id: Q6PEI9 gene_symbol: col1a1b product_type: PROTEIN status: DRAFT taxon: id: NCBITaxon:7955 label: Danio rerio description: >- 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. existing_annotations: - term: id: GO:0001501 label: skeletal system development evidence_type: IMP original_reference_id: PMID:28835471 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-180503-7 review: 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. action: ACCEPT 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). supported_by: - reference_id: PMID:28835471 supporting_text: while the dmh29 mutants exhibit mutations in a glycine residue of the col1a1b gene (G1123D), leading to a very similar phenotype. - reference_id: PMID:30082390 supporting_text: with col1a1bdmh29/+ fish displaying the most severe skeletal phenotype with kyphoscoliosis and shorter, thicker, and overmineralized vertebral bodies and frequent rib fractures - reference_id: PMID:30082390 supporting_text: Fish with a complete loss of α3(I), but intact α1(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. - term: id: GO:0005201 label: extracellular matrix structural constituent evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: enables review: summary: >- InterPro2GO/UniRule mapping from the fibrillar collagen C-terminal domain (IPR000885). action: ACCEPT reason: >- Correct but general. The more specific child GO:0030020 (conferring tensile strength) is present by IBA and is used in core_functions. supported_by: - reference_id: PMID:26876635 supporting_text: The identification of α3(I) peptides demonstrated for the first time the translation of the col1a1b gene in zebrafish. - term: id: GO:0005576 label: extracellular region evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: located_in review: summary: >- Automated location from ARBA/UniRule; the procollagen has a signal peptide and is secreted. action: ACCEPT reason: >- Correct, if general. Alpha3(I) is recovered in pepsin-extracted collagen from the matrix of bone, skin and scales. supported_by: - reference_id: PMID:26876635 supporting_text: The existence of the α3 chain was demonstrated at the protein level both in zebrafish embryos and in adult skin, scales and bone. - term: id: GO:0005737 label: cytoplasm evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - PANTHER:PTN002771199 - ZFIN:ZDB-GENE-030131-9102 review: 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). action: REMOVE 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 source_entities: - source_id: PANTHER:PTN002771199 source_label: PTN002771199 source_status: SOURCE_WEAK_OR_INFERRED comment: The node's only listed experimental source is the paralog col1a1a, so the IBD rests on a single mRNA-level observation. - source_id: ZFIN:ZDB-GENE-030131-9102 source_label: col1a1a source_status: SOURCE_BAD comment: Source IDA (PMID:19757382) is a col1a1 mRNA in situ used as a keratinocyte marker, not a protein localization. supported_by: - reference_id: PMID:26876635 supporting_text: The existence of the α3 chain was demonstrated at the protein level both in zebrafish embryos and in adult skin, scales and bone. - term: id: GO:0030020 label: extracellular matrix structural constituent conferring tensile strength evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables supporting_entities: - PANTHER:PTN001166351 - UniProtKB:P02462 - WB:WBGene00002280 review: summary: >- Phylogenetic propagation of the core structural function of collagens. action: ACCEPT 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. supported_by: - reference_id: PMID:30082390 supporting_text: The functional similarity between α1(I) and α3(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 α1(I) and α3(I) into the type I collagen triple helix. - term: id: GO:0030199 label: collagen fibril organization evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:88452 - MGI:MGI:88453 - MGI:MGI:88458 - PANTHER:PTN009074843 - RGD:61817 - RGD:621351 - UniProtKB:P02458 - UniProtKB:P02461 - UniProtKB:P05997 - UniProtKB:P08123 - ZFIN:ZDB-GENE-030131-9102 review: summary: >- IBA for fibrillar collagen chains, including zebrafish col1a1a among the sources. action: ACCEPT 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. supported_by: - reference_id: PMID:26876635 supporting_text: allowing the mature triple helix to self-assemble into fibrils - term: id: GO:0031012 label: extracellular matrix evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in supporting_entities: - FB:FBgn0000299 - FB:FBgn0016075 - MGI:MGI:104687 - MGI:MGI:104688 - MGI:MGI:1858212 - MGI:MGI:2152695 - MGI:MGI:2672118 - MGI:MGI:2685312 - MGI:MGI:88445 - MGI:MGI:88446 - MGI:MGI:88449 - MGI:MGI:88451 - MGI:MGI:88452 - MGI:MGI:88453 - MGI:MGI:88454 - MGI:MGI:88455 - MGI:MGI:88456 - MGI:MGI:88457 - MGI:MGI:88462 - MGI:MGI:88463 - MGI:MGI:88467 - MGI:MGI:88468 - PANTHER:PTN008390299 - RGD:2372 - RGD:2374 - RGD:61817 - RGD:621351 - RGD:70922 - RGD:71029 - UniProtKB:P02458 - UniProtKB:P02461 - UniProtKB:P02462 - UniProtKB:P02467 - UniProtKB:P05997 - UniProtKB:P08123 - UniProtKB:P08572 - UniProtKB:P12107 - UniProtKB:P20849 - UniProtKB:P20908 - UniProtKB:P29400 - UniProtKB:P53420 - UniProtKB:Q01955 - UniProtKB:Q03692 - UniProtKB:Q14031 - UniProtKB:Q14050 - UniProtKB:Q14055 - UniProtKB:Q7SIB2 - WB:WBGene00000527 - WB:WBGene00001263 - WB:WBGene00002280 review: summary: >- Deep collagen-family IBA for extracellular matrix. action: ACCEPT reason: >- Correct. Alpha3(I) is recovered from the collagen matrix of adult bone, skin and scales. supported_by: - reference_id: PMID:26876635 supporting_text: The existence of the α3 chain was demonstrated at the protein level both in zebrafish embryos and in adult skin, scales and bone. - term: id: GO:0043588 label: skin development evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:88453 - MGI:MGI:88467 - PANTHER:PTN002770836 - UniProtKB:P02461 review: summary: >- IBA from the COL1A1/COL3A1 node, based on mammalian skin phenotypes. action: KEEP_AS_NON_CORE 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. supported_by: - reference_id: PMID:26876635 supporting_text: SRM and spectral counting mass spectrometry data shows a statistically significant higher α3(I)/α1(I) ratio in external (skin and scales) versus internal (bone) tissues pointing out to a tissue-specific collagen composition. - term: id: GO:0048705 label: skeletal system morphogenesis evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in supporting_entities: - MGI:MGI:88453 - MGI:MGI:88467 - PANTHER:PTN002770836 review: summary: >- IBA from the COL1A1/COL3A1 node, based on mouse skeletal phenotypes. action: KEEP_AS_NON_CORE 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. supported_by: - reference_id: PMID:30082390 supporting_text: with col1a1bdmh29/+ fish displaying the most severe skeletal phenotype with kyphoscoliosis and shorter, thicker, and overmineralized vertebral bodies and frequent rib fractures - term: id: GO:0005584 label: collagen type I trimer evidence_type: IDA original_reference_id: PMID:26876635 review: 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. action: NEW 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. supported_by: - reference_id: PMID:26876635 supporting_text: The identification of α3(I) peptides demonstrated for the first time the translation of the col1a1b gene in zebrafish. - reference_id: PMID:26876635 supporting_text: 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 - reference_id: PMID:30082390 supporting_text: arguing for a dominant-negative effect on type I bone collagen and thus incorporation of a substantial amount of both α1(I) and α3(I) into the type I collagen triple helix. core_functions: - description: >- Col1a1b (alpha3(I)) is an additional structural chain of zebrafish type I collagen. It is incorporated with alpha1(I) (col1a1a) and alpha2(I) (col1a2) into triple-helical type I collagen of bone, skin and scales, where the three chains are present at about equal amounts, and it contributes to the fibrillar matrix that gives these tissues tensile strength. Its function overlaps that of alpha1(I) and is partly interchangeable with it: loss of alpha3(I) alone is tolerated, but reducing both chains causes bone fragility. Its share is higher in skin and scales than in bone. molecular_function: id: GO:0030020 label: extracellular matrix structural constituent conferring tensile strength directly_involved_in: - id: GO:0030199 label: collagen fibril organization - id: GO:0001501 label: skeletal system development locations: - id: GO:0031012 label: extracellular matrix in_complex: id: GO:0005584 label: collagen type I trimer supported_by: - reference_id: PMID:26876635 supporting_text: Even though in adult bone, skin and scales equal amounts of α1(I), α3(I) and α2(I) chains are present - reference_id: PMID:30082390 supporting_text: Heterozygous loss of either α1(I) or α3(I) did not induce any skeletal abnormalities, while reduced levels of both α1(I) and α3(I) (col1a1a+/−;col1a1b+/− mutants) causes a mild skeletal phenotype with increased bone fragility, arguing for interchangeability and functional redundancy between α1(I) and the homologous α3(I). - reference_id: PMID:28835471 supporting_text: while the dmh29 mutants exhibit mutations in a glycine residue of the col1a1b gene (G1123D), leading to a very similar phenotype. suggested_questions: - question: >- 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? - question: >- 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? - question: >- 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? suggested_experiments: - description: >- 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. experiment_type: structural mass spectrometry - description: >- 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. experiment_type: knock-in allele replacement - description: >- 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. experiment_type: biophysical characterization references: - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:28835471 title: 'Genetic Screen for Postembryonic Development in the Zebrafish (Danio rerio): Dominant Mutations Affecting Adult Form.' findings: - statement: dmh29 is a dominant glycine substitution in col1a1b with a short-stature skeletal phenotype similar to the col1a1a alleles. supporting_text: while the dmh29 mutants exhibit mutations in a glycine residue of the col1a1b gene (G1123D), leading to a very similar phenotype. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; genotype ZDB-GENO-180503-7 = col1a1b^dmh29/+ checked on ZFIN. - id: PMID:26876635 title: 'Zebrafish Collagen Type I: Molecular and Biochemical Characterization of the Major Structural Protein in Bone and Skin.' findings: - statement: col1a1b is translated; alpha3(I) is present in embryonic and adult type I collagen. supporting_text: The identification of α3(I) peptides demonstrated for the first time the translation of the col1a1b gene in zebrafish. - statement: Adult bone, skin and scales contain about equal amounts of the three chains; homotrimers are not significant. supporting_text: a significant presence of α1(I) or α3(I) homotrimers could be excluded in all three tissues - statement: The alpha3(I)/alpha1(I) ratio is higher in skin and scales than in bone. supporting_text: SRM and spectral counting mass spectrometry data shows a statistically significant higher α3(I)/α1(I) ratio in external (skin and scales) versus internal (bone) tissues - statement: col1a1b is co-expressed with col1a1a and col1a2 but not in the fin fold. supporting_text: Interestingly, only col1a1a was shown to be expressed in the median fin fold and in the apical ectodermal ridge of the pectoral fin at 48, 72 and 96 hpf - statement: pro-alpha3(I) lacks one inter-chain C-propeptide cysteine and has a more divergent chain recognition region. supporting_text: Also, the chain recognition region is more divergent in proα3 than in proα1 when compared to mammalian proα1 reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text. The main biochemical study of alpha3(I). - id: PMID:30082390 title: Zebrafish type I collagen mutants faithfully recapitulate human type I collagenopathies. findings: - statement: col1a1b nonsense mutants lack alpha3(I) and are viable; single heterozygotes are normal; double heterozygotes with col1a1a are fragile. supporting_text: Homozygous mutant col1a1b−/− mutants [loss of α3(I)] were present by the age of 3 mo, however at reduced numbers if combined with heterozygous loss of col1a1a (col1a1a+/−;col1a1b−/−). - statement: The authors interpret alpha1(I) as more abundant, i.e. a dosage asymmetry. supporting_text: This suggests a gene/protein dosage effect, where α1(I) is more abundant than α3(I), as hypothesized in our previous work (19). reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text. Not currently cited by any col1a1b GOA row. - id: PMID:14738308 title: Phylogenetic analysis of vertebrate fibrillar collagen locates the position of zebrafish alpha3(I) and suggests an evolutionary link between collagen alpha chains and hox clusters. findings: - statement: Zebrafish alpha3(I) cDNA cloned; alpha3(I) is phylogenetically closest to alpha1(I) and likely arose by its duplication. supporting_text: support the hypothesis that the alpha3(I) chain arose from a duplication of the alpha1(I) gene reference_review: relevance: HIGH correctness: VERIFIED review_notes: Abstract only. - id: PMID:11358497 title: Complete primary structure of rainbow trout type I collagen consisting of alpha1(I)alpha2(I)alpha3(I) heterotrimers. findings: - statement: In trout, skin collagen is alpha1alpha2alpha3 and muscle collagen is (alpha1)2alpha2; alpha3(I) has many Gly-Gly doublets. supporting_text: The subunit compositions of skin and muscle type I collagens from rainbow trout were found to be alpha1(I)alpha2(I)alpha3(I) and [alpha1(I)](2)alpha2(I), respectively. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; trout, not zebrafish. - id: PMID:3677606 title: 'Fish skin type I collagen: wide distribution of an alpha 3 subunit in teleosts.' findings: - statement: alpha3 is found in skin collagen of many but not all teleosts. supporting_text: The skin collagen seems to exist as an alpha 1 alpha 2 alpha 3 heterotrimer in many teleosts and as an (alpha 1)2 alpha 2 heterotrimer in some teleosts. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; protein chemistry, not gene-level. - id: PMID:1617936 title: Wide distribution of the skin type I collagen alpha 3 chain in bony fish. findings: - statement: An alpha3(I)-like chain was detected in white sturgeon skin collagen. supporting_text: The present study, however, has revealed the occurrence of alpha 3(I) in a chondrostean fish, white sturgeon. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only. Chromatographic chain identification; sturgeons have their own lineage-specific polyploidy, so this does not by itself date the col1a1a/col1a1b duplication. - id: PMID:34430038 title: Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences. findings: - statement: alpha3(I) evolves fastest of the three chains and is absent from some teleosts (two cyprinid genera, herring). supporting_text: This chain is, however, apparently absent from two of the five genera of cyprinids reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text. Absence is inferred from database searches. - id: file:DANRE/col1a1b/col1a1b-bioinformatics/RESULTS.md title: C-propeptide cysteine comparison of col1a1a and col1a1b reference_review: relevance: HIGH correctness: VERIFIED review_notes: Manual audit verified this reproducible sidecar supports the limited statement that col1a1b lacks one of the C-propeptide cysteines present in col1a1a; it does not directly test type I collagen trimer assembly. findings: - statement: One C-propeptide cysteine of alpha1(I) (C1265) is a serine in alpha3(I) (S1267); all other NC1-domain cysteines are conserved. supporting_text: col1a1a C1265 <-> col1a1b S1267