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researcher

Patrick Caffrey

Lecturer/Assistant Professor

School Of Biomolecular & Biomed Science
Science Centre - South
Belfield
Dublin 4

Tel: +353 1 7162618
Email: patrick.caffrey@ucd.ie

Professional

             

Employment

Employer: University of Cambridge
Position: Post Doctoral Research Associate
Employer: University College Dublin
Position: College Lecturer

Education

Year 1983 Institution: Trinity College Dublin
Qualification: BA Subject: --none--
Year 1988 Institution: Trinity College Dublin
Qualification: PhD Subject:
         

Publications

 

Book Chapters

Zotchev, S. B., Caffrey, P.; (2009) 'Genetic analysis of nystatin and amphotericin biosynthesis' In: Hopwood, D. A (eds). Methods in Enzymology Volume 459, Complex enzymes in microbial natural product biosynthesis, part B: polyketides, aminocoumarins and carbohydrates. USA: Elsevier. , pp.243-258 [DOI] [Details]
Owen, P., Caffrey, P., Josefsson, L.-G., and Meehan, M. ; (1991) 'Outer membrane proteins: old and new' In: E. Z. Ron and S. Rottem (eds). Microbial surface components and toxins in relation to pathogenesis. New York: Plenum Press. , pp.127-139 [Details]
Caffrey, P., McVeigh, T., and Owen, P.; (1988) 'Western immunoblotting' In: P. Owen and T. J. Foster (eds). P. Owen and T. J. Foster. Amsterdam: Elsevier Science Publishers B. V. , pp.255-266 [Details]
McVeigh, T., Caffrey, P., and P. Owen. ; (1988) 'Silver staining of proteins and lipopolysaccharides in SDS-polyacrylamide gels' In: P. Owen and T. J. Foster (eds). Immunochemical and molecular analysis of bacterial pathogens. Amsterdam: Elsevier Science Publishers B. V. , pp.267-279 [Details]
 

Peer Reviewed Journals

Simon Walmsley, Eimear De Poire, Bernard Rawlings, Patrick Caffrey (2017) 'Engineered biosynthesis and characterisation of disaccharide-modified 8-deoxyamphoteronolides'. Applied Microbiology and Biotechnology, . [DOI] Link to full text [Details]
James Sheehan, Cormac Murphy, Patrick Caffrey (2017) 'New insights into polyene macrolide biosynthesis in Couchioplanes caeruleus'. Molecular BioSystems, 13 :866-873. [DOI] [Details]
Paul Sweeney, Cormac Murphy, Patrick Caffrey (2016) 'Exploiting the genome sequence of Streptomyces nodosus for enhanced antibiotic production'. Applied Microbiology and Biotechnology, 100 :1285-1295. [DOI] Link to full text [Details]
Patrick Caffrey, Eimear De Poire, James Sheehan, Paul Sweeney (2016) 'Polyene macrolide biosynthesis in streptomycetes and related bacteria: recent advances from genome sequencing and experimental studies'. Applied Microbiology and Biotechnology, 100 (9):3893-3908. [DOI] Link to full text [Details]
Tomoya Yamamoto, Yuichi Umegawa, Hiroshi Tsuchikawa, Nobuaki Matsumori, Shinya Hanashima, Michio Murata, Resul Haser, Bernard Rawlings, Patrick Caffrey (2015) 'Role of polyol moiety of amphotericin B in ion channel formation and sterol selectivity in bilayer membrane'. Bioorganic and Medicinal Chemistry, 23 (17):5782-5788. [DOI] [Details]
Eimear De Poire, Niamh Stephens, Bernard Rawlings, Patrick Caffrey (2013) 'Engineered biosynthesis of disaccharide-modified polyene macrolides'. Applied and Environmental Microbiology, 79 (19):6156-6159. [DOI] [Details]
Niamh Stephens, Bernard Rawlings, Patrick Caffrey (2013) 'Versatility of enzymes catalyzing late steps in polyene 67-121C biosynthesis'. Bioscience Biotechnology and Biochemistry, 77 (4):880-883. [DOI] Link to full text [Details]
Stephens N, Rawlings B, Caffrey P (2012) 'Streptomyces nodosus host strains optimised for glycosylation engineering'. Bioscience Biotechnology and Biochemistry, 76 (2):384-387. [DOI] Link to full text [Details]
Patrick Caffrey (2012) 'Dissecting complex polyketide biosynthesis'. Computational and Structural Biotechnology Journal, 3 (4):1-8. [DOI] [Details]
Naseem Khan, Bernard Rawlings, Patrick Caffrey ; (2011) 'A labile point in mutant amphotericin polyketide synthases'. Biotechnology Letters, 33 :1121-1126. [DOI] [Details]
Murphy, B., Anderson, K., Borissow, C., Caffrey, P., Griffith, G., Hearn, J., Ibrahim, O., Khan, N., Lamburn, N., Lee, M., Pugh, K., Rawlings, B. ; (2010) 'Isolation and characterisation of amphotericin B analogues and truncated polyketide intermediates produced by genetic engineering of Streptomyces nodosus'. Organic and Biomolecular Chemistry, 8 :3758-3770. [DOI] [Details]
Eve Hutchinson, Barry Murphy, Terence Dunne, Ciaran Breen, Bernard Rawlings, Patrick Caffrey ; (2010) 'Redesign of polyene macrolide glycosylation: engineered biosynthesis of 19-(O)-perosaminyl-amphoteronolide B'. Chemistry & Biology, 17 :174-182. [DOI] Link to full text [Details]
Laura Nic Lochlainn, Patrick Caffrey; (2009) 'Phosphomannose isomerase and phosphomannomutase gene disruptions in Streptomyces nodosus: impact on amphotericin biosynthesis and implications for glycosylation engineering'. Metabolic Engineering, 11 :40-47. [DOI] Link to full text [Details]
Lara Soler, Patrick Caffrey, Hilary McMahon; (2008) 'Effects of new amphotericin analogues on the scrapie isoform of the prion protein'. Biochimica et biophysica acta, 1780 :1162-1167. [Details]
Caffrey, P., Aparicio, J. F., Malpartida, F., Zotchev, S. B.; (2008) 'Biosynthetic engineering of polyene macrolides for generation of improved antifungal and antiparasitic agents'. Current Topics in Medicinal Chemistry, 8 (8):639-653. [DOI] Link to full text [Details]
Power, P., Dunne, T., Murphy, B., Nic Lochlainn, L., Rai, D., Borissow, C., Rawlings, B., and Caffrey, P. ; (2008) 'Engineered synthesis of 7-oxo- and 15-deoxy-15-oxo-amphotericins: insights into structure-activity relationships in polyene antibiotics'. Chemistry and Biology, 15 :78-86. [DOI] [Details]
Carmody, M., Murphy, B., Byrne, B., Power, P., Rai, D., Rawlings, B., Caffrey, P.; (2005) 'Biosynthesis of amphotericin derivatives lacking exocyclic carboxyl groups'. Journal of Biological Chemistry, 280 (41):34420-34426. [DOI] [Details]
Caffrey, P.; (2005) 'The stereochemistry of ketoreduction'. Chemistry and Biology, 12 (1):1060-1062. [DOI] [Details]
Carmody, M., Byrne, B., Murphy, B., Breen, C., Lynch, S., Flood, E., Finnan, S., and Caffrey, P.; (2004) 'Analysis and manipulation of amphotericin biosynthetic genes by means of modified phage KC515 transduction techniques'. Gene, 343 :107-115. [DOI] [Details]
Caffrey, P.; (2004) 'New start and finish for complex polyketide biosynthesis'. Chemistry & Biology, 11 :155-157. [DOI] [Details]
Aparicio, J. F., Caffrey, P., Gil, J. A. and Zotchev, S. B.; (2003) 'Polyene antibiotic biosynthesis gene clusters'. Applied Microbiology and Biotechnology, 61 :179-188. [DOI] [Details]
Byrne, B., Carmody, M., Gibson, E., Rawlings, B., Caffrey, P.; (2003) 'Biosynthesis of deoxyamphotericins and deoxyamphoteronolides by engineered strains of Streptomyces nodosus'. Chemistry and Biology, 10 :1215-1224. [DOI] [Details]
Caffrey, P.; (2003) 'Conserved amino acid residues correlating with ketoreductase stereospecificity in modular polyketide synthases'. Chembiochem, 4 :654-657. [DOI] [Details]
Caffrey, P., Lynch, S., Flood, E., Finnan, S., and Oliynyk, M.; (2001) 'Amphotericin biosynthesis in Streptomyces nodosus : deductions from analysis of polyketide synthase and late genes'. Chemistry and Biology, 8 :713-723. [DOI] [Details]
Staunton, J., Caffrey, P., Aparicio, J. F., Roberts, G. A., Bethell, S. and Leadlay, P. F.; (1996) 'Evidence for a double-helical structure for modular polyketide synthases'. Nature Structural Biology, 3 :188-192. [DOI] [Details]
Aggarwal, R., Caffrey, P., Leadlay, P. F., Smith, C. J., and Staunton, J.; (1995) 'The thioesterase of the erythromycin-producing polyketide synthase: mechanistic studies in vitro to investigate its mode of action and substrate specificity'. Journal of the Chemical Society-Chemical Communications, :1519-1520. [DOI] [Details]
Schwecke, T., Aparicio, J. F., Molnar, I., Konig, A., Khaw, L., Haydock, S., Oliynyk, M., Caffrey, P., Cortes, J., Bohm, G., Staunton, J. and Leadlay, P.; (1995) 'The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin'. Proceedings of the National Academy of Sciences, 92 :7839-7842. [DOI] [Details]
Aparicio, J. F., Caffrey, P., Marsden, A. F. A., Staunton, J. and Leadlay, P. F.; (1994) 'Limited proteolysis and active site studies of the 6-deoxyerythronolide B synthase 1 component of the erythromycin-producing polyketide synthase'. Journal of Biological Chemistry, 269 :8524-8528. [Details]
Marsden, A. F. A., Caffrey, P., Aparicio, J. F., Loughran, M., Staunton, J. and Leadlay, P. F.; (1994) 'Stereospecific acyl transfers on the erythromycin-producing polyketide synthase'. Science, 263 :378-380. [DOI] [Details]
Leadlay, P. F., Staunton, J., Aparicio, J. F., Bevitt, D. J., Caffrey, P., Cortes, J., Marsden, A., and Roberts, G. A.; (1993) 'The erythromycin-producing polyketide synthase'. Biochemical Society Transactions, 21 :218-222. [DOI] [Details]
Caffrey, P., Bevitt, D., Staunton, J., and Leadlay, P.; (1992) 'Identification of DEBS1, DEBS2 and DEBS3, the multienzyme polypeptides of the erythromycin-producing polyketide synthase from Saccharopolyspora erythraea'. FEBS Letters, 304 :225-228. [DOI] [Details]
Caffrey, P., Green, B., Packman, L. C., Rawlings, B. J., Staunton, J., and Leadlay, P. F.; (1991) 'An acyl-carrier-protein-thioesterase didomain from the 6-deoxyerythronolide B synthase of Saccharopolyspora erythraea, high-level production in Escherichia coli, purification and characterization'. European Journal of Biochemistry, 195 :823-830. [Details]
Caffrey, P., and Owen, P.; (1989) 'Purification and N-terminal sequence of the α-subunit of Antigen 43, a unique protein complex associated with the outer membrane of Escherichia coli'. Journal of Bacteriology, 171 :3634-3640. [Details]
Owen. P. , Caffrey, P., and L.-G. Josefsson; (1987) 'Identification and partial characterization of a novel bipartite protein antigen associated with the outer membrane of Escherichia coli'. Journal of Bacteriology, 169 :3770-3777. [Details]
Doherty, H., Yamada, H., Caffrey, P., and Owen, P.; (1986) 'Identification, immunological characterization and purification of a major lipoprotein antigen associated with the inner (cytoplasmic) membrane of Escherichia coli'. Journal of Bacteriology, 166 :1072-1082. [Details]
                                                                                                                     

Research

Research Interests

Many of the antibiotics used in clinical medicine are derived from natural products synthesised by bacteria and fungi. Micro-organisms also synthesise a number of other important pharmaceuticals. These include anti-cancer drugs such as doxorubicin and epothilone C, immunosuppressants like cyclosporin and rapamycin, and the cholesterol-lowering statins. The need to develop improved treatments for serious diseases has intensified interest in biosynthesis of these compounds. This research group is interested in genetic manipulation of bacterial secondary metabolism to produce useful new compounds. A major focus is the biosynthesis of polyenes; highly effective antifungal antibiotics that disrupt the ergosterol-containing membranes of fungal cells. Polyenes have a broad spectrum of activity and resistance has not emerged as a serious problem after forty years of clinical use. The most serious disadvantages of polyene antibiotics are extreme toxicity and low water-solubility. However, the rising incidence of life-threatening systemic fungal infections is being mirrored by increased resistance to other classes of antifungal antibiotics. Engineered biosynthesis of less toxic polyenes is clearly a worthwhile objective.

The most important polyene is amphotericin B, a heptaene produced by Streptomyces nodosus. The macrolactone core of amphotericin B is assembled from acetate and propionate units by a modular polyketide synthase. The late stages involve oxidation of a methyl branch to a carboxyl group, glycosylation with an aminodeoxyhexose sugar, mycosamine, and hydroxylation. We have characterised the amphotericin biosynthetic gene cluster and developed methods for genetic manipulation of S. nodosus. Analysis of the polyketide synthase sequence has given insights into how these enzymes determine the stereochemistry of chiral centres during assembly of polyketide carbon chains. Targeted gene replacements have yielded several amphotericin analogues. To date, the most promising of these is 16-descarboxyl-16-methyl amphotericin B, which is expected to show a reduction in toxicity similar to that of the semi-synthetic derivative amphotericin B methyl ester.

Most of the engineered strains produce 10 to 50 mg of novel polyene per litre of culture. Future work aims to maximise these yields to produce large quantities for therapeutic testing. In addition to its antifungal action, amphotericin B also has some activity against prion diseases, enveloped viruses and Leishmania parasites. The new amphotericin analogues will also be tested for improvements in these biological activities.

Additional projects include development of methods for genetic manipulation of other antibiotic-producing bacteria and engineering glycosylation of bioactive natural products.

 

Research Projects

Sponsor : Science Foundation Ireland (SFI)
Title : Expanding the therapeutic potential of amphotericin B by engineered biosynthesis
Start Date / End Date : 01-SEP-09 / 31-AUG-14
Sponsor : Higher Education Authority (HEA)
Title : Scholarship
Start Date / End Date : 01-JAN-03 / 31-DEC-05
Sponsor : European Commission FP5
Title : Glycosylation engineering for novel antibiotics
Start Date / End Date : 01-FEB-00 / 31-JAN-03
Sponsor : Enterprise Ireland (EI)
Title : Characterisation of Large Polyketide Synthase Proteins
Start Date / End Date : 01-OCT-96 / 30-SEP-99
Sponsor : The Wellcome Trust (WT)
Title : Biosynthesis of Novel Amphotericin Derivatives
Start Date / End Date : 01-OCT-96 / 30-SEP-99