Isolation, classification and transcription profiles of the AP2/ERF transcription factor superfamily in citrus.
Identifieur interne : 001605 ( Ncbi/Merge ); précédent : 001604; suivant : 001606Isolation, classification and transcription profiles of the AP2/ERF transcription factor superfamily in citrus.
Auteurs : Xiu-Lan Xie [République populaire de Chine] ; Shu-Ling Shen ; Xue-Ren Yin ; Qian Xu ; Chong-De Sun ; Donald Grierson ; Ian Ferguson ; Kun-Song ChenSource :
- Molecular biology reports [ 1573-4978 ] ; 2014.
English descriptors
- KwdEn :
- Amino Acid Motifs, Arabidopsis (genetics), Arabidopsis (metabolism), Citrus (genetics), Citrus (metabolism), DNA-Binding Proteins (classification), DNA-Binding Proteins (genetics), DNA-Binding Proteins (metabolism), Fruit (genetics), Fruit (metabolism), Gene Expression Regulation, Plant, Genome, Plant, Molecular Sequence Data, Organ Specificity, Oryza (genetics), Oryza (metabolism), Phylogeny, Plant Proteins (classification), Plant Proteins (genetics), Plant Proteins (metabolism), Sequence Homology, Amino Acid, Signal Transduction, Species Specificity, Transcription Factor AP-2 (classification), Transcription Factor AP-2 (genetics), Transcription Factor AP-2 (metabolism), Transcription, Genetic.
- MESH :
- chemical , classification : DNA-Binding Proteins, Plant Proteins, Transcription Factor AP-2.
- genetics : Arabidopsis, Citrus, DNA-Binding Proteins, Fruit, Oryza, Plant Proteins, Transcription Factor AP-2.
- metabolism : Arabidopsis, Citrus, DNA-Binding Proteins, Fruit, Oryza, Plant Proteins, Transcription Factor AP-2.
- Amino Acid Motifs, Gene Expression Regulation, Plant, Genome, Plant, Molecular Sequence Data, Organ Specificity, Phylogeny, Sequence Homology, Amino Acid, Signal Transduction, Species Specificity, Transcription, Genetic.
Abstract
The AP2/ERF gene family encodes plant-specific transcription factors. In model plants, AP2/ERF genes have been shown to be expressed in response to developmental and environmental stimuli, and many function downstream of the ethylene, biotic, and abiotic stress signaling pathways. In citrus, ethylene is effective in regulation citrus fruit quality, such as degreening and aroma. However, information about the citrus AP2/ERF family is limited, and would enhance our understanding of fruit responses to environmental stress, fruit development and quality. CitAP2/ERF genes were isolated using the citrus genome database, and their expression patterns analyzed by real-time PCR using various orange organs and samples from a fruit developmental series. 126 sequences with homologies to AP2/ERF proteins were identified from the citrus genome, and, on the basis of their structure and sequence, assigned to the ERF family (102), AP2 family (18), RAV family (4) and Soloist (2). MEME motif analysis predicted the defining AP2/ERF domain and EAR repressor domains. Analysis of transcript accumulation in Citrus sinensis cv. 'Newhall' indicated that CitAP2/ERF genes show organ-specific and temporal expression, and provided a framework for understanding the transcriptional regulatory roles of AP2/ERF gene family members in citrus. Hierarchical cluster analysis and t tests identified regulators that potentially function during orange fruit growth and development.
DOI: 10.1007/s11033-014-3297-0
PubMed: 24566692
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type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Shen, Shu Ling" sort="Shen, Shu Ling" uniqKey="Shen S" first="Shu-Ling" last="Shen">Shu-Ling Shen</name></author><author><name sortKey="Yin, Xue Ren" sort="Yin, Xue Ren" uniqKey="Yin X" first="Xue-Ren" last="Yin">Xue-Ren Yin</name></author><author><name sortKey="Xu, Qian" sort="Xu, Qian" uniqKey="Xu Q" first="Qian" last="Xu">Qian Xu</name></author><author><name sortKey="Sun, Chong De" sort="Sun, Chong De" uniqKey="Sun C" first="Chong-De" last="Sun">Chong-De Sun</name></author><author><name sortKey="Grierson, Donald" sort="Grierson, Donald" uniqKey="Grierson D" first="Donald" last="Grierson">Donald Grierson</name></author><author><name sortKey="Ferguson, Ian" sort="Ferguson, Ian" uniqKey="Ferguson I" first="Ian" last="Ferguson">Ian Ferguson</name></author><author><name sortKey="Chen, Kun Song" sort="Chen, Kun Song" uniqKey="Chen K" first="Kun-Song" 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Campus, Hangzhou, 310058, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058</wicri:regionArea><orgName type="university">Université de Zhejiang</orgName><placeName><settlement type="city">Hangzhou</settlement><region type="province">Zhejiang</region></placeName></affiliation></author><author><name sortKey="Shen, Shu Ling" sort="Shen, Shu Ling" uniqKey="Shen S" first="Shu-Ling" last="Shen">Shu-Ling Shen</name></author><author><name sortKey="Yin, Xue Ren" sort="Yin, Xue Ren" uniqKey="Yin X" first="Xue-Ren" last="Yin">Xue-Ren Yin</name></author><author><name sortKey="Xu, Qian" sort="Xu, Qian" uniqKey="Xu Q" first="Qian" last="Xu">Qian Xu</name></author><author><name sortKey="Sun, Chong De" sort="Sun, Chong De" uniqKey="Sun C" first="Chong-De" last="Sun">Chong-De Sun</name></author><author><name sortKey="Grierson, Donald" sort="Grierson, Donald" uniqKey="Grierson D" first="Donald" last="Grierson">Donald Grierson</name></author><author><name sortKey="Ferguson, Ian" sort="Ferguson, Ian" uniqKey="Ferguson I" first="Ian" last="Ferguson">Ian Ferguson</name></author><author><name sortKey="Chen, Kun Song" sort="Chen, Kun Song" uniqKey="Chen K" first="Kun-Song" last="Chen">Kun-Song Chen</name></author></analytic><series><title level="j">Molecular biology reports</title><idno type="eISSN">1573-4978</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs</term><term>Arabidopsis (genetics)</term><term>Arabidopsis (metabolism)</term><term>Citrus (genetics)</term><term>Citrus (metabolism)</term><term>DNA-Binding Proteins (classification)</term><term>DNA-Binding Proteins (genetics)</term><term>DNA-Binding Proteins (metabolism)</term><term>Fruit (genetics)</term><term>Fruit (metabolism)</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant</term><term>Molecular Sequence Data</term><term>Organ Specificity</term><term>Oryza (genetics)</term><term>Oryza (metabolism)</term><term>Phylogeny</term><term>Plant Proteins (classification)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Sequence Homology, Amino Acid</term><term>Signal Transduction</term><term>Species Specificity</term><term>Transcription Factor AP-2 (classification)</term><term>Transcription Factor AP-2 (genetics)</term><term>Transcription Factor AP-2 (metabolism)</term><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>DNA-Binding Proteins</term><term>Plant Proteins</term><term>Transcription Factor AP-2</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Citrus</term><term>DNA-Binding Proteins</term><term>Fruit</term><term>Oryza</term><term>Plant Proteins</term><term>Transcription Factor AP-2</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Arabidopsis</term><term>Citrus</term><term>DNA-Binding Proteins</term><term>Fruit</term><term>Oryza</term><term>Plant Proteins</term><term>Transcription Factor AP-2</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term><term>Gene Expression Regulation, Plant</term><term>Genome, Plant</term><term>Molecular Sequence Data</term><term>Organ Specificity</term><term>Phylogeny</term><term>Sequence Homology, Amino Acid</term><term>Signal Transduction</term><term>Species Specificity</term><term>Transcription, Genetic</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The AP2/ERF gene family encodes plant-specific transcription factors. In model plants, AP2/ERF genes have been shown to be expressed in response to developmental and environmental stimuli, and many function downstream of the ethylene, biotic, and abiotic stress signaling pathways. In citrus, ethylene is effective in regulation citrus fruit quality, such as degreening and aroma. However, information about the citrus AP2/ERF family is limited, and would enhance our understanding of fruit responses to environmental stress, fruit development and quality. CitAP2/ERF genes were isolated using the citrus genome database, and their expression patterns analyzed by real-time PCR using various orange organs and samples from a fruit developmental series. 126 sequences with homologies to AP2/ERF proteins were identified from the citrus genome, and, on the basis of their structure and sequence, assigned to the ERF family (102), AP2 family (18), RAV family (4) and Soloist (2). MEME motif analysis predicted the defining AP2/ERF domain and EAR repressor domains. Analysis of transcript accumulation in Citrus sinensis cv. 'Newhall' indicated that CitAP2/ERF genes show organ-specific and temporal expression, and provided a framework for understanding the transcriptional regulatory roles of AP2/ERF gene family members in citrus. Hierarchical cluster analysis and t tests identified regulators that potentially function during orange fruit growth and development.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24566692</PMID><DateCreated><Year>2014</Year><Month>6</Month><Day>23</Day></DateCreated><DateCompleted><Year>2015</Year><Month>02</Month><Day>02</Day></DateCompleted><DateRevised><Year>2015</Year><Month>11</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1573-4978</ISSN><JournalIssue CitedMedium="Internet"><Volume>41</Volume><Issue>7</Issue><PubDate><Year>2014</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Molecular biology reports</Title><ISOAbbreviation>Mol. Biol. 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CitAP2/ERF genes were isolated using the citrus genome database, and their expression patterns analyzed by real-time PCR using various orange organs and samples from a fruit developmental series. 126 sequences with homologies to AP2/ERF proteins were identified from the citrus genome, and, on the basis of their structure and sequence, assigned to the ERF family (102), AP2 family (18), RAV family (4) and Soloist (2). MEME motif analysis predicted the defining AP2/ERF domain and EAR repressor domains. Analysis of transcript accumulation in Citrus sinensis cv. 'Newhall' indicated that CitAP2/ERF genes show organ-specific and temporal expression, and provided a framework for understanding the transcriptional regulatory roles of AP2/ERF gene family members in citrus. Hierarchical cluster analysis and t tests identified regulators that potentially function during orange fruit growth and development.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Xie</LastName><ForeName>Xiu-lan</ForeName><Initials>XL</Initials><AffiliationInfo><Affiliation>Laboratory of Fruit Quality Biology/The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, 310058, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Shen</LastName><ForeName>Shu-ling</ForeName><Initials>SL</Initials></Author><Author ValidYN="Y"><LastName>Yin</LastName><ForeName>Xue-ren</ForeName><Initials>XR</Initials></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Qian</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Chong-de</ForeName><Initials>CD</Initials></Author><Author ValidYN="Y"><LastName>Grierson</LastName><ForeName>Donald</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Ferguson</LastName><ForeName>Ian</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Kun-song</ForeName><Initials>KS</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>2014</Year><Month>Feb</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>Mol Biol Rep</MedlineTA><NlmUniqueID>0403234</NlmUniqueID><ISSNLinking>0301-4851</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004268">DNA-Binding Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D050656">Transcription Factor AP-2</NameOfSubstance></Chemical><Chemical><RegistryNumber>164326-51-6</RegistryNumber><NameOfSubstance UI="C093680">ethylene-responsive element binding protein</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020816" MajorTopicYN="N">Amino Acid Motifs</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002957" MajorTopicYN="N">Citrus</DescriptorName><QualifierName UI="Q000235" 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PubStatus="pubmed"><Year>2014</Year><Month>2</Month><Day>26</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>2</Month><Day>3</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24566692</ArticleId><ArticleId IdType="doi">10.1007/s11033-014-3297-0</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Zhejiang</li></region><settlement><li>Hangzhou</li></settlement><orgName><li>Université de Zhejiang</li></orgName></list><tree><noCountry><name sortKey="Chen, Kun Song" sort="Chen, Kun Song" uniqKey="Chen K" first="Kun-Song" last="Chen">Kun-Song Chen</name><name sortKey="Ferguson, Ian" sort="Ferguson, Ian" uniqKey="Ferguson I" first="Ian" last="Ferguson">Ian Ferguson</name><name sortKey="Grierson, Donald" sort="Grierson, Donald" uniqKey="Grierson D" first="Donald" last="Grierson">Donald Grierson</name><name sortKey="Shen, Shu Ling" sort="Shen, Shu Ling" uniqKey="Shen S" first="Shu-Ling" last="Shen">Shu-Ling Shen</name><name sortKey="Sun, Chong De" sort="Sun, Chong De" uniqKey="Sun C" first="Chong-De" last="Sun">Chong-De Sun</name><name sortKey="Xu, Qian" sort="Xu, Qian" uniqKey="Xu Q" first="Qian" last="Xu">Qian Xu</name><name sortKey="Yin, Xue Ren" sort="Yin, Xue Ren" uniqKey="Yin X" first="Xue-Ren" last="Yin">Xue-Ren Yin</name></noCountry><country name="République populaire de Chine"><region name="Zhejiang"><name sortKey="Xie, Xiu Lan" sort="Xie, Xiu Lan" uniqKey="Xie X" first="Xiu-Lan" last="Xie">Xiu-Lan Xie</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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