Actinomycetes have a tremendous potential to produce natural products with medicinal value. The long-term goal of this project is to develop novel agents for the treatment of human disease facilitated by the application of next-generation DNA sequencing to rapidly access actinomycete genetic information. The marine Streptomyces sp. CNH-189 is a producer of structurally fascinating meroterpenoids with potent activity against a broad panel of multi-drug resistant Staphylococcus aureus strains. The overall research objectives are to beta-test Illumina DNA sequencing for rapidly accessing natural product gene cluster sequences in Streptomyces sp. CNH-189, and to use genetics and biochemistry to link meroterpenoid biosynthesis to the identified gene clusters. Preliminary studies include the construction of genomic DNA fragment libraries that are ready for paired-end Illumina sequencing, and the isolation of a fosmid clone that contains a large part of the biosynthetic gene cluster for meroterpenoid biosynthesis. Through a series of experiments, I propose to evaluate how Illumina sequencing can be used to find gene clusters in Streptomyces sp. CNH-189 and other actinomycetes, to obtain a complete coverage of the gene cluster, and to probe the biosynthesis through in vitro biochemistry, gene disruption, and comparative metabolite profiling. The unique chemical structures and biological activities of the natural products isolated from Streptomyces sp. CNH-189 may lead to new chemotherapies and fundamental biochemical knowledge.

Public Health Relevance

Many pharmaceuticals currently used in the clinic are natural product based. Therefore, natural product discovery, understanding of biosynthetic pathways, and engineering the production of natural product analogs are key for the development of new human chemotherapies. Next-generation DNA sequencing and short read assembly ofers a new and potentialy general platform for accessing gene clusters that could facilitate the genome mining and understanding of clustered biosynthetic pathways in microorganisms. The proposed research will for the first time evaluate Illumina sequencing as a platform for rapidly accessing biosynthetic gene clusters in actinomycetes. Successful completion of this research may advance the field of natural product discovery and biosynthesis.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Postdoctoral Individual National Research Service Award (F32)
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Special Emphasis Panel (ZRG1-F08-E (20))
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Lees, Robert G
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University of California San Diego
Schools of Earth Sciences/Natur
La Jolla
United States
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