id: B3DI32 gene_symbol: vcla product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:7955 label: Danio rerio description: vcla (vinculin a) is one of two zebrafish co-orthologs of vertebrate vinculin (VCL), retained from the teleost-specific genome duplication; its paralog is vclb. It encodes a cytoplasmic actin-binding adaptor of cell-matrix (focal adhesion) and cadherin-based cell-cell (adherens) junctions. Its head domain binds talin and alpha-catenin, and its tail binds F-actin and paxillin; tension-dependent recruitment through alpha-catenin and talin reinforces the link between adhesion complexes and the actin cytoskeleton. The vcla protein keeps the binding residues and regulatory phosphosites of mammalian vinculin, including Y822, and the gene can encode the muscle metavinculin isoform. GFP-tagged Vcla localizes to focal adhesions and, via the alpha-catenin vinculin-binding site, to adherens junctions. Maternal-zygotic vcla mutants are viable and fertile without overt defects. Loss of vcla together with vclb causes mild transient cardiac edema, leakage of small molecules from embryonic blood vessels and lethality before adulthood. vcla mutant alleles whose transcripts undergo nonsense-mediated decay upregulate vclb mRNA (transcriptional adaptation), whereas a vcla locus deletion does not. 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:0003181 label: atrioventricular valve morphogenesis evidence_type: IMP original_reference_id: PMID:30635353 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-GENO-200113-3 review: summary: Endocardial overexpression of a dominant-negative vinculin head domain (cloned from vcla) blocks AV endocardial cell migration and valve leaflet formation. action: KEEP_AS_NON_CORE reason: The experiment is sound and shows that vinculin engagement at focal adhesions is needed for AV valve morphogenesis. It is attributed to vcla only because the DN fragment was cloned from vcla; a head-domain DN competes for talin/alpha-catenin binding sites and therefore blocks vinculin function generally, not vcla specifically. In the heart, vcla is expressed at low levels and vclb predominates, and vclb single mutants had no strong valve delay. Kept, but as a non-core process whose endogenous paralog is not identified; it should not be read as evidence of a vcla-specific role. supported_by: - reference_id: PMID:30635353 supporting_text: We proceeded to analyze the functional consequences of blocking FA signaling and generated an upstream activating sequence (UAS)–driven DN Vinculin transgene, Tg(UAS:DN-Vcl-EGFP), which expresses a form of Vinculin containing only its head domain (Fig. 3 A). - reference_id: PMID:30635353 supporting_text: To generate the DN Vinculin transgene, the first 774 bp of the vcla coding sequence was amplified by PCR using the following primers - reference_id: PMID:30635353 supporting_text: The microarray data show that tln1 and apbb1ip are expressed at high levels in embryonic hearts (Fig. S1 A), but vcla is expressed at low levels (data not shown); no probe for vclb was included in the array. - 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). - reference_id: PMID:30635353 supporting_text: However, we found that vclb mutants did not exhibit strong delays in AV EC migration and valve formation - 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 vcla and vclb alike; nothing in the vcla 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 vcla and vclb alike; nothing in the vcla 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 vcla and vclb alike; nothing in the vcla 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 vcla and vclb alike; nothing in the vcla 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 vcla 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 vcla and vclb alike; nothing in the vcla 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: IDA original_reference_id: PMID:26954676 qualifier: is_active_in review: summary: Vinculin immunostaining at focal adhesion sites (costameres) in 72 hpf zebrafish hearts. action: ACCEPT reason: The antibody is not paralog-specific, so this row alone does not show that vcla (rather than vclb) is at cardiac focal adhesions. Focal adhesion localization of vcla itself is independently established with GFP-tagged vcla (PMID:28767718), so the term is correct for vcla. supported_by: - reference_id: PMID:26954676 supporting_text: Whereas in control morphant hearts Vinculin properly localized to focal adhesion sites, Vinculin was mislocalized and seems to get degraded in morphant hearts (Fig 5A–5C). - 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: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:0005925 label: focal adhesion evidence_type: IMP original_reference_id: PMID:26954676 qualifier: is_active_in supporting_entities: - ZFIN:ZDB-MRPHLNO-100114-3 review: summary: Location term supported by a morphant (paxillin/FAK knockdown) experiment in which vinculin mislocalizes. action: ACCEPT reason: 'Using IMP for a location is unusual: the data show that paxillin and FAK are needed to keep vinculin at focal adhesions. The location itself is correct for vcla (GFP-vcla localizes to focal adhesions), so the term is accepted on the combined evidence.' supported_by: - reference_id: PMID:26954676 supporting_text: Whereas in control morphant hearts Vinculin properly localized to focal adhesion sites, Vinculin was mislocalized and seems to get degraded in morphant hearts (Fig 5A–5C). - 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 vcla and vclb alike; nothing in the vcla 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: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: ACCEPT reason: Vinculin binds beta-catenin at cadherin junctions in mammals, and vcla keeps Y822, the phosphotyrosine required for the beta-catenin interaction in mammalian cells. Both TGD copies descend from the PANTHER PTN005285701 vinculin node, so the IBA is expected on vcla and vclb alike; nothing in the vcla sequence or phenotype argues for loss of the function. supported_by: - reference_id: PMID:28767718 supporting_text: Notably, besides α-catenin- and talin-dependent tension-induced recruitment, vinculin also binds to other proteins at both integrin and cadherin adhesions such as paxillin and β-catenin [19]. - 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 vcla and vclb alike; nothing in the vcla 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:0045214 label: sarcomere organization evidence_type: IMP original_reference_id: PMID:19800866 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-100114-3 review: summary: vcla morpholino knockdown causes cardiac systolic dysfunction; sarcomere organization inferred from morphants. action: UNDECIDED reason: The only evidence is a zygotic vcla splice morpholino (ZDB-MRPHLNO-100114-3), and the cached paper is abstract-only. Maternal-zygotic vcla mutants are fully viable, and zygotic vcla;vclb double mutants have normal skeletal muscle and only mild, transient cardiac edema; the mutant authors consider the morpholino effects most likely non-specific. Against that, vinculin is reported to be essential for cardiomyocyte myofilament maturation in zebrafish (PMID:31495694, abstract only; paralog and alleles not stated), and vcla PTC alleles that decay trigger vclb upregulation, which could mask a single-mutant phenotype. A role for vinculin in cardiac sarcomere organization is plausible, but a vcla-specific IMP cannot be adjudicated from these data. supported_by: - reference_id: PMID:19800866 supporting_text: Consistently, knock-down of the here selected human DCM genes leads to severe heart failure with impairment of systolic cardiac function in zebrafish. - reference_id: PMID:28767718 supporting_text: While we cannot fully exclude the latter, the most likely explanation is that the reported effects of the used vinculin A morpholinos are non-specific. - reference_id: PMID:28767718 supporting_text: While we do see cardiac edemas in vinculin-null mutants, skeletal muscle tissue seems unaffected. - reference_id: PMID:31495694 supporting_text: Here, we first show that the forces of the contracting heart regulate the localization and activation of the cytoskeletal protein vinculin (VCL), which we find to be essential for myofilament maturation. - 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 vcla and vclb alike; nothing in the vcla 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:0060047 label: heart contraction evidence_type: IMP original_reference_id: PMID:19800866 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-100114-3 review: summary: vcla morpholino knockdown impairs systolic function (heart contraction). action: UNDECIDED reason: Morpholino-only evidence (abstract-only cache). MZvcla mutants show no cardiac phenotype, and the mutant study found no rise in vinculin protein from vclb, while noting the morpholino targeted zygotic vcla only and judging its effects most likely non-specific. vcla PTC alleles do trigger transcriptional adaptation of vclb mRNA, so masking cannot be excluded. Vinculin is required for cardiomyocyte maturation (PMID:31495694) and for heart function in mammals, so the process is plausible for vinculin in general, but whether vcla contributes is unresolved. supported_by: - reference_id: PMID:19800866 supporting_text: Consistently, knock-down of the here selected human DCM genes leads to severe heart failure with impairment of systolic cardiac function in zebrafish. - reference_id: PMID:28767718 supporting_text: Moreover, the splice-site morpholino that was used, only targeted the zygotic vinculin A isoform, keeping maternally supplied mRNA and vinculin B intact. - reference_id: PMID:28767718 supporting_text: This result strongly indicates that mutation of the vcla gene leads to loss of most of the functional vinculin protein in zebrafish embryos and that this is not compensated for by increased expression of vinculin B. - reference_id: PMID:30944477 supporting_text: hbegfa, vcla, hif1ab, vegfaa, egfl7 and alcama zebrafish mutants exhibit increased mRNA levels of a paralogue or family member (hereafter referred to as ‘adapting gene’), namely hbegfb, vclb, epas1a and epas1b, vegfab, emilin3a and alcamb, respectively - term: id: GO:0060047 label: heart contraction evidence_type: IMP original_reference_id: PMID:26954676 qualifier: involved_in supporting_entities: - ZFIN:ZDB-MRPHLNO-100114-3 review: summary: The same vcla morpholino reduces ventricular fractional shortening (supplementary data). action: UNDECIDED reason: Same morpholino (ZDB-MRPHLNO-100114-3) as PMID:19800866, re-tested as a supplementary control; the paper is about paxillin/FAK. The mutant data (MZvcla viable; double zygotic mutants with mild transient edema only) conflict with the severe morphant contractility defect. Undecided for the same reasons as the PMID:19800866 row. supported_by: - reference_id: PMID:26954676 supporting_text: Finally, we found that targeted gene knock-down of vinculin, similar to Paxillin and FAK ablation, results in severe ventricular contractile dysfunction in zebrafish embryos [5] (S4A–S4D Fig). - reference_id: PMID:28767718 supporting_text: Taken together, the results show that vcla is not essential for zebrafish development or adult life. - reference_id: PMID:28767718 supporting_text: While we cannot fully exclude the latter, the most likely explanation is that the reported effects of the used vinculin A morpholinos are non-specific. - term: id: GO:0086013 label: membrane repolarization during cardiac muscle cell action potential evidence_type: IMP original_reference_id: PMID:24952909 qualifier: acts_upstream_of_or_within supporting_entities: - ZFIN:ZDB-MRPHLNO-100114-3 review: summary: vcl morpholino knockdown alters cardiac action potential repolarization (supplementary figure of a proteomics/GWAS paper). action: MARK_AS_OVER_ANNOTATED reason: Vinculin is a cytoskeletal adaptor, not a channel or channel subunit; the paper places it in a CAV3/SNTA1 interaction network. A morphant change in action potential duration is a downstream physiological readout (morpholino only, disputed by mutant data), not evidence that vinculin does work in membrane repolarization. The participation bar for this specific electrophysiological process is not met. supported_by: - reference_id: PMID:24952909 supporting_text: We furthermore confirmed the involvement of VCL in cardiac repolarization by knockdown experiments of the ortholog, vcl, in zebrafish, which had a direct effect on cardiac repolarization in vivo (Supplementary Figure 13). - reference_id: PMID:24952909 supporting_text: Second, VCL encodes a cytoskeletal protein, vinculin, which we show interacts with CAV3 and SNTA1. - reference_id: PMID:28767718 supporting_text: While we cannot fully exclude the latter, the most likely explanation is that the reported effects of the used vinculin A morpholinos are non-specific. - 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:19800866 title: In-vivo characterization of human dilated cardiomyopathy genes in zebrafish. findings: [] reference_review: relevance: MEDIUM correctness: LOW_QUALITY review_notes: Abstract only; morpholino-only evidence for vcla, disputed by later mutant data (PMID:28767718). - id: PMID:24952909 title: Annotation of loci from genome-wide association studies using tissue-specific quantitative interaction proteomics. findings: [] reference_review: relevance: LOW correctness: LOW_QUALITY review_notes: Full text; the vcl morpholino repolarization data are a supplementary figure in a GWAS/proteomics paper. - id: PMID:26954676 title: Paxillin and Focal Adhesion Kinase (FAK) Regulate Cardiac Contractility in the Zebrafish Heart. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text; paper is about paxillin/FAK; vinculin morpholino is a supplementary experiment; antibody not paralog-specific. - 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; defines vcla/vclb, MZvcla and double mutants, localization of both GFP-tagged proteins, Y822F in vclb. - 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; DN construct derived from vcla head domain; vclb mutants lack strong valve phenotype. - id: PMID:36427314 title: Parental mutations influence wild-type offspring via transcriptional adaptation. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; vcla RNA-less allele lacks TA; inherited vclb upregulation in wild-type offspring. - id: PMID:30944477 title: Genetic compensation triggered by mutant mRNA degradation. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; vclaΔ13 triggers vclb upregulation dependent on mutant mRNA decay. - id: PMID:36260739 title: Vinculin strengthens the endothelial barrier during vascular development. findings: [] reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text; vcla;vclb double and vcla-/-;vclb+/- 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; vinculin deletion (both copies) prevents endothelial junctional fingers. - id: PMID:27578788 title: Vinculin b deficiency causes epicardial hyperplasia and coronary vessel disorganization in zebrafish. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Abstract only; states vcla is myocardial and not epicardial. - id: PMID:31495694 title: Mechanical Forces Regulate Cardiomyocyte Myofilament Maturation via the VCL-SSH1-CFL Axis. findings: [] reference_review: relevance: MEDIUM correctness: UNVERIFIED review_notes: Abstract only; paralog and allele used not stated in abstract. - id: PMID:38697108 title: Notochord segmentation in zebrafish controlled by iterative mechanical signaling. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Full text; vcla transcripts enriched in notochord sheath cells. - id: PMID:40128410 title: Induction of a transcriptional adaptation response by RNA destabilization events. findings: [] reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: Full text; cites Cas13d cleavage of vcla mRNA raising vclb. - id: PMID:36314606 title: Dynamically regulated focal adhesions coordinate endothelial cell remodelling in developing vasculature. findings: [] reference_review: relevance: LOW correctness: VERIFIED review_notes: Full text; uses a vclb transgene; states vclb is most prominently expressed in endothelium. - id: file:DANRE/vcla/vcla-bioinformatics/RESULTS.md title: vcla/vclb/human VCL protein comparison (metavinculin insert, Y822) reference_review: relevance: HIGH correctness: VERIFIED review_notes: Manual audit verified this sidecar supports the cached vcla and vclb entries as metavinculin-type and vinculin-type isoforms, respectively, and confirms the vclb Y822F substitution without testing splicing. findings: - statement: vcla UniProt B3DI32 is the metavinculin-type isoform; Y822 conserved in vcla, F in vclb. supporting_text: B3DI32 is the metavinculin-type isoform of vcla core_functions: - description: Actin-binding adaptor at integrin-based focal adhesions and cadherin-based adherens junctions, recruited via talin and alpha-catenin and linking them to F-actin; molecular function equivalent to vclb and to mammalian vinculin. 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:28767718 supporting_text: This strongly indicates that both vcla and vclb genes in zebrafish generate fully functional vinculin proteins. - description: Alpha-catenin binding at tensioned cell-cell junctions; with vclb, strengthens endothelial junctions so embryonic vessels retain 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: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: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: Together, the data show that vinculin tightens endothelial junctions in blood vessels. suggested_questions: - question: Does a vcla RNA-less (locus-deletion) allele, which does not upregulate vclb, reveal cardiac, muscle or vascular phenotypes absent from the PTC alleles? - question: Is the vclb mRNA rise in vcla PTC mutants translated into more Vclb protein in the tissues where the copies overlap (notochord sheath, vasculature, myocardium), given that whole-larva Western blots of another PTC allele showed no compensation? - question: Which zebrafish vinculin copy carries the metavinculin exon in cardiac and skeletal muscle? suggested_experiments: - hypothesis: vcla protein function is masked in PTC mutants by transcriptional adaptation of vclb. description: Compare vcla PTC (bns241) and RNA-less (bns605) homozygotes, each also crossed into vclb heterozygotes, for cardiac contractility, myofibril maturation and 10 kDa dextran leakage; measure Vclb protein by paralog-specific antibody or knock-in tag. experiment_type: allele-series comparison - hypothesis: The two vinculin proteins are interchangeable in vivo. description: Knock the vclb coding sequence into the vcla locus (and vice versa) and test rescue of double-mutant phenotypes. experiment_type: cross-rescue