Poplar carbohydrate-active enzymes. Gene identification and expression analyses.
Identifieur interne : 003D45 ( Main/Exploration ); précédent : 003D44; suivant : 003D46Poplar carbohydrate-active enzymes. Gene identification and expression analyses.
Auteurs : Jane Geisler-Lee [Suède] ; Matt Geisler ; Pedro M. Coutinho ; Bo Segerman ; Nobuyuki Nishikubo ; Junko Takahashi ; Henrik Aspeborg ; Soraya Djerbi ; Emma Master ; Sara Andersson-Gunner S ; Björn Sundberg ; Stanislaw Karpinski ; Tuula T. Teeri ; Leszek A. Kleczkowski ; Bernard Henrissat ; Ewa J. MellerowiczSource :
- Plant physiology [ 0032-0889 ] ; 2006.
Descripteurs français
- KwdFr :
- ARN des plantes (métabolisme), Amidon (métabolisme), Analyse de profil d'expression de gènes (MeSH), Arabidopsis (génétique), Carbone (métabolisme), Enzymes (classification), Enzymes (génétique), Enzymes (métabolisme), Famille multigénique (MeSH), Génome végétal (MeSH), Modèles biologiques (MeSH), Métabolisme glucidique (MeSH), Paroi cellulaire (métabolisme), Populus (enzymologie), Populus (génétique), Protéines végétales (classification), Protéines végétales (génétique), Protéines végétales (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Saccharose (métabolisme), Saisons (MeSH), Séquençage par oligonucléotides en batterie (MeSH), Variation génétique (MeSH), Étiquettes de séquences exprimées (MeSH).
- MESH :
- classification : Enzymes, Protéines végétales.
- enzymologie : Populus.
- génétique : Arabidopsis, Enzymes, Populus, Protéines végétales.
- métabolisme : ARN des plantes, Amidon, Carbone, Enzymes, Paroi cellulaire, Protéines végétales, Saccharose.
- Analyse de profil d'expression de gènes, Famille multigénique, Génome végétal, Modèles biologiques, Métabolisme glucidique, Régulation de l'expression des gènes végétaux, Saisons, Séquençage par oligonucléotides en batterie, Variation génétique, Étiquettes de séquences exprimées.
English descriptors
- KwdEn :
- Arabidopsis (genetics), Carbohydrate Metabolism (MeSH), Carbon (metabolism), Cell Wall (metabolism), Enzymes (classification), Enzymes (genetics), Enzymes (metabolism), Expressed Sequence Tags (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Genetic Variation (MeSH), Genome, Plant (MeSH), Models, Biological (MeSH), Multigene Family (MeSH), Oligonucleotide Array Sequence Analysis (MeSH), Plant Proteins (classification), Plant Proteins (genetics), Plant Proteins (metabolism), Populus (enzymology), Populus (genetics), RNA, Plant (metabolism), Seasons (MeSH), Starch (metabolism), Sucrose (metabolism).
- MESH :
- chemical , classification : Enzymes, Plant Proteins.
- chemical , genetics : Enzymes, Plant Proteins.
- chemical , metabolism : Carbon, Enzymes, Plant Proteins, RNA, Plant, Starch, Sucrose.
- enzymology : Populus.
- genetics : Arabidopsis, Populus.
- metabolism : Cell Wall.
- Carbohydrate Metabolism, Expressed Sequence Tags, Gene Expression Profiling, Gene Expression Regulation, Plant, Genetic Variation, Genome, Plant, Models, Biological, Multigene Family, Oligonucleotide Array Sequence Analysis, Seasons.
Abstract
Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr. & Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar (Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis (Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.
DOI: 10.1104/pp.105.072652
PubMed: 16415215
PubMed Central: PMC1400564
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Gene identification and expression analyses.</title><author><name sortKey="Geisler Lee, Jane" sort="Geisler Lee, Jane" uniqKey="Geisler Lee J" first="Jane" last="Geisler-Lee">Jane Geisler-Lee</name><affiliation wicri:level="1"><nlm:affiliation>Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center</wicri:regionArea><wicri:noRegion>Umeå Plant Science Center</wicri:noRegion></affiliation></author><author><name sortKey="Geisler, Matt" sort="Geisler, Matt" uniqKey="Geisler M" first="Matt" last="Geisler">Matt Geisler</name></author><author><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M" last="Coutinho">Pedro M. Coutinho</name></author><author><name sortKey="Segerman, Bo" sort="Segerman, Bo" uniqKey="Segerman B" first="Bo" last="Segerman">Bo Segerman</name></author><author><name sortKey="Nishikubo, Nobuyuki" sort="Nishikubo, Nobuyuki" uniqKey="Nishikubo N" first="Nobuyuki" last="Nishikubo">Nobuyuki Nishikubo</name></author><author><name sortKey="Takahashi, Junko" sort="Takahashi, Junko" uniqKey="Takahashi J" first="Junko" last="Takahashi">Junko Takahashi</name></author><author><name sortKey="Aspeborg, Henrik" sort="Aspeborg, Henrik" uniqKey="Aspeborg H" first="Henrik" last="Aspeborg">Henrik Aspeborg</name></author><author><name sortKey="Djerbi, Soraya" sort="Djerbi, Soraya" uniqKey="Djerbi S" first="Soraya" last="Djerbi">Soraya Djerbi</name></author><author><name sortKey="Master, Emma" sort="Master, Emma" uniqKey="Master E" first="Emma" last="Master">Emma Master</name></author><author><name sortKey="Andersson Gunner S, Sara" sort="Andersson Gunner S, Sara" uniqKey="Andersson Gunner S S" first="Sara" last="Andersson-Gunner S">Sara Andersson-Gunner S</name></author><author><name sortKey="Sundberg, Bjorn" sort="Sundberg, Bjorn" uniqKey="Sundberg B" first="Björn" last="Sundberg">Björn Sundberg</name></author><author><name sortKey="Karpinski, Stanislaw" sort="Karpinski, Stanislaw" uniqKey="Karpinski S" first="Stanislaw" last="Karpinski">Stanislaw Karpinski</name></author><author><name sortKey="Teeri, Tuula T" sort="Teeri, Tuula T" uniqKey="Teeri T" first="Tuula T" last="Teeri">Tuula T. Teeri</name></author><author><name sortKey="Kleczkowski, Leszek A" sort="Kleczkowski, Leszek A" uniqKey="Kleczkowski L" first="Leszek A" last="Kleczkowski">Leszek A. Kleczkowski</name></author><author><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name></author><author><name sortKey="Mellerowicz, Ewa J" sort="Mellerowicz, Ewa J" uniqKey="Mellerowicz E" first="Ewa J" last="Mellerowicz">Ewa J. Mellerowicz</name></author></analytic><series><title level="j">Plant physiology</title><idno type="ISSN">0032-0889</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Arabidopsis (genetics)</term><term>Carbohydrate Metabolism (MeSH)</term><term>Carbon (metabolism)</term><term>Cell Wall (metabolism)</term><term>Enzymes (classification)</term><term>Enzymes (genetics)</term><term>Enzymes (metabolism)</term><term>Expressed Sequence Tags (MeSH)</term><term>Gene Expression Profiling (MeSH)</term><term>Gene Expression Regulation, Plant (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Models, Biological (MeSH)</term><term>Multigene Family (MeSH)</term><term>Oligonucleotide Array Sequence Analysis (MeSH)</term><term>Plant Proteins (classification)</term><term>Plant Proteins (genetics)</term><term>Plant Proteins (metabolism)</term><term>Populus (enzymology)</term><term>Populus (genetics)</term><term>RNA, Plant (metabolism)</term><term>Seasons (MeSH)</term><term>Starch (metabolism)</term><term>Sucrose (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN des plantes (métabolisme)</term><term>Amidon (métabolisme)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Arabidopsis (génétique)</term><term>Carbone (métabolisme)</term><term>Enzymes (classification)</term><term>Enzymes (génétique)</term><term>Enzymes (métabolisme)</term><term>Famille multigénique (MeSH)</term><term>Génome végétal (MeSH)</term><term>Modèles biologiques (MeSH)</term><term>Métabolisme glucidique (MeSH)</term><term>Paroi cellulaire (métabolisme)</term><term>Populus (enzymologie)</term><term>Populus (génétique)</term><term>Protéines végétales (classification)</term><term>Protéines végétales (génétique)</term><term>Protéines végétales (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Saccharose (métabolisme)</term><term>Saisons (MeSH)</term><term>Séquençage par oligonucléotides en batterie (MeSH)</term><term>Variation génétique (MeSH)</term><term>Étiquettes de séquences exprimées (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="classification" xml:lang="en"><term>Enzymes</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Enzymes</term><term>Plant Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Carbon</term><term>Enzymes</term><term>Plant Proteins</term><term>RNA, Plant</term><term>Starch</term><term>Sucrose</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="fr"><term>Enzymes</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Arabidopsis</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Arabidopsis</term><term>Enzymes</term><term>Populus</term><term>Protéines végétales</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Cell Wall</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ARN des plantes</term><term>Amidon</term><term>Carbone</term><term>Enzymes</term><term>Paroi cellulaire</term><term>Protéines végétales</term><term>Saccharose</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Carbohydrate Metabolism</term><term>Expressed Sequence Tags</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Models, Biological</term><term>Multigene Family</term><term>Oligonucleotide Array Sequence Analysis</term><term>Seasons</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Famille multigénique</term><term>Génome végétal</term><term>Modèles biologiques</term><term>Métabolisme glucidique</term><term>Régulation de l'expression des gènes végétaux</term><term>Saisons</term><term>Séquençage par oligonucléotides en batterie</term><term>Variation génétique</term><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr. & Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar (Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis (Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16415215</PMID><DateCompleted><Year>2006</Year><Month>05</Month><Day>31</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0032-0889</ISSN><JournalIssue CitedMedium="Print"><Volume>140</Volume><Issue>3</Issue><PubDate><Year>2006</Year><Month>Mar</Month></PubDate></JournalIssue><Title>Plant physiology</Title><ISOAbbreviation>Plant Physiol</ISOAbbreviation></Journal><ArticleTitle>Poplar carbohydrate-active enzymes. Gene identification and expression analyses.</ArticleTitle><Pagination><MedlinePgn>946-62</MedlinePgn></Pagination><Abstract><AbstractText>Over 1,600 genes encoding carbohydrate-active enzymes (CAZymes) in the Populus trichocarpa (Torr. & Gray) genome were identified based on sequence homology, annotated, and grouped into families of glycosyltransferases, glycoside hydrolases, carbohydrate esterases, polysaccharide lyases, and expansins. Poplar (Populus spp.) had approximately 1.6 times more CAZyme genes than Arabidopsis (Arabidopsis thaliana). Whereas most families were proportionally increased, xylan and pectin-related families were underrepresented and the GT1 family of secondary metabolite-glycosylating enzymes was overrepresented in poplar. CAZyme gene expression in poplar was analyzed using a collection of 100,000 expressed sequence tags from 17 different tissues and compared to microarray data for poplar and Arabidopsis. Expression of genes involved in pectin and hemicellulose metabolism was detected in all tissues, indicating a constant maintenance of transcripts encoding enzymes remodeling the cell wall matrix. The most abundant transcripts encoded sucrose synthases that were specifically expressed in wood-forming tissues along with cellulose synthase and homologs of KORRIGAN and ELP1. Woody tissues were the richest source of various other CAZyme transcripts, demonstrating the importance of this group of enzymes for xylogenesis. In contrast, there was little expression of genes related to starch metabolism during wood formation, consistent with the preferential flux of carbon to cell wall biosynthesis. Seasonally dormant meristems of poplar showed a high prevalence of transcripts related to starch metabolism and surprisingly retained transcripts of some cell wall synthesis enzymes. The data showed profound changes in CAZyme transcriptomes in different poplar tissues and pointed to some key differences in CAZyme genes and their regulation between herbaceous and woody plants.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Geisler-Lee</LastName><ForeName>Jane</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Geisler</LastName><ForeName>Matt</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Coutinho</LastName><ForeName>Pedro M</ForeName><Initials>PM</Initials></Author><Author ValidYN="Y"><LastName>Segerman</LastName><ForeName>Bo</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Nishikubo</LastName><ForeName>Nobuyuki</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Takahashi</LastName><ForeName>Junko</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Aspeborg</LastName><ForeName>Henrik</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Djerbi</LastName><ForeName>Soraya</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Master</LastName><ForeName>Emma</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>Andersson-Gunnerås</LastName><ForeName>Sara</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Sundberg</LastName><ForeName>Björn</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Karpinski</LastName><ForeName>Stanislaw</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Teeri</LastName><ForeName>Tuula T</ForeName><Initials>TT</Initials></Author><Author ValidYN="Y"><LastName>Kleczkowski</LastName><ForeName>Leszek A</ForeName><Initials>LA</Initials></Author><Author ValidYN="Y"><LastName>Henrissat</LastName><ForeName>Bernard</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Mellerowicz</LastName><ForeName>Ewa J</ForeName><Initials>EJ</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>2006</Year><Month>01</Month><Day>13</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="D004798">Enzymes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance></Chemical><Chemical><RegistryNumber>57-50-1</RegistryNumber><NameOfSubstance UI="D013395">Sucrose</NameOfSubstance></Chemical><Chemical><RegistryNumber>7440-44-0</RegistryNumber><NameOfSubstance UI="D002244">Carbon</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-25-8</RegistryNumber><NameOfSubstance UI="D013213">Starch</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D050260" MajorTopicYN="Y">Carbohydrate Metabolism</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002244" MajorTopicYN="N">Carbon</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004798" MajorTopicYN="N">Enzymes</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="N">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018506" MajorTopicYN="Y">Gene Expression Regulation, Plant</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014644" MajorTopicYN="N">Genetic 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