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Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq.

Identifieur interne : 000228 ( Main/Exploration ); précédent : 000227; suivant : 000229

Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq.

Auteurs : Jianqiao Wang [Japon] ; Tomohiro Suzuki [Japon] ; Hideo Dohra [Japon] ; Shoko Takigami [Japon] ; Hiroko Kako [Japon] ; Ayumi Soga [Japon] ; Ichiro Kamei [Japon] ; Toshio Mori [Japon] ; Hirokazu Kawagishi [Japon] ; Hirofumi Hirai [Japon]

Source :

RBID : pubmed:27515927

Descripteurs français

English descriptors

Abstract

BACKGROUND

The white-rot fungus Phlebia sp. MG-60 shows valuable properties such as high ethanol yield from several lignocellulosic materials, although white-rot fungi commonly degrade woody components to CO2 and H2O. In order to identify genes involved in ethanol production by Phlebia sp. MG-60, we compared genes differentially expressed by the ethanol producing fungus Phlebia sp. MG-60 and the model white-rot fungus Phanerochaete chrysosporium under ethanol fermenting and non-fermenting conditions using next-generation sequencing technologies.

RESULTS

mRNAs from mycelia of Phlebia sp. MG-60 and P. chrysosporium under fermenting and non-fermenting conditions were sequenced using the MiSeq system. To detect differentially expressed genes, expression levels were measured in fragments per kilobase of exon per million mapped reads (FPKM). Differentially expressed genes were annotated using BLAST searches, Gene Ontology classifications, and KEGG pathway analysis. Functional analyses of differentially expressed genes revealed that genes involved in glucose uptake, glycolysis, and ethanol synthesis were widely upregulated in Phlebia sp. MG-60 under fermenting conditions.

CONCLUSIONS

In this study, we provided novel transcriptomic information on Phlebia sp. MG-60, and these RNA-seq data were useful in targeting genes involved in ethanol production for future genetic engineering.


DOI: 10.1186/s12864-016-2977-7
PubMed: 27515927
PubMed Central: PMC4982002


Affiliations:


Links toward previous steps (curation, corpus...)


Le document en format XML

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<name sortKey="Dohra, Hideo" sort="Dohra, Hideo" uniqKey="Dohra H" first="Hideo" last="Dohra">Hideo Dohra</name>
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<name sortKey="Kako, Hiroko" sort="Kako, Hiroko" uniqKey="Kako H" first="Hiroko" last="Kako">Hiroko Kako</name>
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<name sortKey="Soga, Ayumi" sort="Soga, Ayumi" uniqKey="Soga A" first="Ayumi" last="Soga">Ayumi Soga</name>
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<name sortKey="Kamei, Ichiro" sort="Kamei, Ichiro" uniqKey="Kamei I" first="Ichiro" last="Kamei">Ichiro Kamei</name>
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<nlm:affiliation>Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-kibanadai-nishi, Miyazaki, 889-2192, Japan.</nlm:affiliation>
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<name sortKey="Mori, Toshio" sort="Mori, Toshio" uniqKey="Mori T" first="Toshio" last="Mori">Toshio Mori</name>
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<nlm:affiliation>Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.</nlm:affiliation>
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<name sortKey="Kawagishi, Hirokazu" sort="Kawagishi, Hirokazu" uniqKey="Kawagishi H" first="Hirokazu" last="Kawagishi">Hirokazu Kawagishi</name>
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<name sortKey="Hirai, Hirofumi" sort="Hirai, Hirofumi" uniqKey="Hirai H" first="Hirofumi" last="Hirai">Hirofumi Hirai</name>
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<title level="j">BMC genomics</title>
<idno type="eISSN">1471-2164</idno>
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<date when="2016" type="published">2016</date>
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<keywords scheme="KwdEn" xml:lang="en">
<term>Biomass (MeSH)</term>
<term>Carbohydrate Metabolism (MeSH)</term>
<term>Ethanol (metabolism)</term>
<term>Fermentation (MeSH)</term>
<term>Fungal Proteins (genetics)</term>
<term>Fungal Proteins (metabolism)</term>
<term>Gene Expression Profiling (MeSH)</term>
<term>Gene Expression Regulation, Fungal (MeSH)</term>
<term>Gene Ontology (MeSH)</term>
<term>Glucose (metabolism)</term>
<term>High-Throughput Nucleotide Sequencing (MeSH)</term>
<term>Molecular Sequence Annotation (MeSH)</term>
<term>Phanerochaete (genetics)</term>
<term>Phanerochaete (metabolism)</term>
<term>Polyporales (genetics)</term>
<term>Polyporales (metabolism)</term>
<term>Wood (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr">
<term>Analyse de profil d'expression de gènes (MeSH)</term>
<term>Annotation de séquence moléculaire (MeSH)</term>
<term>Biomasse (MeSH)</term>
<term>Bois (métabolisme)</term>
<term>Fermentation (MeSH)</term>
<term>Gene Ontology (MeSH)</term>
<term>Glucose (métabolisme)</term>
<term>Métabolisme glucidique (MeSH)</term>
<term>Phanerochaete (génétique)</term>
<term>Phanerochaete (métabolisme)</term>
<term>Polyporales (génétique)</term>
<term>Polyporales (métabolisme)</term>
<term>Protéines fongiques (génétique)</term>
<term>Protéines fongiques (métabolisme)</term>
<term>Régulation de l'expression des gènes fongiques (MeSH)</term>
<term>Séquençage nucléotidique à haut débit (MeSH)</term>
<term>Éthanol (métabolisme)</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>Ethanol</term>
<term>Fungal Proteins</term>
<term>Glucose</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en">
<term>Phanerochaete</term>
<term>Polyporales</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr">
<term>Phanerochaete</term>
<term>Polyporales</term>
<term>Protéines fongiques</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en">
<term>Phanerochaete</term>
<term>Polyporales</term>
<term>Wood</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr">
<term>Bois</term>
<term>Glucose</term>
<term>Phanerochaete</term>
<term>Polyporales</term>
<term>Protéines fongiques</term>
<term>Éthanol</term>
</keywords>
<keywords scheme="MESH" xml:lang="en">
<term>Biomass</term>
<term>Carbohydrate Metabolism</term>
<term>Fermentation</term>
<term>Gene Expression Profiling</term>
<term>Gene Expression Regulation, Fungal</term>
<term>Gene Ontology</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Molecular Sequence Annotation</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr">
<term>Analyse de profil d'expression de gènes</term>
<term>Annotation de séquence moléculaire</term>
<term>Biomasse</term>
<term>Fermentation</term>
<term>Gene Ontology</term>
<term>Métabolisme glucidique</term>
<term>Régulation de l'expression des gènes fongiques</term>
<term>Séquençage nucléotidique à haut débit</term>
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<front>
<div type="abstract" xml:lang="en">
<p>
<b>BACKGROUND</b>
</p>
<p>The white-rot fungus Phlebia sp. MG-60 shows valuable properties such as high ethanol yield from several lignocellulosic materials, although white-rot fungi commonly degrade woody components to CO2 and H2O. In order to identify genes involved in ethanol production by Phlebia sp. MG-60, we compared genes differentially expressed by the ethanol producing fungus Phlebia sp. MG-60 and the model white-rot fungus Phanerochaete chrysosporium under ethanol fermenting and non-fermenting conditions using next-generation sequencing technologies.</p>
</div>
<div type="abstract" xml:lang="en">
<p>
<b>RESULTS</b>
</p>
<p>mRNAs from mycelia of Phlebia sp. MG-60 and P. chrysosporium under fermenting and non-fermenting conditions were sequenced using the MiSeq system. To detect differentially expressed genes, expression levels were measured in fragments per kilobase of exon per million mapped reads (FPKM). Differentially expressed genes were annotated using BLAST searches, Gene Ontology classifications, and KEGG pathway analysis. Functional analyses of differentially expressed genes revealed that genes involved in glucose uptake, glycolysis, and ethanol synthesis were widely upregulated in Phlebia sp. MG-60 under fermenting conditions.</p>
</div>
<div type="abstract" xml:lang="en">
<p>
<b>CONCLUSIONS</b>
</p>
<p>In this study, we provided novel transcriptomic information on Phlebia sp. MG-60, and these RNA-seq data were useful in targeting genes involved in ethanol production for future genetic engineering.</p>
</div>
</front>
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<Title>BMC genomics</Title>
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<ArticleTitle>Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq.</ArticleTitle>
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<AbstractText Label="BACKGROUND">The white-rot fungus Phlebia sp. MG-60 shows valuable properties such as high ethanol yield from several lignocellulosic materials, although white-rot fungi commonly degrade woody components to CO2 and H2O. In order to identify genes involved in ethanol production by Phlebia sp. MG-60, we compared genes differentially expressed by the ethanol producing fungus Phlebia sp. MG-60 and the model white-rot fungus Phanerochaete chrysosporium under ethanol fermenting and non-fermenting conditions using next-generation sequencing technologies.</AbstractText>
<AbstractText Label="RESULTS">mRNAs from mycelia of Phlebia sp. MG-60 and P. chrysosporium under fermenting and non-fermenting conditions were sequenced using the MiSeq system. To detect differentially expressed genes, expression levels were measured in fragments per kilobase of exon per million mapped reads (FPKM). Differentially expressed genes were annotated using BLAST searches, Gene Ontology classifications, and KEGG pathway analysis. Functional analyses of differentially expressed genes revealed that genes involved in glucose uptake, glycolysis, and ethanol synthesis were widely upregulated in Phlebia sp. MG-60 under fermenting conditions.</AbstractText>
<AbstractText Label="CONCLUSIONS">In this study, we provided novel transcriptomic information on Phlebia sp. MG-60, and these RNA-seq data were useful in targeting genes involved in ethanol production for future genetic engineering.</AbstractText>
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<Affiliation>Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka, 422-8529, Japan.</Affiliation>
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<AffiliationInfo>
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<name sortKey="Kawagishi, Hirokazu" sort="Kawagishi, Hirokazu" uniqKey="Kawagishi H" first="Hirokazu" last="Kawagishi">Hirokazu Kawagishi</name>
<name sortKey="Kawagishi, Hirokazu" sort="Kawagishi, Hirokazu" uniqKey="Kawagishi H" first="Hirokazu" last="Kawagishi">Hirokazu Kawagishi</name>
<name sortKey="Kawagishi, Hirokazu" sort="Kawagishi, Hirokazu" uniqKey="Kawagishi H" first="Hirokazu" last="Kawagishi">Hirokazu Kawagishi</name>
<name sortKey="Mori, Toshio" sort="Mori, Toshio" uniqKey="Mori T" first="Toshio" last="Mori">Toshio Mori</name>
<name sortKey="Soga, Ayumi" sort="Soga, Ayumi" uniqKey="Soga A" first="Ayumi" last="Soga">Ayumi Soga</name>
<name sortKey="Suzuki, Tomohiro" sort="Suzuki, Tomohiro" uniqKey="Suzuki T" first="Tomohiro" last="Suzuki">Tomohiro Suzuki</name>
<name sortKey="Takigami, Shoko" sort="Takigami, Shoko" uniqKey="Takigami S" first="Shoko" last="Takigami">Shoko Takigami</name>
</country>
</tree>
</affiliations>
</record>

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