Discovery and Functional Analysis of Microbial Natural Products: From Burkholderia thailandensis to Other Microorganisms

Abstract

Microbial natural products have long provided a source of inspiration for drug discovery and development. Recently, the identification of an abundance of lowly-expressed or 'silent' natural product gene clusters has drawn attention to the vast underestimated biosynthetic potential of microorganisms. Activation of these silent gene clusters would enhance our repertoire of small molecules and potential drug leads.

Herein, we apply high-throughput elicitor screening (HiTES) to Burkholderia thailandensis E264 and study its enhanced secondary metabolome in the presence of the elicitor trimethoprim. This work led to the discovery of two new groups of natural products that we call acybolin and thailandiels. Expanding on the approach, we also implement a genetics-free strategy for inducing cryptic natural product by integrating HiTES with imaging mass spectrometry. This strategy was successfully applied to diverse microorganisms, leading to the identification of a cryptic lasso peptide with a novel post-translational modification and a new glycopeptide chemotype that is more potent in inhibiting respiratory syncytial virus than the currently-used drug ribavirin.

We also report mode of action (MOA) studies on natural products that are elicited by trimethoprim in B. thailandensis. A combination of bacterial cytological profiling, primary metabolite analysis, and biochemical assays was used to deduce the MOA of 4-hydroxy-3-methyl-2-(2-nonenyl)-quinoline (HMNQ). We find that HMNQ has dual targets and interrupts both the proton motive force and pyrimidine biosynthesis. MOA studies on thailandamide, a linear polyene natural product, revealed potent antimicrobial bioactivity and identified acetyl-CoA carboxylase, an enzyme that catalyzes the first committed step in fatty acid biosynthesis, as its biological target.