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In Silico Analysis Reveals 75 Members of Mitogen-Activated Protein Kinase Kinase Kinase Gene Family in Rice
Mitogen-Activated Protein Kinase Kinase Kinases (MAPKKKs) are important components of MAPK cascades, which are universal signal transduction modules and play important role in plant growth and development. In the sequenced Arabidopsis genome 80 MAPKKKs were identified and currently being analysed fo...
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Published in: | DNA research 2010-06, Vol.17 (3), p.139-153 |
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description | Mitogen-Activated Protein Kinase Kinase Kinases (MAPKKKs) are important components of MAPK cascades, which are universal signal transduction modules and play important role in plant growth and development. In the sequenced Arabidopsis genome 80 MAPKKKs were identified and currently being analysed for its role in different stress. In rice, economically important monocot cereal crop only five MAPKKKs were identified so far. In this study using computational analysis of sequenced rice genome we have identified 75 MAPKKKs. EST hits and full-length cDNA sequences (from KOME or Genbank database) of 75 MAPKKKs supported their existence. Phylogenetic analyses of MAPKKKs from rice and Arabidopsis have classified them into three subgroups, which include Raf, ZIK and MEKK. Conserved motifs in the deduced amino acid sequences of rice MAPKKKs strongly supported their identity as members of Raf, ZIK and MEKK subfamilies. Further expression analysis of the MAPKKKs in MPSS database revealed that their transcripts were differentially regulated in various stress and tissue-specific libraries. |
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In the sequenced Arabidopsis genome 80 MAPKKKs were identified and currently being analysed for its role in different stress. In rice, economically important monocot cereal crop only five MAPKKKs were identified so far. In this study using computational analysis of sequenced rice genome we have identified 75 MAPKKKs. EST hits and full-length cDNA sequences (from KOME or Genbank database) of 75 MAPKKKs supported their existence. Phylogenetic analyses of MAPKKKs from rice and Arabidopsis have classified them into three subgroups, which include Raf, ZIK and MEKK. Conserved motifs in the deduced amino acid sequences of rice MAPKKKs strongly supported their identity as members of Raf, ZIK and MEKK subfamilies. Further expression analysis of the MAPKKKs in MPSS database revealed that their transcripts were differentially regulated in various stress and tissue-specific libraries.</description><identifier>ISSN: 1340-2838</identifier><identifier>EISSN: 1756-1663</identifier><identifier>DOI: 10.1093/dnares/dsq011</identifier><identifier>PMID: 20395279</identifier><language>eng</language><publisher>Oxford: Oxford University Press</publisher><subject>Amino Acid Sequence ; Arabidopsis ; Arabidopsis - genetics ; Biological and medical sciences ; Computational Biology ; Fundamental and applied biological sciences. Psychology ; Gene Expression Regulation, Plant ; General aspects ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Plant ; MAP Kinase Kinase Kinases - classification ; MAP Kinase Kinase Kinases - genetics ; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) ; Molecular and cellular biology ; Molecular genetics ; Molecular Sequence Data ; Oryza - genetics ; Oryza sativa ; Phylogeny ; Plant Proteins - genetics ; Sequence Homology, Amino Acid ; Species Specificity</subject><ispartof>DNA research, 2010-06, Vol.17 (3), p.139-153</ispartof><rights>2015 INIST-CNRS</rights><rights>The Author 2010. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. 2010</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c514t-ecfd05a6cc229afee497d2880d7b4950d1395f897c039f9915b490a5bd8b35d43</citedby><cites>FETCH-LOGICAL-c514t-ecfd05a6cc229afee497d2880d7b4950d1395f897c039f9915b490a5bd8b35d43</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885274/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885274/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=22896939$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/20395279$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>KUDUPUDI PRABHAKARA RAO</creatorcontrib><creatorcontrib>RICHA, Tambi</creatorcontrib><creatorcontrib>KUMART, Kundan</creatorcontrib><creatorcontrib>RAGHURAM, Badmi</creatorcontrib><creatorcontrib>ALOK KRISHNA SINHA</creatorcontrib><title>In Silico Analysis Reveals 75 Members of Mitogen-Activated Protein Kinase Kinase Kinase Gene Family in Rice</title><title>DNA research</title><addtitle>DNA Res</addtitle><description>Mitogen-Activated Protein Kinase Kinase Kinases (MAPKKKs) are important components of MAPK cascades, which are universal signal transduction modules and play important role in plant growth and development. In the sequenced Arabidopsis genome 80 MAPKKKs were identified and currently being analysed for its role in different stress. In rice, economically important monocot cereal crop only five MAPKKKs were identified so far. In this study using computational analysis of sequenced rice genome we have identified 75 MAPKKKs. EST hits and full-length cDNA sequences (from KOME or Genbank database) of 75 MAPKKKs supported their existence. Phylogenetic analyses of MAPKKKs from rice and Arabidopsis have classified them into three subgroups, which include Raf, ZIK and MEKK. Conserved motifs in the deduced amino acid sequences of rice MAPKKKs strongly supported their identity as members of Raf, ZIK and MEKK subfamilies. Further expression analysis of the MAPKKKs in MPSS database revealed that their transcripts were differentially regulated in various stress and tissue-specific libraries.</description><subject>Amino Acid Sequence</subject><subject>Arabidopsis</subject><subject>Arabidopsis - genetics</subject><subject>Biological and medical sciences</subject><subject>Computational Biology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Gene Expression Regulation, Plant</subject><subject>General aspects</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Genome, Plant</subject><subject>MAP Kinase Kinase Kinases - classification</subject><subject>MAP Kinase Kinase Kinases - genetics</subject><subject>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Molecular Sequence Data</subject><subject>Oryza - genetics</subject><subject>Oryza sativa</subject><subject>Phylogeny</subject><subject>Plant Proteins - genetics</subject><subject>Sequence Homology, Amino Acid</subject><subject>Species Specificity</subject><issn>1340-2838</issn><issn>1756-1663</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><recordid>eNqFkUtvGyEUhVHVqHbSLrut2FRdTQLDMAObSlaUl-IoVR5rxMCdlHYGHBhb8r8vlp1Hs8nd3Cv4dDiXg9BXSg4pkezIeh0hHdn0SCj9gKa04XVB65p9zDOrSFEKJiZoP6U_hFSUs-YTmpSESV42cor-Xnh863pnAp553a-TS_gGVqD7hBuOr2BoISYcOnzlxvAAvpiZ0a30CBb_imEE5_Gl8zrBm3YGHvCpHly_xpm5cQY-o70u68KXXT9A96cnd8fnxfz67OJ4Ni8Mp9VYgOks4bo2piyl7gAq2dhSCGKbtpKcWJrNd0I2Jm_RSUl5Piaat1a0jNuKHaCfW93Fsh3AGvBj1L1aRDfouFZBO_X_jXe_1UNYqfxI_pWNwI-dQAyPS0ijGlwy0PfaQ1gm1VQ1ETUt6fskyyWp2JDFljQxpBShe_ZDidokqbZJqm2Smf_2eoln-im6DHzfAToZ3XdRe-PSC1cKWUsm2T-ARak5</recordid><startdate>20100601</startdate><enddate>20100601</enddate><creator>KUDUPUDI PRABHAKARA RAO</creator><creator>RICHA, Tambi</creator><creator>KUMART, Kundan</creator><creator>RAGHURAM, Badmi</creator><creator>ALOK KRISHNA SINHA</creator><general>Oxford University Press</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7TM</scope><scope>5PM</scope></search><sort><creationdate>20100601</creationdate><title>In Silico Analysis Reveals 75 Members of Mitogen-Activated Protein Kinase Kinase Kinase Gene Family in Rice</title><author>KUDUPUDI PRABHAKARA RAO ; RICHA, Tambi ; KUMART, Kundan ; RAGHURAM, Badmi ; ALOK KRISHNA SINHA</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c514t-ecfd05a6cc229afee497d2880d7b4950d1395f897c039f9915b490a5bd8b35d43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Amino Acid Sequence</topic><topic>Arabidopsis</topic><topic>Arabidopsis - genetics</topic><topic>Biological and medical sciences</topic><topic>Computational Biology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Gene Expression Regulation, Plant</topic><topic>General aspects</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Genome, Plant</topic><topic>MAP Kinase Kinase Kinases - classification</topic><topic>MAP Kinase Kinase Kinases - genetics</topic><topic>Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Molecular Sequence Data</topic><topic>Oryza - genetics</topic><topic>Oryza sativa</topic><topic>Phylogeny</topic><topic>Plant Proteins - genetics</topic><topic>Sequence Homology, Amino Acid</topic><topic>Species Specificity</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>KUDUPUDI PRABHAKARA RAO</creatorcontrib><creatorcontrib>RICHA, Tambi</creatorcontrib><creatorcontrib>KUMART, Kundan</creatorcontrib><creatorcontrib>RAGHURAM, Badmi</creatorcontrib><creatorcontrib>ALOK KRISHNA SINHA</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Nucleic Acids Abstracts</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>DNA research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>KUDUPUDI PRABHAKARA RAO</au><au>RICHA, Tambi</au><au>KUMART, Kundan</au><au>RAGHURAM, Badmi</au><au>ALOK KRISHNA SINHA</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>In Silico Analysis Reveals 75 Members of Mitogen-Activated Protein Kinase Kinase Kinase Gene Family in Rice</atitle><jtitle>DNA research</jtitle><addtitle>DNA Res</addtitle><date>2010-06-01</date><risdate>2010</risdate><volume>17</volume><issue>3</issue><spage>139</spage><epage>153</epage><pages>139-153</pages><issn>1340-2838</issn><eissn>1756-1663</eissn><abstract>Mitogen-Activated Protein Kinase Kinase Kinases (MAPKKKs) are important components of MAPK cascades, which are universal signal transduction modules and play important role in plant growth and development. 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subjects | Amino Acid Sequence Arabidopsis Arabidopsis - genetics Biological and medical sciences Computational Biology Fundamental and applied biological sciences. Psychology Gene Expression Regulation, Plant General aspects Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Genome, Plant MAP Kinase Kinase Kinases - classification MAP Kinase Kinase Kinases - genetics Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects) Molecular and cellular biology Molecular genetics Molecular Sequence Data Oryza - genetics Oryza sativa Phylogeny Plant Proteins - genetics Sequence Homology, Amino Acid Species Specificity |
title | In Silico Analysis Reveals 75 Members of Mitogen-Activated Protein Kinase Kinase Kinase Gene Family in Rice |
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