Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events
Identifieur interne : 001C58 ( Ncbi/Checkpoint ); précédent : 001C57; suivant : 001C59Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events
Auteurs : Tapan Kumar Mohanta [Corée du Sud] ; Nibedita Mohanta ; Yugal Kishore Mohanta ; Pratap Parida ; Hanhong Bae [Corée du Sud]Source :
- BMC Plant Biology [ 1471-2229 ] ; 2015.
Abstract
Calcium ions, the most versatile secondary messenger found in plants, are involved in the regulation of diverse arrays of plant growth and development, as well as biotic and abiotic stress responses. The calcineurin B-like proteins are one of the most important genes that act as calcium sensors.
In this study, we identified calcineurin B-like gene family members from 38 different plant species and assigned a unique nomenclature to each of them. Sequence analysis showed that, the CBL proteins contain three calcium binding EF-hand domain that contains several conserved Asp and Glu amino acid residues. The third EF-hand of the CBL protein was found to posses the D/E-x-D calcium binding sensor motif. Phylogenetic analysis showed that, the CBL genes fall into six different groups. Additionally, except group B CBLs, all the CBL proteins were found to contain N-terminal palmitoylation and myristoylation sites. An evolutionary study showed that, CBL genes are evolved from a common ancestor and subsequently diverged during the course of evolution of land plants. Tajima’s neutrality test showed that, CBL genes are highly polymorphic and evolved via decreasing population size due to balanced selection. Differential expression analysis with cold and heat stress treatment led to differential modulation of OsCBL genes.
The basic architecture of plant CBL genes is conserved throughout the plant kingdom. Evolutionary analysis showed that, these genes are evolved from a common ancestor of lower eukaryotic plant lineage and led to broadening of the calcium signaling events in higher eukaryotic organisms.
The online version of this article (doi:10.1186/s12870-015-0543-0) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12870-015-0543-0
PubMed: 26245459
PubMed Central: 4527274
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events</title><author><name sortKey="Mohanta, Tapan Kumar" sort="Mohanta, Tapan Kumar" uniqKey="Mohanta T" first="Tapan Kumar" last="Mohanta">Tapan Kumar Mohanta</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook, 712-749 Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook</wicri:regionArea><wicri:noRegion>Gyeongbook</wicri:noRegion></affiliation></author><author><name sortKey="Mohanta, Nibedita" sort="Mohanta, Nibedita" uniqKey="Mohanta N" first="Nibedita" last="Mohanta">Nibedita Mohanta</name><affiliation><nlm:aff id="Aff2">Department of Biotechnology, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa 757003 India</nlm:aff><wicri:noCountry code="subfield">Orissa 757003 India</wicri:noCountry></affiliation></author><author><name sortKey="Mohanta, Yugal Kishore" sort="Mohanta, Yugal Kishore" uniqKey="Mohanta Y" first="Yugal Kishore" last="Mohanta">Yugal Kishore Mohanta</name><affiliation><nlm:aff id="Aff3">Department of Botany, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa 757003 India</nlm:aff><wicri:noCountry code="subfield">Orissa 757003 India</wicri:noCountry></affiliation></author><author><name sortKey="Parida, Pratap" sort="Parida, Pratap" uniqKey="Parida P" first="Pratap" last="Parida">Pratap Parida</name><affiliation><nlm:aff id="Aff4">Center for studies in Biotechnology, Dibrugarh University, Dibrugarh, 786004 Assam India</nlm:aff><wicri:noCountry code="subfield">786004 Assam India</wicri:noCountry></affiliation></author><author><name sortKey="Bae, Hanhong" sort="Bae, Hanhong" uniqKey="Bae H" first="Hanhong" last="Bae">Hanhong Bae</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook, 712-749 Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook</wicri:regionArea><wicri:noRegion>Gyeongbook</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26245459</idno><idno type="pmc">4527274</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4527274</idno><idno type="RBID">PMC:4527274</idno><idno type="doi">10.1186/s12870-015-0543-0</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000632</idno><idno type="wicri:Area/Pmc/Curation">000631</idno><idno type="wicri:Area/Pmc/Checkpoint">000485</idno><idno type="wicri:Area/Ncbi/Merge">001C58</idno><idno type="wicri:Area/Ncbi/Curation">001C58</idno><idno type="wicri:Area/Ncbi/Checkpoint">001C58</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-wide identification of Calcineurin B-Like (CBL) gene family of plants reveals novel conserved motifs and evolutionary aspects in calcium signaling events</title><author><name sortKey="Mohanta, Tapan Kumar" sort="Mohanta, Tapan Kumar" uniqKey="Mohanta T" first="Tapan Kumar" last="Mohanta">Tapan Kumar Mohanta</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook, 712-749 Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook</wicri:regionArea><wicri:noRegion>Gyeongbook</wicri:noRegion></affiliation></author><author><name sortKey="Mohanta, Nibedita" sort="Mohanta, Nibedita" uniqKey="Mohanta N" first="Nibedita" last="Mohanta">Nibedita Mohanta</name><affiliation><nlm:aff id="Aff2">Department of Biotechnology, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa 757003 India</nlm:aff><wicri:noCountry code="subfield">Orissa 757003 India</wicri:noCountry></affiliation></author><author><name sortKey="Mohanta, Yugal Kishore" sort="Mohanta, Yugal Kishore" uniqKey="Mohanta Y" first="Yugal Kishore" last="Mohanta">Yugal Kishore Mohanta</name><affiliation><nlm:aff id="Aff3">Department of Botany, North Orissa University, Sri Ramchandra Vihar, Takatpur, Baripada, Mayurbhanj, Orissa 757003 India</nlm:aff><wicri:noCountry code="subfield">Orissa 757003 India</wicri:noCountry></affiliation></author><author><name sortKey="Parida, Pratap" sort="Parida, Pratap" uniqKey="Parida P" first="Pratap" last="Parida">Pratap Parida</name><affiliation><nlm:aff id="Aff4">Center for studies in Biotechnology, Dibrugarh University, Dibrugarh, 786004 Assam India</nlm:aff><wicri:noCountry code="subfield">786004 Assam India</wicri:noCountry></affiliation></author><author><name sortKey="Bae, Hanhong" sort="Bae, Hanhong" uniqKey="Bae H" first="Hanhong" last="Bae">Hanhong Bae</name><affiliation wicri:level="1"><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook, 712-749 Republic of Korea</nlm:aff><country xml:lang="fr">Corée du Sud</country><wicri:regionArea>School of Biotechnology, Yeungnam University Gyeongsan, Gyeongbook</wicri:regionArea><wicri:noRegion>Gyeongbook</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Plant Biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Calcium ions, the most versatile secondary messenger found in plants, are involved in the regulation of diverse arrays of plant growth and development, as well as biotic and abiotic stress responses. The calcineurin B-like proteins are one of the most important genes that act as calcium sensors.</p></sec><sec><title>Results</title><p>In this study, we identified calcineurin B-like gene family members from 38 different plant species and assigned a unique nomenclature to each of them. Sequence analysis showed that, the CBL proteins contain three calcium binding EF-hand domain that contains several conserved Asp and Glu amino acid residues. The third EF-hand of the CBL protein was found to posses the D/E-x-D calcium binding sensor motif. Phylogenetic analysis showed that, the CBL genes fall into six different groups. Additionally, except group B CBLs, all the CBL proteins were found to contain N-terminal palmitoylation and myristoylation sites. An evolutionary study showed that, CBL genes are evolved from a common ancestor and subsequently diverged during the course of evolution of land plants. Tajima’s neutrality test showed that, CBL genes are highly polymorphic and evolved via decreasing population size due to balanced selection. Differential expression analysis with cold and heat stress treatment led to differential modulation of OsCBL genes.</p></sec><sec><title>Conclusions</title><p>The basic architecture of plant CBL genes is conserved throughout the plant kingdom. Evolutionary analysis showed that, these genes are evolved from a common ancestor of lower eukaryotic plant lineage and led to broadening of the calcium signaling events in higher eukaryotic organisms.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12870-015-0543-0) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hamel, L P" uniqKey="Hamel L">L-P Hamel</name></author><author><name sortKey="Sheen, J" uniqKey="Sheen J">J Sheen</name></author><author><name sortKey="Seguin, A" uniqKey="Seguin A">A Séguin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tuteja, N" uniqKey="Tuteja N">N Tuteja</name></author><author><name sortKey="Mahajan, S" uniqKey="Mahajan S">S Mahajan</name></author></analytic></biblStruct><biblStruct><analytic><author><name 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Umen</name></author><author><name sortKey="Nedelcu, Am" uniqKey="Nedelcu A">AM Nedelcu</name></author><author><name sortKey="Hallmann, A" uniqKey="Hallmann A">A Hallmann</name></author><author><name sortKey="Miller, Sm" uniqKey="Miller S">SM Miller</name></author><author><name sortKey="Nishii, I" uniqKey="Nishii I">I Nishii</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Galperin, My" uniqKey="Galperin M">MY Galperin</name></author><author><name sortKey="Koonin, Ev" uniqKey="Koonin E">EV Koonin</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tajima, F" uniqKey="Tajima F">F Tajima</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Tajima, F" uniqKey="Tajima F">F Tajima</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Goodstein, Dm" uniqKey="Goodstein D">DM Goodstein</name></author><author><name sortKey="Shu, S" uniqKey="Shu S">S Shu</name></author><author><name sortKey="Howson, R" uniqKey="Howson R">R Howson</name></author><author><name sortKey="Neupane, R" uniqKey="Neupane R">R Neupane</name></author><author><name sortKey="Hayes, Rd" uniqKey="Hayes R">RD Hayes</name></author><author><name sortKey="Fazo, J" uniqKey="Fazo J">J Fazo</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Larkin, M" uniqKey="Larkin M">M Larkin</name></author><author><name sortKey="Blackshields, G" uniqKey="Blackshields G">G Blackshields</name></author><author><name sortKey="Brown, Np" uniqKey="Brown N">NP Brown</name></author><author><name sortKey="Chenna, R" uniqKey="Chenna R">R Chenna</name></author><author><name sortKey="Mcgettigan, P" uniqKey="Mcgettigan P">P McGettigan</name></author><author><name sortKey="Mcwilliam, H" uniqKey="Mcwilliam H">H McWilliam</name></author></analytic></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Corée du Sud</li></country></list><tree><noCountry><name sortKey="Mohanta, Nibedita" sort="Mohanta, Nibedita" uniqKey="Mohanta N" first="Nibedita" last="Mohanta">Nibedita Mohanta</name><name sortKey="Mohanta, Yugal Kishore" sort="Mohanta, Yugal Kishore" uniqKey="Mohanta Y" first="Yugal Kishore" last="Mohanta">Yugal Kishore Mohanta</name><name sortKey="Parida, Pratap" sort="Parida, Pratap" uniqKey="Parida P" first="Pratap" last="Parida">Pratap Parida</name></noCountry><country name="Corée du Sud"><noRegion><name sortKey="Mohanta, Tapan Kumar" sort="Mohanta, Tapan Kumar" uniqKey="Mohanta T" first="Tapan Kumar" last="Mohanta">Tapan Kumar Mohanta</name></noRegion><name sortKey="Bae, Hanhong" sort="Bae, Hanhong" uniqKey="Bae H" first="Hanhong" last="Bae">Hanhong Bae</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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