Metabolic engineering is the directed manipulation of chemistry inside cells. The Keasling Lab has developed tools to aid metabolic engineering of microorganisms and then used these tools to produce a variety of products, including pharmaceuticals, nutraceuticals, commodity and specialty chemicals, and biofuels.
Isoprenoids are produced by every organism on the planet, and isoprenoids are widely used as pharmaceuticals, flavors and colorants in foods, fragrances in perfumes and colognes, and biofuels. The Keasling Lab has a long history in engineering isoprenoid metabolism in a variety of organisms, including Escherichia coli and Saccharomyces cerevisiae, for production of valuable isoprenoids. We have engineered cells with heterologous biosynthesis pathways to increase production of desired final products, discovered novel terpene synthases and terpene modifying enzymes from plants and other organisms, and engineered terpene enzymes to produce unnatural products. One of the signature projects of the Keasling Lab is the engineering of E. coli and S. cerevisiae for production of the antimalarial drug artemisinin. Example publications include:
- J. Kirby, K. L. Dietzel, G. Wichmann, R. Chan, E. Antipov, N. Moss, E. E. Baidoo, P. Jackson, S. P. Gaucher, S. Gottlieb, J. LaBarge, T. Mahatdejkul, K. M. Hawkins, S. Muley, J. D. Newman, P. Liu, J. D. Keasling, and L. Zhao. 2017. Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae.” Metab. Eng.
- R. Phelan, O. N. Sekurova, J. D. Keasling, and S. B. Zotchev. 2015. Engineering terpene biosynthesis in Streptomyces for production of the advanced biofuel precursor bisabolene. ACS Syn. Biol.
- J. Kirby, M. Nishimoto, R. W. Chow, E. E. Baidoo, G. Wang. J. Martin, W. Schackwitz, R. Chan, J. L. Fortman, and J. D. Keasling. 2015. Enhancing terpene yield from sugars via novel routes to 1-deoxy-d-xylulose 5-phosphate. Appl. Environ. Microbiol.
- J. Alonso-Gutierrez, R. Chan, T. S. Batth, P. D. Adams, J. D. Keasling, C. J. Petzold, and T. S. Lee. 2013. Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production. Met. Eng.
- H. H. Chou and J. D. Keasling. 2012.Five-carbon alcohols are produced from isopentenyl diphosphate using a synthetic pathway. Appl. Environ. Microbiol.
- P. P. Peralta-Yahya, M. Ouellet, R. Chan, A. Mukhopadhyay, J. D. Keasling, and T. S. Lee. 2011. Identification and microbial production of a terpene-based advanced biofuel. Nat. Comm.
- D-K. Ro, E. M. Paradise, M. Ouellet, K. J. Fisher, K. L. Newman, J. M. Ndungu, K. A. Ho, R. A. Eachus, R. S. Ham, J. Kirby, M. C. Y. Chang, S. T. Withers, Y. Shiba, R. Sarpong, and J. D. Keasling. 2006.Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature
- V. J. J. Martin, D. J. Pitera, S. T. Withers, J. D. Newman, and J. D. Keasling. 2003.Engineering the mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol.
Fatty acid metabolism
Fatty acids are used by most organisms as the membrane around cells and as energy and carbon storage. Fatty acid-derived molecules have been widely used as flavorings in foods, as surfactants in soaps and shampoos, and as biofuels. To produce these important molecules, the Keasling Lab has engineered fatty acid metabolism in E. coli and S. cerevisiae. This work has entailed redirecting native pathways into desired products as well as imported heterologous enzymes and pathways into these hosts to make a variety of fatty acid products that the cell would not naturally synthesize. Example publications include:
- L. d’Espaux, A. Ghosh, W. Runguphan, M. Wehrs, F. Xu, O. Konzock, I. Dev, M. Nhan, J. Gin, A. Reider Apel, C. J. Petzold, S. Singh, B. Simmons, A. Mukhopadhyay, H. García-Martín, and J. D. Keasling. 2017. Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks. Met. Eng.
- R. W. Haushalter, R. M. Phelan, K. M. Hoh, C. Su, G. Wang, E. E. Baidoo, and J. D. Keasling. 2017.Production of odd-carbon dicarboxylic acids in Escherichia coli using an engineered biotin-fatty acid biosynthetic pathway. J. Am. Chem. Soc.
- Ghosh, D. Ando, J. Gin, W. Runguphan, C. Denby, G. Wang, E. E. K. Baidoo, C. Shymansky, J. D. Keasling and H. García Martín. 2016. 13-C metabolic flux analysis for systematic metabolic engineering of S. cerevisiae for overproduction of fatty acids.Front. Bioeng. Biotechnol.
- R. W. Haushalter, D. Groff, S. Deutsch, L. The, T. A. Chavkin, S. F. Brunner, L. Katz, and J. D. Keasling. 2015.Development of an orthogonal fatty acid biosynthesis system in E. coli for oleochemical production. Metab. Eng.
- R. W. Haushalter, W. Kim, T. A. Chavkin, L. The, M. E. Garber, M. Nhan, C. J. Petzold, L. Katz, and J. D. Keasling. 2014. Production of anteiso-branched fatty acids in Escherichia coli; next generation biofuels with improved cold-flow properties. Met. Eng.
- W. Runguphan and J. D. Keasling. 2014. Metabolic engineering of Saccharomyces cerevisiae for production of fatty acid-derived biofuels and chemicals. Met. Eng.
- F. Zhang, J. M. Carothers, and J. D. Keasling. 2012. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol.
- E. J. Steen, Y. Kang, G. Bokinsky, Z. Hu, A. Schirmer, A. McClure, S. B. del Cardayre, and J. D. Keasling. 2010.Microbial production of fatty acid-derived fuels and chemicals from plant biomass. Nature
Polyketides are related to fatty acids but have much more structural and chemical diversity. Many of the most widely used antibiotics are polyketides. Type I polyketides are synthesized by large, multi-modular enzymes that can be rearranged and recombined with components of other polyketide synthases to produce chemicals that they would not normally produce. The Keasling Lab has engineered polyketide synthases for production of commodity and specialty chemicals as well as biofuels. Because many aspects of polyketide biosynthesis are not yet known, the Keasling Lab also does basic biochemistry and enzymology to understand how polyketide synthases function. We also engineer hosts to better express these large enzymes, particularly for production of chemicals and fuels. Representative publications include:
- S. Yuzawa, K. Deng, G. Wang, E. E. Baidoo, T. R. Northen, P. D. Adams, L. Katz, and J. D. Keasling. 2017. “Comprehensive in vitro analysis of acyltransferase domain exchanges in modular polyketide synthases and its application for short-chain ketone production.” ACS Syn. Biol. 6(1):139-147. DOI: 10.1021/acssynbio.6b00176.
- R. M. Phelan, D. Sachs, S. J. Petkiewicz, J. F. Barajas, J. M. Blake-Hedges, M. G. Thompson, A. R. Apel, B. J. Rasor, L. Katz, and J. D. Keasling. 2016. “Development of next generation synthetic biology tools for use in Streptomyces venezuelae.” ACS Syn. Biol. 6(1):159–166. DOI: 10.1021/acssynbio.6b00202.
- C. H. Eng, S. Yuzawa, E. E. Baidoo, L. Katz, and J. D. Keasling. 2016. “Alteration of polyketide stereochemistry from anti to syn by a ketoreductase domain exchange in a Type I modular polyketide synthase subunit.” Biochemistry 55(12):1677-1680. DOI: 10.1021/acs.biochem.6b00129.
- Hagen, S. Poust, T. de Rond, L. Katz, C. J. Petzold, and J. D. Keasling. 2016. “Engineering a polyketide synthase for in vitro production of adipic acid.” ACS Synth. Biol. 5:21-27.
S. Yuzawa, N. Chiba, L. Katz, and J. D. Keasling. 2012. “Construction of a part of a 3-hydroxypropionate cycle for heterologous polyketide biosynthesis in Escherichia coli.” Biochemistry 51:9779-9781.