Conserved structural features anchor biofilm‐associated <scp>RTX</scp>–adhesins to the outer membrane of bacteria
Bibliographic record
Abstract
Repeats‐in‐toxin ( RTX ) adhesins are present in many Gram‐negative bacteria to facilitate biofilm formation. Previously, we reported that the 1.5‐ MD a RTX adhesin ( Mp IBP ) from the Antarctic bacterium, Marinomonas primoryensis , is tethered to the bacterial cell surface via its N‐terminal Region I ( RI ). Here, we show the detailed structural features of RI . It has an N‐terminal periplasmic retention domain ( RIN ), a central domain ( RIM ) that can insert into the β‐barrel of an outer‐membrane pore protein during Mp IBP secretion, and three extracellular domains at its C terminus ( RIC ) that transition the protein into the extender region ( RII ). RIN has a novel β‐sandwich fold with a similar shape to βγ‐crystallins and tryptophan RNA attenuation proteins. Because RIM undergoes fast and extensive degradation in vitro , its narrow cylindrical shape was rapidly measured by small‐angle X‐ray scattering before proteolysis could occur. The crystal structure of RIC comprises three tandem β‐sandwich domains similar to those in RII , but increasing in their hydrophobicity with proximity to the outer membrane. In addition, the key Ca 2+ ion that rigidifies the linkers between RII domains is not present between the first two of these RIC domains. This more flexible RI linker near the cell surface can act as a ‘pivot’ to help the 0.6‐μm‐long Mp IBP sweep over larger volumes to find its binding partners. Since the physical features of RI are well conserved in the RTX adhesins of many Gram‐negative bacteria, our detailed structural and bioinformatic analyses serve as a model for investigating the surface retention of biofilm‐forming bacteria, including human pathogens.
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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) | 0.000 | 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) | 0.001 | 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".