Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation.
Identifieur interne : 001869 ( Main/Exploration ); précédent : 001868; suivant : 001870Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation.
Auteurs : Oleksandr Skyba [Canada] ; Dan Cullen [États-Unis] ; Carl J. Douglas [Canada] ; Shawn D. Mansfield [Canada]Source :
- Applied and environmental microbiology [ 1098-5336 ] ; 2016.
Descripteurs français
- KwdFr :
- MESH :
- composition chimique : Bois.
- croissance et développement : Polyporales.
- génétique : Polyporales.
- microbiologie : Bois, Populus.
- métabolisme : Polyporales.
- Analyse de profil d'expression de gènes, Analyse sur microréseau, Gènes fongiques.
English descriptors
- KwdEn :
- MESH :
- chemistry : Wood.
- genetics : Polyporales.
- growth & development : Polyporales.
- metabolism : Polyporales.
- microbiology : Populus, Wood.
- Gene Expression Profiling, Genes, Fungal, Microarray Analysis.
Abstract
UNLABELLED
Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode "proteins of unknown function," and determining their role in lignocellulose degradation presents opportunities and challenges for future research.
IMPORTANCE
This study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.
DOI: 10.1128/AEM.00134-16
PubMed: 27208101
PubMed Central: PMC4959194
Affiliations:
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Douglas</name><affiliation wicri:level="4"><nlm:affiliation>Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Botany, University of British Columbia, Vancouver, British Columbia</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author><author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name><affiliation wicri:level="4"><nlm:affiliation>Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada shawn.mansfield@ubc.ca.</nlm:affiliation><country wicri:rule="url">Canada</country><wicri:regionArea>Department of Wood Science, University of British Columbia, Vancouver, British Columbia</wicri:regionArea><orgName type="university">Université de la Colombie-Britannique</orgName><placeName><settlement type="city">Vancouver</settlement><region type="state">Colombie-Britannique </region></placeName></affiliation></author></analytic><series><title level="j">Applied and environmental microbiology</title><idno type="eISSN">1098-5336</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Gene Expression Profiling (MeSH)</term><term>Genes, Fungal (MeSH)</term><term>Microarray Analysis (MeSH)</term><term>Polyporales (genetics)</term><term>Polyporales (growth & development)</term><term>Polyporales (metabolism)</term><term>Populus (microbiology)</term><term>Wood (chemistry)</term><term>Wood (microbiology)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Analyse sur microréseau (MeSH)</term><term>Bois (composition chimique)</term><term>Bois (microbiologie)</term><term>Gènes fongiques (MeSH)</term><term>Polyporales (croissance et développement)</term><term>Polyporales (génétique)</term><term>Polyporales (métabolisme)</term><term>Populus (microbiologie)</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Wood</term></keywords><keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Bois</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Polyporales</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Polyporales</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Polyporales</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Polyporales</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Polyporales</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Bois</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Populus</term><term>Wood</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Polyporales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Genes, Fungal</term><term>Microarray Analysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Analyse sur microréseau</term><term>Gènes fongiques</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>UNLABELLED</b></p><p>Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode "proteins of unknown function," and determining their role in lignocellulose degradation presents opportunities and challenges for future research.</p></div><div type="abstract" xml:lang="en"><p><b>IMPORTANCE</b></p><p>This study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">27208101</PMID><DateCompleted><Year>2017</Year><Month>10</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-Print"><Journal><ISSN IssnType="Electronic">1098-5336</ISSN><JournalIssue CitedMedium="Internet"><Volume>82</Volume><Issue>14</Issue><PubDate><Year>2016</Year><Month>07</Month><Day>15</Day></PubDate></JournalIssue><Title>Applied and environmental microbiology</Title><ISOAbbreviation>Appl Environ Microbiol</ISOAbbreviation></Journal><ArticleTitle>Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation.</ArticleTitle><Pagination><MedlinePgn>4387-4400</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1128/AEM.00134-16</ELocationID><Abstract><AbstractText Label="UNLABELLED">Identification of the specific genes and enzymes involved in the fungal degradation of lignocellulosic biomass derived from feedstocks with various compositions is essential to the development of improved bioenergy processes. In order to elucidate the effect of substrate composition on gene expression in wood-rotting fungi, we employed microarrays based on the annotated genomes of the brown- and white-rot fungi, Rhodonia placenta (formerly Postia placenta) and Phanerochaete chrysosporium, respectively. We monitored the expression of genes involved in the enzymatic deconstruction of the cell walls of three 4-year-old Populus trichocarpa (poplar) trees of genotypes with distinct cell wall chemistries, selected from a population of several hundred trees grown in a common garden. The woody substrates were incubated with wood decay fungi for 10, 20, and 30 days. An analysis of transcript abundance in all pairwise comparisons highlighted 64 and 84 differentially expressed genes (>2-fold, P < 0.05) in P. chrysosporium and P. placenta, respectively. Cross-fungal comparisons also revealed an array of highly differentially expressed genes (>4-fold, P < 0.01) across different substrates and time points. These results clearly demonstrate that gene expression profiles of P. chrysosporium and P. placenta are influenced by wood substrate composition and the duration of incubation. Many of the significantly expressed genes encode "proteins of unknown function," and determining their role in lignocellulose degradation presents opportunities and challenges for future research.</AbstractText><AbstractText Label="IMPORTANCE">This study describes the variation in expression patterns of two wood-degrading fungi (brown- and white-rot fungi) during colonization and incubation on three different naturally occurring poplar substrates of differing chemical compositions, over time. The results clearly show that the two fungi respond differentially to their substrates and that several known and, more interestingly, currently unknown genes are highly misregulated in response to various substrate compositions. These findings highlight the need to characterize several unknown proteins for catalytic function but also as potential candidate proteins to improve the efficiency of enzymatic cocktails to degrade lignocellulosic substrates in industrial applications, such as in a biochemically based bioenergy platform.</AbstractText><CopyrightInformation>Copyright © 2016, American Society for Microbiology. All Rights Reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Skyba</LastName><ForeName>Oleksandr</ForeName><Initials>O</Initials><AffiliationInfo><Affiliation>Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cullen</LastName><ForeName>Dan</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>USDA Forest Service, Forest Products Laboratory, Madison, Wisconsin, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Douglas</LastName><ForeName>Carl J</ForeName><Initials>CJ</Initials><AffiliationInfo><Affiliation>Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Mansfield</LastName><ForeName>Shawn D</ForeName><Initials>SD</Initials><AffiliationInfo><Affiliation>Department of Wood Science, University of British Columbia, Vancouver, British Columbia, Canada shawn.mansfield@ubc.ca.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>06</Month><Day>30</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Appl Environ Microbiol</MedlineTA><NlmUniqueID>7605801</NlmUniqueID><ISSNLinking>0099-2240</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005800" MajorTopicYN="N">Genes, Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D046228" MajorTopicYN="N">Microarray Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020072" MajorTopicYN="N">Polyporales</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000382" MajorTopicYN="N">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014934" MajorTopicYN="N">Wood</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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Douglas</name><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name></country><country name="États-Unis"><region name="Wisconsin"><name sortKey="Cullen, Dan" sort="Cullen, Dan" uniqKey="Cullen D" first="Dan" last="Cullen">Dan Cullen</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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|texte= Gene Expression Patterns of Wood Decay Fungi Postia placenta and Phanerochaete chrysosporium Are Influenced by Wood Substrate Composition during Degradation.
}}
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