title: Clostridium thermocellum transcriptomic profiles after exposure to furfural or heat stress.
abstract: BACKGROUND
  The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. A previous C. thermocellum ethanol stress study showed that the largest transcriptomic response was in genes and proteins related to nitrogen uptake and metabolism.
  
  
  RESULTS
  In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate general and specific physiological and regulatory stress responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and fermentation product determinations and compared to a published dataset from an ethanol stress study. Urea uptake genes were induced following furfural stress, but not to the same extent as ethanol stress and transcription from these genes was largely unaffected by heat stress. The largest transcriptomic response to furfural stress was genes for sulfate transporter subunits and enzymes in the sulfate assimilatory pathway, although these genes were also affected late in the heat and ethanol stress responses. Lactate production was higher in furfural treated culture, although the lactate dehydrogenase gene was not differentially expressed under this condition. Other redox related genes such as a copy of the rex gene, a bifunctional acetaldehyde-CoA/alcohol dehydrogenase and adjacent genes did show lower expression after furfural stress compared to the control, heat and ethanol fermentation profiles. Heat stress induced expression from chaperone related genes and overlap was observed with the responses to the other stresses. This study suggests the involvement of C. thermocellum genes with functions in oxidative stress protection, electron transfer, detoxification, sulfur and nitrogen acquisition, and DNA repair mechanisms in its stress responses and the use of different regulatory networks to coordinate and control adaptation.
  
  
  CONCLUSIONS
  This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism's physiology and regulation.
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA.|BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Charlotte M
authors.initials: CM
authors.lastname: Wilson
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA.|BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.|Present address: National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA.
authors.forename: Shihui
authors.initials: S
authors.lastname: Yang
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA.|BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Miguel
authors.initials: M
authors.lastname: Rodriguez
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.|Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA.
authors.forename: Qin
authors.initials: Q
authors.lastname: Ma
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA.|BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Courtney M
authors.initials: CM
authors.lastname: Johnson
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA.|BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Lezlee
authors.initials: L
authors.lastname: Dice
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.|Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, Computational Systems Biology Laboratory, University of Georgia, Athens, GA 30602, USA.|College of Computer Science and Technology, Jilin University, Changchun, Jilin, China.
authors.forename: Ying
authors.initials: Y
authors.lastname: Xu
authors.affiliation: Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, 37831 TN, USA.|BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
references.citation: Appl Biochem Biotechnol. 2000 Spring;84-86:617-32
references.pmid: 10849822
references.citation: Methods Enzymol. 2012;510:317-30
references.pmid: 22608734
references.citation: Appl Environ Microbiol. 2011 Dec;77(23):8288-94
references.pmid: 21965408
references.citation: J Bacteriol. 2011 Jun;193(11):2906-7
references.pmid: 21460082
references.citation: Appl Microbiol Biotechnol. 2012 Feb;93(4):1777-84
references.pmid: 22218768
references.citation: Bioinformatics. 2013 Sep 15;29(18):2261-8
references.pmid: 23846744
references.citation: Biotechnol Lett. 2012 Sep;34(9):1643-9
references.pmid: 22618238
references.citation: Nucleic Acids Res. 2011 Apr;39(7):e42
references.pmid: 21149261
references.citation: Appl Environ Microbiol. 2011 Feb;77(4):1243-53
references.pmid: 21169455
references.citation: Nucleic Acids Res. 2002 Apr 1;30(7):1575-84
references.pmid: 11917018
references.citation: Bioresour Technol. 2012 Jan;103(1):293-9
references.pmid: 22055095
references.citation: Curr Opin Biotechnol. 2005 Oct;16(5):577-83
references.pmid: 16154338
references.citation: Ann N Y Acad Sci. 2008 Mar;1125:298-307
references.pmid: 18378600
references.citation: J Bacteriol. 1983 Nov;156(2):818-27
references.pmid: 6630152
references.citation: Proc Natl Acad Sci U S A. 2011 Aug 16;108(33):13752-7
references.pmid: 21825121
references.citation: PLoS One. 2009;4(4):e5271
references.pmid: 19384422
references.citation: BMC Genomics. 2009 Jan 20;10:34
references.pmid: 19154596
references.citation: Proteome Sci. 2009 Sep 21;7:36
references.pmid: 19772559
references.citation: Annu Rev Microbiol. 2004;58:521-54
references.pmid: 15487947
references.citation: BMC Microbiol. 2012 Sep 21;12:214
references.pmid: 22994686
references.citation: Microbiol Mol Biol Rev. 2002 Sep;66(3):506-77, table of contents
references.pmid: 12209002
references.citation: BMC Syst Biol. 2010 Mar 22;4:31
references.pmid: 20307315
references.citation: BMC Microbiol. 2011 Jun 14;11:134
references.pmid: 21672225
references.citation: Nucleic Acids Res. 2012 Oct;40(19):9887-96
references.pmid: 22879377
references.citation: Science. 1997 Oct 24;278(5338):631-7
references.pmid: 9381173
references.citation: J Bacteriol. 2012 Jun;194(12):3290-1
references.pmid: 22628515
references.citation: Chem Rec. 2008;8(6):364-77
references.pmid: 19107866
references.citation: Appl Microbiol Biotechnol. 2011 Apr;90(2):625-34
references.pmid: 21318364
references.citation: BMC Genomics. 2012 Jul 23;13:336
references.pmid: 22823947
references.citation: Appl Environ Microbiol. 1984 May;47(5):1126-9
references.pmid: 16346540
references.citation: Proc Natl Acad Sci U S A. 2007 Mar 6;104(10):3747-52
references.pmid: 17360424
references.citation: Biotechnol Biofuels. 2010 Jan 15;3:2
references.pmid: 20150993
references.citation: Appl Environ Microbiol. 2009 Oct;75(19):6132-41
references.pmid: 19684179
references.citation: Biotechnol Biofuels. 2013 May 04;6(1):66
references.pmid: 23642190
references.citation: Appl Microbiol Biotechnol. 2006 Jul;71(3):339-49
references.pmid: 16222531
references.citation: Cell Stress Chaperones. 2003 Fall;8(3):207-17
references.pmid: 14984053
references.citation: Appl Microbiol Biotechnol. 2011 Oct;92(1):199-209
references.pmid: 21837436
references.citation: J Bacteriol. 2009 Jan;191(1):203-9
references.pmid: 18952792
references.citation: J Bacteriol. 2005 Jan;187(1):99-106
references.pmid: 15601693
references.citation: Appl Environ Microbiol. 1989 Dec;55(12):3131-9
references.pmid: 16348075
references.citation: Proc Natl Acad Sci U S A. 2010 Oct 12;107(41):17727-32
references.pmid: 20837514
references.citation: Bioresour Technol. 2010 Aug;101(16):6291-6
references.pmid: 20363622
references.citation: Appl Biochem Biotechnol. 2002 Spring;98-100:327-40
references.pmid: 12018260
references.citation: Science. 1995 Oct 6;270(5233):59-67
references.pmid: 7569952
references.citation: Appl Environ Microbiol. 2007 Apr;73(8):2522-31
references.pmid: 17308175
references.citation: FEMS Microbiol Lett. 2010 Jul 1;308(1):84-93
references.pmid: 20487018
references.citation: Anal Chem. 2003 Jan 15;75(2):219-27
references.pmid: 12553755
references.citation: Appl Environ Microbiol. 2010 Oct;76(19):6591-9
references.pmid: 20693441
references.citation: J Bacteriol. 2010 Dec;192(24):6494-6
references.pmid: 20889752
references.citation: Nucleic Acids Res. 2009 Jul;37(Web Server issue):W202-8
references.pmid: 19458158
references.citation: J Biol Chem. 2012 Dec 14;287(51):42962-71
references.pmid: 23091052