title: Pentose sugars inhibit metabolism and increase expression of an AgrD-type cyclic pentapeptide in Clostridium thermocellum.
abstract: Clostridium thermocellum could potentially be used as a microbial biocatalyst to produce renewable fuels directly from lignocellulosic biomass due to its ability to rapidly solubilize plant cell walls. While the organism readily ferments sugars derived from cellulose, pentose sugars from xylan are not metabolized. Here, we show that non-fermentable pentoses inhibit growth and end-product formation during fermentation of cellulose-derived sugars. Metabolomic experiments confirmed that xylose is transported intracellularly and reduced to the dead-end metabolite xylitol. Comparative RNA-seq analysis of xylose-inhibited cultures revealed several up-regulated genes potentially involved in pentose transport and metabolism, which were targeted for disruption. Deletion of the ATP-dependent transporter, CbpD partially alleviated xylose inhibition. A putative xylitol dehydrogenase, encoded by Clo1313_0076, was also deleted resulting in decreased total xylitol production and yield by 41% and 46%, respectively. Finally, xylose-induced inhibition corresponds with the up-regulation and biogenesis of a cyclical AgrD-type, pentapeptide. Medium supplementation with the mature cyclical pentapeptide also inhibits bacterial growth. Together, these findings provide new foundational insights needed for engineering improved pentose utilizing strains of C. thermocellum and reveal the first functional Agr-type cyclic peptide to be produced by a thermophilic member of the Firmicutes.
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Tobin J
authors.initials: TJ
authors.lastname: Verbeke
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Giannone
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Dawn M
authors.initials: DM
authors.lastname: Klingeman
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Nancy L
authors.initials: NL
authors.lastname: Engle
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Rydzak
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Adam M
authors.initials: AM
authors.lastname: Guss
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Timothy J
authors.initials: TJ
authors.lastname: Tschaplinski
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Steven D
authors.initials: SD
authors.lastname: Brown
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.|Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
authors.forename: James G
authors.initials: JG
authors.lastname: Elkins
mesh_terms: D002482:Cellulose / Q000378:metabolism; D048013:Acetivibrio thermocellus / Q000187:drug effects* / Q000254:growth & development / Q000378:metabolism; D005285:Fermentation; D015870:Gene Expression; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000187:drug effects*; D006131:Growth Inhibitors / Q000378:metabolism*; D053858:Metabolic Networks and Pathways / Q000187:drug effects*; D055432:Metabolomics; D009842:Oligopeptides / Q000096:biosynthesis*; D010429:Pentoses / Q000378:metabolism*; D010456:Peptides, Cyclic / Q000096:biosynthesis*
chemical_list: D006131:Growth Inhibitors; D009842:Oligopeptides; D010429:Pentoses; D010456:Peptides, Cyclic; D002482:Cellulose