Soj (ParA) DNA binding is mediated by conserved arginines and is essential for plasmid segregation
Bibliographic record
Abstract
Soj is a member of the ParA family of ATPases involved in plasmid and chromosomal segregation. It binds nonspecifically and cooperatively to DNA although the function of this binding is unknown. Here, we show that mutation of conserved arginine residues that map to the surface of Bacillus subtilis Soj caused only minimal effects on nucleotide-dependent dimerization but had dramatic effects on DNA binding. Using a model plasmid partitioning system in Escherichia coli, we find that Soj DNA-binding mutants are deficient in plasmid segregation. The location of the arginines on the Soj structure explains why DNA binding depends on dimerization and was used to orient the Soj dimer on the DNA, revealing the axis of Soj polymerization. The arginine residues are conserved among other chromosomal homologues, including the ParAs from Caulobacter crescentus, Pseudomonas aeruginosa, Pseudomonas putida, Streptomyces coelicolor, and chromosome I of Vibrio cholerae indicating that DNA binding is a common feature of members of this family.
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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 | 0.001 | 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 | 0.001 |
| 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".