Investigation of lignocellulolytic enzymes during different growth phases of Ganoderma lucidum strain G0119 using genomic, transcriptomic and secretomic analyses.
Identifieur interne : 000408 ( Main/Exploration ); précédent : 000407; suivant : 000409Investigation of lignocellulolytic enzymes during different growth phases of Ganoderma lucidum strain G0119 using genomic, transcriptomic and secretomic analyses.
Auteurs : Shuai Zhou [République populaire de Chine] ; Jingsong Zhang [République populaire de Chine] ; Fuying Ma [République populaire de Chine] ; Chuanhong Tang [République populaire de Chine] ; Qingjiu Tang [République populaire de Chine] ; Xiaoyu Zhang [République populaire de Chine]Source :
- PloS one [ 1932-6203 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Enzymes.
- chemical , metabolism : Enzymes, Lignin, Polysaccharides.
- enzymology : Ganoderma.
- genetics : Ganoderma.
- growth & development : Ganoderma.
- metabolism : Ganoderma.
- Gene Expression Profiling, Genomics, Hydrolysis.
Abstract
Ganoderma lucidum is a medicinal mushroom that is well known for its ability to enhance human health, and products made from this fungus have been highly profitable. The substrate-degrading ability of G. lucidum could be related to its growth. CAZy proteins were more abundant in its genome than in the other white rot fungi models. Among these CAZy proteins, changes in lignocellulolytic enzymes during growth have not been well studied. Using genomic, transcriptomic and secretomic analyses, this study focuses on the lignocellulolytic enzymes of G. lucidum strain G0119 to determine which of these degradative enzymes contribute to its growth. From the genome sequencing data, genes belonging to CAZy protein families, especially genes involved in lignocellulose degradation, were investigated. The gene expression, protein abundance and enzymatic activity of lignocellulolytic enzymes in mycelia over a growth cycle were analysed. The overall expression cellulase was higher than that of hemicellulase and lignin-modifying enzymes, particularly during the development of fruiting bodies. The cellulase and hemicellulase abundances and activities increased after the fruiting bodies matured, when basidiospores were produced in massive quantities till the end of the growth cycle. Additionally, the protein abundances of the lignin-modifying enzymes and the expression of their corresponding genes, including laccases and lignin-degrading heme peroxidases, were highest when the mycelia fully spread in the compost bag. Type I cellobiohydrolase was observed to be the most abundant extracellular lignocellulolytic enzyme produced by the G. lucidum strain G0119. The AA2 family haem peroxidases were the dominant lignin-modifying enzyme expressed during the mycelial growth phase, and several laccases might play roles during the formation of the primordium. This study provides insight into the changes in the lignocellulose degradation ability of G. lucidum during its growth and will facilitate the discovery of new approaches to accelerate the growth of G. lucidum in culture.
DOI: 10.1371/journal.pone.0198404
PubMed: 29852018
PubMed Central: PMC5979026
Affiliations:
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sortKey="Tang, Qingjiu" sort="Tang, Qingjiu" uniqKey="Tang Q" first="Qingjiu" last="Tang">Qingjiu Tang</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Xiaoyu" sort="Zhang, Xiaoyu" uniqKey="Zhang X" first="Xiaoyu" last="Zhang">Xiaoyu Zhang</name><affiliation wicri:level="3"><nlm:affiliation>Key Laboratory of 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type="région">Hubei</region></placeName></affiliation><affiliation wicri:level="1"><nlm:affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Jingsong" sort="Zhang, Jingsong" uniqKey="Zhang J" first="Jingsong" last="Zhang">Jingsong Zhang</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Ma, Fuying" sort="Ma, Fuying" uniqKey="Ma F" first="Fuying" last="Ma">Fuying Ma</name><affiliation wicri:level="3"><nlm:affiliation>Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key 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Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Tang, Qingjiu" sort="Tang, Qingjiu" uniqKey="Tang Q" first="Qingjiu" last="Tang">Qingjiu Tang</name><affiliation wicri:level="1"><nlm:affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai</wicri:regionArea><wicri:noRegion>Shanghai</wicri:noRegion></affiliation></author><author><name sortKey="Zhang, Xiaoyu" sort="Zhang, Xiaoyu" uniqKey="Zhang X" first="Xiaoyu" last="Zhang">Xiaoyu Zhang</name><affiliation wicri:level="3"><nlm:affiliation>Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan</wicri:regionArea><placeName><settlement type="city">Wuhan</settlement><region type="région">Hubei</region></placeName></affiliation></author></analytic><series><title level="j">PloS one</title><idno type="eISSN">1932-6203</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Enzymes (genetics)</term><term>Enzymes (metabolism)</term><term>Ganoderma (enzymology)</term><term>Ganoderma (genetics)</term><term>Ganoderma (growth & development)</term><term>Ganoderma (metabolism)</term><term>Gene Expression Profiling (MeSH)</term><term>Genomics (MeSH)</term><term>Hydrolysis (MeSH)</term><term>Lignin (metabolism)</term><term>Polysaccharides (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Enzymes (génétique)</term><term>Enzymes (métabolisme)</term><term>Ganoderma (croissance et développement)</term><term>Ganoderma (enzymologie)</term><term>Ganoderma (génétique)</term><term>Ganoderma (métabolisme)</term><term>Génomique (MeSH)</term><term>Hydrolyse (MeSH)</term><term>Lignine (métabolisme)</term><term>Polyosides (métabolisme)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Enzymes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Enzymes</term><term>Lignin</term><term>Polysaccharides</term></keywords><keywords scheme="MESH" qualifier="croissance et développement" xml:lang="fr"><term>Ganoderma</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Ganoderma</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Ganoderma</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Ganoderma</term></keywords><keywords scheme="MESH" qualifier="growth & development" xml:lang="en"><term>Ganoderma</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Enzymes</term><term>Ganoderma</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Ganoderma</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Enzymes</term><term>Ganoderma</term><term>Lignine</term><term>Polyosides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Gene Expression Profiling</term><term>Genomics</term><term>Hydrolysis</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Génomique</term><term>Hydrolyse</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Ganoderma lucidum is a medicinal mushroom that is well known for its ability to enhance human health, and products made from this fungus have been highly profitable. The substrate-degrading ability of G. lucidum could be related to its growth. CAZy proteins were more abundant in its genome than in the other white rot fungi models. Among these CAZy proteins, changes in lignocellulolytic enzymes during growth have not been well studied. Using genomic, transcriptomic and secretomic analyses, this study focuses on the lignocellulolytic enzymes of G. lucidum strain G0119 to determine which of these degradative enzymes contribute to its growth. From the genome sequencing data, genes belonging to CAZy protein families, especially genes involved in lignocellulose degradation, were investigated. The gene expression, protein abundance and enzymatic activity of lignocellulolytic enzymes in mycelia over a growth cycle were analysed. The overall expression cellulase was higher than that of hemicellulase and lignin-modifying enzymes, particularly during the development of fruiting bodies. The cellulase and hemicellulase abundances and activities increased after the fruiting bodies matured, when basidiospores were produced in massive quantities till the end of the growth cycle. Additionally, the protein abundances of the lignin-modifying enzymes and the expression of their corresponding genes, including laccases and lignin-degrading heme peroxidases, were highest when the mycelia fully spread in the compost bag. Type I cellobiohydrolase was observed to be the most abundant extracellular lignocellulolytic enzyme produced by the G. lucidum strain G0119. The AA2 family haem peroxidases were the dominant lignin-modifying enzyme expressed during the mycelial growth phase, and several laccases might play roles during the formation of the primordium. This study provides insight into the changes in the lignocellulose degradation ability of G. lucidum during its growth and will facilitate the discovery of new approaches to accelerate the growth of G. lucidum in culture.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29852018</PMID><DateCompleted><Year>2018</Year><Month>11</Month><Day>26</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>26</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Electronic">1932-6203</ISSN><JournalIssue CitedMedium="Internet"><Volume>13</Volume><Issue>5</Issue><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>PloS one</Title><ISOAbbreviation>PLoS One</ISOAbbreviation></Journal><ArticleTitle>Investigation of lignocellulolytic enzymes during different growth phases of Ganoderma lucidum strain G0119 using genomic, transcriptomic and secretomic analyses.</ArticleTitle><Pagination><MedlinePgn>e0198404</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1371/journal.pone.0198404</ELocationID><Abstract><AbstractText>Ganoderma lucidum is a medicinal mushroom that is well known for its ability to enhance human health, and products made from this fungus have been highly profitable. The substrate-degrading ability of G. lucidum could be related to its growth. CAZy proteins were more abundant in its genome than in the other white rot fungi models. Among these CAZy proteins, changes in lignocellulolytic enzymes during growth have not been well studied. Using genomic, transcriptomic and secretomic analyses, this study focuses on the lignocellulolytic enzymes of G. lucidum strain G0119 to determine which of these degradative enzymes contribute to its growth. From the genome sequencing data, genes belonging to CAZy protein families, especially genes involved in lignocellulose degradation, were investigated. The gene expression, protein abundance and enzymatic activity of lignocellulolytic enzymes in mycelia over a growth cycle were analysed. The overall expression cellulase was higher than that of hemicellulase and lignin-modifying enzymes, particularly during the development of fruiting bodies. The cellulase and hemicellulase abundances and activities increased after the fruiting bodies matured, when basidiospores were produced in massive quantities till the end of the growth cycle. Additionally, the protein abundances of the lignin-modifying enzymes and the expression of their corresponding genes, including laccases and lignin-degrading heme peroxidases, were highest when the mycelia fully spread in the compost bag. Type I cellobiohydrolase was observed to be the most abundant extracellular lignocellulolytic enzyme produced by the G. lucidum strain G0119. The AA2 family haem peroxidases were the dominant lignin-modifying enzyme expressed during the mycelial growth phase, and several laccases might play roles during the formation of the primordium. This study provides insight into the changes in the lignocellulose degradation ability of G. lucidum during its growth and will facilitate the discovery of new approaches to accelerate the growth of G. lucidum in culture.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Shuai</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Jingsong</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ma</LastName><ForeName>Fuying</ForeName><Initials>F</Initials><AffiliationInfo><Affiliation>Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Chuanhong</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tang</LastName><ForeName>Qingjiu</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>National Engineering Research Centre of Edible Fungi, Key Laboratory of Applied Mycological Resources and Utilisation, Ministry of Agriculture, Institute of Edible Fungi, Shanghai Academy of Agriculture Sciences, Shanghai, People's Republic of China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Xiaoyu</ForeName><Initials>X</Initials><Identifier Source="ORCID">0000-0002-2021-3084</Identifier><AffiliationInfo><Affiliation>Key Laboratory of Biophysics of MOE, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, People's Republic of China.</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>2018</Year><Month>05</Month><Day>31</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PLoS One</MedlineTA><NlmUniqueID>101285081</NlmUniqueID><ISSNLinking>1932-6203</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004798">Enzymes</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D011134">Polysaccharides</NameOfSubstance></Chemical><Chemical><RegistryNumber>11132-73-3</RegistryNumber><NameOfSubstance UI="C036909">lignocellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>8024-50-8</RegistryNumber><NameOfSubstance UI="C007916">hemicellulose</NameOfSubstance></Chemical><Chemical><RegistryNumber>9005-53-2</RegistryNumber><NameOfSubstance UI="D008031">Lignin</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004798" MajorTopicYN="N">Enzymes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D032902" MajorTopicYN="N">Ganoderma</DescriptorName><QualifierName UI="Q000201" MajorTopicYN="Y">enzymology</QualifierName><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="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="Y">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006868" MajorTopicYN="N">Hydrolysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D011134" MajorTopicYN="N">Polysaccharides</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading></MeshHeadingList><CoiStatement>The authors have declared that no competing interests exist.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>02</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>05</Month><Day>20</Day></PubMedPubDate><PubMedPubDate 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IdType="pubmed">23935031</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>République populaire de Chine</li></country><region><li>Hubei</li></region><settlement><li>Wuhan</li></settlement></list><tree><country name="République populaire de Chine"><region name="Hubei"><name sortKey="Zhou, Shuai" sort="Zhou, Shuai" uniqKey="Zhou S" first="Shuai" last="Zhou">Shuai Zhou</name></region><name sortKey="Ma, Fuying" sort="Ma, Fuying" uniqKey="Ma F" first="Fuying" last="Ma">Fuying Ma</name><name sortKey="Tang, Chuanhong" sort="Tang, Chuanhong" uniqKey="Tang C" first="Chuanhong" last="Tang">Chuanhong Tang</name><name sortKey="Tang, Qingjiu" sort="Tang, Qingjiu" uniqKey="Tang Q" first="Qingjiu" last="Tang">Qingjiu Tang</name><name sortKey="Zhang, Jingsong" sort="Zhang, Jingsong" uniqKey="Zhang J" first="Jingsong" last="Zhang">Jingsong Zhang</name><name sortKey="Zhang, Xiaoyu" sort="Zhang, Xiaoyu" uniqKey="Zhang X" first="Xiaoyu" last="Zhang">Xiaoyu Zhang</name><name sortKey="Zhou, Shuai" sort="Zhou, Shuai" uniqKey="Zhou S" first="Shuai" last="Zhou">Shuai Zhou</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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