Understanding metabolic and regulatory control of antibiotic production in filamentous actinobacteria

Project Summary Bioactive molecules from nature are valuable templates for essential medicines. Filamentous actinobacteria are gifted producers of such molecules and rank among the richest sources yet discovered. They produce >50% of clinical antibiotics, plus numerous other medicines including immunotherapeutics and anticancer agents. These organisms dedicate a substantial fraction of their genomes to gene clusters predicted to encode drug-like compounds. Our research centers on a critical question: Why do the vast majority of actinobacterial biosynthetic gene clusters fail to yield anticipated products? There is an urgent need for new drug scaffolds and this problem transects multiple therapeutic areas. Gaining access to the plethora of yet-undiscovered drug-like molecules encoded within actinobacterial genomes could broadly revolutionize medicinal discovery and development. Coaxing actinobacteria to “turn-on” quiescent pathways is a challenge whose solution is fundamentally rooted in microbial physiology. Building on methodology and research insights established in our prior works, we here outline a multidisciplinary program that investigates two families of antibiotic molecules as models to reveal new mechanisms controlling production phenotypes. These molecules, polycyclic tetramate macrolactams and piperazyl-peptides, are broadly distributed among filamentous actinomycetes. They are largely chemically and biosynthetically distinct but share a common link via ornithine metabolism. Goal 1) Our prior works establish small nucleotide changes in transcriptional promoters can “tune” antibiotic production. How do these promoter polymorphisms exert their control? How can this knowledge be applied to override poor production traits? Goal 2) Certain piperazyl pathways respond positively to ornithine and related pathway intermediates. This suggests a mechanism of metabolic control. We ask: Because both types of antibiotics we study require ornithine precursors, might cellular ornithine status constitute an important regulatory component that could empower discovery strategies for both? Goal 3) We recently established a positive relationship between cellular growth on solid surfaces and polycyclic tetramate macrolactam production in certain strains. We hypothesize this intriguing relationship may extend to other antibiotic production pathways as well. We ask: How do actinobacterial surface interactions modulate bioactive molecule production, and might answering this deliver novel insights for broad-scale biosynthetic activation?