Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins.
Identifieur interne : 000789 ( Main/Corpus ); précédent : 000788; suivant : 000790Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins.
Auteurs : Amber Vanden Wymelenberg ; Patrick Minges ; Grzegorz Sabat ; Diego Martinez ; Andrea Aerts ; Asaf Salamov ; Igor Grigoriev ; Harris Shapiro ; Nik Putnam ; Paula Belinky ; Carlos Dosoretz ; Jill Gaskell ; Phil Kersten ; Dan CullenSource :
- Fungal genetics and biology : FG & B [ 1087-1845 ] ; 2006.
English descriptors
- KwdEn :
- Carboxylic Ester Hydrolases (chemistry), Carboxylic Ester Hydrolases (genetics), Carboxylic Ester Hydrolases (metabolism), Computational Biology (MeSH), Culture Media (chemistry), Databases, Nucleic Acid (MeSH), Fungal Proteins (chemistry), Fungal Proteins (genetics), Fungal Proteins (metabolism), Genome, Fungal (MeSH), Glycoside Hydrolases (chemistry), Glycoside Hydrolases (genetics), Glycoside Hydrolases (metabolism), Lipase (chemistry), Lipase (genetics), Lipase (metabolism), Mass Spectrometry (MeSH), Peptide Hydrolases (chemistry), Peptide Hydrolases (genetics), Peptide Hydrolases (metabolism), Peroxidases (chemistry), Peroxidases (genetics), Peroxidases (metabolism), Phanerochaete (genetics), Phanerochaete (metabolism), Phosphoric Monoester Hydrolases (chemistry), Phosphoric Monoester Hydrolases (genetics), Phosphoric Monoester Hydrolases (metabolism), Protein Transport (MeSH), Sequence Homology, Amino Acid (MeSH).
- MESH :
- chemical , chemistry : Carboxylic Ester Hydrolases, Culture Media, Fungal Proteins, Glycoside Hydrolases, Lipase, Peptide Hydrolases, Peroxidases, Phosphoric Monoester Hydrolases.
- chemical , genetics : Carboxylic Ester Hydrolases, Fungal Proteins, Glycoside Hydrolases, Lipase, Peptide Hydrolases, Peroxidases, Phosphoric Monoester Hydrolases.
- chemical , metabolism : Carboxylic Ester Hydrolases, Fungal Proteins, Glycoside Hydrolases, Lipase, Peptide Hydrolases, Peroxidases, Phosphoric Monoester Hydrolases.
- genetics : Phanerochaete.
- metabolism : Phanerochaete.
- Computational Biology, Databases, Nucleic Acid, Genome, Fungal, Mass Spectrometry, Protein Transport, Sequence Homology, Amino Acid.
Abstract
The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.
DOI: 10.1016/j.fgb.2006.01.003
PubMed: 16524749
Links to Exploration step
pubmed:16524749Le document en format XML
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ligninolytic cultures reveal complex mixtures of secreted proteins.</title><author><name sortKey="Vanden Wymelenberg, Amber" sort="Vanden Wymelenberg, Amber" uniqKey="Vanden Wymelenberg A" first="Amber" last="Vanden Wymelenberg">Amber Vanden Wymelenberg</name><affiliation><nlm:affiliation>Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Minges, Patrick" sort="Minges, Patrick" uniqKey="Minges P" first="Patrick" last="Minges">Patrick Minges</name></author><author><name sortKey="Sabat, Grzegorz" sort="Sabat, Grzegorz" uniqKey="Sabat G" first="Grzegorz" last="Sabat">Grzegorz Sabat</name></author><author><name sortKey="Martinez, Diego" sort="Martinez, Diego" uniqKey="Martinez D" first="Diego" last="Martinez">Diego Martinez</name></author><author><name sortKey="Aerts, Andrea" sort="Aerts, Andrea" uniqKey="Aerts A" first="Andrea" last="Aerts">Andrea Aerts</name></author><author><name sortKey="Salamov, 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uniqKey="Kersten P" first="Phil" last="Kersten">Phil Kersten</name></author><author><name sortKey="Cullen, Dan" sort="Cullen, Dan" uniqKey="Cullen D" first="Dan" last="Cullen">Dan Cullen</name></author></analytic><series><title level="j">Fungal genetics and biology : FG & B</title><idno type="ISSN">1087-1845</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Carboxylic Ester Hydrolases (chemistry)</term><term>Carboxylic Ester Hydrolases (genetics)</term><term>Carboxylic Ester Hydrolases (metabolism)</term><term>Computational Biology (MeSH)</term><term>Culture Media (chemistry)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Fungal Proteins (chemistry)</term><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Genome, Fungal (MeSH)</term><term>Glycoside Hydrolases (chemistry)</term><term>Glycoside Hydrolases (genetics)</term><term>Glycoside Hydrolases (metabolism)</term><term>Lipase (chemistry)</term><term>Lipase (genetics)</term><term>Lipase (metabolism)</term><term>Mass Spectrometry (MeSH)</term><term>Peptide Hydrolases (chemistry)</term><term>Peptide Hydrolases (genetics)</term><term>Peptide Hydrolases (metabolism)</term><term>Peroxidases (chemistry)</term><term>Peroxidases (genetics)</term><term>Peroxidases (metabolism)</term><term>Phanerochaete (genetics)</term><term>Phanerochaete (metabolism)</term><term>Phosphoric Monoester Hydrolases (chemistry)</term><term>Phosphoric Monoester Hydrolases (genetics)</term><term>Phosphoric Monoester Hydrolases (metabolism)</term><term>Protein Transport (MeSH)</term><term>Sequence Homology, Amino Acid (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Carboxylic Ester Hydrolases</term><term>Culture Media</term><term>Fungal Proteins</term><term>Glycoside Hydrolases</term><term>Lipase</term><term>Peptide Hydrolases</term><term>Peroxidases</term><term>Phosphoric Monoester Hydrolases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Carboxylic Ester Hydrolases</term><term>Fungal Proteins</term><term>Glycoside Hydrolases</term><term>Lipase</term><term>Peptide Hydrolases</term><term>Peroxidases</term><term>Phosphoric Monoester Hydrolases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Carboxylic Ester Hydrolases</term><term>Fungal Proteins</term><term>Glycoside Hydrolases</term><term>Lipase</term><term>Peptide Hydrolases</term><term>Peroxidases</term><term>Phosphoric Monoester Hydrolases</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phanerochaete</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Phanerochaete</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Databases, Nucleic Acid</term><term>Genome, Fungal</term><term>Mass Spectrometry</term><term>Protein Transport</term><term>Sequence Homology, Amino Acid</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16524749</PMID><DateCompleted><Year>2006</Year><Month>07</Month><Day>26</Day></DateCompleted><DateRevised><Year>2016</Year><Month>11</Month><Day>28</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1087-1845</ISSN><JournalIssue CitedMedium="Print"><Volume>43</Volume><Issue>5</Issue><PubDate><Year>2006</Year><Month>May</Month></PubDate></JournalIssue><Title>Fungal genetics and biology : FG & B</Title><ISOAbbreviation>Fungal Genet Biol</ISOAbbreviation></Journal><ArticleTitle>Computational analysis of the Phanerochaete chrysosporium v2.0 genome database and mass spectrometry identification of peptides in ligninolytic cultures reveal complex mixtures of secreted proteins.</ArticleTitle><Pagination><MedlinePgn>343-56</MedlinePgn></Pagination><Abstract><AbstractText>The white-rot basidiomycete Phanerochaete chrysosporium employs extracellular enzymes to completely degrade the major polymers of wood: cellulose, hemicellulose, and lignin. Analysis of a total of 10,048 v2.1 gene models predicts 769 secreted proteins, a substantial increase over the 268 models identified in the earlier database (v1.0). Within the v2.1 'computational secretome,' 43% showed no significant similarity to known proteins, but were structurally related to other hypothetical protein sequences. In contrast, 53% showed significant similarity to known protein sequences including 87 models assigned to 33 glycoside hydrolase families and 52 sequences distributed among 13 peptidase families. When grown under standard ligninolytic conditions, peptides corresponding to 11 peptidase genes were identified in culture filtrates by mass spectrometry (LS-MS/MS). Five peptidases were members of a large family of aspartyl proteases, many of which were localized to gene clusters. Consistent with a role in dephosphorylation of lignin peroxidase, a mannose-6-phosphatase (M6Pase) was also identified in carbon-starved cultures. Beyond proteases and M6Pase, 28 specific gene products were identified including several representatives of gene families. These included 4 lignin peroxidases, 3 lipases, 2 carboxylesterases, and 8 glycosyl hydrolases. The results underscore the rich genetic diversity and complexity of P. chrysosporium's extracellular enzyme systems.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vanden Wymelenberg</LastName><ForeName>Amber</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Bacteriology, University of Wisconsin, Madison, WI 53706, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Minges</LastName><ForeName>Patrick</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Sabat</LastName><ForeName>Grzegorz</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Martinez</LastName><ForeName>Diego</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Aerts</LastName><ForeName>Andrea</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Salamov</LastName><ForeName>Asaf</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Grigoriev</LastName><ForeName>Igor</ForeName><Initials>I</Initials></Author><Author ValidYN="Y"><LastName>Shapiro</LastName><ForeName>Harris</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Putnam</LastName><ForeName>Nik</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Belinky</LastName><ForeName>Paula</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Dosoretz</LastName><ForeName>Carlos</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Gaskell</LastName><ForeName>Jill</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Kersten</LastName><ForeName>Phil</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Cullen</LastName><ForeName>Dan</ForeName><Initials>D</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>03</Month><Day>09</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="D003470">Culture Media</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.11.1.-</RegistryNumber><NameOfSubstance UI="D010544">Peroxidases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.11.1.-</RegistryNumber><NameOfSubstance UI="C042858">lignin peroxidase</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.1.-</RegistryNumber><NameOfSubstance UI="D002265">Carboxylic Ester Hydrolases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.1.3</RegistryNumber><NameOfSubstance UI="D008049">Lipase</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.3.-</RegistryNumber><NameOfSubstance UI="C023553">mannose-6-phosphatase</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.1.3.2</RegistryNumber><NameOfSubstance UI="D010744">Phosphoric Monoester Hydrolases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.-</RegistryNumber><NameOfSubstance UI="D006026">Glycoside Hydrolases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.4.-</RegistryNumber><NameOfSubstance UI="D010447">Peptide Hydrolases</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002265" MajorTopicYN="N">Carboxylic Ester Hydrolases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="Y">Computational Biology</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003470" MajorTopicYN="N">Culture Media</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D030561" MajorTopicYN="N">Databases, Nucleic Acid</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="N">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006026" MajorTopicYN="N">Glycoside Hydrolases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008049" MajorTopicYN="N">Lipase</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013058" MajorTopicYN="Y">Mass Spectrometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010447" MajorTopicYN="N">Peptide Hydrolases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010544" MajorTopicYN="N">Peroxidases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020075" MajorTopicYN="N">Phanerochaete</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010744" MajorTopicYN="N">Phosphoric Monoester Hydrolases</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021381" MajorTopicYN="N">Protein Transport</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2005</Year><Month>11</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2005</Year><Month>12</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2006</Year><Month>01</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>3</Month><Day>10</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>7</Month><Day>27</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>3</Month><Day>10</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16524749</ArticleId><ArticleId IdType="pii">S1087-1845(06)00019-3</ArticleId><ArticleId IdType="doi">10.1016/j.fgb.2006.01.003</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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