Analysis of chondroitin degradation by components of a Bacteroides caccae polysaccharide utilization locus
Bibliographic record
Abstract
The human gut microbiota (HGM) possesses an enormously diverse capacity to metabolize both host and dietary glycans. Glycosaminoglycans (GAG) are complex polysaccharides that may be in the diet (e.g., from animal products) or may be presented by host tissues. These polysaccharides are known to be prioritized as a nutrient source by some members of the HGM. While significant advances in understanding how GAGs are metabolized by the HGM have been made, the varied architectures of the numerous polysaccharide utilization loci (PULs) targeting varied polysaccharides suggest that all the mechanisms of GAG degradation may not have been uncovered. Here we show that components of a (PUL) from Bacteroides caccae have activities consistent with comprising a unique pathway for depolymerization of chondroitin sulfate, a common GAG. After prior desulfation by an endo-sulfatase, BcSulf, to produce unsulfated chondroitin from chondroitin sulfate, the depolymerization pathway begins with the activity of a polysaccharide lyase from family 35, BcPL35. BcPL35 activity is coupled with BcGH88, an exo-β-uronyl hydrolase, and presumably BcGH109, a confirmed α/β-N-acetylgalactosaminidase. The most unique feature of the pathway is a β-D-glucuronate dehydratase, BcGDH, which we show through structural and functional analyses primes saturated non-reducing end β-D-glucuronate residues for hydrolysis by BcGH88. BcGDH is a member of a large family previously classified as glycoside hydrolase family 154. The potential reclassification of GH154 enzymes as uronate sugar dehydratases not only improves our understanding of chondroitin metabolism by B. caccae but will be broadly applicable to predicting the function of other pathways relevant to uronate sugar metabolism.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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) | 0.000 | 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 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".