Skip to content

627d95ee00000955 Chondroitin sulfate catabolic process Mouse

Let me review this GO-CAM model "Chondroitin sulfate catabolic process (Mouse)" based on my knowledge of GO-CAM best practices. Here's my review:

GO-CAM Model Review: gomodel:627d95ee00000955

Title and Scope

  • Title: Chondroitin sulfate catabolic process (Mouse)
  • Taxon: Mouse (NCBITaxon:10090)
  • Status: Production
  • Comments: Sourced from gomodel:R-HSA-2024101

Model Overview

This GO-CAM represents the chondroitin sulfate catabolic process (GO:0030207) in mouse, depicting the enzymatic degradation pathway of chondroitin sulfate occurring in lysosomes.

Molecular Activities and Causal Flow Assessment

The model includes 7 activities connected in a causal flow using the "provides input for" (RO:0002413) predicate:

  1. Galns (MGI:MGI:1355303) - N-acetylgalactosamine-6-sulfatase activity (GO:0043890)

  2. Provides input for Hyal1, Hyal3 and Hyal4 activities

  3. Arsb (MGI:MGI:88075) - N-acetylgalactosamine-4-sulfatase activity (GO:0003943)

  4. Provides input for Hyal1, Hyal3 and Hyal4 activities

  5. Hyal1 (MGI:MGI:96298) - Chondroitin hydrolase activity (GO:0052757)

  6. Provides input for Gusb activity

  7. Hyal3 (MGI:MGI:1330288) - Chondroitin hydrolase activity (GO:0052757)

  8. Provides input for Gusb activity

  9. Hyal4 (MGI:MGI:1924292) - Chondroitin hydrolase activity (GO:0052757)

  10. Provides input for Gusb activity

  11. Gusb (MGI:MGI:95872) - Beta-glucuronidase activity (GO:0004566)

  12. Provides input for Hexb activity

  13. Hexb (MGI:MGI:96074) - Hexosaminidase activity (GO:0015929)

  14. Terminal activity in the pathway

Evidence Assessment

  • Most activities have evidence codes and PMIDs supporting them
  • Evidence codes used: ECO:0000315 (mutant phenotype evidence), ECO:0000266 (sequence orthology evidence), ECO:0000314 (direct assay evidence)

Cellular Location

  • All activities occur in lysosomes (GO:0005764), which is appropriate for this degradation process

Strengths

  1. Consistent biological process annotation: All activities are accurately associated with chondroitin sulfate catabolic process (GO:0030207)
  2. Appropriate cellular location: Lysosomal localization is correct for this degradation pathway
  3. Causal flow logic: The causal relationships using RO:0002413 correctly represent the sequential enzymatic activities in the degradation pathway
  4. Evidence support: Most activities have appropriate evidence with references

Issues and Recommendations

  1. Missing evidence for Hyal3 activity: The molecular function, cellular location, and biological process associations for Hyal3 lack evidence codes. I recommend adding appropriate evidence.

  2. Causal flow verification: While the model shows sulfatases (Galns, Arsb) providing input to hyaluronidases (Hyal1, Hyal3, Hyal4), the biological sequence of events should be verified. Typically, hyaluronidases break down the polymer, while sulfatases remove sulfate groups. The current flow suggests that sulfate removal happens before polymer cleavage.

  3. Completeness check: The model focuses on key enzymes but might be missing some steps in the complete chondroitin sulfate degradation pathway. Consider if other enzymes like iduronate-2-sulfatase or alpha-L-iduronidase might be relevant.

Summary

This GO-CAM model accurately represents the chondroitin sulfate catabolic process in mouse lysosomes with appropriate molecular functions, cellular locations, and causal relationships. The model is parsimonious and easy to understand, showing the enzymatic cascade involved in breaking down chondroitin sulfate. The primary recommendation is to add evidence for the Hyal3 activity and verify the biological sequence of events in the causal flow.