Genome mining of rare actinomycetes

Vikeli, Eleni (2018) Genome mining of rare actinomycetes. Doctoral thesis, University of East Anglia.

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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.

Item Type: Thesis (Doctoral)
Faculty \ School: Faculty of Science > School of Biological Sciences
Depositing User: Jennifer Whitaker
Date Deposited: 11 Jun 2019 11:01
Last Modified: 07 Jun 2020 00:38

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