Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood.
Identifieur interne : 000479 ( Main/Exploration ); précédent : 000478; suivant : 000480Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood.
Auteurs : Jacqueline Macdonald [Canada] ; Matt Doering ; Thomas Canam ; Yunchen Gong ; David S. Guttman ; Malcolm M. Campbell ; Emma R. MasterSource :
- Applied and environmental microbiology [ 1098-5336 ] ; 2011.
Descripteurs français
- KwdFr :
- Abies (microbiologie), Acer (microbiologie), Analyse de profil d'expression de gènes (MeSH), Bois (microbiologie), Enzymes (biosynthèse), Enzymes (génétique), Phanerochaete (croissance et développement), Phanerochaete (génétique), Picea (microbiologie), Pinus (microbiologie), Protéines fongiques (biosynthèse), Protéines fongiques (génétique).
- MESH :
- biosynthèse : Enzymes, Protéines fongiques.
- croissance et développement : Phanerochaete.
- génétique : Enzymes, Phanerochaete, Protéines fongiques.
- microbiologie : Abies, Acer, Bois, Picea, Pinus.
- Analyse de profil d'expression de gènes.
English descriptors
- KwdEn :
- Abies (microbiology), Acer (microbiology), Enzymes (biosynthesis), Enzymes (genetics), Fungal Proteins (biosynthesis), Fungal Proteins (genetics), Gene Expression Profiling (MeSH), Phanerochaete (genetics), Phanerochaete (growth & development), Picea (microbiology), Pinus (microbiology), Wood (microbiology).
- MESH :
- chemical , biosynthesis : Enzymes, Fungal Proteins.
- chemical , genetics : Enzymes, Fungal Proteins.
- genetics : Phanerochaete.
- growth & development : Phanerochaete.
- microbiology : Abies, Acer, Picea, Pinus, Wood.
- Gene Expression Profiling.
Abstract
To identify enzymes that could be developed to reduce the recalcitrance of softwood resources, the transcriptomes of the softwood-degrading white-rot fungus Phanerochaete carnosa were evaluated after growth on lodgepole pine, white spruce, balsam fir, and sugar maple and compared to the transcriptome of P. carnosa after growth on liquid nutrient medium. One hundred fifty-two million paired-end reads were obtained, and 63% of these reads were mapped to 10,257 gene models from P. carnosa. Five-hundred thirty-three of these genes had transcripts that were at least four times more abundant during growth on at least one wood medium than on nutrient medium. The 30 transcripts that were on average over 100 times more abundant during growth on wood than on nutrient medium included 6 manganese peroxidases, 5 cellulases, 2 hemicellulases, a lignin peroxidase, glyoxal oxidase, and a P450 monooxygenase. Notably, among the genes encoding putative cellulases, one encoding a glycosyl hydrolase family 61 protein had the highest relative transcript abundance during growth on wood. Overall, transcripts predicted to encode lignin-degrading activities were more abundant than those predicted to encode carbohydrate-active enzymes. Transcripts predicted to encode three MnPs represented the most highly abundant transcripts in wood-grown cultivations compared to nutrient medium cultivations. Gene set enrichment analyses did not distinguish transcriptomes resulting from softwood and hardwood cultivations, suggesting that similar sets of enzyme activities are elicited by P. carnosa grown on different wood substrates, albeit to different expression levels.
DOI: 10.1128/AEM.02490-10
PubMed: 21441342
PubMed Central: PMC3126436
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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One hundred fifty-two million paired-end reads were obtained, and 63% of these reads were mapped to 10,257 gene models from P. carnosa. Five-hundred thirty-three of these genes had transcripts that were at least four times more abundant during growth on at least one wood medium than on nutrient medium. The 30 transcripts that were on average over 100 times more abundant during growth on wood than on nutrient medium included 6 manganese peroxidases, 5 cellulases, 2 hemicellulases, a lignin peroxidase, glyoxal oxidase, and a P450 monooxygenase. Notably, among the genes encoding putative cellulases, one encoding a glycosyl hydrolase family 61 protein had the highest relative transcript abundance during growth on wood. Overall, transcripts predicted to encode lignin-degrading activities were more abundant than those predicted to encode carbohydrate-active enzymes. Transcripts predicted to encode three MnPs represented the most highly abundant transcripts in wood-grown cultivations compared to nutrient medium cultivations. Gene set enrichment analyses did not distinguish transcriptomes resulting from softwood and hardwood cultivations, suggesting that similar sets of enzyme activities are elicited by P. carnosa grown on different wood substrates, albeit to different expression levels.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21441342</PMID><DateCompleted><Year>2011</Year><Month>08</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1098-5336</ISSN><JournalIssue CitedMedium="Internet"><Volume>77</Volume><Issue>10</Issue><PubDate><Year>2011</Year><Month>May</Month></PubDate></JournalIssue><Title>Applied and environmental microbiology</Title><ISOAbbreviation>Appl Environ Microbiol</ISOAbbreviation></Journal><ArticleTitle>Transcriptomic responses of the softwood-degrading white-rot fungus Phanerochaete carnosa during growth on coniferous and deciduous wood.</ArticleTitle><Pagination><MedlinePgn>3211-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1128/AEM.02490-10</ELocationID><Abstract><AbstractText>To identify enzymes that could be developed to reduce the recalcitrance of softwood resources, the transcriptomes of the softwood-degrading white-rot fungus Phanerochaete carnosa were evaluated after growth on lodgepole pine, white spruce, balsam fir, and sugar maple and compared to the transcriptome of P. carnosa after growth on liquid nutrient medium. One hundred fifty-two million paired-end reads were obtained, and 63% of these reads were mapped to 10,257 gene models from P. carnosa. Five-hundred thirty-three of these genes had transcripts that were at least four times more abundant during growth on at least one wood medium than on nutrient medium. The 30 transcripts that were on average over 100 times more abundant during growth on wood than on nutrient medium included 6 manganese peroxidases, 5 cellulases, 2 hemicellulases, a lignin peroxidase, glyoxal oxidase, and a P450 monooxygenase. Notably, among the genes encoding putative cellulases, one encoding a glycosyl hydrolase family 61 protein had the highest relative transcript abundance during growth on wood. Overall, transcripts predicted to encode lignin-degrading activities were more abundant than those predicted to encode carbohydrate-active enzymes. Transcripts predicted to encode three MnPs represented the most highly abundant transcripts in wood-grown cultivations compared to nutrient medium cultivations. Gene set enrichment analyses did not distinguish transcriptomes resulting from softwood and hardwood cultivations, suggesting that similar sets of enzyme activities are elicited by P. carnosa grown on different wood substrates, albeit to different expression levels.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>MacDonald</LastName><ForeName>Jacqueline</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S3E5, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Doering</LastName><ForeName>Matt</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Canam</LastName><ForeName>Thomas</ForeName><Initials>T</Initials></Author><Author ValidYN="Y"><LastName>Gong</LastName><ForeName>Yunchen</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Guttman</LastName><ForeName>David S</ForeName><Initials>DS</Initials></Author><Author ValidYN="Y"><LastName>Campbell</LastName><ForeName>Malcolm M</ForeName><Initials>MM</Initials></Author><Author ValidYN="Y"><LastName>Master</LastName><ForeName>Emma R</ForeName><Initials>ER</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>03</Month><Day>25</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Appl Environ Microbiol</MedlineTA><NlmUniqueID>7605801</NlmUniqueID><ISSNLinking>0099-2240</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance 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Campbell</name><name sortKey="Canam, Thomas" sort="Canam, Thomas" uniqKey="Canam T" first="Thomas" last="Canam">Thomas Canam</name><name sortKey="Doering, Matt" sort="Doering, Matt" uniqKey="Doering M" first="Matt" last="Doering">Matt Doering</name><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name><name sortKey="Guttman, David S" sort="Guttman, David S" uniqKey="Guttman D" first="David S" last="Guttman">David S. Guttman</name><name sortKey="Master, Emma R" sort="Master, Emma R" uniqKey="Master E" first="Emma R" last="Master">Emma R. Master</name></noCountry><country name="Canada"><region name="Ontario"><name sortKey="Macdonald, Jacqueline" sort="Macdonald, Jacqueline" uniqKey="Macdonald J" first="Jacqueline" last="Macdonald">Jacqueline Macdonald</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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