Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725
Abstract
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-richmore »
- Authors:
-
- 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
- Publication Date:
- Research Org.:
- 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 Org.:
- USDOE Office of Science (SC), Basic Energy Sciences (BES)
- OSTI Identifier:
- 1625475
- Grant/Contract Number:
- AC52-06NA25396; AC02-05CH11231; AC05-00OR22725; AC52-07NA27344
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 39; Journal Issue: 8; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Biochemistry & Molecular Biology
Citation Formats
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, and Adams, Michael W. W. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. United States: N. p., 2011.
Web. doi:10.1093/nar/gkq1281.
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. Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. United States. https://doi.org/10.1093/nar/gkq1281
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, and Adams, Michael W. W. Mon .
"Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725". United States. https://doi.org/10.1093/nar/gkq1281. https://www.osti.gov/servlets/purl/1625475.
@article{osti_1625475,
title = {Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725},
author = {Dam, Phuongan and Kataeva, Irina and Yang, Sung-Jae and Zhou, Fengfeng and Yin, Yanbin and Chou, Wenchi and Poole, Farris L. and Westpheling, Janet and Hettich, Robert and Giannone, Richard and Lewis, Derrick L. and Kelly, Robert and Gilbert, Harry J. and Henrissat, Bernard and Xu, Ying and Adams, Michael W. W.},
abstractNote = {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.},
doi = {10.1093/nar/gkq1281},
journal = {Nucleic Acids Research},
number = 8,
volume = 39,
place = {United States},
year = {Mon Jan 10 00:00:00 EST 2011},
month = {Mon Jan 10 00:00:00 EST 2011}
}
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