Discovery and Biosynthetic Characterization of Darumycins Expand the Chemical Space of Sesterterpene Antibiotics

Abstract

The global rise of antibiotic resistance poses a public health challenge, emphasizing the urgent need for novel antibiotics featuring unique chemical scaffolds and mechanisms of action. Here, we report the discovery and characterization of darumycins, guanidine-containing pentacyclic sesterterpene antibiotics that exhibit potent activity against high-priority Gram-positive pathogens and mycobacteria. The darumycin biosynthetic gene cluster was identified through genome mining in the Actinobacterium Micromonospora rubida and heterologously expressed in Streptomyces chassis strains. Gene cluster engineering facilitated the discovery of novel darumycin derivatives, thereby expanding the chemical diversity within the sesterterpene class of natural products and revealing nuanced variations in their bioactivity. Targeted gene deletions, along with LC–MS and NMR analyses, enabled us to propose a darumycin biosynthetic pathway, further complemented by in vitro biochemical characterization of two O-methyltransferase tailoring enzymes, DarM and DarG. The high-resolution crystal structure of DarM in complex with SAH provided valuable insights into the enzymatic mechanism and revealed a distinct architecture compared to other methyltransferases acting on terpene scaffolds.