title: Integrated omics analyses reveal the details of metabolic adaptation ofClostridium thermocellumto lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass.
abstract: BACKGROUND
  Clostridium thermocellumis capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression ofC. thermocellumgrown on switchgrass to assess the metabolic and protein changes that occur during the conversion of plant biomass to ethanol.
  
  
  RESULTS
  The most striking feature of the metabolome was the observed accumulation of long-chain, branched fatty acids over time, implying an adaptive restructuring ofC. thermocellum'scellular membrane as the culture progresses. This is undoubtedly a response to the gradual accumulation of lignocellulose-derived inhibitory compounds as the organism deconstructs the switchgrass to access the embedded cellulose. Corroborating the metabolomics data, proteomic analysis revealed a corresponding time-dependent increase in various enzymes, including those involved in the interconversion of branched amino acids valine, leucine, and isoleucine to iso- and anteiso-fatty acid precursors. Additionally, the metabolic accumulation of hemicellulose-derived sugars and sugar alcohols concomitant with increased abundance of enzymes involved in C5 sugar metabolism/pentose phosphate pathway indicates thatC. thermocellumshifts glycolytic intermediates to alternate pathways to modulate overall carbon flux in response to C5 sugar metabolites that increase during lignocellulose deconstruction.
  
  
  CONCLUSIONS
  Integrated omic platforms provided complementary systems biological information that highlightC. thermocellum's specific response to cytotoxic inhibitors released during the deconstruction and utilization of switchgrass. These additional viewpoints allowed us to fully realize the level to which the organism adapts to an increasingly challenging culture environment-information that will prove critical toC. thermocellum's industrial efficacy.
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.|Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA.
authors.forename: Suresh
authors.initials: S
authors.lastname: Poudel
authors.affiliation: Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Giannone
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.
authors.forename: Miguel
authors.initials: M
authors.lastname: Rodriguez
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.|Dow AgroSciences, 9330 Zionsville Road, Indianapolis, IN 46268 USA.
authors.forename: Babu
authors.initials: B
authors.lastname: Raman
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.
authors.forename: Madhavi Z
authors.initials: MZ
authors.lastname: Martin
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Engle
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.
authors.forename: Jonathan R
authors.initials: JR
authors.lastname: Mielenz
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.|Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA.
authors.forename: Intawat
authors.initials: I
authors.lastname: Nookaew
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.|Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Tschaplinski
authors.affiliation: Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.|Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205 USA.
authors.forename: David
authors.initials: D
authors.lastname: Ussery
authors.affiliation: Chemical Sciences Division, Oak Ridge National Lab, Oak Ridge, TN 37831 USA.|Department of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996 USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
keywords: Biofuel; Cellulosome; Clostridium thermocellum; Ethanol; Lignocellulosic; Mass spectrometry; Metabolomics; Proteomics; Switchgrass; Transcriptomics