Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae.
Identifieur interne : 003244 ( Main/Exploration ); précédent : 003243; suivant : 003245Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae.
Auteurs : Lorenzo Carretero-Paulet [Espagne] ; Anahit Galstyan ; Irma Roig-Villanova ; Jaime F. Martínez-García ; Jose R. Bilbao-Castro ; David L. RobertsonSource :
- Plant physiology [ 1532-2548 ] ; 2010.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de séquence d'ADN (MeSH), Animaux (MeSH), Arabidopsis (génétique), Bryopsida (génétique), Données de séquences moléculaires (MeSH), Eucaryotes (génétique), Facteurs de transcription à motif basique hélice-boucle-hélice (composition chimique), Facteurs de transcription à motif basique hélice-boucle-hélice (génétique), Facteurs de transcription à motif basique hélice-boucle-hélice (métabolisme), Famille multigénique (génétique), Génome végétal (génétique), Introns (génétique), Multimérisation de protéines (MeSH), Oryza (génétique), Phylogenèse (MeSH), Plantes (génétique), Populus (génétique), Séquence consensus (génétique), Séquence d'acides aminés (MeSH), Techniques de double hybride (MeSH), Évolution moléculaire (MeSH).
- MESH :
- composition chimique : Facteurs de transcription à motif basique hélice-boucle-hélice.
- génétique : ADN des plantes, Arabidopsis, Bryopsida, Eucaryotes, Facteurs de transcription à motif basique hélice-boucle-hélice, Famille multigénique, Génome végétal, Introns, Oryza, Plantes, Populus, Séquence consensus.
- métabolisme : Facteurs de transcription à motif basique hélice-boucle-hélice.
- Analyse de séquence d'ADN, Animaux, Données de séquences moléculaires, Multimérisation de protéines, Phylogenèse, Séquence d'acides aminés, Techniques de double hybride, Évolution moléculaire.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Animals (MeSH), Arabidopsis (genetics), Basic Helix-Loop-Helix Transcription Factors (chemistry), Basic Helix-Loop-Helix Transcription Factors (genetics), Basic Helix-Loop-Helix Transcription Factors (metabolism), Bryopsida (genetics), Consensus Sequence (genetics), DNA, Plant (genetics), Eukaryota (genetics), Evolution, Molecular (MeSH), Genome, Plant (genetics), Introns (genetics), Molecular Sequence Data (MeSH), Multigene Family (genetics), Oryza (genetics), Phylogeny (MeSH), Plants (genetics), Populus (genetics), Protein Multimerization (MeSH), Sequence Analysis, DNA (MeSH), Two-Hybrid System Techniques (MeSH).
- MESH :
- chemical , chemistry : Basic Helix-Loop-Helix Transcription Factors.
- genetics : Arabidopsis, Basic Helix-Loop-Helix Transcription Factors, Bryopsida, Consensus Sequence, DNA, Plant, Eukaryota, Genome, Plant, Introns, Multigene Family, Oryza, Plants, Populus.
- chemical , metabolism : Basic Helix-Loop-Helix Transcription Factors.
- Amino Acid Sequence, Animals, Evolution, Molecular, Molecular Sequence Data, Phylogeny, Protein Multimerization, Sequence Analysis, DNA, Two-Hybrid System Techniques.
Abstract
Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.
DOI: 10.1104/pp.110.153593
PubMed: 20472752
PubMed Central: PMC2899937
Affiliations:
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A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20472752</PMID><DateCompleted><Year>2010</Year><Month>10</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-2548</ISSN><JournalIssue CitedMedium="Internet"><Volume>153</Volume><Issue>3</Issue><PubDate><Year>2010</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Plant physiology</Title><ISOAbbreviation>Plant Physiol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae.</ArticleTitle><Pagination><MedlinePgn>1398-412</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1104/pp.110.153593</ELocationID><Abstract><AbstractText>Basic helix-loop-helix proteins (bHLHs) are found throughout the three eukaryotic kingdoms and constitute one of the largest families of transcription factors. A growing number of bHLH proteins have been functionally characterized in plants. However, some of these have not been previously classified. We present here an updated and comprehensive classification of the bHLHs encoded by the whole sequenced genomes of Arabidopsis (Arabidopsis thaliana), Populus trichocarpa, Oryza sativa, Physcomitrella patens, and five algae species. We define a plant bHLH consensus motif, which allowed the identification of novel highly diverged atypical bHLHs. Using yeast two-hybrid assays, we confirm that (1) a highly diverged bHLH has retained protein interaction activity and (2) the two most conserved positions in the consensus play an essential role in dimerization. Phylogenetic analysis permitted classification of the 638 bHLH genes identified into 32 subfamilies. Evolutionary and functional relationships within subfamilies are supported by intron patterns, predicted DNA-binding motifs, and the architecture of conserved protein motifs. Our analyses reveal the origin and evolutionary diversification of plant bHLHs through differential expansions, domain shuffling, and extensive sequence divergence. At the functional level, this would translate into different subfamilies evolving specific DNA-binding and protein interaction activities as well as differential transcriptional regulatory roles. Our results suggest a role for bHLH proteins in generating plant phenotypic diversity and provide a solid framework for further investigations into the role carried out in the transcriptional regulation of key growth and developmental processes.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Carretero-Paulet</LastName><ForeName>Lorenzo</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Department of Applied Biology , University of Almería, 04120 Almería, Spain. lpaulet@ual.es</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Galstyan</LastName><ForeName>Anahit</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Roig-Villanova</LastName><ForeName>Irma</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Martínez-García</LastName><ForeName>Jaime F</ForeName><Initials>JF</Initials></Author><Author ValidYN="Y"><LastName>Bilbao-Castro</LastName><ForeName>Jose R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Robertson</LastName><ForeName>David L</ForeName><Initials>DL</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>2010</Year><Month>05</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Physiol</MedlineTA><NlmUniqueID>0401224</NlmUniqueID><ISSNLinking>0032-0889</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D051792">Basic Helix-Loop-Helix Transcription Factors</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018744">DNA, Plant</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D051792" MajorTopicYN="N">Basic Helix-Loop-Helix Transcription Factors</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019068" MajorTopicYN="N">Bryopsida</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016384" MajorTopicYN="N">Consensus Sequence</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018744" MajorTopicYN="N">DNA, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D056890" MajorTopicYN="N">Eukaryota</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="Y">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D007438" MajorTopicYN="N">Introns</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010944" MajorTopicYN="N">Plants</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D055503" MajorTopicYN="N">Protein Multimerization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020798" MajorTopicYN="N">Two-Hybrid System Techniques</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>5</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>5</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2010</Year><Month>10</Month><Day>12</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">20472752</ArticleId><ArticleId IdType="pii">pp.110.153593</ArticleId><ArticleId IdType="doi">10.1104/pp.110.153593</ArticleId><ArticleId 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Bilbao-Castro</name><name sortKey="Galstyan, Anahit" sort="Galstyan, Anahit" uniqKey="Galstyan A" first="Anahit" last="Galstyan">Anahit Galstyan</name><name sortKey="Martinez Garcia, Jaime F" sort="Martinez Garcia, Jaime F" uniqKey="Martinez Garcia J" first="Jaime F" last="Martínez-García">Jaime F. Martínez-García</name><name sortKey="Robertson, David L" sort="Robertson, David L" uniqKey="Robertson D" first="David L" last="Robertson">David L. Robertson</name><name sortKey="Roig Villanova, Irma" sort="Roig Villanova, Irma" uniqKey="Roig Villanova I" first="Irma" last="Roig-Villanova">Irma Roig-Villanova</name></noCountry><country name="Espagne"><region name="Andalousie"><name sortKey="Carretero Paulet, Lorenzo" sort="Carretero Paulet, Lorenzo" uniqKey="Carretero Paulet L" first="Lorenzo" last="Carretero-Paulet">Lorenzo Carretero-Paulet</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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