dyf-13 (C. elegans) research notes

UniProt: Q95QT8 (IFT56_CAEEL). WormBase: WBGene00001129 / C27H5.7. Gene name from Starich
et al. 1995 dye-filling-defective screen.

Molecular identity (verified from UniProt record)

• RecName: Intraflagellar transport protein 56 homolog; AltName: Abnormal dye filling protein 13. Belongs to the IFT56 family (SIMILARITY block). PANTHER family
  PTHR14781 "INTRAFLAGELLAR TRANSPORT PROTEIN 56"; InterPro IPR030511 TTC26.
• Therefore dyf-13 is the C. elegans ortholog of vertebrate TTC26 / IFT56 / IFT-B protein
  56. 574 aa, contains multiple TPR repeats (UniProt annotates TPR 1/2/3; Pfam
  PF14559 TPR_19; SUPFAM TPR-like). Architecture = tetratricopeptide-repeat (α-solenoid)
  scaffold protein, the canonical fold of many IFT-B peripheral subunits.
• Two isoforms by alternative splicing: Q95QT8-1 (displayed) and Q95QT8-2 ("b", VSP_057361,
  missing residues 1–22). No evidence of isoform-specific function.
• ComplexPortal: CPX-1290 "Intraflagellar transport complex B".

KNOWN (well supported)

Core identity: a novel core IFT component required for cilium function

• dyf-13 was cloned by Blacque et al. 2005 and shown to be the gene disrupted in dyf-13(mn396):
  PMID:15916950. The gene product undergoes IFT like other
  IFT proteins: PMID:15916950 Conclusion of that paper:
  PMID:15916950

Localization: cilium / undergoes IFT

• DYF-13::GFP is a bona fide IFT reporter that localizes along amphid channel cilia (TZ, middle
  and distal segments) and is transported: PMID:18316409 (used as an IFT reporter, strain Ex[DYF-13∷GFP]).
• UniProt SUBCELLULAR LOCATION: Cell projection, cilium (by similarity to mouse Q5PR66).
• ComplexPortal (NAS, PMID:28479320) locates it to the cilium.

Part of IFT-B complex

• Yi et al. 2017 identified dyf-13 as a component of IFT complex B by affinity purification /
  mass spectrometry: UniProt SUBUNIT: "Component of the IFT complex B composed of at least che-2,
  che-13, dyf-1, dyf-3, dyf-6, dyf-11, dyf-13, ift-20, ift-74, ift-81, ifta-2, osm-1, osm-5 and
  osm-6" {ECO:0000269|PubMed:28479320}. The paper shows disruption of the IFT-B complex abolishes
  dynein-2's ciliary localization: PMID:28479320
• Mammalian TTC26/IFT56 was assigned to the IFT-B core subcomplex by Katoh et al. 2016:
  PMID:26980730

Function: anterograde transport / cilium assembly

• UniProt FUNCTION: "Component of the intraflagellar transport (IFT) complex B required for
  transport of proteins in the motile cilium (PubMed:15916950, PubMed:28479320). May be required
  for ciliary entrance and transport of specific ciliary cargo proteins such as che-3 which are
  related to motility (PubMed:28479320)." Note: the "motile cilium" phrasing is UniProt boilerplate
  transferred from the vertebrate ortholog; C. elegans sensory cilia are non-motile, but the
  IFT/assembly role is conserved.
• Disruption phenotype (structural): UniProt DISRUPTION PHENOTYPE "Structural cilia defect: cilia
  are short and lack distal portions." {ECO:0000269|PubMed:15916950}. Consistent with an IFT-B/
  anterograde defect (distal-segment loss).
• The dyf-13 mutant shows partial IFT-cargo defects: PMID:18316409

Dye-filling / sensory phenotype and X-box regulation

• Named for the Dyf (dye-filling defective) phenotype indicative of general cilium structural
  defects; part of the dyf-1..dyf-13 class: PMID:16957054 dyf-13 is a DAF-19/RFX X-box-regulated ciliary
  gene, cloned via the X-box motif: PMID:16957054.
• Conserved IFT component enriched in the Chlamydomonas flagellar proteome:
  PMID:18369462.

NOT known / open questions

• Molecular activity beyond "IFT-B particle binding" is undefined. dyf-13/TTC26/IFT56 is a
  TPR-scaffold subunit; which specific IFT-B subunit(s) it contacts and which cargo(es) it directly
  binds within the worm complex are not experimentally mapped. UniProt frames cargo specificity as
  a hypothesis ("May be required for ... transport of specific ciliary cargo proteins such as che-3").
  This is the classic structural-subunit MF-dark/ontology-gap situation described in
  projects/FUNCTION_KNOWLEDGE_GAPS.md.
• Core vs. peripheral position of the worm protein is not directly determined. Mammalian
  TTC26/IFT56 was placed in the IFT-B core by Katoh 2016 (PMID:26980730); whether C. elegans
  dyf-13 occupies the same sub-architectural position has not been shown biochemically.
• No direct enzymatic activity is expected or reported (TPR scaffold; no catalytic motifs).
• Basal body vs. ciliary-base pool: the IBA annotations place it at the ciliary basal body and
  ciliary base, but there is no worm-specific experimental sub-ciliary localization beyond
  "along the cilium".

Annotation review orientation

GOA has 11 annotations:
- 6 IBA (GO_REF:0000033) from PANTHER PTHR14781: ciliary basal body, intraciliary transport
particle B, intraciliary anterograde transport, intraciliary transport involved in cilium
assembly, ciliary base, intraciliary transport particle B binding. All consistent with an
IFT-B subunit — ACCEPT (the last three are core; basal body/base are supporting locations).
- 1 IEA (GO_REF:0000044, UniProt SubCell) cilium — ACCEPT (redundant with NAS cilium).
- 4 NAS (PMID:28479320, ComplexPortal): cilium, intraciliary transport particle B, intraciliary
transport, cilium assembly. All consistent — ACCEPT; the two most specific (IFT particle B,
cilium assembly / intraciliary transport) are core.

No REMOVE candidates: every annotation is on-pathway for an IFT-B/TTC26 ortholog. No experimental
annotations are being second-guessed. The IBA/NAS evidence is coherent with strong primary
experimental literature (PMID:15916950, PMID:28479320).

References used

• PMID:15916950 Blacque et al. 2005, Curr Biol — cloning of dyf-13; core IFT component. HIGH.
• PMID:28479320 Yi et al. 2017, Curr Biol — dyf-13 in IFT-B by MS; IFT-B needed for dynein-2 entry. HIGH.
• PMID:18316409 Jauregui et al. 2008, JCB — DYF-13::GFP IFT reporter, cargo (OSM-6) defect. MEDIUM.
• PMID:16957054 Efimenko/Blacque et al. 2006, Mol Biol Cell — dyf gene class, X-box regulation. MEDIUM.
• PMID:18369462 Bacaj et al. 2008 (DYF-11), Curr Biol — DYF-13 as conserved IFT component. LOW/MEDIUM.
• PMID:26980730 Katoh et al. 2016, Mol Biol Cell — mammalian TTC26/IFT56 IFT-B architecture. MEDIUM (ortholog).
  
  

Deep research (falcon / Edison) synthesis — added after review draft

A genuine falcon deep-research report (dyf-13-deep-research-falcon.md, Edison Scientific
Literature, ~28 min, 10 citations) completed and corroborates the review. Key points (its
internal citation keys, e.g. ishikawa2014ttc26dyf13isan, xin2017ift56regulatesvertebrate,
zhang2012knockdownofttc26, are falcon-internal and were NOT independently verified against
cached PMIDs, so they are not used as supporting_text in the YAML):

• IFT56/TTC26/DYF-13 is a cargo-selective IFT-B adapter, not an enzyme; TPR/α-solenoid
  scaffold. Placed in the IFT-B1 (B1b) branch (with IFT46, IFT52, IFT70, IFT88).
• Cross-species nuance: in Chlamydomonas and some vertebrate systems IFT56/TTC26 is
  dispensable for basic IFT train assembly/motility but required for import of a subset of
  cargo (notably motility-related axonemal proteins). This contrasts with the C. elegans
  dyf-13(mn396) structural phenotype (short cilia lacking distal segments; Blacque 2005,
  PMID:15916950), which the review anchors on. The species difference (cargo-selectivity vs.
  overt structural defect) is itself part of the open question about DYF-13's precise role.
• Vertebrate orthologs: mouse Ift56/hop mutants mislocalize Gli2/Gli3 (Hedgehog signaling);
  zebrafish ttc26 morphants have short photoreceptor/pronephric cilia; human TTC26/IFT56 linked
  to severe biliary ciliopathy. These are ortholog data, not C. elegans-specific.

This supports the two knowledge_gaps recorded (undefined direct cargo/partner contacts; core vs
peripheral sub-architecture of the worm protein) and the framing of DYF-13 as an IFT-B
structural/adapter subunit.