Protein–DNA interactions at the<i>Sulfolobus</i>spindle-shaped virus-1 (SSV1) T5 and T6 gene promoters
Bibliographic record
Abstract
Ultraviolet irradiation upregulates transcription from the Sulfolobus spindle-shaped virus 1 (SSV-1) T5, T(ind), and T6 genes promoters and also triggers viral DNA replication, but nothing is known about the proteins involved in this process. A notable feature of T5 and T6 promoters is that they contain 4 copies of a highly conserved DNA sequence 5'-ATAGATAGAGT-3'; 2 copies of this repeat are found in tandem upstream of the A-box, whereas 2 additional tandem copies span the initiator region from which transcription originates. By employing electrophoretic mobility gel-shift assays (EMSAs) and chemical modification interference analyses, I have identified a protein STRIP (SSV-1 T5/T6 region-interacting protein) in Sulfolobus shibatae extract that binds specifically to this sequence. Unique to S. shibatae, STRIP induces a 28 degrees bend in DNA. Surprisingly, despite the fact that STRIP binding masks the initiator region and can potentially interfere with preinitiation complex assembly, it does not appear to effect transcription driven from T5 and T6 promoters in vitro. Based on these results, I discuss the potential roles of STRIP in T5 and T6 transcription and in initiating SSV-1 DNA replication.
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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) | 0.001 | 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".