The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown.
Identifieur interne : 000505 ( Main/Exploration ); précédent : 000504; suivant : 000506The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown.
Auteurs : Shingo Miyauchi [France] ; David Navarro [France] ; Sacha Grisel [France] ; Didier Chevret [France] ; Jean-Guy Berrin [France] ; Marie-Noelle Rosso [France]Source :
- PloS one [ 1932-6203 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- enzymologie : Pycnoporus.
- génétique : Protéines fongiques, Pycnoporus.
- métabolisme : Lignine, Pectine, Polyosides, Protéines fongiques.
- Analyse de profil d'expression de gènes, Bois, Transcriptome.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Fungal Proteins.
- chemical , metabolism : Fungal Proteins, Lignin, Pectins, Polysaccharides.
- enzymology : Pycnoporus.
- genetics : Pycnoporus.
- Gene Expression Profiling, Transcriptome, Wood.
Abstract
Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.
DOI: 10.1371/journal.pone.0175528
PubMed: 28394946
PubMed Central: PMC5386290
Affiliations:
Links toward previous steps (curation, corpus...)
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when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Gene Expression Profiling (MeSH)</term><term>Lignin (metabolism)</term><term>Pectins (metabolism)</term><term>Polysaccharides (metabolism)</term><term>Pycnoporus (enzymology)</term><term>Pycnoporus (genetics)</term><term>Transcriptome (MeSH)</term><term>Wood (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Bois (MeSH)</term><term>Lignine (métabolisme)</term><term>Pectine (métabolisme)</term><term>Polyosides (métabolisme)</term><term>Protéines fongiques (génétique)</term><term>Protéines fongiques (métabolisme)</term><term>Pycnoporus (enzymologie)</term><term>Pycnoporus (génétique)</term><term>Transcriptome (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fungal Proteins</term><term>Lignin</term><term>Pectins</term><term>Polysaccharides</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Pycnoporus</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Pycnoporus</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Pycnoporus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Protéines fongiques</term><term>Pycnoporus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Lignine</term><term>Pectine</term><term>Polyosides</term><term>Protéines fongiques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Transcriptome</term><term>Wood</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Bois</term><term>Transcriptome</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28394946</PMID><DateCompleted><Year>2017</Year><Month>09</Month><Day>05</Day></DateCompleted><DateRevised><Year>2019</Year><Month>02</Month><Day>08</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><Issue>4</Issue><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown.</ArticleTitle><Pagination><MedlinePgn>e0175528</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0175528</ELocationID><Abstract><AbstractText>Innovative green technologies are of importance for converting plant wastes into renewable sources for materials, chemicals and energy. However, recycling agricultural and forestry wastes is a challenge. A solution may be found in the forest. Saprotrophic white-rot fungi are able to convert dead plants into consumable carbon sources. Specialized fungal enzymes can be utilized for breaking down hard plant biopolymers. Thus, understanding the enzymatic machineries of such fungi gives us hints for the efficient decomposition of plant materials. Using the saprotrophic white-rot fungus Pycnoporus coccineus as a fungal model, we examined the dynamics of transcriptomic and secretomic responses to different types of lignocellulosic substrates at two time points. Our integrative omics pipeline (SHIN+GO) enabled us to compress layers of biological information into simple heatmaps, allowing for visual inspection of the data. We identified co-regulated genes with corresponding co-secreted enzymes, and the biological roles were extrapolated with the enriched Carbohydrate-Active Enzyme (CAZymes) and functional annotations. We observed the fungal early responses for the degradation of lignocellulosic substrates including; 1) simultaneous expression of CAZy genes and secretion of the enzymes acting on diverse glycosidic bonds in cellulose, hemicelluloses and their side chains or lignin (i.e. hydrolases, esterases and oxido-reductases); 2) the key role of lytic polysaccharide monooxygenases (LPMO); 3) the early transcriptional regulation of lignin active peroxidases; 4) the induction of detoxification processes dealing with biomass-derived compounds; and 5) the frequent attachments of the carbohydrate binding module 1 (CBM1) to enzymes from the lignocellulose-responsive genes. Our omics combining methods and related biological findings may contribute to the knowledge of fungal systems biology and facilitate the optimization of fungal enzyme cocktails for various industrial applications.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Miyauchi</LastName><ForeName>Shingo</ForeName><Initials>S</Initials><Identifier Source="ORCID">http://orcid.org/0000-0002-0620-5547</Identifier><AffiliationInfo><Affiliation>Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Navarro</LastName><ForeName>David</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grisel</LastName><ForeName>Sacha</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chevret</LastName><ForeName>Didier</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>PAPPSO, Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Berrin</LastName><ForeName>Jean-Guy</ForeName><Initials>JG</Initials><AffiliationInfo><Affiliation>Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Rosso</LastName><ForeName>Marie-Noelle</ForeName><Initials>MN</Initials><AffiliationInfo><Affiliation>Aix-Marseille Université, INRA, UMR 1163, Biodiversité et Biotechnologie Fongiques, BBF, Marseille, France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>04</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011134">Polysaccharides</NameOfSubstance></Chemical><Chemical><RegistryNumber>11132-73-3</RegistryNumber><NameOfSubstance UI="C036909">lignocellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>8024-50-8</RegistryNumber><NameOfSubstance 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Didier" sort="Chevret, Didier" uniqKey="Chevret D" first="Didier" last="Chevret">Didier Chevret</name><name sortKey="Grisel, Sacha" sort="Grisel, Sacha" uniqKey="Grisel S" first="Sacha" last="Grisel">Sacha Grisel</name><name sortKey="Navarro, David" sort="Navarro, David" uniqKey="Navarro D" first="David" last="Navarro">David Navarro</name><name sortKey="Rosso, Marie Noelle" sort="Rosso, Marie Noelle" uniqKey="Rosso M" first="Marie-Noelle" last="Rosso">Marie-Noelle Rosso</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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