Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data.
Identifieur interne : 000770 ( Main/Exploration ); précédent : 000769; suivant : 000771Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data.
Auteurs : Vikash Kumar [Suède] ; Matthieu Hainaut [France] ; Nicolas Delhomme [Suède] ; Chanaka Mannapperuma [Suède] ; Peter Immerzeel [Suède] ; Nathaniel R. Street [Suède] ; Bernard Henrissat [France] ; Ewa J. Mellerowicz [Suède]Source :
- The Plant journal : for cell and molecular biology [ 1365-313X ] ; 2019.
Descripteurs français
- KwdFr :
- Bois (génétique), Bois (métabolisme), Génomique (MeSH), Paroi cellulaire (génétique), Paroi cellulaire (métabolisme), Populus (génétique), Populus (métabolisme), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (génétique), Régulation de l'expression des gènes végétaux (physiologie), Séquençage du génome entier (MeSH).
- MESH :
- génétique : Bois, Paroi cellulaire, Populus, Protéines végétales, Régulation de l'expression des gènes végétaux.
- métabolisme : Bois, Paroi cellulaire, Populus, Protéines végétales.
- physiologie : Régulation de l'expression des gènes végétaux.
- Génomique, Séquençage du génome entier.
English descriptors
- KwdEn :
- Cell Wall (genetics), Cell Wall (metabolism), Gene Expression Regulation, Plant (genetics), Gene Expression Regulation, Plant (physiology), Genomics (MeSH), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (genetics), Populus (metabolism), Whole Genome Sequencing (MeSH), Wood (genetics), Wood (metabolism).
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Cell Wall, Gene Expression Regulation, Plant, Populus, Wood.
- metabolism : Cell Wall, Plant Proteins, Populus, Wood.
- physiology : Gene Expression Regulation, Plant.
- Genomics, Whole Genome Sequencing.
Abstract
Carbohydrate-active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re-annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high-resolution RNA-Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood-forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.
DOI: 10.1111/tpj.14417
PubMed: 31111606
PubMed Central: PMC6852159
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Center, Plant Physiology Department, Umeå University, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Immerzeel, Peter" sort="Immerzeel, Peter" uniqKey="Immerzeel P" first="Peter" last="Immerzeel">Peter Immerzeel</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea</wicri:regionArea><wicri:noRegion>Umea</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>Chemical Engineering, Karlstad University, Karlstad, 65188, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Chemical Engineering, Karlstad University, Karlstad, 65188</wicri:regionArea><wicri:noRegion>65188</wicri:noRegion></affiliation></author><author><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Center, Plant Physiology Department, Umeå University, Umeå, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Center, Plant Physiology Department, Umeå University, Umeå</wicri:regionArea><wicri:noRegion>Umeå</wicri:noRegion></affiliation></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><affiliation wicri:level="3"><nlm:affiliation>Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, Marseille, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, Marseille</wicri:regionArea><placeName><region type="region">Provence-Alpes-Côte d'Azur</region><region type="old region">Provence-Alpes-Côte d'Azur</region><settlement type="city">Marseille</settlement></placeName></affiliation><affiliation wicri:level="3"><nlm:affiliation>INRA, USC 1408 AFMB, Marseille, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>INRA, USC 1408 AFMB, Marseille</wicri:regionArea><placeName><region type="region">Provence-Alpes-Côte d'Azur</region><region type="old region">Provence-Alpes-Côte d'Azur</region><settlement type="city">Marseille</settlement></placeName></affiliation></author><author><name sortKey="Mellerowicz, Ewa J" sort="Mellerowicz, Ewa J" uniqKey="Mellerowicz E" first="Ewa J" last="Mellerowicz">Ewa J. Mellerowicz</name><affiliation wicri:level="1"><nlm:affiliation>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea</wicri:regionArea><wicri:noRegion>Umea</wicri:noRegion></affiliation></author></analytic><series><title level="j">The Plant journal : for cell and molecular biology</title><idno type="eISSN">1365-313X</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Cell Wall (genetics)</term><term>Cell Wall (metabolism)</term><term>Gene Expression Regulation, Plant (genetics)</term><term>Gene Expression Regulation, Plant (physiology)</term><term>Genomics (MeSH)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Populus (genetics)</term><term>Populus (metabolism)</term><term>Whole Genome Sequencing (MeSH)</term><term>Wood (genetics)</term><term>Wood (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bois (génétique)</term><term>Bois (métabolisme)</term><term>Génomique (MeSH)</term><term>Paroi cellulaire (génétique)</term><term>Paroi cellulaire (métabolisme)</term><term>Populus (génétique)</term><term>Populus (métabolisme)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (génétique)</term><term>Régulation de l'expression des gènes végétaux (physiologie)</term><term>Séquençage du génome entier (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Wall</term><term>Gene Expression Regulation, Plant</term><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Bois</term><term>Paroi cellulaire</term><term>Populus</term><term>Protéines végétales</term><term>Régulation de l'expression des gènes végétaux</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Cell Wall</term><term>Plant Proteins</term><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Bois</term><term>Paroi cellulaire</term><term>Populus</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Régulation de l'expression des gènes végétaux</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Gene Expression Regulation, Plant</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Genomics</term><term>Whole Genome Sequencing</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Génomique</term><term>Séquençage du génome entier</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Carbohydrate-active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re-annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high-resolution RNA-Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood-forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">31111606</PMID><DateCompleted><Year>2020</Year><Month>06</Month><Day>08</Day></DateCompleted><DateRevised><Year>2020</Year><Month>06</Month><Day>08</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1365-313X</ISSN><JournalIssue CitedMedium="Internet"><Volume>99</Volume><Issue>4</Issue><PubDate><Year>2019</Year><Month>08</Month></PubDate></JournalIssue><Title>The Plant journal : for cell and molecular biology</Title><ISOAbbreviation>Plant J</ISOAbbreviation></Journal><ArticleTitle>Poplar carbohydrate-active enzymes: whole-genome annotation and functional analyses based on RNA expression data.</ArticleTitle><Pagination><MedlinePgn>589-609</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/tpj.14417</ELocationID><Abstract><AbstractText>Carbohydrate-active enzymes (CAZymes) catalyze the formation and modification of glycoproteins, glycolipids, starch, secondary metabolites and cell wall biopolymers. They are key enzymes for the biosynthesis of food and renewable biomass. Woody biomass is particularly important for long-term carbon storage and as an abundant renewable natural resource for many industrial applications. This study presents a re-annotation of CAZyme genes in the current Populus trichocarpa genome assembly and in silico functional characterization, based on high-resolution RNA-Seq data sets. Altogether, 1914 CAZyme and expansin genes were annotated in 101 families. About 1797 of these genes were found expressed in at least one Populus organ. We identified genes involved in the biosynthesis of different cell wall polymers and their paralogs. Whereas similar families exist in poplar and Arabidopsis thaliana (with the exception of CBM13 found only in poplar), a few families had significantly different copy numbers between the two species. To identify the transcriptional coordination and functional relatedness within the CAZymes and other proteins, we performed co-expression network analysis of CAZymes in wood-forming tissues using the AspWood database (http://aspwood.popgenie.org/aspwood-v3.0/) for Populus tremula. This provided an overview of the transcriptional changes in CAZymes during the transition from primary to secondary wall formation, and the clustering of transcripts into potential regulons. Candidate enzymes involved in the biosynthesis of polysaccharides were identified along with many tissue-specific uncharacterized genes and transcription factors. These collections offer a rich source of targets for the modification of secondary cell wall biosynthesis and other developmental processes in woody plants.</AbstractText><CopyrightInformation>© 2019 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kumar</LastName><ForeName>Vikash</ForeName><Initials>V</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hainaut</LastName><ForeName>Matthieu</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, Marseille, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>INRA, USC 1408 AFMB, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Delhomme</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mannapperuma</LastName><ForeName>Chanaka</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center, Plant Physiology Department, Umeå University, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Immerzeel</LastName><ForeName>Peter</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Chemical Engineering, Karlstad University, Karlstad, 65188, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Street</LastName><ForeName>Nathaniel R</ForeName><Initials>NR</Initials><AffiliationInfo><Affiliation>Umeå Plant Science Center, Plant Physiology Department, Umeå University, Umeå, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Henrissat</LastName><ForeName>Bernard</ForeName><Initials>B</Initials><AffiliationInfo><Affiliation>Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille University, Marseille, France.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>INRA, USC 1408 AFMB, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mellerowicz</LastName><ForeName>Ewa J</ForeName><Initials>EJ</Initials><Identifier Source="ORCID">0000-0001-6817-1031</Identifier><AffiliationInfo><Affiliation>Umeå Plant Science Center, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umea, Sweden.</Affiliation></AffiliationInfo></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>2019</Year><Month>07</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Plant J</MedlineTA><NlmUniqueID>9207397</NlmUniqueID><ISSNLinking>0960-7412</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>Plant J. 2019 Aug;99(4):587-588</RefSource><PMID 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IdType="pubmed">24450583</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>France</li><li>Suède</li></country><region><li>Provence-Alpes-Côte d'Azur</li></region><settlement><li>Marseille</li></settlement></list><tree><country name="Suède"><noRegion><name sortKey="Kumar, Vikash" sort="Kumar, Vikash" uniqKey="Kumar V" first="Vikash" last="Kumar">Vikash Kumar</name></noRegion><name sortKey="Delhomme, Nicolas" sort="Delhomme, Nicolas" uniqKey="Delhomme N" first="Nicolas" last="Delhomme">Nicolas Delhomme</name><name sortKey="Immerzeel, Peter" sort="Immerzeel, Peter" uniqKey="Immerzeel P" first="Peter" last="Immerzeel">Peter Immerzeel</name><name sortKey="Immerzeel, Peter" sort="Immerzeel, Peter" uniqKey="Immerzeel P" first="Peter" last="Immerzeel">Peter Immerzeel</name><name sortKey="Mannapperuma, Chanaka" sort="Mannapperuma, Chanaka" uniqKey="Mannapperuma C" first="Chanaka" last="Mannapperuma">Chanaka Mannapperuma</name><name sortKey="Mellerowicz, Ewa J" sort="Mellerowicz, Ewa J" uniqKey="Mellerowicz E" first="Ewa J" last="Mellerowicz">Ewa J. Mellerowicz</name><name sortKey="Street, Nathaniel R" sort="Street, Nathaniel R" uniqKey="Street N" first="Nathaniel R" last="Street">Nathaniel R. Street</name></country><country name="France"><region name="Provence-Alpes-Côte d'Azur"><name sortKey="Hainaut, Matthieu" sort="Hainaut, Matthieu" uniqKey="Hainaut M" first="Matthieu" last="Hainaut">Matthieu Hainaut</name></region><name sortKey="Hainaut, Matthieu" sort="Hainaut, Matthieu" uniqKey="Hainaut M" first="Matthieu" last="Hainaut">Matthieu Hainaut</name><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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