this with annotations you find in gene/protein databases, but these can be outdated or inaccurate. Falcon Edison Scientific Literature 10 citations 1 artifacts 2026-07-04T19:27:30.270211

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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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.

We are interested in where in or outside the cell the gene product carries out its function.

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.

Comprehensive Research Report: dyf-13 (IFT56/TTC26) in Caenorhabditis elegans

1. Gene and Protein Identity

The C. elegans gene dyf-13 (ORF name C27H5.7; UniProt Q95QT8) encodes intraflagellar transport protein 56 homolog (IFT56), also known in vertebrates as tetratricopeptide repeat domain 26 (TTC26). The protein is a highly conserved member of the IFT56 family, present in all ciliated organisms but absent from non-ciliated species, underscoring its dedicated role in ciliary biology (ishikawa2014ttc26dyf13isan pages 3-4, ishikawa2014ttc26dyf13isan pages 15-17). IFT56 (also known as TTC26, DYF-13, and PIFTC3) is a highly conserved intraflagellar transport complex B (IFT-B) protein (xin2017ift56regulatesvertebrate pages 1-2, ishikawa2014ttc26dyf13isan pages 1-2). The protein contains TPR-like helical domain superfamily features and TTC26/TPR_19 domains, consistent with tetratricopeptide repeat-mediated protein–protein interactions typical of IFT scaffold/adapter proteins (ishikawa2014ttc26dyf13isan pages 13-15).

The following table summarizes the key properties of dyf-13/IFT56/TTC26:

Property Description
Gene names and aliases dyf-13 in Caenorhabditis elegans; orthologous/alias names include TTC26, IFT56, and PIFTC3. Literature explicitly equates TTC26/DYF13/IFT56 across ciliated organisms, validating that the requested gene identity matches the UniProt entry for the worm dyf-13 protein (ishikawa2014ttc26dyf13isan pages 12-13, ishikawa2014ttc26dyf13isan pages 1-2, xin2017ift56regulatesvertebrate pages 1-2).
Organism The target gene/protein is from Caenorhabditis elegans, where it functions in sensory cilia of amphid and phasmid neurons; cross-species functional data are available from zebrafish, mouse, mammalian cultured cells, and Chlamydomonas ortholog studies (efimenko2006caenorhabditiselegansdyf2an pages 2-3, zhang2012knockdownofttc26 pages 1-2, xin2017ift56regulatesvertebrate pages 1-2).
Protein family DYF-13 belongs to the conserved IFT56/TTC26 family, a cilia-associated family present in ciliated organisms and absent from non-ciliated organisms, consistent with a dedicated role in intraflagellar transport and ciliary biology (ishikawa2014ttc26dyf13isan pages 3-4, ishikawa2014ttc26dyf13isan pages 15-17, xin2017ift56regulatesvertebrate pages 1-2).
Domain structure UniProt annotates DYF-13/Q95QT8 with TPR-like helical superfamily features and TTC26 / TPR_19 domains, consistent with tetratricopeptide repeat-mediated protein interaction/adaptor functions typical of IFT-associated scaffold proteins; this agrees with the experimentally supported role of IFT56/TTC26 as an IFT-B-associated adaptor rather than an enzyme (ishikawa2014ttc26dyf13isan pages 13-15, ishikawa2014ttc26dyf13isan pages 12-13).
IFT-B subcomplex position IFT56/TTC26/DYF-13 is a component of IFT complex B, specifically placed in the IFT-B1b subgroup together with IFT46, IFT52, IFT70, and IFT88. Recent assembly work indicates IFT56 is part of the IFT-B1 branch and is linked through the IFT46-IFT52 module to other IFT-B subcomplexes (ishikawa2014ttc26dyf13isan pages 7-9, tasaki2025assemblyandmother pages 1-5).
Primary function The best-supported primary function is as a cargo-selective IFT-B-associated adapter/regulator, not a catalytic protein. IFT56/TTC26/DYF-13 is dispensable for basic IFT train assembly/motility in some systems but is required for transport of a subset of ciliary cargoes, especially motility-related proteins such as inner dynein arm components, dynein regulatory complex proteins, and central pair-associated factors (ishikawa2014ttc26dyf13isan pages 10-12, ishikawa2014ttc26dyf13isan pages 7-9, ishikawa2014ttc26dyf13isan pages 12-13, ishikawa2014ttc26dyf13isan pages 13-15).
Subcellular localization IFT56/TTC26/DYF-13 localizes to cilia/flagella and basal body-associated regions, with a punctate distribution characteristic of IFT proteins. In mammalian cells it undergoes bidirectional IFT; in zebrafish and photoreceptors, Ttc26 was also observed at the transition zone. Reported mammalian transport speeds for TTC26-GFP are ~1.22 ± 0.17 μm/s anterograde and 0.92 ± 0.24 μm/s retrograde (ishikawa2014ttc26dyf13isan pages 2-3, ishikawa2014ttc26dyf13isan pages 6-7, zhang2012knockdownofttc26 pages 1-2, zhang2012knockdownofttc26 pages 2-4).
Key phenotypes in C. elegans dyf-13 is one of the classic Dyf (dye-filling defective) genes required for proper amphid/phasmid sensory cilium function. The Dyf class is associated with failed DiI filling of sensory neurons and abnormal ciliary structure. Prior work cited in later studies indicates shortened cilia in C. elegans dyf-13 mutants, and dyf-13 has been linked to regulation of OSM-3-kinesin/IFT-B behavior in sensory cilia (efimenko2006caenorhabditiselegansdyf2an pages 2-3, ishikawa2014ttc26dyf13isan pages 2-3, ishikawa2014ttc26dyf13isan pages 12-13).
Key phenotypes in other organisms In zebrafish, ttc26 knockdown causes shortened or missing photoreceptor outer segments, pronephric cilia defects, kidney duct dilation, body curvature, edema, abnormal fluid flow, and reduced cilia length/number in Kupffer’s vesicle. In mouse/vertebrate systems, Ift56 loss causes developmental patterning defects, male sterility, gait abnormalities, shortened/abnormal cilia, and disorganized axonemal microtubules (zhang2012knockdownofttc26 pages 1-2, zhang2012knockdownofttc26 pages 6-7, zhang2012knockdownofttc26 pages 4-5, ishikawa2014ttc26dyf13isan pages 3-4, xin2017ift56regulatesvertebrate pages 1-2, xin2017ift56regulatesvertebrate pages 5-7).
Signaling pathway involvement IFT56 is implicated in cilium-dependent Hedgehog signaling. In mouse Ift56/hop mutants, cilia form but fail to properly accumulate Gli2 and Gli3 at ciliary tips, while Smoothened localization can remain relatively normal; this leads to defective Shh-dependent patterning in limb and neural tube development. Thus, IFT56 supports signaling competence by maintaining IFT-B integrity and ciliary architecture needed for Gli trafficking (xin2017ift56regulatesvertebrate pages 4-5, xin2017ift56regulatesvertebrate pages 1-2, xin2017ift56regulatesvertebrate pages 2-3, xin2017ift56regulatesvertebrate pages 3-4).
Human disease associations Human TTC26/IFT56 has been linked to severe biliary ciliopathy by biallelic mutation studies, and broader cross-species work places IFT56 among IFT-B components whose dysfunction can contribute to ciliopathy phenotypes. Although the detailed clinical text was not retrievable here, the paper metadata and abstract identify TTC26 as a human disease gene in severe biliary ciliopathy (xin2017ift56regulatesvertebrate pages 5-7).

Table: This table condenses the main verified properties of the C. elegans dyf-13 gene product and its orthologs, including molecular function, localization, phenotypes, and pathway relevance. It is useful as a quick-reference functional annotation summary grounded in the retrieved evidence.

2. Primary Function: Cargo-Selective Adapter in Intraflagellar Transport

DYF-13/IFT56/TTC26 is not an enzyme or transporter in the classical sense; rather, it functions as a cargo-selective adapter protein within the intraflagellar transport (IFT) machinery. The landmark study by Ishikawa et al. (2014) in eLife demonstrated that TTC26/DYF13 is an IFT complex B protein required for the transport of motility-related proteins into flagella (ishikawa2014ttc26dyf13isan pages 10-12, ishikawa2014ttc26dyf13isan pages 2-3). Unlike core IFT-B components, whose loss abolishes ciliogenesis, IFT56 is not required for assembly or movement of IFT particles themselves (ishikawa2014ttc26dyf13isan pages 7-9, ishikawa2014ttc26dyf13isan pages 10-12). Instead, dyf13 mutant flagella in Chlamydomonas reinhardtii still assemble and IFT particle speed remains normal, but a specific subset of ciliary proteins is selectively depleted (ishikawa2014ttc26dyf13isan pages 10-12).

Proteomic and biochemical analyses of C. reinhardtii dyf13 mutant flagella revealed that the proteins requiring DYF13 for import are predominantly motility-related, including:
- Inner dynein arm components (species a, f, and g)
- Dynein regulatory complex proteins (e.g., PF2/DRC4)
- Central pair complex proteins
- Additional flagellar proteins such as FAP59, tektin, centrin, and enolase (ishikawa2014ttc26dyf13isan pages 13-15, ishikawa2014ttc26dyf13isan pages 10-12)

This led to the concept that IFT56 functions as an adaptor between the main IFT complex and its cargo proteins, possibly by recruiting PIH proteins (specifically TWI1) that pre-assemble dynein arms to the IFT complex for transport (ishikawa2014ttc26dyf13isan pages 12-13). The mechanism by which IFT56 binds its various cargo proteins remains unclear; unlike tubulin, which has specific binding domains on IFT74 and IFT81, it is unknown whether IFT56 contains similarly specific binding sites for all of its cargoes (ishikawa2014ttc26dyf13isan pages 13-15).

This finding supports the broader concept that different IFT proteins are responsible for different cargo subsets, providing a possible explanation for the complexity of the IFT machinery with its >20 subunits (ishikawa2014ttc26dyf13isan pages 2-3).

3. Position within the IFT-B Complex Architecture

IFT56/TTC26/DYF-13 is a component of the IFT-B1b subgroup within the larger IFT-B complex. The 16-subunit IFT-B complex is subdivided into two major subcomplexes: IFT-B1 and IFT-B2 (tasaki2025assemblyandmother pages 1-5). IFT-B1 is further divided into IFT-B1a (containing IFT22, IFT25, IFT27, IFT74, IFT81) and IFT-B1b (containing IFT46, IFT52, IFT56, IFT70, and IFT88) (tasaki2025assemblyandmother pages 1-5). The IFT-B1b subgroup connects to IFT-B1a through an interaction between the IFT46-IFT52 dimer (from IFT-B1b) and the IFT74-IFT81 dimer (from IFT-B1a) (tasaki2025assemblyandmother pages 1-5).

Through tandem affinity purification (TAP) analysis, TTC26/DYF13 was shown to physically interact with all known IFT complex B proteins but not with IFT complex A proteins or motor proteins (ishikawa2014ttc26dyf13isan pages 7-9). Sucrose density gradient analysis confirmed that TTC26/DYF13 comigrates with other IFT complex B proteins such as IFT46 and IFT74 (ishikawa2014ttc26dyf13isan pages 12-13, ishikawa2014ttc26dyf13isan pages 7-9). IFT56 interacts directly with IFT46 as part of the IFTB-1 subcomplex (xin2017ift56regulatesvertebrate pages 5-7). The IFT46–IFT56 dimer has been identified as the minimum entity needed for interaction with ANKRD55, a multiple sclerosis-associated protein, in microglial cells, further underscoring their close physical association within the IFT-B architecture (tasaki2025assemblyandmother pages 1-5).

Despite being an IFT-B component, IFT56 acts as a peripheral rather than core structural component; its loss does not entirely abolish IFT-B complex assembly or IFT train movement, consistent with its role as a cargo-adapter module rather than a structural requirement for the transport machinery itself (ishikawa2014ttc26dyf13isan pages 12-13, ishikawa2014ttc26dyf13isan pages 7-9).

4. Subcellular Localization

IFT56/TTC26/DYF-13 localizes to primary cilia and basal bodies, displaying a punctate distribution along the ciliary length that is characteristic of IFT proteins (ishikawa2014ttc26dyf13isan pages 2-3, ishikawa2014ttc26dyf13isan pages 3-4). The protein undergoes bidirectional intraflagellar transport along the ciliary axoneme. In mammalian cells, TTC26-GFP moves at anterograde speeds of 1.22 ± 0.17 μm/s and retrograde speeds of 0.92 ± 0.24 μm/s, comparable to the established IFT protein IFT88 (ishikawa2014ttc26dyf13isan pages 6-7). These speeds indicate that TTC26 moves together with other IFT proteins as part of the complex (ishikawa2014ttc26dyf13isan pages 6-7).

In zebrafish, Ttc26 was specifically localized to the transition zone of both photoreceptor sensory cilia and primary cilia in cultured renal cells (zhang2012knockdownofttc26 pages 1-2, zhang2012knockdownofttc26 pages 2-4). In C. elegans, DYF-13 protein undergoes IFT motion in sensory cilia of amphid and phasmid neurons (ishikawa2014ttc26dyf13isan pages 6-7). The protein is present in both motile flagella and non-motile primary and sensory cilia, suggesting functions beyond motility cargo transport alone (ishikawa2014ttc26dyf13isan pages 15-17).

5. Phenotypes in C. elegans

The gene name dyf-13 derives from the Dye-Filling defective (Dyf) phenotype class in C. elegans. The dyf class consists of 13 members (dyf-1 to dyf-13), all exhibiting reduced fluorescent dye (DiI) filling of amphid and phasmid sensory neurons, indicative of structural defects in the environmentally exposed cilia of these neurons (efimenko2006caenorhabditiselegansdyf2an pages 2-3). dyf-13 mutants display abnormally short cilia, consistent with a role for DYF-13 in determining proper cilium length (ishikawa2014ttc26dyf13isan pages 12-13, ishikawa2014ttc26dyf13isan pages 2-3).

Previous studies suggested that DYF-13 may function as an IFT regulator that modulates either the activity of the OSM-3-kinesin motor or its association with IFT subcomplex B in C. elegans sensory cilia (ishikawa2014ttc26dyf13isan pages 12-13, ishikawa2014ttc26dyf13isan pages 2-3). In the C. elegans sensory cilium, IFT is driven cooperatively by two kinesin motors: heterotrimeric kinesin-II and homodimeric OSM-3/KIF17. In the middle segment, both motors work redundantly, while in the distal segment, only OSM-3 drives anterograde transport (efimenko2006caenorhabditiselegansdyf2an pages 2-3, efimenko2006caenorhabditiselegansdyf2an pages 1-2). DYF-13 appears to contribute to the regulation of this bipartite motor system.

Importantly, dyf-13 mutants display a distinct phenotype compared to other IFT-B mutants in C. elegans when probed by quantitative imaging of ARL-13/ARL13B compartmentalization. In wild-type worms, ARL-13 is restricted to the middle segment of amphid/phasmid cilia, but in most IFT-B mutants, ARL-13 accumulates strongly at the periciliary membrane (PCM). Notably, dyf-13/TTC26 mutants showed only moderate periciliary ARL-13 accumulation and moderately fast FRAP (fluorescence recovery after photobleaching) rates between ciliary and PCM pools (half-time recovery of ~50–78 seconds), distinct from other IFT-B mutants that displayed much slower exchange (cevik2013activetransportand pages 6-8). Furthermore, dyf-13;nphp-4 double mutants possessed even faster bidirectional recovery kinetics (half-time ~14–34 seconds), suggesting partially redundant functions for these genes in regulating ARL-13 diffusion at the ciliary/PCM boundary (cevik2013activetransportand pages 6-8). These data indicate that DYF-13 has roles in establishing and maintaining protein compartmentalization within the cilium, particularly at the transition zone diffusion barrier.

The dyf-13 gene has also been implicated in anthelmintic drug uptake. DYF-13 was identified among genes involved in dynein import, alongside OSM-1 and DAF-6, that contribute to intraflagellar transport in the ciliary distal segment of amphid neurons and influence avermectin susceptibility in C. elegans (brinzer2021theuptakeof pages 4-7).

6. Conserved Functions: Evidence from Other Organisms

Zebrafish: Morpholino knockdown of ttc26 in zebrafish embryos produced multiple cilia-related defects: shortened or absent photoreceptor outer segments, pronephric cilia defects with disrupted and disorganized cilia, pronephric duct dilation, body curvature, cardiac edema, reduced cilia length and number in Kupffer's vesicle, and abolished directional fluid flow (zhang2012knockdownofttc26 pages 1-2, zhang2012knockdownofttc26 pages 6-7, zhang2012knockdownofttc26 pages 4-5, ishikawa2014ttc26dyf13isan pages 3-4). In mIMCD3 cultured kidney cells, shRNA knockdown of Ttc26 led to significantly shortened cilia with enlarged ends (zhang2012knockdownofttc26 pages 4-5).

Chlamydomonas reinhardtii: Mutation of DYF13 in Chlamydomonas produced short flagella with pronounced motility defects, while IFT particle assembly and speed were normal—the key finding that established IFT56 as a cargo-specific adapter (ishikawa2014ttc26dyf13isan pages 10-12, ishikawa2014ttc26dyf13isan pages 7-9).

Mouse: The Ift56^hop (Hsp90-opposing protein) mutant mouse provided critical insights into vertebrate IFT56 function. Ift56^hop mutants form normal numbers of cilia but the cilia lack IFT56 protein (xin2017ift56regulatesvertebrate pages 2-3). These mutant cilia exhibit disorganized microtubule structures (8+0 or 7+0 arrangements instead of normal 9+0), indicating IFT56 is essential for maintaining proper ciliary microtubule architecture (xin2017ift56regulatesvertebrate pages 5-7). IFT81 and IFT27 are significantly reduced in Ift56^hop cilia, while IFT88 accumulates abnormally at the ciliary base rather than distributing along the axoneme, demonstrating IFT56's importance for IFT-B complex integrity (xin2017ift56regulatesvertebrate pages 5-7, xin2017ift56regulatesvertebrate pages 4-5). The mutant mice display preaxial polydactyly, gait abnormalities, and male sterility (xin2017ift56regulatesvertebrate pages 1-2).

7. Signaling Pathway Involvement: Hedgehog Signaling

A major function revealed by the mouse Ift56^hop mutant is the requirement for IFT56 in cilium-dependent Hedgehog (Hh) signaling. Both Gli2 and Gli3 show significantly reduced localization to ciliary tips in Ift56^hop cells, with over half of mutant cilia lacking detectable Gli2 and approximately 80% lacking Gli3 (xin2017ift56regulatesvertebrate pages 4-5, xin2017ift56regulatesvertebrate pages 1-2). Importantly, ciliary Smoothened (Smo) distribution and intensity remain relatively unaffected when the Hh pathway is activated, indicating the defect is specifically in Gli protein trafficking to ciliary tips (xin2017ift56regulatesvertebrate pages 3-4). The Ift56^hop phenotype results primarily from impaired Gli repressor (GliR) function rather than ectopic Shh pathway activation, leading to developmental patterning defects including preaxial polydactyly (an extra anterior digit) and differential effects in rostral versus caudal neural tube specification (xin2017ift56regulatesvertebrate pages 3-4, xin2017ift56regulatesvertebrate pages 2-3). The reduction in IFT27 in Ift56^hop cilia is particularly notable, as IFT27 has been independently linked to Hedgehog signaling through BBSome regulation (xin2017ift56regulatesvertebrate pages 4-5). While C. elegans lacks a canonical Hedgehog signaling pathway, these vertebrate findings illuminate the broader conserved role of IFT56 in maintaining IFT-B complex integrity for ciliary cargo trafficking.

8. Human Disease Relevance

Human TTC26 mutations have been linked to severe biliary ciliopathy through biallelic mutation studies, where patient cells displayed disrupted ciliary staining for IFT-B markers and abnormal sonic hedgehog signaling. This places TTC26/IFT56 among IFT-B components whose dysfunction can contribute to the spectrum of ciliopathy phenotypes. These findings were corroborated by the Ift56^hop mouse phenotype, which contrasts with other IFT-B mutants in that cilia still form but have impaired function (xin2017ift56regulatesvertebrate pages 5-7, xin2017ift56regulatesvertebrate pages 7-8). The relatively mild phenotype compared to mutations in core IFT-B components such as IFT88 or IFT172 is consistent with IFT56's peripheral, cargo-selective role within the complex.

9. Summary and Conclusions

DYF-13 (Q95QT8) in C. elegans is the nematode ortholog of vertebrate TTC26/IFT56, a tetratricopeptide repeat-containing component of the IFT-B1b subgroup within the intraflagellar transport complex B. The protein is not an enzyme or transporter but functions as a cargo-selective adapter that facilitates the transport of specific ciliary cargo proteins—particularly motility-related components such as inner dynein arms, dynein regulatory complex proteins, and central pair components—via IFT trains from the cell body into cilia and flagella. In C. elegans, DYF-13 localizes to the sensory cilia of amphid and phasmid neurons, undergoes bidirectional IFT movement, and is required for proper cilium length, ciliary protein compartmentalization, and sensory neuron dye-filling. Through cross-species studies, IFT56 has been shown to maintain IFT-B complex integrity and ciliary microtubule architecture, and to be essential for Hedgehog signaling-dependent developmental patterning in vertebrates via Gli2/Gli3 trafficking to ciliary tips. Its loss leads to ciliopathy phenotypes across species, from dye-filling defects in worms to photoreceptor degeneration and polydactyly in vertebrates and biliary ciliopathy in humans.

References

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Artifacts

Citations

  1. tasaki2025assemblyandmother pages 1-5
  2. cevik2013activetransportand pages 6-8
  3. brinzer2021theuptakeof pages 4-7
  4. https://doi.org/10.7554/elife.01566,
  5. https://doi.org/10.1242/jcs.205013,
  6. https://doi.org/10.1091/mbc.e06-04-0260,
  7. https://doi.org/10.1091/mbc.e12-01-0019,
  8. https://doi.org/10.1247/csf.25027,
  9. https://doi.org/10.1371/journal.pgen.1003977,
  10. https://doi.org/10.1101/2021.10.22.465401,