Characterization of Variation in Natural Product Production Under Chemical Elicitation Using Parallel Stable Isotope Labeling

Most microorganisms produce far fewer secondary metabolites
under
laboratory culture conditions than would be expected based on the
number of biosynthetic gene clusters (BGCs) present in their genomes.
One strategy for inducing secondary metabolite production is to add
chemical elicitors that disrupt bacterial metabolism. This one-strain-many-compounds
(OSMAC) strategy has been used successfully to discover a broad range
of natural products. However, traditional strategies for detecting
changes in natural product production are not well suited to characterizing
variations in the full secondary metabolome under elicitation conditions.
One efficient tool to differentiate metabolites between experiments
is IsoAnalyst, a parallel stable isotope labeling method that connects
secondary metabolites to BGCs by determining the rates of incorporation
for a set of isotopically labeled secondary metabolism building blocks.
In this study three strains of Paraburkholderia were profiled under a range of OSMAC conditions and changes in secondary
metabolism characterized using a combination of analytical tools including
IsoAnalyst. Using these profiles, we assessed the degree of novel
secondary metabolite production under different elicitation conditions.
Prioritization of one compound class strongly induced in the presence
of the antibiotic rifaximin led to the discovery of 2-hydroxyacyl
putrescine compounds putrescinamides A (1) and B (2). The structures of these new metabolites were determined
through a combination of multidimensional NMR experiments and total
synthesis, which permitted the determination of their full absolute
configurations. Together these stable isotope labeling experiments
provide a unique perspective on system-wide variation in de novo secondary
metabolite biosynthesis under elicitor conditions and highlight the
impact of elicitor selection on metabolite induction in Burkholderiales
strains.