Uncovering the Molecular Landscape of Tetracycline Family Natural Products through Bacterial Genome Mining

Tetracycline (TC) family natural products have attracted
significant
attention due to their diverse chemical structures and important role
in drug development. As one of the most successful classes of drugs,
TC antibiotics have been used clinically for over 70 years and remain
crucial in treating infections. Despite their importance, systematic
exploration of novel TC natural products has been limited, leaving
the molecular landscape of the TC family poorly understood and hindering
further development of these compounds for therapeutic applications.
Here, we developed a targeted strategy to identify TC biosynthetic
gene clusters (BGCs) based on specific cyclase signatures involved
in assembling the TC scaffold. This led to the discovery of 82 representative
BGCs with the potential to produce structurally diverse TCs. Among
them, we uncovered three groups of novel natural productsmisiomycins,
varsomycins, and hibarimicins J–Land identified their
biosynthetic pathways. These compounds display distinctive structural
features, with misiomycin A and hibarimicin L among the most highly
modified TCs identified to date. Misiomycin A biosynthesis involves
extensive glycosylation, while biosynthesis of varsomycin A, featuring
a unique six-membered lactone ring structure, requires the coordinated
action of two TC BGCs. The biosynthesis of hibarimicins J–L,
derived from TC monomer dimerization, undergoes complex oxidative
modifications involving seven oxygenases. Several TCs exhibited potent
activity against drug-resistant Gram-positive pathogens. Our work
further expands the structural diversity within the TC family and
underscores the potential of these BGCs for generating new TC structures,
providing valuable insights for the discovery and development of novel
TC-based therapeutics.