Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive gene clustering.
Identifieur interne : 000831 ( Main/Exploration ); précédent : 000830; suivant : 000832Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive gene clustering.
Auteurs : Harshavardhan Doddapaneni [États-Unis] ; Ranajit Chakraborty ; Jagjit S. YadavSource :
- BMC genomics [ 1471-2164 ] ; 2005.
Descripteurs français
- KwdFr :
- ADN complémentaire (métabolisme), Analyse de regroupements (MeSH), Clonage moléculaire (MeSH), Cytochrome P-450 enzyme system (génétique), Données de séquences moléculaires (MeSH), Duplication de gène (MeSH), Famille multigénique (MeSH), Génome fongique (MeSH), Mixed function oxygenases (génétique), Modèles génétiques (MeSH), Oxygène (métabolisme), Phanerochaete (génétique), Phylogenèse (MeSH), Similitude de séquences d'acides aminés (MeSH), Structure tertiaire des protéines (MeSH), Séquence d'acides aminés (MeSH), Épissage alternatif (MeSH), Évolution moléculaire (MeSH).
- MESH :
- génétique : Cytochrome P-450 enzyme system, Mixed function oxygenases, Phanerochaete.
- métabolisme : ADN complémentaire, Oxygène.
- Analyse de regroupements, Clonage moléculaire, Données de séquences moléculaires, Duplication de gène, Famille multigénique, Génome fongique, Modèles génétiques, Phylogenèse, Similitude de séquences d'acides aminés, Structure tertiaire des protéines, Séquence d'acides aminés, Épissage alternatif, Évolution moléculaire.
English descriptors
- KwdEn :
- Alternative Splicing (MeSH), Amino Acid Sequence (MeSH), Cloning, Molecular (MeSH), Cluster Analysis (MeSH), Cytochrome P-450 Enzyme System (genetics), DNA, Complementary (metabolism), Evolution, Molecular (MeSH), Gene Duplication (MeSH), Genome, Fungal (MeSH), Mixed Function Oxygenases (genetics), Models, Genetic (MeSH), Molecular Sequence Data (MeSH), Multigene Family (MeSH), Oxygen (metabolism), Phanerochaete (genetics), Phylogeny (MeSH), Protein Structure, Tertiary (MeSH), Sequence Homology, Amino Acid (MeSH).
- MESH :
- chemical , genetics : Cytochrome P-450 Enzyme System, Mixed Function Oxygenases.
- chemical , metabolism : DNA, Complementary, Oxygen.
- genetics : Phanerochaete.
- Alternative Splicing, Amino Acid Sequence, Cloning, Molecular, Cluster Analysis, Evolution, Molecular, Gene Duplication, Genome, Fungal, Models, Genetic, Molecular Sequence Data, Multigene Family, Phylogeny, Protein Structure, Tertiary, Sequence Homology, Amino Acid.
Abstract
BACKGROUND
Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning efforts in P. chrysosporium and its subsequent whole genome sequencing have revealed an extraordinary P450 repertoire ("P450ome") containing at least 150 P450 genes with yet unknown function. In order to understand the functional diversity and the evolutionary mechanisms and significance of these hemeproteins, here we report a genome-wide structural and evolutionary analysis of the P450ome of this fungus.
RESULTS
Our analysis showed that P. chrysosporium P450ome could be classified into 12 families and 23 sub-families and is characterized by the presence of multigene families. A genome-level structural analysis revealed 16 organizationally homogeneous and heterogeneous clusters of tandem P450 genes. Analysis of our cloned cDNAs revealed structurally conserved characteristics (intron numbers and locations, and functional domains) among members of the two representative multigene P450 families CYP63 and CYP505 (P450foxy). Considering the unusually complex structural features of the P450 genes in this genome, including microexons (2-10 aa) and frequent small introns (45-55 bp), alternative splicing, as experimentally observed for CYP63, may be a more widespread event in the P450ome of this fungus. Clan-level phylogenetic comparison revealed that P. chrysosporium P450 families fall under 11 fungal clans and the majority of these multigene families appear to have evolved locally in this genome from their respective progenitor genes, as a result of extensive gene duplications and rearrangements.
CONCLUSION
P. chrysosporium P450ome, the largest known to date among fungi, is characterized by tandem gene clusters and multigene families. This enormous P450 gene diversity has evolved by extensive gene duplications and intragenomic recombinations of the progenitor genes presumably to meet the exceptionally high metabolic demand of this biodegradative group of basidiomycetous fungi in ecological niches. In this context, alternative splicing appears to further contribute to the evolution of functional diversity of the P450ome in this fungus. The evolved P450 diversity is consistent with the known vast biotransformation potential of P. chrysosporium. The presented analysis will help design future P450 functional studies to understand the underlying mechanisms of secondary metabolism and oxidative biotransformation pathways in this model white rot fungus.
DOI: 10.1186/1471-2164-6-92
PubMed: 15955240
PubMed Central: PMC1184071
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning efforts in P. chrysosporium and its subsequent whole genome sequencing have revealed an extraordinary P450 repertoire ("P450ome") containing at least 150 P450 genes with yet unknown function. In order to understand the functional diversity and the evolutionary mechanisms and significance of these hemeproteins, here we report a genome-wide structural and evolutionary analysis of the P450ome of this fungus.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Our analysis showed that P. chrysosporium P450ome could be classified into 12 families and 23 sub-families and is characterized by the presence of multigene families. A genome-level structural analysis revealed 16 organizationally homogeneous and heterogeneous clusters of tandem P450 genes. Analysis of our cloned cDNAs revealed structurally conserved characteristics (intron numbers and locations, and functional domains) among members of the two representative multigene P450 families CYP63 and CYP505 (P450foxy). Considering the unusually complex structural features of the P450 genes in this genome, including microexons (2-10 aa) and frequent small introns (45-55 bp), alternative splicing, as experimentally observed for CYP63, may be a more widespread event in the P450ome of this fungus. Clan-level phylogenetic comparison revealed that P. chrysosporium P450 families fall under 11 fungal clans and the majority of these multigene families appear to have evolved locally in this genome from their respective progenitor genes, as a result of extensive gene duplications and rearrangements.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>P. chrysosporium P450ome, the largest known to date among fungi, is characterized by tandem gene clusters and multigene families. This enormous P450 gene diversity has evolved by extensive gene duplications and intragenomic recombinations of the progenitor genes presumably to meet the exceptionally high metabolic demand of this biodegradative group of basidiomycetous fungi in ecological niches. In this context, alternative splicing appears to further contribute to the evolution of functional diversity of the P450ome in this fungus. The evolved P450 diversity is consistent with the known vast biotransformation potential of P. chrysosporium. The presented analysis will help design future P450 functional studies to understand the underlying mechanisms of secondary metabolism and oxidative biotransformation pathways in this model white rot fungus.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">15955240</PMID><DateCompleted><Year>2006</Year><Month>04</Month><Day>13</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>6</Volume><PubDate><Year>2005</Year><Month>Jun</Month><Day>14</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Genome-wide structural and evolutionary analysis of the P450 monooxygenase genes (P450ome) in the white rot fungus Phanerochaete chrysosporium: evidence for gene duplications and extensive gene clustering.</ArticleTitle><Pagination><MedlinePgn>92</MedlinePgn></Pagination><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Phanerochaete chrysosporium, the model white rot basidiomycetous fungus, has the extraordinary ability to mineralize (to CO2) lignin and detoxify a variety of chemical pollutants. Its cytochrome P450 monooxygenases have recently been implied in several of these biotransformations. Our initial P450 cloning efforts in P. chrysosporium and its subsequent whole genome sequencing have revealed an extraordinary P450 repertoire ("P450ome") containing at least 150 P450 genes with yet unknown function. In order to understand the functional diversity and the evolutionary mechanisms and significance of these hemeproteins, here we report a genome-wide structural and evolutionary analysis of the P450ome of this fungus.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Our analysis showed that P. chrysosporium P450ome could be classified into 12 families and 23 sub-families and is characterized by the presence of multigene families. A genome-level structural analysis revealed 16 organizationally homogeneous and heterogeneous clusters of tandem P450 genes. Analysis of our cloned cDNAs revealed structurally conserved characteristics (intron numbers and locations, and functional domains) among members of the two representative multigene P450 families CYP63 and CYP505 (P450foxy). Considering the unusually complex structural features of the P450 genes in this genome, including microexons (2-10 aa) and frequent small introns (45-55 bp), alternative splicing, as experimentally observed for CYP63, may be a more widespread event in the P450ome of this fungus. Clan-level phylogenetic comparison revealed that P. chrysosporium P450 families fall under 11 fungal clans and the majority of these multigene families appear to have evolved locally in this genome from their respective progenitor genes, as a result of extensive gene duplications and rearrangements.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">P. chrysosporium P450ome, the largest known to date among fungi, is characterized by tandem gene clusters and multigene families. This enormous P450 gene diversity has evolved by extensive gene duplications and intragenomic recombinations of the progenitor genes presumably to meet the exceptionally high metabolic demand of this biodegradative group of basidiomycetous fungi in ecological niches. In this context, alternative splicing appears to further contribute to the evolution of functional diversity of the P450ome in this fungus. The evolved P450 diversity is consistent with the known vast biotransformation potential of P. chrysosporium. The presented analysis will help design future P450 functional studies to understand the underlying mechanisms of secondary metabolism and oxidative biotransformation pathways in this model white rot fungus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Doddapaneni</LastName><ForeName>Harshavardhan</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Environmental Genetics and Molecular Toxicology Division, Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH 45267-0056, USA. d_harshavardhan@yahoo.co.in</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chakraborty</LastName><ForeName>Ranajit</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>R01 ES010210</GrantID><Acronym>ES</Acronym><Agency>NIEHS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R01-ES10210</GrantID><Acronym>ES</Acronym><Agency>NIEHS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2005</Year><Month>06</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018076">DNA, Complementary</NameOfSubstance></Chemical><Chemical><RegistryNumber>9035-51-2</RegistryNumber><NameOfSubstance UI="D003577">Cytochrome P-450 Enzyme System</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 1.-</RegistryNumber><NameOfSubstance UI="D006899">Mixed Function Oxygenases</NameOfSubstance></Chemical><Chemical><RegistryNumber>S88TT14065</RegistryNumber><NameOfSubstance UI="D010100">Oxygen</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D017398" MajorTopicYN="N">Alternative Splicing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003001" MajorTopicYN="N">Cloning, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016000" MajorTopicYN="N">Cluster Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003577" MajorTopicYN="N">Cytochrome P-450 Enzyme System</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D018076" MajorTopicYN="N">DNA, Complementary</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020440" MajorTopicYN="Y">Gene Duplication</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016681" MajorTopicYN="Y">Genome, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006899" MajorTopicYN="N">Mixed Function Oxygenases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008957" MajorTopicYN="N">Models, Genetic</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010100" MajorTopicYN="N">Oxygen</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020075" MajorTopicYN="N">Phanerochaete</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017434" MajorTopicYN="N">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017386" MajorTopicYN="N">Sequence Homology, Amino Acid</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2004</Year><Month>11</Month><Day>24</Day></PubMedPubDate><PubMedPubDate 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last="Yadav">Jagjit S. Yadav</name></noCountry><country name="États-Unis"><region name="Ohio"><name sortKey="Doddapaneni, Harshavardhan" sort="Doddapaneni, Harshavardhan" uniqKey="Doddapaneni H" first="Harshavardhan" last="Doddapaneni">Harshavardhan Doddapaneni</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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