Elucidating the function of the unknown Escherichia coli GTPase YjeQ through genetic interactions
Bibliographic record
Abstract
The protein YjeQ is a small GTPase that associates with the 30S ribosomal subunit. The slow steady state GTPase activity of YjeQ of 10 h −1 is stimulated 160 fold by this interaction, implicating the ribosome as the site of YjeQ function in the cell. Although dispensable in both Escherichia coli and Bacillus subtilis , strains lacking this protein are severely comprised for growth. Additionally, we have shown that this protein is a virulence determinant in a Staphylococcus aureus mouse infection model, implicating it as a potential target for the development of new antimicrobial agents. In this study we are looking at the genetic interactions of yjeQ to more precisely determine its role in the cell. Two methods were used to identify genetic interactions with yjeQ . The first was a screen of overexpression strains for correction of the yjeQ deletion slow growth phenotype. Using this method all essential E. coli genes were screened as well as 40 non‐essential translation related genes. A number of suppressors were identified, with one third functioning in translation or ribosome biogenesis. The suppressors were further screened for mechanism of suppression, and infB , era , and glnS were found to partially correct a ribosome defect associated with yjeQ deletion. As a second method to identify genetic interactions with yjeQ , double deletion strains were created with yjeQ and the non‐essential translation related genes. These double deletions were characterized for growth and implicate a number of genes as functionally related to yjeQ . Using this data we are creating a network of genes that interact with yjeQ and if they function up‐ or downstream in the cell. This work was funded by CIHR.
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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) | 0.001 | 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 | 0.001 |
| 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".