-long genes, while PpCBL1 (Pp1s28_66V6.2) and PpCBL4 (Pp1s64_196V6.1) are longer (1960 bp and 2268 bp) in size and their coding sequences are distributed in eight coding regions. However, both PpCBL1 and PpCBL2 encode peptides of same length (213 aa) and possess MGXXXS motif, whereas PpCBL3 and PpCBL4 do not have this motif. Therefore, Physcomitrella possesses CBL genes with both simple and complex gene structures and its CBL genes encode proteins with and without myristoylation motif. Multiexonic CvCBL1 gene shows initiation of complex gene structure in unicellular algae. It appears that CBL proteins with or without N-myristoylation motif have different origins. Notably, CBL proteins appear to be absent in algae Volvox carteri and Chlamydomonas rheinhardtii, which are phylogenetically placed between Chlorella and Physcomitrella suggesting different calcium-signaling mechanism in these species. Re-appearance of CBL gene family in moss Physcomitrella with both mono- and multi-exonic genes and proteins with or without N-myristoylation motif indicates a convergence of both the types of CBL genes in this species.


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)

The exon/Intron structure of representative CBL genes from various plant species.Introns and exons are represented by lines and black boxes, respectively. The length of lines and boxes correspond to intron-exon size accordingly. The exon-intron structures of CaCBL genes were determined by aligning their cDNA sequences to the corresponding gene sequences using Gene Structure Display Server 2.0 program. Exon/Intron structures of all the PpCBL and CaCBL genes are shown in S3 Fig.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0123640.g002: The exon/Intron structure of representative CBL genes from various plant species.Introns and exons are represented by lines and black boxes, respectively. The length of lines and boxes correspond to intron-exon size accordingly. The exon-intron structures of CaCBL genes were determined by aligning their cDNA sequences to the corresponding gene sequences using Gene Structure Display Server 2.0 program. Exon/Intron structures of all the PpCBL and CaCBL genes are shown in S3 Fig.
Mentions: Comparison of gene and peptide sequences of CBL gene family reveals an evolution of gene structure. 604 base pair (bp)-long calcineurin B gene of yeast encodes a 175 aa-long peptide derived from two coding regions and the protein possesses a motif for N-myristoylation. The only CBL gene of Ostreococcus (Ot16g00900, OtCBL1) is of simple structure without any intron (Fig 2 and S3 Fig) and the protein is devoid of conserved motif for N-myristoylation (S2 Fig). OtCBL1 peptide sequence shows only about 30% amino acid identity with the yeast calcineurin B, indicating that the OtCBL1 might not have been derived from yeast calcineurin B or it has lost myristoylation motif and intron in the evolution. The Chlorella CBL gene (FJ901249.1, CvCBL1) is longer (1617 bp) than those encoding yeast calcineurin B (604 bp) and OtCBL1 (630 bp) and its protein coding sequence (CDS) is distributed in five coding regions showing appearance of complex gene structure with evolution. Increase in intron number is seen as an increase in the probability of differential splicing and ability to absorb mutations. The Chlorella CBL possesses motif for myristoylation. Physcomitrella CBL genes could be divided into two groups according to their gene structure. PpCBL2 (Pp1s4_347V6.1) and PpCBL3 (Pp1s107_63V6.1) are encoded by single coding regions of their ~650 bp-long genes, while PpCBL1 (Pp1s28_66V6.2) and PpCBL4 (Pp1s64_196V6.1) are longer (1960 bp and 2268 bp) in size and their coding sequences are distributed in eight coding regions. However, both PpCBL1 and PpCBL2 encode peptides of same length (213 aa) and possess MGXXXS motif, whereas PpCBL3 and PpCBL4 do not have this motif. Therefore, Physcomitrella possesses CBL genes with both simple and complex gene structures and its CBL genes encode proteins with and without myristoylation motif. Multiexonic CvCBL1 gene shows initiation of complex gene structure in unicellular algae. It appears that CBL proteins with or without N-myristoylation motif have different origins. Notably, CBL proteins appear to be absent in algae Volvox carteri and Chlamydomonas rheinhardtii, which are phylogenetically placed between Chlorella and Physcomitrella suggesting different calcium-signaling mechanism in these species. Re-appearance of CBL gene family in moss Physcomitrella with both mono- and multi-exonic genes and proteins with or without N-myristoylation motif indicates a convergence of both the types of CBL genes in this species.

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.