KRIT1 (Krev interaction trapped protein 1, CCM1) is a non-enzymatic cytoplasmic scaffold of the cerebral cavernous malformation (CCM) signaling system. It has an N-terminal pseudo-Nudix region with NPxY/F motifs that bind ICAP1/ITGB1BP1 and CCM2, a series of ankyrin repeats, and a C-terminal FERM domain. In mammalian endothelium, GTP-bound Rap1 binds the FERM F1 lobe and releases KRIT1 from microtubules. The HEG1 cytoplasmic tail, bound in a groove at the F1/F3 interface, then anchors KRIT1 at cell-cell junctions. There KRIT1 stabilizes adherens junctions, suppresses RhoA/ROCK and MEKK3-ERK5 signaling, and keeps the endothelium quiescent; it also binds PIP2-containing membranes. This entry, A0A9L0SR44 (719 aa), is one of several alternative products of the horse KRIT1 gene (Ensembl ENSECAG00000016850). It is identical to the 736-aa horse product A0A3Q2GZV2 except for a different C-terminal end. Residues equivalent to human 715-731 are missing, including Leu717 and Leu721, which form the HEG1-binding groove. The Rap1-binding F1 region, including Arg452, is intact. No horse KRIT1 product has been studied experimentally. Its functions are inferred from human and mouse KRIT1, which sit in the same PANTHER subfamily (PTHR13283:SF11).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005856 cytoskeleton | IEA GO_REF:0000044 | MODIFY | Summary: KRIT1 associates with microtubules. The correct but general term cytoskeleton should be refined to microtubule cytoskeleton. Reason: The SubCell "Cytoplasm, cytoskeleton" mapping is correct for KRIT1. Recombinant KRIT1 co-sediments with microtubules, and YFP-KRIT1 decorates microtubules in cells. Active Rap1 and ICAP1 release it (PMID:17916086, PMID:21633110). The evidence is specifically for microtubules, so the general cytoskeleton term is refined to microtubule cytoskeleton (GO:0015630), a child of cytoskeleton. Transfer to horse rests on membership of the same PANTHER subfamily (PTHR13283:SF11) as the characterized human and mouse proteins. One caveat applies to this product, which is an alternative C-terminal variant. Microtubule binding maps to both the N- and C-terminal regions. The N-terminal region is fully conserved, but this product lacks residues equivalent to human 715-731 (file:HORSE/KRIT1/KRIT1-bioinformatics/RESULTS-rereview.md). Its own microtubule association has not been tested. Proposed replacements: microtubule cytoskeleton Supporting Evidence: PMID:17916086 Krit1 binds in vitro to microtubules through its N- and C-termini PMID:21633110 Rap1 binding released KRIT1 from microtubules |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | ACCEPT | Summary: KRIT1 is a peripheral plasma-membrane protein, recruited by Rap1 and binding PIP2-containing membranes. Reason: Human KRIT1 binds PIP2-containing liposomes, and active Rap1 enhances this binding. Wild-type KRIT1 localizes to the endothelial plasma membrane at junctions, whereas the Rap1-binding mutant R452E does not (PMID:17916086, PMID:21633110). PAINT places plasma membrane at a deep family node (PTN004412369), which covers KRIT1 and FRMD8, and the 736-aa horse KRIT1 product carries this IBA. This product retains the FERM F1/F2 region and Arg452, both needed for Rap1-dependent membrane recruitment. Plasma membrane is therefore kept as the location of the product's core Rap1-effector function. Supporting Evidence: PMID:17916086 Krit1 binds to phosphatidylinositol PMID:21633110 Wild-type KRIT1 but not the KRIT1(R452E) mutant localized to the plasma membrane at endothelial junctions. file:HORSE/KRIT1/KRIT1-bioinformatics/RESULTS-rereview.md S430->S430, R452->R452 |
| GO:0051093 negative regulation of developmental process | IEA GO_REF:0000117 | MODIFY | Summary: This general ARBA term is true of KRIT1, but the specific supported process is negative regulation of angiogenesis. Reason: In primary human endothelial cells, KRIT1/CCM1 inhibits proliferation, migration, lumen formation and sprouting angiogenesis (PMID:20616044). PAINT propagates negative regulation of angiogenesis (GO:0016525) from node PTN002665064, and the 736-aa horse KRIT1 product carries this IBA. GO:0016525 is a descendant of this term (via negative regulation of vasculature development), so the general term is refined to it. It is not treated as core for this product. Junction-dependent KRIT1 activities need HEG1 anchoring through the C-terminal Leu717/Leu721 groove (PMID:23007647), and this product lacks those residues. Proposed replacements: negative regulation of angiogenesis Supporting Evidence: PMID:20616044 CCM1 represents an antiangiogenic protein to keep the human endothelium quiescent. |
| GO:0070161 anchoring junction | IEA GO_REF:0000044 | UNDECIDED | Summary: The canonical KRIT1 product is at endothelial cell-cell junctions. This alternative product lacks the HEG1-binding residues that anchor KRIT1 there. Reason: Full-length KRIT1 localizes to endothelial cell-cell (adherens) junctions (PMID:20332120, PMID:21633110). For that product the annotation would be refined to cell-cell junction (GO:0005911). Junctional anchoring needs HEG1 binding in a groove formed by the FERM F1 and F3 subdomains. KRIT1(L717,721A), although well folded, fails to target to endothelial junctions (PMID:23007647). Rap1 binding is also required (PMID:21633110). A0A9L0SR44 keeps the Rap1-binding F1 region and Arg452, but residues equivalent to human 715-731, including Leu717 and Leu721, are absent (file:HORSE/KRIT1/KRIT1-bioinformatics/RESULTS-rereview.md). By the human mutant data, this product would bind Rap1 but would not be anchored at junctions by HEG1, and possibly not anchored at all. Nobody has tested whether it is expressed or where it localizes, so the junctional location of this product can be neither confirmed nor rejected. Supporting Evidence: PMID:23007647 failed to target to EC PMID:21633110 KRIT1 binds HEG1 to localize to endothelial cell–cell junctions file:HORSE/KRIT1/KRIT1-bioinformatics/RESULTS-rereview.md A715->gap, L717->gap, L721->gap, P731->gap |
| GO:2000026 regulation of multicellular organismal development | IEA GO_REF:0000117 | MODIFY | Summary: This broad ARBA term is true of KRIT1 but uninformative. The supported specific process is negative regulation of angiogenesis. Reason: The KRIT1 developmental role with direct support is restraint of endothelial sprouting and angiogenesis (PMID:20616044). PAINT propagates negative regulation of angiogenesis (GO:0016525) to the KRIT1 clade (PTN002665064), and GO:0016525 is a descendant of this term. The general term is therefore refined, as for the GO:0051093 row. Cardiovascular-development phenotypes of Krit1 mutants are organismal consequences and are not proposed as separate process terms. As for GO:0051093, the effect may be reduced in this C-terminal variant, which lacks the HEG1-anchoring residues. Proposed replacements: negative regulation of angiogenesis Supporting Evidence: PMID:20616044 CCM1 represents an antiangiogenic protein to keep the human endothelium quiescent. |
| GO:0031267 small GTPase binding | IBA GO_REF:0000033 | NEW | Summary: Proposed. KRIT1 is a direct, GTP-dependent Rap1 effector, and this product retains the Rap1 interface. Reason: Native human KRIT1 binds the effector loop of active Rap1A but not H-Ras. The R452E interface mutant reduces Rap1 affinity about 40-fold (PMID:21633110). This is the best-established molecular activity of KRIT1, and the human review refines GTPase regulator activity to this term. A0A9L0SR44 is in the same PANTHER subfamily (PTHR13283:SF11) and keeps Arg452 and the 430-452 Rap1B-interaction region (file:HORSE/KRIT1/KRIT1-bioinformatics/RESULTS-rereview.md). The binding is part of the product's own function, as an effector, so the participation bar is met. The evidence code is a placeholder for phylogenetic transfer within the SF11 subfamily. Supporting Evidence: PMID:21633110 KRIT1 is an authentic Rap1-specific effector that binds strongly to the effector loop of active Rap1A file:HORSE/KRIT1/KRIT1-bioinformatics/RESULTS-rereview.md S430->S430, R452->R452 |
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Download this section (compressed HTML)Q: Is the 719-aa horse KRIT1 product (ENSECAT00000146800) supported by transcript evidence, with a distinct terminal exon, or is it a gene-model artefact? If it is expressed, does it lose HEG1-dependent junctional anchoring and act as a Rap1-binding, junction-incompetent variant?
Q: Should GO annotations on non-canonical alternative products that lack known interaction residues (here the HEG1 groove) be restricted relative to the canonical gene product?
Experiment: RT-PCR or long-read sequencing of horse endothelial tissue to confirm the alternative 3' exon of ENSECAT00000146800. Then express the 719-aa and 736-aa horse products in endothelial cells and compare HEG1-tail binding, Rap1A-GTP binding and junctional localization.
Type: transcript validation and localization/binding assays
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