In situ activation and heterologous production of a cryptic lantibiotic from a plant-ant derived Saccharopolyspora species

Abstract

Most clinical antibiotics are derived from actinomycete natural products 19 (NPs) discovered at least 60 years ago. Repeated rediscovery of known compounds 20 led the pharmaceutical industry to largely discard microbial NPs as a source of new 21 chemical diversity but advances in genome sequencing revealed that these organisms 22 have the potential to make many more NPs than previously thought. Approaches to 23 unlock NP biosynthesis by genetic manipulation of the strain, by the application of 24 chemical genetics, or by microbial co-cultivation have resulted in the identification of 25 new antibacterial compounds. Concomitantly, intensive exploration of coevolved 26 ecological niches, such as insect-microbe defensive symbioses, has revealed these 27 to be a rich source of chemical novelty. Here we report the novel lanthipeptide 28 antibiotic kyamicin generated through the activation of a cryptic biosynthetic gene 29 2 cluster identified by genome mining Saccharopolyspora species found in the obligate 30 domatia-dwelling ant Tetraponera penzigi of the ant plant Vachellia drepanolobium. 31 Heterologous production and purification of kyamicin allowed its structural 32 characterisation and bioactivity determination. Our activation strategy was also 33 successful for the expression of lantibiotics from other genera, paving the way for a 34 synthetic heterologous expression platform for the discovery of lanthipeptides that are 35 not detected under laboratory conditions or that are new to nature. 37Importance. The discovery of novel antibiotics to tackle the growing threat of 38 antimicrobial resistance is impeded by difficulties in accessing the full biosynthetic 39 potential of microorganisms. The development of new tools to unlock the biosynthesis 40 of cryptic bacterial natural products will greatly increase the repertoire of natural 41 product scaffolds. Here we report an activation strategy that can be rapidly applied to 42 activate the biosynthesis of cryptic lanthipeptide biosynthetic gene clusters. This 43 allowed the discovery of a new lanthipeptide antibiotic directly from the native host and 44 via heterologous expression.45 46Antimicrobial resistance (AMR) is arguably the greatest health threat facing humanity 47 in the 21 st century (1-3). It is predicted that without urgent action, infectious disease 48 will become the biggest killer of humans by 2050 (1). The majority of clinically used 49 antibiotics are based on microbial natural products, isolated mostly from soil-dwelling 50 Streptomyces species and other filamentous actinomycete bacteria, and these 51 organisms remain a promising source of new antibiotics. Although the discovery 52 pipeline began to dry up in the 1960s, blighted by the rediscovery of known 53 compounds, we know from large scale genome sequencing that up to 90% of microbial 54 natural products are not produced under laboratory conditions (4). Thus, there exists 55 a wealth of novel chemistry waiting to be discovered by mining the genomes of these 56 organisms. Bearing in m...

Chemical warfare between fungus-growing ants and their pathogens

“…These symbiotic interactions are widespread in the plant and animal kingdoms and are all likely driven by chemical communication and chemical warfare. For example, a Kenyan fungus growing plant-ant system is already proving to be an exciting resource for the discovery of new chemical diversity [ 57 , 58 ]. Understanding the roles and regulation of microbial specialized metabolites in their natural habitats is crucial if we are to unlock and discover the vast range of activities encoded by these organisms.…”

Heterologous expression of a cryptic gene cluster from a marine proteobacterium Thalassomonas actiniarum affords new lanthipeptides thalassomonasins A and B

“…A new duramycin/cinnamycin analogous peptide named kyamicin was produced using a cryptic BGC of the actinobacterium Saccharopolyspora sp. in the host actinobacterium Streptomyces coelicolor (Vikeli et al, 2020). A new two-component lantibiotic roseocin was produced by heterologous gene expression using a cryptic BGC of the actinobacterium Streptomyces roseosporus (Singh et al, 2020).…”