Rubcn encodes Rubicon (RUN domain Beclin-1-interacting and cysteine-rich domain-containing protein), a negative regulator of late-stage autophagy and endolysosomal maturation. Its middle PI3K-binding region associates with the UVRAG-containing class III phosphatidylinositol 3-kinase complex II (Beclin 1-VPS34-VPS15-UVRAG) and inhibits VPS34 lipid kinase activity, while its C-terminal zinc-cluster Rubicon homology (RH) domain binds GTP-bound Rab7 to target it to late endosomes and lysosomes. By restraining PI3KC3-C2 and sequestering UVRAG from the HOPS tethering complex, Rubicon slows autophagosome maturation, autophagosome-lysosome fusion and degradative endocytic trafficking. Rubicon levels rise with age and under lipid overload in mouse tissues; tissue-specific or whole-body Rubcn knockout mice show increased autophagy with reduced hepatic steatosis on a high-fat diet, reduced kidney fibrosis and alpha-synuclein accumulation in aging, and altered adipose responses to fasting. Rubicon is also implicated in phagocyte innate immunity, including NADPH oxidase-associated phagosome functions and feedback inhibition of CARD9 signalling.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:25594178 A kinase-independent role for EGF receptor in autophagy init... | REMOVE | Summary: Mouse Rubcn co-immunoprecipitates with (human) EGFR in the EGFR-LAPTM4B-Sec5 study; the interaction is plausible but the generic protein binding term conveys no function. Reason: Protein binding is uninformative. In the cited study EGFR sequesters Rubicon away from Beclin 1 to release the Beclin 1 complex; Rubicon is the regulated party, so there is no informative molecular function of Rubcn to substitute (EGFR binding would only restate the interaction). Removal does not imply the interaction is false. Supporting Evidence: PMID:25594178 This EGFR complex binds the autophagy inhibitor Rubicon resulting in its disassociation from Beclin 1 |
| GO:0005654 nucleoplasm | ISO GO_REF:0000119 | REMOVE | Summary: Nucleoplasm is transferred from a human RUBCN annotation; no Rubicon literature reports a nucleoplasmic pool. Reason: All experimental localization data place Rubicon on late endosomes/lysosomes (with a minor early endosome pool) and on Rab7-positive compartments; the human donor nucleoplasm row is no longer present in the current human GOA file, and no published study supports a nuclear function. The ISO transfer therefore propagates an unsupported (likely high-throughput imaging) localization. Propagation Review Root cause: SOURCE STALE OR MISSING Failure modes: SOURCE EVIDENCE WEAK Sources checked: UniProtKB:Q92622 Β· RUBCN SOURCE STALE OR MISSING No nucleoplasm row for human RUBCN remains in the current human GOA file, and no published Rubicon study reports a nuclear pool; the donor localization is not supported. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome file:mouse/Rubcn/Rubcn-uniprot.txt Late endosome {ECO:0000269|PubMed:19270693} |
| GO:0005764 lysosome | IEA GO_REF:0000044 | ACCEPT | Summary: Lysosome localization is experimentally supported for mouse Rubicon (Zhong et al. 2009). Reason: UniProt cites PMID:19270693 for the lysosome location of mouse Rubcn; Rubicon accumulates on late endosomal/lysosomal structures where it restrains maturation. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Lysosome {ECO:0000269|PubMed:19270693} file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome PMID:19270693 forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation |
| GO:0005764 lysosome | ISO GO_REF:0000119 | ACCEPT | Summary: Lysosome localization, transferred from human RUBCN, agrees with mouse data. Reason: Consistent with mouse experimental localization (PMID:19270693) and human data. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Lysosome {ECO:0000269|PubMed:19270693} PMID:19270693 forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation |
| GO:0005769 early endosome | IBA GO_REF:0000033 | ACCEPT | Summary: Early endosome localization is supported but represents a minor pool of Rubicon. Reason: Mouse Rubicon is only partially detected on early endosomes, predominantly on late endosomes/lysosomes; the early endosome location is real and fits its role restraining endosome maturation. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Early endosome {ECO:0000269|PubMed:19270693} file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome PMID:20974968 prevents endosome maturation through differential interactions with Rab7 and UVRAG |
| GO:0005769 early endosome | IEA GO_REF:0000120 | ACCEPT | Summary: Early endosome localization is supported but represents a minor pool of Rubicon. Reason: Mouse Rubicon is only partially detected on early endosomes, predominantly on late endosomes/lysosomes; the early endosome location is real and fits its role restraining endosome maturation. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Early endosome {ECO:0000269|PubMed:19270693} file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome PMID:20974968 prevents endosome maturation through differential interactions with Rab7 and UVRAG |
| GO:0005769 early endosome | ISO GO_REF:0000119 | ACCEPT | Summary: Early endosome localization is supported but represents a minor pool of Rubicon. Reason: Mouse Rubicon is only partially detected on early endosomes, predominantly on late endosomes/lysosomes; the early endosome location is real and fits its role restraining endosome maturation. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Early endosome {ECO:0000269|PubMed:19270693} file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome PMID:20974968 prevents endosome maturation through differential interactions with Rab7 and UVRAG |
| GO:0005770 late endosome | IBA GO_REF:0000033 | ACCEPT | Summary: Late endosome is the principal site of Rubicon action, where its RH domain binds Rab7-GTP. Reason: Late endosome localization is experimentally shown for mouse Rubicon (PMID:19270693) and mechanistically explained by RH-domain binding to Rab7-GTP (PMID:32632011); the PTN002915566 IBA placement in the Euteleostomi RUBCN clade is sound. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Late endosome {ECO:0000269|PubMed:19270693} file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP |
| GO:0005770 late endosome | IEA GO_REF:0000120 | ACCEPT | Summary: Late endosome is the principal site of Rubicon action, where its RH domain binds Rab7-GTP. Reason: Late endosome localization is experimentally shown for mouse Rubicon (PMID:19270693) and mechanistically explained by RH-domain binding to Rab7-GTP (PMID:32632011); the PTN002915566 IBA placement in the Euteleostomi RUBCN clade is sound. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Late endosome {ECO:0000269|PubMed:19270693} file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP |
| GO:0005770 late endosome | ISO GO_REF:0000119 | ACCEPT | Summary: Late endosome is the principal site of Rubicon action, where its RH domain binds Rab7-GTP. Reason: Late endosome localization is experimentally shown for mouse Rubicon (PMID:19270693) and mechanistically explained by RH-domain binding to Rab7-GTP (PMID:32632011); the PTN002915566 IBA placement in the Euteleostomi RUBCN clade is sound. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Late endosome {ECO:0000269|PubMed:19270693} file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP |
| GO:0005829 cytosol | ISO GO_REF:0000119 | KEEP AS NON CORE | Summary: Cytosol localization reflects the soluble pool of a peripheral membrane protein that is recruited to Rab7-positive membranes. Reason: Rubicon has no transmembrane segment and is recruited to late endosomes via Rab7-GTP and the PI3KC3-C2 complex, so a cytosolic pool is expected, but its functional site is the endolysosomal membrane. Supporting Evidence: PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP file:mouse/Rubcn/Rubcn-uniprot.txt Predominantly located in late endosomes/lysosomes, only partially detected in early endosome |
| GO:0010507 negative regulation of autophagy | IEA GO_REF:0000107 | ACCEPT | Summary: Rubicon is a negative regulator of autophagy; this is directly supported in mouse cells and mouse genetics. Reason: Mouse Rubicon reduces Vps34 activity and downregulates autophagy (PMID:19270693); hepatocyte-, adipocyte-specific and whole-body Rubcn knockout mice show increased autophagic activity and amelioration of age-related or diet-induced pathology (PMID:27637015, PMID:35282767, PMID:30783089). The more specific core process is negative regulation of autophagosome maturation. Supporting Evidence: PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy PMID:27637015 Up-regulation of Rubicon was associated with suppression of the late stage of autophagy PMID:30783089 Rubicon knockout mice exhibits reductions in interstitial fibrosis in kidney and reduced Ξ±-synuclein accumulation in the brain PMID:35282767 Adipose-specific rubcn-knockout mice exhibited systemic fat loss that was not accelerated by fasting |
| GO:0010507 negative regulation of autophagy | ISO GO_REF:0000119 | ACCEPT | Summary: Rubicon is a negative regulator of autophagy; this is directly supported in mouse cells and mouse genetics. Reason: Mouse Rubicon reduces Vps34 activity and downregulates autophagy (PMID:19270693); hepatocyte-, adipocyte-specific and whole-body Rubcn knockout mice show increased autophagic activity and amelioration of age-related or diet-induced pathology (PMID:27637015, PMID:35282767, PMID:30783089). The more specific core process is negative regulation of autophagosome maturation. Supporting Evidence: PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy PMID:27637015 Up-regulation of Rubicon was associated with suppression of the late stage of autophagy PMID:30783089 Rubicon knockout mice exhibits reductions in interstitial fibrosis in kidney and reduced Ξ±-synuclein accumulation in the brain PMID:35282767 Adipose-specific rubcn-knockout mice exhibited systemic fat loss that was not accelerated by fasting |
| GO:0045806 negative regulation of endocytosis | IBA GO_REF:0000033 | ACCEPT | Summary: Rubicon restrains endosome maturation and degradative endocytic trafficking. Reason: Rubicon inhibits UVRAG-PI3KC3-C2 and sequesters UVRAG from HOPS, delaying endosome maturation and degradative endocytic trafficking (PMID:20974968; mouse UniProt). The GO term "negative regulation of endocytosis" is used by GO for this endocytic-trafficking branch; the PTN002915566 placement is sound for the RUBCN clade. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Negatively regulates endosome maturation and degradative endocytic trafficking PMID:20974968 sequesters UVRAG from C-VPS/HOPS PMID:20974968 prevents endosome maturation through differential interactions with Rab7 and UVRAG |
| GO:0045806 negative regulation of endocytosis | IEA GO_REF:0000107 | ACCEPT | Summary: Rubicon restrains endosome maturation and degradative endocytic trafficking. Reason: Rubicon inhibits UVRAG-PI3KC3-C2 and sequesters UVRAG from HOPS, delaying endosome maturation and degradative endocytic trafficking (PMID:20974968; mouse UniProt). The GO term "negative regulation of endocytosis" is used by GO for this endocytic-trafficking branch; the PTN002915566 placement is sound for the RUBCN clade. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Negatively regulates endosome maturation and degradative endocytic trafficking PMID:20974968 sequesters UVRAG from C-VPS/HOPS PMID:20974968 prevents endosome maturation through differential interactions with Rab7 and UVRAG |
| GO:0045806 negative regulation of endocytosis | ISO GO_REF:0000119 | ACCEPT | Summary: Rubicon restrains endosome maturation and degradative endocytic trafficking. Reason: Rubicon inhibits UVRAG-PI3KC3-C2 and sequesters UVRAG from HOPS, delaying endosome maturation and degradative endocytic trafficking (PMID:20974968; mouse UniProt). The GO term "negative regulation of endocytosis" is used by GO for this endocytic-trafficking branch; the PTN002915566 placement is sound for the RUBCN clade. Supporting Evidence: file:mouse/Rubcn/Rubcn-uniprot.txt Negatively regulates endosome maturation and degradative endocytic trafficking PMID:20974968 sequesters UVRAG from C-VPS/HOPS PMID:20974968 prevents endosome maturation through differential interactions with Rab7 and UVRAG |
| GO:0051898 negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | IEA GO_REF:0000107 | MODIFY | Summary: The PI3K/AKT signaling term misrepresents Rubicon, which inhibits the class III PI3K (VPS34) rather than class I PI3K/AKT signaling. Reason: The source human annotation (IDA, PMID:21062745) reports inhibition of PI3KC3/hVps34 lipid kinase activity, which is unrelated to PI3K/PKB signal transduction. Replace with phosphatidylinositol 3-kinase inhibitor activity, consistent with the human RUBCN review. Propagation Review Root cause: SOURCE BAD Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:Q92622 Β· RUBCN SOURCE BAD Ensembl Compara transfer of the same human IDA row (PMID:21062745) that measured class III PI3K inhibition, not PI3K/PKB signalling. Proposed replacements: phosphatidylinositol 3-kinase inhibitor activity Supporting Evidence: PMID:21062745 inhibition of PI3KC3 lipid kinase activity by Rubicon PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy |
| GO:0051898 negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction | ISO GO_REF:0000119 | MODIFY | Summary: The PI3K/AKT signaling term misrepresents Rubicon, which inhibits the class III PI3K (VPS34) rather than class I PI3K/AKT signaling. Reason: The source human annotation (IDA, PMID:21062745) reports inhibition of PI3KC3/hVps34 lipid kinase activity, which is unrelated to PI3K/PKB signal transduction. Replace with phosphatidylinositol 3-kinase inhibitor activity, consistent with the human RUBCN review. Propagation Review Root cause: SOURCE BAD Failure modes: GRANULARITY MISMATCH Sources checked: UniProtKB:Q92622 Β· RUBCN SOURCE BAD Human IDA (PMID:21062745) measured inhibition of class III PI3K (hVps34) lipid kinase activity, which is not PI3K/PKB signal transduction; the human review also proposes MODIFY to GO:0141039. Proposed replacements: phosphatidylinositol 3-kinase inhibitor activity Supporting Evidence: PMID:21062745 inhibition of PI3KC3 lipid kinase activity by Rubicon PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy |
| GO:0141039 phosphatidylinositol 3-kinase inhibitor activity | IEA GO_REF:0000107 | ACCEPT | Summary: Phosphatidylinositol 3-kinase inhibitor activity is the core molecular function of Rubicon, shown directly for mouse Rubicon. Reason: Co-expression of mouse Rubicon with Vps34-Vps15 reduces Vps34 lipid kinase activity (PMID:19270693), and the human RUN/PIKBD-dependent inhibition is well established (PMID:21062745). Supporting Evidence: PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy PMID:19270693 This result suggests that over-expression of Rubicon inhibits the Vps34 kinase activity, and this effect does not require Beclin 1 PMID:21062745 inhibition of PI3KC3 lipid kinase activity by Rubicon file:mouse/Rubcn/Rubcn-uniprot.txt Inhibits PIK3C3 activity |
| GO:1901097 negative regulation of autophagosome maturation | IBA GO_REF:0000033 | ACCEPT | Summary: Negative regulation of autophagosome maturation is the central Rubicon process. Reason: Forced expression of mouse Rubicon impairs autophagosome maturation (PMID:19270693); Rubicon inhibits the UVRAG-containing PI3KC3-C2 that drives late-stage maturation, and its RH domain targets it to Rab7-GTP (PMID:32632011). The PTN002915566 placement is sound. Supporting Evidence: PMID:19270693 forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP PMID:27637015 Up-regulation of Rubicon was associated with suppression of the late stage of autophagy |
| GO:1901097 negative regulation of autophagosome maturation | IEA GO_REF:0000107 | ACCEPT | Summary: Negative regulation of autophagosome maturation is the central Rubicon process. Reason: Forced expression of mouse Rubicon impairs autophagosome maturation (PMID:19270693); Rubicon inhibits the UVRAG-containing PI3KC3-C2 that drives late-stage maturation, and its RH domain targets it to Rab7-GTP (PMID:32632011). The PTN002915566 placement is sound. Supporting Evidence: PMID:19270693 forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP PMID:27637015 Up-regulation of Rubicon was associated with suppression of the late stage of autophagy |
| GO:1901097 negative regulation of autophagosome maturation | ISO GO_REF:0000119 | ACCEPT | Summary: Negative regulation of autophagosome maturation is the central Rubicon process. Reason: Forced expression of mouse Rubicon impairs autophagosome maturation (PMID:19270693); Rubicon inhibits the UVRAG-containing PI3KC3-C2 that drives late-stage maturation, and its RH domain targets it to Rab7-GTP (PMID:32632011). The PTN002915566 placement is sound. Supporting Evidence: PMID:19270693 forced expression of Rubicon results in aberrant late endosomal/lysosomal structures and impaired autophagosome maturation PMID:19270693 Rubicon reduces Vps34 activity and downregulates autophagy PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP PMID:27637015 Up-regulation of Rubicon was associated with suppression of the late stage of autophagy |
| GO:1901981 phosphatidylinositol phosphate binding | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phosphatidylinositol phosphate binding is inherited from a Eukaryota-root PAINT node seeded only by RUBCNL/Pacer; direct lipid binding has not been demonstrated for Rubicon. Reason: The only experimental seed for PTN002915557 is Pacer (RUBCNL). For Rubicon itself, Rubicon-EGFP was not pulled down by PtdIns(3)P beads (PMID:19270693), and the RH-domain crystal structure shows that its FYVE-like zinc cluster lacks the basic residues required for PI(3)P binding, the authors noting that Rubicon has not been reported to bind phospholipids (PMID:32632011). Rubicon membrane targeting is explained by Rab7-GTP and PI3KC3-C2 binding instead. Lipid binding may be a Pacer-lineage property rather than an ancestral one, so the inference is likely an over-annotation for the RUBCN clade. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN002915557 Β· PTN002915557 SUPPORTS SOURCE BUT NOT TARGET Eukaryota-root node seeded only by RUBCNL/Pacer (Q9H714, IDA PMID:28306502). Rubicon was negative in a PtdIns(3)P bead pull-down (PMID:19270693) and its FYVE-like zinc cluster lacks the basic PI3P-binding residues (PMID:32632011), so lipid binding is not established for the RUBCN clade. Supporting Evidence: PMID:19270693 Rubicon-EGFP was not pulled down by PtdIns(3)P-conjugated sepharose beads PMID:32632011 Rubicon has not been reported to bind specifically to phospholipids PMID:32632011 However, the Rubicon Zn cluster 1 lacks some of the basic residues required for canonical FYVE domain phosphatidylinositol 3-phosphate (PI[3]P) binding PMID:32632011 Rubicon-mediated inhibition of autophagy requires the interaction of the C-terminal Rubicon homology (RH) domain of Rubicon with Rab7-GTP |
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Download this section (compressed HTML)Q: Is phosphatidylinositol phosphate binding (GO:1901981) at the Eukaryota root node PTN002915557 an ancestral property of the family, or a Pacer/RUBCNL-specific gain? Rubicon was negative in a PtdIns(3)P bead pull-down and its FYVE-like zinc cluster lacks the canonical basic residues.
Suggested experts: PAINT curators, GO phylogenetic annotation editors
Q: Should Rubicon be annotated as part_of PI3KC3-C2 (GO:0034272) given that it binds the complex through the Beclin 1 BARA domain, or does it remain an inhibitory binding partner outside the core complex?
Suggested experts: ComplexPortal curators, GO autophagy editors
Experiment: Quantitative liposome flotation or SPR with purified mouse Rubicon RH domain versus Pacer RH domain on PI3P/PI4P/PI5P-containing membranes, with and without Rab7-GTP.
Hypothesis: The RH domain of Pacer, but not of Rubicon, binds phosphoinositides directly; Rubicon membrane recruitment depends on Rab7-GTP.
Type: in vitro lipid-binding assay
Experiment: Knock-in mice carrying PIKBD (PI3KC3-C2-binding) or RH (Rab7-binding) point mutations in Rubcn, analysed for liver autophagy flux, steatosis on high-fat diet and age-related kidney fibrosis.
Hypothesis: PI3KC3-C2 inhibition targeted by Rab7 accounts for the in vivo autophagy-suppressive phenotypes of Rubicon.
Type: separation-of-function knock-in mice
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