Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.
Identifieur interne : 003906 ( Main/Exploration ); précédent : 003905; suivant : 003907Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.
Auteurs : An-Yuan Guo [République populaire de Chine] ; Qi-Hui Zhu ; Xiaocheng Gu ; Song Ge ; Ji Yang ; Jingchu LuoSource :
- Gene [ 0378-1119 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : MicroRNAs.
- Binding Sites, Conserved Sequence, Evolution, Molecular, Genes, Plant, Genome, Plant, Multigene Family, Phylogeny, Transcription Factors, Zinc Fingers.
Abstract
We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.
DOI: 10.1016/j.gene.2008.03.016
PubMed: 18495384
Affiliations:
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sortKey="Zhu, Qi Hui" sort="Zhu, Qi Hui" uniqKey="Zhu Q" first="Qi-Hui" last="Zhu">Qi-Hui Zhu</name></author><author><name sortKey="Gu, Xiaocheng" sort="Gu, Xiaocheng" uniqKey="Gu X" first="Xiaocheng" last="Gu">Xiaocheng Gu</name></author><author><name sortKey="Ge, Song" sort="Ge, Song" uniqKey="Ge S" first="Song" last="Ge">Song Ge</name></author><author><name sortKey="Yang, Ji" sort="Yang, Ji" uniqKey="Yang J" first="Ji" last="Yang">Ji Yang</name></author><author><name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18495384</idno><idno type="pmid">18495384</idno><idno type="doi">10.1016/j.gene.2008.03.016</idno><idno type="wicri:Area/Main/Corpus">003885</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">003885</idno><idno 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type="university">Université de Pékin</orgName><placeName><settlement type="city">Pékin</settlement><region type="capitale">Pékin</region></placeName></affiliation></author><author><name sortKey="Zhu, Qi Hui" sort="Zhu, Qi Hui" uniqKey="Zhu Q" first="Qi-Hui" last="Zhu">Qi-Hui Zhu</name></author><author><name sortKey="Gu, Xiaocheng" sort="Gu, Xiaocheng" uniqKey="Gu X" first="Xiaocheng" last="Gu">Xiaocheng Gu</name></author><author><name sortKey="Ge, Song" sort="Ge, Song" uniqKey="Ge S" first="Song" last="Ge">Song Ge</name></author><author><name sortKey="Yang, Ji" sort="Yang, Ji" uniqKey="Yang J" first="Ji" last="Yang">Ji Yang</name></author><author><name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name></author></analytic><series><title level="j">Gene</title><idno type="ISSN">0378-1119</idno><imprint><date when="2008" 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xml:lang="en"><term>MicroRNAs</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>microARN</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Conserved Sequence</term><term>Evolution, Molecular</term><term>Genes, Plant</term><term>Genome, Plant</term><term>Multigene Family</term><term>Phylogeny</term><term>Transcription Factors</term><term>Zinc Fingers</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Doigts de zinc</term><term>Facteurs de transcription</term><term>Famille multigénique</term><term>Gènes de plante</term><term>Génome végétal</term><term>Phylogenèse</term><term>Sites de fixation</term><term>Séquence conservée</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18495384</PMID><DateCompleted><Year>2008</Year><Month>08</Month><Day>15</Day></DateCompleted><DateRevised><Year>2008</Year><Month>06</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0378-1119</ISSN><JournalIssue CitedMedium="Print"><Volume>418</Volume><Issue>1-2</Issue><PubDate><Year>2008</Year><Month>Jul</Month><Day>15</Day></PubDate></JournalIssue><Title>Gene</Title><ISOAbbreviation>Gene</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification and evolutionary analysis of the plant specific SBP-box transcription factor family.</ArticleTitle><Pagination><MedlinePgn>1-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gene.2008.03.016</ELocationID><Abstract><AbstractText>We made genome-wide analyses to explore the evolutionary process of the SBP-box gene family. We identified 120 SBP-box genes from nine species representing the main green plant lineages: green alga, moss, lycophyte, gymnosperm and angiosperm. A maximum-likelihood phylogenetic tree was constructed using the protein sequences of the DNA-binding domain of SBP-box genes (SBP-domain). Our results revealed that all SBP-box genes of green alga clustered into a single clade (CR group), while all genes from land-plants fell into two distinct groups. Group I had a single copy in each species except for poplar while group II had several members in each species and can be divided into several subgroups. The SBP-domain encoded by all SBP-box genes possesses two zinc fingers. The C-terminal zinc finger of both group I and group II had the same C2HC motif while their N-terminal zinc finger showed different signatures, C4 in group I and C3H in group II. The patterns of exon-intron structure in Arabidopsis and rice SBP-box genes were consistent with the phylogenetic results. A target site of microRNA miR156 was highly conserved among land-plant SBP-box genes. Our results suggested that the SBP-box gene family might have originated from a common ancestor of green plants, followed by duplication and divergence in each lineage including exon-intron loss processes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Guo</LastName><ForeName>An-Yuan</ForeName><Initials>AY</Initials><AffiliationInfo><Affiliation>College of Life Sciences, Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing, 100871, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhu</LastName><ForeName>Qi-Hui</ForeName><Initials>QH</Initials></Author><Author ValidYN="Y"><LastName>Gu</LastName><ForeName>Xiaocheng</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Ge</LastName><ForeName>Song</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Ji</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Luo</LastName><ForeName>Jingchu</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>04</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Gene</MedlineTA><NlmUniqueID>7706761</NlmUniqueID><ISSNLinking>0378-1119</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D035683">MicroRNAs</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="Y">Genome, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="Y">analysis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="Y">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="Y">Transcription Factors</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016335" MajorTopicYN="N">Zinc Fingers</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2007</Year><Month>07</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2008</Year><Month>03</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2008</Year><Month>03</Month><Day>26</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>5</Month><Day>23</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>8</Month><Day>16</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>5</Month><Day>23</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">18495384</ArticleId><ArticleId IdType="pii">S0378-1119(08)00136-4</ArticleId><ArticleId IdType="doi">10.1016/j.gene.2008.03.016</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Pékin</li></region><settlement><li>Pékin</li></settlement><orgName><li>Université de Pékin</li></orgName></list><tree><noCountry><name sortKey="Ge, Song" sort="Ge, Song" uniqKey="Ge S" first="Song" last="Ge">Song Ge</name><name sortKey="Gu, Xiaocheng" sort="Gu, Xiaocheng" uniqKey="Gu X" first="Xiaocheng" last="Gu">Xiaocheng Gu</name><name sortKey="Luo, Jingchu" sort="Luo, Jingchu" uniqKey="Luo J" first="Jingchu" last="Luo">Jingchu Luo</name><name sortKey="Yang, Ji" sort="Yang, Ji" uniqKey="Yang J" first="Ji" last="Yang">Ji Yang</name><name sortKey="Zhu, Qi Hui" sort="Zhu, Qi Hui" uniqKey="Zhu Q" first="Qi-Hui" last="Zhu">Qi-Hui Zhu</name></noCountry><country name="République populaire de Chine"><region name="Pékin"><name sortKey="Guo, An Yuan" sort="Guo, An Yuan" uniqKey="Guo A" first="An-Yuan" last="Guo">An-Yuan Guo</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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