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6258b8f300000188 Chondroitin sulfate biosynthetic process 1 chondroitin 6 sulfate proteoglycans Mouse

Let me review this GO-CAM model based on the information provided. The model describes the chondroitin sulfate biosynthetic process in mouse, focusing on chondroitin 6-sulfate proteoglycans.

Model Summary

  • Model ID: gomodel:6258b8f300000188
  • Title: Chondroitin sulfate biosynthetic process 1, chondroitin 6-sulfate proteoglycans (Mouse)
  • Taxon: Mouse (NCBITaxon:10090)
  • Status: Production
  • Source: gomodel:R-HSA-2022870

Review of the Model Structure

This GO-CAM represents the chondroitin sulfate biosynthetic process (GO:0030206), occurring in the Golgi apparatus (GO:0005794). The model includes multiple proteins involved in this process, with various molecular functions connected by causal relationships.

Key Proteins and Activities

The model includes several key proteins with specific molecular functions:

  1. Chondroitin synthesis enzymes:
  2. Csgalnact1 (MGI:MGI:2442354) - glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)
  3. Csgalnact2 (MGI:MGI:1926002) - glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)
  4. Chsy1 (MGI:MGI:2681120) - N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510) and glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)
  5. Chsy3 (MGI:MGI:1926173) - Similar activities as Chsy1
  6. Chpf (MGI:MGI:106576) - Both transferase activities

  7. Chpf2 (MGI:MGI:1917522) - N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)

  8. Sulfotransferases:

  9. Chst3 (MGI:MGI:1858224) - chondroitin 6-sulfotransferase activity (GO:0008459)
  10. Chst7 (MGI:MGI:1891767) - chondroitin 6-sulfotransferase activity (GO:0008459)

Causal Flow

The model represents a clear flow of activities in the biosynthetic pathway: - Initial transferase activities (Csgalnact1, Csgalnact2) provide input for subsequent transferase activities - These lead to the sulfotransferase activities (Chst3, Chst7) at the end of the chain

All activities are connected through the "provides input for" (RO:0002413) causal relation, which is appropriate for a biosynthetic pathway where the product of one reaction becomes the substrate for the next.

Quality Control Assessment

Biological Content Consistency

The model accurately represents the chondroitin sulfate biosynthetic process as described in the literature. The enzymes involved and their sequential activities in the pathway are well-represented.

GO-CAM Best Practices

  1. Cellular Component: All activities are correctly assigned to the Golgi apparatus (GO:0005794), which is the known location for chondroitin sulfate biosynthesis.

  2. Causal Relations: The model uses appropriate causal relationships (RO:0002413 "provides input for") to connect sequential enzymatic activities in the biosynthetic pathway.

  3. Evidence: Each activity is supported by evidence codes and literature references, which is excellent practice.

  4. Parsimony: The model is well-structured and focuses on the key aspects of the pathway without extraneous elements.

Evidence and References

The model includes appropriate evidence codes for the assertions: - ECO:0000314 (direct assay evidence) - ECO:0000315 (mutant phenotype evidence) - ECO:0000316 (genetic interaction evidence) - ECO:0000266 (sequence orthology evidence)

Each activity has references to primary literature (PMIDs) supporting the annotations.

Minor Improvement Suggestions

  1. Potential Addition: The model could potentially benefit from including the final product of the pathway (chondroitin 6-sulfate proteoglycan) as an output entity, although this is not strictly necessary as the pathway is already well-defined.

  2. Complex Representation: Given the collaborative nature of some of these enzymes in the biosynthetic process, considering whether any of these proteins work as a complex might be worth evaluating. However, based on the current evidence represented in the model, the individual representation of each enzyme and its activity appears appropriate.

Conclusion

This GO-CAM model gomodel:6258b8f300000188 is a high-quality representation of the chondroitin sulfate biosynthetic process in mouse. It follows GO-CAM best practices, includes appropriate evidence, and accurately represents the biological pathway with clear causal connections between activities. The model is scientifically sound and does not require significant revisions.