Genome mining of rare actinomycetes

The rise of antibiotic-resistant microbes, combined with an absence of novel antimicrobials in the development pipeline, raises the spectre of a post-antibiotic era and has prompted a resurgence of interest in antibiotic discovery and development. This project focuses on combining advanced genomics and bioinformatics with traditional bioassays and untargeted metabolomics, with the aim to explore the natural product repertoire of three Saccharopolyspora strains isolated from the cuticles of the Kenyan plant ants, Tetraponera penzigi. The three strains were sequenced using the PacBio RSII platform. Bioinformatics suggested the presence of at least 23 biosynthetic gene clusters (BGCs) in each strain. Interestingly, several of these are predicted to encode novel and uncommon members of chemotypes known to possess potent biological activity, including several potential anti-infective agents. We observed that the genomes of all three strains encode a cinnamycin-like BGC that proved silent despite culturing under a varied range of conditions. The isolate Saccharopolyspora sp. KY21 proved most tractable under laboratory conditions and was chosen as the basis for further study. I report the activation of this BGC by expression of two native genes under a constitutive promoter, kyaL and kyaR1. kyaL encodes a phosphatidyl ethanolamine methyl transferase gene which represents a self-immunity mechanism; resistance – kyaR1 encodes a pathway specific positive regulator of the SARP family. This led to the isolation and characterisation of kyamicin, a novel type B lantibiotic with activity against a range of Gram-positive bacteria. Furthermore, I describe the engineering of a platform for expression of type B lantibiotics, based on the kyamicin machinery. Additionally, I report the discovery of a novel NRPS-derived siderophore via the exploitation of untargeted metabolomics data, as well as preliminary attempts to isolate an antifungal compound via a bioassay-guided approach. Finally, I discuss the biosynthesis of sporeamicin from Saccharopolyspora sp. L53-18, an erythromycin-like macrolide antibiotic

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

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

Differential regulation of genes for cyclic-di-GMP metabolism orchestrates adaptive changes during rhizosphere colonization by Pseudomonas fluorescens

Bacteria belonging to the Pseudomonas genus are highly successful colonizers of the plant rhizosphere. The ability of different Pseudomonas species to live either commensal lifestyles or to act as agents of plant-growth promotion or disease is reflected in a large, highly flexible accessory genome. Nevertheless, adaptation to the plant environment involves a commonality of phenotypic outputs such as changes to motility, coupled with synthesis of nutrient uptake systems, stress-response molecules and adherence factors including exopolysaccharides. Cyclic-di-GMP (cdG) is a highly important second messenger involved in the integration of environmental signals with appropriate adaptive responses and is known to play a central role in mediating effective rhizosphere colonization. In this study, we examined the transcription of multiple, reportedly plant-upregulated cdG metabolism genes during colonization of the wheat rhizosphere by the plant-growth-promoting strain P. fluorescens SBW25. While transcription of the tested genes generally increased in the rhizosphere environment, we additionally observed a tightly orchestrated response to environmental cues, with a distinct transcriptional pattern seen for each gene throughout the colonization process. Extensive phenotypical analysis of deletion and overexpression strains was then conducted and used to propose cellular functions for individual cdG signaling genes. Finally, in-depth genetic analysis of an important rhizosphere colonization regulator revealed a link between cdG control of growth, motility and stress response, and the carbon sources available in the rhizosphere

Diversity of Pod Shape in Pisum

The seed-containing pod is the defining structure of plants in the legume family, yet pods exhibit a wide range of morphological variation. Within a species pod characters are likely to be correlated with reproductive strategy, and within cultivated forms will correspond to aspects of yield determination and/or end use. Here variation in pod size, described as pod length: pod width ratio, has been analyzed in pea germplasm represented by 597 accessions. This pod size variation is discussed with respect to population structure and to known classical pod morphology mutants. Variability of the pod length: width ratio can be explained by allelic variation at two genetic loci that may correspond to organ-specific negative regulators of growth