Discovery of a family of γ-aminobutyrate ureas via rational derepression of a silent bacterial gene cluster

Abstract

Gaburedins, a family of g-aminobutyrate (GABA)-derived ureas, have been discovered by deletion of gbnR, an arpA-like putative transcriptional repressor in Streptomyces venezuelae ATCC 10712. Comparison of metabolite profiles in the wild type and mutant strains revealed six metabolites in the mutant that are lacking from the wild type. The structure of gaburedin A was established by HRMS combined with 1-and 2-D NMR spectroscopy and was confirmed by total synthesis. The other metabolites were confirmed as congeners using HRMS, MS/MS and feeding of putative biosynthetic precursors. Two genes, gbnA and gbnB, are proposed to be involved in gaburedin biosynthesis. Consistent with this hypothesis, deletion of gbnB in the gbnR mutant abolished gaburedin production. This is the first report to disclose the discovery of novel natural products via rational deletion of a putative pathway-specific regulatory gene.

Targeted activation of silent natural product biosynthesis pathways by reporter-guided mutant selection

“…Furthermore, many methods limit the manipulation attempts to the target gene cluster (e.g. manipulation of pathway specific regulatory genes (Bergmann et al, 2007;Bunet et al, 2011;Gottelt et al, 2010;Laureti et al, 2011;Sidda et al, 2014) or promoter exchange experiments (Luo et al, 2013;Olano et al, 2014)), whereas RGMS is able to probe the whole genome to drive expression of the selected secondary metabolic pathway. In other words, RGMS is a method to manipulate target gene(s) expression via genome-wide trans mutations.…”

“…Only a recently developed screening platform for small molecule elicitors hold some promise for specific activation of selected gene cluster without heterologous expression (Seyedsayamdost, 2014). Manipulation of either pathway specific or global regulatory genes (Bergmann et al, 2007;Bunet et al, 2011;Gottelt et al, 2010;Laureti et al, 2011;Olano et al, 2014;Sidda et al, 2014) by genetic engineering may also result in the activation of another pathway instead of the desired gene cluster. Promoter exchange experiments (Luo et al, 2013;Olano et al, 2014) are able to connect the activation to a targeted genetic locus, but are only feasible in relatively simple systems that are composed of few operons.…”

Omics-based natural product discovery and the lexicon of genome mining

“…Despite these significant unknowns, there are numerous examples where orphan BGCs have yielded new compounds[34,40,62–64], thus supporting the concept that genome mining and associated omic approaches hold considerable promise for NP discovery. The continued development and application of these technologies will help fill the knowledge gaps discussed above and allow for the better exploitation of NP resources.…”

Using natural products for drug discovery: the impact of the genomics era

“…, including the production of an unprecedented 51-membered glycosylated macrolide [53]. On the other hand, deletion of pathway-specific repressors has been demonstrated to activate a number of silent BGCs and trigger metabolite production [54, 55, 56]. Likewise, manipulation of transcription factors in plants has yielded the overproduction of desired metabolites [57].…”