ASSOCIATE RESEARCH SCIENTIST

EDUCATION:

Ph.D. in Molecular Biology
University of Aberdeen
Scotland, UK

B.S. in Industrial Microbiology
University College Dublin
Ireland

CONTACT INFORMATION:

Email …… jimkirby at berkeley dot edu
Phone ….. 510-495-2459
Office …… 4660F
Bench ….. 4550-22
Address
Keasling Research Group
Joint BioEnergy Institute
University of California, Berkeley
5885 Hollis St., 4th Floor
Emeryville, CA 94608

Current Research

Engineering terpene biofuels in pine (Pinus taeda). ARPA-E PETRO program. (Overview Video).

Metabolic engineering of isoprenoid pathways in Saccharomyces cerevisiae and other yeasts. Collaborative projects with Amyris Inc. and the JBEI Fungal Biotech group.

Microbial biosynthesis of prostratin and related phorbol esters.

Enzyme-Mediated Synthesis of Functionalized Terpene Structures (NIH funded).

 

Publications

  • Kirby J, Nishimoto M, Chow RW, Baidoo EE, Wang G, Martin J, Schackwitz W, Chan R, Fortman JL, Keasling JD. Enhancing Terpene Yield from Sugars via Novel Routes to 1-Deoxy-D-Xylulose 5-Phosphate. Appl Environ Microbiol. (2015) 81:130-8.
  • Kirby J, Nishimoto M, Chow RW, Pasumarthi VN, Chan R, Chan LJ, Petzold CJ, Keasling JD. Use of nonionic surfactants for improvement of terpene production in Saccharomyces cerevisiae. Appl Environ Microbiol. (2014) 80:6685-93.
  • Rodriguez S, Kirby J, Denby CM, Keasling JD. Production and quantification of sesquiterpenes in Saccharomyces cerevisiae, including extraction, detection and quantification of terpene products and key related metabolites. Nature Protocols (2014) 9:1980-96.
  • Perez-Gil J, Uros EM, Sauret-Güeto S, Lois LM, Kirby J, Nishimoto M, Baidoo EE, Keasling JD, Boronat A, Rodriguez-Concepcion M. Mutations in Escherichia coli aceE and ribB genes allow survival of strains defective in the first step of the isoprenoid biosynthesis pathway. PLoS One. 2012;7(8):e43775.
  • Xie X, Kirby J, Keasling JD. Functional characterization of four sesquiterpene synthases from Ricinus communis (castor bean). Phytochemistry. 2012 Jun;78:20-8. Epub 2012 Mar 27.
  • James Kirby, Minobu Nishimoto, J. Genevieve Park, Jeffrey L. Fortman, and Jay D. Keasling “Diterpene Biosynthesis in Ricinus Communis –Modification of Casbene by a Cytochrome P450 Monooxygenase” (oral presentation), Phytochemical Society of North America, Hawaii, December 10-15, 2011
  • Prach L, Kirby J, Keasling JD, Alber T. Diterpene production in Mycobacterium tuberculosis. FEBS J. (2010) 277:3588-95.
  • Kirby J, Nishimoto M, Park JG, Withers ST, Nowroozi F, Behrendt D, Rutledge EJ, Fortman JL, Johnson HE, Anderson JV, Keasling JD. Cloning of casbene and neocembrene synthases from Euphorbiaceae plants and expression in Saccharomyces cerevisiae. Phytochemistry. (2010) 71:1466-73.
  • Kirby J, Keasling JD. Biosynthesis of Plant Isoprenoids: Perspectives for Microbial Engineering. Annu. Rev. Plant Biol. (2009) 60:335-55.
  • Kirby J, Keasling JD. Metabolic engineering of microorganisms for isoprenoid production. Nat Prod Rep. (2008) 25:656-61.
  • Kirby J, Romanini DW, Paradise EM, Keasling JD. Engineering triterpene production in Saccharomyces cerevisiae-beta-amyrin synthase from Artemisia annua. FEBS J. (2008) 275:1852-9.
  • Paradise EM, Kirby J, Chan R, Keasling JD. Redirection of flux through the FPP branch-point in Saccharomyces cerevisiae by down-regulating squalene synthase. Biotechnol Bioeng. (2008) 100:371-8.
  • Shiba Y, Paradise EM, Kirby J, Ro DK, Keasling JD. Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab. Eng. (2007) 9:160-168.
  • Tang YJ, Meadows AL, Kirby J, Keasling JD. Anaerobic Central Metabolic Pathways in Shewanella oneidensis MR-1 Reinterpreted in the Light of Isotopic Metabolite Labelling. J. Bacteriol. (2007) 189:894-901.
  • Ro DK, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang MC, Withers ST, Shiba Y, Sarpong R, Keasling JD. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature (2006) 440:940-943.
  • Kirby J, Kavanagh TA. NAN fusions: a synthetic sialidase reporter gene as a sensitive and versatile partner for GUS. Plant J. (2002) 32:391-400.
  • Rincon MT, McCrae SI, Kirby J, Scott KP, Flint HJ. EndB, a multidomain family 44 cellulase from Ruminococcus flavefaciens 17, binds to cellulose via a novel cellulose-binding module and to another R. flavefaciens protein via a dockerin domain. Appl. Environ. Microbiol. (2001) 67:4426-4431.
  • Kirby J, Wright F, Flint HJ. A cysteine desulphurase gene from the cellulolytic rumen anaerobe Ruminococcus flavefaciens 17. Biochim. Biophys. Acta. (1998) 1386:233-237.
  • Kirby J, Aurilia V, McCrae SI, Martin JC, Flint HJ. Plant cell wall degrading enzyme complexes from the cellulolytic rumen bacterium Ruminococcus flavefaciens. Biochem Soc. Trans. (1998) 26:S169.
  • Kirby J, Martin JC, Daniel AS, Flint HJ. Dockerin-like sequences in cellulases and xylanases from the rumen cellulolytic bacterium Ruminococcus flavefaciens. FEMS Microbiol. Lett. (1997) 149:213-219.

Patents

  • US 20150087042. Engineering the mevalonate pathway in Saccharomyces cerevisiae for overproduction of terpenes.
  • WO 2007024718. Engineering the pyruvate dehydrogenase bypass in S. cerevisiae.
  • US 20130052692. Novel routes for production of 1-deoxy-D-xylulose 5-phosphate (DXP).
  • Three additional applications in progress.

Awards

Poster award at the 1st Brazilian BioEnergy Science and Technology meeting 2011: Novel pathways from plant sugars to isoprenoid-based fuels James Kirby, Minobu Nishimoto, Jeffrey L. Fortman, and Jay D. Keasling.

Winner of the UC Berkeley Technology Breakthrough Competition, 2005.

Winner of the Rowett Institute Cuthbertson Award for the best Ph.D. of 1996.