Elucidating the Structure and Bioactivity of a Rhodococcus fascians Non-Ribosomal Peptide

Ford, Jonathan (2022) Elucidating the Structure and Bioactivity of a Rhodococcus fascians Non-Ribosomal Peptide. Doctoral thesis, University of East Anglia.

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Abstract

The rise of antimicrobial resistance has necessitated the discovery of novel antimicrobial compounds as a matter of urgency. Non-Ribosomal Peptides (NRPs) are a class of structurally diverse natural products used clinically as antibiotic and anticancer agents. Actinonin and the matlystatins are actinobacterial NRPs which inhibit metalloproteinases by the chelation of their catalytic metal ion. This bioactivity is conferred by the N-hydroxyl-2-pentyl succinamic acid group, referred to as the ‘warhead’ group. Actinonin is the most potent natural inhibitor of peptide deformylase (PDF, a key enzyme involved in bacterial protein synthesis) and has been the focus of much research into the development of therapeutic PDF inhibitors as antimicrobials. Therefore, there is interest in the identification of other warhead-containing natural products which may have potent bioactivities.

In this thesis, a genetic probe for warhead-containing NRP biosynthetic gene clusters (BGCs) is identified and a number of putative clusters are presented. One such BGC was present in the pathogenicity-associated megaplasmid of the plant pathogen Rhodococcus fascians. The product of the cluster was isolated from R. fascians and structural analysis indicated that it was the antimycobacterial agent lydiamycin A, originally identified from Streptomyces lydicus. Consideration of the BGC and extensive NMR analysis informed a structural revision of lydiamycin A. Lydiamycin A was confirmed to inhibit PDF in vitro. The LydA PDF is encoded within the lydiamycin BGC and has been experimentally determined to be resistant against lydiamycin A. This result implicates LydA as an important selfimmunity determinant for R. fascians. Finally, in planta competition assays frame lydiamycin as an important ecological factor that may enhance the fitness of R. fascians during niche colonisation.

This study highlights the power of targeted genome mining for the identification of BGCs that may produce structurally related natural products. This enabled structural revision and bioactivity characterisation of lydiamycin A.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	26 Oct 2023 11:02
Last Modified:	26 Oct 2023 11:02
URI:	https://ueaeprints.uea.ac.uk/id/eprint/93479
DOI:

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