FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.
Identifieur interne : 000691 ( Main/Exploration ); précédent : 000690; suivant : 000692FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.
Auteurs : Anthony Levasseur [France] ; François Piumi ; Pedro M. Coutinho ; Corinne Rancurel ; Michèle Asther ; Michel Delattre ; Bernard Henrissat ; Pierre Pontarotti ; Marcel Asther ; Eric RecordSource :
- Fungal genetics and biology : FG & B [ 1096-0937 ] ; 2008.
Descripteurs français
- KwdFr :
- Bases de données de protéines (MeSH), Champignons (enzymologie), Lignine (métabolisme), Oxidoreductases (classification), Oxidoreductases (génétique), Oxidoreductases (métabolisme), Protéines fongiques (classification), Protéines fongiques (génétique), Protéines fongiques (métabolisme), Similitude de séquences d'acides aminés (MeSH).
- MESH :
- classification : Oxidoreductases, Protéines fongiques.
- enzymologie : Champignons.
- génétique : Oxidoreductases, Protéines fongiques.
- métabolisme : Lignine, Oxidoreductases, Protéines fongiques.
- Bases de données de protéines, Similitude de séquences d'acides aminés.
English descriptors
- KwdEn :
- MESH :
- chemical , classification : Fungal Proteins, Oxidoreductases.
- chemical , genetics : Fungal Proteins, Oxidoreductases.
- chemical , metabolism : Fungal Proteins, Lignin, Oxidoreductases.
- enzymology : Fungi.
- Databases, Protein, Sequence Homology, Amino Acid.
Abstract
The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.
DOI: 10.1016/j.fgb.2008.01.004
PubMed: 18308593
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18308593</PMID><DateCompleted><Year>2008</Year><Month>05</Month><Day>06</Day></DateCompleted><DateRevised><Year>2008</Year><Month>04</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1096-0937</ISSN><JournalIssue CitedMedium="Internet"><Volume>45</Volume><Issue>5</Issue><PubDate><Year>2008</Year><Month>May</Month></PubDate></JournalIssue><Title>Fungal genetics and biology : FG & B</Title><ISOAbbreviation>Fungal Genet Biol</ISOAbbreviation></Journal><ArticleTitle>FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds.</ArticleTitle><Pagination><MedlinePgn>638-45</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.fgb.2008.01.004</ELocationID><Abstract><AbstractText>The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Levasseur</LastName><ForeName>Anthony</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>UMR 1163 INRA de Biotechnologie des Champignons Filamenteux, IFR86-BAIM, Universités de Provence et de la Méditerranée, ESIL, 163 Avenue de Luminy, Case Postale 925, 13288 Marseille Cedex 09, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Piumi</LastName><ForeName>François</ForeName><Initials>F</Initials></Author><Author ValidYN="Y"><LastName>Coutinho</LastName><ForeName>Pedro M</ForeName><Initials>PM</Initials></Author><Author ValidYN="Y"><LastName>Rancurel</LastName><ForeName>Corinne</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Asther</LastName><ForeName>Michèle</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Delattre</LastName><ForeName>Michel</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Henrissat</LastName><ForeName>Bernard</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Pontarotti</LastName><ForeName>Pierre</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Asther</LastName><ForeName>Marcel</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Record</LastName><ForeName>Eric</ForeName><Initials>E</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>2008</Year><Month>01</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Fungal Genet Biol</MedlineTA><NlmUniqueID>9607601</NlmUniqueID><ISSNLinking>1087-1845</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.-</RegistryNumber><NameOfSubstance UI="D010088">Oxidoreductases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D030562" MajorTopicYN="Y">Databases, Protein</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005658" MajorTopicYN="N">Fungi</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010088" MajorTopicYN="N">Oxidoreductases</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="Y">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2007</Year><Month>08</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2008</Year><Month>01</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2008</Year><Month>01</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>3</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2008</Year><Month>5</Month><Day>7</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>3</Month><Day>1</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">18308593</ArticleId><ArticleId IdType="pii">S1087-1845(08)00006-6</ArticleId><ArticleId IdType="doi">10.1016/j.fgb.2008.01.004</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>France</li></country><region><li>Provence-Alpes-Côte d'Azur</li></region><settlement><li>Marseille</li></settlement></list><tree><noCountry><name sortKey="Asther, Marcel" sort="Asther, Marcel" uniqKey="Asther M" first="Marcel" last="Asther">Marcel Asther</name><name sortKey="Asther, Michele" sort="Asther, Michele" uniqKey="Asther M" first="Michèle" last="Asther">Michèle Asther</name><name sortKey="Coutinho, Pedro M" sort="Coutinho, Pedro M" uniqKey="Coutinho P" first="Pedro M" last="Coutinho">Pedro M. Coutinho</name><name sortKey="Delattre, Michel" sort="Delattre, Michel" uniqKey="Delattre M" first="Michel" last="Delattre">Michel Delattre</name><name sortKey="Henrissat, Bernard" sort="Henrissat, Bernard" uniqKey="Henrissat B" first="Bernard" last="Henrissat">Bernard Henrissat</name><name sortKey="Piumi, Francois" sort="Piumi, Francois" uniqKey="Piumi F" first="François" last="Piumi">François Piumi</name><name sortKey="Pontarotti, Pierre" sort="Pontarotti, Pierre" uniqKey="Pontarotti P" first="Pierre" last="Pontarotti">Pierre Pontarotti</name><name sortKey="Rancurel, Corinne" sort="Rancurel, Corinne" uniqKey="Rancurel C" first="Corinne" last="Rancurel">Corinne Rancurel</name><name sortKey="Record, Eric" sort="Record, Eric" uniqKey="Record E" first="Eric" last="Record">Eric Record</name></noCountry><country name="France"><region name="Provence-Alpes-Côte d'Azur"><name sortKey="Levasseur, Anthony" sort="Levasseur, Anthony" uniqKey="Levasseur A" first="Anthony" last="Levasseur">Anthony Levasseur</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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