MESing around with a primula obconica type III polyketide synthase
Why this work is in the frame
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Bibliographic record
Abstract
Polyketide-derived compounds are key components of many pharmacologically relevant molecules; plants are a major source of polyketides and produce them using type III polyketide synthases (PKS). This research project investigates the role of a putative type III PKS (PoPKS) and a putative polyketide cyclase (PKC; PoDABB) in the biosynthesis of the benzoquinone primin produced by Primula obconica (primula). I hypothesized that primula uses these enzymes to produce olivetolic acid, which is further modified to primin in planta. Using heterologously expressed protein, the function of PoPKS and PoDABB were assayed in vitro and compared to that of a functionally similar type III PKS and PKC from Cannabis sativa, CsTKS and CsOAC. I was able to demonstrate that, like CsTKS, PoPKS is a type III PKS and is able to catalyze the synthesis of a triketide lactone, tetraketide lactone, and a linear tetraketide. PoDABB did not show any PKC activity but did increase the catalytic activity of PoPKS, suggesting that the protein may have another role in the primin pathway in planta. Interactions between the commonly used buffer MES and type III PKSs were observed that altered the activity of both PoPKS and CsTKS, allowing the enzymes to catalyze additional extension steps. An investigation of the compounds produced in the MES buffer systems suggest that PoPKS is able to catalyze the synthesis of pentaketide and hexaketide products as well as catalyze the cyclization of resorcylic acids, including olivetolic acid, without the need for a PKC. A homology model of PoPKS was developed and used to predict a novel type III PKS hydrogen binding network used to catalyze the release of a linear polyketide free acid; a tyrosine residue in this network may also participate in the cyclization of resorcylic acids.
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Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| 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 | 0.001 |
| 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 it