Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation.
Identifieur interne : 000162 ( Main/Exploration ); précédent : 000161; suivant : 000163Metadata Analysis of Phanerochaete chrysosporium Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation.
Auteurs : Ayyappa Kumar Sista Kameshwar [Canada] ; Wensheng Qin [Canada]Source :
- International journal of biological sciences [ 1449-2288 ] ; 2017.
Descripteurs français
- KwdFr :
- MESH :
- enzymologie : Phanerochaete.
- génétique : Phanerochaete, Protéines fongiques, Transcriptome.
- métabolisme : Cellulose, Phanerochaete, Polyosides, Protéines fongiques.
- Métadonnées.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Fungal Proteins.
- chemical , metabolism : Cellulose, Fungal Proteins, Polysaccharides.
- enzymology : Phanerochaete.
- genetics : Phanerochaete, Transcriptome.
- metabolism : Phanerochaete.
- Metadata.
Abstract
In literature, extensive studies have been conducted on popular wood degrading white rot fungus, Phanerochaete chrysosporium about its lignin degrading mechanisms compared to the cellulose and hemicellulose degrading abilities. This study delineates cellulose and hemicellulose degrading mechanisms through large scale metadata analysis of P. chrysosporium gene expression data (retrieved from NCBI GEO) to understand the common expression patterns of differentially expressed genes when cultured on different growth substrates. Genes encoding glycoside hydrolase classes commonly expressed during breakdown of cellulose such as GH-5,6,7,9,44,45,48 and hemicellulose are GH-2,8,10,11,26,30,43,47 were found to be highly expressed among varied growth conditions including simple customized and complex natural plant biomass growth mediums. Genes encoding carbohydrate esterase class enzymes CE (1,4,8,9,15,16) polysaccharide lyase class enzymes PL-8 and PL-14, and glycosyl transferases classes GT (1,2,4,8,15,20,35,39,48) were differentially expressed in natural plant biomass growth mediums. Based on these results, P. chrysosporium, on natural plant biomass substrates was found to express lignin and hemicellulose degrading enzymes more than cellulolytic enzymes except GH-61 (LPMO) class enzymes, in early stages. It was observed that the fate of P. chrysosporium transcriptome is significantly affected by the wood substrate provided. We believe, the gene expression findings in this study plays crucial role in developing genetically efficient microbe with effective cellulose and hemicellulose degradation abilities.
DOI: 10.7150/ijbs.17390
PubMed: 28123349
PubMed Central: PMC5264264
Affiliations:
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(metabolism)</term><term>Transcriptome (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cellulose (métabolisme)</term><term>Métadonnées (MeSH)</term><term>Phanerochaete (enzymologie)</term><term>Phanerochaete (génétique)</term><term>Phanerochaete (métabolisme)</term><term>Polyosides (métabolisme)</term><term>Protéines fongiques (génétique)</term><term>Protéines fongiques (métabolisme)</term><term>Transcriptome (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cellulose</term><term>Fungal Proteins</term><term>Polysaccharides</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Phanerochaete</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Phanerochaete</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Phanerochaete</term><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Phanerochaete</term><term>Protéines fongiques</term><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Phanerochaete</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Cellulose</term><term>Phanerochaete</term><term>Polyosides</term><term>Protéines fongiques</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Metadata</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Métadonnées</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">In literature, extensive studies have been conducted on popular wood degrading white rot fungus, <i>Phanerochaete chrysosporium</i> about its lignin degrading mechanisms compared to the cellulose and hemicellulose degrading abilities. This study delineates cellulose and hemicellulose degrading mechanisms through large scale metadata analysis of <i>P. chrysosporium</i> gene expression data (retrieved from NCBI GEO) to understand the common expression patterns of differentially expressed genes when cultured on different growth substrates. Genes encoding glycoside hydrolase classes commonly expressed during breakdown of cellulose such as GH-5,6,7,9,44,45,48 and hemicellulose are GH-2,8,10,11,26,30,43,47 were found to be highly expressed among varied growth conditions including simple customized and complex natural plant biomass growth mediums. Genes encoding carbohydrate esterase class enzymes CE (1,4,8,9,15,16) polysaccharide lyase class enzymes PL-8 and PL-14, and glycosyl transferases classes GT (1,2,4,8,15,20,35,39,48) were differentially expressed in natural plant biomass growth mediums. Based on these results, <i>P. chrysosporium,</i> on natural plant biomass substrates was found to express lignin and hemicellulose degrading enzymes more than cellulolytic enzymes except GH-61 (LPMO) class enzymes, in early stages. It was observed that the fate of <i>P. chrysosporium</i> transcriptome is significantly affected by the wood substrate provided. We believe, the gene expression findings in this study plays crucial role in developing genetically efficient microbe with effective cellulose and hemicellulose degradation abilities.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">28123349</PMID><DateCompleted><Year>2017</Year><Month>11</Month><Day>07</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1449-2288</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>1</Issue><PubDate><Year>2017</Year></PubDate></JournalIssue><Title>International journal of biological sciences</Title><ISOAbbreviation>Int J Biol Sci</ISOAbbreviation></Journal><ArticleTitle>Metadata Analysis of <i>Phanerochaete chrysosporium</i> Gene Expression Data Identified Common CAZymes Encoding Gene Expression Profiles Involved in Cellulose and Hemicellulose Degradation.</ArticleTitle><Pagination><MedlinePgn>85-99</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7150/ijbs.17390</ELocationID><Abstract><AbstractText>In literature, extensive studies have been conducted on popular wood degrading white rot fungus, <i>Phanerochaete chrysosporium</i> about its lignin degrading mechanisms compared to the cellulose and hemicellulose degrading abilities. This study delineates cellulose and hemicellulose degrading mechanisms through large scale metadata analysis of <i>P. chrysosporium</i> gene expression data (retrieved from NCBI GEO) to understand the common expression patterns of differentially expressed genes when cultured on different growth substrates. Genes encoding glycoside hydrolase classes commonly expressed during breakdown of cellulose such as GH-5,6,7,9,44,45,48 and hemicellulose are GH-2,8,10,11,26,30,43,47 were found to be highly expressed among varied growth conditions including simple customized and complex natural plant biomass growth mediums. Genes encoding carbohydrate esterase class enzymes CE (1,4,8,9,15,16) polysaccharide lyase class enzymes PL-8 and PL-14, and glycosyl transferases classes GT (1,2,4,8,15,20,35,39,48) were differentially expressed in natural plant biomass growth mediums. Based on these results, <i>P. chrysosporium,</i> on natural plant biomass substrates was found to express lignin and hemicellulose degrading enzymes more than cellulolytic enzymes except GH-61 (LPMO) class enzymes, in early stages. It was observed that the fate of <i>P. chrysosporium</i> transcriptome is significantly affected by the wood substrate provided. We believe, the gene expression findings in this study plays crucial role in developing genetically efficient microbe with effective cellulose and hemicellulose degradation abilities.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Kameshwar</LastName><ForeName>Ayyappa Kumar Sista</ForeName><Initials>AK</Initials><AffiliationInfo><Affiliation>Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Qin</LastName><ForeName>Wensheng</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>01</Month><Day>01</Day></ArticleDate></Article><MedlineJournalInfo><Country>Australia</Country><MedlineTA>Int J Biol Sci</MedlineTA><NlmUniqueID>101235568</NlmUniqueID><ISSNLinking>1449-2288</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011134">Polysaccharides</NameOfSubstance></Chemical><Chemical><RegistryNumber>8024-50-8</RegistryNumber><NameOfSubstance UI="C007916">hemicellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>9004-34-6</RegistryNumber><NameOfSubstance UI="D002482">Cellulose</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D002482" MajorTopicYN="N">Cellulose</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005656" MajorTopicYN="N">Fungal Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D000071253" MajorTopicYN="N">Metadata</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020075" MajorTopicYN="N">Phanerochaete</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011134" MajorTopicYN="N">Polysaccharides</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D059467" 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