title: Genome-scale resources for Thermoanaerobacterium saccharolyticum.
abstract: BACKGROUND
  Thermoanaerobacterium saccharolyticum is a hemicellulose-degrading thermophilic anaerobe that was previously engineered to produce ethanol at high yield. A major project was undertaken to develop this organism into an industrial biocatalyst, but the lack of genome information and resources were recognized early on as a key limitation.
  
  
  RESULTS
  Here we present a set of genome-scale resources to enable the systems level investigation and development of this potentially important industrial organism. Resources include a complete genome sequence for strain JW/SL-YS485, a genome-scale reconstruction of metabolism, tiled microarray data showing transcription units, mRNA expression data from 71 different growth conditions or timepoints and GC/MS-based metabolite analysis data from 42 different conditions or timepoints. Growth conditions include hemicellulose hydrolysate, the inhibitors HMF, furfural, diamide, and ethanol, as well as high levels of cellulose, xylose, cellobiose or maltodextrin. The genome consists of a 2.7 Mbp chromosome and a 110 Kbp megaplasmid. An active prophage was also detected, and the expression levels of CRISPR genes were observed to increase in association with those of the phage. Hemicellulose hydrolysate elicited a response of carbohydrate transport and catabolism genes, as well as poorly characterized genes suggesting a redox challenge. In some conditions, a time series of combined transcription and metabolite measurements were made to allow careful study of microbial physiology under process conditions. As a demonstration of the potential utility of the metabolic reconstruction, the OptKnock algorithm was used to predict a set of gene knockouts that maximize growth-coupled ethanol production. The predictions validated intuitive strain designs and matched previous experimental results.
  
  
  CONCLUSIONS
  These data will be a useful asset for efforts to develop T. saccharolyticum for efficient industrial production of biofuels. The resources presented herein may also be useful on a comparative basis for development of other lignocellulose degrading microbes, such as Clostridium thermocellum.
authors.affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. Devin.H.Currie.GR@dartmouth.edu.
authors.forename: Devin H
authors.initials: DH
authors.lastname: Currie
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. raman.babu@gmail.com.|Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN, 46268, USA. raman.babu@gmail.com.
authors.forename: Babu
authors.initials: B
authors.lastname: Raman
authors.affiliation: Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, Virginia, 23284, USA. chris.gowen@utoronto.ca.|Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada. chris.gowen@utoronto.ca.
authors.forename: Christopher M
authors.initials: CM
authors.lastname: Gowen
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. tschaplinstj@ornl.gov.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Tschaplinski
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. landml@ornl.gov.
authors.forename: Miriam L
authors.initials: ML
authors.lastname: Land
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. brownsd@ornl.gov.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
authors.affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. scovalla@mascoma.com.
authors.forename: Sean F
authors.initials: SF
authors.lastname: Covalla
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. klingemandm@ornl.gov.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Klingeman
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. yangz@ornl.gov.
authors.forename: Zamin K
authors.initials: ZK
authors.lastname: Yang
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. englenl@ornl.gov.
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Engle
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. Courtney.Johnson10@fsis.usda.gov.
authors.forename: Courtney M
authors.initials: CM
authors.lastname: Johnson
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. rodriguezmjr@ornl.gov.
authors.forename: Miguel
authors.initials: M
authors.lastname: Rodriguez
authors.affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. joeshawiv@gmail.com.|Novogy Inc, Cambridge, MA, 02138, USA. joeshawiv@gmail.com.
authors.forename: A Joe
authors.initials: AJ
authors.lastname: Shaw
authors.affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. wkenealy@mascoma.com.
authors.forename: William R
authors.initials: WR
authors.lastname: Kenealy
authors.affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. lee.r.lynd@dartmouth.edu.|Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA. lee.r.lynd@dartmouth.edu.
authors.forename: Lee R
authors.initials: LR
authors.lastname: Lynd
authors.affiliation: Chemical and Life Science Engineering, Virginia Commonwealth University, P.O. Box 843028, Richmond, Virginia, 23284, USA. ssfong@vcu.edu.
authors.forename: Stephen S
authors.initials: SS
authors.lastname: Fong
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. mielenzjr@ornl.gov.
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Mielenz
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, TN, 37831, USA. davisonbh@ornl.gov.
authors.forename: Brian H
authors.initials: BH
authors.lastname: Davison
authors.affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. dhogsett@opxbio.com.
authors.forename: David A
authors.initials: DA
authors.lastname: Hogsett
authors.affiliation: Mascoma Corporation, 67 Etna Rd, 03766, Lebanon, NH, USA. chrisherringfish@gmail.com.|Thayer School of Engineering, Dartmouth College, 14 Engineering Drive, Hanover, NH, 03755, USA. chrisherringfish@gmail.com.
authors.forename: Christopher D
authors.initials: CD
authors.lastname: Herring
mesh_terms: D001483:Base Sequence; D056804:Biofuels / Q000382:microbiology; D005662:Furaldehyde / Q000031:analogs & derivatives / Q000494:pharmacology; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics / Q000379:methods*; D007221:Industry; D008954:Models, Biological; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D011134:Polysaccharides / Q000494:pharmacology; D046950:Thermoanaerobacterium / Q000187:drug effects / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D056804:Biofuels; D011134:Polysaccharides; C008046:5-hydroxymethylfurfural; C007916:hemicellulose; D005662:Furaldehyde