Discovering and Deciphering Natural Product Biosynthetic Pathways In the Era of Synthetic Biology

The combination of genome-sequencing and synthetic biology is greatly facilitating natural product discovery. Biosynthetic pathways for natural products are being identified from sequencing projects and manipulated with aid of synthetic biology in order to identify new compounds and new chemical transformations. Here we identified the biosynthetic pathway for holomycin, a potent antibiotic with broad-spectrum activities, by mining the genome of the producer Streptomyces clavuligerus. We showed that the holomycin pathway consists of a unique set of enzymes including a single-module nonribosomal peptide synthetase (NRPS) and four flavin-dependent oxidoreductases. Biochemical and genetic studies were employed to characterize individual enzymatic transformations and related substrate scopes. Bioinformatic analyses of sequenced genomes reveal a number of homologous pathways in various microbes, thus providing the basis for discovery of new, naturally occurring analogs. These efforts enter several new and unique transformations into the ever-expanding synthetic biology toolbox.