Genome-Wide Identification and Characterization of RBR Ubiquitin Ligase Genes in Soybean
Identifieur interne : 001184 ( Pmc/Curation ); précédent : 001183; suivant : 001185Genome-Wide Identification and Characterization of RBR Ubiquitin Ligase Genes in Soybean
Auteurs : Pei Chen ; Xiaolian Zhang ; Tuanjie Zhao ; Yan Li ; Junyi GaiSource :
- PLoS ONE [ 1932-6203 ] ; 2014.
Abstract
RBR (
Url:
DOI: 10.1371/journal.pone.0087282
PubMed: 24489889
PubMed Central: 3904995
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genome-Wide Identification and Characterization of RBR Ubiquitin Ligase Genes in Soybean</title><author><name sortKey="Chen, Pei" sort="Chen, Pei" uniqKey="Chen P" first="Pei" last="Chen">Pei Chen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhang, Xiaolian" sort="Zhang, Xiaolian" uniqKey="Zhang X" first="Xiaolian" last="Zhang">Xiaolian Zhang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhao, Tuanjie" sort="Zhao, Tuanjie" uniqKey="Zhao T" first="Tuanjie" last="Zhao">Tuanjie Zhao</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Li, Yan" sort="Li, Yan" uniqKey="Li Y" first="Yan" last="Li">Yan Li</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Gai, Junyi" sort="Gai, Junyi" uniqKey="Gai J" first="Junyi" last="Gai">Junyi Gai</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24489889</idno><idno type="pmc">3904995</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904995</idno><idno type="RBID">PMC:3904995</idno><idno type="doi">10.1371/journal.pone.0087282</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">001185</idno><idno type="wicri:Area/Pmc/Curation">001184</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Genome-Wide Identification and Characterization of RBR Ubiquitin Ligase Genes in Soybean</title><author><name sortKey="Chen, Pei" sort="Chen, Pei" uniqKey="Chen P" first="Pei" last="Chen">Pei Chen</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhang, Xiaolian" sort="Zhang, Xiaolian" uniqKey="Zhang X" first="Xiaolian" last="Zhang">Xiaolian Zhang</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Zhao, Tuanjie" sort="Zhao, Tuanjie" uniqKey="Zhao T" first="Tuanjie" last="Zhao">Tuanjie Zhao</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Li, Yan" sort="Li, Yan" uniqKey="Li Y" first="Yan" last="Li">Yan Li</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author><author><name sortKey="Gai, Junyi" sort="Gai, Junyi" uniqKey="Gai J" first="Junyi" last="Gai">Junyi Gai</name><affiliation><nlm:aff id="aff1"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>RBR (<underline>R</underline>ING1-I<underline>B</underline>R-<underline>R</underline>ING2) proteins play an important role in protein ubiquitination and are involved in many cellular processes. Recent studies showed plant RBR genes were induced by abiotic and biotic stresses. However, detailed studies on RBR genes in the important oil crop, soybean (<italic>Glycine max</italic> (L.) Merr.), is still lacking. Here we performed a genome-wide search and identified 24 RBR domain-containing genes from the soybean genome sequence and cloned 11 of them. Most soybean RBR proteins contain a highly conserved RBR supra-domain. Phylogenetic analyses indicated all 24 soybean RBR proteins are most related to the RBR proteins from <italic>Phaseolus vulgaris</italic>, and could be classified into seven groups including Ariadne A, Ariadne B, ARA54, Plant IIA, Plant IIB, Plant IIC, and Helicase. Tandem duplication and block duplication were found among the Ariadne B and Plant IIC group of soybean RBR genes. Despite the conserved RBR supra-domain, there are extensive variations in the additional protein motifs and exon-intron structures between different groups, which indicate they might have diverse functions. Most soybean RBR proteins are predicted to localize in nucleus, and four of them were experimentally confirmed by GFP fusion proteins. Soybean RBR genes are broadly expressed in many tissue types with a little more abundant in the roots and flowers than leaves, stems, and seeds. The expression of <italic>GmRTRTP3</italic> (Plant IIB) and <italic>GmRTRTP5</italic> (Plant IIC) are induced by NaCl treatment, which suggests these RBR genes might be involved in soybean response to abiotic stresses.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Okiyoneda, T" uniqKey="Okiyoneda T">T Okiyoneda</name></author><author><name sortKey="Apaja, Pm" uniqKey="Apaja P">PM Apaja</name></author><author><name sortKey="Lukacs, Gl" uniqKey="Lukacs G">GL Lukacs</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lin, Ss" uniqKey="Lin S">SS Lin</name></author><author><name sortKey="Martin, R" uniqKey="Martin R">R Martin</name></author><author><name sortKey="Mongrand, S" uniqKey="Mongrand S">S Mongrand</name></author><author><name sortKey="Vandenabeele, S" uniqKey="Vandenabeele S">S Vandenabeele</name></author><author><name sortKey="Chen, Kc" uniqKey="Chen K">KC 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">24489889</article-id><article-id pub-id-type="pmc">3904995</article-id><article-id pub-id-type="publisher-id">PONE-D-13-36293</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0087282</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Agriculture</subject><subj-group><subject>Crops</subject></subj-group></subj-group><subj-group subj-group-type="Discipline-v2"><subject>Biology</subject><subj-group><subject>Computational Biology</subject><subj-group><subject>Molecular Genetics</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group></subj-group><subj-group><subject>Evolutionary Biology</subject><subj-group><subject>Evolutionary Systematics</subject><subj-group><subject>Phylogenetics</subject></subj-group></subj-group></subj-group><subj-group><subject>Genetics</subject><subj-group><subject>Plant Genetics</subject><subj-group><subject>Crop Genetics</subject></subj-group></subj-group><subj-group><subject>Gene Expression</subject></subj-group></subj-group><subj-group><subject>Molecular Cell Biology</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group><subj-group><subject>Plant Science</subject><subj-group><subject>Plant Biotechnology</subject><subj-group><subject>Plant Genomics</subject></subj-group></subj-group><subj-group><subject>Plant Genetics</subject><subject>Plant Genomics</subject><subject>Plant Phylogenetics</subject></subj-group></subj-group></subj-group></article-categories><title-group><article-title>Genome-Wide Identification and Characterization of RBR Ubiquitin Ligase Genes in Soybean</article-title><alt-title alt-title-type="running-head">Soybean RBR Ubiquitin Ligases</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Pei</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Zhang</surname><given-names>Xiaolian</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Zhao</surname><given-names>Tuanjie</given-names></name><xref ref-type="aff" rid="aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Li</surname><given-names>Yan</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gai</surname><given-names>Junyi</given-names></name><xref ref-type="aff" rid="aff1"></xref><xref ref-type="corresp" rid="cor1"><sup>*</sup></xref></contrib></contrib-group><aff id="aff1"><addr-line>Soybean Research Institute, National Center for Soybean Improvement, MOA Key Laboratory for Biology and Genetic Improvement of Soybean (General), National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu, China</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Schönbach</surname><given-names>Christian</given-names></name><role>Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Nazarbayev University, Kazakhstan</addr-line></aff><author-notes><corresp id="cor1">* E-mail: <email>yanli1@njau.edu.cn (YL)</email>; <email>sri@njau.edu.cn (JG)</email></corresp><fn fn-type="conflict"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con"><p>Conceived and designed the experiments: PC YL JG. Performed the experiments: PC XZ. Analyzed the data: PC XZ TZ YL JG. Contributed reagents/materials/analysis tools: PC TZ YL JG. Wrote the paper: PC YL JG. Revised the manuscript: PC XZ TZ YL JG.</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>28</day><month>1</month><year>2014</year></pub-date><volume>9</volume><issue>1</issue><elocation-id>e87282</elocation-id><history><date date-type="received"><day>4</day><month>9</month><year>2013</year></date><date date-type="accepted"><day>20</day><month>12</month><year>2013</year></date></history><permissions><copyright-year>2014</copyright-year><copyright-holder>Chen et al</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open-access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.</license-p></license></permissions><abstract><p>RBR (<underline>R</underline>ING1-I<underline>B</underline>R-<underline>R</underline>ING2) proteins play an important role in protein ubiquitination and are involved in many cellular processes. Recent studies showed plant RBR genes were induced by abiotic and biotic stresses. However, detailed studies on RBR genes in the important oil crop, soybean (<italic>Glycine max</italic> (L.) Merr.), is still lacking. Here we performed a genome-wide search and identified 24 RBR domain-containing genes from the soybean genome sequence and cloned 11 of them. Most soybean RBR proteins contain a highly conserved RBR supra-domain. Phylogenetic analyses indicated all 24 soybean RBR proteins are most related to the RBR proteins from <italic>Phaseolus vulgaris</italic>, and could be classified into seven groups including Ariadne A, Ariadne B, ARA54, Plant IIA, Plant IIB, Plant IIC, and Helicase. Tandem duplication and block duplication were found among the Ariadne B and Plant IIC group of soybean RBR genes. Despite the conserved RBR supra-domain, there are extensive variations in the additional protein motifs and exon-intron structures between different groups, which indicate they might have diverse functions. Most soybean RBR proteins are predicted to localize in nucleus, and four of them were experimentally confirmed by GFP fusion proteins. Soybean RBR genes are broadly expressed in many tissue types with a little more abundant in the roots and flowers than leaves, stems, and seeds. The expression of <italic>GmRTRTP3</italic> (Plant IIB) and <italic>GmRTRTP5</italic> (Plant IIC) are induced by NaCl treatment, which suggests these RBR genes might be involved in soybean response to abiotic stresses.</p></abstract><funding-group><funding-statement>This work was supported by the National Key Basic Research Program of China (2011CB1093, 2010CB1259), the National Hightech R & D Program of China (2011AA10A105, 2012AA101106), the Natural Science Foundation of China (31071442), the Program for New Century Excellent Talents in University (NCET-12-0891), the MOE 111 Project (B08025), the MOA Public Profit Program (200803060), and the Jiangsu Higher Education PAPD Program. The funders had no role in study design, data collection and analysis, decision or preparation of the manuscript.</funding-statement></funding-group><counts><page-count count="13"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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