SPAAR (small regulatory polypeptide of amino acid response; formerly the lncRNA LINC00961) is a mammalian microprotein of 90 aa (canonical) or 75 aa (short isoform, conserved with mouse) with a single transmembrane helix, a short lumenal N-terminus and a cytoplasmic C-terminus. It resides in the membrane of late endosomes and lysosomes, where it associates with the lysosomal V-type proton ATPase (interacting with the V0 a1 and a2 subunits ATP6V0A1/ATP6V0A2). SPAAR selectively restrains mTORC1 activation by amino acids, but not by growth factors: it favours a tightly bound V-ATPase-Ragulator-Rag GTPase supercomplex that fails to recruit mTORC1 to the lysosome. In mouse skeletal muscle the peptide is downregulated after acute injury, and its loss enhances mTORC1 activation and muscle regeneration. The peptide is expressed in lung, heart, skeletal muscle and endothelium; overexpression in endothelial cells promotes network formation, while the host RNA has separable, opposing effects on angiogenesis.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005765 lysosomal membrane | IDA PMID:28024296 mTORC1 and muscle regeneration are regulated by the LINC0096... | ACCEPT | Summary: Late endosome/lysosome membrane localisation of SPAAR shown directly in the primary characterisation paper; consistent with a single-pass TM topology with cytoplasmic C-terminus. Reason: Direct localisation evidence from Matsumoto et al. 2017; lysosomal membrane is where SPAAR engages the V-ATPase/Ragulator/Rag machinery to restrain amino-acid-induced mTORC1 recruitment, so this is the core location. Supporting Evidence: PMID:28024296 is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation |
| GO:0005765 lysosomal membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0157 Lysosome membrane), itself based on PMID:28024296. Reason: Mapping is correct and concordant with the IDA row from the same underlying evidence. Supporting Evidence: PMID:28024296 is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation |
| GO:0031902 late endosome membrane | IDA PMID:28024296 mTORC1 and muscle regeneration are regulated by the LINC0096... | ACCEPT | Summary: SPAAR localises to late endosome as well as lysosome membranes in the primary paper. Reason: Direct experimental localisation; late endosome and lysosome membranes form a continuum and both are appropriate. Supporting Evidence: PMID:28024296 is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation |
| GO:0031902 late endosome membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping (SL-0151 Late endosome membrane). Reason: Correct mapping, concordant with the IDA annotation. Supporting Evidence: PMID:28024296 is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation |
| GO:0043416 regulation of skeletal muscle tissue regeneration | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: Ensembl Compara transfer from mouse Spaar (A0A1B0GSZ0), where a peptide-specific knockout (host lncRNA preserved) enhanced mTORC1 activation and muscle regeneration after injury. Reason: The mouse evidence is robust and peptide-specific, and the human and mouse short forms are orthologous. However, muscle regeneration is a tissue-level outcome of SPAAR's cellular role in restraining amino-acid-driven mTORC1 activation, so it is kept as non-core. Supporting Evidence: PMID:28024296 use CRISPR/Cas9 engineering to develop a SPAR-polypeptide-specific knockout mouse while maintaining expression of the host lncRNA PMID:28024296 SPAR downregulation enables efficient activation of mTORC1 and promotes muscle regeneration |
| GO:0043416 regulation of skeletal muscle tissue regeneration | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: UniProt curator transfer from mouse Spaar of the muscle regeneration phenotype. Reason: Same basis as the IEA row: valid ortholog transfer of an in vivo phenotype that is downstream of the core mTORC1-regulatory function. Supporting Evidence: PMID:28024296 SPAR downregulation enables efficient activation of mTORC1 and promotes muscle regeneration |
| GO:0046611 lysosomal proton-transporting V-type ATPase complex | IDA PMID:28024296 mTORC1 and muscle regeneration are regulated by the LINC0096... | ACCEPT | Summary: SPAAR interacts with the lysosomal V-ATPase (ATP6V0A1, ATP6V0A2 per UniProt) and co-localises with it; annotated with colocalizes_with rather than part_of. Reason: SPAAR is an interactor/regulator of the lysosomal V-ATPase, not a structural subunit of the proton pump, and there is no evidence that it contributes to proton transport. The colocalizes_with qualifier correctly records physical association without asserting complex membership, so the row is accepted on that reading; it should not be upgraded to part_of. Note that an HA-SPAAR pull-down in HUVECs did not recover V-ATPase subunits, so the association may be cell-context dependent. Supporting Evidence: PMID:28024296 is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation PMID:31990292 SPAAR has been previously shown to bind the v-ATPase complex in HEK293.23 However, these proteins were not found in the SPAAR pull-down in HUVECs, suggesting a different function for SPAAR in ECs. |
| GO:0071230 cellular response to amino acid stimulus | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara transfer from mouse Spaar of cellular response to amino acid stimulus. Reason: SPAAR acts specifically on the amino-acid input to mTORC1, as a negative regulator of that response; the term is appropriate though less informative than GO:1904262. Supporting Evidence: PMID:28024296 This regulation of mTORC1 is specific to activation of mTORC1 by amino acid stimulation, rather than by growth factors |
| GO:0071230 cellular response to amino acid stimulus | IMP PMID:28024296 mTORC1 and muscle regeneration are regulated by the LINC0096... | ACCEPT | Summary: SPAAR depletion/overexpression alters mTORC1 activation by amino acid stimulation specifically, not by growth factors. Reason: The amino-acid specificity is the defining feature of SPAAR (hence its name). SPAAR participates in the cellular response to amino acids as a brake on lysosomal mTORC1 recruitment. Supporting Evidence: PMID:28024296 This regulation of mTORC1 is specific to activation of mTORC1 by amino acid stimulation, rather than by growth factors PMID:28388426 LINC00961 generates SPAR polypeptide that acts via the lysosome to suppress amino-acid-mediated mTORC1 activity |
| GO:1904262 negative regulation of TORC1 signaling | IEA GO_REF:0000107 | ACCEPT | Summary: Ensembl Compara transfer from mouse Spaar of negative regulation of TORC1 signaling. Reason: Correct transfer of the core process, supported by both human and mouse data. Supporting Evidence: PMID:28024296 is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation |
| GO:1904262 negative regulation of TORC1 signaling | IMP PMID:28024296 mTORC1 and muscle regeneration are regulated by the LINC0096... | ACCEPT | Summary: SPAAR negatively regulates amino-acid-induced mTORC1 activation by preventing mTORC1 recruitment to lysosomes. Reason: Core function of SPAAR: loss of the peptide enhances, and its expression suppresses, amino-acid-driven mTORC1 activation; the mechanism is lysosomal and via the V-ATPase-Ragulator-Rag axis. Supporting Evidence: PMID:28024296 is localized to the late endosome/lysosome and interacts with the lysosomal v-ATPase to negatively regulate mTORC1 activation PMID:28024296 This regulation of mTORC1 is specific to activation of mTORC1 by amino acid stimulation, rather than by growth factors PMID:28024296 SPAR downregulation enables efficient activation of mTORC1 and promotes muscle regeneration |
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Download this section (compressed HTML)Q: What molecular activity does SPAAR exert on the V-ATPase-Ragulator-Rag assembly: does it directly bridge the V0 a subunit to Ragulator/Rag, or allosterically lock the V-ATPase in an amino-acid-insensitive state? The answer determines whether a molecular adaptor or an enzyme/GTPase regulator MF term is appropriate.
Q: Is the lysosomal V-ATPase interaction cell-type specific? HA-SPAAR pull-down in endothelial cells did not recover V-ATPase subunits, and the pro-angiogenic effect of SPAAR overexpression may operate through a different mechanism (e.g. SYNE1).
Q: Does the primate-specific 90-aa isoform 1 share the localisation and mTORC1-regulatory function of the conserved 75-aa isoform 2, to which UniProt attributes the function?
Experiment: Generate peptide-specific (start-codon mutant, lncRNA-preserving) knockout endothelial cells or mice, as done for muscle, and test angiogenesis, lysosomal mTORC1 recruitment after amino-acid restimulation, and rescue with wild-type versus V-ATPase-binding-deficient SPAAR.
Hypothesis: SPAAR's pro-angiogenic effect in endothelial cells depends on its mTORC1-regulatory function at the lysosome.
Type: genetic knockout and rescue
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