Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants
Identifieur interne : 000594 ( Main/Exploration ); précédent : 000593; suivant : 000595Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants
Auteurs : Tapan Kumar Mohanta ; Pankaj Kumar Arora ; Nibedita Mohanta ; Pratap Parida ; Hanhong BaeSource :
- BMC Genomics [ 1471-2164 ] ; 2015.
Abstract
Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes.
A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with
We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development.
The online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1244-7
PubMed: 25888265
PubMed Central: 4363184
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants</title><author><name sortKey="Mohanta, Tapan Kumar" sort="Mohanta, Tapan Kumar" uniqKey="Mohanta T" first="Tapan Kumar" last="Mohanta">Tapan Kumar Mohanta</name><affiliation><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook 712749 Republic of Korea</nlm:aff><wicri:noCountry code="subfield">Gyeonsangbook 712749 Republic of Korea</wicri:noCountry></affiliation></author><author><name sortKey="Arora, Pankaj Kumar" sort="Arora, Pankaj Kumar" uniqKey="Arora P" first="Pankaj Kumar" last="Arora">Pankaj Kumar Arora</name><affiliation><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook 712749 Republic of Korea</nlm:aff><wicri:noCountry code="subfield">Gyeonsangbook 712749 Republic of Korea</wicri:noCountry></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="Parida, Pratap" sort="Parida, Pratap" uniqKey="Parida P" first="Pratap" last="Parida">Pratap Parida</name><affiliation><nlm:aff id="Aff3">Center for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam 786004 India</nlm:aff><wicri:noCountry code="subfield">Assam 786004 India</wicri:noCountry></affiliation></author><author><name sortKey="Bae, Hanhong" sort="Bae, Hanhong" uniqKey="Bae H" first="Hanhong" last="Bae">Hanhong Bae</name><affiliation><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook 712749 Republic of Korea</nlm:aff><wicri:noCountry code="subfield">Gyeonsangbook 712749 Republic of Korea</wicri:noCountry></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25888265</idno><idno type="pmc">4363184</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4363184</idno><idno type="RBID">PMC:4363184</idno><idno type="doi">10.1186/s12864-015-1244-7</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000582</idno><idno type="wicri:Area/Pmc/Curation">000581</idno><idno type="wicri:Area/Pmc/Checkpoint">000465</idno><idno type="wicri:Area/Ncbi/Merge">001A95</idno><idno type="wicri:Area/Ncbi/Curation">001A95</idno><idno type="wicri:Area/Ncbi/Checkpoint">001A95</idno><idno type="wicri:Area/Main/Merge">000594</idno><idno type="wicri:Area/Main/Curation">000594</idno><idno type="wicri:Area/Main/Exploration">000594</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Identification of new members of the MAPK gene family in plants shows diverse conserved domains and novel activation loop variants</title><author><name sortKey="Mohanta, Tapan Kumar" sort="Mohanta, Tapan Kumar" uniqKey="Mohanta T" first="Tapan Kumar" last="Mohanta">Tapan Kumar Mohanta</name><affiliation><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook 712749 Republic of Korea</nlm:aff><wicri:noCountry code="subfield">Gyeonsangbook 712749 Republic of Korea</wicri:noCountry></affiliation></author><author><name sortKey="Arora, Pankaj Kumar" sort="Arora, Pankaj Kumar" uniqKey="Arora P" first="Pankaj Kumar" last="Arora">Pankaj Kumar Arora</name><affiliation><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook 712749 Republic of Korea</nlm:aff><wicri:noCountry code="subfield">Gyeonsangbook 712749 Republic of Korea</wicri:noCountry></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="Parida, Pratap" sort="Parida, Pratap" uniqKey="Parida P" first="Pratap" last="Parida">Pratap Parida</name><affiliation><nlm:aff id="Aff3">Center for Studies in Biotechnology, Dibrugarh University, Dibrugarh, Assam 786004 India</nlm:aff><wicri:noCountry code="subfield">Assam 786004 India</wicri:noCountry></affiliation></author><author><name sortKey="Bae, Hanhong" sort="Bae, Hanhong" uniqKey="Bae H" first="Hanhong" last="Bae">Hanhong Bae</name><affiliation><nlm:aff id="Aff1">School of Biotechnology, Yeungnam University, Daehak Gyeongsan, Gyeonsangbook 712749 Republic of Korea</nlm:aff><wicri:noCountry code="subfield">Gyeonsangbook 712749 Republic of Korea</wicri:noCountry></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</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>Mitogen Activated Protein Kinase (MAPK) signaling is of critical importance in plants and other eukaryotic organisms. The MAPK cascade plays an indispensible role in the growth and development of plants, as well as in biotic and abiotic stress responses. The MAPKs are constitute the most downstream module of the three tier MAPK cascade and are phosphorylated by upstream MAP kinase kinases (MAPKK), which are in turn are phosphorylated by MAP kinase kinase kinase (MAPKKK). The MAPKs play pivotal roles in regulation of many cytoplasmic and nuclear substrates, thus regulating several biological processes.</p></sec><sec><title>Results</title><p>A total of 589 MAPKs genes were identified from the genome wide analysis of 40 species. The sequence analysis has revealed the presence of several N- and C-terminal conserved domains. The MAPKs were previously believed to be characterized by the presence of TEY/TDY activation loop motifs. The present study showed that, in addition to presence of activation loop TEY/TDY motifs, MAPKs are also contain MEY, TEM, TQM, TRM, TVY, TSY, TEC and TQY activation loop motifs. Phylogenetic analysis of all predicted MAPKs were clustered into six different groups (group A, B, C, D, E and F), and all predicted MAPKs were assigned with specific names based on their orthology based evolutionary relationships with <italic>Arabidopsis</italic> or <italic>Oryza</italic> MAPKs.</p></sec><sec><title>Conclusion</title><p>We conducted global analysis of the MAPK gene family of plants from lower eukaryotes to higher eukaryotes and analyzed their genomic and evolutionary aspects. Our study showed the presence of several new activation loop motifs and diverse conserved domains in MAPKs. Advance study of newly identified activation loop motifs can provide further information regarding the downstream signaling cascade activated in response to a wide array of stress conditions, as well as plant growth and development.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1244-7) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Ellis, Be" uniqKey="Ellis B">BE Ellis</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Besteiro, Mag" uniqKey="Besteiro M">MAG Besteiro</name></author><author><name sortKey="Ulm, R" uniqKey="Ulm R">R Ulm</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Caunt, Cj" uniqKey="Caunt C">CJ Caunt</name></author><author><name sortKey="Keyse, Sm" uniqKey="Keyse S">SM 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