Many of the commodity chemicals that are used in many of the products we encounter on a daily basis are derived from petroleum. As such, the prices of these chemicals fluctuate with the price of petroleum and will become more expensive and scarce as petroleum supplies dwindle. The Keasling laboratory is modifying microbial metabolism to produce the very same chemicals that would otherwise be derived from petroleum. In the common biotechnological host E. coli, we have produced the commodity chemical adipic acid, a precursor to some forms of nylon and responsible for 10% of the man-made emissions of the greenhouse gas nitrous oxide.

In addition, the Keasling laboratory is modifying metabolism to produce chemicals that could not economically be produced from petroleum. When these chemicals are introduced into polymers, they will make much more durable plastics and fibers than have been possible using the simple chemicals derived from petroleum using conventional catalysts.

FUNDING

http://www.nsf.gov/

http://www.energy.gov/eere/bioenergy/bioenergy-technologies-office

LINKS

http://www.synberc.org/

REPRESENTATIVE PUBLICATIONS
  • S.-W. Kim and J. D. Keasling. 2001. “Metabolic engineering of the nonmevalonate isopentenyl diphosphate synthesis pathway in Escherichia coli enhances lycopene production.” Biotechnol. Bioeng. 72:408-415.
  • I. Aldor and J. D. Keasling. 2001. “Metabolic engineering of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) composition in recombinant Salmonella enterica serovar Typhimurium.” Biotechnol. Bioeng. 76:108-114.
  • C. D. Smolke, V. J. J. Martin, and J. D. Keasling. 2001. “Controlling the metabolic flux through the carotenoid pathway using directed mRNA processing and stabilization.” Met. Eng. 3:313-321.
  • V. J. J. Martin, Y. Yoshikuni, and J. D. Keasling. 2001. “The in vivo synthesis of plant sesquiterpenes in Escherichia coli.” Biotechnol. Bioeng. 75:497-503.
  • V. J. J. Martin, C. D. Smolke, and J. D. Keasling. 2002. “Redesigning cells for production of complex organic molecules.” ASM News 68:336-343.
  • I. S. Aldor, S.-W. Kim, K. L. Jones, and J. D. Keasling. 2002. “Metabolic engineering of a novel propionate-independent pathway for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in recombinant Salmonella enterica serovar Typhimurium.” Appl. Environ. Microbiol. 68:3848-3854.
  • N. L. Goeden-Wood, V. P. Conticello, S. J. Muller, and J. D. Keasling. 2002. “Improved assembly of multimeric genes for the biosynthetic production of protein polymers.” Biomacromolecules 3:874-879.
  • G.-Y. Wang and J. D. Keasling. 2002. “Amplification of HMG-CoA reductase production enhances carotenoid accumulation in Neurospora crassa.” Met. Eng. 4:193-201.
  • D. J. Scott, B. M.T. da Costa, S. C. Espy, J. D. Keasling, and Katrina Cornish. 2003. “Activation and inhibition of rubber transferases by metal cofactors and pyrophosphate substrates.” Phytochemistry 64:123-134.
  • I. S. Aldor and J. D. Keasling. 2003. “Process design for microbial plastic factories: metabolic engineering of polyhydroxyalkanoates.” Curr. Opin. Biotechnol. 14:475-483.
  • K. K. Reiling, Y. Yoshikuni, V. J. J. Martin, J. Newman, J. Bohlmann, and J. D. Keasling. 2004. “Mono and diterpene production in Escherichia coli.” Biotechnol. Bioeng. 87:200-212.
  • B. M. T. da Costa, J. D. Keasling, and K. Cornish. 2005. “Regulation of rubber biosynthetic rate and molecular weight in Hevea brasiliensis by metal cofactor.” Biomacromolecules 6:279-289.
  • M. J. Kang, Y. M. Lee, S. H. Yoon, J. H. Kim, S. W. Ock, K. H. Jung, Y. C. Shin, J. D. Keasling, and S. W. Kim. 2005. “Identification of genes affecting lycopene accumulation in Escherichia coli using a shot-gun method.” Biotechnol. Bioeng. 91:636-642.
  • Y. Yoshikuni, V. J. J. Martin, T. E. Ferrin, and J. D. Keasling. 2006. “Engineering cotton (+)-?-cadinene synthase to an altered function: germacrene D-4-ol synthase.” Chem. Biol. 13:91-98.
  • Y. Yoshikuni, T. E. Ferrin, and J. D. Keasling. 2006. “Designed divergent evolution of enzyme function.” Nature 440:1078-1082.
  • S. C. Espy, J. D. Keasling, J. Castillon, and K. Cornish. 2006. “Initiator-independent and initiator-dependent rubber biosynthesis in Ficus elastica.” Arch. Biochem. Biophys. 448:13-22.
  • B. M. T. da Costa, J. D. Keasling, C. M. McMahon, and K. Cornish. 2006. “Magnesium regulation of in vitro rubber biosynthesis by Parthenium argentatum Gray.” Phytochemistry 67:1621-1628.
  • S. H. Yoon, Y. M. Lee, J. E. Kim, S. H. Lee, J. H. Lee, J. Y. Kim, K. H. Jung, Y. C. Shin, J. D. Keasling, and S. W. Kim. 2006. “Enhanced lycopene production in Escherichia coli engineered to synthesize isopentenyl diphosphate and dimethylallyl diphosphate from mevalonate.” Biotechnol. Bioeng. 94:1025-1032.
  • B. F. Pfleger, D. J. Pitera, C. D. Smolke, and J. D. Keasling. 2006. “Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes.” Nat. Biotechnol. 24:1027-1032.
  • H. S. Zahiri, S. H. Yoon, J. D. Keasling, S. H. Lee, K. S. Won, S. C. Yoon, and Y. C. Shin. 2006. “Coenzyme Q(10) production in recombinant Escherichia coli strains engineered with a heterologous decaprenyl diphosphate synthase gene and foreign mevalonate pathway.” Metab. Eng. 8:406-416.
  • S. T. Withers and J. D. Keasling. 2007. “Biosynthesis and engineering of isoprenoid small molecules.” Appl. Microbiol. Biotechnol. 73:980-990.
  • S. H. Yoon, J. E. Kim, S. H. Lee, H. M. Park, M. S. Choi, J. Y. Kim, S. H. Lee, Y. C. Shin, J. D. Keasling, and S. W. Kim. 2007. “Engineering the lycopene synthetic pathway in E. coli by comparison of the carotenoid genes of Pantoea agglomerans and Pantoea ananatis.” Appl. Microbiol. Biotechnol. 74:131-139.
  • D. J. Pitera, C. J. Paddon, J. D. Newman, and J. D. Keasling. 2007. “Balancing a heterologous mevalonate pathway for improved isoprenoid production in Escherichia coli.” Metab. Eng. 9:193-207.
  • M. C. Y. Chang, R. A. Eachus, W. Trieu, D.-K. Ro, and J. D. Keasling. 2007. “Engineering Escherichia coli for production of functionalized terpenoids using plant P450s.” Nature Chem. Biol. 3:274-277.
  • S. H. Yoon, H. M. Park, J. E. Kim, S. H. Lee, M. S. Choi, J. Y. Kim, D. K. Oh, J. D. Keasling, and S. W. Kim. 2007. “Increased beta-carotene production in recombinant Escherichia coli harboring an engineered isoprenoid precursor Pathway with mevalonate addition.” Biotechnol. Prog. 23:599-605.
  • B. M. T. da Costa, K. Cornish, and J. D. Keasling. 2007. “Manipulation of intracellular magnesium levels in Saccharomyces cerevisiae with deletion of magnesium transporters.” Appl. Microbiol. Biotechnol. 77:411-425.
  • W. D. Marner, A. S. Shaikh, S. J. Muller, and J. D. Keasling. 2008. “Morphology of artificial silica matrices formed via autosilification of a silaffin/protein polymer chimera.” Biomacromol. 9:1-5.
  • J. D. Keasling. 2008. “Synthetic biology for synthetic chemistry.” ACS Chem. Biol. 3:64-76.
  • J. Kirby, D. W. Romanini, E. M. Paradise, and J. D. Keasling. 2008. “Engineering triterpene production in Saccharomyces cerevisiae – beta-amyrin synthase from Artemisia annua.” FEBS J. 275:1852-1859.
  • L. Kizer, D. J. Pitera, B. Pfleger, and J. D. Keasling. 2008. “Functional genomics for pathway optimization: application to isoprenoid production.” Appl. Environ. Microbiol. 74:3229-3241.
  • J. Kirby and J. D. Keasling. 2008. “Metabolic engineering of microorganisms for isoprenoid production.” Nat. Prod. Rep. 25:656-661.
  • W. D. Marner, A. Shaikh, S. J. Muller, and J. D. Keasling. 2009. “Enzyme immobilization via silaffin-mediated autoencapsulation in a biosilica support.” Biotech. Prog. 25:417-423.
  • J. Kirby and J. D. Keasling. 2009. “Biosynthesis of plant isoprenoids: perspectives for microbial engineering.” Annu. Rev. Plant Biol. 60:335.355.
  • S. H. Yoon, S. H. Lee, A. Das, H. K. Ryu, H. J. Jang, J. Y. Kim, D. K. Oh, J. D. Keasling, and S. W. Kim. 2009. “Combinatorial expression of bacterial whole mevalonate pathway for production of beta-carotene in E. coli.” J. Biotechnol. 140:218-226.
  • J. E. Dueber, G. C. Wu, G. R. Malmirchegini, T. S. Moon, C. J. Petzold, A. V. Ullal, K. J. Prather, and J. D. Keasling. 2009. “Synthetic protein scaffolds provide modular control over metabolic flux.” Nat. Biotechnol. 27:753-759.
  • J. M. Carothers, J. A. Goler, and J. D. Keasling. 2009. “Chemical synthesis using synthetic biology.” Curr. Opin. Biotechnol. 20:498-503.
  • 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 463:559-562.
  • H. R. Beller, E.-B. Goh, and J. D. Keasling. 2010. “Genes involved in long-chain alkene biosynthesis in Micrococcus luteus.” Appl. Environ. Microbiol. 76:1212-1223.
  • J. A. Dietrich, A. E. McKee, and J. D. Keasling. 2010. “High-throughput metabolic engineering: advances in small-molecule screening and selection.” Annu. Rev. Biochem. 79:563-590.
  • J. Kirby, M. Nishimoto, J. G. Park, S. T. Withers, F. Nowroozi, D. Behrendt, E. J. Rutledge, J. L. Fortman, H. E. Johnson, J. V. Anderson, and J. D. Keasling. 2010. “Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae.” Phytochem. 71:1466-1473.
  • C. Wang, S. H. Yoon, A. A. Shah, Y. R. Chung, J. Y. Kim, E. S. Choi, J. D. Keasling, and S. W. Kim. 2010. “Farnesol production from Escherichia coli by harnessing the exogenous mevalonate pathway.” Biotechnol. Bioeng. 107:421-429.
  • J. D. Keasling. 2010. “Manufacturing molecules through metabolic engineering.” Science 330:1355-1358.
  • A. Eudes, E. E. Baidoo, F. Yang, H. Burd, M. Z. Hadi, F. W. Collins, J. D. Keasling, and D. Loqué. 2010. “Production of tranilast [N-(3′,4′-dimethoxycinnamoyl)-anthranilic acid] and its analogs in yeast Saccharomyces cerevisiae.” Appl. Microbiol. Biotechnol. 89:989-1000.
  • A. M. Redding-Johanson, T. S. Batth, R. Chan, R. Krupa, H. L. Szmidt, P. D. Adams, J. D. Keasling, T. S. Lee, A. Mukhopadhyay, C. J. Petzold. 2011. “Targeted proteomics for metabolic pathway optimization: application to terpene production.” Metab. Eng. 13:194-203.
  • S. M. Ma, D. E. Garcia, A. M. Redding-Johanson, G. D. Friedland, R. Chan, T. S. Batth, J. R. Haliburton, D. Chivian, J. D. Keasling, C. J. Petzold, T. S. Lee, S. R. Chhabra. 2011. “Optimization of a heterologous mevalonate pathway through use of variant HMG-CoA reductases.” Met. Eng. 13:588-597.
  • H. R. Beller, E. B. Goh, and J. D. Keasling. 2011. “Definitive alkene identification needed for in vitro studies with ole (olefin biosynthesis) proteins.” J. Biol. Chem. 286:1e11.
  • D. Juminaga, E. E. Baidoo, A. M. Redding-Johanson, T. S. Batth, H. Burd, A. Mukhopadhyay, C. J. Petzold, and J. D. Keasling. 2012. “Modular engineering of L-tyrosine production in Escherichia coli.” Appl. Environ. Microbiol. 78:89-98.
  • Y. Satoh, K. Tajima, M. Munekata, J. D. Keasling, and T. S. Lee. 2012. “Engineering of a tyrosol-producing pathway, utilizing simple sugar and the central metabolite tyrosine, in Escherichia coli.” J. Agric. Food Chem. 60:979-984.
  • S. Kumar, F. M. Hahn, E. Baidoo, T. S. Kahlon, D. F. Wood, C. M. McMahan, K. Cornish, J. D. Keasling, H. Daniell, and M. C. Whalen. 2012. “Remodeling the isoprenoid pathway in tobacco by expressing the cytoplasmic mevalonate pathway in chloroplasts.” Met. Eng. 14:19-28.
  • J. D. Keasling. 2012. “Synthetic biology and the development of tools for metabolic engineering.” Met. Eng. 14:189-195.
  • 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. 30:354-359.
  • X. Xie, J. Kirby, and J. D. Keasling. 2012. “Functional characterization of four sesquiterpene synthases from Ricinus communis (Caster Bean).” Phytochemistry 78:20-28.
  • J. Perez-Gil, E. M. Uros, S. Sauret-Gueto, L. M. Lois, J. Kirby, M. Nishimoto, E. E. K. Baidoo, J. D. Keasling, A. Boronat, and M. Rodriguez-Concepcion. 2012. “Mutations in Escherichia coli aceE and rib genes allow survival of strains defective in the first step of the isoprenoid biosynthesis pathway.” PLoS One 7(8):e43775.
  • S. Yuzawa, W. Kim, L. Katz, and J. D. Keasling. 2012. “Heterologous production of polyketides by modular type I polyketide synthases in Escherichia coli.” Curr. Opin. Biotechnol. 23:725-735.
  • J. D. Keasling, A. Mendoza, and P. S. Baran. 2012. “Synthesis: A constructive debate.” Nature 492:188-189.
  • Y. Satoh, K. Tajima, M. Munekata, J. D. Keasling, and T. S. Lee. 2012. “Engineering of L-tyrosine oxidation in Escherichia coli and microbial production of hydroxytyrosol.” Met. Eng. 14:603-610.
  • J. D. Keasling. 2012. “Engineering biology for drugs and fuels.” Proc. Amer. Philosoph. Soc. 156:283-294.
  • 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.
  • J. A. Dietrich, D. L. Shis, A. Alikhani, and J. D. Keasling. 2013. “Transcription factor-based screens and synthetic selections for microbial small-molecule biosynthesis.” ACS Synth. Biol. 2:47-58.
  • G. Bokinsky, E. E.K. Baidoo, S. Akella, H. Burd, D. Weaver, J. Alonso-Gutierrez, H. García-Martín, T. S. Lee, J. D. Keasling. 2013. “HipA-triggered growth arrest and ?-lactam tolerance in Escherichia coli is mediated by RelA-dependent ppGpp synthesis.” J. Bacteriol. 195:3173-3182.
  • 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. 19:33-41.
  • A. Eudes, D. Juminaga, E. E. Baidoo, F. W. Collins, J. D. Keasling, and D. Loque. 2013. “Production of hydroxycinnamoyl anthranilates from glucose in Escherichia coli.” Microb. Cell Fact. 12:62
  • H. H. Chou and J. D. Keasling. 2013. “Programming adaptive control to evolve increased metabolite production.” Nat. Commun. 4:2595. DOI: 10:1038/ncomms3595.
  • H. L Szmidt-Middleton, M. Ouellet, P.  D Adams, J. D Keasling, and A. Mukhopadhyay. 2013. “Utilizing a highly responsive gene, yhjX, in E. coli based production of 1,4-butanediol.” Chem. Eng. Sci. 103:68-73.
  • S. Rodriguez, J. Kirby, C. M. Denby, and J. D. Keasling. 2014. “Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and ket related metabolites.” Nat. Protoc. 9(8):1980-96. doi: 10.1038/nprot.2014.132.
  • J. Kirby, M. Nishimoto, R. W. Chow, V. N. Pasumarthi, R. Chan, L. J. Chan, C. J. Petzold, and J. D. Keasling. 2014. “Use of non-ionic surfactants for improvement of terpene production in Saccharomyces cerevisiae.” Appl. Environ. MIcrobiol. 80(21):6685-6693.
  • L. J. Weaver, M. M. Sousa, G. Wang, E. Baidoo, C. J. Petzold, and J. D. Keasling. 2015. “A kinetic-based approach to understanding heterologous mevalonate pathway function in E. coli.” Biotechnol. Bioeng. 112(1):111-119.
  • 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. 81:130-138.
  • J. Alonso-Gutierrez, E.-M. Kim; T. S. Batth, N. Cho, Q. Hu, L. J. G. Chan, C. J. Petzold, Nathan J Hillson, P. D. Adams, J. D. Keasling, H. Garcia-Martin, and T. S. Lee. 2015. “Principal component analysis of proteomics (PCAP) as a tool to direct metabolic engineering.” Met. Eng. 28:123-133.
  • Hagen A, Poust S, Rond Td, Fortman JL, Katz L, Petzold CJ, Keasling JD. 2016. “Engineering a polyketide synthase for in vitro production of adipic acid.” ACS. Synth. Biol. 15:21-27