R&D Biological Sciences

Portrait of James Kirby

Education

B.S. in Industrial Microbiology, University College Dublin, Ireland (1993)

Ph.D. in Molecular Biology, Rowett Research Institute/University of Aberdeen, U.K. (1997)

Research Interests

Kirby's research interest is primarily metabolic engineering of microbes for the sustainable production of bioproducts. Much of his focus over the last decade has been on yeast (Saccharomyces cerevisiae), but his current work is focused on an interesting fungus, Rhodosporidium toruloides, which can utilize a wider variety of carbon sources than yeast and also accumulates lipids to a high percentage of biomass. He is particularly interested in terpenes, which comprise a massive family of bioproducts including most of the volatile oils made by plants.

Selected Publications

Kirby J, Dietzel KL, Wichmann G, Chan R, Antipov E, Moss N, Baidoo EE, Jackson P, Gaucher SP, Gottlieb S, LaBarge J, Mahatdejkul T, Hawkins KM, Muley S, Newman JD, Liu P, Keasling JD, Zhao L. Engineering a functional 1-deoxy-D-xylulose 5-phosphate (DXP) pathway in Saccharomyces cerevisiae. Metab Eng. (2016) 38:494-503.

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:e43775.

Xie X, Kirby J, Keasling JD. Functional characterization of four sesquiterpene synthases from Ricinus communis (Castor bean). Phytochemistry (2012) 78:20-8.

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, 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.