A homing endonuclease‐rps3 gene fusion in Ophiostoma novo‐ulmi (Dutch Elm disease fungus)
Bibliographic record
Abstract
In O. novo‐ulmi a homing endonuclease gene (HEG) is sometimes located within the mitochondrial (mt) rnl gene, rps3. Homing endonucleases (HE) are DNA cutting enzymes that cleave at asymmetric recognition sites (12‐40bp) and HEGs are mobile elements that can be free standing or encoded within group I or group II introns. Here we characterize the LAGLIDADG type homing endonuclease: I‐Onu 1, that exists as part of a fusion protein, as the HEG inserted in‐frame into the C‐terminus of the mt‐rps3 gene. Within the filamentous ascomycetes fungi rps3 is encoded by a group I intron located within the mt‐rnl gene. Sequencing analysis of rps3 HEG (−) and HEG (+) strains suggests the presence of 4bp direct repeats (GAAT) flanking the HEG insertion sites. This is unexpected as exonucleolytic activity associated with HEG mobility is thought to remove any overhangs generated by the HE. In vitro endonuclease assays using plasmid DNA that contains the rps3 HEG (−) allele (pRPS3) confirmed HE activity. The cleavage sites were mapped using P 32 5′end‐labeled 201bp PCR fragment (with predicted HE target site) derived from rps3. The results showed that the HE cuts at GAAT generating a 3′ GAAT overhang confirming the sequence data analysis. Overall this endonuclease is unique as it inserts into an essential gene and generates 4bp direct repeats usually not observed in HEG mobility events. In general, the rare cutting HEases with characterized target/recognition and cleavage sites with 3′ overhangs are useful in genetic engineering and genomics.
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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 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 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".