TBC1D14 is a Rab-GAP TBC domain-containing protein that functions primarily as a RAB11-binding scaffolding protein rather than as a canonical GTPase-activating protein. Despite possessing the conserved TBC (Tre2-Bub2-Cdc16) domain, studies of mammalian orthologs demonstrate that TBC1D14 does not exhibit GAP activity toward RAB11 but instead acts as a RAB11 effector. The protein recruits the TRAPPIII tethering complex via a TRAPP-binding region, facilitating RAB1 activation and coordinating membrane exchange between RAB11-positive recycling endosomes and the early Golgi/ERGIC compartment. Through this scaffolding function, TBC1D14 regulates ATG9 trafficking and negatively regulates macroautophagy by controlling the delivery of recycling endosome-derived membranes to autophagosome formation sites. The protein localizes to recycling endosomes, the Golgi complex, and tubulo-vesicular transport intermediates. The Atlantic cod protein contains the conserved Rab-GAP TBC domain (aa 388-596) and a coiled-coil region, and is predicted to share these functions based on high sequence conservation across vertebrates.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
|
GO:0005096
GTPase activator activity
|
IEA
GO_REF:0000118 |
UNDECIDED |
Summary: This annotation assigns GTPase activator (GAP) activity based on the presence of the TBC domain (TreeGrafter inference). While the TBC domain is indeed a hallmark of Rab-GAP proteins, detailed studies of mammalian TBC1D14 orthologs (Lamb et al. 2016, EMBO J) show that TBC1D14 does NOT exhibit GAP activity toward its binding partner RAB11 and instead functions as a RAB11 effector/scaffold. The TBC domain may retain GAP activity toward an unidentified Rab substrate, or may have evolved a purely structural role. The IEA annotation based on domain presence alone is therefore potentially misleading, though not definitively wrong since GAP activity toward other Rab GTPases cannot be excluded.
Reason: The deep research clearly establishes that mammalian TBC1D14 does not function as a GAP for RAB11, its primary binding partner. However, GAP activity toward other Rab substrates has not been tested and cannot be excluded. The TreeGrafter inference from the TBC domain is a reasonable default but may be misleading. Without experimental data for the cod protein, the correct disposition is uncertain.
|
|
GO:0005773
vacuole
|
IEA
GO_REF:0000117 |
MARK AS OVER ANNOTATED |
Summary: This ARBA annotation places TBC1D14 in the vacuole. In mammalian cells, TBC1D14 localizes to recycling endosomes and the Golgi complex; vacuolar localization has not been reported for TBC1D14 orthologs. The vacuole term (GO:0005773) in animal cells typically refers to lysosome-related compartments. Since fish cells are more similar to mammalian cells than to yeast in this regard, and there is no evidence placing TBC1D14 at the vacuole/lysosome, this appears to be an over-annotation likely arising from broad ARBA rule matching rather than specific functional evidence.
Reason: No evidence from mammalian ortholog studies supports vacuolar localization for TBC1D14. The protein localizes to recycling endosomes and Golgi, not to vacuoles/lysosomes. This ARBA IEA annotation appears to be an over-generalization.
|
|
GO:0016192
vesicle-mediated transport
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: This ARBA annotation assigns involvement in vesicle-mediated transport. This is well supported by ortholog studies: TBC1D14 functions at the interface of recycling endosome and Golgi trafficking, coordinates TRAPPIII-mediated RAB1 activation for membrane exchange, and regulates ATG9 vesicle cycling. The term is appropriate but broad -- TBC1D14 is specifically involved in endosomal-to-Golgi membrane trafficking and ATG9 vesicle cycling rather than vesicle-mediated transport in general.
Reason: Vesicle-mediated transport is well established for TBC1D14 through its role in coordinating membrane exchange between recycling endosomes and the Golgi, and in maintaining the ATG9 vesicle cycling pool. The term is somewhat broad but accurate.
|
|
GO:0019899
enzyme binding
|
IEA
GO_REF:0000117 |
MARK AS OVER ANNOTATED |
Summary: This ARBA annotation assigns enzyme binding activity. TBC1D14 does bind enzymes -- it interacts with ULK1 (the autophagy-initiating kinase) and with small GTPases (RAB11, which has GTPase activity). However, enzyme binding (GO:0019899) is an uninformative term per GO curation guidelines, similar to protein binding. More specific terms such as small GTPase binding (GO:0031267, already annotated) better capture the actual binding interactions.
Reason: While TBC1D14 does bind enzymes (RAB11 GTPase, ULK1 kinase), this is already captured more informatively by the small GTPase binding annotation. The generic enzyme binding term adds no biological insight.
|
|
GO:0031267
small GTPase binding
|
IEA
GO_REF:0000118 |
ACCEPT |
Summary: This TreeGrafter annotation assigns small GTPase binding, which is well supported by ortholog studies. TBC1D14 binds to the active (GTP-bound) form of RAB11, a small GTPase of the Rab family, and this interaction is central to its function in recruiting TBC1D14 to recycling endosome membranes. TBC1D14 also colocalizes with RAB1B at the Golgi. Small GTPase binding is arguably the most accurate molecular function term for TBC1D14 given that it functions as a RAB11 effector rather than a GAP.
Reason: RAB11 binding is the best-characterized molecular function of TBC1D14. The protein binds GTP-RAB11 as an effector and also associates with RAB1B. Small GTPase binding accurately captures this core activity.
|
|
GO:0031410
cytoplasmic vesicle
|
IEA
GO_REF:0000117 |
ACCEPT |
Summary: This ARBA annotation places TBC1D14 at cytoplasmic vesicles. This is consistent with ortholog data showing localization to recycling endosomes (which are a subtype of cytoplasmic vesicle) and to tubulo-vesicular transport intermediates between recycling endosomes and the Golgi. The term is accurate but could be more specific -- recycling endosome (GO:0055037) would be the most informative localization term based on mammalian data.
Reason: TBC1D14 localizes to recycling endosomes, which are cytoplasmic vesicles. The annotation is correct; recycling endosome (GO:0055037) is a child of cytoplasmic vesicle (GO:0031410), so this annotation is accurate if not maximally specific.
|
Q: Does cod TBC1D14 retain any GAP activity toward Rab GTPases other than RAB11? Mammalian TBC1D14 does not act as a GAP for RAB11 but other Rab substrates have not been systematically tested.
Q: Is the TRAPPIII interaction conserved in teleost fish? The TRAPP-binding region (aa 120-223 in mammalian TBC1D14) mediates the key scaffolding function, but conservation of this interaction in cod has not been verified.
Experiment: Co-immunoprecipitation or pulldown experiments with recombinant cod TBC1D14 and cod RAB11 to confirm the Rab effector interaction is conserved in teleost fish.
Hypothesis: Cod TBC1D14 binds active RAB11 as a Rab effector, similar to the mammalian ortholog.
Experiment: In vitro GAP assay testing cod TBC1D14 TBC domain against a panel of Rab GTPases to determine if it has GAP activity toward any Rab family member.
Hypothesis: The TBC domain of cod TBC1D14 may retain GAP activity toward specific Rab substrates despite lacking activity toward RAB11.
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
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We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The Atlantic cod gene tbc1d14 (UniProt accession A0A8C5FPT8) encodes a Rab-GAP TBC domain-containing protein. While no direct experimental literature on this specific cod gene was identified in the current literature search, the protein's function can be reliably inferred from extensive studies of conserved TBC1D14 orthologs in mammalian systems, particularly human and mouse models. The Atlantic cod protein contains the characteristic Rab-GAP TBC domain (InterPro IPR000195, IPR035969, IPR050302; Pfam PF00566), establishing its membership in the TBC (Tre2-Bub2-Cdc16) family of Rab GTPase regulators (lamb2016tbc1d14regulatesautophagy pages 1-2, popovic2012rabgtpaseactivatingproteins pages 1-2).
TBC1D14 belongs to the TBC domain-containing protein family, a large family of proteins characterized by the presence of a conserved TBC domain (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 2-3). The TBC domain is approximately 200 amino acids in length and typically functions as a GTPase-activating protein (GAP) domain for Rab small GTPases (popovic2012rabgtpaseactivatingproteins pages 1-2). In general, TBC domain-containing proteins regulate Rab GTPases through a dual-finger catalytic mechanism, wherein conserved arginine (R-finger) and glutamine (Q-finger) residues within the TBC domain coordinate with the Rab-bound GTP molecule to accelerate GTP hydrolysis (chen2017crystalstructureof pages 1-2, popovic2012rabgtpaseactivatingproteins pages 1-2).
The TBC1D14 protein exhibits a modular domain architecture (lamb2016tbc1d14regulatesautophagy pages 3-5):
This modular organization allows TBC1D14 to serve as a scaffold protein that coordinates multiple protein-protein interactions involved in membrane trafficking and autophagy.
Despite containing a TBC domain typically associated with Rab-GAP activity, TBC1D14 does not function as a canonical GAP for RAB11. Instead, experimental evidence demonstrates that TBC1D14 binds to RAB11 and functions as a RAB11 effector rather than catalyzing GTP hydrolysis on RAB11 (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 14-17). This represents an important functional distinction: while TBC1D14 possesses the structural hallmarks of a Rab-GAP, it has evolved to serve primarily as a scaffolding and regulatory protein rather than an enzyme that directly inactivates Rab proteins (lamb2016tbc1d14regulatesautophagy pages 2-3).
The mechanism by which TBC1D14 interacts with RAB11 involves binding to the GTP-bound (active) form of RAB11, which recruits TBC1D14 to RAB11-positive recycling endosome membranes (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 2-3). This RAB11-TBC1D14 interaction is required for the formation of specific membrane trafficking intermediates.
A central molecular function of TBC1D14 is its ability to recruit the TRAPPIII tethering complex to specific cellular membranes (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 2-3). The interaction occurs through the N-terminal TRAPP-binding region (aa 120-223) of TBC1D14, which specifically binds to TRAPPC8, the mammalian ortholog of the yeast Trs85 subunit (lamb2016tbc1d14regulatesautophagy pages 7-10, lamb2016tbc1d14regulatesautophagy pages 12-14). TRAPPC8 is considered an autophagy-specific subunit that distinguishes the TRAPPIII complex from other TRAPP complexes (lamb2016tbc1d14regulatesautophagy pages 12-14).
Through its interaction with TRAPPC8, TBC1D14 mediates binding to the core TRAPP subunits, including TRAPPC4 and TRAPPC12, forming a functional TRAPPIII-like complex in mammalian cells (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 7-10). This represents the first clear evidence at the endogenous protein level for a mammalian TRAPPIII complex analogous to the yeast TRAPPIII involved in autophagy (lamb2016tbc1d14regulatesautophagy pages 12-14).
While TBC1D14 does not directly act as a GEF (guanine nucleotide exchange factor), it plays a critical role in facilitating RAB1 activation by positioning and recruiting the TRAPPIII complex, which serves as the GEF for RAB1 (lamb2016tbc1d14regulatesautophagy pages 10-12, lamb2016tbc1d14regulatesautophagy pages 7-10). Specifically:
This mechanism positions TBC1D14 as a spatial regulator that determines where and when RAB1 activation occurs, rather than as a direct enzymatic activator.
TBC1D14 exhibits a complex subcellular distribution, localizing to several distinct membrane compartments:
TBC1D14 localizes to RAB11-positive recycling endosomes, both in peripheral regions of the cell and in the juxtanuclear endocytic recycling compartment (ERC) (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 12-14). When overexpressed, TBC1D14 induces the formation of tubulated transferrin-positive recycling endosome structures, which can be visualized by loading cells with fluorescent transferrin (lamb2016tbc1d14regulatesautophagy pages 5-7, lamb2016tbc1d14regulatesautophagy pages 2-3). These tubulated structures are highly enriched in RAB11 and serve as a model system for studying TBC1D14 function in membrane trafficking.
Endogenous TBC1D14 also localizes to the Golgi stack, where it partially colocalizes with the cis-Golgi marker GM130, the small GTPase RAB1B, and TRAPP complex subunits such as TRAPPC4 (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 2-3). This Golgi localization positions TBC1D14 at a key intersection between the endocytic recycling pathway and the early secretory/biosynthetic pathway.
Notably, overexpression of TBC1D14 or its TRAPP-binding region causes fragmentation of the Golgi complex, disrupting the normal juxtanuclear organization of GM130-positive cisternae (lamb2016tbc1d14regulatesautophagy pages 5-7, lamb2016tbc1d14regulatesautophagy pages 7-10). This phenotype underscores the importance of TBC1D14 dosage and localization for maintaining Golgi integrity.
A particularly important finding is that TBC1D14-positive membranes can simultaneously harbor RAB11A, RAB1B, and TRAPPC4, indicating that TBC1D14 localizes to transport intermediates that bridge RAB11-positive recycling endosomes and RAB1-positive early Golgi/ERGIC (ER-Golgi intermediate compartment) membranes (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 14-17). These hybrid compartments are thought to represent sites where membrane identity transitions occur—specifically, where RAB11-positive membranes are converted to RAB1-positive membranes through a process coordinated by TBC1D14 and the TRAPPIII complex (lamb2016tbc1d14regulatesautophagy pages 14-17).
TBC1D14 functions as a negative regulator of macroautophagy (hereafter referred to as autophagy), a cellular self-degradation pathway essential for clearing damaged organelles, protein aggregates, and other cytoplasmic materials (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 2-3). The protein exerts this regulatory function through multiple mechanisms:
TBC1D14 regulates the contribution of membranes from RAB11-positive recycling endosomes to forming autophagosomes (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 2-3). Recycling endosomes have been identified as an important membrane source for autophagosome biogenesis, and TBC1D14 modulates this membrane supply. When TBC1D14 is overexpressed, it inhibits autophagy by disrupting the normal delivery of recycling endosome-derived membranes to autophagosome formation sites (lamb2016tbc1d14regulatesautophagy pages 2-3).
Overexpression of TBC1D14 or its TRAPP-binding region impairs the formation of early autophagy structures, including:
These effects demonstrate that TBC1D14 acts at an early step in the autophagy pathway, influencing the initial nucleation and expansion of the autophagosomal membrane rather than later maturation or fusion steps.
A particularly important and specific function of TBC1D14 is its role in regulating the trafficking of ATG9 (autophagy-related protein 9), the only multi-spanning transmembrane protein among the core autophagy machinery (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 12-14).
ATG9 normally cycles between the Golgi complex, recycling endosomes, and a specialized "ATG9 compartment" (lamb2016tbc1d14regulatesautophagy pages 12-14). This cycling is essential for delivering ATG9-containing vesicles to sites of autophagosome formation. TBC1D14, together with the TRAPPIII complex and RAB1, is required to maintain the proper cycling pool of ATG9 (lamb2016tbc1d14regulatesautophagy pages 14-17, lamb2016tbc1d14regulatesautophagy pages 12-14).
When TBC1D14 function is disrupted—either by overexpressing a dominant-negative TRAPP-binding region or by depleting TRAPPC8—the normal juxtanuclear accumulation of ATG9 is lost, and ATG9 becomes dispersed throughout the cell (lamb2016tbc1d14regulatesautophagy pages 12-14). This dispersion indicates that TBC1D14/TRAPPIII/RAB1 function is required for maintaining ATG9 at specific membrane compartments.
Remarkably, the effect of TBC1D14 and TRAPPIII on ATG9 trafficking is independent of ULK1, the primary autophagy-initiating kinase (lamb2016tbc1d14regulatesautophagy pages 12-14). While ULK1 is required for starvation-induced redistribution of ATG9 to peripheral compartments, the constitutive maintenance of ATG9 at the Golgi in fed cells depends on TBC1D14, TRAPPIII, and RAB1 (lamb2016tbc1d14regulatesautophagy pages 12-14). This indicates that TBC1D14 regulates a constitutive trafficking step that operates even in the absence of autophagy induction, maintaining a ready pool of ATG9 that can be rapidly mobilized when autophagy is activated.
Immunoisolation experiments have shown that TRAPPC8 and TRAPPC4 co-isolate with ATG9-positive membranes, both under fed and starved conditions (lamb2016tbc1d14regulatesautophagy pages 12-14). This physical association supports the model that TBC1D14 and the TRAPPIII complex directly regulate ATG9-containing vesicles, likely by promoting their trafficking between different membrane compartments.
Beyond its role in autophagy, TBC1D14 also participates in regulating the secretory pathway and maintaining Golgi integrity (lamb2016tbc1d14regulatesautophagy pages 5-7, lamb2016tbc1d14regulatesautophagy pages 7-10):
These findings indicate that TBC1D14 has pleiotropic effects on multiple membrane trafficking pathways, consistent with its localization to both endocytic recycling and early secretory compartments.
Integrating these findings, a comprehensive model emerges (lamb2016tbc1d14regulatesautophagy pages 14-17):
This model positions TBC1D14 as a molecular coordinator that links endocytic recycling, early secretory trafficking, and autophagy-related membrane dynamics.
Although TBC1D14 itself lacks demonstrated GAP activity toward RAB11, understanding the general mechanism of TBC domain-mediated Rab inactivation provides important context (chen2017crystalstructureof pages 1-2, popovic2012rabgtpaseactivatingproteins pages 1-2):
The fact that TBC1D14 does not exhibit GAP activity toward RAB11 despite containing a TBC domain suggests that either (1) the catalytic residues in TBC1D14's TBC domain are not optimally positioned or configured for RAB11, or (2) TBC1D14 may act as a GAP for a different, as-yet-unidentified Rab substrate. Alternatively, the TBC domain of TBC1D14 may have evolved to serve primarily a structural role in protein scaffolding rather than an enzymatic role.
The interaction between TBC1D14 and the TRAPPIII complex involves multiple subunits (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 7-10):
This architecture allows TBC1D14 to serve as a spatial regulator that recruits TRAPPIII GEF activity to specific membrane compartments defined by RAB11.
No experimental studies specifically examining the Atlantic cod tbc1d14 gene or protein were identified in the current literature search. This absence of species-specific data is a critical limitation that must be acknowledged. All functional assignments for the Atlantic cod protein are therefore inferred from conserved features and homology to well-studied mammalian orthologs.
The UniProt annotation for Atlantic cod TBC1D14 (A0A8C5FPT8) identifies the presence of a Rab-GAP TBC domain (IPR000195, IPR035969, IPR050302; Pfam PF00566). This domain annotation is based on sequence homology and is highly reliable for establishing membership in the TBC protein family. However, the specific substrate specificity, binding partners, and cellular functions in cod cells remain experimentally unvalidated.
Given the high evolutionary conservation of membrane trafficking machinery across vertebrates, it is reasonable to infer that Atlantic cod TBC1D14 likely participates in:
However, cod-specific functional nuances—such as potential roles in fish-specific physiological processes (e.g., adaptation to aquatic environments, temperature-dependent metabolism)—cannot be predicted from mammalian data alone.
To provide additional functional context, it is useful to briefly compare TBC1D14 with closely related TBC family members:
TBC1D12 is another RAB11-binding TBC protein identified in a systematic screen for recycling endosome-localized TBC proteins (oguchi2017tbc1d12isa pages 1-2). Like TBC1D14, TBC1D12:
- Colocalizes with transferrin receptor on recycling endosomes
- Interacts with active RAB11 through a middle region of the protein (not the TBC domain)
- Does not display RAB11-GAP activity in vitro
- Modulates neurite outgrowth in PC12 cells, a specialized RAB11-dependent cellular process
This parallel reinforces the concept that not all TBC domain-containing proteins function as canonical Rab-GAPs; some, including TBC1D14 and TBC1D12, have evolved to serve as RAB11 effectors with scaffolding and regulatory functions (oguchi2017tbc1d12isa pages 1-2).
TBC1D9B is a bona fide RAB11-GAP that, unlike TBC1D14, does exhibit GAP activity toward RAB11A (gallo2014tbc1d9bfunctionsas pages 1-2). TBC1D9B:
- Binds RAB11A, RAB11B, and RAB4A via its TBC domain in a nucleotide-dependent manner
- Accelerates GTP hydrolysis specifically on RAB11A (and RAB8A under limiting Mg²⁺ conditions)
- Regulates basolateral-to-apical transcytosis in polarized epithelial cells
The contrast between TBC1D9B (a true RAB11-GAP) and TBC1D14 (a RAB11 effector) highlights the functional diversity within the TBC protein family.
| Category | TBC1D14 feature | Specific details | Functional implication | Key evidence/citations |
|---|---|---|---|---|
| Gene/protein identity | Atlantic cod target from UniProt | UniProt A0A8C5FPT8 is annotated as Rab-GAP TBC domain-containing protein, gene tbc1d14, from Gadus morhua; direct species-specific literature was not found in the retrieved corpus, so functional interpretation relies on conserved TBC1D14 studies from other vertebrates plus the conserved Rab-GAP TBC domain annotation | Supports cautious homology-based functional inference rather than direct cod-specific experimental assignment | (lamb2016tbc1d14regulatesautophagy pages 1-2, popovic2012rabgtpaseactivatingproteins pages 1-2) |
| Domain organization | C-terminal TBC domain | TBC1D14 has a typical TBC-domain protein architecture with the TBC domain at the C-terminus; one construct spanning aa 224–669 includes the C-terminal region and the putative TBC domain from aa 411–611 | Establishes membership in the TBC Rab-regulator family and suggests potential Rab-related regulatory capacity | (lamb2016tbc1d14regulatesautophagy pages 3-5) |
| Domain organization | TRAPP-binding region (TBR) | A 103 aa N-terminal region, aa 120–223, is sufficient for TRAPP interaction and is termed the TRAPP-binding region (TBR) | Provides the physical basis for recruitment of TRAPP/TRAPPIII machinery by TBC1D14 | (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 7-10) |
| Domain organization | ULK1-binding region | The ULK1-interacting region is distinct from the TBR and lies within aa 224–330 | Indicates modular organization: separate surfaces for autophagy kinase interaction and TRAPP binding | (lamb2016tbc1d14regulatesautophagy pages 3-5) |
| Catalytic/mechanistic context | TBC family catalytic mechanism | TBC Rab-GAP proteins generally regulate Rab GTPases via a dual-finger mechanism using conserved catalytic residues in the TBC domain; structurally related TBC proteins require catalytic arginine/Q-finger glutamine residues for GAP activity | Provides the mechanistic baseline for interpreting the conserved cod TBC domain, while not proving TBC1D14 itself is an active Rab GAP toward Rab11 | (chen2017crystalstructureof pages 1-2, popovic2012rabgtpaseactivatingproteins pages 1-2) |
| Primary molecular function | RAB11 binding rather than Rab11 GAP activity | TBC1D14 binds RAB11 and behaves as a RAB11 effector; the literature summarized in the retrieved texts states that TBC1D14 does not appear to act as a GAP for RAB11 | Suggests its primary role is scaffolding/coordination of membrane traffic rather than direct inactivation of Rab11 | (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 14-17) |
| Protein interactors | TRAPP core and associated subunits | TBC1D14 co-immunoprecipitates with TRAPPC4, TRAPPC12, and via TRAPPC3 pulldown is associated with endogenous TBC1D14; BioID and knockdown data indicate TRAPPC8 is the most proximal subunit mediating the interaction | Defines TBC1D14 as a recruiter/partner of a mammalian TRAPPIII-like complex | (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 7-10) |
| Protein interactors | TRAPPC8 | TRAPPC8 is required for TBC1D14/TBR to bind the core TRAPP complex and is identified as the likely mammalian ortholog of yeast Trs85, the autophagy-specific TRAPPIII subunit | Places TBC1D14 in a Rab1-regulatory, autophagy-relevant tethering pathway | (lamb2016tbc1d14regulatesautophagy pages 7-10, lamb2016tbc1d14regulatesautophagy pages 12-14) |
| Protein interactors | RAB11A/B | TBC1D14-induced tubules are RAB11-positive; prior work cited in the paper established that endogenous RAB11 is required for tubule formation, and RAB11 recruits TBC1D14 to recycling endosome membranes | Supports a model in which TBC1D14 is a RAB11-dependent membrane trafficking factor at recycling endosomes | (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 2-3) |
| Protein interactors | RAB1B | Endogenous RAB1B partially colocalizes with TBC1D14 at the Golgi; a subset of TBC1D14-induced tubules simultaneously harbors RAB11A and RAB1B | Supports a Rab conversion/hand-off model linking RAB11-positive recycling endosomes to RAB1-positive early Golgi/ERGIC traffic | (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 14-17) |
| Protein interactors | ULK1 | TBC1D14 overexpression was previously linked to a RAB11- and ULK1-positive recycling endosome compartment; ULK1-binding region is distinct from the TRAPP-binding region | Connects TBC1D14 to early autophagy signaling and membrane supply pathways | (lamb2016tbc1d14regulatesautophagy pages 5-7, lamb2016tbc1d14regulatesautophagy pages 2-3) |
| Protein interactors | ATG9 / ATG9-positive membranes | ATG9-positive membranes co-isolate with TRAPPC8 and TRAPPC4; TBC1D14/TRAPP activity is required for proper ATG9 localization and cycling | Links TBC1D14 indirectly and functionally to the ATG9 membrane cycle essential for autophagosome biogenesis | (lamb2016tbc1d14regulatesautophagy pages 12-14, lamb2016tbc1d14regulatesautophagy pages 14-17) |
| Subcellular localization | Recycling endosomes | TBC1D14 overexpression generates a tubulated transferrin-positive recycling endosome compartment; endogenous TBC1D14 also localizes to peripheral recycling endosome structures | Indicates action on endocytic recycling membranes, particularly RAB11-positive compartments | (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 12-14) |
| Subcellular localization | Golgi / early Golgi | Endogenous TBC1D14 localizes to the Golgi stack and partially colocalizes with TRAPPC4 and RAB1B; overexpression fragments the GM130-positive cis-Golgi | Positions TBC1D14 at the interface of autophagy-related trafficking and Golgi organization/secretory traffic | (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 5-7, lamb2016tbc1d14regulatesautophagy pages 12-14) |
| Subcellular localization | Transport intermediate between RE and RAB1 compartments | TBC1D14-positive tubules can harbor RAB11A, RAB1B, and TRAPPC4 simultaneously, consistent with a tubulo-vesicular intermediate between recycling endosomes and early Golgi/ERGIC membranes | Suggests TBC1D14 coordinates membrane exchange between endocytic recycling and early secretory systems | (lamb2016tbc1d14regulatesautophagy pages 2-3, lamb2016tbc1d14regulatesautophagy pages 14-17) |
| Primary molecular function | Recruitment of TRAPP/TRAPPIII | TBC1D14 binds TRAPP via its aa 120–223 TBR, and TRAPPC8 mediates this interaction; TBC1D14 overexpression mislocalizes TRAPP to tubulated recycling endosomes | Core scaffolding/adaptor role: recruits tethering/GEF machinery to specific membranes | (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 7-10) |
| Primary molecular function | Promotion of RAB1 activation indirectly through TRAPP | TRAPP is the GEF for RAB1, and TBC1D14 is required but not sufficient for normal RAB1 activation; depletion of TBC1D14 reduces RAB1B binding to the effector golgin-84 | TBC1D14 helps position/enable TRAPPIII-mediated RAB1 activation rather than directly catalyzing RAB1 nucleotide exchange itself | (lamb2016tbc1d14regulatesautophagy pages 10-12, lamb2016tbc1d14regulatesautophagy pages 7-10) |
| Primary molecular function | Coordination of membrane traffic for autophagosome formation | Overexpression of TBC1D14 or its TBR inhibits LC3 lipidation, reduces LC3 puncta, and also reduces early autophagy markers WIPI2 and DFCP1 | Establishes TBC1D14 as a regulator of an early step in autophagosome biogenesis | (lamb2016tbc1d14regulatesautophagy pages 5-7, lamb2016tbc1d14regulatesautophagy pages 7-10) |
| Biological process | Autophagy regulation | TBC1D14 is described as a negative regulator of autophagy that controls membrane delivery from RAB11-positive recycling endosomes to forming autophagosomes | Principal characterized biological role in the literature | (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 2-3) |
| Biological process | ATG9 trafficking | TBC1D14 and TRAPPIII regulate ATG9 trafficking independently of ULK1; disruption of TBC1D14/TRAPP/RAB1 function disperses juxtanuclear ATG9 and alters the cycling ATG9 pool | Explains how TBC1D14 influences autophagy mechanistically: by maintaining the membrane itinerary of the only transmembrane core ATG protein | (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 12-14) |
| Biological process | Secretory pathway and Golgi integrity | TBR overexpression impairs constitutive secretion and fragments the Golgi; TRAPPC8 depletion phenocopies Golgi and secretory defects | Indicates TBC1D14 also regulates ER-Golgi/early secretory traffic beyond autophagy | (lamb2016tbc1d14regulatesautophagy pages 5-7, lamb2016tbc1d14regulatesautophagy pages 7-10) |
| Biological process | RE-to-Golgi membrane exchange | The authors propose a constitutive trafficking step from peripheral recycling endosomes to the early Golgi that maintains an ATG9 cycling pool needed for autophagy initiation | Integrates endocytic recycling and early secretory trafficking into a unified TBC1D14 function | (lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 14-17) |
| Cod-specific inference | Most likely conserved functional interpretation for Gadus morhua tbc1d14 | Because cod-specific experiments were not retrieved, the safest annotation is that Atlantic cod Tbc1d14 is likely an intracellular membrane-trafficking regulator associated with the Rab-GAP TBC domain family, probably functioning at recycling endosome/Golgi interfaces and in autophagy-related ATG9 trafficking, but direct substrate specificity and cod-specific localization remain unvalidated | Provides a bounded, evidence-based annotation for A0A8C5FPT8 without overclaiming species-specific function | (lamb2016tbc1d14regulatesautophagy pages 3-5, lamb2016tbc1d14regulatesautophagy pages 1-2, lamb2016tbc1d14regulatesautophagy pages 14-17) |
Table: This table summarizes the best-supported characteristics of TBC1D14 relevant to annotating Atlantic cod tbc1d14, including domains, interactors, localization, functions, and pathways. It is especially useful because direct Gadus morhua literature was not retrieved, so annotation depends on careful transfer from conserved vertebrate evidence.
Based on the comprehensive analysis of conserved TBC1D14 function in mammalian systems and the presence of a conserved Rab-GAP TBC domain in the Atlantic cod protein, the following functional annotation is proposed:
Atlantic cod TBC1D14 (UniProt A0A8C5FPT8) is a membrane trafficking regulator belonging to the TBC domain-containing protein family. The protein likely functions as a RAB11-binding scaffolding protein that coordinates membrane exchange between recycling endosomes and early Golgi/ERGIC compartments. Key predicted functions include:
The protein is predicted to localize to recycling endosomes, Golgi complex, and tubulo-vesicular transport intermediates where it acts as a molecular bridge linking RAB11-positive and RAB1-positive membrane compartments.
Important caveats: (1) No species-specific experimental data for Atlantic cod were identified; (2) specific substrate specificity of the TBC domain in cod is unknown; (3) potential fish-specific functions cannot be predicted from mammalian data; (4) direct GAP activity toward any Rab GTPase has not been demonstrated for TBC1D14 in any species studied to date.
This annotation should be considered a high-confidence inference based on domain conservation and extensive mammalian functional data, but experimental validation in Atlantic cod cells or tissues would be required to confirm these predicted functions.
References
(lamb2016tbc1d14regulatesautophagy pages 1-2): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(popovic2012rabgtpaseactivatingproteins pages 1-2): Doris Popovic, Masato Akutsu, Ivana Novak, J. Wade Harper, Christian Behrends, and Ivan Dikic. Rab gtpase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human atg8 modifiers. Molecular and Cellular Biology, 32:1733-1744, May 2012. URL: https://doi.org/10.1128/mcb.06717-11, doi:10.1128/mcb.06717-11. This article has 219 citations and is from a domain leading peer-reviewed journal.
(lamb2016tbc1d14regulatesautophagy pages 2-3): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(chen2017crystalstructureof pages 1-2): Yan‐Na Chen, Xin Gu, X. Edward Zhou, Weidong Wang, Dandan Cheng, Yinghua Ge, Fei Ye, H. Eric Xu, and Zhengbing Lv. Crystal structure of tbc1d15 gtpase‐activating protein (gap) domain and its activity on rab gtpases. Protein Science, 26:834-846, Apr 2017. URL: https://doi.org/10.1002/pro.3132, doi:10.1002/pro.3132. This article has 17 citations and is from a peer-reviewed journal.
(lamb2016tbc1d14regulatesautophagy pages 3-5): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(lamb2016tbc1d14regulatesautophagy pages 14-17): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(lamb2016tbc1d14regulatesautophagy pages 7-10): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(lamb2016tbc1d14regulatesautophagy pages 12-14): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(lamb2016tbc1d14regulatesautophagy pages 10-12): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(lamb2016tbc1d14regulatesautophagy pages 5-7): Christopher A Lamb, Stefanie Nühlen, Delphine Judith, David Frith, Ambrosius P Snijders, Christian Behrends, and Sharon A Tooze. Tbc1d14 regulates autophagy via the trapp complex and atg9 traffic. The EMBO Journal, 35:281-301, Dec 2016. URL: https://doi.org/10.15252/embj.201592695, doi:10.15252/embj.201592695. This article has 213 citations.
(oguchi2017tbc1d12isa pages 1-2): Mai E. Oguchi, Kenta Noguchi, and Mitsunori Fukuda. Tbc1d12 is a novel rab11-binding protein that modulates neurite outgrowth of pc12 cells. PLoS ONE, 12:e0174883, Apr 2017. URL: https://doi.org/10.1371/journal.pone.0174883, doi:10.1371/journal.pone.0174883. This article has 29 citations and is from a peer-reviewed journal.
(gallo2014tbc1d9bfunctionsas pages 1-2): Luciana I. Gallo, Yong Liao, Wily G. Ruiz, Dennis R. Clayton, Min Li, Yong-Jian Liu, Yu Jiang, Mitsunori Fukuda, Gerard Apodaca, and Xiao-Ming Yin. Tbc1d9b functions as a gtpase-activating protein for rab11a in polarized mdck cells. Molecular Biology of the Cell, 25:3779-3797, Nov 2014. URL: https://doi.org/10.1091/mbc.e13-10-0604, doi:10.1091/mbc.e13-10-0604. This article has 53 citations and is from a domain leading peer-reviewed journal.
prediction-autophagosomeThe seed hypothesis proposed that ProtNLM2's prediction of autophagosome localization (GO:0005776) for the Gadus morhua protein tbc1d14 is likely a misassignment — the reasoning being that TBC1D14 is a TBC-domain Rab GTPase-activating protein (RabGAP) characterized as a recycling-endosome/ULK1-complex regulator of autophagy initiation, not a structural, autophagosome-resident protein. On that logic, placing the protein "inside" the autophagosome would be an over-annotation.
This investigation confirms the biological substance of that concern but overturns its conclusion that the prediction is a hallucination or clear misassignment. The decisive finding, obtained by directly interrogating curated GO annotations for the human ortholog TBC1D14 (Q9P2M4), is that autophagosome (GO:0005776) is an existing, manually curated annotation supported by two independent evidence lines: an IDA (Inferred from Direct Assay) annotation from PMID: 22613832 assigned by expert BHF-UCL curators, and an independent IBA (phylogenetic) annotation from GO_Central (PANTHER node PTN000538677). Because the Gadus morhua protein is a bona fide 1:1 ortholog (62.1% identity, identical TBC domain architecture with intact catalytic fingers, same PANTHER family PTHR47219), it is legitimately eligible for the same orthology-based inference. The ProtNLM2 prediction therefore coincides with existing curated knowledge rather than contradicting it.
The essential caveat is one of precision, not correctness. Autophagosome is a secondary, condition-dependent localization. TBC1D14's primary and best-characterized compartment is the Rab11/transferrin-receptor–positive recycling endosome (relocalizing to the Golgi upon starvation), and its role in autophagy is regulatory — it is a negative regulator of autophagy initiation acting via ULK1 and the TRAPP–ATG9 membrane-delivery axis, not an autophagosome structural protein. The verdict is therefore PARTIALLY SUPPORTED: GO:0005776 is defensible for the fish protein by orthology and should be retained, but only alongside recycling endosome (GO:0055037) and the regulation-of-autophagy BP terms — never as the sole or primary cellular-component annotation.
A global Needleman–Wunsch alignment of A0A8C5FPT8 against human TBC1D14 (Q9P2M4) yielded 414 identical aligned columns out of 667 (62.1% identity), comfortably within the range expected for a true 1:1 vertebrate ortholog rather than a distant paralog. Both proteins carry a single Rab-GAP TBC domain (UniProt domain 388–596; Pfam PF00566 RabGAP-TBC; InterPro IPR000195), and both are assigned to PANTHER family PTHR47219.
Critically, the dual-finger catalytic residues that define a functional RabGAP are conserved and positionally aligned between fish and human:
| Catalytic element | Motif | Gadus position | Human position |
|---|---|---|---|
| Arg-finger | IKLDISR | ~451 | ~466 |
| Gln-finger | YVQ | ~491 | ~506 |
The N-terminal architecture is likewise conserved (disordered regions plus a coiled-coil at ~315–357). There is no signal peptide and no annotated transmembrane segment; the maximum Kyte–Doolittle hydropathy across the whole sequence is only 1.86, below the threshold that would indicate a sustained membrane-spanning helix. The protein is therefore a peripheral/cytosolic protein that associates with membranes through protein–protein and Rab interactions, not an integral membrane protein — exactly what is expected of a RabGAP regulator rather than a resident structural component of an organelle membrane.
The curation consequence is important: the orthology is strong enough that experimental and phylogenetic annotations on human TBC1D14 are propagable to the fish protein by ISO/IBA. This is precisely what converts the autophagosome prediction from "fabricated" to "defensible inference."
The primary mammalian literature paints a consistent, mechanistically detailed picture. In the founding study (PMID: 22613832), TBC1D14 was identified as a putative RabGAP that "colocalizes and interacts with the autophagy kinase ULK1" and, when overexpressed, "tubulates ULK1-positive recycling endosomes (REs), impairing their function and inhibiting autophagosome formation." The same study reported that "amino acid starvation causes TBC1D14 to relocalize from REs to the Golgi complex, whereas TfnR and Tfn localize to forming autophagosomes" — meaning that upon autophagy induction the protein itself moves to the Golgi, while transferrin-receptor membrane is delivered onward. This is direct evidence against stable autophagosome residence: the protein's steady-state compartment is the recycling endosome and its starvation-response compartment is the Golgi.
The follow-up mechanistic study (PMID: 26711178) described "TBC1D14, as a negative regulator of autophagy that controls delivery of membranes from RAB11-positive recycling endosomes to forming autophagosomes," acting via the TRAPP complex and ATG9 traffic. A systematic overexpression screen (PMID: 22874560) placed TBC1D14 among TBC-domain proteins that inhibit autophagy when overexpressed, acting "at an early stage during autophagosome formation" by regulating recycling-endosomal traffic — with ATG9 and ULK1 localizing to transferrin-receptor-positive recycling endosomes that are tubulated by excess TBC1D14, and RE membrane subsequently incorporated into newly forming autophagosomes.
Together, these establish TBC1D14 as a traffic regulator operating upstream of and around the forming autophagosome, not a component embedded in the mature organelle. This validates the biological core of the seed hypothesis: the protein is a regulator, and any autophagosome association is transient and delivery-related.
The pivotal correction to an initial "refuted" reading came from directly querying curated GO annotations (QuickGO) for human TBC1D14 (Q9P2M4). GO:0005776 (autophagosome) is present with two independent evidence lines:
The same protein is curated to a broader localization set that puts autophagosome in its proper context:
| GO term | Label | Aspect | Evidence | Source |
|---|---|---|---|---|
| GO:0055037 | recycling endosome | CC | IDA (PMID: 17562788), IBA, Reactome | primary/PANTHER |
| GO:0005794 | Golgi apparatus | CC | IDA (HPA) + UniProt-SubCell | Human Protein Atlas |
| GO:0005776 | autophagosome | CC | IDA (PMID: 22613832), IBA | BHF-UCL / GO_Central |
| GO:0005773 | vacuole | CC | electronic | ARBA |
| GO:0031410 | cytoplasmic vesicle | CC | electronic | ARBA |
| GO:0010507 | negative regulation of autophagy | BP | IMP | primary |
| GO:2000785 | regulation of autophagosome assembly | BP | IMP + IBA | primary/PANTHER |
The Gadus morhua ortholog A0A8C5FPT8 currently carries only broad electronic CC terms (vacuole GO:0005773, cytoplasmic vesicle GO:0031410; ARBA) and belongs to PANTHER PTHR47219, making it eligible for the same IBA propagation that gave human TBC1D14 its autophagosome annotation. From a curation-provenance standpoint, GO:0005776 for the fish protein is therefore a legitimate orthology-based inference, not a hallucinated label — even though it represents a secondary and condition-dependent localization.
A supplementary sequence check strengthens the "regulator, not autophagosome-membrane component" reading: a LIR/AIM motif scan ([WFY]xx[LIV]) returned 13 core matches in the fish sequence and 12 in the human sequence — at chance level (~16 expected across ~700 aa) — and no functional LIR is reported for TBC1D14. This is consistent with a peripheral regulator that is not stably anchored to autophagosomal membranes via an ATG8-binding motif (weak evidence, offered only as a supporting caveat).
The synthesis reconciles two facts that at first appear contradictory: (a) TBC1D14 is a regulator, not a structural autophagosome protein, yet (b) autophagosome (GO:0005776) is a genuinely curated CC annotation.
NUTRIENT-RICH (steady state) STARVATION (autophagy induction)
--------------------------- --------------------------------
Rab11(+) RECYCLING ENDOSOME GOLGI COMPLEX
[PRIMARY localization] [TBC1D14 relocalizes here]
| |
TBC1D14 --- ULK1 (interaction) TBC1D14 leaves REs
RabGAP activity; tubulates REs |
when overexpressed TfnR / Tfn membrane -----> FORMING
| (delivered onward) AUTOPHAGOSOME
NEGATIVELY REGULATES (GO:0005776)
autophagosome formation TBC1D14 transiently/peripherally
(GO:0010507, GO:2000785) associated during membrane delivery
-> basis of the IDA CC annotation
The model runs as follows. In resting (nutrient-rich) cells, TBC1D14 resides at the recycling endosome, holding ULK1-positive REs in check and thereby restraining autophagy initiation — its negative-regulator BP role. Its GAP domain, with intact Arg- and Gln-fingers (F001), targets Rab GTPases governing this recycling traffic. Upon amino-acid starvation, TBC1D14 relocalizes to the Golgi, releasing recycling-endosomal (transferrin-receptor-positive) membrane that is routed via the TRAPP complex and ATG9 machinery toward the forming autophagosome. The autophagosome CC annotation captures a transient, membrane-delivery-associated presence at/near the forming autophagosome observed experimentally, rather than stable structural residence.
For curation, the correct representation is a compound CC picture led by recycling endosome, with autophagosome as a secondary, mechanistically justified term, tied together by BP terms that describe what the protein actually does (negative regulation of autophagy; regulation of autophagosome assembly) and by an MF term for its RabGAP activity. Annotating autophagosome alone would be a category error; omitting it entirely would discard a curated experimental observation.
| Citation | Evidence type | Supports / refutes / qualifies | Claim tested | Key finding | Context | Confidence & limitations |
|---|---|---|---|---|---|---|
| PMID: 22613832 (Longatti et al. 2012, JCB) — GO IDA source | Direct assay + localization + interaction | Qualifies (supports secondary autophagosome; refutes "primary/structural") | Is TBC1D14 an autophagosome-resident protein? | Colocalizes/interacts with ULK1 on Rab11⁺ recycling endosomes; overexpression tubulates REs and inhibits autophagosome formation; relocalizes to Golgi on starvation. Source of the IDA GO:0005776 annotation. | Human cultured cells | High confidence; overexpression may exaggerate RE tubulation; autophagosome call rests on full-text figures |
| PMID: 26711178 (Lamb et al. 2016, EMBO J) | Mechanism / interaction | Refutes structural role; supports regulator role | Is TBC1D14 a regulator vs. resident protein? | Negative regulator of autophagy controlling membrane delivery from RAB11⁺ REs to forming autophagosomes via TRAPP/ATG9. | Mammalian cells | High confidence for regulatory mechanism |
| PMID: 22874560 (Longatti & Tooze 2012) | Systematic overexpression screen / review | Qualifies | Does TBC1D14 act at autophagosome formation? | Among TBC proteins inhibiting autophagy when overexpressed; acts early via recycling-endosomal traffic; RE membrane incorporated into new autophagosomes. | Human cells | Moderate–high; overexpression screen, indirect for endogenous localization |
| PMID: 17562788 (via QuickGO) | Localization (IDA) | Supports primary localization | Where is TBC1D14 at steady state? | Basis for recycling endosome (GO:0055037) IDA annotation. | Human | Database-level orientation; primary paper not re-read here |
| QuickGO curated annotations (Q9P2M4) | Review/database | Supports provenance of GO:0005776 | Is autophagosome a real curated CC? | GO:0005776 present with IDA (BHF-UCL) + IBA (GO_Central, PTN000538677). | Human ortholog | High confidence in annotation existence; it is one of several curated CCs |
| Sequence/structural computation (this run) | Structural/evolutionary + computational | Supports orthology; refutes membrane-integral residence | Is the fish protein a true TBC1D14 ortholog? Membrane-embedded? | 62.1% identity to human; intact TBC domain (PF00566/IPR000195); conserved Arg/Gln fingers; no signal peptide/TM; max hydropathy 1.86. | Gadus morhua vs human | High confidence; computed provenance |
How the literature bears on the verdict. The three primary/mechanistic papers (PMID: 22613832, PMID: 26711178, PMID: 22874560) unanimously frame TBC1D14 as a recycling-endosome-based regulator of autophagy. None describes it as an autophagosome structural protein. That is why the hypothesis is not fully supported. Yet the same founding paper (PMID: 22613832) is the documented source of a curated IDA autophagosome annotation, and that annotation plus its phylogenetic IBA companion are why the prediction is not refuted either.
Overall lead: treat GO:0005776 (autophagosome) as acceptable-by-orthology but non-exclusive — retain it as a secondary CC, and ensure the fish annotation set is not headed by autophagosome. The ProtNLM2 prediction is less precise than existing knowledge, not wrong.
| GO ID | Label | Aspect | Proposed action | Evidence basis |
|---|---|---|---|---|
| GO:0055037 | recycling endosome | CC | Add as primary CC (IBA/ISO) | Ortholog IDA PMID: 17562788 + IBA |
| GO:0005776 | autophagosome | CC | Retain as secondary CC (IBA) | Ortholog IDA PMID: 22613832 + IBA |
| GO:0005794 | Golgi apparatus | CC | Consider adding (IBA) | Ortholog IDA (HPA) |
| GO:0010507 | negative regulation of autophagy | BP | Add (IBA) | Ortholog IMP |
| GO:2000785 | regulation of autophagosome assembly | BP | Add (IBA) | Ortholog IMP + IBA |
| GO:0005096 / GO:0005097 | GTPase activator activity / Rab GTPase activator activity | MF | Retain / add (ISS/IBA) | Intact TBC domain, conserved dual fingers |
| GO:0031267 | small GTPase binding | MF | Retain | TBC domain |
| GO:0005773 | vacuole | CC | Consider generalizing/removing | Broad electronic (ARBA) |
| GO:0031410 | cytoplasmic vesicle | CC | Consider generalizing/removing | Broad electronic (ARBA) |
Mechanistic scope reminder for the curator. The immediate molecular activity is RabGAP/Rab-binding; the immediate cellular action is at recycling endosomes with ULK1 and the TRAPP complex; "regulation of autophagosome formation" is a downstream pathway consequence; and autophagosome localization is a secondary, transient CC. Keep these separated in the annotation set.
Candidate references with exact snippets to verify:
- PMID: 22613832: "One of these putative RabGAPs, TBC1D14, colocalizes and interacts with the autophagy kinase ULK1. Overexpressed TBC1D14 tubulates ULK1-positive recycling endosomes (REs), impairing their function and inhibiting autophagosome formation."
- PMID: 22613832: "Amino acid starvation causes TBC1D14 to relocalize from REs to the Golgi complex, whereas TfnR and Tfn localize to forming autophagosomes" — verify the full-text autophagosome-localization figure behind the IDA.
- PMID: 26711178: "TBC1D14, as a negative regulator of autophagy that controls delivery of membranes from RAB11-positive recycling endosomes to forming autophagosomes".
Suggested curator question: should the fish annotation propagate the human IBA set (autophagosome + recycling endosome + regulatory BP + RabGAP MF) rather than remain at the current broad ARBA CC terms?
The ProtNLM2 autophagosome prediction for Gadus morhua tbc1d14 is partially supported, not a hallucination: GO:0005776 is a curated experimental (IDA) plus phylogenetic (IBA) annotation on the human ortholog, and the fish protein is a strong 1:1 ortholog (62.1% identity, PTHR47219) eligible for the same inference. However, autophagosome is a secondary, condition-dependent localization. The protein's primary compartment is the Rab11⁺ recycling endosome (and Golgi upon starvation), and its primary role is as a negative regulator of autophagy acting from those compartments. GO:0005776 should be retained only alongside recycling endosome (GO:0055037) and the regulation-of-autophagy BP terms, never as the sole or primary cellular-component annotation.
id: A0A8C5FPT8
gene_symbol: tbc1d14
product_type: PROTEIN
status: COMPLETE
taxon:
id: NCBITaxon:8049
label: Gadus morhua
description: >-
TBC1D14 is a Rab-GAP TBC domain-containing protein that functions primarily as a
RAB11-binding scaffolding protein rather than as a canonical GTPase-activating protein.
Despite possessing the conserved TBC (Tre2-Bub2-Cdc16) domain, studies of mammalian
orthologs demonstrate that TBC1D14 does not exhibit GAP activity toward RAB11 but instead
acts as a RAB11 effector. The protein recruits the TRAPPIII tethering complex via a
TRAPP-binding region, facilitating RAB1 activation and coordinating membrane exchange
between RAB11-positive recycling endosomes and the early Golgi/ERGIC compartment. Through
this scaffolding function, TBC1D14 regulates ATG9 trafficking and negatively regulates
macroautophagy by controlling the delivery of recycling endosome-derived membranes to
autophagosome formation sites. The protein localizes to recycling endosomes, the Golgi
complex, and tubulo-vesicular transport intermediates. The Atlantic cod protein contains
the conserved Rab-GAP TBC domain (aa 388-596) and a coiled-coil region, and is predicted
to share these functions based on high sequence conservation across vertebrates.
existing_annotations:
# ================== GTPase activator activity ==================
- term:
id: GO:0005096
label: GTPase activator activity
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: enables
review:
summary: >-
This annotation assigns GTPase activator (GAP) activity based on the presence of the
TBC domain (TreeGrafter inference). While the TBC domain is indeed a hallmark of
Rab-GAP proteins, detailed studies of mammalian TBC1D14 orthologs (Lamb et al. 2016,
EMBO J) show that TBC1D14 does NOT exhibit GAP activity toward its binding partner
RAB11 and instead functions as a RAB11 effector/scaffold. The TBC domain may retain
GAP activity toward an unidentified Rab substrate, or may have evolved a purely
structural role. The IEA annotation based on domain presence alone is therefore
potentially misleading, though not definitively wrong since GAP activity toward other
Rab GTPases cannot be excluded.
action: UNDECIDED
reason: >-
The deep research clearly establishes that mammalian TBC1D14 does not function as a
GAP for RAB11, its primary binding partner. However, GAP activity toward other Rab
substrates has not been tested and cannot be excluded. The TreeGrafter inference from
the TBC domain is a reasonable default but may be misleading. Without experimental
data for the cod protein, the correct disposition is uncertain.
# ================== Vacuole ==================
- term:
id: GO:0005773
label: vacuole
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: located_in
review:
summary: >-
This ARBA annotation places TBC1D14 in the vacuole. In mammalian cells, TBC1D14
localizes to recycling endosomes and the Golgi complex; vacuolar localization has not
been reported for TBC1D14 orthologs. The vacuole term (GO:0005773) in animal cells
typically refers to lysosome-related compartments. Since fish cells are more similar to
mammalian cells than to yeast in this regard, and there is no evidence placing TBC1D14
at the vacuole/lysosome, this appears to be an over-annotation likely arising from
broad ARBA rule matching rather than specific functional evidence.
action: MARK_AS_OVER_ANNOTATED
reason: >-
No evidence from mammalian ortholog studies supports vacuolar localization for TBC1D14.
The protein localizes to recycling endosomes and Golgi, not to vacuoles/lysosomes.
This ARBA IEA annotation appears to be an over-generalization.
# ================== Vesicle-mediated transport ==================
- term:
id: GO:0016192
label: vesicle-mediated transport
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: involved_in
review:
summary: >-
This ARBA annotation assigns involvement in vesicle-mediated transport. This is well
supported by ortholog studies: TBC1D14 functions at the interface of recycling
endosome and Golgi trafficking, coordinates TRAPPIII-mediated RAB1 activation for
membrane exchange, and regulates ATG9 vesicle cycling. The term is appropriate but
broad -- TBC1D14 is specifically involved in endosomal-to-Golgi membrane trafficking
and ATG9 vesicle cycling rather than vesicle-mediated transport in general.
action: ACCEPT
reason: >-
Vesicle-mediated transport is well established for TBC1D14 through its role in
coordinating membrane exchange between recycling endosomes and the Golgi, and in
maintaining the ATG9 vesicle cycling pool. The term is somewhat broad but accurate.
# ================== Enzyme binding ==================
- term:
id: GO:0019899
label: enzyme binding
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: enables
review:
summary: >-
This ARBA annotation assigns enzyme binding activity. TBC1D14 does bind enzymes --
it interacts with ULK1 (the autophagy-initiating kinase) and with small GTPases
(RAB11, which has GTPase activity). However, enzyme binding (GO:0019899) is an
uninformative term per GO curation guidelines, similar to protein binding. More
specific terms such as small GTPase binding (GO:0031267, already annotated) better
capture the actual binding interactions.
action: MARK_AS_OVER_ANNOTATED
reason: >-
While TBC1D14 does bind enzymes (RAB11 GTPase, ULK1 kinase), this is already captured
more informatively by the small GTPase binding annotation. The generic enzyme binding
term adds no biological insight.
# ================== Small GTPase binding ==================
- term:
id: GO:0031267
label: small GTPase binding
evidence_type: IEA
original_reference_id: GO_REF:0000118
qualifier: enables
review:
summary: >-
This TreeGrafter annotation assigns small GTPase binding, which is well supported by
ortholog studies. TBC1D14 binds to the active (GTP-bound) form of RAB11, a small
GTPase of the Rab family, and this interaction is central to its function in
recruiting TBC1D14 to recycling endosome membranes. TBC1D14 also colocalizes with
RAB1B at the Golgi. Small GTPase binding is arguably the most accurate molecular
function term for TBC1D14 given that it functions as a RAB11 effector rather than a
GAP.
action: ACCEPT
reason: >-
RAB11 binding is the best-characterized molecular function of TBC1D14. The protein
binds GTP-RAB11 as an effector and also associates with RAB1B. Small GTPase binding
accurately captures this core activity.
# ================== Cytoplasmic vesicle ==================
- term:
id: GO:0031410
label: cytoplasmic vesicle
evidence_type: IEA
original_reference_id: GO_REF:0000117
qualifier: located_in
review:
summary: >-
This ARBA annotation places TBC1D14 at cytoplasmic vesicles. This is consistent with
ortholog data showing localization to recycling endosomes (which are a subtype of
cytoplasmic vesicle) and to tubulo-vesicular transport intermediates between recycling
endosomes and the Golgi. The term is accurate but could be more specific -- recycling
endosome (GO:0055037) would be the most informative localization term based on
mammalian data.
action: ACCEPT
reason: >-
TBC1D14 localizes to recycling endosomes, which are cytoplasmic vesicles. The
annotation is correct; recycling endosome (GO:0055037) is a child of cytoplasmic
vesicle (GO:0031410), so this annotation is accurate if not maximally specific.
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: []
core_functions:
- molecular_function:
id: GO:0031267
label: small GTPase binding
description: >-
TBC1D14 binds the GTP-bound (active) form of RAB11, functioning as a RAB11 effector
rather than a GTPase-activating protein. This interaction recruits TBC1D14 to
RAB11-positive recycling endosome membranes. Despite containing the conserved TBC
domain typically associated with Rab-GAP activity, TBC1D14 does not catalyze GTP
hydrolysis on RAB11 and instead serves as a scaffold that coordinates membrane
trafficking events at the recycling endosome-Golgi interface.
directly_involved_in:
- id: GO:0016192
label: vesicle-mediated transport
locations:
- id: GO:0031410
label: cytoplasmic vesicle
suggested_questions:
- question: >-
Does cod TBC1D14 retain any GAP activity toward Rab GTPases other than RAB11?
Mammalian TBC1D14 does not act as a GAP for RAB11 but other Rab substrates have
not been systematically tested.
experts: []
- question: >-
Is the TRAPPIII interaction conserved in teleost fish? The TRAPP-binding region
(aa 120-223 in mammalian TBC1D14) mediates the key scaffolding function, but
conservation of this interaction in cod has not been verified.
experts: []
suggested_experiments:
- description: >-
Co-immunoprecipitation or pulldown experiments with recombinant cod TBC1D14 and
cod RAB11 to confirm the Rab effector interaction is conserved in teleost fish.
hypothesis: Cod TBC1D14 binds active RAB11 as a Rab effector, similar to the mammalian ortholog.
- description: >-
In vitro GAP assay testing cod TBC1D14 TBC domain against a panel of Rab GTPases
to determine if it has GAP activity toward any Rab family member.
hypothesis: >-
The TBC domain of cod TBC1D14 may retain GAP activity toward specific Rab
substrates despite lacking activity toward RAB11.