Genome-wide analysis and expression profiling of the ERF transcription factor family in potato (Solanum tuberosum L.).
Identifieur interne : 000555 ( PubMed/Corpus ); précédent : 000554; suivant : 000556Genome-wide analysis and expression profiling of the ERF transcription factor family in potato (Solanum tuberosum L.).
Auteurs : Mariam Charfeddine ; Mohamed Najib Saïdi ; Safa Charfeddine ; Asma Hammami ; Radhia Gargouri BouzidSource :
- Molecular biotechnology [ 1559-0305 ] ; 2015.
English descriptors
- KwdEn :
- Cluster Analysis (MeSH), Databases, Genetic (MeSH), Gene Expression Profiling (MeSH), Genome, Plant (genetics), Phylogeny (MeSH), Plant Proteins (analysis), Plant Proteins (genetics), Plant Proteins (metabolism), Solanum tuberosum (genetics), Solanum tuberosum (metabolism), Transcription Factors (analysis), Transcription Factors (genetics), Transcription Factors (metabolism).
- MESH :
- chemical , analysis : Plant Proteins, Transcription Factors.
- genetics : Genome, Plant, Plant Proteins, Solanum tuberosum, Transcription Factors.
- chemical , metabolism : Plant Proteins, Solanum tuberosum, Transcription Factors.
- Cluster Analysis, Databases, Genetic, Gene Expression Profiling, Phylogeny.
Abstract
The ERF transcription factors belong to the AP2/ERF superfamily, one of the largest transcription factor families in plants. They play important roles in plant development processes, as well as in the response to biotic, abiotic, and hormone signaling. In the present study, 155 putative ERF transcription factor genes were identified from the potato (Solanum tuberosum) genome database, and compared with those from Arabidopsis thaliana. The StERF proteins are divided into ten phylogenetic groups. Expression analyses of five StERFs were carried out by semi-quantitative RT-PCR and compared with published RNA-seq data. These latter analyses were used to distinguish tissue-specific, biotic, and abiotic stress genes as well as hormone-responsive StERF genes. The results are of interest to better understand the role of the AP2/ERF genes in response to diverse types of stress in potatoes. A comprehensive analysis of the physiological functions and biological roles of the ERF family genes in S. tuberosum is required to understand crop stress tolerance mechanisms.
DOI: 10.1007/s12033-014-9828-z
PubMed: 25491236
Links to Exploration step
pubmed:25491236Le document en format XML
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They play important roles in plant development processes, as well as in the response to biotic, abiotic, and hormone signaling. In the present study, 155 putative ERF transcription factor genes were identified from the potato (Solanum tuberosum) genome database, and compared with those from Arabidopsis thaliana. The StERF proteins are divided into ten phylogenetic groups. Expression analyses of five StERFs were carried out by semi-quantitative RT-PCR and compared with published RNA-seq data. These latter analyses were used to distinguish tissue-specific, biotic, and abiotic stress genes as well as hormone-responsive StERF genes. The results are of interest to better understand the role of the AP2/ERF genes in response to diverse types of stress in potatoes. A comprehensive analysis of the physiological functions and biological roles of the ERF family genes in S. tuberosum is required to understand crop stress tolerance mechanisms. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25491236</PMID><DateCompleted><Year>2015</Year><Month>12</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1559-0305</ISSN><JournalIssue CitedMedium="Internet"><Volume>57</Volume><Issue>4</Issue><PubDate><Year>2015</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Molecular biotechnology</Title><ISOAbbreviation>Mol Biotechnol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide analysis and expression profiling of the ERF transcription factor family in potato (Solanum tuberosum L.).</ArticleTitle><Pagination><MedlinePgn>348-58</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s12033-014-9828-z</ELocationID><Abstract><AbstractText>The ERF transcription factors belong to the AP2/ERF superfamily, one of the largest transcription factor families in plants. They play important roles in plant development processes, as well as in the response to biotic, abiotic, and hormone signaling. In the present study, 155 putative ERF transcription factor genes were identified from the potato (Solanum tuberosum) genome database, and compared with those from Arabidopsis thaliana. The StERF proteins are divided into ten phylogenetic groups. Expression analyses of five StERFs were carried out by semi-quantitative RT-PCR and compared with published RNA-seq data. These latter analyses were used to distinguish tissue-specific, biotic, and abiotic stress genes as well as hormone-responsive StERF genes. The results are of interest to better understand the role of the AP2/ERF genes in response to diverse types of stress in potatoes. A comprehensive analysis of the physiological functions and biological roles of the ERF family genes in S. tuberosum is required to understand crop stress tolerance mechanisms. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Charfeddine</LastName><ForeName>Mariam</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Unité d'Enzymes et Bioconversion, Ecole Nationale d'Ingénieurs de Sfax, Route Soukra Km 4, BP 1173, 3038, Sfax, Tunisia, charfeddine.mariam@yahoo.fr.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saïdi</LastName><ForeName>Mohamed Najib</ForeName><Initials>MN</Initials></Author><Author ValidYN="Y"><LastName>Charfeddine</LastName><ForeName>Safa</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Hammami</LastName><ForeName>Asma</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Gargouri Bouzid</LastName><ForeName>Radhia</ForeName><Initials>R</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></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Biotechnol</MedlineTA><NlmUniqueID>9423533</NlmUniqueID><ISSNLinking>1073-6085</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000032" MajorTopicYN="N">analysis</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011198" MajorTopicYN="N">Solanum tuberosum</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" 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IdType="doi">10.1007/s12033-014-9828-z</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Plant Cell. 2001 May;13(5):1035-46</Citation><ArticleIdList><ArticleId IdType="pubmed">11340180</ArticleId></ArticleIdList></Reference><Reference><Citation>Planta. 2011 Sep;234(3):429-44</Citation><ArticleIdList><ArticleId IdType="pubmed">21509693</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2010 Dec 20;11:719</Citation><ArticleIdList><ArticleId IdType="pubmed">21171999</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol Biochem. 2012 Nov;60:98-108</Citation><ArticleIdList><ArticleId IdType="pubmed">22922109</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell Physiol. 2011 Feb;52(2):344-60</Citation><ArticleIdList><ArticleId IdType="pubmed">21169347</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2011;6(10):e26801</Citation><ArticleIdList><ArticleId IdType="pubmed">22046362</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2005 Nov;139(3):1185-93</Citation><ArticleIdList><ArticleId IdType="pubmed">16227468</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 2011 Oct;28(10):2731-9</Citation><ArticleIdList><ArticleId IdType="pubmed">21546353</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochem Biophys Res Commun. 2002 Jan 25;290(3):998-1009</Citation><ArticleIdList><ArticleId IdType="pubmed">11798174</ArticleId></ArticleIdList></Reference><Reference><Citation>J Plant Physiol. 2012 Jul 15;169(11):1112-20</Citation><ArticleIdList><ArticleId IdType="pubmed">22459326</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Plant Biol. 2012 Oct 11;12:190</Citation><ArticleIdList><ArticleId IdType="pubmed">23057995</ArticleId></ArticleIdList></Reference><Reference><Citation>Planta. 2007 Sep;226(4):827-38</Citation><ArticleIdList><ArticleId IdType="pubmed">17541631</ArticleId></ArticleIdList></Reference><Reference><Citation>Gene. 2010 Jun 1;457(1-2):1-12</Citation><ArticleIdList><ArticleId IdType="pubmed">20193749</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Plant. 2008 Jan;1(1):42-57</Citation><ArticleIdList><ArticleId IdType="pubmed">20031913</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Genet Genomics. 2010 Dec;284(6):455-75</Citation><ArticleIdList><ArticleId IdType="pubmed">20922546</ArticleId></ArticleIdList></Reference><Reference><Citation>Eur J Biochem. 1999 Jun;262(2):247-57</Citation><ArticleIdList><ArticleId IdType="pubmed">10336605</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Gen Genet. 1993 Jan;236(2-3):331-40</Citation><ArticleIdList><ArticleId IdType="pubmed">8437577</ArticleId></ArticleIdList></Reference><Reference><Citation>Yi Chuan. 2007 Aug;29(8):1023-6</Citation><ArticleIdList><ArticleId IdType="pubmed">17681935</ArticleId></ArticleIdList></Reference><Reference><Citation>Genet Mol Biol. 2011 Oct;34(4):624-33</Citation><ArticleIdList><ArticleId IdType="pubmed">22215967</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Rep. 2011 Apr;38(4):2801-11</Citation><ArticleIdList><ArticleId IdType="pubmed">21127996</ArticleId></ArticleIdList></Reference><Reference><Citation>J Exp Bot. 2008;59(15):4095-107</Citation><ArticleIdList><ArticleId IdType="pubmed">18832187</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biochem Mol Biol. 2005 Jul 31;38(4):440-6</Citation><ArticleIdList><ArticleId IdType="pubmed">16053711</ArticleId></ArticleIdList></Reference><Reference><Citation>FEBS Lett. 2006 Feb 20;580(5):1303-8</Citation><ArticleIdList><ArticleId IdType="pubmed">16457823</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2008 Oct;148(2):993-1003</Citation><ArticleIdList><ArticleId IdType="pubmed">18715958</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Cell. 2000 Mar;12(3):393-404</Citation><ArticleIdList><ArticleId IdType="pubmed">10715325</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36</Citation><ArticleIdList><ArticleId IdType="pubmed">7584402</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Genet Genomics. 2005 Jun;273(4):326-35</Citation><ArticleIdList><ArticleId IdType="pubmed">15812649</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biotechnol. 2013 Jul;54(3):803-17</Citation><ArticleIdList><ArticleId IdType="pubmed">23250722</ArticleId></ArticleIdList></Reference><Reference><Citation>J Integr Plant Biol. 2011 Jul;53(7):570-85</Citation><ArticleIdList><ArticleId IdType="pubmed">21676172</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Plant Biol. 2009 May 29;9:66</Citation><ArticleIdList><ArticleId IdType="pubmed">19480686</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Plant Sci. 2005 Feb;10(2):54-6</Citation><ArticleIdList><ArticleId IdType="pubmed">15708341</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2013 Aug 23;14:573</Citation><ArticleIdList><ArticleId IdType="pubmed">23972083</ArticleId></ArticleIdList></Reference><Reference><Citation>J Hered. 2002 Jan-Feb;93(1):77-8</Citation><ArticleIdList><ArticleId IdType="pubmed">12011185</ArticleId></ArticleIdList></Reference><Reference><Citation>Methods Enzymol. 2006;411:134-93</Citation><ArticleIdList><ArticleId IdType="pubmed">16939790</ArticleId></ArticleIdList></Reference><Reference><Citation>Planta. 2003 Nov;218(1):1-14</Citation><ArticleIdList><ArticleId IdType="pubmed">14513379</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2008 Dec;68(6):533-55</Citation><ArticleIdList><ArticleId IdType="pubmed">18754079</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochem Biophys Res Commun. 2008 Jul 4;371(3):468-74</Citation><ArticleIdList><ArticleId IdType="pubmed">18442469</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant J. 2007 Apr;50(1):54-69</Citation><ArticleIdList><ArticleId IdType="pubmed">17346263</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Physiol. 2006 Feb;140(2):411-32</Citation><ArticleIdList><ArticleId IdType="pubmed">16407444</ArticleId></ArticleIdList></Reference><Reference><Citation>Nucleic Acids Res. 1989 Mar 25;17(6):2362</Citation><ArticleIdList><ArticleId IdType="pubmed">2468132</ArticleId></ArticleIdList></Reference><Reference><Citation>Plant Mol Biol. 2011 Mar;75(4-5):321-31</Citation><ArticleIdList><ArticleId IdType="pubmed">21246258</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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