Ph.D. (1980) John Innes Institute, Norwich, England
The rate-limiting step in the conversion of lignocellulosic biomass from crop plants such as Poplar or Switchgrass to biofuels, such as ethanol and biomaterials is the recalcitrance of these complex substrates. A critical component of the development of bio-based alternative fuels, such as ethanol and hydrogen, is the identification, characterization and manipulation of microorganisms and biocatalysts for biomass conversion. Organisms and enzymes that can function at high temperature, 80-100 °C are especially useful for this conversion because the biomass material is typically pretreated at high temperature before microbial or enzymatic conversion. Although the pursuit of biological routes to alternative fuels has been ongoing for several decades, recently available genomics-based approaches offer unprecedented access to novel enzymes and pathways for biomass conversions, making rational, genome-wide approaches for biocatalyst discovery and pathway identification that lead to enzyme production and metabolic engineering possible. An essential component of the application of modern technology to microbial and enzymatic biomass conversion is the ability to genetically manipulate extreme thermophilic microbes and the enzymes they produce. The focus of our research is to use functional and structural genomics-based methods, in conjunction with classical genetics and biochemical approaches, to identify novel biocatalytic (purified enzymes) and metabolic strategies (using whole cells) for bioenergy conversion. We have developed genetic tools for manipulation of Pyrococcus furiosus, a hyperthermophilic fermentative anaerobic archaean that produces hydrogen at or above temperatures of 100 °C and Caldicellulosiruptor species, thermophilic, anaerobic Gram-positive bacterium, unique in its ability to efficiently utilize untreated cellulosic biomass. This work fits into the larger intellectual context of using classical (high temperature microbial bioprocessing, large-scale protein purification) and modern (structural genomics, bioinformatics, transcriptional response analysis, gene replacement/mutational analysis) approaches to study extremophile biology and biotechnology as this relates to bioenergy conversion.
- Daehwan Chung, Minseok Cha and Janet Westpheling. (2014) Direct Conversion of Plant Biomass to Ethanol by Engineered Caldicellulosiruptor bescii. Proceedings of the National Academy of Sciences 2014 111 (24) 8931-8936; published ahead of print June 2, 2014, doi:10.1073/pnas.1402210111.
- Joseph Groom, Daehwan Chung, Jenna Young and Janet Westpheling. (2014) Heterologous Complementation of a pyrF Deletion in Caldicellulosiruptor hydrothermalis Generates a New Host for the Analysis of Biomass Deconstruction. Biotechnology for Biofuels, in press.
- Cha, C., D. Chung, J. Elkins, A. Guss and J. Westpheling. 2013. Metabolic Engineering of the Caldicellulosiruptor bescii Yields Increased Hydrogen Production from Lignocellulosic Biomass, Biotechnology for Biofuels, 6: 85. doi: 10.1186/1754-6834-6-85.
- Chung, D., M. Cha, J. Farkas and J. Wespheling. 2013. Overcoming Restriction as a Barrier to DNA Transformation in Caldicellulosiruptor species Results Efficient Marker Replacement. Biotechnology for Biofuels, 6: 82. doi: 10.1186/1754-6834-6-82
- Chung, D., C. Cha, J. Farkas and J. Westpheling. 2013. A stable replicating shuttle vector for Caldicellulosiruptor species: Use for Overcoming Restriction as a Barrier to Extending Genetic Methodologies to Members of This Genus. PLoS ONE. Link to Article.
- Chung, D., J. Farkas and J. Westpheling. 2013. Detection of a Novel Active Transposable Element in Caldicellulosiruptor hydrothermalis and a New Search for Elements in this Genus. Journal of Industrial Microbiology and Biotechnology, 40: 517-521.
- Farkas, J., D. Chung, M. Cha, J. Copeland, P. Grayeski and J. Westpheling. 2013. Improved Growth Media and Culture Techniques for Genetic Analysis and Assessment of Biomass Utilization by Caldicellulosiruptor bescii. Journal of Industrial Microbiology and Biotechnology, 40: 41-49.
- Chung, D., J. Farkas, J. Huddleston, E. Olivar and J. Westpheling. 2012. Methylation by a Unique beta-class N4-Cytosine Methyltransferase is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725. PLoS ONE. Link to Article.
- Farkas J., D.-H. Chung, M. DeBarry, M.W. Adams and J. Westpheling. 2011. Defining Components of the Chromosomal Origin of Replication of the Hyperthermophilic Archaeon, Pyrococcus furiosus, Needed for Construction of a Stable Replicating Shuttle Vector. Applied and Environmental Microbiology, in press.
- Chung, D.-H., J. Huddleston, J. Farkas and J. Westpheling. 2011. Identification and Characterization of CbeI, a Novel Thermostable Restriction Enzyme from Caldicellulosiruptor bescii DSM 6725 and a Member of a New Subfamily of HaeIII-like Enzymes. Journal of Industrial Microbiology and Biotechnology, in press.
- Lipscomb, G., K. Stirrett, G. Schut, F. Yang, F. Jenney, R. Scott, M.W. Adams and J. Westpheling. 2011. Natural competence in the hyperthermophilic archaeon Pyrococcus furiosus facilitates genetic manipulation: construction of multiple markerless deletions of genes encoding the two cytoplasmic hydrogenases. Applied and Environmental Microbiology 77: 2232-2238.
- Dam P., I. Kataeva, S.J. Yang, F. Zhou, Y. Yin, W. Chou, F. Poole, J. Westpheling, R. Hettich, R. Giannone, D. Lewis, R. Kelly, H. Gilbert, B. Henrissat, Y. Xu and M.W. Adams. Insights into Plant Biomass Conversion from the Genome of the Anaerobic Thermophilic Bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acid Research, in press.
- Yang S.J., I. Kataeva, J. Wiegel, Y. Yin, P. Dam, Y. Xu, J. Westpheling and M.W. Adams. 2010. Classification of 'Anaerocellum thermophilum' strain DSM 6725 as Caldicellulosiruptor bescii sp. nov. International Journal of Systems and Evolutionary Microbiology 60: 2011-5.
- Yang S.J., I. Kataeva, S.D. Hamilton-Brehm, N.L. Engle, T.J. Tschaplinski, C. Doeppke, M. Davis, J. Westpheling and M.W. Adams. 2009. Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe "Anaerocellum thermophilum" DSM 6725. Applied and Environmental Microbiology 75: 4762-9.
- Kataeva I.A., S.J. Yang, P. Dam, F.L. Poole 2nd, Y. Yin, F. Zhou, W.C. Chou, Y. Xu, L. Goodwin, D.R. Sims, J.C. Detter, L.J. Hauser, J. Westpheling and M.W. Adams. 2009. Genome sequence of the anaerobic, thermophilic, and cellulolytic bacterium "Anaerocellum thermophilum" DSM 6725. Journal of Bacteriology 191: 3760-1.
- Stirrett K., C. Denoya and J. Westpheling. 2009. Branched-chain amino acid catabolism provides precursors for the Type II polyketide antibiotic, actinorhodin, via pathways that are nutrient dependent. Journal of Industrial Microbiology and Biotechnology 36: 129-37.
- Blumer-Schuette S.E., I. Kataeva, J. Westpheling, M.W. Adams and R.M. Kelly. 2008. Extremely thermophilic microorganisms for biomass conversion: status and prospects.
Current Opinion in Biotechnology 19: 210-7.
- Hillerich, B. and J. Westpheling. 2008. A new TetR family transcriptional regulator required for morphogenesis in Streptomyces coelicolor. Journal of Bacteriology 190: 61-67.