In Situ Activation and Heterologous Production of a Cryptic Lantibiotic from an African Plant Ant-Derived Saccharopolyspora Species

Abstract

Most clinical antibiotics are derived from actinomycete natural products discovered at least 60 years ago. However, the repeated rediscovery of known compounds led the pharmaceutical industry to largely discard microbial natural products (NPs) as a source of new chemical diversity. Recent advances in genome sequencing have revealed that these organisms have the potential to make many more NPs than previously thought. Approaches to unlock NP biosynthesis by genetic manipulation of strains, by the application of chemical genetics, or by microbial cocultivation have resulted in the identification of new antibacterial compounds. Concomitantly, intensive exploration of coevolved ecological niches, such as insect-microbe defensive symbioses, has revealed these to be a rich source of chemical novelty. Here, we report the new lanthipeptide antibiotic kyamicin, which was generated through the activation of a cryptic biosynthetic gene cluster identified by genome mining Saccharopolyspora species found in the obligate domatium-dwelling ant Tetraponera penzigi of the ant plant Vachellia drepanolobium. Transcriptional activation of this silent gene cluster was achieved by ectopic expression of a pathway-specific activator under the control of a constitutive promoter. Subsequently, a heterologous production platform was developed which enabled the purification of kyamicin for structural characterization and bioactivity determination. This strategy was also successful for the production of lantibiotics from other genera, paving the way for a synthetic heterologous expression platform for the discovery of lanthipeptides that are not detected under laboratory conditions or that are new to nature. IMPORTANCE The discovery of novel antibiotics to tackle the growing threat of antimicrobial resistance is impeded by difficulties in accessing the full biosynthetic potential of microorganisms. The development of new tools to unlock the biosynthesis of cryptic bacterial natural products will greatly increase the repertoire of natural product scaffolds. Here, we report a strategy for the ectopic expression of pathway-specific positive regulators that can be rapidly applied to activate the biosynthesis of cryptic lanthipeptide biosynthetic gene clusters. This allowed the discovery of a new lanthipeptide antibiotic directly from the native host and via heterologous expression.

Marine Actinobacteria: Screening for Predation Leads to the Discovery of Potential New Drugs against Multidrug-Resistant Bacteria

“…Cryptic gene clusters in Actinobacteria are now regarded as an untapped source of bacterial secondary metabolites [17]. Consequently, nowadays, various approaches are being tested to stimulate the production of microbial secondary metabolites by Actinobacteria [13,[18][19][20][21].…”

Structural Analysis of Class I Lanthipeptides from Pedobacter lusitanus NL19 Reveals an Unusual Ring Pattern

“…These observations highlight both the challenges of a genome mining strategy that prioritizes lanthipeptide precursor peptides that are as different as possible from previously characterized family members and the opportunities for discovering new functions of natural products in microbial ecology. Indeed, only a subset of lanthipeptides identified thus far by genome mining have identifiable bioactivities, and this subset has often consisted of structural analogues of known lantibiotics. ,,,− On the contrary, many others with novel ring patterns are still awaiting identification of their functions. ,,,,− Historically natural products with antimicrobial activity have been prioritized for their potential application as therapeutics, but the RiPPs now discovered by genome mining provide the opportunity to learn more about chemical ecology in the microbial world. − …”

Discovery and characterisation of an amidine-containing ribosomally-synthesised peptide that is widely distributed in nature

“…The small size of streptamidine and the lack of conventional (ox/thi)azoles prompted further MS analysis using methodology optimised for larger peptides. 50 In some S. coelicolor M1146-pCAPSalbC cultures, a potential pathway-related compound with m / z 414.69 was observed (Fig. S8 † ), but this was never observed in S. albidoflavus J1074 (Fig.…”