The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak.
Identifieur interne : 000601 ( Main/Exploration ); précédent : 000600; suivant : 000602The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak.
Auteurs : Shin Sato [États-Unis] ; F Alex Feltus ; Prashanti Iyer ; Ming TienSource :
- Current genetics [ 1432-0983 ] ; 2009.
Descripteurs français
- KwdFr :
- ADN complémentaire (composition chimique), ADN complémentaire (génétique), ARN messager (génétique), ARN messager (métabolisme), Analyse de profil d'expression de gènes (MeSH), Analyse de regroupements (MeSH), Analyse de séquence d'ADN (MeSH), Banque de gènes (MeSH), Cellulases (génétique), Cellulases (métabolisme), Cellulose (métabolisme), Données de séquences moléculaires (MeSH), Génome fongique (génétique), Lignine (métabolisme), Phanerochaete (croissance et développement), Phanerochaete (génétique), Polyosides (métabolisme), Protéines fongiques (génétique), Protéines fongiques (métabolisme), Quercus (microbiologie), RT-PCR (MeSH), Séquence nucléotidique (MeSH), bêta-Glucosidase (génétique), bêta-Glucosidase (métabolisme), Étiquettes de séquences exprimées (MeSH).
- MESH :
- composition chimique : ADN complémentaire.
- croissance et développement : Phanerochaete.
- génétique : ADN complémentaire, ARN messager, Cellulases, Génome fongique, Phanerochaete, Protéines fongiques, bêta-Glucosidase.
- microbiologie : Quercus.
- métabolisme : ARN messager, Cellulases, Cellulose, Lignine, Polyosides, Protéines fongiques, bêta-Glucosidase.
- Analyse de profil d'expression de gènes, Analyse de regroupements, Analyse de séquence d'ADN, Banque de gènes, Données de séquences moléculaires, RT-PCR, Séquence nucléotidique, Étiquettes de séquences exprimées.
English descriptors
- KwdEn :
- Base Sequence (MeSH), Cellulases (genetics), Cellulases (metabolism), Cellulose (metabolism), Cluster Analysis (MeSH), DNA, Complementary (chemistry), DNA, Complementary (genetics), Expressed Sequence Tags (MeSH), Fungal Proteins (genetics), Fungal Proteins (metabolism), Gene Expression Profiling (MeSH), Gene Library (MeSH), Genome, Fungal (genetics), Lignin (metabolism), Molecular Sequence Data (MeSH), Phanerochaete (genetics), Phanerochaete (growth & development), Polysaccharides (metabolism), Quercus (microbiology), RNA, Messenger (genetics), RNA, Messenger (metabolism), Reverse Transcriptase Polymerase Chain Reaction (MeSH), Sequence Analysis, DNA (MeSH), beta-Glucosidase (genetics), beta-Glucosidase (metabolism).
- MESH :
- chemical , chemistry : DNA, Complementary.
- chemical , genetics : Cellulases, DNA, Complementary, Fungal Proteins, RNA, Messenger, beta-Glucosidase.
- chemical , metabolism : Cellulases, Cellulose, Fungal Proteins, Lignin, Polysaccharides, RNA, Messenger, beta-Glucosidase.
- genetics : Genome, Fungal, Phanerochaete.
- growth & development : Phanerochaete.
- microbiology : Quercus.
- Base Sequence, Cluster Analysis, Expressed Sequence Tags, Gene Expression Profiling, Gene Library, Molecular Sequence Data, Reverse Transcriptase Polymerase Chain Reaction, Sequence Analysis, DNA.
Abstract
As part of an effort to determine all the gene products involved in wood degradation, we have performed massively parallel pyrosequencing on an expression library from the white rot fungus Phanerochaete chrysosporium grown in shallow stationary cultures with red oak as the carbon source. Approximately 48,000 high quality sequence tags (246 bp average length) were generated. 53% of the sequence tags aligned to 4,262 P. chrysosporium gene models, and an additional 18.5% of the tags reliably aligned to the P. chrysosporium genome providing evidence for 961 putative novel fragmented gene models. Due to their role in lignocellulose degradation, the secreted proteins were focused upon. Our results show that the four enzymes required for cellulose degradation: endocellulase, exocellulase CBHI, exocellulase CBHII, and beta-glucosidase are all produced. For hemicellulose degradation, not all known enzymes were produced, but endoxylanases, acetyl xylan esterases and mannosidases were detected. For lignin degradation, the role of peroxidases has been questioned; however, our results show that lignin peroxidase is highly expressed along with the H(2)O(2) generating enzyme, alcohol oxidase. The transcriptome snapshot reveals that H(2)O(2) generation and utilization are central in wood degradation. Our results also reveal new transcripts that encode extracellular proteins with no known function.
DOI: 10.1007/s00294-009-0243-0
PubMed: 19396602
Affiliations:
Links toward previous steps (curation, corpus...)
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nucléotidique</term><term>Étiquettes de séquences exprimées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">As part of an effort to determine all the gene products involved in wood degradation, we have performed massively parallel pyrosequencing on an expression library from the white rot fungus Phanerochaete chrysosporium grown in shallow stationary cultures with red oak as the carbon source. Approximately 48,000 high quality sequence tags (246 bp average length) were generated. 53% of the sequence tags aligned to 4,262 P. chrysosporium gene models, and an additional 18.5% of the tags reliably aligned to the P. chrysosporium genome providing evidence for 961 putative novel fragmented gene models. Due to their role in lignocellulose degradation, the secreted proteins were focused upon. Our results show that the four enzymes required for cellulose degradation: endocellulase, exocellulase CBHI, exocellulase CBHII, and beta-glucosidase are all produced. For hemicellulose degradation, not all known enzymes were produced, but endoxylanases, acetyl xylan esterases and mannosidases were detected. For lignin degradation, the role of peroxidases has been questioned; however, our results show that lignin peroxidase is highly expressed along with the H(2)O(2) generating enzyme, alcohol oxidase. The transcriptome snapshot reveals that H(2)O(2) generation and utilization are central in wood degradation. Our results also reveal new transcripts that encode extracellular proteins with no known function.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19396602</PMID><DateCompleted><Year>2009</Year><Month>09</Month><Day>28</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1432-0983</ISSN><JournalIssue CitedMedium="Internet"><Volume>55</Volume><Issue>3</Issue><PubDate><Year>2009</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Current genetics</Title><ISOAbbreviation>Curr Genet</ISOAbbreviation></Journal><ArticleTitle>The first genome-level transcriptome of the wood-degrading fungus Phanerochaete chrysosporium grown on red oak.</ArticleTitle><Pagination><MedlinePgn>273-86</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1007/s00294-009-0243-0</ELocationID><Abstract><AbstractText>As part of an effort to determine all the gene products involved in wood degradation, we have performed massively parallel pyrosequencing on an expression library from the white rot fungus Phanerochaete chrysosporium grown in shallow stationary cultures with red oak as the carbon source. Approximately 48,000 high quality sequence tags (246 bp average length) were generated. 53% of the sequence tags aligned to 4,262 P. chrysosporium gene models, and an additional 18.5% of the tags reliably aligned to the P. chrysosporium genome providing evidence for 961 putative novel fragmented gene models. Due to their role in lignocellulose degradation, the secreted proteins were focused upon. Our results show that the four enzymes required for cellulose degradation: endocellulase, exocellulase CBHI, exocellulase CBHII, and beta-glucosidase are all produced. For hemicellulose degradation, not all known enzymes were produced, but endoxylanases, acetyl xylan esterases and mannosidases were detected. For lignin degradation, the role of peroxidases has been questioned; however, our results show that lignin peroxidase is highly expressed along with the H(2)O(2) generating enzyme, alcohol oxidase. The transcriptome snapshot reveals that H(2)O(2) generation and utilization are central in wood degradation. Our results also reveal new transcripts that encode extracellular proteins with no known function.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sato</LastName><ForeName>Shin</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, 16802, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Feltus</LastName><ForeName>F Alex</ForeName><Initials>FA</Initials></Author><Author ValidYN="Y"><LastName>Iyer</LastName><ForeName>Prashanti</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Tien</LastName><ForeName>Ming</ForeName><Initials>M</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>04</Month><Day>26</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Curr Genet</MedlineTA><NlmUniqueID>8004904</NlmUniqueID><ISSNLinking>0172-8083</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018076">DNA, Complementary</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011134">Polysaccharides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical><Chemical><RegistryNumber>8024-50-8</RegistryNumber><NameOfSubstance UI="C007916">hemicellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>9004-34-6</RegistryNumber><NameOfSubstance UI="D002482">Cellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.-</RegistryNumber><NameOfSubstance UI="D044602">Cellulases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.21</RegistryNumber><NameOfSubstance UI="D001617">beta-Glucosidase</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D044602" MajorTopicYN="N">Cellulases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002482" MajorTopicYN="N">Cellulose</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D018076" MajorTopicYN="N">DNA, Complementary</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020224" MajorTopicYN="N">Expressed Sequence Tags</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015723" MajorTopicYN="N">Gene Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="N">Genome, Fungal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020075" MajorTopicYN="N">Phanerochaete</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011134" MajorTopicYN="N">Polysaccharides</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D029963" MajorTopicYN="N">Quercus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001617" MajorTopicYN="N">beta-Glucosidase</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2008</Year><Month>12</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2009</Year><Month>04</Month><Day>07</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2009</Year><Month>03</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>4</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>4</Month><Day>28</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>9</Month><Day>29</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19396602</ArticleId><ArticleId IdType="doi">10.1007/s00294-009-0243-0</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Curr Genet. 2005 Jan;47(1):49-56</Citation><ArticleIdList><ArticleId 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IdType="pubmed">690075</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Pennsylvanie</li></region><settlement><li>University Park (Pennsylvanie)</li></settlement><orgName><li>Université d'État de Pennsylvanie</li></orgName></list><tree><noCountry><name sortKey="Feltus, F Alex" sort="Feltus, F Alex" uniqKey="Feltus F" first="F Alex" last="Feltus">F Alex Feltus</name><name sortKey="Iyer, Prashanti" sort="Iyer, Prashanti" uniqKey="Iyer P" first="Prashanti" last="Iyer">Prashanti Iyer</name><name sortKey="Tien, Ming" sort="Tien, Ming" uniqKey="Tien M" first="Ming" last="Tien">Ming Tien</name></noCountry><country name="États-Unis"><region name="Pennsylvanie"><name sortKey="Sato, Shin" sort="Sato, Shin" uniqKey="Sato S" first="Shin" last="Sato">Shin Sato</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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