Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production.
ABSTRACT Modern methods to develop microbe-based biomass conversion processes require a system-level understanding of the microbes involved. Clostridium species have long been recognized as ideal candidates for processes involving biomass conversion and production of various biofuels and other industrial products. To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacteraceae. Species were chosen based on representation in the experimental literature as model organisms, ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial systems biology.
Published Ahead of Print 1 October 2010.
2010, 192(24):6494. DOI: 10.1128/JB.01064-10. J. Bacteriol.
Rubin and Jizhong Zhou
Himmel, Safiyh Taghavi, Daniël van der Lelie, Edward M.
Huhnke, Jonathan R. Mielenz, Shi-You Ding, Michael E.
Dong, Defeng Xing, Nanqi Ren, Aijie Wang, Raymond L.
Stevenson, Michael J. McInerney, Yunfeng Yang, Hailiang
Fields, Adam P. Arkin, Christopher W. Schadt, Bradley S.
Ralph S. Tanner, Lee R. Lynd, Juergen Wiegel, Matthew W.
Nostrand, Bernard Henrissat, Qiang He, Paul A. Lawson,
Van Kyrpides, Natalia Mikhailova, Zhili He, Liyou Wu, Joy D.
Han, Sam Pitluck, Miriam L. Land, Loren J. Hauser, Nikos
Elizabeth Saunders, Thomas Brettin, John C. Detter, Cliff S.
Copeland, Alla Lapidus, Tijana Glavina del Rio, Hope Tice,
Gengxin Zhang, Lynne Goodwin, Susan Lucas, Alex
Christopher L. Hemme, Housna Mouttaki, Yong-Jin Lee,
and Biofuel Production
Genomes Related to Biomass Conversion
Sequencing of Multiple Clostridial
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JOURNAL OF BACTERIOLOGY, Dec. 2010, p. 6494–6496
Copyright © 2010, American Society for Microbiology. All Rights Reserved.
Vol. 192, No. 24
Sequencing of Multiple Clostridial Genomes Related to Biomass
Conversion and Biofuel Production?
Christopher L. Hemme,1,2Housna Mouttaki,1,2,3Yong-Jin Lee,1,2Gengxin Zhang,14Lynne Goodwin,5
Susan Lucas,4Alex Copeland,4Alla Lapidus,4Tijana Glavina del Rio,4Hope Tice,4
Elizabeth Saunders,5Thomas Brettin,5,6John C. Detter,5Cliff S. Han,5Sam Pitluck,4
Miriam L. Land,6Loren J. Hauser,6Nikos Kyrpides,4Natalia Mikhailova,4Zhili He,1,2
Liyou Wu,1,2Joy D. Van Nostrand,1,2Bernard Henrissat,7Qiang He,8
Paul A. Lawson,1Ralph S. Tanner,1Lee R. Lynd,9Juergen Wiegel,10
Matthew W. Fields,11Adam P. Arkin,12Christopher W. Schadt,13
Bradley S. Stevenson,1Michael J. McInerney,1Yunfeng Yang,13
Hailiang Dong,14Defeng Xing,15Nanqi Ren,15Aijie Wang,15
Raymond L. Huhnke,16Jonathan R. Mielenz,17Shi-You Ding,18
Michael E. Himmel,18Safiyh Taghavi,19Danie ¨l van der Lelie,19
Edward M. Rubin,4and Jizhong Zhou1,2*
Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma1; Institute for Environmental Genomics,
University of Oklahoma, Norman, Oklahoma2; German Research Center for Environment and Health, Neuherberg,
Germany3; Joint Genome Institute Production Genomics Facility, Walnut Creek, California4; Joint Genome Institute,
Los Alamos National Laboratory, Los Alamos, New Mexico5; Computational Biology and Bioinformatics Group,
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee6; CNRS, Universite ´s Aix-Marseille,
13628 Aix-en-Provence, France7; Department of Civil and Environmental Engineering, University of
Tennessee—Knoxville, Knoxville, Tennessee8; Department of Biological Sciences, Dartmouth College,
Hanover, New Hampshire9; Department of Microbiology, University of Georgia, Athens, Georgia10;
Department of Microbiology, Montana State University, Bozeman, Montana11; University of
California—Berkeley, Berkeley, California12; Molecular Microbial Ecology Group, Biosciences Division,
Oak Ridge National Laboratory, Oak Ridge, Tennessee13; Miami University, Oxford, Ohio14;
State Key Lab of Urban Water Resource and Environment, Harbin 160090, People’s Republic of
China15; Oklahoma State University, Stillwater, Oklahoma16; Bioconversion and Science
Technology Group, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge,
Tennessee17; National Renewable Energy Laboratory, Golden, Colorado18; and
Brookhaven National Laboratory, Upton, New York19
Received 7 September 2010/Accepted 20 September 2010
Modern methods to develop microbe-based biomass conversion processes require a system-level under-
standing of the microbes involved. Clostridium species have long been recognized as ideal candidates for
processes involving biomass conversion and production of various biofuels and other industrial products.
To expand the knowledge base for clostridial species relevant to current biofuel production efforts, we have
sequenced the genomes of 20 species spanning multiple genera. The majority of species sequenced fall
within the class III cellulosome-encoding Clostridium and the class V saccharolytic Thermoanaerobacter-
aceae. Species were chosen based on representation in the experimental literature as model organisms,
ability to degrade cellulosic biomass either by free enzymes or by cellulosomes, ability to rapidly ferment
hexose and pentose sugars to ethanol, and ability to ferment synthesis gas to ethanol. The sequenced
strains significantly increase the number of noncommensal/nonpathogenic clostridial species and provide
a key foundation for future studies of biomass conversion, cellulosome composition, and clostridial
Clostridial genomes were sequenced using a combination of
Sanger (3? coverage, 8 kb, pMCL200), 454 (20? coverage),
and Solexa methods. Standardsequencingprotocolsarelistedon
the Joint Genome Institute (JGI) website (http://www.jgi.doe.gov
/sequencing/protocols/prots_production.html). Sanger and 454
reads were assembled as previously described (5). Automatic
annotations were conducted for all draft genomes using the
JGI-Oak Ridge National Laboratory (ORNL) annotation
pipeline, and all draft genomes and annotations were loaded
into the JGI Integrated Microbial Resource (IMG) for analysis
(11). Due to difficulties in assembling and finishing low-GC,
high-repeat genomes, many of the genomes targeted for
sequencing could not be finished and are presented as a high-
* Corresponding author. Mailing address: Stephenson Research and
Technology Center, University of Oklahoma, Norman, OK 73019.
Phone: (405) 325-6073. Fax: (405) 325-7552. E-mail: email@example.com.
?Published ahead of print on 1 October 2010.
on March 9, 2012 by UNIV OF OKLA LIBRARIES
quality permanent draft. Sequences available at the time of this
analysis are listed in Table 1 and are categorized based on the
latest Bergey’s taxonomy (9).
The biomass-converting clostridium sequencing project was initiated
by the Clostridium Sequencing Consortium (see author list) through
the Joint Genome Institute. The genome sequencing work was per-
formed under the auspices of the U.S. Department of Energy’s Office
of Science, Biological and Environmental Research Program, and by
the University of California, Lawrence Berkeley National Laboratory,
under contract no. DE-AC02-05CH11231, Lawrence Livermore Na-
tional Laboratory, under contract no. DE-AC52-07NA27344, Los
Alamos National Laboratory,
06NA25396, and Oak Ridge National Laboratory, under contract no.
DE-AC05-00OR22725. This work was supported by NSF-EPSC.R
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TABLE 1. Clostridium genome sequencing projects related to biomass conversion and biofuels production
Organism name Reference(s)
% GC CDSb
Clostridium sensu stricto
Clostridium cellulovorans 743B
Clostridium carboxidivorans P7
Clostridium ragsdalei P11
Acetivibrio cellulolyticus CD2
Clostridium cellulolyticum H10
Clostridium papyrosolvens DSM 2782
Clostridium thermocellum JW20 DSM 4150
Clostridium thermocellum LQRI DSM 2360
Thermoanaerobacter wiegelii Rt8.B1
Thermoanaerobacter brockii sp. finnii Ako-1
Thermoanaerobacter sp. CCSD1
Thermoanaerobacter sp. X513
Thermoanaerobacter sp. X561
Thermoanaerobacter pseudethanolicus 39E
Thermoanaerobacter sp. X514
Thermoanaerobacter italicus Ab9
Thermoanaerobacter mathranii subsp. mathranii A3
Thermoanaerobacter ethanolicus JW200
Thermoanaerobacter siderophilus L-64
Thermoanaerobacterium xylanolyticum LX11
2.2 37634.02423 ACXY00000000
2.71 34.12,161 CP002171
7D 2.5 91 34.82,509 Pending
Clostridium saccharolyticum DSM 2544
Ethanoligenens harbinense YUAN-3
aSequencing status: F, finished; PD, permanent high-quality draft; D, draft (ongoing); P, sequence pending.
bNo. of annotated protein coding sequences.
cGenBank accession number.
VOL. 192, 2010GENOME ANNOUNCEMENTS6495
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