Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq.
Identifieur interne : 002313 ( Main/Exploration ); précédent : 002312; suivant : 002314Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq.
Auteurs : Hui Wei [États-Unis] ; Yan Fu [États-Unis] ; Lauren Magnusson [États-Unis] ; John O. Baker [États-Unis] ; Pin-Ching Maness [États-Unis] ; Qi Xu [États-Unis] ; Shihui Yang [États-Unis] ; Andrew Bowersox [États-Unis] ; Igor Bogorad [États-Unis] ; Wei Wang [États-Unis] ; Melvin P. Tucker [États-Unis] ; Michael E. Himmel [États-Unis] ; Shi-You Ding [États-Unis]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2014.
Abstract
The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism.
DOI: 10.3389/fmicb.2014.00142
PubMed: 24782837
PubMed Central: PMC3990059
Affiliations:
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Baker</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Maness, Pin Ching" sort="Maness, Pin Ching" uniqKey="Maness P" first="Pin-Ching" last="Maness">Pin-Ching Maness</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Xu, Qi" sort="Xu, Qi" uniqKey="Xu Q" first="Qi" last="Xu">Qi Xu</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Yang, Shihui" sort="Yang, Shihui" uniqKey="Yang S" first="Shihui" last="Yang">Shihui Yang</name><affiliation wicri:level="2"><nlm:affiliation>National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Bioenergy Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Bowersox, Andrew" sort="Bowersox, Andrew" uniqKey="Bowersox A" first="Andrew" last="Bowersox">Andrew Bowersox</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Bogorad, Igor" sort="Bogorad, Igor" uniqKey="Bogorad I" first="Igor" last="Bogorad">Igor Bogorad</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Wang, Wei" sort="Wang, Wei" uniqKey="Wang W" first="Wei" last="Wang">Wei Wang</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Tucker, Melvin P" sort="Tucker, Melvin P" uniqKey="Tucker M" first="Melvin P" last="Tucker">Melvin P. Tucker</name><affiliation wicri:level="2"><nlm:affiliation>National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Bioenergy Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Himmel, Michael E" sort="Himmel, Michael E" uniqKey="Himmel M" first="Michael E" last="Himmel">Michael E. Himmel</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author><author><name sortKey="Ding, Shi You" sort="Ding, Shi You" uniqKey="Ding S" first="Shi-You" last="Ding">Shi-You Ding</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Center, National Renewable Energy Laboratory Golden, CO</wicri:regionArea><placeName><region type="state">Colorado</region></placeName></affiliation></author></analytic><series><title level="j">Frontiers in microbiology</title><idno type="ISSN">1664-302X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">24782837</PMID><DateCompleted><Year>2014</Year><Month>04</Month><Day>30</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>30</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>5</Volume><PubDate><Year>2014</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>Comparison of transcriptional profiles of Clostridium thermocellum grown on cellobiose and pretreated yellow poplar using RNA-Seq.</ArticleTitle><Pagination><MedlinePgn>142</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2014.00142</ELocationID><Abstract><AbstractText>The anaerobic, thermophilic bacterium, Clostridium thermocellum, secretes multi-protein enzyme complexes, termed cellulosomes, which synergistically interact with the microbial cell surface and efficiently disassemble plant cell wall biomass. C. thermocellum has also been considered a potential consolidated bioprocessing (CBP) organism due to its ability to produce the biofuel products, hydrogen, and ethanol. We found that C. thermocellum fermentation of pretreated yellow poplar (PYP) produced 30 and 39% of ethanol and hydrogen product concentrations, respectively, compared to fermentation of cellobiose. RNA-seq was used to analyze the transcriptional profiles of these cells. The PYP-grown cells taken for analysis at the late stationary phase showed 1211 genes up-regulated and 314 down-regulated by more than two-fold compared to the cellobiose-grown cells. These affected genes cover a broad spectrum of specific functional categories. The transcriptional analysis was further validated by sub-proteomics data taken from the literature; as well as by quantitative reverse transcription-PCR (qRT-PCR) analyses of selected genes. Specifically, 47 cellulosomal protein-encoding genes, genes for 4 pairs of SigI-RsgI for polysaccharide sensing, 7 cellodextrin ABC transporter genes, and a set of NAD(P)H hydogenase and alcohol dehydrogenase genes were up-regulated for cells growing on PYP compared to cellobiose. These genes could be potential candidates for future studies aimed at gaining insight into the regulatory mechanism of this organism as well as for improvement of C. thermocellum in its role as a CBP organism. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wei</LastName><ForeName>Hui</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fu</LastName><ForeName>Yan</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Center for Plant Genomics, Iowa State University Ames, IA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Magnusson</LastName><ForeName>Lauren</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Baker</LastName><ForeName>John O</ForeName><Initials>JO</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Maness</LastName><ForeName>Pin-Ching</ForeName><Initials>PC</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Xu</LastName><ForeName>Qi</ForeName><Initials>Q</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Shihui</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bowersox</LastName><ForeName>Andrew</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA ; National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bogorad</LastName><ForeName>Igor</ForeName><Initials>I</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Wei</ForeName><Initials>W</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tucker</LastName><ForeName>Melvin P</ForeName><Initials>MP</Initials><AffiliationInfo><Affiliation>National Bioenergy Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Himmel</LastName><ForeName>Michael E</ForeName><Initials>ME</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ding</LastName><ForeName>Shi-You</ForeName><Initials>SY</Initials><AffiliationInfo><Affiliation>Biosciences Center, National Renewable Energy Laboratory Golden, CO, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>04</Month><Day>11</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>Front Microbiol</MedlineTA><NlmUniqueID>101548977</NlmUniqueID><ISSNLinking>1664-302X</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Clostridium thermocellum</Keyword><Keyword MajorTopicYN="N">RNA-Seq</Keyword><Keyword MajorTopicYN="N">cellobiose</Keyword><Keyword MajorTopicYN="N">cellulosome</Keyword><Keyword MajorTopicYN="N">ethanol</Keyword><Keyword MajorTopicYN="N">hydrogen</Keyword><Keyword MajorTopicYN="N">pretreated yellow poplar (PYP)</Keyword><Keyword MajorTopicYN="N">transcriptomics</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>11</Month><Day>21</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>03</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>5</Month><Day>1</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>5</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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