GLIPR2, also called GAPR-1, is a compact CAP-domain protein that lacks a signal peptide and associates with lipid-enriched microdomains on the cytosolic leaflet of Golgi membranes through N-terminal myristoylation, electrostatic contacts, and protein interactions. It forms structurally dynamic homodimers and binds the BARA region of BECN1 and the ATG14-containing class III phosphatidylinositol 3-kinase complex I. GLIPR2 reduces complex association with membranes and directly inhibits its lipid kinase activity, thereby restraining basal macroautophagy; deletion increases autophagic flux in human cells and mouse tissues. In renal and hepatocellular-carcinoma cell models, elevated GLIPR2 also promotes ERK1/2-dependent epithelial-to-mesenchymal transition and migration, while a separate study implicates it in TLR4-induced type-I-interferon signaling. These context-dependent signaling phenotypes have not yet been mechanistically connected to its core autophagy-inhibitory activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005576 extracellular region | IBA GO_REF:0000033 | REMOVE | Summary: PAINT propagated extracellular-region activity from a broad CAP-family node that contains many signal-peptide-bearing secreted proteins. Reason: GLIPR2 is a documented exception to the usual CAP-family topology. It has no signal peptide and localizes to the cytosolic face of Golgi/endosomal membranes, where it inhibits a cytosolic BECN1-containing PI3K complex. Therefore extracellular region is not a supported site of GLIPR2 activity. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000036124 · broad PTHR10334 CAP-family ancestral node SUPPORTS SOURCE BUT NOT TARGET The node spans numerous secreted CAP-family proteins, whereas GLIPR2 is a directly demonstrated nonsecreted cytosolic Golgi protein. Supporting Evidence: PMID:11865038 localizes to the cytosolic site of the endomembrane system in mammalian cells. file:human/GLIPR2/GLIPR2-deep-research-manual.md The extracellular IBA and InterPro-derived IEA should therefore be removed. |
| GO:0010718 positive regulation of epithelial to mesenchymal transition | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: This narrow PAINT inference is seeded by direct human GLIPR2 evidence and is corroborated in two human epithelial-cell contexts. Reason: GLIPR2 overexpression produces EMT-like marker changes, and knockdown attenuates hypoxia-induced EMT-like changes in human HCC cells. The process is experimentally supported but is a disease/cell-culture context rather than the protein's core biochemical role. Supporting Evidence: PMID:24204846 These results revealed that suppression of GLIPR-2 expression in human HCC cells attenuated ERK1/2 activation and EMT-like process following by migration and invasion in response to hypoxia. |
| GO:0060090 molecular adaptor activity | IBA GO_REF:0000033 | MODIFY | Summary: PAINT propagated a broad adaptor term from mouse Glipr1l1, an acrosomal sperm paralog, across the deep CAP-family node to GLIPR2. Reason: The Glipr1l1 source does not support transfer to GLIPR2. Independent human evidence shows a more specific activity: purified GLIPR2 binds and directly inhibits the ATG14-containing class III phosphatidylinositol 3-kinase complex I. Phosphatidylinositol 3-kinase inhibitor activity captures the experimentally demonstrated molecular function without relying on the unrelated paralog seed. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: WRONG ORTHOLOG OR PARALOG FUNCTIONAL DIVERGENCE GRANULARITY MISMATCH Sources checked: MGI:MGI:1916536 · mouse Glipr1l1 SUPPORTS SOURCE BUT NOT TARGET This is a specialized sperm outer-acrosomal-membrane paralog and does not establish GLIPR2's molecular activity. PANTHER:PTN000036124 · broad PTHR10334 ancestral node UNRESOLVED The node spans functionally diverse CAP proteins and is too broad for a Glipr1l1-specific adaptor transfer. Proposed replacements: phosphatidylinositol 3-kinase inhibitor activity Supporting Evidence: PMID:33222586 These findings demonstrate that GLIPR2 directly inactivates the PtdIns3K-C1 complex. |
| GO:0000139 Golgi membrane | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt subcellular-location mapping places GLIPR2 at the Golgi membrane. Reason: This mapping is independently supported by direct immunofluorescence, membrane fractionation, myristoylation, and later autophagy studies. GLIPR2 associates with the cytosolic leaflet rather than entering the Golgi lumen. Supporting Evidence: PMID:11865038 localizes to the cytosolic site of the endomembrane system in mammalian cells. |
| GO:0005576 extracellular region | IEA GO_REF:0000002 | REMOVE | Summary: InterPro transferred the extracellular association of the CAP signature to GLIPR2. Reason: The domain-level mapping fails for this unusual CAP protein. GLIPR2 lacks a signal peptide and direct experiments place it on the cytosolic Golgi leaflet. Exosome proteomics does not establish constitutive extracellular residence or activity. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE COMPARTMENT OR COMPLEX MISMATCH Sources checked: InterPro:IPR018244 · Allrgn_V5/Tpx1 CAP-family signature SUPPORTS SOURCE BUT NOT TARGET Extracellular topology is common in the family but contradicted by direct GLIPR2 localization and sequence topology. Supporting Evidence: PMID:11865038 localizes to the cytosolic site of the endomembrane system in mammalian cells. |
| GO:0070062 extracellular exosome | HDA PMID:18570454 Proteomic analysis of exosomes from human neural stem cells ... | KEEP AS NON CORE | Summary: GLIPR2 was identified in a high-throughput proteomic analysis of exosome preparations from human neural stem cells. Reason: The HDA dataset supports occasional extracellular-vesicle cargo, but the cached abstract does not expose the GLIPR2 peptide row. This context-specific proteomic localization does not define the cytosolic Golgi protein's core site of activity. |
| GO:0070062 extracellular exosome | HDA PMID:23533145 In-depth proteomic analyses of exosomes isolated from expres... | KEEP AS NON CORE | Summary: GLIPR2 was identified in pooled expressed-prostatic-secretion/urine exosome proteomes. Reason: The full paper establishes a large exosome proteome, while the protein-level GLIPR2 row resides in supplementary data not represented in the cached article. The HDA localization is retained as vesicle-cargo context, not as evidence for extracellular function. |
| GO:0000139 Golgi membrane | IDA PMID:11865038 Identification and characterization of a novel human plant p... | ACCEPT | Summary: The original biochemical and imaging study directly localized GAPR-1 to lipid-enriched microdomains of the Golgi membrane. Reason: Immunofluorescence, isolated-Golgi membrane fractionation, myristoylation, and persistent detergent-resistant membrane association establish this as GLIPR2's characteristic cellular location. Supporting Evidence: PMID:11865038 localizes to the cytosolic site of the endomembrane system in mammalian cells. |
| GO:0010634 positive regulation of epithelial cell migration | IDA PMID:23516513 GLIPR-2 overexpression in HK-2 cells promotes cell EMT and m... | KEEP AS NON CORE | Summary: Stable overexpression of GLIPR2 increased migration of human HK-2 renal epithelial cells, alongside EMT-like changes. Reason: The phenotype is directly supported and corroborated by knockdown in human HCC cells under hypoxia. It is retained as a context-dependent cellular consequence rather than treated as the core biochemical function. Supporting Evidence: PMID:24204846 Cells motility and invasiveness were also decreased after suppression of GLIPR-2 in hypoxia |
| GO:0010718 positive regulation of epithelial to mesenchymal transition | IDA PMID:23516513 GLIPR-2 overexpression in HK-2 cells promotes cell EMT and m... | KEEP AS NON CORE | Summary: GLIPR2 overexpression in HK-2 cells decreased epithelial markers and increased mesenchymal markers, ERK activation, and migration. Reason: Direct human-cell evidence supports an EMT-promoting effect, and an independent overexpression/knockdown study reproduces it in hypoxic HCC cells. The evidence is restricted to pathological cell models and does not define the conserved core activity. Supporting Evidence: PMID:23516513 Taken together, these results suggest that the high expression of GLIPR-2 in epithelial cells may promote an EMT. |
| GO:0042803 protein homodimerization activity | IDA PMID:15123429 Structural analysis of the human Golgi-associated plant path... | ACCEPT | Summary: Yeast two-hybrid, biochemical, biophysical, and crystallographic analyses demonstrate GLIPR2 self-association. Reason: Homodimerization is directly observed and is modulated by conserved interface residues, inositol hexakisphosphate, negatively charged membranes, and metal/redox conditions. It is a genuine mechanistic property even though its precise relationship to PI3K inhibition remains unresolved. Supporting Evidence: PMID:15123429 GAPR-1 may form dimers in vitro and in vivo, as determined PMID:22560898 phytic acid (inositol hexakisphosphate) induces dimerization of GAPR-1 in solution. |
| GO:0070374 positive regulation of ERK1 and ERK2 cascade | IDA PMID:23516513 GLIPR-2 overexpression in HK-2 cells promotes cell EMT and m... | KEEP AS NON CORE | Summary: GLIPR2 overexpression increased phospho-ERK1/2 in HK-2 cells; MEK inhibition or ERK1/2 knockdown reversed downstream EMT and migration phenotypes. Reason: The result is direct and is corroborated by GLIPR2 knockdown in hypoxic HCC cells. ERK activation is a context-dependent downstream signaling outcome, not the directly established molecular activity of GLIPR2. Supporting Evidence: PMID:23516513 the GLIPR-2-transfected HK-2 cells had an increased level of phospho-ERK1/2. |
| GO:0070062 extracellular exosome | HDA PMID:19056867 Large-scale proteomics and phosphoproteomics of urinary exos... | KEEP AS NON CORE | Summary: GLIPR2 was recovered in a large-scale proteomic survey of human urinary exosome preparations. Reason: The curated HDA finding is compatible with vesicular export from renal epithelia, but the cached main article does not enumerate the GLIPR2 peptide row. It is retained as a context-specific cargo localization, not a core extracellular site of action. |
| GO:0016242 negative regulation of macroautophagy | IMP PMID:33222586 GLIPR2 is a negative regulator of autophagy and the BECN1-AT... | NEW | Summary: Proposed new direct human annotation. CRISPR deletion of GLIPR2 in three HeLa clones increased basal autophagic flux by four complementary assays, and wild-type reconstitution reversed the phenotype. Reason: Human-cell knockout/rescue, direct PtdIns3K-C1 inhibition, and Glipr2-null mouse-tissue data converge on a conserved role in restraining basal macroautophagy. IMP captures the causal human genetic perturbation. Supporting Evidence: PMID:33222586 Thus, using four independent assays, we demonstrate that GLIPR2 negatively regulates autophagy in cultured cells. |
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Download this section (compressed HTML)Q: At which endogenous membrane compartment does GLIPR2 inhibit PtdIns3K-C1, and does cytosolic Golgi tethering of BECN1 cause the inhibition?
Suggested experts: autophagy and class III PI3K structural biologists, Golgi membrane-trafficking specialists
Q: Does GLIPR2 inhibit the UVRAG-containing PtdIns3K-C2 complex, and how does it compete or cooperate with GORASP2 at the BECN1 BARA domain?
Suggested experts: autophagy-complex biochemists
Q: Are the ERK/EMT and TLR4/type-I-interferon phenotypes consequences of BECN1/PtdIns3K-C1 inhibition, or separable GLIPR2 activities?
Suggested experts: renal and cancer cell-signaling biologists, innate-immunity and autophagy specialists
Q: Do lipid-, zinc-, or copper-regulated GLIPR2 oligomers and amyloid-like assemblies form in living cells and contribute to normal function?
Suggested experts: CAP-domain structural biochemists
Experiment: Reconstitute GLIPR2-null human cells at endogenous abundance with wild-type, G2A nonmyristoylated, BECN1-groove pentad, and dimer-interface mutants; measure PtdIns3K-C1 binding, membrane association, PtdIns3P, WIPI2, autophagic flux, and Golgi morphology in parallel.
Hypothesis: Golgi membrane anchoring and the BECN1-binding groove are independently required for GLIPR2 to inhibit PtdIns3K-C1, while a specific oligomeric state gates access to BECN1.
Type: CRISPR rescue and separation-of-function analysis
Experiment: Reconstitute purified PtdIns3K-C1 and PtdIns3K-C2 on Golgi-like membranes with GLIPR2 and GORASP2, then combine lipid-kinase assays with cryo-EM or HDX-MS and membrane-flotation measurements.
Hypothesis: GLIPR2 inhibits one or both class III PI3K complexes by restricting BECN1 BARA-domain membrane engagement, with GORASP2 providing complex-specific competition.
Type: comparative complex biochemistry and structural analysis
Experiment: In primary human renal epithelial cells and monocytes, compare GLIPR2 knockout and separation-of-function rescue during hypoxia or TLR4 stimulation, with autophagy epistasis using BECN1 mutants and selective class III PI3K perturbations.
Hypothesis: The ERK/EMT and interferon phenotypes depend on the same BECN1/PtdIns3K-C1 inhibitory activity that restrains basal autophagy.
Type: pathway epistasis in physiologically relevant human cells
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The endogenous site and complete molecular mechanism of PtdIns3K-C1 inhibition by GLIPR2 remain unresolved.
OPEN BIOLOGY MF_DARK
What is known: Purified GLIPR2 binds and inhibits PtdIns3K-C1 and lowers its liposome association, while cellular knockout increases PtdIns3P and autophagic flux; however, it is unknown where endogenous inhibition occurs and whether Golgi sequestration or dispersion is causal.
Significance: Resolving compartment and structural state is necessary to distinguish direct membrane competition, BECN1 sequestration, and allosteric inhibition.
What would resolve it: Endogenous-level localization mutants, proximity labeling, live-cell PtdIns3P reporters, and structures of GLIPR2-bound PtdIns3K-C1 should resolve the mechanism.
Provenance (the field's own admissions):
Gap: It is unknown whether GLIPR2 also inhibits PtdIns3K-C2 and how GORASP2 competition changes complex specificity.
OPEN BIOLOGY MF_DARK
What is known: Direct biochemical inhibition has been shown only for ATG14-containing PtdIns3K-C1, while the BECN1-binding surface is also regulatory in PtdIns3K-C2.
Significance: PtdIns3K-C2 controls autophagosome maturation and endocytic pathways, so inhibition would materially broaden GLIPR2's core function.
What would resolve it: Purified-complex kinase, membrane-association, and binding assays should test PtdIns3K-C2 directly with and without GORASP2.
Provenance (the field's own admissions):
Gap: The relationship between core autophagy inhibition and the reported EMT/ERK and TLR4/type-I-interferon phenotypes is unknown.
OPEN BIOLOGY BP_DARK
What is known: Each phenotype is experimentally supported, but existing studies do not use GLIPR2 mutants that separate BECN1/PtdIns3K-C1 inhibition from membrane, dimerization, or TMED7 interactions.
Significance: Mechanistic unification would determine whether these are physiological outputs of one core activity or distinct context-specific functions.
What would resolve it: Autophagy epistasis and endogenous-level separation-of-function rescues in renal epithelial, HCC, and monocyte models can distinguish the alternatives.
Provenance (the field's own admissions):
Gap: The physiological relevance of GLIPR2's lipid- and metal-regulated amyloid-like assemblies is unknown.
OPEN BIOLOGY MF_DARK
What is known: Purified GLIPR2 forms oligomers and fibrils with anionic lipids, heparin, zinc, or copper, but no study has demonstrated these assemblies in normal cells or linked them causally to autophagy inhibition.
Significance: The assemblies could be regulatory CAP-domain states or nonphysiological consequences of high-concentration in vitro conditions.
What would resolve it: Conformation-specific probes, endogenous crosslinking, and live-cell assembly measurements under controlled metal and membrane-lipid perturbations are required.
Provenance (the field's own admissions):
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