Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants.
Identifieur interne : 003532 ( Main/Exploration ); précédent : 003531; suivant : 003533Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants.
Auteurs : Malona V. Alinsug [Taïwan] ; Chun-Wei Yu ; Keqiang WuSource :
- BMC plant biology [ 1471-2229 ] ; 2009.
Descripteurs français
- KwdFr :
- ADN des plantes (génétique), Analyse de profil d'expression de gènes (MeSH), Analyse de séquence d'ADN (MeSH), Biologie informatique (MeSH), Histone deacetylases (génétique), Phylogenèse (MeSH), Plantes (enzymologie), Plantes (génétique), Protéines de Saccharomyces cerevisiae (génétique), Protéines végétales (génétique), Régulation de l'expression des gènes végétaux (MeSH), Saccharomyces cerevisiae (génétique), Séquence conservée (MeSH), Évolution moléculaire (MeSH).
- MESH :
- enzymologie : Plantes.
- génétique : ADN des plantes, Histone deacetylases, Plantes, Protéines de Saccharomyces cerevisiae, Protéines végétales, Saccharomyces cerevisiae.
- Analyse de profil d'expression de gènes, Analyse de séquence d'ADN, Biologie informatique, Phylogenèse, Régulation de l'expression des gènes végétaux, Séquence conservée, Évolution moléculaire.
English descriptors
- KwdEn :
- Computational Biology (MeSH), Conserved Sequence (MeSH), DNA, Plant (genetics), Evolution, Molecular (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Histone Deacetylases (genetics), Phylogeny (MeSH), Plant Proteins (genetics), Plants (enzymology), Plants (genetics), Saccharomyces cerevisiae (genetics), Saccharomyces cerevisiae Proteins (genetics), Sequence Analysis, DNA (MeSH).
- MESH :
- chemical , genetics : DNA, Plant, Histone Deacetylases, Plant Proteins, Saccharomyces cerevisiae Proteins.
- enzymology : Plants.
- genetics : Plants, Saccharomyces cerevisiae.
- Computational Biology, Conserved Sequence, Evolution, Molecular, Gene Expression Profiling, Gene Expression Regulation, Plant, Phylogeny, Sequence Analysis, DNA.
Abstract
BACKGROUND
Although histone deacetylases from model organisms have been previously identified, there is no clear basis for the classification of histone deacetylases under the RPD3/HDA1 superfamily, particularly on plants. Thus, this study aims to reconstruct a phylogenetic tree to determine evolutionary relationships between RPD3/HDA1 histone deacetylases from six different plants representing dicots with Arabidopsis thaliana, Populus trichocarpa, and Pinus taeda, monocots with Oryza sativa and Zea mays, and the lower plants with Physcomitrella patens.
RESULTS
Sixty two histone deacetylases of RPD3/HDA1 family from the six plant species were phylogenetically analyzed to determine corresponding orthologues. Three clusters were formed separating Class I, Class II, and Class IV. We have confirmed lower and higher plant orthologues for AtHDA8 and AtHDA14, classifying both genes as Class II histone deacetylases in addition to AtHDA5, AtHDA15, and AtHDA18. Since Class II histone deacetylases in other eukaryotes have been known to undergo nucleocytoplasmic transport, it remains unknown whether such functional regulation also happens in plants. Thus, bioinformatics studies using different programs and databases were conducted to predict their corresponding localization sites, nuclear export signal, nuclear localization signal, as well as expression patterns. We also found new conserved domains in most of the RPD3/HDA1 histone deacetylases which were similarly conserved in its corresponding orthologues. Assessing gene expression patterns using Genevestigator, it appears that RPD3/HDA1 histone deacetylases are expressed all throughout the plant parts and developmental stages of the plant.
CONCLUSION
The RPD3/HDA1 histone deacetylase family in plants is divided into three distinct groups namely, Class I, Class II, and Class IV suggesting functional diversification. Class II comprises not only AtHDA5, AtHDA15, and AtHDA18 but also includes AtHDA8 and AtHDA14. New conserved domains have also been identified in most of the RPD3/HDA1 family indicating further versatile roles other than histone deacetylation.
DOI: 10.1186/1471-2229-9-37
PubMed: 19327164
PubMed Central: PMC2671507
Affiliations:
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Alinsug</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan. malinsug@yahoo.com</nlm:affiliation><country xml:lang="fr">Taïwan</country><wicri:regionArea>Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei</wicri:regionArea><wicri:noRegion>Taipei</wicri:noRegion></affiliation></author><author><name sortKey="Yu, Chun Wei" sort="Yu, Chun Wei" uniqKey="Yu C" first="Chun-Wei" last="Yu">Chun-Wei Yu</name></author><author><name sortKey="Wu, Keqiang" sort="Wu, Keqiang" uniqKey="Wu K" first="Keqiang" last="Wu">Keqiang Wu</name></author></analytic><series><title level="j">BMC plant biology</title><idno type="eISSN">1471-2229</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology (MeSH)</term><term>Conserved Sequence (MeSH)</term><term>DNA, Plant (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Histone Deacetylases (genetics)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plants (enzymology)</term><term>Plants (genetics)</term><term>Saccharomyces cerevisiae (genetics)</term><term>Saccharomyces cerevisiae Proteins (genetics)</term><term>Sequence Analysis, DNA (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN des plantes (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Biologie informatique (MeSH)</term><term>Histone deacetylases (génétique)</term><term>Phylogenèse (MeSH)</term><term>Plantes (enzymologie)</term><term>Plantes (génétique)</term><term>Protéines de Saccharomyces cerevisiae (génétique)</term><term>Protéines végétales (génétique)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Saccharomyces cerevisiae (génétique)</term><term>Séquence conservée (MeSH)</term><term>Évolution moléculaire (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Plant</term><term>Histone Deacetylases</term><term>Plant Proteins</term><term>Saccharomyces cerevisiae Proteins</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Plantes</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Plants</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plants</term><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN des plantes</term><term>Histone deacetylases</term><term>Plantes</term><term>Protéines de Saccharomyces cerevisiae</term><term>Protéines végétales</term><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Conserved Sequence</term><term>Evolution, Molecular</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Phylogenèse</term><term>Régulation de l'expression des gènes végétaux</term><term>Séquence conservée</term><term>Évolution moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Although histone deacetylases from model organisms have been previously identified, there is no clear basis for the classification of histone deacetylases under the RPD3/HDA1 superfamily, particularly on plants. Thus, this study aims to reconstruct a phylogenetic tree to determine evolutionary relationships between RPD3/HDA1 histone deacetylases from six different plants representing dicots with Arabidopsis thaliana, Populus trichocarpa, and Pinus taeda, monocots with Oryza sativa and Zea mays, and the lower plants with Physcomitrella patens.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Sixty two histone deacetylases of RPD3/HDA1 family from the six plant species were phylogenetically analyzed to determine corresponding orthologues. Three clusters were formed separating Class I, Class II, and Class IV. We have confirmed lower and higher plant orthologues for AtHDA8 and AtHDA14, classifying both genes as Class II histone deacetylases in addition to AtHDA5, AtHDA15, and AtHDA18. Since Class II histone deacetylases in other eukaryotes have been known to undergo nucleocytoplasmic transport, it remains unknown whether such functional regulation also happens in plants. Thus, bioinformatics studies using different programs and databases were conducted to predict their corresponding localization sites, nuclear export signal, nuclear localization signal, as well as expression patterns. We also found new conserved domains in most of the RPD3/HDA1 histone deacetylases which were similarly conserved in its corresponding orthologues. Assessing gene expression patterns using Genevestigator, it appears that RPD3/HDA1 histone deacetylases are expressed all throughout the plant parts and developmental stages of the plant.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>The RPD3/HDA1 histone deacetylase family in plants is divided into three distinct groups namely, Class I, Class II, and Class IV suggesting functional diversification. Class II comprises not only AtHDA5, AtHDA15, and AtHDA18 but also includes AtHDA8 and AtHDA14. New conserved domains have also been identified in most of the RPD3/HDA1 family indicating further versatile roles other than histone deacetylation.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19327164</PMID><DateCompleted><Year>2009</Year><Month>04</Month><Day>30</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2229</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><PubDate><Year>2009</Year><Month>Mar</Month><Day>28</Day></PubDate></JournalIssue><Title>BMC plant biology</Title><ISOAbbreviation>BMC Plant Biol</ISOAbbreviation></Journal><ArticleTitle>Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants.</ArticleTitle><Pagination><MedlinePgn>37</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2229-9-37</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Although histone deacetylases from model organisms have been previously identified, there is no clear basis for the classification of histone deacetylases under the RPD3/HDA1 superfamily, particularly on plants. Thus, this study aims to reconstruct a phylogenetic tree to determine evolutionary relationships between RPD3/HDA1 histone deacetylases from six different plants representing dicots with Arabidopsis thaliana, Populus trichocarpa, and Pinus taeda, monocots with Oryza sativa and Zea mays, and the lower plants with Physcomitrella patens.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Sixty two histone deacetylases of RPD3/HDA1 family from the six plant species were phylogenetically analyzed to determine corresponding orthologues. Three clusters were formed separating Class I, Class II, and Class IV. We have confirmed lower and higher plant orthologues for AtHDA8 and AtHDA14, classifying both genes as Class II histone deacetylases in addition to AtHDA5, AtHDA15, and AtHDA18. Since Class II histone deacetylases in other eukaryotes have been known to undergo nucleocytoplasmic transport, it remains unknown whether such functional regulation also happens in plants. Thus, bioinformatics studies using different programs and databases were conducted to predict their corresponding localization sites, nuclear export signal, nuclear localization signal, as well as expression patterns. We also found new conserved domains in most of the RPD3/HDA1 histone deacetylases which were similarly conserved in its corresponding orthologues. Assessing gene expression patterns using Genevestigator, it appears that RPD3/HDA1 histone deacetylases are expressed all throughout the plant parts and developmental stages of the plant.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">The RPD3/HDA1 histone deacetylase family in plants is divided into three distinct groups namely, Class I, Class II, and Class IV suggesting functional diversification. Class II comprises not only AtHDA5, AtHDA15, and AtHDA18 but also includes AtHDA8 and AtHDA14. New conserved domains have also been identified in most of the RPD3/HDA1 family indicating further versatile roles other than histone deacetylation.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Alinsug</LastName><ForeName>Malona V</ForeName><Initials>MV</Initials><AffiliationInfo><Affiliation>Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan. malinsug@yahoo.com</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yu</LastName><ForeName>Chun-Wei</ForeName><Initials>CW</Initials></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Keqiang</ForeName><Initials>K</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 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|area= PoplarV1
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|étape= Exploration
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|clé= pubmed:19327164
|texte= Phylogenetic analysis, subcellular localization, and expression patterns of RPD3/HDA1 family histone deacetylases in plants.
}}
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