Discovery of lydiamycin biosynthetic gene cluster in a plant pathogen guides structural revision and identification of molecular target

Ford, Jonathan J., Santos-Aberturas, Javier, Hems, Edward S., Sallmen, Joseph W., Bögeholz, Lena A. K., Polturak, Guy, Osbourn, Anne, Wright, Joseph A., Rodnina, Marina V., Vereecke, Danny, Francis, Isolde M. and Truman, Andrew W. (2025) Discovery of lydiamycin biosynthetic gene cluster in a plant pathogen guides structural revision and identification of molecular target. Proceedings of the National Academy of Sciences of the United States of America (PNAS), 122 (21). ISSN 0027-8424

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Abstract

The natural products actinonin and matlystatin feature an N-hydroxy-2-pentyl-succinamyl (HPS) chemophore that facilitates metal chelation and confers their metalloproteinase inhibitory activity. Actinonin is the most potent natural inhibitor of peptide deformylase (PDF) and exerts antimicrobial and herbicidal bioactivity by disrupting protein synthesis. Here, we used a genomics-led approach to identify candidate biosynthetic gene clusters (BGCs) hypothesized to produce HPS-containing natural products. We show that one of these BGCs is on the pathogenicity megaplasmid of the plant pathogen Rhodococcus fascians and produces lydiamycin A, a macrocyclic pentapeptide. The presence of genes predicted to make an HPS-like chemophore informed the structural recharacterization of lydiamycin via NMR and crystallography to show that it features a rare 2-pentyl-succinyl chemophore. We demonstrate that lydiamycin A inhibits bacterial PDF in vitro and show that a cluster-situated PDF gene confers resistance to lydiamycin A, representing an uncommon self-immunity mechanism associated with the production of a PDF inhibitor. In planta competition assays showed that lydiamycin enhances the fitness of R. fascians during plant colonization. This study highlights how a BGC can inform the structure, biochemical target, and ecological function of a natural product.

Item Type:	Article
Additional Information:	Data, Materials, and Software Availability: Mass spectrometry data are available in the MassIVE repository with accession MSV000097741 (94). All other data are included in the manuscript and/or SI Appendix. Funding Information: This work was funded by a UK Research and Innovation Biotechnology and Biological Sciences Research Council (BBSRC) Norwich Research Park Doctoral Training Partnership grant (BB/M011216/1) for J.J.F. The work was also supported by BBSRC Institute Strategic Programme grants (BBS/E/J/000PR9790 and BB/X01097X/1) for the John Innes Centre (JIC). J.W.S. was funded by BBSRC grant BB/T015349/1. We wish to acknowledge the Diamond Light Source for access to beamline i04 under proposal MX32728.
Faculty \ School:	Faculty of Science > School of Biological Sciences Faculty of Science > School of Chemistry, Pharmacy and Pharmacology
Depositing User:	LivePure Connector
Date Deposited:	20 May 2025 09:30
Last Modified:	27 May 2025 03:30
URI:	https://ueaeprints.uea.ac.uk/id/eprint/99309
DOI:	10.1073/pnas.2424388122

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