col1a1b (collagen type I alpha 1b; also known as col1a3) encodes the pro-alpha3(I) chain, a third type I collagen alpha chain found in most bony fishes but absent from tetrapods. It is one of two zebrafish co-orthologs of human COL1A1; its paralog col1a1a encodes alpha1(I), and the two arose by duplication of the ancestral alpha1(I) gene, most likely in the teleost-specific genome duplication. The 1449-aa secreted procollagen has the full fibrillar collagen architecture (signal peptide, von Willebrand factor type C domain in the N-propeptide, uninterrupted Gly-X-Y triple helix, fibrillar collagen NC1 C-propeptide) and is 78% identical to pro-alpha1(I). It differs from alpha1(I) at one of the inter-chain C-propeptide cysteines, in a more divergent chain recognition region, and in a higher Gly-Gly content of the helix. Alpha3(I) is translated in embryos and is a regular component of type I collagen in adult bone, skin and scales, where the three chains occur at about equal amounts, with a relatively higher alpha3(I) share in skin and scales than in bone. col1a1b is co-expressed with col1a1a and col1a2 in osteoblasts, tendon and ligament fibroblasts, myosepta and basal epidermis, but not in the fin fold. A dominant helix glycine substitution (dmh29) causes a severe osteogenesis imperfecta-like skeletal phenotype, showing that alpha3(I) is incorporated into bone collagen. Null mutants are viable with only mild bone changes, while combined heterozygous loss of col1a1a and col1a1b causes bone fragility.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0001501 skeletal system development | IMP PMID:28835471 Genetic Screen for Postembryonic Development in the Zebrafis... | ACCEPT | Summary: Genotype col1a1b^dmh29/+ (ZFIN). dmh29 is a dominant glycine substitution in the col1a1b triple helix, isolated in an adult screen for short stature, with strong vertebral deformation and excess bone formation. In the follow-up phenomic survey it is the most severe of the helix glycine alleles tested in the col1a1 paralogs. Reason: A dominant glycine substitution acts through the mutant chain being built into trimers, so this allele shows directly that alpha3(I) is part of skeletal type I collagen. col1a1b contributes structure to bone matrix, so the role is direct. The single-copy null phenotype is milder (fractures and increased mineral density in some fish), which fits a structural chain partly backed up by alpha1(I). Supporting Evidence: PMID:28835471 while the dmh29 mutants exhibit mutations in a glycine residue of the col1a1b gene (G1123D), leading to a very similar phenotype. PMID:30082390 with col1a1bdmh29/+ fish displaying the most severe skeletal phenotype with kyphoscoliosis and shorter, thicker, and overmineralized vertebral bodies and frequent rib fractures PMID:30082390 Fish with a complete loss of Ξ±3(I), but intact Ξ±1(I) did not show significant alterations of bone morphology (SI Appendix, Fig. S7), although some fish showed evidence of fractures (Fig. 1 and Table 2) and increased TMD throughout the vertebral column, indicating an impaired bone quality. |
| GO:0005201 extracellular matrix structural constituent | IEA GO_REF:0000120 | ACCEPT | Summary: InterPro2GO/UniRule mapping from the fibrillar collagen C-terminal domain (IPR000885). Reason: Correct but general. The more specific child GO:0030020 (conferring tensile strength) is present by IBA and is used in core_functions. Supporting Evidence: PMID:26876635 The identification of Ξ±3(I) peptides demonstrated for the first time the translation of the col1a1b gene in zebrafish. |
| GO:0005576 extracellular region | IEA GO_REF:0000120 | ACCEPT | Summary: Automated location from ARBA/UniRule; the procollagen has a signal peptide and is secreted. Reason: Correct, if general. Alpha3(I) is recovered in pepsin-extracted collagen from the matrix of bone, skin and scales. Supporting Evidence: PMID:26876635 The existence of the Ξ±3 chain was demonstrated at the protein level both in zebrafish embryos and in adult skin, scales and bone. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | REMOVE | Summary: IBA from PTN002771199, whose only listed experimental source is the paralog col1a1a (ZFIN:ZDB-GENE-030131-9102). That source is an IDA based on col1a1 mRNA in situ hybridization used as a keratinocyte marker (PMID:19757382). Reason: The only grounding is an mRNA localization of the paralog, which says nothing about where the protein acts. Alpha3(I) is a secreted matrix collagen whose structural activity is exerted in the extracellular matrix. The same row is removed from col1a1a for consistency. Propagation Review Root cause: SOURCE BAD Failure modes: SOURCE EVIDENCE WEAK COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN002771199 Β· PTN002771199 SOURCE WEAK OR INFERRED The node's only listed experimental source is the paralog col1a1a, so the IBD rests on a single mRNA-level observation. ZFIN:ZDB-GENE-030131-9102 Β· col1a1a SOURCE BAD Source IDA (PMID:19757382) is a col1a1 mRNA in situ used as a keratinocyte marker, not a protein localization. Supporting Evidence: PMID:26876635 The existence of the Ξ±3 chain was demonstrated at the protein level both in zebrafish embryos and in adult skin, scales and bone. |
| GO:0030020 extracellular matrix structural constituent conferring tensile strength | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic propagation of the core structural function of collagens. Reason: Alpha3(I) keeps the uninterrupted triple helix and the cross-linking lysines of alpha1(I). It is built into type I collagen of bone, skin and scales, and a dominant helix mutation causes bone fragility. The molecular function is conserved, so the IBA is correct for this duplicate. Supporting Evidence: PMID:30082390 The functional similarity between Ξ±1(I) and Ξ±3(I) is further illustrated by the fact that glycine substitutions in both genes can cause severe skeletal phenotypes, arguing for a dominant-negative effect on type I bone collagen and thus incorporation of a substantial amount of both Ξ±1(I) and Ξ±3(I) into the type I collagen triple helix. |
| GO:0030199 collagen fibril organization | IBA GO_REF:0000033 | ACCEPT | Summary: IBA for fibrillar collagen chains, including zebrafish col1a1a among the sources. Reason: As a subunit of fibril-forming type I collagen, alpha3(I) contributes structure to the fibrils. No col1a1b-specific fibril data exist, but nothing suggests loss of this ancestral property. Supporting Evidence: PMID:26876635 allowing the mature triple helix to self-assemble into fibrils |
| GO:0031012 extracellular matrix | IBA GO_REF:0000033 | ACCEPT | Summary: Deep collagen-family IBA for extracellular matrix. Reason: Correct. Alpha3(I) is recovered from the collagen matrix of adult bone, skin and scales. Supporting Evidence: PMID:26876635 The existence of the Ξ±3 chain was demonstrated at the protein level both in zebrafish embryos and in adult skin, scales and bone. |
| GO:0043588 skin development | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from the COL1A1/COL3A1 node, based on mammalian skin phenotypes. Reason: col1a1b is expressed in the basal epidermis. Alpha3(I) is a component of skin and scale collagen, relatively enriched there compared with bone. The term is plausible by inheritance, but no zebrafish skin phenotype has been reported for col1a1b, so it is non-core, as for col1a1a. Supporting Evidence: PMID:26876635 SRM and spectral counting mass spectrometry data shows a statistically significant higher Ξ±3(I)/Ξ±1(I) ratio in external (skin and scales) versus internal (bone) tissues pointing out to a tissue-specific collagen composition. |
| GO:0048705 skeletal system morphogenesis | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from the COL1A1/COL3A1 node, based on mouse skeletal phenotypes. Reason: Consistent with the dmh29 phenotype of kyphoscoliosis and short, thick vertebral bodies. The broader skeletal system development term already covers this role, so this one is kept as non-core, as for col1a1a. Supporting Evidence: PMID:30082390 with col1a1bdmh29/+ fish displaying the most severe skeletal phenotype with kyphoscoliosis and shorter, thicker, and overmineralized vertebral bodies and frequent rib fractures |
| GO:0005584 collagen type I trimer | IDA PMID:26876635 Zebrafish Collagen Type I: Molecular and Biochemical Charact... | NEW | Summary: Proposed location. Alpha3(I) peptides are identified by mass spectrometry in pepsin-extracted type I collagen from 48 hpf embryos and from adult bone, skin and scales. Amino acid composition (the Ile/Leu ratio) supports about equal amounts of alpha1(I), alpha2(I) and alpha3(I) and excludes significant homotrimers. Dominant helix glycine substitutions in col1a1b act dominantly on bone collagen. Reason: This is the complex alpha3(I) is a subunit of, and it is the central point for this paralog: col1a1b encodes an additional chain of the same complex, not a separate collagen type. GO:0005584 is defined as a collagen trimer containing alpha(I) chains, which includes the teleost alpha1(I)alpha2(I)alpha3(I) heterotrimer. The exact trimer stoichiometry, whether alpha1alpha2alpha3 alone or a mixture with (alpha1)2alpha2 and (alpha3)2alpha2, is unresolved, but the membership is established. The same term is proposed for col1a1a, and human COL1A1 carries it by IDA. Supporting Evidence: PMID:26876635 The identification of Ξ±3(I) peptides demonstrated for the first time the translation of the col1a1b gene in zebrafish. PMID:26876635 We demonstrated that, both in zebrafish embryos and adult tissues, three instead of two types of alpha chains contribute to the formation of the collagen type I triple helix PMID:30082390 arguing for a dominant-negative effect on type I bone collagen and thus incorporation of a substantial amount of both Ξ±1(I) and Ξ±3(I) into the type I collagen triple helix. |
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Download this section (compressed HTML)Q: What is the actual trimer composition in each tissue: alpha1alpha2alpha3 only, or a mixture with (alpha1)2alpha2 and (alpha3)2alpha2? How does the missing inter-chain C-propeptide cysteine of alpha3(I) constrain chain selection?
Q: Does alpha3(I) change the properties of the collagen it is part of, for example lower thermal stability from its high Gly-Gly content, or different cross-linking in skin and scales? Or is it a dosage copy of alpha1(I) with a neutral sequence drift?
Q: ZFIN has not annotated col1a1b from PMID:30082390 (the null sa12931 and the dominant dmh29 phenotypes); instead, a dmh29 genotype row is attached to col1a1a. Should that evidence be moved to col1a1b?
Experiment: Chain-resolved proteomics of cross-linked peptides (or intact trimers) from wild-type skin, scale and bone, to establish which trimer species exist and whether alpha3(I) pairs with alpha1(I) in the same molecule.
Type: structural mass spectrometry
Experiment: Swap test: knock the col1a1a coding sequence into the col1a1b locus (and the reverse) to ask whether alpha1(I) can fully replace alpha3(I) in skin and scale collagen and whether alpha3(I) can support actinotrichia.
Type: knock-in allele replacement
Experiment: Thermal stability (DSC) and fibril diameter of skin and scale collagen from col1a1b-/- fish compared with wild type, to test whether alpha3(I) changes the material properties of type I collagen.
Type: biophysical characterization
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