Transcriptome-Proteome Profiling in <i>Burkholderia thailandensis</i> during the Transition from Exponential to Stationary Phase
Bibliographic record
Abstract
species. Like other bacterial cells, it commonly exists in the stationary phase, for instance, within a host cell. Understanding the molecular mechanisms that characterize the transition from exponential to stationary phases is therefore critical to understanding responses to stress or nutrient limitation. We present here an integrated transcriptomic and proteomic analysis of mRNA and protein abundance changes during entry into the stationary phase. We identified 928 differentially accumulating mRNAs and 832 differentially accumulating proteins. mRNAs encoding proteins involved in benzoate degradation and O-antigen nucleotide sugar biosynthesis were elevated in the stationary phase, whereas processes such as translation and flagellar biosynthesis were downregulated. Proteins related to fatty acid degradation and butanoate metabolism accumulated in the stationary phase along with proteins involved in the synthesis of secondary metabolites. Markedly downregulated proteins in the stationary phase included ribosomal proteins as well as the house-keeping iron-sulfur biogenesis proteins. An only modest correlation between transcriptome and proteome changes was seen, and the RpoS sigma factor was not significantly increased during the stationary phase; RpoS is typically abundant during the stationary phase and critical for expression of stress-response genes. Our data point to distinct adaptive mechanisms, possibly including post-translational regulation.
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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 | 0.002 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.002 |
| 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) | 0.000 | 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".