Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella.
Identifieur interne : 003840 ( Main/Corpus ); précédent : 003839; suivant : 003841Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella.
Auteurs : Clarice De Azevedo Souza ; Brad Barbazuk ; Steven G. Ralph ; Joerg Bohlmann ; Bjoern Hamberger ; Carl J. DouglasSource :
- The New phytologist [ 1469-8137 ] ; 2008.
English descriptors
- KwdEn :
- Arabidopsis (enzymology), Arabidopsis (genetics), Base Sequence (MeSH), Bryopsida (enzymology), Bryopsida (genetics), Chloroplasts (chemistry), Coenzyme A Ligases (analysis), Coenzyme A Ligases (genetics), Coenzyme A Ligases (physiology), Computational Biology (MeSH), Evolution, Molecular (MeSH), Gene Expression (MeSH), Genome, Plant (MeSH), Multigene Family (MeSH), Oryza (enzymology), Oryza (genetics), Peroxisomes (chemistry), Phylogeny (MeSH), Plant Proteins (analysis), Plant Proteins (genetics), Plant Proteins (physiology), Plants (enzymology), Plants (genetics), Plants, Genetically Modified (metabolism), Plants, Genetically Modified (ultrastructure), Populus (enzymology), Populus (genetics), Sequence Alignment (MeSH), Tobacco (genetics).
- MESH :
- chemical , analysis : Coenzyme A Ligases, Plant Proteins.
- chemistry : Chloroplasts, Peroxisomes.
- enzymology : Arabidopsis, Bryopsida, Oryza, Plants, Populus.
- genetics : Arabidopsis, Bryopsida, Coenzyme A Ligases, Oryza, Plant Proteins, Plants, Populus, Tobacco.
- metabolism : Plants, Genetically Modified.
- chemical , physiology : Coenzyme A Ligases, Plant Proteins.
- ultrastructure : Plants, Genetically Modified.
- Base Sequence, Computational Biology, Evolution, Molecular, Gene Expression, Genome, Plant, Multigene Family, Phylogeny, Sequence Alignment.
Abstract
The plant enzyme 4-coumarate:coenzyme A ligase (4CL) is part of a family of adenylate-forming enzymes present in all organisms. Analysis of genome sequences shows the presence of '4CL-like' enzymes in plants and other organisms, but their evolutionary relationships and functions remain largely unknown. 4CL and 4CL-like genes were identified by BLAST searches in Arabidopsis, Populus, rice, Physcomitrella, Chlamydomonas and microbial genomes. Evolutionary relationships were inferred by phylogenetic analysis of aligned amino acid sequences. Expression patterns of a conserved set of Arabidopsis and poplar 4CL-like acyl-CoA synthetase (ACS) genes were assayed. The conserved ACS genes form a land plant-specific class. Angiosperm ACS genes grouped into five clades, each of which contained representatives in three fully sequenced genomes. Expression analysis revealed conserved developmental and stress-induced expression patterns of Arabidopsis and poplar genes in some clades. Evolution of plant ACS enzymes occurred early in land plants. Differential gene expansion of angiosperm ACS clades has occurred in some lineages. Evolutionary and gene expression data, combined with in vitro and limited in vivo protein function data, suggest that angiosperm ACS enzymes play conserved roles in octadecanoid and fatty acid metabolism, and play roles in organ development, for example in anthers.
DOI: 10.1111/j.1469-8137.2008.02534.x
PubMed: 18627494
Links to Exploration step
pubmed:18627494Le document en format XML
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Ralph</name></author><author><name sortKey="Bohlmann, Joerg" sort="Bohlmann, Joerg" uniqKey="Bohlmann J" first="Joerg" last="Bohlmann">Joerg Bohlmann</name></author><author><name sortKey="Hamberger, Bjoern" sort="Hamberger, Bjoern" uniqKey="Hamberger B" first="Bjoern" last="Hamberger">Bjoern Hamberger</name></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. 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Ralph</name></author><author><name sortKey="Bohlmann, Joerg" sort="Bohlmann, Joerg" uniqKey="Bohlmann J" first="Joerg" last="Bohlmann">Joerg Bohlmann</name></author><author><name sortKey="Hamberger, Bjoern" sort="Hamberger, Bjoern" uniqKey="Hamberger B" first="Bjoern" last="Hamberger">Bjoern Hamberger</name></author><author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name></author></analytic><series><title level="j">The New phytologist</title><idno type="eISSN">1469-8137</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (enzymology)</term><term>Arabidopsis (genetics)</term><term>Base Sequence (MeSH)</term><term>Bryopsida (enzymology)</term><term>Bryopsida (genetics)</term><term>Chloroplasts (chemistry)</term><term>Coenzyme A Ligases (analysis)</term><term>Coenzyme A Ligases (genetics)</term><term>Coenzyme A Ligases (physiology)</term><term>Computational Biology (MeSH)</term><term>Evolution, Molecular (MeSH)</term><term>Gene Expression (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Multigene Family (MeSH)</term><term>Oryza (enzymology)</term><term>Oryza (genetics)</term><term>Peroxisomes (chemistry)</term><term>Phylogeny (MeSH)</term><term>Plant Proteins (analysis)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (physiology)</term><term>Plants (enzymology)</term><term>Plants (genetics)</term><term>Plants, Genetically Modified (metabolism)</term><term>Plants, Genetically Modified (ultrastructure)</term><term>Populus (enzymology)</term><term>Populus (genetics)</term><term>Sequence Alignment (MeSH)</term><term>Tobacco (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Coenzyme A Ligases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Chloroplasts</term><term>Peroxisomes</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Arabidopsis</term><term>Bryopsida</term><term>Oryza</term><term>Plants</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Bryopsida</term><term>Coenzyme A Ligases</term><term>Oryza</term><term>Plant Proteins</term><term>Plants</term><term>Populus</term><term>Tobacco</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Plants, Genetically Modified</term></keywords><keywords scheme="MESH" type="chemical" qualifier="physiology" xml:lang="en"><term>Coenzyme A Ligases</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="ultrastructure" xml:lang="en"><term>Plants, Genetically Modified</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Computational Biology</term><term>Evolution, Molecular</term><term>Gene Expression</term><term>Genome, Plant</term><term>Multigene Family</term><term>Phylogeny</term><term>Sequence Alignment</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The plant enzyme 4-coumarate:coenzyme A ligase (4CL) is part of a family of adenylate-forming enzymes present in all organisms. Analysis of genome sequences shows the presence of '4CL-like' enzymes in plants and other organisms, but their evolutionary relationships and functions remain largely unknown. 4CL and 4CL-like genes were identified by BLAST searches in Arabidopsis, Populus, rice, Physcomitrella, Chlamydomonas and microbial genomes. Evolutionary relationships were inferred by phylogenetic analysis of aligned amino acid sequences. Expression patterns of a conserved set of Arabidopsis and poplar 4CL-like acyl-CoA synthetase (ACS) genes were assayed. The conserved ACS genes form a land plant-specific class. Angiosperm ACS genes grouped into five clades, each of which contained representatives in three fully sequenced genomes. Expression analysis revealed conserved developmental and stress-induced expression patterns of Arabidopsis and poplar genes in some clades. Evolution of plant ACS enzymes occurred early in land plants. Differential gene expansion of angiosperm ACS clades has occurred in some lineages. Evolutionary and gene expression data, combined with in vitro and limited in vivo protein function data, suggest that angiosperm ACS enzymes play conserved roles in octadecanoid and fatty acid metabolism, and play roles in organ development, for example in anthers.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18627494</PMID><DateCompleted><Year>2008</Year><Month>11</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1469-8137</ISSN><JournalIssue CitedMedium="Internet"><Volume>179</Volume><Issue>4</Issue><PubDate><Year>2008</Year></PubDate></JournalIssue><Title>The New phytologist</Title><ISOAbbreviation>New Phytol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide analysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella.</ArticleTitle><Pagination><MedlinePgn>987-1003</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1469-8137.2008.02534.x</ELocationID><Abstract><AbstractText>The plant enzyme 4-coumarate:coenzyme A ligase (4CL) is part of a family of adenylate-forming enzymes present in all organisms. Analysis of genome sequences shows the presence of '4CL-like' enzymes in plants and other organisms, but their evolutionary relationships and functions remain largely unknown. 4CL and 4CL-like genes were identified by BLAST searches in Arabidopsis, Populus, rice, Physcomitrella, Chlamydomonas and microbial genomes. Evolutionary relationships were inferred by phylogenetic analysis of aligned amino acid sequences. Expression patterns of a conserved set of Arabidopsis and poplar 4CL-like acyl-CoA synthetase (ACS) genes were assayed. The conserved ACS genes form a land plant-specific class. Angiosperm ACS genes grouped into five clades, each of which contained representatives in three fully sequenced genomes. Expression analysis revealed conserved developmental and stress-induced expression patterns of Arabidopsis and poplar genes in some clades. Evolution of plant ACS enzymes occurred early in land plants. Differential gene expansion of angiosperm ACS clades has occurred in some lineages. Evolutionary and gene expression data, combined with in vitro and limited in vivo protein function data, suggest that angiosperm ACS enzymes play conserved roles in octadecanoid and fatty acid metabolism, and play roles in organ development, for example in anthers.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Souza</LastName><ForeName>Clarice de Azevedo</ForeName><Initials>Cde A</Initials><AffiliationInfo><Affiliation>Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Barbazuk</LastName><ForeName>Brad</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Ralph</LastName><ForeName>Steven G</ForeName><Initials>SG</Initials></Author><Author ValidYN="Y"><LastName>Bohlmann</LastName><ForeName>Joerg</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Hamberger</LastName><ForeName>Bjoern</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Douglas</LastName><ForeName>Carl J</ForeName><Initials>CJ</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>England</Country><MedlineTA>New Phytol</MedlineTA><NlmUniqueID>9882884</NlmUniqueID><ISSNLinking>0028-646X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 6.2.1.-</RegistryNumber><NameOfSubstance UI="D003066">Coenzyme A Ligases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" 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UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="N">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014026" MajorTopicYN="N">Tobacco</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>7</Month><Day>17</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>11</Month><Day>19</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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