Characterization of an orphan specialized metabolite biosynthetic gene cluster in the potato common scab pathogen Streptomyces scabiei
Bibliographic record
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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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".