Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725

Dam, Phuongan; Kataeva, Irina; Yang, Sung-Jae; Zhou, Fengfeng; Yin, Yanbin; Chou, Wenchi; Poole, Farris L.; Westpheling, Janet; Hettich, Robert; Giannone, Richard; Lewis, Derrick L.; Kelly, Robert; Gilbert, Harry J.; Henrissat, Bernard; Xu, Ying; Adams, Michael W.  W.

doi:10.1093/nar/gkq1281

Title: Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725

Journal Article · Mon Jan 10 00:00:00 EST 2011 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkq1281· OSTI ID:1625475

Dam, Phuongan ^[1]; Kataeva, Irina ^[2]; Yang, Sung-Jae ^[2]; Zhou, Fengfeng ^[1]; Yin, Yanbin ^[1]; Chou, Wenchi ^[3]; Poole, Farris L. ^[2]; Westpheling, Janet ^[4]; Hettich, Robert ^[5]; Giannone, Richard ^[5]; Lewis, Derrick L. ^[6]; Kelly, Robert ^[6]; Gilbert, Harry J. ^[7]; Henrissat, Bernard ^[8]; Xu, Ying ^[1]; Adams, Michael W. W. ^[2]

Univ. of Georgia, Athens, GA (United States). Inst. of Bioinformatics; Univ. of Georgia, Athens, GA (United States). Dept. of Biochemistry and Molecular Biology; Univ. of Georgia, Athens, GA (United States). BioEnergy Science Center
Univ. of Georgia, Athens, GA (United States). Dept. of Biochemistry and Molecular Biology; Univ. of Georgia, Athens, GA (United States). BioEnergy Science Center
Univ. of Georgia, Athens, GA (United States). Inst. of Bioinformatics; Univ. of Georgia, Athens, GA (United States). BioEnergy Science Center
Univ. of Georgia, Athens, GA (United States). BioEnergy Science Center; Univ. of Georgia, Athens, GA (United States). Dept. of Genetics
Univ. of Georgia, Athens, GA (United States). BioEnergy Science Center
Univ. of Georgia, Athens, GA (United States). BioEnergy Science Center; North Carolina State Univ., Raleigh, NC (United States). Dept. of Chemical and Biomolecular Engineering
Univ. of Georgia, Athens, GA (United States). Dept. of Biochemistry and Molecular Biology; Univ. of Georgia, Athens, GA (United States). Complex Carbohydrate Research Center
Aix-Marseille Univ., Marseille (France); Centre National de la Recherche Scientifique (CNRS), Marseille (France). Architecture et Fonction des Macromolecules Biologiques

Caldicellulosiruptor bescii DSM 6725 utilizes various polysaccharides and grows efficiently on untreated high-lignin grasses and hardwood at an optimum temperature of 80C. It is a promising anaerobic bacterium for studying high-temperature biomass conversion. Its genome contains 2666 proteincoding sequences organized into 1209 operons. Expression of 2196 genes (83%) was confirmed experimentally. At least 322 genes appear to have been obtained by lateral gene transfer (LGT). Putative functions were assigned to 364 conserved/hypothetical protein (C/HP) genes. The genome contains 171 and 88 genes related to carbohydrate transport and utilization, respectively. Growth on cellulose led to the up-regulation of 32 carbohydrate-active (CAZy), 61 sugar transport, 25 transcription factor and 234 C/HP genes. Some C/HPs were overproduced on cellulose or xylan, suggesting their involvement in polysaccharide conversion. A unique feature of the genome is enrichment with genes encoding multi-modular, multi-functional CAZy proteins organized into one large cluster, the products of which are proposed to act synergistically on different components of plant cell walls and to aid the ability of C. bescii to convert plant biomass. The high duplication of CAZy domains coupled with the ability to acquire foreign genes by LGT may have allowed the bacterium to rapidly adapt to changing plant biomass-rich environments.

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Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: AC52-06NA25396; AC02-05CH11231; AC05-00OR22725; AC52-07NA27344

OSTI ID:: 1625475

Journal Information:: Nucleic Acids Research, Vol. 39, Issue 8; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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Improved growth media and culture techniques for genetic analysis and assessment of biomass utilization by Caldicellulosiruptor bescii Farkas, Joel; Chung, Daehwan; Cha, Minseok Journal of Industrial Microbiology & Biotechnology, Vol. 40, Issue 1, p. 41-49 https://doi.org/10.1007/s10295-012-1202-1	journal	November 2012
Construction of a Stable Replicating Shuttle Vector for Caldicellulosiruptor Species: Use for Extending Genetic Methodologies to Other Members of This Genus Chung, Daehwan; Cha, Minseok; Farkas, Joel PLoS ONE, Vol. 8, Issue 5, Article No. e62881 https://doi.org/10.1371/journal.pone.0062881	journal	May 2013
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Expression of the Acidothermus cellulolyticus E1 endoglucanase in Caldicellulosiruptor bescii enhances its ability to deconstruct crystalline cellulose Chung, Daehwan; Young, Jenna; Cha, Minseok Biotechnology for Biofuels, Vol. 8, Issue 1 https://doi.org/10.1186/s13068-015-0296-x	journal	August 2015
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Insights into the roles of non-catalytic residues in the active site of a GH10 xylanase with activity on cellulose Chu, Yindi; Tu, Tao; Penttinen, Leena Journal of Biological Chemistry, Vol. 292, Issue 47 https://doi.org/10.1074/jbc.m117.807768	journal	October 2017
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SGNH hydrolase-type esterase domain containing Cbes-AcXE2: a novel and thermostable acetyl xylan esterase from Caldicellulosiruptor bescii Soni, Surabhi; Sathe, Sneha S.; Odaneth, Annamma A. Extremophiles, Vol. 21, Issue 4 https://doi.org/10.1007/s00792-017-0934-2	journal	April 2017
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Supplementing with Non-Glycoside Hydrolase Proteins Enhances Enzymatic Deconstruction of Plant Biomass Su, Xiaoyun; Zhang, Jing; Mackie, Roderick I. PLoS ONE, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pone.0043828	journal	August 2012
Methylation by a Unique α-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725 Chung, Daehwan; Farkas, Joel; Huddleston, Jennifer R. PLoS ONE, Vol. 7, Issue 8 https://doi.org/10.1371/journal.pone.0043844	journal	August 2012
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