Regulation of transcription by acetate in <i>Escherichia coli</i>: <i>in vivo</i> and <i>in vitro</i> comparisons
Bibliographic record
Abstract
Acetate, even at neutral pH, induces changes in gene expression that allow Escherichia coli to adapt to the diverse chemical stresses of the gastrointestinal tract. These include differential effects on transcription, including both activation and repression. The in vivo studies presented here show that cyclopropane fatty acid synthase transcription induced by neutral acetate proceeds via both the sigma70 and sigma38 forms of RNA polymerase. Upstream DNA elements are required in both cases, but in vitro studies demonstrate that the binding of regulatory factors is not needed. Sigma70 promoters respond towards acetate with very significant differences in vitro, with effects ranging from inhibition to lack of effect to weak stimulation to strong stimulation. By contrast, the effects of acetate on sigma38 transcription at these same promoters in vitro are generally stimulatory. Thus, acetate directly alters transcription complexes in vitro in ways that lead to significant differential transcription, contributing to the diverse effects that are known to allow adaptation in vivo.
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 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 | 0.000 |
| 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 teacher head, 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".