id: A0A8C5FPT8 gene_symbol: tbc1d14 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:8049 label: Gadus morhua description: >- tbc1d14 encodes a TBC (Tre2-Bub2-Cdc16) Rab-GAP-domain protein of the vertebrate TBC1D14 orthology group. In vertebrates it acts as a non-catalytic regulator of membrane traffic between recycling endosomes and the early Golgi. Characterised mammalian TBC1D14 binds the GTP-bound forms of RAB11A and RAB11B, but it shows no detectable GAP activity toward RAB11 or a broad panel of other Rabs, and it behaves as a RAB11 effector. Its N-terminal region binds the TRAPPIII tethering complex through TRAPPC8, which is needed for RAB1 activation. The protein also binds the autophagy kinase ULK1. TBC1D14 sits on RAB11-positive recycling endosomes and moves toward the Golgi under amino-acid starvation. It controls the supply of recycling-endosome membrane and the cycling of ATG9 to sites of autophagosome formation, and so acts as a negative regulator of starvation-induced macroautophagy. The Atlantic cod protein shares this architecture: an N-terminal disordered region, a TRAPP-binding segment aligned to the mammalian region, a coiled coil, and a C-terminal TBC domain (residues 388-596) that keeps the arginine- and glutamine-finger residues. existing_annotations: - term: id: GO:0005096 label: GTPase activator activity evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: enables review: summary: >- TreeGrafter transfer from PANTHER node PTN009208344. The cod protein was placed in PTHR47219:SF15 (the TBC1D12 subfamily) and inherits GAP activity from a deep node seeded by RABGAP1/RABGAP1L. The re-review tree puts cod tbc1d14 inside the vertebrate TBC1D14 clade, not with TBC1D12, so the correct comparator is TBC1D14. Human TBC1D14 binds GTP-locked RAB11A and RAB11B. In a screen of 47 [32P]GTP-loaded Rabs, recombinant TBC1D14 showed no detectable GAP activity, and the authors describe it as having no GAP activity. The arginine- and glutamine-finger positions are retained in the cod sequence (R457/Q493). Keeping these residues does not show catalysis. action: MARK_AS_OVER_ANNOTATED reason: >- The direct experimental test on the ortholog is negative: no GAP activity toward RAB11 or 46 other Rabs. The ortholog's function is that of a Rab11 effector and TRAPPIII scaffold. The term reaches cod only through a subfamily placement that the phylogeny does not support. PAINT does propagate GTPase activator activity to human TBC1D14 from a deep TBC-family node, and a substrate outside the tested panel cannot be ruled out formally, so this is recorded as an over-annotation rather than a removal. supported_by: - reference_id: PMID:22613832 supporting_text: We then performed a GAP assay screen using a panel of 47 Rabs loaded with [32P]GTP but were unable to detect GAP activity with either recombinant GST-TBC1D14 - reference_id: PMID:22613832 supporting_text: S4 shows that TBC1D14 has no GAP activity toward a panel of GTP-loaded mammalian Rab proteins. - reference_id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-deep-research-falcon.md supporting_text: TBC1D14 does not function as a canonical GAP for RAB11 - reference_id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-bioinformatics/RESULTS-rereview.md supporting_text: The catalytic residues are retained, but retaining them does not show GAP activity. - term: id: GO:0005773 label: vacuole evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: located_in review: summary: >- ARBA rule-based location. In GO, the only route from TBC1D14 biology to vacuole is autophagosome (GO:0005776), which is_a vacuole. Mammalian TBC1D14 is mainly on recycling endosomes and moves to the Golgi on starvation. Its contact with autophagosome-forming membrane comes from overexpressed protein on ULK1-positive tubules. No lysosomal or vacuolar residence has been reported. action: MARK_AS_OVER_ANNOTATED reason: >- Vacuole is not where the ortholog has been seen. The documented compartments are recycling endosome and Golgi, and residence on the autophagosome itself is weakly supported. The ARBA rule gives no protein-specific evidence. supported_by: - reference_id: PMID:22613832 supporting_text: Amino acid starvation causes TBC1D14 to relocalize from REs to the - term: id: GO:0016192 label: vesicle-mediated transport evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: involved_in review: summary: >- ARBA rule-based process. The mammalian ortholog regulates membrane traffic from RAB11-positive recycling endosomes. The proposed model is a constitutive step from peripheral recycling endosomes to the early Golgi, mediated by TRAPPIII and RAB1, that maintains the cycling ATG9 pool. More specific GO transport terms (e.g. GO:0042147 retrograde transport, endosome to Golgi) are not annotated to the experimentally studied ortholog. The precise transport step is a proposed model, not a measured transport reaction. action: ACCEPT reason: >- The term is correct and is as specific as the evidence allows. TBC1D14 is part of the membrane-trafficking machinery: it binds RAB11, recruits TRAPPIII and is required for RAB1 activation. The exact transport step it carries out is not established well enough to justify a narrower process term. supported_by: - reference_id: PMID:26711178 supporting_text: We also demonstrate that TBC1D14 is required for activation of RAB1 through its TRAPP‐binding ability. - reference_id: PMID:26711178 supporting_text: In support of an interaction of TBC1D14 and TRAPPIII, it has been shown that exchange between the transferrin/RAB11‐positive RE and the RAB1‐positive ERGIC/early Golgi can occur - term: id: GO:0019899 label: enzyme binding evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: enables review: summary: >- ARBA rule-based function. The term is true but uninformative. The enzyme partners documented for the ortholog are the small GTPases RAB11A/B, bound in the GTP-loaded form, and the autophagy kinase ULK1. Both are better described by specific descendants of enzyme binding: small GTPase binding (GO:0031267, already carried by this gene) and protein kinase binding (GO:0019901). action: MODIFY reason: >- The term is correct but too general. Replace it with the specific supported descendants small GTPase binding (RAB11) and protein kinase binding (ULK1). proposed_replacement_terms: - id: GO:0031267 label: small GTPase binding - id: GO:0019901 label: protein kinase binding supported_by: - reference_id: PMID:22613832 supporting_text: TBC1D14 binds specifically to both Rab11a and 11b but not to any of the other 55 Rabs tested - reference_id: PMID:22613832 supporting_text: TBC1D14 and ULK1 interact and colocalize on TBC1D14-induced tubules - term: id: GO:0031267 label: small GTPase binding evidence_type: IEA original_reference_id: GO_REF:0000118 qualifier: enables review: summary: >- TreeGrafter transfer. It arrives through the SF15 placement, but the function is independently supported for the true ortholog group. Human TBC1D14 binds GTP-locked RAB11A and RAB11B selectively in a yeast two-hybrid screen of GTP-locked Rabs. RAB11 binding recruits the protein to recycling endosomes, and loss of RAB11 prevents TBC1D14-induced tubulation. The cod protein falls in the TBC1D14 clade and keeps the TBC domain through which Rab binding occurs. The more specific Rab GTPase binding term (GO:0017137) is obsolete, so small GTPase binding is the appropriate term. action: ACCEPT reason: >- Binding of active RAB11 is the best-characterised molecular activity of TBC1D14 orthologs, and the cod protein is a phylogenetic member of that orthology group. supported_by: - reference_id: PMID:22613832 supporting_text: TBC1D14 binds specifically to both Rab11a and 11b but not to any of the other 55 Rabs tested - reference_id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-bioinformatics/RESULTS-rereview.md supporting_text: the two cod tbc1d14 models fall inside the vertebrate TBC1D14 clade - term: id: GO:0031410 label: cytoplasmic vesicle evidence_type: IEA original_reference_id: GO_REF:0000117 qualifier: located_in review: summary: >- ARBA rule-based location. It is correct but general. The ortholog's documented compartment is the RAB11- and transferrin receptor-positive recycling endosome, and GO:0055037 recycling endosome is a descendant of cytoplasmic vesicle (via endosome and intracellular vesicle). PAINT places recycling endosome on the TBC1D14 clade (PTN000538677), which the cod protein belongs to by the re-review tree. Cod did not receive that IBA because PANTHER mis-assigned it to SF15. action: MODIFY reason: >- Replace with the more specific recycling endosome, the compartment supported by the ortholog data. proposed_replacement_terms: - id: GO:0055037 label: recycling endosome supported_by: - reference_id: PMID:22613832 supporting_text: Amino acid starvation causes TBC1D14 to relocalize from REs to the - reference_id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-bioinformatics/RESULTS-rereview.md supporting_text: the two cod tbc1d14 models fall inside the vertebrate TBC1D14 clade - term: id: GO:2000785 label: regulation of autophagosome assembly evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: >- Proposed new annotation. PAINT placed regulation of autophagosome assembly on node PTN008586039, seeded by human TBC1D14 IMP data, which covers the TBC1D14 clade. The cod protein belongs to that clade by phylogeny but was routed by TreeGrafter through SF15 and so did not inherit the term. TBC1D14 does part of the regulatory work itself: it binds RAB11 and TRAPPIII and is required for RAB1 activation and ATG9 cycling. This is the role the curators assigned, not a downstream phenotype. action: NEW reason: >- The term matches the ortholog's established role and the PAINT node that covers the TBC1D14 clade. It is missing in cod only because of a subfamily mis-assignment shown by the re-review tree. supported_by: - reference_id: PMID:26711178 supporting_text: We show here TBC1D14 acts as a negative regulator of autophagy by modulating the contribution of both RE and Golgi membranes to the growing autophagosome through its interaction with Rab11 and TRAPPIII. - reference_id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-bioinformatics/RESULTS-rereview.md supporting_text: the two cod tbc1d14 models fall inside the vertebrate TBC1D14 clade references: - id: GO_REF:0000117 title: Electronic Gene Ontology annotations created by ARBA machine learning models findings: [] - id: GO_REF:0000118 title: TreeGrafter-generated GO annotations findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: PMID:22613832 title: TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes. findings: - statement: >- Human TBC1D14 binds GTP-locked RAB11A/B selectively and has no detectable GAP activity against a panel of 47 Rabs; it localizes to recycling endosomes and moves to the Golgi on starvation. supporting_text: TBC1D14 binds specifically to both Rab11a and 11b but not to any of the other 55 Rabs tested reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text cached; primary characterisation of the human ortholog (Rab11 binding, negative GAP screen, RE/Golgi localisation, ULK1 interaction). - id: PMID:26711178 title: TBC1D14 regulates autophagy via the TRAPP complex and ATG9 traffic. findings: - statement: >- TBC1D14 binds TRAPPIII via TRAPPC8 through an N-terminal region and is required for RAB1 activation and ATG9 trafficking; it acts as a negative regulator of autophagy. supporting_text: We also demonstrate that TBC1D14 is required for activation of RAB1 through its TRAPP‐binding ability. reference_review: relevance: HIGH correctness: VERIFIED review_notes: Full text cached; defines the TRAPPIII scaffold mechanism in mammalian cells. - id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-bioinformatics/RESULTS-rereview.md title: Re-review sequence analysis of cod tbc1d14 (gene model, orthology, catalytic residues) findings: - statement: >- All cod tbc1d14 entries are transcripts of ENSGMOG00000018292; A0A8C5FPT8 is an alternative model with a non-conserved N-terminus and a non-conserved 48-residue C-terminal tail; it groups with vertebrate TBC1D14, not TBC1D12, despite PANTHER SF15. supporting_text: A0A8C5FPT8 is therefore a near-complete alternative gene model. - id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-deep-research-falcon.md title: Falcon deep research report for cod tbc1d14 findings: [] - id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-uniprot.txt title: UniProt record A0A8C5FPT8 findings: [] core_functions: - molecular_function: id: GO:0031267 label: small GTPase binding description: >- Binds GTP-bound RAB11 as an effector rather than a GAP. This binding places the protein on RAB11-positive recycling endosomes, where it scaffolds the TRAPPIII complex and supports RAB1 activation at the recycling endosome to early Golgi interface. Inferred from the characterised mammalian ortholog. The cod protein falls in the TBC1D14 orthology clade. directly_involved_in: - id: GO:0016192 label: vesicle-mediated transport - id: GO:2000785 label: regulation of autophagosome assembly locations: - id: GO:0055037 label: recycling endosome supported_by: - reference_id: PMID:22613832 supporting_text: TBC1D14 binds specifically to both Rab11a and 11b but not to any of the other 55 Rabs tested - reference_id: PMID:26711178 supporting_text: We also demonstrate that TBC1D14 is required for activation of RAB1 through its TRAPP‐binding ability. - reference_id: file:GADMO/A0A8C5FPT8/A0A8C5FPT8-bioinformatics/RESULTS-rereview.md supporting_text: the two cod tbc1d14 models fall inside the vertebrate TBC1D14 clade suggested_questions: - question: >- Should PANTHER move teleost and coelacanth tbc1d14 from PTHR47219:SF15 (TBC1D12) to SF21 (TBC1D14)? A distance tree puts them in the TBC1D14 clade, and the SF15 placement routes TBC1D12/RABGAP1 node annotations to them while blocking the TBC1D14-clade PAINT terms. experts: [] - question: >- Does cod tbc1d14 retain any GAP activity toward a Rab outside the 47-Rab panel tested for the human ortholog, given that its arginine and glutamine fingers are intact? experts: [] - question: >- Is the non-conserved 48-residue C-terminal tail of the A0A8C5FPT8 model supported by transcript evidence, or is it a read-through artefact relative to the A0A8C5FCB4 model? experts: [] suggested_experiments: - description: >- Pulldown of recombinant cod tbc1d14 with GTP- and GDP-locked cod rab11a/rab11b, and co-immunoprecipitation with trappc8, to test whether the effector and TRAPPIII-scaffold interactions are conserved in teleosts. hypothesis: Cod tbc1d14 binds active Rab11 and TRAPPIII as the mammalian ortholog does. - description: >- RT-PCR or long-read sequencing across the 3' end of ENSGMOG00000018292 to determine which C-terminal exon (conserved ...QKDQERSSPVLRR versus the A0A8C5FPT8 tail) is used in vivo. hypothesis: The conserved C-terminus of the A0A8C5FCB4 model is the predominant product.