Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.
Identifieur interne : 000457 ( Main/Exploration ); précédent : 000456; suivant : 000458Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.
Auteurs : Hitoshi Suzuki [Canada] ; Jacqueline Macdonald ; Khajamohiddin Syed ; Asaf Salamov ; Chiaki Hori ; Andrea Aerts ; Bernard Henrissat ; Ad Wiebenga ; Patricia A. Vankuyk ; Kerrie Barry ; Erika Lindquist ; Kurt Labutti ; Alla Lapidus ; Susan Lucas ; Pedro Coutinho ; Yunchen Gong ; Masahiro Samejima ; Radhakrishnan Mahadevan ; Mamdouh Abou-Zaid ; Ronald P. De Vries ; Kiyohiko Igarashi ; Jagjit S. Yadav ; Igor V. Grigoriev ; Emma R. MasterSource :
- BMC genomics [ 1471-2164 ] ; 2012.
Descripteurs français
- KwdFr :
- MESH :
- enzymologie : Phanerochaete, Polyporaceae.
- génétique : Glycosidases, Génome fongique, Phanerochaete, Polyporaceae, Protéines fongiques.
- microbiologie : Bois.
- métabolisme : Protéines fongiques.
- méthodes : Génomique.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Fungal Proteins, Glycoside Hydrolases.
- chemical , metabolism : Fungal Proteins.
- enzymology : Phanerochaete, Polyporaceae.
- genetics : Genome, Fungal, Phanerochaete, Polyporaceae.
- methods : Genomics.
- microbiology : Wood.
Abstract
BACKGROUND
Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.
RESULTS
P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.
CONCLUSIONS
The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.
DOI: 10.1186/1471-2164-13-444
PubMed: 22937793
PubMed Central: PMC3463431
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Vankuyk</name></author><author><name sortKey="Barry, Kerrie" sort="Barry, Kerrie" uniqKey="Barry K" first="Kerrie" last="Barry">Kerrie Barry</name></author><author><name sortKey="Lindquist, Erika" sort="Lindquist, Erika" uniqKey="Lindquist E" first="Erika" last="Lindquist">Erika Lindquist</name></author><author><name sortKey="Labutti, Kurt" sort="Labutti, Kurt" uniqKey="Labutti K" first="Kurt" last="Labutti">Kurt Labutti</name></author><author><name sortKey="Lapidus, Alla" sort="Lapidus, Alla" uniqKey="Lapidus A" first="Alla" last="Lapidus">Alla Lapidus</name></author><author><name sortKey="Lucas, Susan" sort="Lucas, Susan" uniqKey="Lucas S" first="Susan" last="Lucas">Susan Lucas</name></author><author><name sortKey="Coutinho, Pedro" sort="Coutinho, Pedro" uniqKey="Coutinho P" first="Pedro" last="Coutinho">Pedro Coutinho</name></author><author><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name></author><author><name sortKey="Samejima, Masahiro" sort="Samejima, Masahiro" uniqKey="Samejima M" first="Masahiro" last="Samejima">Masahiro Samejima</name></author><author><name sortKey="Mahadevan, Radhakrishnan" sort="Mahadevan, Radhakrishnan" uniqKey="Mahadevan R" first="Radhakrishnan" last="Mahadevan">Radhakrishnan Mahadevan</name></author><author><name sortKey="Abou Zaid, Mamdouh" sort="Abou Zaid, Mamdouh" uniqKey="Abou Zaid M" first="Mamdouh" last="Abou-Zaid">Mamdouh Abou-Zaid</name></author><author><name sortKey="De Vries, Ronald P" sort="De Vries, Ronald P" uniqKey="De Vries R" first="Ronald P" last="De Vries">Ronald P. De Vries</name></author><author><name sortKey="Igarashi, Kiyohiko" sort="Igarashi, Kiyohiko" uniqKey="Igarashi K" first="Kiyohiko" last="Igarashi">Kiyohiko Igarashi</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><author><name sortKey="Grigoriev, Igor V" sort="Grigoriev, Igor V" uniqKey="Grigoriev I" first="Igor V" last="Grigoriev">Igor V. Grigoriev</name></author><author><name sortKey="Master, Emma R" sort="Master, Emma R" uniqKey="Master E" first="Emma R" last="Master">Emma R. Master</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Genome, Fungal (genetics)</term><term>Genomics (methods)</term><term>Glycoside Hydrolases (genetics)</term><term>Phanerochaete (enzymology)</term><term>Phanerochaete (genetics)</term><term>Polyporaceae (enzymology)</term><term>Polyporaceae (genetics)</term><term>Wood (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bois (microbiologie)</term><term>Glycosidases (génétique)</term><term>Génome fongique (génétique)</term><term>Génomique (méthodes)</term><term>Phanerochaete (enzymologie)</term><term>Phanerochaete (génétique)</term><term>Polyporaceae (enzymologie)</term><term>Polyporaceae (génétique)</term><term>Protéines fongiques (génétique)</term><term>Protéines fongiques (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term><term>Glycoside Hydrolases</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Phanerochaete</term><term>Polyporaceae</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Phanerochaete</term><term>Polyporaceae</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Genome, Fungal</term><term>Phanerochaete</term><term>Polyporaceae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Glycosidases</term><term>Génome fongique</term><term>Phanerochaete</term><term>Polyporaceae</term><term>Protéines fongiques</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Genomics</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Bois</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Wood</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines fongiques</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Génomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">22937793</PMID><DateCompleted><Year>2013</Year><Month>02</Month><Day>06</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>13</Volume><PubDate><Year>2012</Year><Month>Sep</Month><Day>02</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize.</ArticleTitle><Pagination><MedlinePgn>444</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-13-444</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Softwood is the predominant form of land plant biomass in the Northern hemisphere, and is among the most recalcitrant biomass resources to bioprocess technologies. The white rot fungus, Phanerochaete carnosa, has been isolated almost exclusively from softwoods, while most other known white-rot species, including Phanerochaete chrysosporium, were mainly isolated from hardwoods. Accordingly, it is anticipated that P. carnosa encodes a distinct set of enzymes and proteins that promote softwood decomposition. To elucidate the genetic basis of softwood bioconversion by a white-rot fungus, the present study reports the P. carnosa genome sequence and its comparative analysis with the previously reported P. chrysosporium genome.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">P. carnosa encodes a complete set of lignocellulose-active enzymes. Comparative genomic analysis revealed that P. carnosa is enriched with genes encoding manganese peroxidase, and that the most divergent glycoside hydrolase families were predicted to encode hemicellulases and glycoprotein degrading enzymes. Most remarkably, P. carnosa possesses one of the largest P450 contingents (266 P450s) among the sequenced and annotated wood-rotting basidiomycetes, nearly double that of P. chrysosporium. Along with metabolic pathway modeling, comparative growth studies on model compounds and chemical analyses of decomposed wood components showed greater tolerance of P. carnosa to various substrates including coniferous heartwood.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The P. carnosa genome is enriched with genes that encode P450 monooxygenases that can participate in extractives degradation, and manganese peroxidases involved in lignin degradation. The significant expansion of P450s in P. carnosa, along with differences in carbohydrate- and lignin-degrading enzymes, could be correlated to the utilization of heartwood and sapwood preparations from both coniferous and hardwood species.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Suzuki</LastName><ForeName>Hitoshi</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, ON, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>MacDonald</LastName><ForeName>Jacqueline</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Syed</LastName><ForeName>Khajamohiddin</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Salamov</LastName><ForeName>Asaf</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Hori</LastName><ForeName>Chiaki</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Aerts</LastName><ForeName>Andrea</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Henrissat</LastName><ForeName>Bernard</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Wiebenga</LastName><ForeName>Ad</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>VanKuyk</LastName><ForeName>Patricia A</ForeName><Initials>PA</Initials></Author><Author ValidYN="Y"><LastName>Barry</LastName><ForeName>Kerrie</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Lindquist</LastName><ForeName>Erika</ForeName><Initials>E</Initials></Author><Author ValidYN="Y"><LastName>LaButti</LastName><ForeName>Kurt</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Lapidus</LastName><ForeName>Alla</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Lucas</LastName><ForeName>Susan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Coutinho</LastName><ForeName>Pedro</ForeName><Initials>P</Initials></Author><Author ValidYN="Y"><LastName>Gong</LastName><ForeName>Yunchen</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Samejima</LastName><ForeName>Masahiro</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Mahadevan</LastName><ForeName>Radhakrishnan</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Abou-Zaid</LastName><ForeName>Mamdouh</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>de Vries</LastName><ForeName>Ronald P</ForeName><Initials>RP</Initials></Author><Author ValidYN="Y"><LastName>Igarashi</LastName><ForeName>Kiyohiko</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Yadav</LastName><ForeName>Jagjit S</ForeName><Initials>JS</Initials></Author><Author ValidYN="Y"><LastName>Grigoriev</LastName><ForeName>Igor V</ForeName><Initials>IV</Initials></Author><Author ValidYN="Y"><LastName>Master</LastName><ForeName>Emma R</ForeName><Initials>ER</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>2012</Year><Month>09</Month><Day>02</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="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 3.2.1.-</RegistryNumber><NameOfSubstance UI="D006026">Glycoside Hydrolases</NameOfSubstance></Chemical><Chemical><RegistryNumber>EC 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Yadav</name></noCountry><country name="Canada"><region name="Ontario"><name sortKey="Suzuki, Hitoshi" sort="Suzuki, Hitoshi" uniqKey="Suzuki H" first="Hitoshi" last="Suzuki">Hitoshi Suzuki</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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