Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain

Calcium ions are considered ubiquitous second messengers in eukaryotic signal transduction pathways. Intracellular Ca2+ concentration are modulated by various signals such as hormones and biotic and abiotic stresses. Modulation of Ca2+ ion leads to stimulation of calcium dependent protein kinase gen...

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Main Authors:	Mohanta, Tapan K., Mohanta, Nibedita, Mohanta, Yugal K., Bae, Hanhong
Format:	Online
Language:	English
Published:	Frontiers Media S.A. 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690006/

id	pubmed-4690006
recordtype	oai_dc
spelling	pubmed-46900062016-01-05 Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain Mohanta, Tapan K. Mohanta, Nibedita Mohanta, Yugal K. Bae, Hanhong Plant Science Calcium ions are considered ubiquitous second messengers in eukaryotic signal transduction pathways. Intracellular Ca2+ concentration are modulated by various signals such as hormones and biotic and abiotic stresses. Modulation of Ca2+ ion leads to stimulation of calcium dependent protein kinase genes (CPKs), which results in regulation of gene expression and therefore mediates plant growth and development as well as biotic and abiotic stresses. Here, we reported the CPK gene family of 40 different plant species (950 CPK genes) and provided a unified nomenclature system for all of them. In addition, we analyzed their genomic, biochemical and structural conserved features. Multiple sequence alignment revealed that the kinase domain, auto-inhibitory domain and EF-hands regions of regulatory domains are highly conserved in nature. Additionally, the EF-hand domains of higher plants were found to contain four D-x-D and two D-E-L motifs, while lower eukaryotic plants had two D-x-D and one D-x-E motifs in their EF-hands. Phylogenetic analysis showed that CPK genes are clustered into four different groups. By studying the CPK gene family across the plant lineage, we provide the first evidence of the presence of D-x-D motif in the calcium binding EF-hand domain of CPK proteins. Frontiers Media S.A. 2015-12-24 /pmc/articles/PMC4690006/ /pubmed/26734045 http://dx.doi.org/10.3389/fpls.2015.01146 Text en Copyright © 2015 Mohanta, Mohanta, Mohanta and Bae. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Mohanta, Tapan K. Mohanta, Nibedita Mohanta, Yugal K. Bae, Hanhong
spellingShingle	Mohanta, Tapan K. Mohanta, Nibedita Mohanta, Yugal K. Bae, Hanhong Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain
author_facet	Mohanta, Tapan K. Mohanta, Nibedita Mohanta, Yugal K. Bae, Hanhong
author_sort	Mohanta, Tapan K.
title	Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain
title_short	Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain
title_full	Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain
title_fullStr	Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain
title_full_unstemmed	Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain
title_sort	genome-wide identification of calcium dependent protein kinase gene family in plant lineage shows presence of novel d-x-d and d-e-l motifs in ef-hand domain
description	Calcium ions are considered ubiquitous second messengers in eukaryotic signal transduction pathways. Intracellular Ca2+ concentration are modulated by various signals such as hormones and biotic and abiotic stresses. Modulation of Ca2+ ion leads to stimulation of calcium dependent protein kinase genes (CPKs), which results in regulation of gene expression and therefore mediates plant growth and development as well as biotic and abiotic stresses. Here, we reported the CPK gene family of 40 different plant species (950 CPK genes) and provided a unified nomenclature system for all of them. In addition, we analyzed their genomic, biochemical and structural conserved features. Multiple sequence alignment revealed that the kinase domain, auto-inhibitory domain and EF-hands regions of regulatory domains are highly conserved in nature. Additionally, the EF-hand domains of higher plants were found to contain four D-x-D and two D-E-L motifs, while lower eukaryotic plants had two D-x-D and one D-x-E motifs in their EF-hands. Phylogenetic analysis showed that CPK genes are clustered into four different groups. By studying the CPK gene family across the plant lineage, we provide the first evidence of the presence of D-x-D motif in the calcium binding EF-hand domain of CPK proteins.
publisher	Frontiers Media S.A.
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4690006/
_version_	1613516368871686144

Genome-Wide Identification of Calcium Dependent Protein Kinase Gene Family in Plant Lineage Shows Presence of Novel D-x-D and D-E-L Motifs in EF-Hand Domain

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