Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants.
Identifieur interne : 000818 ( Main/Exploration ); précédent : 000817; suivant : 000819Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants.
Auteurs : Nan Chao [République populaire de Chine] ; Wen-Ting Jiang [République populaire de Chine] ; Xue-Chun Wang [République populaire de Chine] ; Xiang-Ning Jiang [République populaire de Chine] ; Ying Gai [République populaire de Chine]Source :
- Tree physiology [ 1758-4469 ] ; 2019.
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Abstract
Cinnamoyl-coenzyme A reductases (CCRs) have been reported as key enzymes involved in monolignol biosynthesis. In this study, a motif-aware workflow based on a new signature motif effectively distinguished CCRs from CCR-like proteins. The divergence of CCRs and CCR-like sequences in Populus tomentosa Carr, Panicum virgatum L, Oryza sativa L and Selaginella moellendorffii Hieron suggests that NWYCY is not efficient for CCR recognition. The novel motif H202(X)2K205 (CCR-SBM or CCR substrate binding motif) was introduced to distinguish between CCRs and CCR-like proteins. The site-directed mutant R205K in Os(I)CCR-like and H202 in PtoCCR7 resulted in the rescue and loss of activity, respectively, further validating the fact that CCR-SBM is critical for maintaining CCR activity. The molecular docking using feruloyl-cinnamoyl-coenzyme A (CoA) as the ligand and binary PhCCR-NADP structures as receptors indicated an interaction between H202 and K205 with CoA moiety. The genuine CCRs and CCR-like proteins from several angiosperms and gymnosperms were screened using a motif-aware workflow and were validated using a biochemical assay. Our results suggest that the motif-aware workflow is efficient and effective for the identification of CCRs and CCR-like proteins in land plants and can be used as a more accurate way of identifying genuine CCRs among land plants.
DOI: 10.1093/treephys/tpz098
PubMed: 31748812
Affiliations:
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sortKey="Chao, Nan" sort="Chao, Nan" uniqKey="Chao N" first="Nan" last="Chao">Nan Chao</name><affiliation wicri:level="1"><nlm:affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>School of Biotechnology, Jiangsu University of Science and Technology, ZhenJiang, Jiangsu 212003, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>School of Biotechnology, Jiangsu University of Science and Technology, ZhenJiang, Jiangsu 212003</wicri:regionArea><wicri:noRegion>Jiangsu 212003</wicri:noRegion></affiliation></author><author><name sortKey="Jiang, Wen Ting" sort="Jiang, Wen Ting" uniqKey="Jiang W" first="Wen-Ting" last="Jiang">Wen-Ting Jiang</name><affiliation wicri:level="1"><nlm:affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Wang, Xue Chun" sort="Wang, Xue Chun" uniqKey="Wang X" first="Xue-Chun" last="Wang">Xue-Chun Wang</name><affiliation wicri:level="1"><nlm:affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author><author><name sortKey="Jiang, Xiang Ning" sort="Jiang, Xiang Ning" uniqKey="Jiang X" first="Xiang-Ning" last="Jiang">Xiang-Ning Jiang</name><affiliation wicri:level="1"><nlm:affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Biotechnology, Beijing Forestry 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Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083</wicri:regionArea><placeName><settlement type="city">Pékin</settlement></placeName></affiliation></author></analytic><series><title level="j">Tree physiology</title><idno type="eISSN">1758-4469</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Molecular Docking Simulation (MeSH)</term><term>Populus (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Populus (MeSH)</term><term>Simulation de docking moléculaire (MeSH)</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Molecular Docking Simulation</term><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Populus</term><term>Simulation de docking moléculaire</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Cinnamoyl-coenzyme A reductases (CCRs) have been reported as key enzymes involved in monolignol biosynthesis. In this study, a motif-aware workflow based on a new signature motif effectively distinguished CCRs from CCR-like proteins. The divergence of CCRs and CCR-like sequences in Populus tomentosa Carr, Panicum virgatum L, Oryza sativa L and Selaginella moellendorffii Hieron suggests that NWYCY is not efficient for CCR recognition. The novel motif H202(X)2K205 (CCR-SBM or CCR substrate binding motif) was introduced to distinguish between CCRs and CCR-like proteins. The site-directed mutant R205K in Os(I)CCR-like and H202 in PtoCCR7 resulted in the rescue and loss of activity, respectively, further validating the fact that CCR-SBM is critical for maintaining CCR activity. The molecular docking using feruloyl-cinnamoyl-coenzyme A (CoA) as the ligand and binary PhCCR-NADP structures as receptors indicated an interaction between H202 and K205 with CoA moiety. The genuine CCRs and CCR-like proteins from several angiosperms and gymnosperms were screened using a motif-aware workflow and were validated using a biochemical assay. Our results suggest that the motif-aware workflow is efficient and effective for the identification of CCRs and CCR-like proteins in land plants and can be used as a more accurate way of identifying genuine CCRs among land plants.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Automated" Owner="NLM"><PMID Version="1">31748812</PMID><DateCompleted><Year>2020</Year><Month>05</Month><Day>18</Day></DateCompleted><DateRevised><Year>2020</Year><Month>05</Month><Day>18</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1758-4469</ISSN><JournalIssue CitedMedium="Internet"><Volume>39</Volume><Issue>12</Issue><PubDate><Year>2019</Year><Month>12</Month><Day>01</Day></PubDate></JournalIssue><Title>Tree physiology</Title><ISOAbbreviation>Tree Physiol</ISOAbbreviation></Journal><ArticleTitle>Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants.</ArticleTitle><Pagination><MedlinePgn>2019-2026</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/treephys/tpz098</ELocationID><Abstract><AbstractText>Cinnamoyl-coenzyme A reductases (CCRs) have been reported as key enzymes involved in monolignol biosynthesis. In this study, a motif-aware workflow based on a new signature motif effectively distinguished CCRs from CCR-like proteins. The divergence of CCRs and CCR-like sequences in Populus tomentosa Carr, Panicum virgatum L, Oryza sativa L and Selaginella moellendorffii Hieron suggests that NWYCY is not efficient for CCR recognition. The novel motif H202(X)2K205 (CCR-SBM or CCR substrate binding motif) was introduced to distinguish between CCRs and CCR-like proteins. The site-directed mutant R205K in Os(I)CCR-like and H202 in PtoCCR7 resulted in the rescue and loss of activity, respectively, further validating the fact that CCR-SBM is critical for maintaining CCR activity. The molecular docking using feruloyl-cinnamoyl-coenzyme A (CoA) as the ligand and binary PhCCR-NADP structures as receptors indicated an interaction between H202 and K205 with CoA moiety. The genuine CCRs and CCR-like proteins from several angiosperms and gymnosperms were screened using a motif-aware workflow and were validated using a biochemical assay. Our results suggest that the motif-aware workflow is efficient and effective for the identification of CCRs and CCR-like proteins in land plants and can be used as a more accurate way of identifying genuine CCRs among land plants.</AbstractText><CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chao</LastName><ForeName>Nan</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>School of Biotechnology, Jiangsu University of Science and Technology, ZhenJiang, Jiangsu 212003, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Wen-Ting</ForeName><Initials>WT</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Xue-Chun</ForeName><Initials>XC</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jiang</LastName><ForeName>Xiang-Ning</ForeName><Initials>XN</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gai</LastName><ForeName>Ying</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>College of Biological Sciences and Biotechnology, Beijing Forestry University, No 35, Qinghua East Road, Haidian District, Beijing 100083, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Laboratory for Tree Breeding, the Tree and Ornamental Plant Breeding and Biotechnology Laboratory of Chinese Forestry Administration, Beijing 100083, People's Republic of China.</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></Article><MedlineJournalInfo><Country>Canada</Country><MedlineTA>Tree Physiol</MedlineTA><NlmUniqueID>100955338</NlmUniqueID><ISSNLinking>0829-318X</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D062105" MajorTopicYN="N">Molecular Docking Simulation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="Y">Populus</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">CCR substrate binding motif</Keyword><Keyword MajorTopicYN="Y">cinnamoyl-coenzyme A reductase</Keyword><Keyword MajorTopicYN="Y">divergence</Keyword><Keyword MajorTopicYN="Y">genuine CCR</Keyword><Keyword MajorTopicYN="Y">motif-aware workflow</Keyword><Keyword MajorTopicYN="Y">signature motif</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2019</Year><Month>07</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>08</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>09</Month><Day>09</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>11</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>5</Month><Day>19</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>11</Month><Day>22</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">31748812</ArticleId><ArticleId IdType="pii">5585514</ArticleId><ArticleId IdType="doi">10.1093/treephys/tpz098</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><settlement><li>Pékin</li></settlement></list><tree><country name="République populaire de Chine"><noRegion><name sortKey="Chao, Nan" sort="Chao, Nan" uniqKey="Chao N" first="Nan" last="Chao">Nan Chao</name></noRegion><name sortKey="Chao, Nan" sort="Chao, Nan" uniqKey="Chao N" first="Nan" last="Chao">Nan Chao</name><name sortKey="Gai, Ying" sort="Gai, Ying" uniqKey="Gai Y" first="Ying" last="Gai">Ying Gai</name><name sortKey="Gai, Ying" sort="Gai, Ying" uniqKey="Gai Y" first="Ying" last="Gai">Ying Gai</name><name sortKey="Jiang, Wen Ting" sort="Jiang, Wen Ting" uniqKey="Jiang W" first="Wen-Ting" last="Jiang">Wen-Ting Jiang</name><name sortKey="Jiang, Xiang Ning" sort="Jiang, Xiang Ning" uniqKey="Jiang X" first="Xiang-Ning" last="Jiang">Xiang-Ning Jiang</name><name sortKey="Jiang, Xiang Ning" sort="Jiang, Xiang Ning" uniqKey="Jiang X" first="Xiang-Ning" last="Jiang">Xiang-Ning Jiang</name><name sortKey="Wang, Xue Chun" sort="Wang, Xue Chun" uniqKey="Wang X" first="Xue-Chun" last="Wang">Xue-Chun Wang</name></country></tree></affiliations></record>Pour manipuler ce document 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