Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels

Petit, Elsa; Coppi, Maddalena V.; Hayes, James C.; Tolonen, Andrew C.; Warnick, Thomas; Latouf, William G.; Amisano, Danielle; Biddle, Amy; Mukherjee, Supratim; Ivanova, Natalia; Lykidis, Athanassios; Land, Miriam; Hauser, Loren; Kyrpides, Nikos; Henrissat, Bernard; Lau, Joanne; Schnell, Danny J.; Church, George M.; Leschine, Susan B.; Blanchard, Jeffrey L.

doi:10.1371/journal.pone.0118285

Title: Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels

Journal Article · Tue Jun 02 00:00:00 EDT 2015 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0118285· OSTI ID:1265527

Petit, Elsa ^[1]; Coppi, Maddalena V. ^[1]; Hayes, James C. ^[2]; Tolonen, Andrew C. ^[3]; Warnick, Thomas ^[1]; Latouf, William G. ^[4]; Amisano, Danielle ^[1]; Biddle, Amy ^[4]; Mukherjee, Supratim ^[4]; Ivanova, Natalia ^[5]; Lykidis, Athanassios ^[5]; Land, Miriam ^[6]; Hauser, Loren ^[6]; Kyrpides, Nikos ^[5]; Henrissat, Bernard ^[7]; Lau, Joanne ^[1]; Schnell, Danny J. ^[8]; Church, George M. ^[9]; Leschine, Susan B. ^[10]; Blanchard, Jeffrey L. ^[11]

Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology
Univ. of Massachusetts, Amherst, MA (United States). Graduate Program in Molecular and Cellular Biology; Univ. of Massachusetts, Amherst, MA (United States). Inst. for Cellular Engineering
National Center for Scientific Research (CNRS), Evry (France). Alternative Energies and Atomic Energy Commission (CEA)-Genoscope. Mixed Research Unit (UMR)-8030
Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology; Univ. of Massachusetts, Amherst, MA (United States). Inst. for Cellular Engineering
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States). Genome Biology Program. Production Genomics Facility
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Life Sciences Division
Aix-Marseille Univ. I and II, Marseille (France). National Center for Scientific Research (CNRS). Architecture and Function of Biological Macromolecules. Mixed Research Unit (UMR)-6098
Univ. of Massachusetts, Amherst, MA (United States). Dept. of Biochemistry and Molecular Biology
Harvard Medical School, Boston, MA (United States). Dept. of Genetics
Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology; Univ. of Massachusetts, Amherst, MA (United States). Inst. for Cellular Engineering; Univ. of Massachusetts, Amherst, MA (United States). Dept. of Veterinary and Animal Sciences
Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology; Univ. of Massachusetts, Amherst, MA (United States). Graduate Program in Molecular and Cellular Biology; Univ. of Massachusetts, Amherst, MA (United States). Inst. for Cellular Engineering; Univ. of Massachusetts, Amherst, MA (United States). Graduate Program in Organismal and Evolutionary Biology; Univ. of Massachusetts, Amherst, MA (United States). Dept. of Biology

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. In this paper, 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. Finally, these characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.

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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Oak Ridge Y-12 Plant (Y-12), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Contributing Organization:: Univ. of Massachusetts, Amherst, MA (United States)

Grant/Contract Number:: AC02-05CH11231; FG02-02ER15330; FG02-02ER1533; 0722802

OSTI ID:: 1265527

Alternate ID(s):: OSTI ID: 1260614

Journal Information:: PLoS ONE, Vol. 10, Issue 6; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

Citation Metrics:

Cited by: 16 works

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09 BIOMASS FUELS
59 BASIC BIOLOGICAL SCIENCES
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