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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 our 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. Lastly, these characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.

Authors:
 [1];  [1];  [2];  [3];  [1];  [4];  [1];  [5];  [6];  [7];  [7];  [8];  [8];  [7];  [9];  [1];  [10];  [11];  [12];  [13]
  1. Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology
  2. 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
  3. National Center for Scientific Research (CNRS), Evry (France). Atomic Energy and Energy Alternatives Commission
  4. Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology; Univ. of Massachusetts, Amherst, MA (United States). Inst.for Cellular Engineering
  5. Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology; Univ. of Massachusetts, Amherst, MA (United States). Inst. for Cellular Engineering
  6. Univ. of Massachusetts, Amherst, MA (United States). Dept. of Microbiology; Univ. of Massachusetts, Amherst, MA (United States). Inst. for Cellular Engineering
  7. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  8. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Life Sciences Division
  9. Aix-Marseille Univ., and CNRS, Marseille (France)
  10. Univ. of Massachusetts, Amherst, MA (United States). Dept. of of Biochemistry and Molecular Biology
  11. Harvard Medical School, Boston, MA (United States)
  12. 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
  13. 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
Publication Date:
Research Org.:
Oak Ridge Y-12 Plant (Y-12), Oak Ridge, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
Contributing Org.:
Univ. of Massachusetts, Amherst, MA (United States)
OSTI Identifier:
1260614
Alternate Identifier(s):
OSTI ID: 1265527
Grant/Contract Number:  
FG02-02ER1533; 0722802; AC02-05CH11231; FG02-02ER15330
Resource Type:
Accepted Manuscript
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 10; Journal Issue: 6; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; clostridium; ethanol; genomic databases; cellulose; gene regulation; database searching; fermentation; microarrays

Citation Formats

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., and Blanchard, Jeffrey L. Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. United States: N. p., 2015. Web. doi:10.1371/journal.pone.0118285.
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. Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. United States. doi:10.1371/journal.pone.0118285.
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., and Blanchard, Jeffrey L. Tue . "Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels". United States. doi:10.1371/journal.pone.0118285. https://www.osti.gov/servlets/purl/1260614.
@article{osti_1260614,
title = {Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels},
author = {Petit, Elsa and Coppi, Maddalena V. and Hayes, James C. and Tolonen, Andrew C. and Warnick, Thomas and Latouf, William G. and Amisano, Danielle and Biddle, Amy and Mukherjee, Supratim and Ivanova, Natalia and Lykidis, Athanassios and Land, Miriam and Hauser, Loren and Kyrpides, Nikos and Henrissat, Bernard and Lau, Joanne and Schnell, Danny J. and Church, George M. and Leschine, Susan B. and Blanchard, Jeffrey L.},
abstractNote = {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 our 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. Lastly, these characteristics make C. phytofermentans an attractive resource for improving the efficiency and speed of biomass conversion to biofuels.},
doi = {10.1371/journal.pone.0118285},
journal = {PLoS ONE},
number = 6,
volume = 10,
place = {United States},
year = {2015},
month = {6}
}

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