Discovery of the amipurimycin and miharamycins biosynthetic gene clusters and insight into the biosynthesis of nogalamycin

Advancements in our ability to obtain high quality bacterial whole genome sequences have increased the rate natural product biosynthetic gene clusters are identified, but these projects require computational methods for gene annotation which are limited by their reliance on comparison to previously annotated genes. Thus, even in a well-defined cluster with a known product it may be difficult to predict how structural characteristics arise if they have no known precedent. Without further work, such limitations will continue to impede the utility of sequenced bacterial genomes. Biosyntheses of the peptidyl nucleoside antibiotics and atypical anthracyclines like nogalamycin are topics which exemplify these challenges. The peptidyl nucleoside antibiotics (PNAs) are a structurally complex group of natural products with diverse biological activities which could be useful for the development of novel antimicrobials. Amipurimycin and the miharamycins are remarkably similar PNAs elaborated by the bacteria Streptomyces miharaensis ATCC 19440 and Streptomyces novoguineensis CBS 199.78, respectively. Their dissimilarity to other well-characterized groups of antibiotics has presented a challenge to the study of their unique structural features. Herein, we describe the identification of the amipurimycin and miharamycins biosynthetic gene clusters though a comparative genomics approach. Besides providing insight into the biosynthesis of the rare amino acids adorning these PNA, our analysis revealed a plausible biosynthetic route to the unique 2-aminopurine nucleobase and suggests the core saccharides are generated by a polyketide synthase. The anthracyclines are a mainstay of chemotherapy, but their use is limited by fatal cardiotoxicity and tumor resistance. The structures of the anthracyclines are sensitive to modification, as even small changes can ablate their biological activity. Nevertheless, the diversification of anthracyclines through semi- or total syntheses is an ongoing effort. Nogalamycin is rare amongst the anthracyclines because of its extended ring system and unusual glycosylation pattern. It is hoped an understanding of the biosynthesis of nogalamycin could allow the incorporation of its uncommon structural features into other anthracyclines to develop novel compounds with improved actitivty. Towards this end, we investigated the biosynthesis of the amino sugar found in nogalamycin, nogalamine, to clarify ambiguous steps in the reported biosynthetic pathway for this sugar.