Discovery and distribution of natural product biosynthesis pathways in the marine actinomycetes Salinispora

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Genome mining and various bioinformatic techniques have broadened traditional screening approaches and become important tools for the discovery of new natural products. We are developing a genome mining approach that can be used to predict secondary metabolite production based on short (ca. 600 bp) fragments of the appropriate biosynthetic genes as opposed to the analysis of complete biosynthetic gene clusters, which can exceed 100 kb. This method is being applied to four unassembled Salinispora genome sequences including two strains of the new species “S. pacifica”. Salinospora species are a prolific source of structurally diverse secondary metabolites including polyketides, nonribosomal peptides and PKS/NRPS hybrids. Phylogenetic analyses of conserved domains responsible for amino acid condensation in nonribosomal peptide synthetases and acyl condensation in polyketide synthases are performed not only to assess the type and number of biosynthetic pathways in four genome sequences but also to infer evolutionary and biogeographical patterns of secondary metabolites in Salinospora species. The project intends to develop a fast and easy to use tool to predict the potent novelty of biosynthetic gene clusters in unassembled sequence data and facilitate the discovery of new compounds.