title: Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels.
abstract: Clostridium phytofermentans was isolated from forest soil and is distinguished by its capacity to directly ferment plant cell wall polysaccharides into ethanol as the primary product, suggesting that it possesses unusual catabolic pathways. The objective of the present study was to understand the molecular mechanisms of biomass conversion to ethanol in a single organism, Clostridium phytofermentans, by analyzing its complete genome and transcriptome during growth on plant carbohydrates. The saccharolytic versatility of C. phytofermentans is reflected in a diversity of genes encoding ATP-binding cassette sugar transporters and glycoside hydrolases, many of which may have been acquired through horizontal gene transfer. These genes are frequently organized as operons that may be controlled individually by the many transcriptional regulators identified in the genome. Preferential ethanol production may be due to high levels of expression of multiple ethanol dehydrogenases and additional pathways maximizing ethanol yield. The genome also encodes three different proteinaceous bacterial microcompartments with the capacity to compartmentalize pathways that divert fermentation intermediates to various products. These characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Elsa
authors.initials: E
authors.lastname: Petit
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Maddalena V
authors.initials: MV
authors.lastname: Coppi
authors.affiliation: Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America; Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: James C
authors.initials: JC
authors.lastname: Hayes
authors.affiliation: Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA)-Genoscope, Unité Mixte de Recherche (UMR)-8030, National Center for Scientific Research (CNRS), Evry, France.
authors.forename: Andrew C
authors.initials: AC
authors.lastname: Tolonen
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Thomas
authors.initials: T
authors.lastname: Warnick
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America; Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: William G
authors.initials: WG
authors.lastname: Latouf
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Danielle
authors.initials: D
authors.lastname: Amisano
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America; Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Amy
authors.initials: A
authors.lastname: Biddle
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America; Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Supratim
authors.initials: S
authors.lastname: Mukherjee
authors.affiliation: Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America.
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.affiliation: Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America.
authors.forename: Athanassios
authors.initials: A
authors.lastname: Lykidis
authors.affiliation: Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America.
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.affiliation: Oak Ridge National Laboratory (ORNL), Life Sciences Division, Oak Ridge, Tennessee, United States of America.
authors.forename: Loren
authors.initials: L
authors.lastname: Hauser
authors.affiliation: Department of Energy (DOE)- Joint Genome Institute, Genome Biology Program, Production Genomics Facility, Walnut Creek, California, United States of America.
authors.forename: Nikos
authors.initials: N
authors.lastname: Kyrpides
authors.affiliation: Architecture et Fonction des Macromolécules Biologiques, Unité mixte de recherche (UMR)-6098, National Center for Scientific Research (CNRS), and Universités d'Aix-Marseille I and II, Marseille, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Henrissat
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Joanne
authors.initials: J
authors.lastname: Lau
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Danny J
authors.initials: DJ
authors.lastname: Schnell
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America.
authors.forename: George M
authors.initials: GM
authors.lastname: Church
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America; Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America; Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Susan B
authors.initials: SB
authors.lastname: Leschine
authors.affiliation: Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, United States of America; Graduate Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts, United States of America; Institute for Cellular Engineering, University of Massachusetts, Amherst, Massachusetts, United States of America; Graduate Program in Organismal and Evolutionary Biology, University of Massachusetts, Amherst, Massachusetts, United States of America; Department of Biology, University of Massachusetts, Amherst, Massachusetts, United States of America.
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Blanchard
mesh_terms: D000426:Alcohol Dehydrogenase / Q000235:genetics / Q000378:metabolism; D056804:Biofuels; D001692:Biological Transport; D050260:Carbohydrate Metabolism / Q000235:genetics*; D003013:Clostridium / Q000235:genetics* / Q000378:metabolism*; D004798:Enzymes / Q000235:genetics / Q000378:metabolism*; D000431:Ethanol / Q000378:metabolism; D005285:Fermentation; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D010802:Phylogeny; D010944:Plants / Q000378:metabolism*; D012336:RNA, Ribosomal, 16S; D059467:Transcriptome
chemical_list: D056804:Biofuels; D004798:Enzymes; D012336:RNA, Ribosomal, 16S; D000431:Ethanol; D000426:Alcohol Dehydrogenase