Jay Keasling


Work and research


En savoir plusResearch interests

Metabolic engineering of microorganisms


The research in the Keasling Laboratory focuses on the metabolic engineering of microorganisms for degradation of environmental contaminants or for environmentally friendly synthesis. To that end, we have developed a number of new genetic and mathematical tools to allow more precise and reproducible control of metabolism. These tools are being used in such applications as synthesis of biodegradable polymers, accumulation of phosphate and heavy metals, and degradation of chlorinated and aromatic hydrocarbons, biodesulfurization of fossil fuels, and complete mineralization of organophosphate nerve agents and pesticides.

En savoir plusKeasling Laboratoty
 
Synthetic biology is is the design and construction of new biological entities such as enzymes, genetic circuits, and cells or the redesign of existing biological systems. Synthetic biology builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components (parts of enzymes, genetic circuits, metabolic pathways, etc.) that can be modeled, understood, and tuned to meet specific performance criteria, and the assembly of these smaller parts and devices into larger integrated systems that solve specific problems. Just as engineers now design integrated circuits based on the known physical properties of materials and then fabricate functioning circuits and entire processors (with relatively high reliability), synthetic biologists will soon design and build engineered biological systems.
The Keasling laboratory has a long history in the development of basic biological components, including low-copy expression vectors, regulatable promoters with consistent expression in all cells of a culture, mRNA processing elements for expression of multiple genes in an operon, flip elements for on-off gene expression regulation, and scaffolds for metabolic pathway construction.  Most of these components have been engineered for use in controlling the expression of genes in metabolic pathways.

En savoir plusSynberc
 
"At Synberc, we believe that by responsibly leading the field of synthetic biology, we will enable transformative technologies to meet global challenges and improve lives. Our mission is to build the foundations of synthetic biology by catalyzing multidisciplinary collaborations in research and education.

Synberc. Building the future with biology.

In 2006, the NSF funded the first synthetic biology engineering research center – Synberc – to develop engineered biological systems that will catalyze new technologies for processing information, producing energy, manufacturing chemicals and pharmaceuticals and fabricating materials.
Synberc is a consortium of UC Berkeley, UC San Francisco, Stanford, Harvard and MIT. These universities are located in the two “hubs” of synthetic biology: the Boston and San Francisco Bay Area. Synberc PIs are the leaders of synthetic biology, and their labs attract the best and the brightest students in the field. Synberc also has a number of industry partners; these relationships facilitate the technology transfer that will lead to the commercial use of Synberc’s cutting-edge research results."
 

Recent publications

E. B. Goh, E. E. Baidoo, J. D. Keasling, and H. R. Beller.  2012.  “Engineering of bacterial methyl ketone synthesis for biofuels.”  Appl. Environ. Microbiol. 78:70-80.

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.

D. Groff, P. I. Benke, T. S. Batth, G. Bokinsky, C. J. Petzold, P. D. Adams, and J. D. Keasling.  2012.  “Supplementation of intracellular XylR leads to coutilization of hemicellulose sugars.”  Appl. Environ. Microbiol. 78:2221-2229.

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.

P. J. Westfall, D. J. Pitera, J. R. Lenihan, D. Eng, F. Woolard, R. Regentin, T. Horning, Hiroko Tsuruta, D. Melis, A. Owens, S. Fickes, D. Diola, J. D. Keasling, M. D. Leavell, D. McPhee, N. S. Renninger, J. D. Newman, C. J. Paddon.  2012.  “Production of Amorpha-4,11-diene in yeast, and its conversion to dihydroartemisinic acid, precursor to the antimalarial agent artemisinin.”  Proc. Natl. Acad. Sci. USA 109:E111-E118.

Z. Li, J. D. Keasling, and K. Niyogi. 2012. “Overlapping photoprotective function of vitamin E and carotenoids in Chlamydomonas.” Plant Phys. 158:313-323.

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.

C. Rautengarten, B. Ebert, M. Ouellet, M. Nafisi, E. E.K. Baidoo, P. Benke, M. Stranne, A. Mukhopadhyay, J. D. Keasling, Y. Sakuragi, and H. V. Scheller.  2012.  “The Arabidopsis deficient in cutin ferulate (DCF) encodes a transferase required for feruloylation of ω-hydroxy fatty acids in cutin polyester.” Plant Phys. 158:654-665.

K. Deng, K. W. George, W. Reindl, J. D. Keasling, P. D. Adams, T. S. Lee, A. K. Singh, and T. R. Northen.  2012.  “Encoding substrates with mass tags to resolve stereospecific reactions using Nimzyme.” Rapid Commun. Mass Spectrom. 26:611-615.

J. Chen, D. Densmore, T. S. Ham, J. D. Keasling, and N. J. Hillson.  2012.  “DeviceEditor visual biological CAD canvas.”  J. Biol. Eng. 6:1. 

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.

A. Eudes, A. George, P. Mukerjee, J. S. Kim, B. Pollet, P. I. Benke, F. Yang, P. Mitra, L. Sun, O. P. Cetinkol, S. Chabout, G. Mouille, L. Soubigou-Taconnat, S. Balzergue, S. Singh, B. M. Holmes, A. Mukhopadhyay, J. D. Keasling, B. A. Simmons, C. Lapierre, J. Ralph, D. Loqué.  2012.  “Biosynthesis and incorporation of side-chain-truncated lignin monomers to reduce lignin polymerization and enhance saccharification.”  Plant Biotechnol J.  10:609-620.

X. Xie, J. Kirby, and J. D. Keasling.  2012.  “Functional characterization of four sesquiterpene synthases from Ricinus communis (Caster Bean).”  Phytochemistry 78:20-28.

P. Singh, T. S. Batth, D. Juminaga, R. H. Dahl, J. D. Keasling, P. D. Adams, and C. J. Petzold.  2012.  “Application of targeted proteomics to metabolically engineered Escherichia coli.”  Proteomics 12:1289-1299.

J. L. Park, E. J. Steen, H. Burd, S. S. Evans, A. M. Redding-Johanson, T. Batth, P. I. Benke, P. D’haeseleer, N. Sun, K. L. Sale, J. D. Keasling, C. J. Petzold, A. Mukhopadhyay, S. W. Singer, B. A. Simmons, and J. M. Gladden.  2012.  “A thermophilic ionic liquid-tolerant cocktail for the production of cellulosic biofuels.”  PLoS One 7:e37010. 

Z. Chen, G. D. Friedland, J. H. Pereira, S. A. Reveco, R. Chan, J. I. Park, M. P. Thelen, P. D. Adams, A. P. Arkin, J. D. Keasling, H. W. Blanch, B. A. Simmons, D. Chivian, and S. R. Chhabra.  2012.  “Tracing determinants of dual-substrate specificity in glycoside hydrolase family 5.”  J. Biol. Chem. 287:25335-25343.

Y. Xiao, T. Savchenko, E. E. Baidoo, W. E. Chehab, D. M. Hayden, V. Tolstikov, J. A. Corwin, D. J. Kliebenstein, J. D. Keasling, and K. Dehesh.  2012.  “Retrograde signaling by the plastidial metabolite MEcPP regulates expression of nuclear stress-response genes.”  Cell 149:1525-1535.

M. E. Clark, Z. He, A. M. Redding, M. P. Joachimiak, J. D. Keasling, J. Zhou, A. P. Arkin, A. Mukhopadhyay, and M. W. Fields.  2012.  “Transcriptomic and proteomic analyses of Desulfovibrio vulgaris biofilms: carbon and energy flow contribute to the distinct biofilm growth state.”  BMC Genomics 13:138.

P. P. Peralta-Yahya, F. Zhang, S. B. del Cardayre, and J. D. Keasling.  2012.  “Microbial engineering for the production of advanced biofuels.”  Nature 488:320-328.

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. 

E. A. Rennie, S. F. Hansen, E. Baidoo, M. Hadi, J. D. Keasling, H. Scheller.  2012.  “Three members of the Arabidopsis glycosyltransferase family 8 are xylan glucuronosyltransferases.” Plant Physiol. 159:1408-1417.  

N. J. Hillson, R. D. Rosengarten, and J. D. Keasling.  2012.  “j5 DNA assembly design automation software.”  ACS Syn. Biol. 1:14-21.

J. H. Pereira, E.-B. Goh, J. D. Keasling, H. R. Beller, and P. D. Adams.  2012.  “Structure of FabH and factors affecting the distribution of branched fatty acids in Micrococcus luteus.”  Acta Crystallographica D. 68:1320-1328.

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.

C. B. Walker, A. M. Redding-Johanson, E. Baidoo, L. Rajeev, Z. He, E. L Hendrickson, M.P. Joachimiak, S. Stolyar, A. P. Arkin, J. A. Leigh, J. Zhou, J. D. Keasling, A. Mukhopadhyay, and D. A. Stahl.  2012.  “Functional response of methanogenic archaea to syntrophic growth.”  ISME J. 6:2045-2055.

H. H. Chou and J. D. Keasling.  2012.  “Five-carbon alcohols are produced from isopentenyl diphosphate using a synthetic pathway.”  Appl. Environ. Microbiol. 78:7829-7855.

D. Chiniquy, V. Sharma, A. Schultink, E. E. Baidoo, C. Rautengarten, K. Cheng, A. Carroll, P. Ulvskov, J. Harholt, J. D. Keasling, M. Pauly, H. V. Scheller, and P. C. Ronald.  2012.  “XAX1 from glycosyltransferase family 61 mediates xylosyltransfer to rice xylan.”  Proc. Natl. Acad. Sci. USA 109:17117-17122.

T. S. Ham, Z. Dmytriv, H. Plahar, J. Chen, N. J. Hillson, and J. D. Keasling.  2012.  “Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools.”  Nucl. Acids Res. 40:e141 (doi: 10.1093/nar/gks531).

F. Zhang, M. Ouellet, T. Batth, P. D. Adams, C. J. Petzold, A. Mukhopadhyay, and J. D. Keasling.  2012.  “Enhancing fatty acid production by the expression of the regulatory transcription factor FadR.”  Met. Eng. 14:653-660.

A. E. Mckee, B. J. Rutherford, D. C. Chivian, E. K. Baidoo, D. Juminaga, D. Kuo, P. I. Benke, J. A. Dietrich, S. M. Ma, A. P. Arkin, C. J. Petzold, P. D. Adams, J. D. Keasling and S. R. Chhabra.  2012.  “Manipulation of the carbon storage regulator system for metabolite remodeling and biofuel production in Escherichia coli.”  Microb. Cell Fact. 11:79 (doi:10.1186/1475-2859-11-79). 

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. 

Y. Kung, W. Runguphan, and J. D. Keasling. 2012. “From fields to fuels: recent advances in the microbial production of biofuels.”  ACS Synth. Biol. 1:498-513.

S. M. Paap, T. H. West, D. K. Manley, E. J. Steen, H. R. Beller, J. D. Keasling, D. C. Dibble, S. Chana, and B. A. Simmons.  2013.  “Biochemical production of ethanol and fatty acid ethyl esters from switchgrass: A comparative analysis of environmental and economic performance.”  Biomass Bioenergy 49:49-62.

B. Ozaydin, H. Burd, T. S. Lee, and J. D. Keasling.  2013.  “Carotenoid-based phenotypic screen of the yeast deletion collection reveals new genes with roles in isoprenoid production.”  Met. Eng15:174-183.

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. 

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 in press.
 


Contact

UC Berkeley
Dpt of Chemical and Biomolecular Engineering
Office: 5885 Hollis St., 4th Floor Emeryville, CA 94608
UC mailcode: MC 3224

Phone: (510) 642-4862
Fax: (510) 495-2629

Email: keasling@berkeley.edu