Marine Biodiscovery - Screening & Culturing: establish and implement a screening and culturing process for isolation of bioactive compounds from marin

Marine Biodiscovery - Screening & Culturing: establish and implement a screening and culturing process for isolation of bioactive compounds from marine

Funding Body : Beaufort Marine Research Award

Project type:  Post-Doctoral

Period:  June 2007 – June 2015

Researcher: Jonathan Kennedy

Project Description

Culture dependent and independent (metagenomic) based approaches will be employed to study the microbial biodiversity of various marine ecosystems, such as marine sponges. These approaches will be used to identify different microorganisms (or clones from metagenomic libraries), which produce bioactive compounds with potential anti-microbial, anti-fungal and anti-biofouling activities. This will involve the use of novel heterologous expression systems, together with high–throughput screening systems. Candidate microorganisms and clones will be genetically characterised to gain a better understanding of the biochemical pathways involved in the production of these bioactive compounds. In addition efforts will focus on elucidating the effects of these bioactives on the target microorganisms at the molecular level.



1.       Kennedy, J., Baker, P.W., Piper, C., Cotter, P.D., Walsh, M., Mooij, M.J., Bourke, M.B., Rea, M.C., O’Connor, P.M., Ross, R.P., Hill, C., O’Gara, F., Marchesi, J.R. and Dobson, A.D.W.  Isolation and analysis of bacteria with antimicrobial activities from the marine sponge Haliclona simulans isolated from Irish waters.  (2008) Marine Biotechnology (DOI:10.1007/s10126-008-9154-1).

2.       Baker, P.W., Kennedy, J., Dobson, A.D.W., and Marchesi, J.R.  Phylogenetic diversity and antimicrobial activities of fungi associated with Haliclona simulans isolated from Irish coastal waters.  (2008)  Marine Biotechnology (DOI: 10.1007/s10126-008-9169-7)

3.       Kennedy, J. , Marchesi, J.R. and Dobson, A.D.  Marine metagenomics: strategies for the discovery of novel enzymes with biotechnological applications from marine environments.  (2008)  Microbial Cell Factories.  7 p27

4.       Kennedy, J., Codling, C., Jones, B.V., Dobson, A.D.W., and Marchesi, J.R.  Diversity of bacteria associated with the marine sponge Haliclona simulans and identification of polyketide synthase genes from the sponge metagenome. (2008)  Environmental Microbiology  10 pp1888-902     

5.       Kennedy, J.   Mutasynthesis, Chemobiosynthesis, and back to Semi-synthesis: Combining Synthetic Chemistry and Biosynthetic Engineering for Diversifying Natural Products.  (2008) Natural Product Reports .  10 pp25-34

6.       Kennedy, J., Marchesi J.R., and Dobson, A.D.  Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges.  (2007)  Applied Microbiology and Biotechnology.  75 pp11-20

7.       Katz, L., Kennedy, J., Mutka, S.C., Carney, J.R., MacMillan, K.S., and Murli, S.  Novel polyketides from genetic engineering (…and lessons we have learned from making them).  (2007).  Polyketides: Biosynthesis, Biological Activity, and Genetic Engineering.  ACS Publications, S. Baerson, A. Rimondo, eds.

8.       Kennedy, J., Schirmer, A., Murli, S., Reid, R., and Santi, D.V.  Targeted irreversible inhibition of protein kinases by resorcinyl acid lactone polyketides.  (2006)  Proceedings of the National Academy of Sciences.  103 pp4234-9.

9.       Mutka, S.C., Carney, J.R., Lui, Y., and Kennedy, J.  Heterologous production of epothilones C and D in Escherichia coli.   (2006)   Biochemistry.  45 pp1321-30.

10.   Menzella, H.G., Reisinger, S.J., Welch, M., Kealey, J.T., Kennedy, J., Reid, R., Tran, C.Q., and Santi, D.V.  Redesign, synthesis and functional expression of the 6-deoxyerythronolide B polyketide synthase gene cluster. (2006)  Journal of Industrial Microbiology and Biotechnology.  33 pp22-8

11.   Murli, S., MacMillan, K.S., Hu, Z., Ashley, G. W., Dong, S. D., Kealey, J. T., Reeves, C. D. and Kennedy, J.  Chemobiosynthesis of Novel 6-Deoxyerythronolide B Analogues by Mutation of the Loading Module of DEBS1.   (2005).  Applied and Environmental Microbiology. 71 pp4503-9

12.   Kennedy, J. , and Kealey, J. T.  Tools for Metabolic Engineering in Escherichia coli:  Inactivation of panD by a point mutation.  (2004).  Analytical Biochemistry.  327 pp91-6

13.   Regentin, R., Kennedy, J., Wu, N., Carney, J., Licari, P., Galazzo, J., and Desai, R.  Biosynthesis of Novel Triketide Lactones.  (2004).  Biotechnology Progress.  20 pp122-7

14.   Kennedy, J., Murli, S., and Kealey, J. T.  6-Deoxyerythronolide B analogue production in Escherichia coli through metabolic pathway engineering.  (2003).  Biochemistry.  42 pp14342-8

15.   Kennedy, J., Murli, S., Dayem, L. C., Carney, J. R., and Kealey, J. T.  Metabolic Engineering of Escherichia coli for Improved 6-Deoxyerythronolide B Production.  (2003).  Journal of Industrial Microbiology and Biotechnology.  30 pp500-9

16.   Hutchinson, C. R., Kennedy, J., Park, C. S., Auclair, K., and Vederas, J. C.  The Molecular Genetics of Lovastatin Biosynthesis.  (2004)  Industrial Mycology: Past, Present and Future.  Handbook of Industrial Mycology.  Chapter 20.  pp479-492.  Z. An (Ed.). Marcel Dekker

17.   Sorensen, J. L., Auclair, K., Kennedy, J., Hutchinson, C.R., and Vederas, J.C.  Transformations of Cyclic Nonaketides by Aspergillus terreus Mutants Blocked for Lovastatin Biosynthesis at the lovA and lovC Genes.  (2003). Organic and Biomolecular Chemistry 1, pp50-59

18.   Auclair, K., Kennedy, J., Hutchinson, C. R., and Vederas, J. C.  Conversion of cyclic nonaketides to lovastatin and compactin by a lovC deficient mutant of Aspergillus terreus.  (2001).  Bioorganic and Medicinal Chemistry Letters  11,  pp1527-1531

19.   Auclair, K., Sutherland, A., Kennedy, J., Witter, D. J., Van den Heever, J., Hutchinson, C. R., and J. C. Vederas.  Lovastatin Nonaketide Synthase (LNKS) Catalyzes an Intramolecular Diels-Alder Reaction of a Substrate Analog. (2000).  Journal of the American Chemical Society. 122, pp11519-11520

20.   Hutchinson, C. R., Kennedy, J., Park, C. S., Kendrew, S. G., Auclair, K., and John Vederas.  Aspects of the Biosynthesis of Non-Aromatic Fungal Polyketides by Iterative Polyketide Synthases. (2000).  Antonie van Leeuwenhoek78, pp287-95

21.   Kennedy, J., Auclair, K., Kendrew, S. G., Park, C. S., Vederas, J. C., and C. R. Hutchinson.  Modulation of Polyketide Synthase Activity by Accessory Proteins During Lovastatin Biosynthesis. (1999). Science 284, pp1368-1372

22.   Kennedy, J. and C. R. Hutchinson.  Nurturing nature: engineering new antibiotics. (1999). Nature Biotechnology 17, pp538-539

23.   Kennedy, J., Madduri, K., Rivola, G., Inventi-Solari, A., Filippini, S., Zanuso, G., Colombo, A. L., Gewain, K. M., Occi, J. L., MacNeil D. J., and C. R. Hutchinson. (1998) Production of the antitumor drug epirubicin (4’-epidoxorubicin) and its precursor by a genetically engineered strain of Streptomyces peucetius.  Nature Biotechnology, 16, pp 69-74

24.   Kallow, W., Kennedy, J., Arezi, B., Turner, G., and H. von Döhren.  Thioesterase domain of d-(l-a-aminoadipyl)-l-cysteinyl-d-valine synthetase: alteration of stereospecificity by site-directed mutagenesis. (2000).  Journal of Molecular Biology, 297, pp395-408

25.   Kennedy, J. and G. Turner.  ACV synthetase is a rate-limiting enzyme for penicillin production in Aspergillus nidulans. (1996).  Molecular and General Genetics. 253, 189-197.

26.   Etchegaray, A., Dieckmann, R., Kennedy, J., Turner, G., and H. von Döhren.  ACV Synthetase:  Expression of Amino Acid Activating Domains of the Penicillium chrysogenum Enzyme in Aspergillus nidulans.  (1997).  Biochemical and Biophysical Research Communications. 237, 166-169.

27.   Andrews, J., Kennedy, J., and J. MacKinnon.  Humanization of bacterial thymidylate synthetase by site-directed mutagenesis: A model system for rational drug design (1993) Protein Engineering. 6 SS, p109.


28.   Kennedy, J., Park, C. S., and C. R. Hutchinson.  Fungal genes for the production of lovastatin (mevinolin) and related inhibitors of hydroxymethylglutaryl coenzyme A reductase.  (1998) U.S. patent no.  6,391,583.


Environmental Research Institute

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