id: A0A0S2I7K2
gene_symbol: vclb
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:7955
  label: Danio rerio
description: vclb (vinculin b) is one of two zebrafish co-orthologs of vertebrate vinculin (VCL), retained from
  the teleost-specific genome duplication; its paralog is vcla. It encodes a cytoplasmic actin-binding adaptor of
  focal adhesions and adherens junctions that binds talin and alpha-catenin through its head domain and F-actin
  and paxillin through its tail. The protein conserves the binding residues of mammalian vinculin but carries phenylalanine
  at the position of the regulatory tyrosine Y822; GFP-tagged Vclb still localizes to focal adhesions and, via the
  alpha-catenin vinculin-binding site, to adherens junctions. vclb is the predominant vinculin copy in the embryonic
  heart, including epicardium and endocardium, and is the copy most prominently expressed in endothelial cells,
  where it marks focal adhesions and cell-cell junctions. vclb mutants develop epicardial hyperplasia, disorganized
  coronary vessels with elevated FAK and ERK phosphorylation, and die as juveniles. Combined loss with vcla causes
  leakage of small molecules from embryonic vessels. vclb mRNA is upregulated when vcla mutant transcripts undergo
  nonsense-mediated decay (transcriptional adaptation).
existing_annotations:
- term:
    id: GO:0002102
    label: podosome
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0295
  review:
    summary: Podosome localization mapped from the UniProt subcellular location vocabulary (ARBA rule).
    action: KEEP_AS_NON_CORE
    reason: Vinculin is a podosome component in mammalian cells, and the ARBA-derived location is a family-level
      transfer. There is no zebrafish evidence for podosomes containing this copy, and podosomes are not where the
      zebrafish mutant phenotypes lie; kept as a plausible non-core location.
- term:
    id: GO:0003779
    label: actin binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR017997
  review:
    summary: Actin binding from the InterPro vinculin family signature.
    action: ACCEPT
    reason: Vinculin binds F-actin through its tail domain, and the tail helices that mediate F-actin and paxillin
      binding are almost identical between the zebrafish copies and higher vertebrates. Correct, though less specific
      than the co-annotated actin filament binding (GO:0051015).
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: Especially Helices 3–5 which mediate paxillin and F-actin binding (Fig 1E) [52,53] are almost
        completely identical.
- term:
    id: GO:0005198
    label: structural molecule activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR000633
  review:
    summary: Structural molecule activity from an InterPro vinculin conserved-site mapping.
    action: MARK_AS_OVER_ANNOTATED
    reason: Vinculin is a mechanosensitive linker that couples talin and alpha-catenin to F-actin; it is not a structural
      constituent in the sense of a filament or matrix protein. The informative activities (actin filament binding,
      alpha-catenin binding) are already annotated, so this vague parent adds nothing and implies a role the protein
      does not have.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: Vinculin binds the adherens junction component α-catenin, which interacts with cadherin-bound
        β-catenin through its N-terminal head domain, and links the cadherin complex to F-actin using its C-terminal
        tail.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  supporting_entities:
  - MGI:MGI:98927
  - PANTHER:PTN005285701
  - RGD:1311217
  - UniProtKB:P12003
  - UniProtKB:P18206
  - WB:WBGene00000942
  - dictyBase:DDB_G0273107
  - dictyBase:DDB_G0281499
  - dictyBase:DDB_G0285939
  review:
    summary: Cytoplasmic protein (IBA).
    action: ACCEPT
    reason: Vinculin is a cytoplasmic, membrane-associated cytoskeletal protein. Both TGD copies descend from the
      PANTHER PTN005285701 vinculin node, so the IBA is expected on vclb and vcla alike; nothing in the vclb sequence
      or phenotype argues for loss of the function.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
- term:
    id: GO:0005856
    label: cytoskeleton
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  supporting_entities:
  - MGI:MGI:98927
  - PANTHER:PTN005285701
  - RGD:1311217
  - UniProtKB:P12003
  - WB:WBGene00000942
  - dictyBase:DDB_G0273107
  - dictyBase:DDB_G0281499
  review:
    summary: Cytoskeleton (IBA).
    action: ACCEPT
    reason: Vinculin is an actin-cytoskeleton-associated protein at adhesion sites. Both TGD copies descend from
      the PANTHER PTN005285701 vinculin node, so the IBA is expected on vclb and vcla alike; nothing in the vclb
      sequence or phenotype argues for loss of the function.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: Vinculin binds the adherens junction component α-catenin, which interacts with cadherin-bound
        β-catenin through its N-terminal head domain, and links the cadherin complex to F-actin using its C-terminal
        tail.
- term:
    id: GO:0005856
    label: cytoskeleton
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0090
  review:
    summary: Cytoskeleton from UniProt subcellular location mapping.
    action: ACCEPT
    reason: Consistent with the IBA row and the known actin association of vinculin.
- term:
    id: GO:0005886
    label: plasma membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  supporting_entities:
  - FB:FBgn0004397
  - MGI:MGI:98927
  - PANTHER:PTN005285701
  - RGD:1311217
  - UniProtKB:P12003
  - WB:WBGene00000942
  - dictyBase:DDB_G0273107
  review:
    summary: Plasma membrane (IBA); vinculin sits on the cytoplasmic face of adhesion sites.
    action: ACCEPT
    reason: Vinculin is a peripheral protein at the cytoplasmic face of integrin and cadherin adhesions. Both TGD
      copies descend from the PANTHER PTN005285701 vinculin node, so the IBA is expected on vclb and vcla alike;
      nothing in the vclb sequence or phenotype argues for loss of the function.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
- term:
    id: GO:0005911
    label: cell-cell junction
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  supporting_entities:
  - ARBA:ARBA00028427
  review:
    summary: Cell-cell junction (ARBA).
    action: ACCEPT
    reason: Correct but general; the more specific adherens junction term is supported experimentally for both copies
      in the same cell assay.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
- term:
    id: GO:0005912
    label: adherens junction
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  supporting_entities:
  - MGI:MGI:98927
  - PANTHER:PTN005285701
  - UniProtKB:P12003
  - UniProtKB:P18206
  - ZFIN:ZDB-GENE-050506-61
  - ZFIN:ZDB-GENE-131017-1
  review:
    summary: Adherens junction (IBA).
    action: ACCEPT
    reason: 'Both zebrafish copies are among the descendant evidences (ZFIN:ZDB-GENE-050506-61 = vcla, ZFIN:ZDB-GENE-131017-1
      = vclb) used for this node, which is expected: each has its own IDA from PMID:28767718. Recruitment to adherens
      junctions depends on the alpha-catenin vinculin-binding site for both copies. Both TGD copies descend from
      the PANTHER PTN005285701 vinculin node, so the IBA is expected on vclb and vcla alike; nothing in the vclb
      sequence or phenotype argues for loss of the function.'
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
    - reference_id: PMID:28767718
      supporting_text: Here it is apparent that both vinculin A and vinculin B are now excluded from Focal Adherens
        Junctions and Linear Adherens Junctions (arrows), but are still present in Focal Adhesions (arrows).
- term:
    id: GO:0005912
    label: adherens junction
  evidence_type: IDA
  original_reference_id: PMID:28767718
  qualifier: located_in
  review:
    summary: GFP-tagged zebrafish vclb localizes to focal and linear adherens junctions in MDCK cells, dependent
      on the alpha-catenin vinculin-binding site.
    action: ACCEPT
    reason: Direct localization assay of the zebrafish protein in epithelial cells; junctional recruitment is lost
      when alpha-catenin lacks its vinculin-binding site, showing the canonical recruitment mechanism. Both copies
      behave the same in this assay.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
    - reference_id: PMID:28767718
      supporting_text: Here it is apparent that both vinculin A and vinculin B are now excluded from Focal Adherens
        Junctions and Linear Adherens Junctions (arrows), but are still present in Focal Adhesions (arrows).
- term:
    id: GO:0005912
    label: adherens junction
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0009
  review:
    summary: Adherens junction from UniProt subcellular location mapping.
    action: ACCEPT
    reason: Consistent with the IDA and IBA rows for the same term.
- term:
    id: GO:0005925
    label: focal adhesion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  supporting_entities:
  - MGI:MGI:98927
  - PANTHER:PTN005285701
  - RGD:1311217
  - UniProtKB:P12003
  - UniProtKB:P18206
  - ZFIN:ZDB-GENE-050506-61
  - dictyBase:DDB_G0281499
  review:
    summary: Focal adhesion (IBA).
    action: ACCEPT
    reason: Both copies localize to integrin-based focal adhesions independently of alpha-catenin. Both TGD copies
      descend from the PANTHER PTN005285701 vinculin node, so the IBA is expected on vclb and vcla alike; nothing
      in the vclb sequence or phenotype argues for loss of the function.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
    - reference_id: PMID:28767718
      supporting_text: Here it is apparent that both vinculin A and vinculin B are now excluded from Focal Adherens
        Junctions and Linear Adherens Junctions (arrows), but are still present in Focal Adhesions (arrows).
- term:
    id: GO:0005925
    label: focal adhesion
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: located_in
  supporting_entities:
  - ARBA:ARBA00028361
  - UniProtKB-SubCell:SL-0118
  review:
    summary: Focal adhesion (combined IEA).
    action: ACCEPT
    reason: Consistent with experimental localization of both copies to focal adhesions.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
- term:
    id: GO:0007155
    label: cell adhesion
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  supporting_entities:
  - MGI:MGI:98927
  - PANTHER:PTN005285701
  - UniProtKB:P12003
  - UniProtKB:P18206
  review:
    summary: Cell adhesion (IBA).
    action: ACCEPT
    reason: Vinculin reinforces integrin- and cadherin-based adhesions by linking them to actin; this is the core
      process of the protein. Both TGD copies descend from the PANTHER PTN005285701 vinculin node, so the IBA is
      expected on vclb and vcla alike; nothing in the vclb sequence or phenotype argues for loss of the function.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: Vinculin binds the adherens junction component α-catenin, which interacts with cadherin-bound
        β-catenin through its N-terminal head domain, and links the cadherin complex to F-actin using its C-terminal
        tail.
    - reference_id: PMID:36260739
      supporting_text: Together, the data show that vinculin tightens endothelial junctions in blood vessels.
- term:
    id: GO:0007155
    label: cell adhesion
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  supporting_entities:
  - InterPro:IPR000633
  - InterPro:IPR006077
  - InterPro:IPR036723
  review:
    summary: Cell adhesion from InterPro vinculin family signatures.
    action: ACCEPT
    reason: Consistent with the IBA row and the conserved adhesion-linker function.
- term:
    id: GO:0007507
    label: heart development
  evidence_type: IMP
  original_reference_id: PMID:27578788
  qualifier: acts_upstream_of_or_within
  supporting_entities:
  - ZFIN:ZDB-GENO-170321-9
  review:
    summary: vclb gene-trap mutants have multiple cardiac defects, epicardial hyperplasia and coronary vessel disorganization,
      and die as juveniles.
    action: ACCEPT
    reason: Direct loss-of-function evidence for this copy (abstract-only cache; defer to the ZFIN curator for details).
      Consistent with vclb being the predominant vinculin copy in the embryonic heart and the copy expressed in
      epicardium and endocardium. Heart development is broad; the more specific coronary vasculature term below
      captures the best-characterized defect.
    supported_by:
    - reference_id: PMID:27578788
      supporting_text: We report a zebrafish gene-trap vinculin b (vclb) mutant that displays abnormal coronary
        vessel development among multiple cardiac defects.
    - reference_id: PMID:27578788
      supporting_text: The mutant shows overproliferation of epicardium-derived cells and disorganization of coronary
        vessels, and they eventually die off at juvenile stages.
    - reference_id: PMID:30635353
      supporting_text: A recent report showed that vclb is the predominant vcl gene expressed in the embryonic heart
        (Cheng et al., 2016).
- term:
    id: GO:0008013
    label: beta-catenin binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  supporting_entities:
  - PANTHER:PTN005285701
  - UniProtKB:P12003
  - dictyBase:DDB_G0285939
  review:
    summary: Beta-catenin binding (IBA).
    action: UNDECIDED
    reason: The PAINT node is sound for vertebrate vinculin, but vclb carries F at the position of Y822, the tyrosine
      whose phosphorylation was reported to be needed for vinculin-beta-catenin binding, and the Y822F mutation
      of chicken vinculin abrogated the interaction. Vclb still reaches cell-cell junctions in MDCK cells via alpha-catenin,
      which does not test beta-catenin binding. This is a candidate target-specific divergence inside the clade,
      so the inheritance of this particular activity by vclb is unresolved until binding is tested directly.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: The one notable difference between zebrafish vinculin A and B is the change of the otherwise
        conserved Y at position 822 to F in vinculin B.
    - reference_id: PMID:28767718
      supporting_text: Curiously, the 822F residue in zebrafish vinculin B does not perturb its localization to
        cell-cell junctions.
    propagation_review:
      root_cause: UNRESOLVED
      failure_modes:
      - FUNCTIONAL_DIVERGENCE
      residue_claims:
      - claim_type: SUBSTITUTED
        anchor:
          accession: UniProtKB:P18206-2
          position: 822
          residue: Y
        target:
          accession: UniProtKB:A0A0S2I7K2
          position: 822
          residue: F
          sequence_version: 1
        role: Phosphotyrosine reported to be required for vinculin-beta-catenin binding in mammalian cells
        method: MSA
        comment: Global BLOSUM62 alignment (genes/DANRE/vcla/vcla-bioinformatics/compare_vinculins.py); substitution
          also reported by PMID:28767718. vcla retains Y at this position.
      source_entities:
      - source_id: PANTHER:PTN005285701
        comment: Vertebrate/metazoan vinculin node carrying the beta-catenin binding IBD. Sound for vinculin generally;
          vclb is inside the clade but carries a substitution at a residue linked to this specific interaction,
          and binding has not been tested for vclb.
        source_status: UNRESOLVED
- term:
    id: GO:0015629
    label: actin cytoskeleton
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: located_in
  supporting_entities:
  - InterPro:IPR000633
  review:
    summary: Actin cytoskeleton (InterPro).
    action: ACCEPT
    reason: Vinculin binds F-actin at adhesion sites; correct location.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: Vinculin binds the adherens junction component α-catenin, which interacts with cadherin-bound
        β-catenin through its N-terminal head domain, and links the cadherin complex to F-actin using its C-terminal
        tail.
- term:
    id: GO:0016020
    label: membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  supporting_entities:
  - ARBA:ARBA00028763
  review:
    summary: Membrane (ARBA).
    action: ACCEPT
    reason: Correct but uninformative; plasma membrane and adhesion-site terms are more specific.
- term:
    id: GO:0030016
    label: myofibril
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  qualifier: located_in
  supporting_entities:
  - ARBA:ARBA00028265
  review:
    summary: Myofibril (ARBA).
    action: KEEP_AS_NON_CORE
    reason: In the zebrafish heart vinculin immunoreactivity is found at sarcomeric Z-disks and costameres (antibody
      not paralog-specific), consistent with a muscle location, but this is a tissue-specific attachment site, not
      the core location.
    supported_by:
    - reference_id: PMID:26954676
      supporting_text: We show here for the first time that an orchestrated interplay of Paxillin, Focal Adhesion
        Kinase (FAK) and Vinculin localizing to sarcomeric Z-disks and costameres in cardiomyocytes is essential
        for the regulation of cardiac contractility.
- term:
    id: GO:0042383
    label: sarcolemma
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0238
  review:
    summary: Sarcolemma (UniProt subcellular location mapping).
    action: KEEP_AS_NON_CORE
    reason: Costameric vinculin lies at the sarcolemma of cardiomyocytes; the zebrafish antibody data do not distinguish
      the paralogs. Plausible, muscle-specific, non-core.
    supported_by:
    - reference_id: PMID:26954676
      supporting_text: We show here for the first time that an orchestrated interplay of Paxillin, Focal Adhesion
        Kinase (FAK) and Vinculin localizing to sarcomeric Z-disks and costameres in cardiomyocytes is essential
        for the regulation of cardiac contractility.
- term:
    id: GO:0044291
    label: cell-cell contact zone
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  supporting_entities:
  - MGI:MGI:98927
  - PANTHER:PTN005285701
  - RGD:1311217
  - UniProtKB:P18206
  review:
    summary: Cell-cell contact zone (IBA).
    action: ACCEPT
    reason: Vinculin is recruited to tensioned cadherin contacts; both copies reach cell-cell junctions in the same
      assay. Both TGD copies descend from the PANTHER PTN005285701 vinculin node, so the IBA is expected on vclb
      and vcla alike; nothing in the vclb sequence or phenotype argues for loss of the function.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
        Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization
        with α-catenin
- term:
    id: GO:0045294
    label: alpha-catenin binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  supporting_entities:
  - PANTHER:PTN005285701
  - UniProtKB:P12003
  - UniProtKB:P18206
  review:
    summary: Alpha-catenin binding (IBA).
    action: ACCEPT
    reason: Junctional recruitment of both zebrafish copies requires the vinculin-binding site of alpha-catenin,
      and the D1 head residue A50 that mediates talin/alpha-catenin binding is conserved. Both TGD copies descend
      from the PANTHER PTN005285701 vinculin node, so the IBA is expected on vclb and vcla alike; nothing in the
      vclb sequence or phenotype argues for loss of the function.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: Here it is apparent that both vinculin A and vinculin B are now excluded from Focal Adherens
        Junctions and Linear Adherens Junctions (arrows), but are still present in Focal Adhesions (arrows).
    - reference_id: PMID:28767718
      supporting_text: The key residue of which mutation perturbs all of these interactions, A50, is fully conserved
        [47,48].
- term:
    id: GO:0048471
    label: perinuclear region of cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  supporting_entities:
  - UniProtKB-SubCell:SL-0198
  review:
    summary: Perinuclear region of cytoplasm (UniProt subcellular location mapping).
    action: MARK_AS_OVER_ANNOTATED
    reason: No zebrafish or functional basis for a perinuclear vinculin pool; the protein acts at adhesion sites.
      The mapped keyword adds no information about function.
- term:
    id: GO:0051015
    label: actin filament binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  supporting_entities:
  - InterPro:IPR006077
  - InterPro:IPR036723
  review:
    summary: Actin filament binding (InterPro).
    action: ACCEPT
    reason: Core activity of the vinculin tail; the F-actin-binding tail helices are nearly identical to mammalian
      vinculin in both copies.
    supported_by:
    - reference_id: PMID:28767718
      supporting_text: Especially Helices 3–5 which mediate paxillin and F-actin binding (Fig 1E) [52,53] are almost
        completely identical.
- term:
    id: GO:0060977
    label: coronary vasculature morphogenesis
  evidence_type: IMP
  original_reference_id: PMID:27578788
  qualifier: acts_upstream_of_or_within
  supporting_entities:
  - ZFIN:ZDB-GENO-170321-9
  review:
    summary: Vclb is required for organized coronary vessel formation; loss raises FAK/ERK signalling in epicardium
      and endocardium.
    action: ACCEPT
    reason: 'The main phenotype of the vclb mutant and the one that distinguishes the copies: vcla is expressed
      in the myocardium but not the epicardium, so the coronary/epicardial role falls to vclb by expression. The
      mechanism given (paxillin released from the Vclb complex, FAK/ERK hyperphosphorylation) is the ancestral vinculin
      adhesion-site activity acting in a vclb-specific expression domain.'
    supported_by:
    - reference_id: PMID:27578788
      supporting_text: Mechanistically, Vclb deficiency results in the release of another cytoskeletal protein,
        paxillin, from the Vclb complex and the upregulation of ERK and FAK phosphorylation in epicardium and endocardium,
        causing disorganization of endothelial cells and pericytes during coronary vessel development.
    - reference_id: PMID:27578788
      supporting_text: By contrast, cardiac muscle development is relatively normal, probably owing to redundancy
        with Vcla, a vinculin paralog that is expressed in the myocardium but not epicardium.
- term:
    id: GO:0061028
    label: establishment of endothelial barrier
  evidence_type: IGI
  original_reference_id: PMID:36260739
  review:
    summary: Vinculin strengthens endothelial adherens junctions; vcla;vclb double and vcla-/-;vclb+/- embryos leak
      10 kDa dextran from intersegmental vessels.
    action: NEW
    reason: 'Participation: vinculin is recruited to tensioned VE-cadherin junctions through alpha-catenin and reinforces
      their link to actin, so it contributes structure that barrier formation depends on (junctional vinculin, not
      a downstream signal). The in vivo evidence is genetic and involves both copies (vcla-/-;vclb+/- and vcla-/-;vclb-/-
      both leak), so the annotation is made to both copies as IGI rather than to one. vclb is the copy most prominently
      expressed in endothelium (PMID:36314606), so the relative contribution of each copy is not resolved.'
    supported_by:
    - reference_id: PMID:36260739
      supporting_text: Our analysis shows that vcla−/−;vclb+/−and vcl full-KO embryos exhibited increased perivascular
        dextran levels
    - reference_id: PMID:36260739
      supporting_text: we observed vascular leakage specifically for small molecules, 10 kDa, in vinculin knockout
        zebrafish, whereas the vasculature still acted as a barrier for larger molecules
    - reference_id: PMID:36260739
      supporting_text: Together, the data show that vinculin tightens endothelial junctions in blood vessels.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied
    by conservative changes to GO terms applied by UniProt
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:27578788
  title: Vinculin b deficiency causes epicardial hyperplasia and coronary vessel disorganization in zebrafish.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Abstract only; gene-trap vclb mutant; states vcla is myocardial, not epicardial.
- id: PMID:28767718
  title: Zygotic vinculin is not essential for embryonic development in zebrafish.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Full text; vclb hu11202 (PTC at codon 22); Y822F in vclb; localization of GFP-Vclb.
- id: PMID:30944477
  title: Genetic compensation triggered by mutant mRNA degradation.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text; vclb is the adapting gene in vcla PTC mutants.
- id: PMID:36427314
  title: Parental mutations influence wild-type offspring via transcriptional adaptation.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text; inherited vclb upregulation, H3K4me3 at vclb promoter.
- id: PMID:36260739
  title: Vinculin strengthens the endothelial barrier during vascular development.
  findings: []
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Full text; double mutant vascular leakage.
- id: PMID:35417696
  title: Vinculin controls endothelial cell junction dynamics during vascular lumen formation.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Abstract only.
- id: PMID:30635353
  title: Focal adhesions are essential to drive zebrafish heart valve morphogenesis.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text; vclb bns247 mutants; vclb predominant in heart; no strong valve defect.
- id: PMID:36314606
  title: Dynamically regulated focal adhesions coordinate endothelial cell remodelling in developing vasculature.
  findings: []
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Full text; endothelial Vinculinb-eGFP at FAs and junctions; talin1-dependent FA recruitment.
- id: PMID:38697108
  title: Notochord segmentation in zebrafish controlled by iterative mechanical signaling.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Full text; vclb-mScarlet knock-in in notochord sheath, muscle and vasculature.
- id: PMID:26954676
  title: Paxillin and Focal Adhesion Kinase (FAK) Regulate Cardiac Contractility in the Zebrafish Heart.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Full text; cardiac vinculin at Z-disks/costameres, antibody not paralog-specific.
core_functions:
- description: Actin-binding adaptor at focal adhesions and adherens junctions, recruited via talin and alpha-catenin;
    molecular function shared with vcla.
  molecular_function:
    id: GO:0051015
    label: actin filament binding
  directly_involved_in:
  - id: GO:0007155
    label: cell adhesion
  locations:
  - id: GO:0005925
    label: focal adhesion
  - id: GO:0005912
    label: adherens junction
  supported_by:
  - reference_id: PMID:28767718
    supporting_text: In α-catenin rescued cells, both vinculin A and vinculin B localize to integrin-based Focal
      Adhesion structures, as well as to the punctate Focal Adherens Junctions as evidenced by colocalization with
      α-catenin
  - reference_id: PMID:28767718
    supporting_text: Here it is apparent that both vinculin A and vinculin B are now excluded from Focal Adherens
      Junctions and Linear Adherens Junctions (arrows), but are still present in Focal Adhesions (arrows).
  - reference_id: PMID:36314606
    supporting_text: Live imaging of the main axial artery, the dorsal aorta (DA), revealed Vinculinb localisation
      at cell-cell junctions and at FAs in wild-type embryos (Fig.
- description: In epicardium and endocardium (where vcla is not expressed), holds paxillin in the adhesion complex
    and restrains FAK/ERK signalling, needed for organized coronary vessel development.
  molecular_function:
    id: GO:0051015
    label: actin filament binding
  directly_involved_in:
  - id: GO:0060977
    label: coronary vasculature morphogenesis
  locations:
  - id: GO:0005925
    label: focal adhesion
  supported_by:
  - reference_id: PMID:27578788
    supporting_text: Mechanistically, Vclb deficiency results in the release of another cytoskeletal protein, paxillin,
      from the Vclb complex and the upregulation of ERK and FAK phosphorylation in epicardium and endocardium, causing
      disorganization of endothelial cells and pericytes during coronary vessel development.
  - reference_id: PMID:27578788
    supporting_text: By contrast, cardiac muscle development is relatively normal, probably owing to redundancy
      with Vcla, a vinculin paralog that is expressed in the myocardium but not epicardium.
- description: With vcla, alpha-catenin-dependent strengthening of endothelial junctions (barrier to small molecules).
  molecular_function:
    id: GO:0045294
    label: alpha-catenin binding
  directly_involved_in:
  - id: GO:0061028
    label: establishment of endothelial barrier
  locations:
  - id: GO:0005912
    label: adherens junction
  supported_by:
  - reference_id: PMID:36260739
    supporting_text: Our analysis shows that vcla−/−;vclb+/−and vcl full-KO embryos exhibited increased perivascular
      dextran levels
  - reference_id: PMID:36314606
    supporting_text: As vinculinb is most prominently expressed in zebrafish ECs (Lawson et al., 2020), we generated
      a vascular restricted transgenic line, Tg(fli1ep:vinculinb-eGFP)uq2al, whereby Vinculinb is tagged with eGFP
      at the C terminus.
suggested_questions:
- question: Does Vclb (F822) bind beta-catenin, and does the Y822F substitution change junction stabilization in
    a vinculin-null zebrafish background?
- question: Is the juvenile lethality of vclb mutants due to loss of an epicardial/endocardial expression domain
    that vcla lacks, i.e. would vcla expressed from the vclb locus rescue it?
- question: Can the vclb locus encode a metavinculin exon, or is metavinculin made only from vcla?
suggested_experiments:
- hypothesis: vclb-specific coronary phenotypes reflect expression, not protein divergence.
  description: Express vcla (and vclb as control) coding sequence in epicardium (tcf21 driver) of vclb mutants and
    score coronary vessel organization and FAK/ERK phosphorylation.
  experiment_type: cross-rescue
- hypothesis: F822 in Vclb reduces beta-catenin binding relative to Vcla.
  description: Co-immunoprecipitation of tagged Vcla, Vclb and Vclb F822Y with beta-catenin in zebrafish cells or
    embryos.
  experiment_type: protein interaction assay