Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry.
Identifieur interne : 002B50 ( Main/Exploration ); précédent : 002B49; suivant : 002B51Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry.
Auteurs : Christopher M. Shuford [États-Unis] ; Quanzi Li ; Ying-Hsuan Sun ; Hsi-Chuan Chen ; Jack Wang ; Rui Shi ; Ronald R. Sederoff ; Vincent L. Chiang ; David C. MuddimanSource :
- Journal of proteome research [ 1535-3907 ] ; 2012.
Descripteurs français
- KwdFr :
- Données de séquences moléculaires (MeSH), Marquage isotopique (MeSH), Normes de référence (MeSH), Populus (enzymologie), Protéines végétales (composition chimique), Protéines végétales (métabolisme), Protéome (composition chimique), Protéome (métabolisme), Spectrométrie de masse ESI (normes), Séquence d'acides aminés (MeSH), Voies de biosynthèse (MeSH), Xylème (enzymologie).
- MESH :
- composition chimique : Protéines végétales, Protéome.
- enzymologie : Populus, Xylème.
- métabolisme : Protéines végétales, Protéome.
- normes : Spectrométrie de masse ESI.
- Données de séquences moléculaires, Marquage isotopique, Normes de référence, Séquence d'acides aminés, Voies de biosynthèse.
English descriptors
- KwdEn :
- Amino Acid Sequence (MeSH), Biosynthetic Pathways (MeSH), Isotope Labeling (MeSH), Molecular Sequence Data (MeSH), Plant Proteins (chemistry), Plant Proteins (metabolism), Populus (enzymology), Proteome (chemistry), Proteome (metabolism), Reference Standards (MeSH), Spectrometry, Mass, Electrospray Ionization (standards), Xylem (enzymology).
- MESH :
- chemical , chemistry : Plant Proteins, Proteome.
- chemical , metabolism : Plant Proteins, Proteome.
- enzymology : Populus, Xylem.
- standards : Spectrometry, Mass, Electrospray Ionization.
- Amino Acid Sequence, Biosynthetic Pathways, Isotope Labeling, Molecular Sequence Data, Reference Standards.
Abstract
The economic value of wood/pulp from many tree species is largely dictated by the quantity and chemical properties of lignin, which is directly related to the composition and linkages of monolignols comprising the polymer. Although much is known regarding the monolignol biosynthetic pathway, our understanding is still deficient due to the lack of quantitative information at the proteomic level. We developed an assay based on protein cleavage isotope dilution mass spectrometry (PC-IDMS) for the determination of all potential, primary enzymes involved in the biosynthesis of monolignols and the peroxidases responsible for their polymerization to form lignin in the model tree species, Populus trichocarpa. Described is the identification of quantitative surrogate peptides through shotgun analysis of native and recombinant proteins, optimization of trypsin proteolysis using fractional factorial design of experiments, and development of a liquid chromatography-selected reaction monitoring method for specific detection of all targeted peptides. Of the 25 targeted enzymes, three were undetected in the normal xylem tissues, and all but two of the detectable species showed good day-to-day precision (CV < 10%). This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level.
DOI: 10.1021/pr300205a
PubMed: 22524869
Affiliations:
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Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, and ‡Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695</wicri:regionArea><wicri:noRegion>North Carolina 27695</wicri:noRegion></affiliation></author><author><name sortKey="Li, Quanzi" sort="Li, Quanzi" uniqKey="Li Q" first="Quanzi" last="Li">Quanzi Li</name></author><author><name sortKey="Sun, Ying Hsuan" sort="Sun, Ying Hsuan" uniqKey="Sun Y" first="Ying-Hsuan" last="Sun">Ying-Hsuan Sun</name></author><author><name sortKey="Chen, Hsi Chuan" sort="Chen, Hsi Chuan" uniqKey="Chen H" first="Hsi-Chuan" last="Chen">Hsi-Chuan Chen</name></author><author><name sortKey="Wang, Jack" sort="Wang, Jack" uniqKey="Wang J" first="Jack" last="Wang">Jack Wang</name></author><author><name sortKey="Shi, Rui" sort="Shi, Rui" uniqKey="Shi R" first="Rui" last="Shi">Rui Shi</name></author><author><name sortKey="Sederoff, Ronald R" sort="Sederoff, Ronald R" uniqKey="Sederoff R" first="Ronald R" last="Sederoff">Ronald R. 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Muddiman</name></author></analytic><series><title level="j">Journal of proteome research</title><idno type="eISSN">1535-3907</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term><term>Biosynthetic Pathways (MeSH)</term><term>Isotope Labeling (MeSH)</term><term>Molecular Sequence Data (MeSH)</term><term>Plant Proteins (chemistry)</term><term>Plant Proteins (metabolism)</term><term>Populus (enzymology)</term><term>Proteome (chemistry)</term><term>Proteome (metabolism)</term><term>Reference Standards (MeSH)</term><term>Spectrometry, Mass, Electrospray Ionization (standards)</term><term>Xylem (enzymology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Données de séquences moléculaires (MeSH)</term><term>Marquage isotopique (MeSH)</term><term>Normes de référence (MeSH)</term><term>Populus (enzymologie)</term><term>Protéines végétales (composition chimique)</term><term>Protéines végétales (métabolisme)</term><term>Protéome (composition chimique)</term><term>Protéome (métabolisme)</term><term>Spectrométrie de masse ESI (normes)</term><term>Séquence d'acides aminés (MeSH)</term><term>Voies de biosynthèse (MeSH)</term><term>Xylème (enzymologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term><term>Proteome</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Protéines végétales</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Populus</term><term>Xylème</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Populus</term><term>Xylem</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines végétales</term><term>Protéome</term></keywords><keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Spectrométrie de masse ESI</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Spectrometry, Mass, Electrospray Ionization</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term><term>Biosynthetic Pathways</term><term>Isotope Labeling</term><term>Molecular Sequence Data</term><term>Reference Standards</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Données de séquences moléculaires</term><term>Marquage isotopique</term><term>Normes de référence</term><term>Séquence d'acides aminés</term><term>Voies de biosynthèse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The economic value of wood/pulp from many tree species is largely dictated by the quantity and chemical properties of lignin, which is directly related to the composition and linkages of monolignols comprising the polymer. Although much is known regarding the monolignol biosynthetic pathway, our understanding is still deficient due to the lack of quantitative information at the proteomic level. We developed an assay based on protein cleavage isotope dilution mass spectrometry (PC-IDMS) for the determination of all potential, primary enzymes involved in the biosynthesis of monolignols and the peroxidases responsible for their polymerization to form lignin in the model tree species, Populus trichocarpa. Described is the identification of quantitative surrogate peptides through shotgun analysis of native and recombinant proteins, optimization of trypsin proteolysis using fractional factorial design of experiments, and development of a liquid chromatography-selected reaction monitoring method for specific detection of all targeted peptides. Of the 25 targeted enzymes, three were undetected in the normal xylem tissues, and all but two of the detectable species showed good day-to-day precision (CV < 10%). This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22524869</PMID><DateCompleted><Year>2014</Year><Month>11</Month><Day>25</Day></DateCompleted><DateRevised><Year>2014</Year><Month>01</Month><Day>16</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1535-3907</ISSN><JournalIssue CitedMedium="Internet"><Volume>11</Volume><Issue>6</Issue><PubDate><Year>2012</Year><Month>Jun</Month><Day>01</Day></PubDate></JournalIssue><Title>Journal of proteome research</Title><ISOAbbreviation>J Proteome Res</ISOAbbreviation></Journal><ArticleTitle>Comprehensive quantification of monolignol-pathway enzymes in Populus trichocarpa by protein cleavage isotope dilution mass spectrometry.</ArticleTitle><Pagination><MedlinePgn>3390-404</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/pr300205a</ELocationID><Abstract><AbstractText>The economic value of wood/pulp from many tree species is largely dictated by the quantity and chemical properties of lignin, which is directly related to the composition and linkages of monolignols comprising the polymer. Although much is known regarding the monolignol biosynthetic pathway, our understanding is still deficient due to the lack of quantitative information at the proteomic level. We developed an assay based on protein cleavage isotope dilution mass spectrometry (PC-IDMS) for the determination of all potential, primary enzymes involved in the biosynthesis of monolignols and the peroxidases responsible for their polymerization to form lignin in the model tree species, Populus trichocarpa. Described is the identification of quantitative surrogate peptides through shotgun analysis of native and recombinant proteins, optimization of trypsin proteolysis using fractional factorial design of experiments, and development of a liquid chromatography-selected reaction monitoring method for specific detection of all targeted peptides. Of the 25 targeted enzymes, three were undetected in the normal xylem tissues, and all but two of the detectable species showed good day-to-day precision (CV < 10%). This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Shuford</LastName><ForeName>Christopher M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>W.M. Keck FT-ICR Mass Spectrometry Laboratory, Department of Chemistry, and ‡Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, North Carolina 27695, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Quanzi</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Sun</LastName><ForeName>Ying-Hsuan</ForeName><Initials>YH</Initials></Author><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Hsi-Chuan</ForeName><Initials>HC</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jack</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Rui</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Sederoff</LastName><ForeName>Ronald R</ForeName><Initials>RR</Initials></Author><Author ValidYN="Y"><LastName>Chiang</LastName><ForeName>Vincent L</ForeName><Initials>VL</Initials></Author><Author ValidYN="Y"><LastName>Muddiman</LastName><ForeName>David C</ForeName><Initials>DC</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>2012</Year><Month>05</Month><Day>09</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Proteome Res</MedlineTA><NlmUniqueID>101128775</NlmUniqueID><ISSNLinking>1535-3893</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D053898" MajorTopicYN="N">Biosynthetic Pathways</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007553" MajorTopicYN="N">Isotope Labeling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012015" MajorTopicYN="N">Reference Standards</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D021241" MajorTopicYN="N">Spectrometry, Mass, Electrospray Ionization</DescriptorName><QualifierName UI="Q000592" MajorTopicYN="N">standards</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D052584" MajorTopicYN="N">Xylem</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2012</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2012</Year><Month>4</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>12</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">22524869</ArticleId><ArticleId IdType="doi">10.1021/pr300205a</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Chen, Hsi Chuan" sort="Chen, Hsi Chuan" uniqKey="Chen H" first="Hsi-Chuan" last="Chen">Hsi-Chuan Chen</name><name sortKey="Chiang, Vincent L" sort="Chiang, Vincent L" uniqKey="Chiang V" first="Vincent L" last="Chiang">Vincent L. Chiang</name><name sortKey="Li, Quanzi" sort="Li, Quanzi" uniqKey="Li Q" first="Quanzi" last="Li">Quanzi Li</name><name sortKey="Muddiman, David C" sort="Muddiman, David C" uniqKey="Muddiman D" first="David C" last="Muddiman">David C. Muddiman</name><name sortKey="Sederoff, Ronald R" sort="Sederoff, Ronald R" uniqKey="Sederoff R" first="Ronald R" last="Sederoff">Ronald R. Sederoff</name><name sortKey="Shi, Rui" sort="Shi, Rui" uniqKey="Shi R" first="Rui" last="Shi">Rui Shi</name><name sortKey="Sun, Ying Hsuan" sort="Sun, Ying Hsuan" uniqKey="Sun Y" first="Ying-Hsuan" last="Sun">Ying-Hsuan Sun</name><name sortKey="Wang, Jack" sort="Wang, Jack" uniqKey="Wang J" first="Jack" last="Wang">Jack Wang</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Shuford, Christopher M" sort="Shuford, Christopher M" uniqKey="Shuford C" first="Christopher M" last="Shuford">Christopher M. 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