Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid:coenzyme A ligase protein complex formation, regulation, and numerical modeling.
Identifieur interne : 002029 ( Main/Exploration ); précédent : 002028; suivant : 002030Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid:coenzyme A ligase protein complex formation, regulation, and numerical modeling.
Auteurs : Hsi-Chuan Chen [République populaire de Chine] ; Jina Song ; Jack P. Wang ; Ying-Chung Lin ; Joel Ducoste ; Christopher M. Shuford ; Jie Liu ; Quanzi Li ; Rui Shi ; Angelito Nepomuceno ; Fikret Isik ; David C. Muddiman ; Cranos Williams ; Ronald R. Sederoff ; Vincent L. ChiangSource :
- The Plant cell [ 1532-298X ] ; 2014.
Descripteurs français
- KwdFr :
- ARN messager (génétique), Acides coumariques (métabolisme), Biologie des systèmes (MeSH), Coenzyme A ligases (génétique), Coenzyme A ligases (métabolisme), Immunoprécipitation (MeSH), Lignine (biosynthèse), Modèles biologiques (MeSH), Populus (métabolisme), Propionates (MeSH), Spectrométrie de masse (MeSH), Spécificité du substrat (MeSH).
- MESH :
- biosynthèse : Lignine.
- génétique : ARN messager, Coenzyme A ligases.
- métabolisme : Acides coumariques, Coenzyme A ligases, Populus.
- Biologie des systèmes, Immunoprécipitation, Modèles biologiques, Propionates, Spectrométrie de masse, Spécificité du substrat.
English descriptors
- KwdEn :
- Coenzyme A Ligases (genetics), Coenzyme A Ligases (metabolism), Coumaric Acids (metabolism), Immunoprecipitation (MeSH), Lignin (biosynthesis), Mass Spectrometry (MeSH), Models, Biological (MeSH), Populus (metabolism), Propionates (MeSH), RNA, Messenger (genetics), Substrate Specificity (MeSH), Systems Biology (MeSH).
- MESH :
- chemical , biosynthesis : Lignin.
- chemical , genetics : Coenzyme A Ligases, RNA, Messenger.
- chemical , metabolism : Coenzyme A Ligases, Coumaric Acids.
- metabolism : Populus.
- Immunoprecipitation, Mass Spectrometry, Models, Biological, Propionates, Substrate Specificity, Systems Biology.
Abstract
As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein-protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation.
DOI: 10.1105/tpc.113.119685
PubMed: 24619612
PubMed Central: PMC4001399
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Wang</name></author><author><name sortKey="Lin, Ying Chung" sort="Lin, Ying Chung" uniqKey="Lin Y" first="Ying-Chung" last="Lin">Ying-Chung Lin</name></author><author><name sortKey="Ducoste, Joel" sort="Ducoste, Joel" uniqKey="Ducoste J" first="Joel" last="Ducoste">Joel Ducoste</name></author><author><name sortKey="Shuford, Christopher M" sort="Shuford, Christopher M" uniqKey="Shuford C" first="Christopher M" last="Shuford">Christopher M. Shuford</name></author><author><name sortKey="Liu, Jie" sort="Liu, Jie" uniqKey="Liu J" first="Jie" last="Liu">Jie Liu</name></author><author><name sortKey="Li, Quanzi" sort="Li, Quanzi" uniqKey="Li Q" first="Quanzi" last="Li">Quanzi Li</name></author><author><name sortKey="Shi, Rui" sort="Shi, Rui" uniqKey="Shi R" first="Rui" last="Shi">Rui Shi</name></author><author><name sortKey="Nepomuceno, Angelito" sort="Nepomuceno, Angelito" uniqKey="Nepomuceno A" first="Angelito" last="Nepomuceno">Angelito Nepomuceno</name></author><author><name sortKey="Isik, Fikret" sort="Isik, Fikret" uniqKey="Isik F" first="Fikret" last="Isik">Fikret Isik</name></author><author><name sortKey="Muddiman, David C" sort="Muddiman, David C" uniqKey="Muddiman D" first="David C" last="Muddiman">David C. 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Chiang</name></author></analytic><series><title level="j">The Plant cell</title><idno type="eISSN">1532-298X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Coenzyme A Ligases (genetics)</term><term>Coenzyme A Ligases (metabolism)</term><term>Coumaric Acids (metabolism)</term><term>Immunoprecipitation (MeSH)</term><term>Lignin (biosynthesis)</term><term>Mass Spectrometry (MeSH)</term><term>Models, Biological (MeSH)</term><term>Populus (metabolism)</term><term>Propionates (MeSH)</term><term>RNA, Messenger (genetics)</term><term>Substrate Specificity (MeSH)</term><term>Systems Biology (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>Acides coumariques (métabolisme)</term><term>Biologie des systèmes (MeSH)</term><term>Coenzyme A ligases (génétique)</term><term>Coenzyme A ligases (métabolisme)</term><term>Immunoprécipitation (MeSH)</term><term>Lignine (biosynthèse)</term><term>Modèles biologiques (MeSH)</term><term>Populus (métabolisme)</term><term>Propionates (MeSH)</term><term>Spectrométrie de masse (MeSH)</term><term>Spécificité du substrat (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Lignin</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Coenzyme A Ligases</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Coenzyme A Ligases</term><term>Coumaric Acids</term></keywords><keywords scheme="MESH" qualifier="biosynthèse" xml:lang="fr"><term>Lignine</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>Coenzyme A ligases</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Acides coumariques</term><term>Coenzyme A ligases</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Immunoprecipitation</term><term>Mass Spectrometry</term><term>Models, Biological</term><term>Propionates</term><term>Substrate Specificity</term><term>Systems Biology</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Biologie des systèmes</term><term>Immunoprécipitation</term><term>Modèles biologiques</term><term>Propionates</term><term>Spectrométrie de masse</term><term>Spécificité du substrat</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein-protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">24619612</PMID><DateCompleted><Year>2015</Year><Month>02</Month><Day>23</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-298X</ISSN><JournalIssue CitedMedium="Internet"><Volume>26</Volume><Issue>3</Issue><PubDate><Year>2014</Year><Month>Mar</Month></PubDate></JournalIssue><Title>The Plant cell</Title><ISOAbbreviation>Plant Cell</ISOAbbreviation></Journal><ArticleTitle>Systems biology of lignin biosynthesis in Populus trichocarpa: heteromeric 4-coumaric acid:coenzyme A ligase protein complex formation, regulation, and numerical modeling.</ArticleTitle><Pagination><MedlinePgn>876-93</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1105/tpc.113.119685</ELocationID><Abstract><AbstractText>As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein-protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Hsi-Chuan</ForeName><Initials>HC</Initials><AffiliationInfo><Affiliation>State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Song</LastName><ForeName>Jina</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Jack P</ForeName><Initials>JP</Initials></Author><Author ValidYN="Y"><LastName>Lin</LastName><ForeName>Ying-Chung</ForeName><Initials>YC</Initials></Author><Author ValidYN="Y"><LastName>Ducoste</LastName><ForeName>Joel</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Shuford</LastName><ForeName>Christopher M</ForeName><Initials>CM</Initials></Author><Author ValidYN="Y"><LastName>Liu</LastName><ForeName>Jie</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Quanzi</ForeName><Initials>Q</Initials></Author><Author ValidYN="Y"><LastName>Shi</LastName><ForeName>Rui</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Nepomuceno</LastName><ForeName>Angelito</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Isik</LastName><ForeName>Fikret</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Muddiman</LastName><ForeName>David C</ForeName><Initials>DC</Initials></Author><Author ValidYN="Y"><LastName>Williams</LastName><ForeName>Cranos</ForeName><Initials>C</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></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>03</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Cell</MedlineTA><NlmUniqueID>9208688</NlmUniqueID><ISSNLinking>1040-4651</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D003373">Coumaric Acids</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011422">Propionates</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 6.2.1.-</RegistryNumber><NameOfSubstance UI="D003066">Coenzyme A Ligases</NameOfSubstance></Chemical><Chemical><RegistryNumber>IBS9D1EU3J</RegistryNumber><NameOfSubstance UI="C495469">trans-3-(4'-hydroxyphenyl)-2-propenoic acid</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D003066" MajorTopicYN="N">Coenzyme A Ligases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003373" MajorTopicYN="N">Coumaric Acids</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D047468" MajorTopicYN="N">Immunoprecipitation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000096" MajorTopicYN="Y">biosynthesis</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013058" MajorTopicYN="N">Mass Spectrometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008954" MajorTopicYN="N">Models, Biological</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011422" MajorTopicYN="N">Propionates</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" 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Chiang</name><name sortKey="Ducoste, Joel" sort="Ducoste, Joel" uniqKey="Ducoste J" first="Joel" last="Ducoste">Joel Ducoste</name><name sortKey="Isik, Fikret" sort="Isik, Fikret" uniqKey="Isik F" first="Fikret" last="Isik">Fikret Isik</name><name sortKey="Li, Quanzi" sort="Li, Quanzi" uniqKey="Li Q" first="Quanzi" last="Li">Quanzi Li</name><name sortKey="Lin, Ying Chung" sort="Lin, Ying Chung" uniqKey="Lin Y" first="Ying-Chung" last="Lin">Ying-Chung Lin</name><name sortKey="Liu, Jie" sort="Liu, Jie" uniqKey="Liu J" first="Jie" last="Liu">Jie Liu</name><name sortKey="Muddiman, David C" sort="Muddiman, David C" uniqKey="Muddiman D" first="David C" last="Muddiman">David C. Muddiman</name><name sortKey="Nepomuceno, Angelito" sort="Nepomuceno, Angelito" uniqKey="Nepomuceno A" first="Angelito" last="Nepomuceno">Angelito Nepomuceno</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="Shuford, Christopher M" sort="Shuford, Christopher M" uniqKey="Shuford C" first="Christopher M" last="Shuford">Christopher M. Shuford</name><name sortKey="Song, Jina" sort="Song, Jina" uniqKey="Song J" first="Jina" last="Song">Jina Song</name><name sortKey="Wang, Jack P" sort="Wang, Jack P" uniqKey="Wang J" first="Jack P" last="Wang">Jack P. Wang</name><name sortKey="Williams, Cranos" sort="Williams, Cranos" uniqKey="Williams C" first="Cranos" last="Williams">Cranos Williams</name></noCountry><country name="République populaire de Chine"><noRegion><name sortKey="Chen, Hsi Chuan" sort="Chen, Hsi Chuan" uniqKey="Chen H" first="Hsi-Chuan" last="Chen">Hsi-Chuan Chen</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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