A proteomics approach to discovering natural products and their biosynthetic pathways

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Abstract
Nonribosomal peptides and polyketides constitute a large fraction of antibiotic, antitumor and immunosuppressant drugs. Bumpus et al. present a proteomic strategy to identify new natural products and their biosynthetic pathways. Many natural products with antibiotic, anticancer and antifungal properties are synthesized by nonribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs)1. Although genome sequencing has revealed the diversity of these enzymes, identifying new products and their biosynthetic pathways remains challenging2. By taking advantage of the size of these enzymes (often >2,000 amino acids) and unique marker ions derived from their common phosphopantetheinyl cofactor, we adapted mass spectrometry–based proteomics to selectively detect NRPS and PKS gene clusters in microbial proteomes without requiring genome sequence information. We detected known NRPS systems in members of the genera Bacillus and Streptomyces, and screened 22 environmental isolates to uncover production of unknown natural products from the hybrid NRPS-PKS zwittermicin A biosynthetic gene cluster3. We also discovered an NRPS cluster that generates a seven-residue lipopeptide. This 'protein-first' strategy complements bioassay- and sequence-based approaches by finding expressed gene clusters that produce new natural products.