TULP3

TULP3 is a ciliary trafficking adaptor that couples diverse membrane-associated cargoes to the intraflagellar transport machinery for delivery into primary cilia, and additionally functions outside cilia as a metabolic signaling receptor. TULP3 binds the IFT-A complex through its N-terminal region and membrane phosphoinositides through its C-terminal tubby domain β-barrel, and a distinct surface region on the β-barrel (β-strands 8–12) captures both lipidated (ARL13B, INPP5E) and transmembrane cargoes (GPCRs, polycystins, ACE2) for ciliary import (PMID:20889716, PMID:39565681, PMID:36652335). Loss of TULP3-mediated trafficking derepresses Hedgehog signaling downstream of Smoothened and upstream of Gli2, causes neural tube closure defects, and drives renal cystogenesis through mislocalization of polycystin-1/2 and ARL13B with consequent activation of MAPK/ERK, mTOR, and cAMP pathways (PMID:19286674, PMID:11406614, PMID:30799239). Independent of its ciliary role, TULP3 serves as a direct receptor for the bile acid lithocholic acid and allosterically activates SIRT1 to deacetylate the v-ATPase V1E1 subunit, thereby engaging the lysosomal glucose-sensing pathway and AMPK activation—a mechanism conserved across worms, flies, and mammals (PMID:39695235).

1. 2001 High

   Establishing that TULP3 is essential for mammalian neural tube development resolved the question of whether this tubby-family member had a non-redundant in vivo role.

   Evidence Germline knockout in mouse with TUNEL apoptosis and histological analysis

   PMID:11406614

   Open questions at the time

   • Molecular mechanism linking TULP3 loss to neuroepithelial apoptosis was unknown
   • No connection to cilia or signaling pathways had been made
2. 2009 High

   Genetic epistasis placed TULP3 as a negative regulator of Hedgehog signaling downstream of Smoothened but upstream of Gli2/Gli3, and revealed its localization to primary cilia, connecting the neural tube phenotype to a specific signaling pathway.

   Evidence Compound mutant analysis (Tulp3/Shh, Tulp3/Smo, Tulp3/Gli3) in mouse neural tube and limb, immunofluorescence

   PMID:19223390 PMID:19286674 PMID:19334287

   Open questions at the time

   • How TULP3 reached cilia and whether it trafficked other proteins was unknown
   • Whether TULP3 regulated Gli processing or just Gli activity was unclear
3. 2010 High

   Demonstrating that TULP3 directly binds IFT-A and that both IFT-A binding and phosphoinositide binding are required for ciliary GPCR trafficking established TULP3 as a bona fide ciliary trafficking adaptor rather than a signaling modulator per se.

   Evidence Co-immunoprecipitation, phosphoinositide-binding assays, domain mutagenesis, ciliary trafficking assays in mouse embryonic cells

   PMID:20889716

   Open questions at the time

   • Full cargo repertoire beyond a subset of GPCRs was undefined
   • Whether TULP3 directly contacts cargo or acts indirectly was unknown
4. 2018 High

   Extending the cargo list to include ARL13B and INPP5E and confirming IFT-A dependence in human cells broadened TULP3's role from GPCR-specific to a general lipidated and membrane-protein trafficking adaptor.

   Evidence TULP3 knockout in hTERT RPE-1 cells, rescue with wild-type vs. IFT-A-binding-deficient mutant

   PMID:30583862

   Open questions at the time

   • How TULP3 recognizes such structurally diverse cargoes was not resolved
   • Whether phosphoinositide binding was always required for all cargo classes was unclear
5. 2019 High

   Conditional kidney knockout linked TULP3-dependent ciliary trafficking of polycystins and ARL13B to renal cystogenesis and downstream MAPK/mTOR/cAMP hyperactivation, providing a disease-relevant in vivo validation of the trafficking adaptor model.

   Evidence Nephron-specific conditional knockout, forward genetic screen in mouse, genetic interaction with Pkd1

   PMID:30799239 PMID:30799240

   Open questions at the time

   • Whether TULP3 dysfunction contributes to human polycystic kidney disease was untested
   • Relative contributions of individual mislocalized cargoes to cystogenesis were not separated
6. 2022 Medium

   Identification of a patient TULP3 R382W variant that disrupts phosphoinositide binding and ciliary cargo delivery, combined with detection of a TULP3–SIRT1 interaction and increased DNA damage in patient cells, opened an unexpected non-ciliary function and linked TULP3 mutations to human disease.

   Evidence Patient-derived cell Co-IP, DNA damage assays, functional expression of R382W variant in IMCD-3 cells

   PMID:35397207 PMID:36276950

   Open questions at the time

   • The TULP3–SIRT1 interaction's mechanism and whether it is direct awaited biochemical dissection
   • Whether the DNA damage phenotype is a direct consequence of SIRT1 modulation or ciliary dysfunction was not distinguished
7. 2023 High

   Mapping the ARL13B ciliary localization sequence to an N-terminal amphipathic helix that directly contacts the TULP3 tubby domain—independently of palmitoylation and phosphoinositide binding—revealed a cargo-recognition mode distinct from lipid-dependent mechanisms.

   Evidence Mutational analysis of ARL13B and TULP3, Co-IP, rescue in knockout cells

   PMID:36652335

   Open questions at the time

   • Whether other cargoes use analogous amphipathic helices for TULP3 recognition was untested
   • Structural basis of the ARL13B helix–tubby domain interface was not determined
8. 2024 High

   Proximity-labeling and mutagenesis identified a specific β-barrel surface (β-strands 8–12) on the tubby domain as the universal cargo-capture site, distinct from the phosphoinositide-binding pocket, unifying how TULP3 recognizes both transmembrane and lipidated cargoes.

   Evidence Proximity biotinylation-mass spectrometry, structural analysis, mutagenesis, ciliary trafficking rescue assays

   PMID:39565681

   Open questions at the time

   • Atomic-resolution structure of cargo–tubby domain complexes is lacking
   • How cargo selectivity is achieved given a shared binding surface is unresolved
9. 2024 High

   Discovery that TULP3 directly binds lithocholic acid and allosterically activates SIRT1 to deacetylate v-ATPase V1E1 and activate AMPK established a cilia-independent metabolic signaling function conserved from C. elegans to mammals.

   Evidence Biochemical binding assays, in vitro deacetylation, proteomics, mouse muscle-specific expression, genetic experiments in C. elegans (tub-1) and Drosophila (ktub)

   PMID:39695235

   Open questions at the time

   • How TULP3's ciliary trafficking and SIRT1-activating functions are coordinated or segregated in the same cell is unknown
   • Whether other bile acids or endogenous ligands also bind TULP3 is untested
   • Structural basis of the LCA-TULP3-SIRT1 ternary complex is not resolved
10. 2025 Medium

    Extension of TULP3's cargo repertoire to ACE2 and demonstration that TULP3 depletion impairs SARS-CoV-2 pseudovirus entry connected ciliary trafficking to viral tropism.

    Evidence Co-immunoprecipitation, confocal microscopy, siRNA knockdown, IFT-A-binding-deficient TULP3 mutant rescue, pseudovirus infection assay

    PMID:41316318

    Open questions at the time

    • Relevance to authentic SARS-CoV-2 infection in vivo is not established
    • Whether ciliary versus apical membrane ACE2 is the relevant pool for viral entry is not distinguished

• Key open questions include the structural basis of cargo discrimination at the shared β-barrel surface, how the ciliary adaptor and SIRT1-activating functions are partitioned in different cell types, and whether TULP3 mutations cause a defined human ciliopathy or metabolic syndrome.
• No atomic-resolution structure of TULP3 in complex with any cargo or SIRT1 exists
• Genotype-phenotype correlation for human TULP3 mutations across ciliary and metabolic phenotypes is incomplete
• Whether TULP3-SIRT1-AMPK axis is druggable or relevant to human aging remains untested