Most clinically-used antibiotics are bacterially-produced small molecules known as natural products, or their derivatives. However, natural products are not being featured in antibiotic discovery programs due to high rates of rediscovery and low rates of new molecule discovery. This proposal describes a new genomicsbased approach to natural product discovery that employs a combination of bioinformatics, microbial ecology, genetics, and chemistry to identify cryptic biosynthetic loci and stimulate them to produce their encoded natural products. All molecules identified will be characterized for antimicrobial activity.
Specific Aim 1. Use bioinformatics to identify biosynthetic gene clusters and predict their products. New bioinformatic tools will be developed to identify biosynthetic gene clusters in the genomes of actinomycetes and other microbes, and to predict structural elements of their small molecule products. These predictions will be leveraged toward antibiotic discovery by using them as the basis for efforts to stimulate the production of cryptic natural products, as described in Specific Aims 2 and 3:
Specific Aim 2. Stimulate the production of cryptic metabolites by simulating a multispecies environment. Most screens for new natural products have been performed with strains grown as pure cultures in nutrientrich growth media. A new screening format has recently been developed in which strains are grown as microcolonies on nutrient-poor growth media. This microcolony screening methodology will be used to identify cryptic natural products with antimicrobial activity.
Specific Aim 3. Stimulate the production of cryptic metabolites by genetically manipulating producers. Most natural product-encoding gene clusters are thought to be repressed under standard culture conditions. Using actinomycete strains whose biosynthetic gene clusters have been identified by the efforts described in Specific Aim 1, endogenous gene cluster promoters will be systematically replaced with a strong, inducible promoter, enabling the controlled synthesis and isolation of their small molecule products and the subsequent characterization of their antimicrobial activity. .

Public Health Relevance

While most clinically-used antibiotics are small molecules produced by bacteria, these molecules are rarely used in antibiotic discovery programs due to the difficulty of finding new molecules. This proposal describes a new genomics-based approach to natural product discovery increasing the supply of new antibiotic candidates to combat resistant pathogens.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Specialized Center--Cooperative Agreements (U54)
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Special Emphasis Panel (ZAI1-DDS-M)
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Harvard University
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