MESing around with a primula obconica type III polyketide synthase
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.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| 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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".