Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass.
Identifieur interne : 002660 ( Main/Exploration ); précédent : 002659; suivant : 002661Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass.
Auteurs : Charlotte M. Wilson ; Miguel Rodriguez ; Courtney M. Johnson ; Stanton L. Martin ; Tzu Ming Chu ; Russ D. Wolfinger ; Loren J. Hauser ; Miriam L. Land ; Dawn M. Klingeman ; Mustafa H. Syed ; Arthur J. Ragauskas ; Timothy J. Tschaplinski ; Jonathan R. Mielenz ; Steven D. Brown [États-Unis]Source :
- Biotechnology for biofuels [ 1754-6834 ] ; 2013.
Abstract
BACKGROUND
The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. The aim of this study was to investigate C. thermocellum genes required to ferment biomass substrates and to conduct a robust comparison of DNA microarray and RNA sequencing (RNA-seq) analytical platforms.
RESULTS
C. thermocellum ATCC 27405 fermentations were conducted with a 5 g/L solid substrate loading of either pretreated switchgrass or Populus. Quantitative saccharification and inductively coupled plasma emission spectroscopy (ICP-ES) for elemental analysis revealed composition differences between biomass substrates, which may have influenced growth and transcriptomic profiles. High quality RNA was prepared for C. thermocellum grown on solid substrates and transcriptome profiles were obtained for two time points during active growth (12 hours and 37 hours postinoculation). A comparison of two transcriptomic analytical techniques, microarray and RNA-seq, was performed and the data analyzed for statistical significance. Large expression differences for cellulosomal genes were not observed. We updated gene predictions for the strain and a small novel gene, Cthe_3383, with a putative AgrD peptide quorum sensing function was among the most highly expressed genes. RNA-seq data also supported different small regulatory RNA predictions over others. The DNA microarray gave a greater number (2,351) of significant genes relative to RNA-seq (280 genes when normalized by the kernel density mean of M component (KDMM) method) in an analysis of variance (ANOVA) testing method with a 5% false discovery rate (FDR). When a 2-fold difference in expression threshold was applied, 73 genes were significantly differentially expressed in common between the two techniques. Sulfate and phosphate uptake/utilization genes, along with genes for a putative efflux pump system were some of the most differentially regulated transcripts when profiles for C. thermocellum grown on either pretreated switchgrass or Populus were compared.
CONCLUSIONS
Our results suggest that a high degree of agreement in differential gene expression measurements between transcriptomic platforms is possible, but choosing an appropriate normalization regime is essential.
DOI: 10.1186/1754-6834-6-179
PubMed: 24295562
PubMed Central: PMC3880215
Affiliations:
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Martin</name></author><author><name sortKey="Chu, Tzu Ming" sort="Chu, Tzu Ming" uniqKey="Chu T" first="Tzu Ming" last="Chu">Tzu Ming Chu</name></author><author><name sortKey="Wolfinger, Russ D" sort="Wolfinger, Russ D" uniqKey="Wolfinger R" first="Russ D" last="Wolfinger">Russ D. Wolfinger</name></author><author><name sortKey="Hauser, Loren J" sort="Hauser, Loren J" uniqKey="Hauser L" first="Loren J" last="Hauser">Loren J. Hauser</name></author><author><name sortKey="Land, Miriam L" sort="Land, Miriam L" uniqKey="Land M" first="Miriam L" last="Land">Miriam L. Land</name></author><author><name sortKey="Klingeman, Dawn M" sort="Klingeman, Dawn M" uniqKey="Klingeman D" first="Dawn M" last="Klingeman">Dawn M. Klingeman</name></author><author><name sortKey="Syed, Mustafa H" sort="Syed, Mustafa H" uniqKey="Syed M" first="Mustafa H" last="Syed">Mustafa H. 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Wilson</name></author><author><name sortKey="Rodriguez, Miguel" sort="Rodriguez, Miguel" uniqKey="Rodriguez M" first="Miguel" last="Rodriguez">Miguel Rodriguez</name></author><author><name sortKey="Johnson, Courtney M" sort="Johnson, Courtney M" uniqKey="Johnson C" first="Courtney M" last="Johnson">Courtney M. Johnson</name></author><author><name sortKey="Martin, Stanton L" sort="Martin, Stanton L" uniqKey="Martin S" first="Stanton L" last="Martin">Stanton L. Martin</name></author><author><name sortKey="Chu, Tzu Ming" sort="Chu, Tzu Ming" uniqKey="Chu T" first="Tzu Ming" last="Chu">Tzu Ming Chu</name></author><author><name sortKey="Wolfinger, Russ D" sort="Wolfinger, Russ D" uniqKey="Wolfinger R" first="Russ D" last="Wolfinger">Russ D. Wolfinger</name></author><author><name sortKey="Hauser, Loren J" sort="Hauser, Loren J" uniqKey="Hauser L" first="Loren J" last="Hauser">Loren J. Hauser</name></author><author><name sortKey="Land, Miriam L" sort="Land, Miriam L" uniqKey="Land M" first="Miriam L" last="Land">Miriam L. Land</name></author><author><name sortKey="Klingeman, Dawn M" sort="Klingeman, Dawn M" uniqKey="Klingeman D" first="Dawn M" last="Klingeman">Dawn M. Klingeman</name></author><author><name sortKey="Syed, Mustafa H" sort="Syed, Mustafa H" uniqKey="Syed M" first="Mustafa H" last="Syed">Mustafa H. Syed</name></author><author><name sortKey="Ragauskas, Arthur J" sort="Ragauskas, Arthur J" uniqKey="Ragauskas A" first="Arthur J" last="Ragauskas">Arthur J. Ragauskas</name></author><author><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name></author><author><name sortKey="Mielenz, Jonathan R" sort="Mielenz, Jonathan R" uniqKey="Mielenz J" first="Jonathan R" last="Mielenz">Jonathan R. Mielenz</name></author><author><name sortKey="Brown, Steven D" sort="Brown, Steven D" uniqKey="Brown S" first="Steven D" last="Brown">Steven D. Brown</name><affiliation wicri:level="2"><nlm:affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. brownsd@ornl.gov.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831</wicri:regionArea><placeName><region type="state">Tennessee</region></placeName></affiliation></author></analytic><series><title level="j">Biotechnology for biofuels</title><idno type="ISSN">1754-6834</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. The aim of this study was to investigate C. thermocellum genes required to ferment biomass substrates and to conduct a robust comparison of DNA microarray and RNA sequencing (RNA-seq) analytical platforms.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>C. thermocellum ATCC 27405 fermentations were conducted with a 5 g/L solid substrate loading of either pretreated switchgrass or Populus. Quantitative saccharification and inductively coupled plasma emission spectroscopy (ICP-ES) for elemental analysis revealed composition differences between biomass substrates, which may have influenced growth and transcriptomic profiles. High quality RNA was prepared for C. thermocellum grown on solid substrates and transcriptome profiles were obtained for two time points during active growth (12 hours and 37 hours postinoculation). A comparison of two transcriptomic analytical techniques, microarray and RNA-seq, was performed and the data analyzed for statistical significance. Large expression differences for cellulosomal genes were not observed. We updated gene predictions for the strain and a small novel gene, Cthe_3383, with a putative AgrD peptide quorum sensing function was among the most highly expressed genes. RNA-seq data also supported different small regulatory RNA predictions over others. The DNA microarray gave a greater number (2,351) of significant genes relative to RNA-seq (280 genes when normalized by the kernel density mean of M component (KDMM) method) in an analysis of variance (ANOVA) testing method with a 5% false discovery rate (FDR). When a 2-fold difference in expression threshold was applied, 73 genes were significantly differentially expressed in common between the two techniques. Sulfate and phosphate uptake/utilization genes, along with genes for a putative efflux pump system were some of the most differentially regulated transcripts when profiles for C. thermocellum grown on either pretreated switchgrass or Populus were compared.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>Our results suggest that a high degree of agreement in differential gene expression measurements between transcriptomic platforms is possible, but choosing an appropriate normalization regime is essential.</p></div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">24295562</PMID><DateCompleted><Year>2014</Year><Month>01</Month><Day>06</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Print">1754-6834</ISSN><JournalIssue CitedMedium="Print"><Volume>6</Volume><Issue>1</Issue><PubDate><Year>2013</Year><Month>Dec</Month><Day>02</Day></PubDate></JournalIssue><Title>Biotechnology for biofuels</Title><ISOAbbreviation>Biotechnol Biofuels</ISOAbbreviation></Journal><ArticleTitle>Global transcriptome analysis of Clostridium thermocellum ATCC 27405 during growth on dilute acid pretreated Populus and switchgrass.</ArticleTitle><Pagination><MedlinePgn>179</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1754-6834-6-179</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. The aim of this study was to investigate C. thermocellum genes required to ferment biomass substrates and to conduct a robust comparison of DNA microarray and RNA sequencing (RNA-seq) analytical platforms.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">C. thermocellum ATCC 27405 fermentations were conducted with a 5 g/L solid substrate loading of either pretreated switchgrass or Populus. Quantitative saccharification and inductively coupled plasma emission spectroscopy (ICP-ES) for elemental analysis revealed composition differences between biomass substrates, which may have influenced growth and transcriptomic profiles. High quality RNA was prepared for C. thermocellum grown on solid substrates and transcriptome profiles were obtained for two time points during active growth (12 hours and 37 hours postinoculation). A comparison of two transcriptomic analytical techniques, microarray and RNA-seq, was performed and the data analyzed for statistical significance. Large expression differences for cellulosomal genes were not observed. We updated gene predictions for the strain and a small novel gene, Cthe_3383, with a putative AgrD peptide quorum sensing function was among the most highly expressed genes. RNA-seq data also supported different small regulatory RNA predictions over others. The DNA microarray gave a greater number (2,351) of significant genes relative to RNA-seq (280 genes when normalized by the kernel density mean of M component (KDMM) method) in an analysis of variance (ANOVA) testing method with a 5% false discovery rate (FDR). When a 2-fold difference in expression threshold was applied, 73 genes were significantly differentially expressed in common between the two techniques. Sulfate and phosphate uptake/utilization genes, along with genes for a putative efflux pump system were some of the most differentially regulated transcripts when profiles for C. thermocellum grown on either pretreated switchgrass or Populus were compared.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">Our results suggest that a high degree of agreement in differential gene expression measurements between transcriptomic platforms is possible, but choosing an appropriate normalization regime is essential.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wilson</LastName><ForeName>Charlotte M</ForeName><Initials>CM</Initials></Author><Author ValidYN="Y"><LastName>Rodriguez</LastName><ForeName>Miguel</ForeName><Initials>M</Initials><Suffix>Jr</Suffix></Author><Author ValidYN="Y"><LastName>Johnson</LastName><ForeName>Courtney M</ForeName><Initials>CM</Initials></Author><Author ValidYN="Y"><LastName>Martin</LastName><ForeName>Stanton L</ForeName><Initials>SL</Initials></Author><Author ValidYN="Y"><LastName>Chu</LastName><ForeName>Tzu Ming</ForeName><Initials>TM</Initials></Author><Author ValidYN="Y"><LastName>Wolfinger</LastName><ForeName>Russ D</ForeName><Initials>RD</Initials></Author><Author ValidYN="Y"><LastName>Hauser</LastName><ForeName>Loren J</ForeName><Initials>LJ</Initials></Author><Author ValidYN="Y"><LastName>Land</LastName><ForeName>Miriam L</ForeName><Initials>ML</Initials></Author><Author ValidYN="Y"><LastName>Klingeman</LastName><ForeName>Dawn M</ForeName><Initials>DM</Initials></Author><Author ValidYN="Y"><LastName>Syed</LastName><ForeName>Mustafa H</ForeName><Initials>MH</Initials></Author><Author ValidYN="Y"><LastName>Ragauskas</LastName><ForeName>Arthur J</ForeName><Initials>AJ</Initials></Author><Author ValidYN="Y"><LastName>Tschaplinski</LastName><ForeName>Timothy J</ForeName><Initials>TJ</Initials></Author><Author ValidYN="Y"><LastName>Mielenz</LastName><ForeName>Jonathan R</ForeName><Initials>JR</Initials></Author><Author ValidYN="Y"><LastName>Brown</LastName><ForeName>Steven D</ForeName><Initials>SD</Initials><AffiliationInfo><Affiliation>Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. brownsd@ornl.gov.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>12</Month><Day>02</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Biotechnol Biofuels</MedlineTA><NlmUniqueID>101316935</NlmUniqueID><ISSNLinking>1754-6834</ISSNLinking></MedlineJournalInfo></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>08</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2013</Year><Month>11</Month><Day>19</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2013</Year><Month>12</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2013</Year><Month>12</Month><Day>4</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2013</Year><Month>12</Month><Day>4</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">24295562</ArticleId><ArticleId IdType="pii">1754-6834-6-179</ArticleId><ArticleId IdType="doi">10.1186/1754-6834-6-179</ArticleId><ArticleId IdType="pmc">PMC3880215</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Appl Environ Microbiol. 2011 Feb;77(4):1243-53</Citation><ArticleIdList><ArticleId IdType="pubmed">21169455</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2007 Oct;189(19):6787-95</Citation><ArticleIdList><ArticleId IdType="pubmed">17644599</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Biochem Biotechnol. 2003 Spring;105 -108:69-85</Citation><ArticleIdList><ArticleId IdType="pubmed">12721476</ArticleId></ArticleIdList></Reference><Reference><Citation>Biotechnol Biofuels. 2012 Nov 12;5(1):81</Citation><ArticleIdList><ArticleId IdType="pubmed">23146305</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2011 Aug;193(16):4268-9</Citation><ArticleIdList><ArticleId IdType="pubmed">21685289</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2013 Mar 09;14:91</Citation><ArticleIdList><ArticleId IdType="pubmed">23497356</ArticleId></ArticleIdList></Reference><Reference><Citation>Trends Biotechnol. 2006 Dec;24(12):549-56</Citation><ArticleIdList><ArticleId IdType="pubmed">17050014</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2009 Oct;27(10):893-4</Citation><ArticleIdList><ArticleId IdType="pubmed">19816441</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2009 Nov 22;10:552</Citation><ArticleIdList><ArticleId IdType="pubmed">19930606</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 1995 Nov;61(11):4012-5</Citation><ArticleIdList><ArticleId IdType="pubmed">16535164</ArticleId></ArticleIdList></Reference><Reference><Citation>Microbiol Mol Biol Rev. 2008 Jun;72(2):317-64, table of contents</Citation><ArticleIdList><ArticleId IdType="pubmed">18535149</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Genomics Hum Genet. 2008;9:387-402</Citation><ArticleIdList><ArticleId IdType="pubmed">18576944</ArticleId></ArticleIdList></Reference><Reference><Citation>J Biol Chem. 1968 Jun 10;243(11):2899-904</Citation><ArticleIdList><ArticleId IdType="pubmed">5653182</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Microbiol Biotechnol. 2004 Nov;66(1):10-26</Citation><ArticleIdList><ArticleId IdType="pubmed">15300416</ArticleId></ArticleIdList></Reference><Reference><Citation>Microbiology. 2006 Nov;152(Pt 11):3453-65</Citation><ArticleIdList><ArticleId IdType="pubmed">17074913</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2007 Feb 9;315(5813):804-7</Citation><ArticleIdList><ArticleId IdType="pubmed">17289988</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Microbiol. 2005 Dec;3(12):969-78</Citation><ArticleIdList><ArticleId IdType="pubmed">16261177</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Methods. 2008 Jul;5(7):621-8</Citation><ArticleIdList><ArticleId IdType="pubmed">18516045</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2006 Sep;24(9):1151-61</Citation><ArticleIdList><ArticleId IdType="pubmed">16964229</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2006 Jan 27;311(5760):506-8</Citation><ArticleIdList><ArticleId IdType="pubmed">16439656</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Microbiol. 2012 Aug 16;12:180</Citation><ArticleIdList><ArticleId IdType="pubmed">22897981</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2010;11(12):220</Citation><ArticleIdList><ArticleId IdType="pubmed">21176179</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioresour Technol. 2009 Mar;100(5):1809-14</Citation><ArticleIdList><ArticleId IdType="pubmed">19019672</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2006 Aug;188(15):5469-78</Citation><ArticleIdList><ArticleId IdType="pubmed">16855236</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2010 Aug;28(8):827-38</Citation><ArticleIdList><ArticleId IdType="pubmed">20676074</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2009 Jan;191(1):203-9</Citation><ArticleIdList><ArticleId IdType="pubmed">18952792</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2010 Oct 26;107(43):18646-51</Citation><ArticleIdList><ArticleId IdType="pubmed">20937888</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2012 Jun;78(12):4141-8</Citation><ArticleIdList><ArticleId IdType="pubmed">22492454</ArticleId></ArticleIdList></Reference><Reference><Citation>Comp Funct Genomics. 2001;2(3):143-54</Citation><ArticleIdList><ArticleId IdType="pubmed">18628908</ArticleId></ArticleIdList></Reference><Reference><Citation>Microbiol Mol Biol Rev. 2005 Mar;69(1):124-54</Citation><ArticleIdList><ArticleId IdType="pubmed">15755956</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2009 May;191(10):3203-11</Citation><ArticleIdList><ArticleId IdType="pubmed">19304856</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2012 Jan;194(1):195-6</Citation><ArticleIdList><ArticleId IdType="pubmed">22156394</ArticleId></ArticleIdList></Reference><Reference><Citation>Brief Bioinform. 2013 Nov;14(6):671-83</Citation><ArticleIdList><ArticleId IdType="pubmed">22988256</ArticleId></ArticleIdList></Reference><Reference><Citation>Genome Biol. 2007;8(1):102</Citation><ArticleIdList><ArticleId IdType="pubmed">17274839</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2007 Mar 15;23(6):673-9</Citation><ArticleIdList><ArticleId IdType="pubmed">17237039</ArticleId></ArticleIdList></Reference><Reference><Citation>Biosci Biotechnol Biochem. 1997 Mar;61(3):427-31</Citation><ArticleIdList><ArticleId IdType="pubmed">9095547</ArticleId></ArticleIdList></Reference><Reference><Citation>MBio. 2011 Jan 25;2(1):e00340-10</Citation><ArticleIdList><ArticleId IdType="pubmed">21264064</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3976-81</Citation><ArticleIdList><ArticleId IdType="pubmed">19234113</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioresour Technol. 2013 Feb;130:125-35</Citation><ArticleIdList><ArticleId IdType="pubmed">23306120</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2010 Mar 08;11:119</Citation><ArticleIdList><ArticleId IdType="pubmed">20211023</ArticleId></ArticleIdList></Reference><Reference><Citation>J Bacteriol. 2000 Aug;182(16):4478-90</Citation><ArticleIdList><ArticleId IdType="pubmed">10913081</ArticleId></ArticleIdList></Reference><Reference><Citation>Curr Opin Biotechnol. 2005 Oct;16(5):577-83</Citation><ArticleIdList><ArticleId IdType="pubmed">16154338</ArticleId></ArticleIdList></Reference><Reference><Citation>Front Microbiol. 2013 Feb 05;4:7</Citation><ArticleIdList><ArticleId IdType="pubmed">23386844</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Rev Microbiol. 2009 Oct;7(10):715-23</Citation><ArticleIdList><ArticleId IdType="pubmed">19756010</ArticleId></ArticleIdList></Reference><Reference><Citation>Biol Direct. 2009 Apr 16;4:14</Citation><ArticleIdList><ArticleId IdType="pubmed">19371405</ArticleId></ArticleIdList></Reference><Reference><Citation>Appl Environ Microbiol. 2012 Feb;78(4):1113-22</Citation><ArticleIdList><ArticleId IdType="pubmed">22179241</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2009;4(4):e5271</Citation><ArticleIdList><ArticleId IdType="pubmed">19384422</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Genet Genomics. 2002 Dec;268(4):518-24</Citation><ArticleIdList><ArticleId IdType="pubmed">12471449</ArticleId></ArticleIdList></Reference><Reference><Citation>Carbohydr Res. 2010 Oct 13;345(15):2183-93</Citation><ArticleIdList><ArticleId IdType="pubmed">20797699</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Biol Evol. 1999 Apr;16(4):512-24</Citation><ArticleIdList><ArticleId IdType="pubmed">10331277</ArticleId></ArticleIdList></Reference><Reference><Citation>Nature. 2010 Apr 1;464(7289):768-72</Citation><ArticleIdList><ArticleId IdType="pubmed">20220758</ArticleId></ArticleIdList></Reference><Reference><Citation>Biotechnol Biofuels. 2013 Jan 28;6(1):15</Citation><ArticleIdList><ArticleId IdType="pubmed">23356640</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Genomics. 2012 Jul 23;13:336</Citation><ArticleIdList><ArticleId IdType="pubmed">22823947</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Mar 1;28(5):750-1</Citation><ArticleIdList><ArticleId IdType="pubmed">22238270</ArticleId></ArticleIdList></Reference><Reference><Citation>Bioinformatics. 2012 Jun 1;28(11):1542-3</Citation><ArticleIdList><ArticleId IdType="pubmed">22492314</ArticleId></ArticleIdList></Reference><Reference><Citation>Nat Biotechnol. 2008 Oct;26(10):1135-45</Citation><ArticleIdList><ArticleId IdType="pubmed">18846087</ArticleId></ArticleIdList></Reference><Reference><Citation>BMC Bioinformatics. 2010 Feb 18;11:94</Citation><ArticleIdList><ArticleId IdType="pubmed">20167110</ArticleId></ArticleIdList></Reference><Reference><Citation>PLoS One. 2010 May 14;5(5):e10642</Citation><ArticleIdList><ArticleId IdType="pubmed">20498845</ArticleId></ArticleIdList></Reference><Reference><Citation>Science. 2007 Feb 9;315(5813):801-4</Citation><ArticleIdList><ArticleId IdType="pubmed">17289987</ArticleId></ArticleIdList></Reference><Reference><Citation>Proc Natl Acad Sci U S A. 2005 May 17;102(20):7321-5</Citation><ArticleIdList><ArticleId IdType="pubmed">15883376</ArticleId></ArticleIdList></Reference><Reference><Citation>Mol Syst Biol. 2013;9:641</Citation><ArticleIdList><ArticleId IdType="pubmed">23340847</ArticleId></ArticleIdList></Reference><Reference><Citation>Microbiol Mol Biol Rev. 2002 Sep;66(3):506-77, table of contents</Citation><ArticleIdList><ArticleId IdType="pubmed">12209002</ArticleId></ArticleIdList></Reference><Reference><Citation>Annu Rev Biochem. 2010;79:655-81</Citation><ArticleIdList><ArticleId IdType="pubmed">20373916</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Tennessee</li></region></list><tree><noCountry><name sortKey="Chu, Tzu Ming" sort="Chu, Tzu Ming" uniqKey="Chu T" first="Tzu Ming" last="Chu">Tzu Ming Chu</name><name sortKey="Hauser, Loren J" sort="Hauser, Loren J" uniqKey="Hauser L" first="Loren J" last="Hauser">Loren J. Hauser</name><name sortKey="Johnson, Courtney M" sort="Johnson, Courtney M" uniqKey="Johnson C" first="Courtney M" last="Johnson">Courtney M. Johnson</name><name sortKey="Klingeman, Dawn M" sort="Klingeman, Dawn M" uniqKey="Klingeman D" first="Dawn M" last="Klingeman">Dawn M. Klingeman</name><name sortKey="Land, Miriam L" sort="Land, Miriam L" uniqKey="Land M" first="Miriam L" last="Land">Miriam L. Land</name><name sortKey="Martin, Stanton L" sort="Martin, Stanton L" uniqKey="Martin S" first="Stanton L" last="Martin">Stanton L. Martin</name><name sortKey="Mielenz, Jonathan R" sort="Mielenz, Jonathan R" uniqKey="Mielenz J" first="Jonathan R" last="Mielenz">Jonathan R. Mielenz</name><name sortKey="Ragauskas, Arthur J" sort="Ragauskas, Arthur J" uniqKey="Ragauskas A" first="Arthur J" last="Ragauskas">Arthur J. Ragauskas</name><name sortKey="Rodriguez, Miguel" sort="Rodriguez, Miguel" uniqKey="Rodriguez M" first="Miguel" last="Rodriguez">Miguel Rodriguez</name><name sortKey="Syed, Mustafa H" sort="Syed, Mustafa H" uniqKey="Syed M" first="Mustafa H" last="Syed">Mustafa H. Syed</name><name sortKey="Tschaplinski, Timothy J" sort="Tschaplinski, Timothy J" uniqKey="Tschaplinski T" first="Timothy J" last="Tschaplinski">Timothy J. Tschaplinski</name><name sortKey="Wilson, Charlotte M" sort="Wilson, Charlotte M" uniqKey="Wilson C" first="Charlotte M" last="Wilson">Charlotte M. Wilson</name><name sortKey="Wolfinger, Russ D" sort="Wolfinger, Russ D" uniqKey="Wolfinger R" first="Russ D" last="Wolfinger">Russ D. Wolfinger</name></noCountry><country name="États-Unis"><region name="Tennessee"><name sortKey="Brown, Steven D" sort="Brown, Steven D" uniqKey="Brown S" first="Steven D" last="Brown">Steven D. 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