Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions
Bibliographic record
Abstract
Gene expression databases, acquired by proteomics and transcriptomics, describe physiological and developmental programs at the systems level. Here we analyze proteosynthetic profiles in a bacterium undergoing defined metabolic changes. Streptomyces coelicolor cultured in a defined liquid medium displays four distinct patterns of gene expression associated with growth on glutamate, diauxic transition, and growth on maltose and ammonia that terminates by starvation for nitrogen and entry into stationary phase. Principal component and fuzzy cluster analyses of the proteome database of 935 protein spot profiles revealed principal kinetic patterns. Online linkage of the proteome database (SWICZ) to a protein-function database (KEGG) revealed limited correlations between expression profiles and metabolic pathway activities. Proteins belonging to principal metabolic pathways defined characteristic kinetic profiles correlated with the physiological state of the culture. These analyses supported the concept that metabolic flux was regulated not by individual enzymes but rather by groups of enzymes whose synthesis responded to changes in nutritional conditions. Higher-level regulation is reflected by the distribution of all kinetic profiles into only nine groups. The observation that enzymes representing principal metabolic pathways displayed their own distinctive average kinetic profiles suggested that expression of a "high-flux backbone" may dominate regulation of metabolic flux.
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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".