Investigating the specialized metabolism of the novel plant pathogen Streptomyces sp. 11-1-2

Díaz Cruz, Gustavo Adolfo (2023) Investigating the specialized metabolism of the novel plant pathogen Streptomyces sp. 11-1-2. Doctoral (PhD) thesis, Memorial University of Newfoundland.

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Abstract

Streptomyces is a genus of Gram-positive bacteria that are found in a wide range of environments and are capable of producing numerous specialized metabolites with diverse bioactivities. A small group of Streptomyces species is capable of causing plant diseases on a variety of crops. Notably, Streptomyces scabiei is one of the main causal agents of common scab disease, which affects multiple plants but is most relevant in potato production, as it significantly diminishes profits due to unmarketable tubers. To cause the disease, S. scabiei and most CS-causing pathogens use a specialized metabolite called thaxtomin A as the main pathogenicity factor. Recently, several reports have shown the isolation of plant-pathogenic Streptomyces strains that do not produce thaxtomin A, but instead produce other phytotoxic specialized metabolites. One example is Streptomyces sp. 11-1-2 a strain isolated in 2011 from a CS-symptomatic potato tuber in Newfoundland, Canada. This strain was shown to be highly pathogenic against differerent plant hosts, but it does not produce thaxtomin A or other reported phytotoxins. Notably, the phytotoxic activity of the strain was retained by extracts obtained with organic solvent, suggesting that the activity was associated with one or more specialized metabolites. The main objective of this work was to investigate the metabolic potential of Streptomyces sp. 11-1-2 in order to gain insights into the mechanisms used by this strain to inflict tissue damage on living plant hosts. In Chapter 3, the aim was to identify the main specialized metabolite(s) associated with the observed phytotoxic activity of the 11-1-2 strain using a combined genomics and metabolomics approach. Among the metabolites produced by the strain, nigericin and geldanamycin, which have previously been reported to exhibit phytotoxic activity, were identified. Bioassays with the pure compounds showed pitting and necrosis of potato tissue, while nigericin also impacted the development of radish seedlings. In Chapter 4, the aim was to further explore the specialized metabolites that are produced by the 11-1-2 strain and their associated bioactivities. The “One Strain, Many Compounds” (OSMAC) approach was used together with untargeted metabolomics and genomics to evaluate the production of predicted and novel specialized metabolites. It was determined that the 11-1-2 strain can produce elaiophylins, echosides, and niphimycins, and elaiophylin was found to exhibit some phytotoxic activity against potato tuber tissue. In Chapter 5, the aim was to construct mutants of 11-1-2 that were deficient in the synthesis of nigericin and geldanamycin in order to assess the contribution of these metabolites to the pathogenic phenotype of 11-1-2. Different plasmids targeting specific genes in the geldanamycin and nigericin biosynthetic gene clusters (BGC) were designed and constructed. The introduction of DNA into 11-1-2 via intergeneric conjugation was achieved using the integrative plasmid pSET152, but no DNA introduction was accomplished when using the plasmids targeting the nigericin and geldanamycin BGCs. Overall, this study represents an in-depth characterization of the novel plant pathogen Streptomyces sp. 11-1-2, which may utilize a different plant pathogenicity mechanism compared to other Streptomyces species.

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