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Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa.

Identifieur interne : 001D96 ( Main/Exploration ); précédent : 001D95; suivant : 001D97

Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa.

Auteurs : Philip L. Loziuk [États-Unis] ; Jennifer Parker [États-Unis] ; Wei Li [États-Unis] ; Chien-Yuan Lin [États-Unis] ; Jack P. Wang [États-Unis] ; Quanzi Li [République populaire de Chine] ; Ronald R. Sederoff [États-Unis] ; Vincent L. Chiang [États-Unis] ; David C. Muddiman [États-Unis]

Source :

RBID : pubmed:26325666

Descripteurs français

English descriptors

Abstract

Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa.

DOI: 10.1021/acs.jproteome.5b00233
PubMed: 26325666


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Le document en format XML

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<term>Carbohydrate Metabolism (MeSH)</term>
<term>Cellulose (biosynthesis)</term>
<term>Cellulose (genetics)</term>
<term>Chromatography, Liquid (MeSH)</term>
<term>Gene Expression Regulation, Plant (MeSH)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (isolation & purification)</term>
<term>Plant Proteins (metabolism)</term>
<term>Populus (genetics)</term>
<term>Populus (metabolism)</term>
<term>Proteome (genetics)</term>
<term>Proteome (isolation & purification)</term>
<term>Proteome (metabolism)</term>
<term>Proteomics (MeSH)</term>
<term>Tandem Mass Spectrometry (MeSH)</term>
<term>Transcription Factors (genetics)</term>
<term>Transcription Factors (isolation & purification)</term>
<term>Transcription Factors (metabolism)</term>
<term>Wood (chemistry)</term>
<term>Wood (metabolism)</term>
<term>Xylem (genetics)</term>
<term>Xylem (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Annotation de séquence moléculaire (MeSH)</term>
<term>Bois (composition chimique)</term>
<term>Bois (métabolisme)</term>
<term>Cellulose (biosynthèse)</term>
<term>Cellulose (génétique)</term>
<term>Chromatographie en phase liquide (MeSH)</term>
<term>Facteurs de transcription (génétique)</term>
<term>Facteurs de transcription (isolement et purification)</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Métabolisme glucidique (MeSH)</term>
<term>Populus (génétique)</term>
<term>Populus (métabolisme)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (isolement et purification)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Protéome (génétique)</term>
<term>Protéome (isolement et purification)</term>
<term>Protéome (métabolisme)</term>
<term>Protéomique (MeSH)</term>
<term>Régulation de l'expression des gènes végétaux (MeSH)</term>
<term>Spectrométrie de masse en tandem (MeSH)</term>
<term>Xylème (génétique)</term>
<term>Xylème (métabolisme)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en">
<term>Cellulose</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en">
<term>Cellulose</term>
<term>Plant Proteins</term>
<term>Proteome</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en">
<term>Plant Proteins</term>
<term>Proteome</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en">
<term>Plant Proteins</term>
<term>Proteome</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr">
<term>Cellulose</term>
</keywords>
<keywords scheme="MESH" qualifier="chemistry" xml:lang="en">
<term>Wood</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr">
<term>Bois</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Populus</term>
<term>Xylem</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Cellulose</term>
<term>Facteurs de transcription</term>
<term>Populus</term>
<term>Protéines végétales</term>
<term>Protéome</term>
<term>Xylème</term>
</keywords>
<keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr">
<term>Facteurs de transcription</term>
<term>Protéines végétales</term>
<term>Protéome</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en">
<term>Populus</term>
<term>Wood</term>
<term>Xylem</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr">
<term>Bois</term>
<term>Facteurs de transcription</term>
<term>Populus</term>
<term>Protéines végétales</term>
<term>Protéome</term>
<term>Xylème</term>
</keywords>
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<term>Chromatography, Liquid</term>
<term>Gene Expression Regulation, Plant</term>
<term>Molecular Sequence Annotation</term>
<term>Proteomics</term>
<term>Tandem Mass Spectrometry</term>
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<term>Annotation de séquence moléculaire</term>
<term>Chromatographie en phase liquide</term>
<term>Métabolisme glucidique</term>
<term>Protéomique</term>
<term>Régulation de l'expression des gènes végétaux</term>
<term>Spectrométrie de masse en tandem</term>
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<div type="abstract" xml:lang="en">Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa. </div>
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<Month>07</Month>
<Day>08</Day>
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<AbstractText>Cellulose, the main chemical polymer of wood, is the most abundant polysaccharide in nature.1 The ability to perturb the abundance and structure of cellulose microfibrils is of critical importance to the pulp and paper industry as well as for the textile, wood products, and liquid biofuels industries. Although much has been learned at the transcript level about the biosynthesis of cellulose, a quantitative understanding at the proteome level has yet to be established. The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins. Development of an effective discovery proteomic strategy through a combination of subcellular fractionation of stem differentiating xylem tissue (SDX) with recently optimized FASP digestion protocols, StageTip fractionation, as well as optimized instrument parameters for global proteomic analysis using the quadrupole-orbitrap mass spectrometer resulted in the deepest proteomic coverage of SDX protein from P. trichocarpa with 9,146 protein groups being identified (1% FDR). Of these, 20 cellulosic/hemicellulosic enzymes and 43 xylem-specific transcription factor groups were identified. Finally, selection of surrogate peptides led to an assay for absolute quantification of 14 cellulosic proteins in SDX of P. trichocarpa. </AbstractText>
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<Author ValidYN="Y">
<LastName>Chiang</LastName>
<ForeName>Vincent L</ForeName>
<Initials>VL</Initials>
<AffiliationInfo>
<Affiliation>Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States.</Affiliation>
</AffiliationInfo>
</Author>
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<LastName>Muddiman</LastName>
<ForeName>David C</ForeName>
<Initials>DC</Initials>
<AffiliationInfo>
<Affiliation>W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
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<PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
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<ArticleDate DateType="Electronic">
<Year>2015</Year>
<Month>09</Month>
<Day>01</Day>
</ArticleDate>
</Article>
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<Country>United States</Country>
<MedlineTA>J Proteome Res</MedlineTA>
<NlmUniqueID>101128775</NlmUniqueID>
<ISSNLinking>1535-3893</ISSNLinking>
</MedlineJournalInfo>
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<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D020543">Proteome</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
</Chemical>
<Chemical>
<RegistryNumber>9004-34-6</RegistryNumber>
<NameOfSubstance UI="D002482">Cellulose</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList>
<MeshHeading>
<DescriptorName UI="D050260" MajorTopicYN="N">Carbohydrate Metabolism</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D002482" MajorTopicYN="N">Cellulose</DescriptorName>
<QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D002853" MajorTopicYN="N">Chromatography, Liquid</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D018506" MajorTopicYN="N">Gene Expression Regulation, Plant</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D040901" MajorTopicYN="N">Proteomics</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D053719" MajorTopicYN="N">Tandem Mass Spectrometry</DescriptorName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000302" MajorTopicYN="Y">isolation & purification</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName>
</MeshHeading>
<MeshHeading>
<DescriptorName UI="D052584" MajorTopicYN="N">Xylem</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM">
<Keyword MajorTopicYN="N">PC-IDMS</Keyword>
<Keyword MajorTopicYN="N">SRM</Keyword>
<Keyword MajorTopicYN="N">absolute quantification</Keyword>
<Keyword MajorTopicYN="N">cellulose biosynthesis</Keyword>
<Keyword MajorTopicYN="N">shotgun discovery proteomics</Keyword>
<Keyword MajorTopicYN="N">targeted mass spectrometry</Keyword>
<Keyword MajorTopicYN="N">transcription factor</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData>
<History>
<PubMedPubDate PubStatus="entrez">
<Year>2015</Year>
<Month>9</Month>
<Day>2</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="pubmed">
<Year>2015</Year>
<Month>9</Month>
<Day>2</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
<PubMedPubDate PubStatus="medline">
<Year>2016</Year>
<Month>7</Month>
<Day>9</Day>
<Hour>6</Hour>
<Minute>0</Minute>
</PubMedPubDate>
</History>
<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList>
<ArticleId IdType="pubmed">26325666</ArticleId>
<ArticleId IdType="doi">10.1021/acs.jproteome.5b00233</ArticleId>
</ArticleIdList>
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</pubmed>
<affiliations>
<list>
<country>
<li>République populaire de Chine</li>
<li>États-Unis</li>
</country>
<settlement>
<li>Pékin</li>
</settlement>
</list>
<tree>
<country name="États-Unis">
<noRegion>
<name sortKey="Loziuk, Philip L" sort="Loziuk, Philip L" uniqKey="Loziuk P" first="Philip L" last="Loziuk">Philip L. Loziuk</name>
</noRegion>
<name sortKey="Chiang, Vincent L" sort="Chiang, Vincent L" uniqKey="Chiang V" first="Vincent L" last="Chiang">Vincent L. Chiang</name>
<name sortKey="Li, Wei" sort="Li, Wei" uniqKey="Li W" first="Wei" last="Li">Wei Li</name>
<name sortKey="Lin, Chien Yuan" sort="Lin, Chien Yuan" uniqKey="Lin C" first="Chien-Yuan" last="Lin">Chien-Yuan Lin</name>
<name sortKey="Muddiman, David C" sort="Muddiman, David C" uniqKey="Muddiman D" first="David C" last="Muddiman">David C. Muddiman</name>
<name sortKey="Parker, Jennifer" sort="Parker, Jennifer" uniqKey="Parker J" first="Jennifer" last="Parker">Jennifer Parker</name>
<name sortKey="Sederoff, Ronald R" sort="Sederoff, Ronald R" uniqKey="Sederoff R" first="Ronald R" last="Sederoff">Ronald R. Sederoff</name>
<name sortKey="Wang, Jack P" sort="Wang, Jack P" uniqKey="Wang J" first="Jack P" last="Wang">Jack P. Wang</name>
</country>
<country name="République populaire de Chine">
<noRegion>
<name sortKey="Li, Quanzi" sort="Li, Quanzi" uniqKey="Li Q" first="Quanzi" last="Li">Quanzi Li</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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