Characterization of an orphan specialized metabolite biosynthetic gene cluster in the potato common scab pathogen Streptomyces scabiei

Liu, Jingyu (2021) Characterization of an orphan specialized metabolite biosynthetic gene cluster in the potato common scab pathogen Streptomyces scabiei. Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Streptomyces scabiei is the main causative agent of potato common scab (CS) disease, which causes significant economic losses to potato growers worldwide. The ability of S. scabiei to cause CS is primarily based on the production of a phytotoxic specialized metabolite called thaxtomin A, which is an essential virulence factor for the organism. In addition, S. scabiei has the genetic potential to produce other specialized metabolites that might contribute to CS disease development; however, most of the genes predicted to be involved in production of these specialized metabolites are silent under laboratory conditions, and thus there is little known regarding the nature of these metabolites and their role in CS disease. The aim of this research was to characterize one cryptic specialized metabolite that is thought to resemble a phenazine. The putative biosynthetic genes that produce this cryptic metabolite are expressed at low levels or not at all under laboratory conditions, and therefore different strategies were employed to activate or enhance expression of these genes in S. scabiei. Specifically, the first approach taken was to use different bioinformatics tools to predict the boundaries of the biosynthetic gene cluster (BGC), and it is proposed that the BGC is much larger than initially thought. Molecular and culture-based strategies were successfully employed to activate expression of the BGC, and this also enabled a better understanding of the role of predicted regulatory genes in controlling the expression of the BGC. Metabolomics analysis conducted in this study suggests that the BGC is involved in the production of phenazine-related metabolites. This analysis additionally provided new insights into the overall specialized metabolic potential of S. scabiei and enabled the prediction of several novel compounds that were not previously known to be produced by this organism. The phenazine-like BGC is conserved in the genomes of other Actinobacteria, including two phytopathogenic Streptomyces spp. Although the role of the resulting metabolite(s) in the pathogenicity of S. scabiei remains unclear, evidence is presented in this thesis suggesting that the molecule(s) may exhibit antibacterial activity, and thus may have a function in inter-microbial interactions as described for other phenazine-producing organisms.

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