dyf-13 encodes the C. elegans ortholog of tetratricopeptide-repeat protein 26 (TTC26/IFT56/IFT-B protein 56), a tetratricopeptide-repeat (TPR) scaffold subunit of the intraflagellar transport complex B (IFT-B). IFT-B, together with IFT-A and kinesin-2/dynein-2 motors, drives the bidirectional transport of ciliary cargo along the axoneme that builds and maintains cilia. DYF-13 is expressed in ciliated sensory neurons, localizes to the cilium, and itself undergoes intraflagellar transport; its ciliary localization depends on other IFT and BBS proteins. Loss of dyf-13 produces short sensory cilia that lack their distal segments and a dye-filling-defective (Dyf) phenotype, and DYF-13 is a component of the IFT-B complex required for anterograde cargo transport and for ciliary entry of the retrograde dynein-2 motor. The gene is one of the founding dye-filling-defective (dyf-1 to dyf-13) loci and is a target of the RFX transcription factor DAF-19 via an X-box promoter motif.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0036064 ciliary basal body | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IFT proteins, including IFT-B/TTC26 orthologs, accumulate at and turn around at the ciliary base/basal body region. This IBA localization is consistent with DYF-13 being a core IFT component whose transport begins at the ciliary base. Reason: Consistent with the established role of DYF-13 as a core IFT component that accumulates at the ciliary base; a supporting (non-core) location rather than the primary functional assignment. Supporting Evidence: PMID:15916950 encodes a ciliary protein that undergoes IFT |
| GO:0030992 intraciliary transport particle B | IBA GO_REF:0000033 | ACCEPT | Summary: DYF-13/TTC26 is an integral subunit of the IFT-B complex. This is directly supported in C. elegans by affinity-purification/mass-spectrometry identification of dyf-13 within IFT complex B, and in mammals TTC26/IFT56 is assigned to the IFT-B complex. Reason: Core structural assignment; DYF-13 is a bona fide IFT-B subunit (ComplexPortal CPX-1290), confirmed biochemically in worm and mammals. Supporting Evidence: PMID:28479320 intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary PMID:26980730 neither of which was included with certainty in |
| GO:0035720 intraciliary anterograde transport | IBA GO_REF:0000033 | ACCEPT | Summary: As an IFT-B subunit, DYF-13 participates in kinesin-2-driven anterograde transport that carries cargo from the ciliary base toward the tip. Loss of dyf-13 causes distal-segment defects consistent with impaired anterograde delivery. Reason: Core biological process for an IFT-B subunit; anterograde transport is the direction driven by the kinesin-2/IFT-B machinery that DYF-13 belongs to. Supporting Evidence: PMID:15916950 encodes a ciliary protein that undergoes IFT |
| GO:0035735 intraciliary transport involved in cilium assembly | IBA GO_REF:0000033 | ACCEPT | Summary: DYF-13 is required for building and maintaining cilia: dyf-13(mn396) mutants have short cilia lacking distal portions, and the protein is a novel core IFT component required for cilia function. Reason: Core biological process; captures the specific role of IFT in cilium assembly, strongly supported by the dyf-13 mutant structural phenotype. Supporting Evidence: PMID:15916950 is a novel core IFT component required for cilia function |
| GO:0097546 ciliary base | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IFT particles, including DYF-13, are active at the ciliary base where anterograde trains assemble and retrograde trains are remodeled. Consistent with DYF-13 undergoing IFT that initiates at the base. Reason: Supporting (non-core) location consistent with IFT-B biology; complements the primary cilium/axoneme localization. Supporting Evidence: PMID:15916950 encodes a ciliary protein that undergoes IFT |
| GO:0120170 intraciliary transport particle B binding | IBA GO_REF:0000033 | ACCEPT | Summary: The molecular function of DYF-13/TTC26 within the cilium is to associate with the IFT-B particle. As a TPR-repeat scaffold subunit it binds the IFT-B complex; this is the most specific molecular-function term currently available for an IFT-B structural subunit. Reason: Best-available molecular-function term for an IFT-B subunit; more informative than generic protein binding. DYF-13 co-purifies within IFT complex B, and functions as a cargo-selective IFT-B adapter rather than a core-structural requirement (it associates with, but is not essential for, IFT-particle assembly). Supporting Evidence: PMID:28479320 intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary file:worm/dyf-13/dyf-13-deep-research-falcon.md IFT56 is not required for assembly or movement of IFT particles themselves |
| GO:0005929 cilium | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell-derived electronic annotation placing DYF-13 in the cilium. Correct but general; concordant with the experimentally supported ciliary localization. Reason: Correct general localization (cilium), consistent with primary evidence that DYF-13 is a ciliary protein undergoing IFT. Supporting Evidence: PMID:15916950 encodes a ciliary protein that undergoes IFT |
| GO:0005929 cilium | NAS PMID:28479320 Dynein-Driven Retrograde Intraflagellar Transport Is Triphas... | ACCEPT | Summary: ComplexPortal NAS annotation to cilium based on the IFT-B complex membership reported in Yi et al. 2017. Correct but general localization. Reason: Correct ciliary localization; supported by identification of dyf-13 in the ciliary IFT-B complex. Supporting Evidence: PMID:28479320 intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary |
| GO:0030992 intraciliary transport particle B | NAS PMID:28479320 Dynein-Driven Retrograde Intraflagellar Transport Is Triphas... | ACCEPT | Summary: ComplexPortal NAS annotation, from the same study that identified dyf-13 as a component of IFT complex B by affinity purification and mass spectrometry. Reason: Core structural assignment corroborating the IBA IFT-B membership; directly supported by the primary study. Supporting Evidence: PMID:28479320 intraflagellar transport (IFT)-B complex abolishes dynein-2's ciliary |
| GO:0042073 intraciliary transport | NAS PMID:28479320 Dynein-Driven Retrograde Intraflagellar Transport Is Triphas... | KEEP AS NON CORE | Summary: General intraflagellar-transport process annotation for an IFT-B subunit. Correct but less specific than the anterograde/assembly terms; the parent process under which DYF-13 acts. Reason: Correct but general parent term; the more specific anterograde-transport and transport-in-cilium-assembly terms better capture the core function. Supporting Evidence: PMID:15916950 encodes a ciliary protein that undergoes IFT |
| GO:0060271 cilium assembly | NAS PMID:28479320 Dynein-Driven Retrograde Intraflagellar Transport Is Triphas... | ACCEPT | Summary: DYF-13 is required for cilium assembly; dyf-13 mutants have short cilia lacking distal segments. This general BP term is well supported, with the more specific IFT-in-cilium-assembly term giving the mechanism. Reason: Correct biological process; the dyf-13 loss-of-function structural cilia phenotype directly supports a cilium-assembly role. Supporting Evidence: PMID:15916950 is a novel core IFT component required for cilia function |
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Download this section (compressed HTML)What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The molecular activity of DYF-13/TTC26 beyond intraciliary-transport-particle-B binding is undefined. It is unknown which specific IFT-B subunit(s) DYF-13 contacts within the C. elegans complex and which ciliary cargo(es) it directly binds or is required to transport; cargo specificity (e.g. for the retrograde motor che-3/dynein-2) is stated only as a hypothesis.
OPEN BIOLOGYONTOLOGY MF_DARK
What is known: It is firmly established that DYF-13 is an IFT-B subunit (co-purifies within IFT complex B), localizes to the cilium and undergoes IFT, is required for cilium assembly (dyf-13 mutants have short cilia lacking distal segments), and that IFT-B integrity is required for ciliary entry of dynein-2. Its fold is a TPR-repeat (alpha-solenoid) scaffold.
Significance: IFT-B subunits are structural adaptors whose specific cargo/partner contacts determine which proteins a cilium can import; TTC26/IFT56 loss in vertebrates selectively perturbs Hedgehog and motility-related ciliary cargo, so mapping DYF-13's direct interactions would explain the specificity of its transport role. There is also no GO molecular-function term for a structural constituent of an IFT particle, forcing an IFT-B subunit to be annotated with the complex-binding term, which is why the gene reads as MF-dark.
What would resolve it: Proximity/affinity proteomics and cross-linking mass spectrometry to map DYF-13's direct IFT-B neighbors; cargo-specific transport assays in dyf-13 mutants; a GO molecular-function term for an IFT-particle structural constituent.
Provenance (the field's own admissions):
Gap: Whether C. elegans DYF-13 occupies the IFT-B core or peripheral sub-architecture has not been determined biochemically. Mammalian TTC26/IFT56 was assigned to the IFT-B core subcomplex, but the sub-complex position of the worm ortholog and the consequences of its loss for IFT-B stability in vivo are unmapped.
OPEN BIOLOGYCURATION CC_DARK
What is known: DYF-13 is confirmed as part of the IFT-B complex in C. elegans (mass spectrometry) and TTC26/IFT56 is placed in the IFT-B core in the mammalian interaction map, but the two have not been reconciled for the worm protein.
Significance: Knowing whether DYF-13 is a core or peripheral IFT-B subunit predicts how severely its loss should destabilize the whole particle versus a specific cargo-adaptor arm, informing interpretation of the dyf-13 mutant phenotype.
What would resolve it: Salt-dissociation and reconstitution of the C. elegans IFT-B complex, or quantitative proteomics of IFT-B in dyf-13 mutants, to place DYF-13 in the core/peripheral architecture.
Provenance (the field's own admissions):
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