id: Q9H714 gene_symbol: RUBCNL product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- RUBCNL encodes PACER, a Rubicon-like autophagy enhancer that acts at late autophagosome maturation. It is recruited to STX17-positive autophagosome membranes, interacts with UVRAG/STX17, promotes recruitment of PI3K/PI3KC3 and HOPS complexes, stimulates Vps34/PI3KC3-dependent PtdIns(3)P production, and supports autophagosome-endosome/lysosome fusion. RUBCNL functions as an autophagosome-maturation adaptor/recruitment factor associated with PI3KC3-C2 and HOPS. alternative_products: - name: '1' id: Q9H714-5 - name: '5' id: Q9H714-4 sequence_note: VSP_014713 - name: '2' id: Q9H714-3 sequence_note: VSP_014708 - name: '3' id: Q9H714-1 sequence_note: VSP_014711, VSP_014712 - name: '4' id: Q9H714-2 sequence_note: VSP_014709, VSP_014710 - name: '6' id: Q9H714-6 sequence_note: VSP_055260 existing_annotations: - term: id: GO:0000421 label: autophagosome membrane evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: is_active_in review: summary: Autophagosome membrane localization is supported and central to PACER late-autophagy function. action: ACCEPT reason: RUBCNL/PACER is recruited to late autophagic/autophagosome membranes and uses STX17-positive autophagosomes as the platform for PI3KC3 and HOPS recruitment. additional_reference_ids: &id001 - PMID:28306502 - PMID:30704899 - file:human/RUBCNL/RUBCNL-uniprot.txt - file:human/RUBCNL/RUBCNL-notes.md supported_by: &id003 - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Cytoplasmic vesicle, autophagosome membrane - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Associates with late autophagic structure - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Recruitment to autophagosome membrane is promoted by autophagic stimuli - reference_id: PMID:28306502 supporting_text: Pacer localizes to autophagic structures - term: id: GO:0061909 label: autophagosome-lysosome fusion evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: Autophagosome-lysosome fusion is supported as a core late-autophagy process for RUBCNL. action: ACCEPT reason: PACER recruits PI3KC3 and HOPS complexes at STX17-positive autophagosomes, supporting fusion specificity with late endosomes/lysosomes. additional_reference_ids: *id001 supported_by: &id002 - reference_id: PMID:28306502 supporting_text: recruits PI3KC3 and HOPS complexes - reference_id: PMID:28306502 supporting_text: anchoring to the autophagosomal SNARE Stx17 - reference_id: PMID:28306502 supporting_text: HOPS complex mediates the fusion of intracellular vesicles to lysosome - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: regulate the fusion specificity of autophagosomes with late endosomes/lysosomes - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Interacts with STX17 - term: id: GO:0061910 label: autophagosome-endosome fusion evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: Autophagosome-endosome fusion is supported as part of the same late maturation/fusion role. action: ACCEPT reason: The curated mechanism places RUBCNL at STX17-positive autophagosomes where it recruits PI3KC3 and HOPS machinery to regulate fusion with late endosomal/lysosomal compartments. additional_reference_ids: *id001 supported_by: *id002 - term: id: GO:0097352 label: autophagosome maturation evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: Autophagosome maturation is the central RUBCNL biological-process annotation. action: ACCEPT reason: Both functional papers and UniProt support PACER as a positive regulator of late autophagosome maturation through STX17, PI3KC3, HOPS, and regulated phosphorylation/acetylation. additional_reference_ids: *id001 supported_by: &id006 - reference_id: PMID:28306502 supporting_text: positively regulates autophagosome maturation - reference_id: PMID:28306502 supporting_text: stimulate Vps34 kinase activity - reference_id: PMID:28306502 supporting_text: recruits PI3KC3 and HOPS complexes - reference_id: PMID:28306502 supporting_text: anchoring to the autophagosomal SNARE Stx17 - reference_id: PMID:30704899 supporting_text: modulate autophagosome maturation through Pacer - reference_id: PMID:30704899 supporting_text: facilitates HOPS complex recruitment - reference_id: PMID:30704899 supporting_text: required for autophagosome maturation and lipid droplet clearance - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: promotes autophagosome maturation - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: promotes the recruitment of PI3K/PI3KC3 and HOPS complexes - term: id: GO:1901981 label: phosphatidylinositol phosphate binding evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: enables review: summary: The broad phosphatidylinositol phosphate binding term is true but should be replaced by specific lipid-binding terms. action: MODIFY reason: RUBCNL has IDA-supported binding to PtdIns(3)P, PtdIns(4)P, and PtdIns(5)P, so the inherited generic term is less informative than the specific existing annotations. additional_reference_ids: - GO_REF:0000033 - PMID:28306502 - file:human/RUBCNL/RUBCNL-uniprot.txt - file:human/RUBCNL/RUBCNL-notes.md supported_by: &id005 - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Binds phosphoinositides phosphatidylinositol 3-phosphate - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: GO:0032266; F:phosphatidylinositol-3-phosphate binding - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: GO:0070273; F:phosphatidylinositol-4-phosphate binding - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: GO:0010314; F:phosphatidylinositol-5-phosphate binding proposed_replacement_terms: - id: GO:0032266 label: phosphatidylinositol-3-phosphate binding - id: GO:0070273 label: phosphatidylinositol-4-phosphate binding - id: GO:0010314 label: phosphatidylinositol-5-phosphate binding - term: id: GO:0000421 label: autophagosome membrane evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: Autophagosome membrane localization is supported and central to PACER late-autophagy function. action: ACCEPT reason: RUBCNL/PACER is recruited to late autophagic/autophagosome membranes and uses STX17-positive autophagosomes as the platform for PI3KC3 and HOPS recruitment. additional_reference_ids: *id001 supported_by: *id003 - term: id: GO:0000421 label: autophagosome membrane evidence_type: IDA original_reference_id: PMID:28306502 qualifier: located_in review: summary: Autophagosome membrane localization is supported and central to PACER late-autophagy function. action: ACCEPT reason: RUBCNL/PACER is recruited to late autophagic/autophagosome membranes and uses STX17-positive autophagosomes as the platform for PI3KC3 and HOPS recruitment. additional_reference_ids: *id001 supported_by: *id003 - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:28306502 qualifier: enables review: summary: The interaction evidence is real, but generic protein binding obscures the PACER adaptor/recruitment function. action: MARK_AS_OVER_ANNOTATED reason: RUBCNL interaction data should be represented by the specific STX17/UVRAG-dependent adaptor role in PI3KC3/HOPS recruitment and autophagosome maturation, not by generic protein binding. additional_reference_ids: *id001 supported_by: &id004 - reference_id: PMID:28306502 supporting_text: recruits PI3KC3 and HOPS complexes - reference_id: PMID:28306502 supporting_text: anchoring to the autophagosomal SNARE Stx17 - reference_id: PMID:30704899 supporting_text: disrupt the association of Pacer with Stx17 and the HOPS complex - reference_id: PMID:30704899 supporting_text: facilitates HOPS complex recruitment - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Interacts with UVRAG - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Interacts with STX17 - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: association with the PI3K/PI3KC3 and HOPS complexes proposed_replacement_terms: - id: GO:0030674 label: protein-macromolecule adaptor activity - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:30704899 qualifier: enables review: summary: The interaction evidence is real, but generic protein binding obscures the PACER adaptor/recruitment function. action: MARK_AS_OVER_ANNOTATED reason: RUBCNL interaction data should be represented by the specific STX17/UVRAG-dependent adaptor role in PI3KC3/HOPS recruitment and autophagosome maturation, not by generic protein binding. additional_reference_ids: *id001 supported_by: *id004 proposed_replacement_terms: - id: GO:0030674 label: protein-macromolecule adaptor activity - term: id: GO:0010314 label: phosphatidylinositol-5-phosphate binding evidence_type: IDA original_reference_id: PMID:28306502 qualifier: enables review: summary: phosphatidylinositol-5-phosphate binding is directly supported and contributes to autophagosome-membrane recruitment/function. action: ACCEPT reason: The discovery study and UniProt support phosphoinositide binding by PACER, including PtdIns(3)P, PtdIns(4)P, and PtdIns(5)P. additional_reference_ids: - PMID:28306502 - file:human/RUBCNL/RUBCNL-uniprot.txt - file:human/RUBCNL/RUBCNL-notes.md supported_by: *id005 - term: id: GO:0019216 label: regulation of lipid metabolic process evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: involved_in review: summary: Regulation of lipid metabolic process is supported as downstream organismal physiology, not the core PN molecular role. action: KEEP_AS_NON_CORE reason: The direct human evidence centers on autophagosome maturation; lipid and glycogen homeostasis are described as additional or by-similarity biology downstream of PACER-dependent autophagy. additional_reference_ids: - GO_REF:0000024 - PMID:30704899 - file:human/RUBCNL/RUBCNL-uniprot.txt - file:human/RUBCNL/RUBCNL-notes.md supported_by: - reference_id: PMID:30704899 supporting_text: required for autophagosome maturation and lipid droplet clearance - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: acts as a regulator of lipid and glycogen homeostasis - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Acetylated by KAT5/TIP60 under autophagy induction - term: id: GO:0032266 label: phosphatidylinositol-3-phosphate binding evidence_type: IDA original_reference_id: PMID:28306502 qualifier: enables review: summary: phosphatidylinositol-3-phosphate binding is directly supported and contributes to autophagosome-membrane recruitment/function. action: ACCEPT reason: The discovery study and UniProt support phosphoinositide binding by PACER, including PtdIns(3)P, PtdIns(4)P, and PtdIns(5)P. additional_reference_ids: - PMID:28306502 - file:human/RUBCNL/RUBCNL-uniprot.txt - file:human/RUBCNL/RUBCNL-notes.md supported_by: *id005 - term: id: GO:0061909 label: autophagosome-lysosome fusion evidence_type: IDA original_reference_id: PMID:28306502 qualifier: involved_in review: summary: Autophagosome-lysosome fusion is supported as a core late-autophagy process for RUBCNL. action: ACCEPT reason: PACER recruits PI3KC3 and HOPS complexes at STX17-positive autophagosomes, supporting fusion specificity with late endosomes/lysosomes. additional_reference_ids: *id001 supported_by: *id002 - term: id: GO:0061910 label: autophagosome-endosome fusion evidence_type: IDA original_reference_id: PMID:28306502 qualifier: involved_in review: summary: Autophagosome-endosome fusion is supported as part of the same late maturation/fusion role. action: ACCEPT reason: The curated mechanism places RUBCNL at STX17-positive autophagosomes where it recruits PI3KC3 and HOPS machinery to regulate fusion with late endosomal/lysosomal compartments. additional_reference_ids: *id001 supported_by: *id002 - term: id: GO:0070273 label: phosphatidylinositol-4-phosphate binding evidence_type: IDA original_reference_id: PMID:28306502 qualifier: enables review: summary: phosphatidylinositol-4-phosphate binding is directly supported and contributes to autophagosome-membrane recruitment/function. action: ACCEPT reason: The discovery study and UniProt support phosphoinositide binding by PACER, including PtdIns(3)P, PtdIns(4)P, and PtdIns(5)P. additional_reference_ids: - PMID:28306502 - file:human/RUBCNL/RUBCNL-uniprot.txt - file:human/RUBCNL/RUBCNL-notes.md supported_by: *id005 - term: id: GO:0097352 label: autophagosome maturation evidence_type: IDA original_reference_id: PMID:28306502 qualifier: involved_in review: summary: Autophagosome maturation is the central RUBCNL biological-process annotation. action: ACCEPT reason: Both functional papers and UniProt support PACER as a positive regulator of late autophagosome maturation through STX17, PI3KC3, HOPS, and regulated phosphorylation/acetylation. additional_reference_ids: *id001 supported_by: *id006 - term: id: GO:0097352 label: autophagosome maturation evidence_type: IDA original_reference_id: PMID:30704899 qualifier: involved_in review: summary: Autophagosome maturation is the central RUBCNL biological-process annotation. action: ACCEPT reason: Both functional papers and UniProt support PACER as a positive regulator of late autophagosome maturation through STX17, PI3KC3, HOPS, and regulated phosphorylation/acetylation. additional_reference_ids: *id001 supported_by: *id006 - term: id: GO:0030674 label: protein-macromolecule adaptor activity evidence_type: IPI original_reference_id: PMID:28306502 qualifier: enables review: summary: PACER has a supported adaptor/recruitment role at STX17-positive autophagosomes. action: NEW reason: Add this as a more informative molecular-function annotation than generic protein binding. RUBCNL links STX17-positive autophagosomes with UVRAG, PI3KC3, and HOPS machinery to drive autophagosome maturation. additional_reference_ids: *id001 supported_by: *id004 - term: id: GO:0034272 label: phosphatidylinositol 3-kinase complex, class III, type II evidence_type: IPI original_reference_id: PMID:28306502 qualifier: part_of review: summary: RUBCNL should be added as a PI3KC3-C2-associated regulatory/adaptor context component. action: NEW reason: The PN projection highlights missing PI3KC3-C2 context, and the functional evidence shows PACER/UVRAG-dependent recruitment and activation of PI3KC3 at autophagosomes during late autophagy. additional_reference_ids: - PMID:28306502 - file:human/RUBCNL/RUBCNL-uniprot.txt - file:human/RUBCNL/RUBCNL-notes.md supported_by: - reference_id: PMID:28306502 supporting_text: recruits PI3KC3 and HOPS complexes - reference_id: PMID:28306502 supporting_text: stimulate Vps34 kinase activity - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: promotes the recruitment of PI3K/PI3KC3 and HOPS complexes - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Interacts with UVRAG references: - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity 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: PMID:28306502 title: Pacer Mediates the Function of Class III PI3K and HOPS Complexes in Autophagosome Maturation by Engaging Stx17. findings: [] - id: PMID:30704899 title: Pacer Is a Mediator of mTORC1 and GSK3-TIP60 Signaling in Regulation of Autophagosome Maturation and Lipid Metabolism. findings: [] - id: file:human/RUBCNL/RUBCNL-uniprot.txt title: UniProtKB record for human RUBCNL findings: [] - id: file:human/RUBCNL/RUBCNL-notes.md title: RUBCNL review notes findings: [] core_functions: - molecular_function: id: GO:0030674 label: protein-macromolecule adaptor activity description: PACER/RUBCNL acts as a STX17-anchored autophagosome adaptor that recruits UVRAG-associated PI3KC3-C2 and HOPS machinery, stimulates Vps34/PI3KC3-dependent PtdIns(3)P production, and promotes late autophagosome maturation and fusion with endolysosomal compartments. directly_involved_in: - id: GO:0097352 label: autophagosome maturation - id: GO:0061909 label: autophagosome-lysosome fusion - id: GO:0061910 label: autophagosome-endosome fusion locations: - id: GO:0000421 label: autophagosome membrane in_complex: id: GO:0034272 label: phosphatidylinositol 3-kinase complex, class III, type II supported_by: - reference_id: PMID:28306502 supporting_text: positively regulates autophagosome maturation - reference_id: PMID:28306502 supporting_text: stimulate Vps34 kinase activity - reference_id: PMID:28306502 supporting_text: recruits PI3KC3 and HOPS complexes - reference_id: PMID:28306502 supporting_text: anchoring to the autophagosomal SNARE Stx17 - reference_id: PMID:30704899 supporting_text: facilitates HOPS complex recruitment - reference_id: PMID:30704899 supporting_text: required for autophagosome maturation and lipid droplet clearance - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: promotes the recruitment of PI3K/PI3KC3 and HOPS complexes - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Interacts with UVRAG - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Interacts with STX17 - reference_id: file:human/RUBCNL/RUBCNL-uniprot.txt supporting_text: Cytoplasmic vesicle, autophagosome membrane proposed_new_terms: [] suggested_questions: - question: Should RUBCNL/PACER be curated as part_of GO:0034272 PI3KC3-C2, or represented as a PI3KC3/HOPS recruitment adaptor without complex membership? experts: - GO autophagy editors - ComplexPortal curators - question: Should generic RUBCNL protein-binding annotations be replaced by protein-macromolecule adaptor activity for STX17/UVRAG/PI3KC3/HOPS recruitment? experts: - GO molecular function editors - GO autophagy editors - question: Should regulation of lipid metabolic process remain a non-core by-similarity annotation, or should it be tied more explicitly to autophagy-dependent lipid droplet clearance? experts: - GO autophagy editors - GO lipid metabolism editors suggested_experiments: - experiment_type: PACER adaptor separation-of-function rescue hypothesis: RUBCNL requires separable STX17/UVRAG interaction surfaces and phosphoinositide binding to recruit PI3KC3/HOPS and promote autophagosome maturation. description: Use RUBCNL knockout/rescue cells with STX17-binding, UVRAG-binding, and phosphoinositide-binding mutants to quantify PI3P production, HOPS recruitment, and autophagosome-endolysosome fusion. - experiment_type: endogenous live-cell maturation imaging hypothesis: PACER occupancy marks STX17-positive autophagosomes that are competent for PI3KC3/HOPS recruitment and subsequent fusion with endolysosomal compartments. description: Endogenously tag RUBCNL, STX17, UVRAG, a PI3P reporter, and HOPS markers and follow recruitment timing during starvation and recovery.