Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora.
Identifieur interne : 000357 ( Main/Corpus ); précédent : 000356; suivant : 000358Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora.
Auteurs : Khajamohiddin Syed ; David R. Nelson ; Robert Riley ; Jagjit S. YadavSource :
- Mycologia [ 0027-5514 ]
English descriptors
- KwdEn :
- Coriolaceae (classification), Coriolaceae (enzymology), Coriolaceae (genetics), Cytochrome P-450 Enzyme System (genetics), Evolution, Molecular (MeSH), Fungal Proteins (genetics), Genome, Fungal (MeSH), Genomics (MeSH), Molecular Sequence Annotation (MeSH), Multigene Family (MeSH), Phylogeny (MeSH), Polyporales (classification), Polyporales (enzymology), Polyporales (genetics).
- MESH :
- chemical , genetics : Cytochrome P-450 Enzyme System, Fungal Proteins.
- classification : Coriolaceae, Polyporales.
- enzymology : Coriolaceae, Polyporales.
- genetics : Coriolaceae, Polyporales.
- Evolution, Molecular, Genome, Fungal, Genomics, Molecular Sequence Annotation, Multigene Family, Phylogeny.
Abstract
Genomewide annotation of cytochrome P450 monooxygenases (P450s) in three white-rot species of the fungal order Polyporales, namely Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora, revealed a large contingent of P450 genes (P450ome) in their genomes. A total of 199 P450 genes in B. adusta and 209 P450 genes each in Ganoderma sp. and P. brevispora were identified. These P450omes were classified into families and subfamilies as follows: B. adusta (39 families, 86 subfamilies), Ganoderma sp. (41 families, 105 subfamilies) and P. brevispora (42 families, 111 subfamilies). Of note, the B. adusta genome lacked the CYP505 family (P450foxy), a group of P450-CPR fusion proteins. The three polypore species revealed differential enrichment of individual P450 families in their genomes. The largest CYP families in the three genomes were CYP5144 (67 P450s), CYP5359 (46 P450s) and CYP5344 (43 P450s) in B. adusta, Ganoderma sp. and P. brevispora, respectively. Our analyses showed that tandem gene duplications led to expansions in certain P450 families. An estimated 33% (72 P450s), 28% (55 P450s) and 23% (49 P450s) of P450ome genes were duplicated in P. brevispora, B. adusta and Ganoderma sp., respectively. Family-wise comparative analysis revealed that 22 CYP families are common across the three Polypore species. Comparative P450ome analysis with Ganoderma lucidum revealed the presence of 143 orthologs and 56 paralogs in Ganoderma sp. Multiple P450s were found near the characteristic biosynthetic genes for secondary metabolites, namely polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), terpene cyclase and terpene synthase in the three genomes, suggesting a likely role of these P450s in secondary metabolism in these Polyporales. Overall, the three species had a richer P450 diversity both in terms of the P450 genes and P450 subfamilies as compared to the model white-rot and brown-rot polypore species Phanerochaete chrysosporium and Postia placenta.
DOI: 10.3852/13-002
PubMed: 23928414
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pubmed:23928414Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora.</title><author><name sortKey="Syed, Khajamohiddin" sort="Syed, Khajamohiddin" uniqKey="Syed K" first="Khajamohiddin" last="Syed">Khajamohiddin Syed</name><affiliation><nlm:affiliation>Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267-0056.</nlm:affiliation></affiliation></author><author><name sortKey="Nelson, David R" sort="Nelson, David R" uniqKey="Nelson D" first="David R" last="Nelson">David R. Nelson</name></author><author><name sortKey="Riley, Robert" sort="Riley, Robert" uniqKey="Riley R" first="Robert" last="Riley">Robert Riley</name></author><author><name sortKey="Yadav, Jagjit S" sort="Yadav, Jagjit S" uniqKey="Yadav J" first="Jagjit S" last="Yadav">Jagjit S. Yadav</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013 Nov-Dec</date><idno type="RBID">pubmed:23928414</idno><idno type="pmid">23928414</idno><idno type="doi">10.3852/13-002</idno><idno type="wicri:Area/Main/Corpus">000357</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000357</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora.</title><author><name sortKey="Syed, Khajamohiddin" sort="Syed, Khajamohiddin" uniqKey="Syed K" first="Khajamohiddin" last="Syed">Khajamohiddin Syed</name><affiliation><nlm:affiliation>Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267-0056.</nlm:affiliation></affiliation></author><author><name sortKey="Nelson, David R" sort="Nelson, David R" uniqKey="Nelson D" first="David R" last="Nelson">David R. Nelson</name></author><author><name sortKey="Riley, Robert" sort="Riley, Robert" uniqKey="Riley R" first="Robert" last="Riley">Robert Riley</name></author><author><name sortKey="Yadav, Jagjit S" sort="Yadav, Jagjit S" uniqKey="Yadav J" first="Jagjit S" last="Yadav">Jagjit S. Yadav</name></author></analytic><series><title level="j">Mycologia</title><idno type="ISSN">0027-5514</idno></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Coriolaceae (classification)</term><term>Coriolaceae (enzymology)</term><term>Coriolaceae (genetics)</term><term>Cytochrome P-450 Enzyme System (genetics)</term><term>Evolution, Molecular (MeSH)</term><term>Fungal Proteins (genetics)</term><term>Genome, Fungal (MeSH)</term><term>Genomics (MeSH)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Multigene Family (MeSH)</term><term>Phylogeny (MeSH)</term><term>Polyporales (classification)</term><term>Polyporales (enzymology)</term><term>Polyporales (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Cytochrome P-450 Enzyme System</term><term>Fungal Proteins</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Coriolaceae</term><term>Polyporales</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Coriolaceae</term><term>Polyporales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coriolaceae</term><term>Polyporales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Evolution, Molecular</term><term>Genome, Fungal</term><term>Genomics</term><term>Molecular Sequence Annotation</term><term>Multigene Family</term><term>Phylogeny</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genomewide annotation of cytochrome P450 monooxygenases (P450s) in three white-rot species of the fungal order Polyporales, namely Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora, revealed a large contingent of P450 genes (P450ome) in their genomes. A total of 199 P450 genes in B. adusta and 209 P450 genes each in Ganoderma sp. and P. brevispora were identified. These P450omes were classified into families and subfamilies as follows: B. adusta (39 families, 86 subfamilies), Ganoderma sp. (41 families, 105 subfamilies) and P. brevispora (42 families, 111 subfamilies). Of note, the B. adusta genome lacked the CYP505 family (P450foxy), a group of P450-CPR fusion proteins. The three polypore species revealed differential enrichment of individual P450 families in their genomes. The largest CYP families in the three genomes were CYP5144 (67 P450s), CYP5359 (46 P450s) and CYP5344 (43 P450s) in B. adusta, Ganoderma sp. and P. brevispora, respectively. Our analyses showed that tandem gene duplications led to expansions in certain P450 families. An estimated 33% (72 P450s), 28% (55 P450s) and 23% (49 P450s) of P450ome genes were duplicated in P. brevispora, B. adusta and Ganoderma sp., respectively. Family-wise comparative analysis revealed that 22 CYP families are common across the three Polypore species. Comparative P450ome analysis with Ganoderma lucidum revealed the presence of 143 orthologs and 56 paralogs in Ganoderma sp. Multiple P450s were found near the characteristic biosynthetic genes for secondary metabolites, namely polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), terpene cyclase and terpene synthase in the three genomes, suggesting a likely role of these P450s in secondary metabolism in these Polyporales. Overall, the three species had a richer P450 diversity both in terms of the P450 genes and P450 subfamilies as compared to the model white-rot and brown-rot polypore species Phanerochaete chrysosporium and Postia placenta.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23928414</PMID><DateCompleted><Year>2014</Year><Month>01</Month><Day>16</Day></DateCompleted><DateRevised><Year>2013</Year><Month>12</Month><Day>06</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0027-5514</ISSN><JournalIssue CitedMedium="Print"><Volume>105</Volume><Issue>6</Issue><PubDate><MedlineDate>2013 Nov-Dec</MedlineDate></PubDate></JournalIssue><Title>Mycologia</Title><ISOAbbreviation>Mycologia</ISOAbbreviation></Journal><ArticleTitle>Genomewide annotation and comparative genomics of cytochrome P450 monooxygenases (P450s) in the polypore species Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora.</ArticleTitle><Pagination><MedlinePgn>1445-55</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3852/13-002</ELocationID><Abstract><AbstractText>Genomewide annotation of cytochrome P450 monooxygenases (P450s) in three white-rot species of the fungal order Polyporales, namely Bjerkandera adusta, Ganoderma sp. and Phlebia brevispora, revealed a large contingent of P450 genes (P450ome) in their genomes. A total of 199 P450 genes in B. adusta and 209 P450 genes each in Ganoderma sp. and P. brevispora were identified. These P450omes were classified into families and subfamilies as follows: B. adusta (39 families, 86 subfamilies), Ganoderma sp. (41 families, 105 subfamilies) and P. brevispora (42 families, 111 subfamilies). Of note, the B. adusta genome lacked the CYP505 family (P450foxy), a group of P450-CPR fusion proteins. The three polypore species revealed differential enrichment of individual P450 families in their genomes. The largest CYP families in the three genomes were CYP5144 (67 P450s), CYP5359 (46 P450s) and CYP5344 (43 P450s) in B. adusta, Ganoderma sp. and P. brevispora, respectively. Our analyses showed that tandem gene duplications led to expansions in certain P450 families. An estimated 33% (72 P450s), 28% (55 P450s) and 23% (49 P450s) of P450ome genes were duplicated in P. brevispora, B. adusta and Ganoderma sp., respectively. Family-wise comparative analysis revealed that 22 CYP families are common across the three Polypore species. Comparative P450ome analysis with Ganoderma lucidum revealed the presence of 143 orthologs and 56 paralogs in Ganoderma sp. Multiple P450s were found near the characteristic biosynthetic genes for secondary metabolites, namely polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), terpene cyclase and terpene synthase in the three genomes, suggesting a likely role of these P450s in secondary metabolism in these Polyporales. Overall, the three species had a richer P450 diversity both in terms of the P450 genes and P450 subfamilies as compared to the model white-rot and brown-rot polypore species Phanerochaete chrysosporium and Postia placenta.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Syed</LastName><ForeName>Khajamohiddin</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267-0056.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nelson</LastName><ForeName>David R</ForeName><Initials>DR</Initials></Author><Author ValidYN="Y"><LastName>Riley</LastName><ForeName>Robert</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Yadav</LastName><ForeName>Jagjit S</ForeName><Initials>JS</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R01ES015543</GrantID><Acronym>ES</Acronym><Agency>NIEHS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>08</Month><Day>08</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mycologia</MedlineTA><NlmUniqueID>0400764</NlmUniqueID><ISSNLinking>0027-5514</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>9035-51-2</RegistryNumber><NameOfSubstance UI="D003577">Cytochrome P-450 Enzyme System</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D055453" MajorTopicYN="N">Coriolaceae</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D003577" MajorTopicYN="N">Cytochrome P-450 Enzyme System</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="Y">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020072" MajorTopicYN="N">Polyporales</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Bjerkandera adusta</Keyword><Keyword MajorTopicYN="N">Cytochrome P450 monooxygenases</Keyword><Keyword MajorTopicYN="N">Ganoderma sp.</Keyword><Keyword MajorTopicYN="N">P450ome</Keyword><Keyword MajorTopicYN="N">Phanerochaete chrysosporium</Keyword><Keyword MajorTopicYN="N">Phlebia brevispora</Keyword><Keyword MajorTopicYN="N">Postia placenta</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>8</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>8</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2014</Year><Month>1</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">23928414</ArticleId><ArticleId IdType="pii">13-002</ArticleId><ArticleId IdType="doi">10.3852/13-002</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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