{"gene":"TULP3","run_date":"2026-04-28T21:43:00","timeline":{"discoveries":[{"year":2010,"finding":"TULP3 directly binds to the IFT-A complex, and this interaction is required for ciliary entry of TULP3 itself and for trafficking of a subset of GPCRs (but not Smoothened) into primary cilia. Both IFT-A binding and phosphoinositide-binding properties of the TULP3 tubby domain are required for ciliary GPCR localization.","method":"Co-immunoprecipitation, phosphoinositide-binding assays, genetic epistasis in mouse embryo, loss-of-function ciliary trafficking assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1-2 — multiple orthogonal methods (Co-IP, lipid binding, mouse genetics, ciliary trafficking assays), foundational paper with 358 citations, replicated by subsequent studies","pmids":["20889716"],"is_preprint":false},{"year":2009,"finding":"TULP3 acts as a negative regulator of Sonic Hedgehog (Shh) signaling downstream of Shh and Smoothened but upstream of Gli2, as established by genetic epistasis in mouse neural tube; TULP3 localizes to the tips of primary cilia.","method":"Genetic epistasis (Tulp3−/−, Tulp3−/−/Shh−/−, Tulp3−/−/Smo compound mutants), immunofluorescence localization","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — epistasis with multiple compound mutants, independently replicated by three labs in the same year (PMIDs 19286674, 19223390, 19334287)","pmids":["19286674","19223390","19334287"],"is_preprint":false},{"year":2009,"finding":"Tulp3 acts genetically downstream of Shh and Smo in neural tube patterning and exhibits a genetic interaction with Gli3 in limb development, without affecting Gli3 expression or processing.","method":"Genetic epistasis with Shh, Smo, and Gli3 mutants; immunofluorescence; in situ hybridization","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — clean genetic epistasis with multiple alleles, replicated across labs","pmids":["19223390"],"is_preprint":false},{"year":2001,"finding":"Tulp3 knockout in mice causes failure of neural tube closure and increased neuroepithelial apoptosis specifically in the hindbrain and caudal neural tube, demonstrating an essential role in neural development.","method":"Homologous recombination knockout in mouse, TUNEL apoptosis assay, immunohistochemistry","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 — clean germline KO with specific cellular phenotype, foundational paper","pmids":["11406614"],"is_preprint":false},{"year":2019,"finding":"TULP3 is required for ciliary trafficking of polycystin-1, polycystin-2, and Arl13b in kidney collecting duct cells without affecting ciliogenesis; nephron-specific Tulp3 knockout causes renal cystogenesis with increased MAPK/ERK, mTOR, and cAMP signaling.","method":"Conditional knockout mouse model, immunofluorescence, co-immunoprecipitation, signaling pathway analysis","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 — tissue-specific KO with defined molecular phenotype, independently replicated by two concurrent papers (PMIDs 30799239, 30799240)","pmids":["30799239","30799240"],"is_preprint":false},{"year":2019,"finding":"A hypomorphic missense mutation in the conserved Tubby domain of Tulp3 abolishes trafficking of Arl13b into kidney cilia without affecting ciliogenesis, causing renal cystic disease; simultaneous Tulp3 loss ameliorates cystic disease in adult inducible Pkd1 knockout mice.","method":"Forward genetic screen in mouse, conditional knockout, immunofluorescence, genetic interaction with Pkd1","journal":"Current biology : CB","confidence":"High","confidence_rationale":"Tier 2 — forward genetic screen plus conditional KO with defined ciliary trafficking phenotype","pmids":["30799240"],"is_preprint":false},{"year":2018,"finding":"TULP3 is required for localization of membrane-associated proteins ARL13B and INPP5E to primary cilia; a TULP3 mutant lacking IFT-A binding fails to rescue these defects in TULP3-KO cells, indicating IFT-A interaction is essential for this function.","method":"TULP3 knockout in hTERT RPE-1 cells by gene editing, immunofluorescence, rescue with wild-type vs. IFT-A-binding-deficient mutant TULP3","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 2 — KO plus structure-function mutagenesis rescue experiments with orthogonal readouts","pmids":["30583862"],"is_preprint":false},{"year":2023,"finding":"TULP3 transports the palmitoylated GTPase ARL13B into cilia via a ciliary localization sequence (CLS); an N-terminal amphipathic helix of ARL13B interacts with the TULP3 tubby domain for ciliary trafficking, independently of palmitoylation; this trafficking requires TULP3 binding to IFT-A but not to phosphoinositides.","method":"Mutational analysis of ARL13B and TULP3, co-immunoprecipitation, immunofluorescence in knockout cells, rescue experiments","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1-2 — structure-function mutagenesis combined with multiple biochemical and cell biological assays","pmids":["36652335"],"is_preprint":false},{"year":2024,"finding":"A specific surface region on one side of the TULP3 tubby domain β-barrel (overlooking β-strands 8–12), distinct from the phosphoinositide binding site, mediates ciliary trafficking of both lipidated and transmembrane cargoes and determines proximity to diverse cargoes in vivo without affecting TULP3 ciliary localization or phosphoinositide binding.","method":"Proximity biotinylation-mass spectrometry, structural analysis, mutagenesis, functional rescue in ciliary trafficking assays","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1 — proximity labeling MS combined with structural analysis and mutagenesis","pmids":["39565681"],"is_preprint":false},{"year":2024,"finding":"TULP3 is a direct receptor for lithocholic acid (LCA); LCA-bound TULP3 allosterically activates sirtuins (SIRT1), which then deacetylate the V1E1 subunit of v-ATPase, leading to AMPK activation through the lysosomal glucose-sensing pathway.","method":"Co-immunoprecipitation proteomics, biochemical binding assays, in vitro deacetylation assays, mutagenesis, in vivo mouse muscle-specific expression, genetic experiments in C. elegans (tub-1) and Drosophila (ktub)","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — multiple orthogonal methods including proteomics, biochemical assays, mutagenesis, and in vivo validation across species","pmids":["39695235"],"is_preprint":false},{"year":2022,"finding":"TULP3 interacts with the nuclear deacetylase SIRT1; patient-derived cells with TULP3 mutations show increased DNA damage, implicating the TULP3-SIRT1 interaction in DNA damage repair.","method":"Co-immunoprecipitation in primary cells from affected individuals, ex vivo DNA damage assays, transcriptomic analysis","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP with functional correlate in patient cells, single lab","pmids":["35397207"],"is_preprint":false},{"year":2022,"finding":"The TULP3 R382W patient missense variant within the Tubby domain severely reduces the ability to localize ARL13b, INPP5E, and GPR161 to the cilium, establishing Arg382 as a critical residue for TULP3-mediated phosphoinositide binding and ciliary protein trafficking.","method":"Expression of patient variant in IMCD-3 cells, immunofluorescence for ciliary cargo localization","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 2-3 — structure-function mutation in cellular assay, single lab, single paper","pmids":["36276950"],"is_preprint":false},{"year":2025,"finding":"TULP3 facilitates ACE2 localization to the primary cilium through physical association with ACE2; TULP3 depletion removes ACE2 from ciliary axonemes and impairs SARS-CoV-2 pseudovirus entry; ciliary localization of ACE2 is partially dependent on TULP3's IFT-A interaction.","method":"Co-immunoprecipitation, co-immunofluorescence/confocal microscopy, siRNA knockdown, IFT-A-binding-deficient TULP3 mutant rescue, pseudovirus infection assay","journal":"Cell communication and signaling : CCS","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus functional pseudovirus assay and mutagenesis, but single lab","pmids":["41316318"],"is_preprint":false},{"year":2024,"finding":"Both the N- and C-terminal domains of TULP3 are necessary for interaction with SIRT1 and SIRT2; TULP3 is not a deacetylation substrate for SIRT1.","method":"Biochemical and biophysical binding assays (in vitro interaction experiments with domain deletion constructs, in vitro deacetylation assay)","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — biochemical domain mapping with in vitro deacetylation assay, but preprint only","pmids":["bio_10.1101_2024.12.23.630205"],"is_preprint":true},{"year":2023,"finding":"TULP3 localizes to kinocilia of cochlear and vestibular hair cells during early postnatal development and subsequently redistributes to microtubule bundles in non-sensory Pillar and Deiters cells, suggesting distinct functional roles at different developmental stages.","method":"Immunofluorescence microscopy in mouse inner ear","journal":"Frontiers in neuroscience","confidence":"Low","confidence_rationale":"Tier 3 — localization data only, no direct functional consequence demonstrated","pmids":["37144094"],"is_preprint":false}],"current_model":"TULP3 is a ciliary trafficking adaptor that binds the IFT-A complex via its N-terminal region and membrane phosphoinositides via its C-terminal tubby domain β-barrel; together, a specific β-barrel surface region of the tubby domain captures diverse cargoes—including GPCRs, polycystins, ARL13B (via its amphipathic helix), INPP5E, and ACE2—for transport into primary cilia, thereby controlling Hedgehog signaling, renal cystic disease, and SARS-CoV-2 tropism; additionally, TULP3 functions outside cilia as a receptor for lithocholic acid that allosterically activates SIRT1 to deacetylate v-ATPase and activate AMPK, linking it to caloric-restriction-mimetic aging pathways."},"narrative":{"teleology":[{"year":2001,"claim":"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","pmids":["11406614"],"confidence":"High","gaps":["Molecular mechanism linking TULP3 loss to neuroepithelial apoptosis was unknown","No connection to cilia or signaling pathways had been made"]},{"year":2009,"claim":"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","pmids":["19286674","19223390","19334287"],"confidence":"High","gaps":["How TULP3 reached cilia and whether it trafficked other proteins was unknown","Whether TULP3 regulated Gli processing or just Gli activity was unclear"]},{"year":2010,"claim":"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","pmids":["20889716"],"confidence":"High","gaps":["Full cargo repertoire beyond a subset of GPCRs was undefined","Whether TULP3 directly contacts cargo or acts indirectly was unknown"]},{"year":2018,"claim":"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","pmids":["30583862"],"confidence":"High","gaps":["How TULP3 recognizes such structurally diverse cargoes was not resolved","Whether phosphoinositide binding was always required for all cargo classes was unclear"]},{"year":2019,"claim":"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","pmids":["30799239","30799240"],"confidence":"High","gaps":["Whether TULP3 dysfunction contributes to human polycystic kidney disease was untested","Relative contributions of individual mislocalized cargoes to cystogenesis were not separated"]},{"year":2022,"claim":"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","pmids":["35397207","36276950"],"confidence":"Medium","gaps":["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"]},{"year":2023,"claim":"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","pmids":["36652335"],"confidence":"High","gaps":["Whether other cargoes use analogous amphipathic helices for TULP3 recognition was untested","Structural basis of the ARL13B helix–tubby domain interface was not determined"]},{"year":2024,"claim":"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","pmids":["39565681"],"confidence":"High","gaps":["Atomic-resolution structure of cargo–tubby domain complexes is lacking","How cargo selectivity is achieved given a shared binding surface is unresolved"]},{"year":2024,"claim":"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)","pmids":["39695235"],"confidence":"High","gaps":["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"]},{"year":2025,"claim":"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","pmids":["41316318"],"confidence":"Medium","gaps":["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"]},{"year":null,"claim":"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.","evidence":"","pmids":[],"confidence":"High","gaps":["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"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,8,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,6,7,8]},{"term_id":"GO:0038024","term_label":"cargo receptor activity","supporting_discovery_ids":[0,7,8,12]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1,6,7,8]}],"pathway":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[0,1]}],"complexes":["IFT-A complex"],"partners":["IFT140","ARL13B","INPP5E","GPR161","SIRT1","PKD1","PKD2","ACE2"],"other_free_text":[]},"mechanistic_narrative":"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]."},"prefetch_data":{"uniprot":{"accession":"O75386","full_name":"Tubby-related protein 3","aliases":["Tubby-like protein 3"],"length_aa":442,"mass_kda":49.6,"function":"Negative regulator of the Shh signaling transduction pathway: recruited to primary cilia via association with the IFT complex A (IFT-A) and is required for recruitment of G protein-coupled receptor GPR161 to cilia, a promoter of PKA-dependent basal repression machinery in Shh signaling. Binds to phosphorylated inositide (phosphoinositide) lipids. Both IFT-A- and phosphoinositide-binding properties are required to regulate ciliary G protein-coupled receptor trafficking. During adipogenesis, regulates ciliary trafficking of FFAR4 in preadipocytes","subcellular_location":"Nucleus; Cell membrane; Cell projection, cilium; Cytoplasm; Secreted","url":"https://www.uniprot.org/uniprotkb/O75386/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TULP3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ANKRD54","stoichiometry":0.2},{"gene":"CTTN","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TULP3","total_profiled":1310},"omim":[{"mim_id":"619902","title":"HEPATORENOCARDIAC DEGENERATIVE FIBROSIS; HRCDF","url":"https://www.omim.org/entry/619902"},{"mim_id":"612250","title":"G PROTEIN-COUPLED RECEPTOR 161: GPR161","url":"https://www.omim.org/entry/612250"},{"mim_id":"604730","title":"TUB-LIKE PROTEIN 3; TULP3","url":"https://www.omim.org/entry/604730"},{"mim_id":"604114","title":"PHOSPHOLIPASE C, BETA-2; PLCB2","url":"https://www.omim.org/entry/604114"},{"mim_id":"601197","title":"TUB BIPARTITE TRANSCRIPTION FACTOR; TUB","url":"https://www.omim.org/entry/601197"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Primary cilium","reliability":"Supported"},{"location":"Nucleoli","reliability":"Additional"},{"location":"Plasma membrane","reliability":"Additional"},{"location":"Mitotic spindle","reliability":"Additional"},{"location":"Primary cilium transition zone","reliability":"Additional"},{"location":"Basal body","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TULP3"},"hgnc":{"alias_symbol":["TUBL3"],"prev_symbol":[]},"alphafold":{"accession":"O75386","domains":[{"cath_id":"3.20.90.10","chopping":"178-291_298-442","consensus_level":"medium","plddt":89.1896,"start":178,"end":442}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O75386","model_url":"https://alphafold.ebi.ac.uk/files/AF-O75386-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O75386-F1-predicted_aligned_error_v6.png","plddt_mean":72.25},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TULP3","jax_strain_url":"https://www.jax.org/strain/search?query=TULP3"},"sequence":{"accession":"O75386","fasta_url":"https://rest.uniprot.org/uniprotkb/O75386.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O75386/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O75386"}},"corpus_meta":[{"pmid":"20889716","id":"PMC_20889716","title":"TULP3 bridges the IFT-A complex and membrane phosphoinositides to promote trafficking of G protein-coupled receptors into primary cilia.","date":"2010","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/20889716","citation_count":358,"is_preprint":false},{"pmid":"19286674","id":"PMC_19286674","title":"Tubby-like protein 3 (TULP3) regulates patterning in the mouse embryo through inhibition of Hedgehog signaling.","date":"2009","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19286674","citation_count":96,"is_preprint":false},{"pmid":"19223390","id":"PMC_19223390","title":"Mouse hitchhiker mutants have spina bifida, dorso-ventral patterning defects and polydactyly: identification of Tulp3 as a novel negative regulator of the Sonic hedgehog pathway.","date":"2009","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/19223390","citation_count":78,"is_preprint":false},{"pmid":"11406614","id":"PMC_11406614","title":"Neural tube defects and neuroepithelial cell death in Tulp3 knockout mice.","date":"2001","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11406614","citation_count":63,"is_preprint":false},{"pmid":"9828123","id":"PMC_9828123","title":"Molecular characterization of a novel tubby gene family member, TULP3, in mouse and humans.","date":"1998","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/9828123","citation_count":59,"is_preprint":false},{"pmid":"30799240","id":"PMC_30799240","title":"Tulp3 Is a Ciliary Trafficking Gene that Regulates Polycystic Kidney Disease.","date":"2019","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/30799240","citation_count":57,"is_preprint":false},{"pmid":"30799239","id":"PMC_30799239","title":"Tulp3 Regulates Renal Cystogenesis by Trafficking of Cystoproteins to Cilia.","date":"2019","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/30799239","citation_count":52,"is_preprint":false},{"pmid":"39695235","id":"PMC_39695235","title":"Lithocholic acid binds TULP3 to activate sirtuins and AMPK to slow down ageing.","date":"2024","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/39695235","citation_count":51,"is_preprint":false},{"pmid":"30583862","id":"PMC_30583862","title":"TULP3 is required for localization of membrane-associated proteins ARL13B and INPP5E to primary cilia.","date":"2018","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/30583862","citation_count":51,"is_preprint":false},{"pmid":"19334287","id":"PMC_19334287","title":"Tulp3 is a critical repressor of mouse hedgehog signaling.","date":"2009","source":"Developmental dynamics : an official publication of the American Association of Anatomists","url":"https://pubmed.ncbi.nlm.nih.gov/19334287","citation_count":42,"is_preprint":false},{"pmid":"35397207","id":"PMC_35397207","title":"Progressive liver, kidney, and heart degeneration in children and adults affected by TULP3 mutations.","date":"2022","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35397207","citation_count":40,"is_preprint":false},{"pmid":"36652335","id":"PMC_36652335","title":"Interactions between TULP3 tubby domain and ARL13B amphipathic helix promote lipidated protein transport to cilia.","date":"2023","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/36652335","citation_count":32,"is_preprint":false},{"pmid":"31868202","id":"PMC_31868202","title":"STAT3-induced up-regulation of lncRNA NEAT1 as a ceRNA facilitates abdominal aortic aneurysm formation by elevating TULP3.","date":"2020","source":"Bioscience reports","url":"https://pubmed.ncbi.nlm.nih.gov/31868202","citation_count":31,"is_preprint":false},{"pmid":"36276950","id":"PMC_36276950","title":"A pathogenic variant of TULP3 causes renal and hepatic fibrocystic disease.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36276950","citation_count":13,"is_preprint":false},{"pmid":"30640939","id":"PMC_30640939","title":"TULP3: A potential biomarker in colorectal cancer?","date":"2019","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/30640939","citation_count":12,"is_preprint":false},{"pmid":"39565681","id":"PMC_39565681","title":"A defined tubby domain β-barrel surface region of TULP3 mediates ciliary trafficking of diverse cargoes.","date":"2024","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/39565681","citation_count":6,"is_preprint":false},{"pmid":"35344762","id":"PMC_35344762","title":"TULP3 silencing suppresses cell proliferation, migration and invasion in gastric cancer via the PTEN/Akt/Snail pathway.","date":"2022","source":"Cancer treatment and research communications","url":"https://pubmed.ncbi.nlm.nih.gov/35344762","citation_count":4,"is_preprint":false},{"pmid":"40282234","id":"PMC_40282234","title":"TULP3 Regulates Proliferation and Differentiation of 3T3-L1 Preadipocytes Through the Hedgehog Signaling Pathway.","date":"2025","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/40282234","citation_count":0,"is_preprint":false},{"pmid":"40579123","id":"PMC_40579123","title":"Biallelic pathogenic TULP3 variants presenting as neonatal cholestasis, liver fibrosis and neurological manifestations.","date":"2025","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40579123","citation_count":0,"is_preprint":false},{"pmid":"41316318","id":"PMC_41316318","title":"Primary cilium and TULP3-dependent ciliary targeting of ACE2 in SARS-CoV-2 tropism.","date":"2025","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/41316318","citation_count":0,"is_preprint":false},{"pmid":"37144094","id":"PMC_37144094","title":"Distribution of ciliary adaptor proteins tubby and TULP3 in the organ of Corti.","date":"2023","source":"Frontiers in neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/37144094","citation_count":0,"is_preprint":false},{"pmid":"41091799","id":"PMC_41091799","title":"Tulp3 quantitative alleles titrate requirements for viability, brain development, and kidney homeostasis but do not suppress Zfp423 mutations in mice.","date":"2025","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41091799","citation_count":0,"is_preprint":false},{"pmid":"41000950","id":"PMC_41000950","title":"Tulp3 quantitative alleles titrate requirements for viability, brain development, and kidney homeostasis but do not suppress Zfp423 mutations in mice.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/41000950","citation_count":0,"is_preprint":false},{"pmid":"40066670","id":"PMC_40066670","title":"Ciliopathy due to genetic alterations of TULP3 as an uncommon cause of hepatorenocardiac fibrosis.","date":"2025","source":"Revista espanola de enfermedades digestivas","url":"https://pubmed.ncbi.nlm.nih.gov/40066670","citation_count":0,"is_preprint":false},{"pmid":"40226390","id":"PMC_40226390","title":"Unearthing TULP3 Mutation as a Rare Cause of Cryptogenic Cirrhosis: A Case Report and Review of the Literature.","date":"2025","source":"Journal of clinical and experimental hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/40226390","citation_count":0,"is_preprint":false},{"pmid":"40940409","id":"PMC_40940409","title":"Tulp3 deficiency results in ciliopathy phenotypes during zebrafish embryogenesis.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/40940409","citation_count":0,"is_preprint":false},{"pmid":"35510584","id":"PMC_35510584","title":"TULP3 NLS inhibition: an in silico study to hamper cargo transport to nucleus.","date":"2022","source":"Journal of biomolecular structure & dynamics","url":"https://pubmed.ncbi.nlm.nih.gov/35510584","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.04.25.650726","title":"<i>Tulp3</i> quantitative alleles titrate requirements for viability, brain development, and kidney homeostasis but do not suppress <i>Zfp423</i> mutations in mice","date":"2025-04-29","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.25.650726","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.12.23.630205","title":"Deciphering the molecular mechanism associated with the interaction of TULP3 and Histone deacetylases, SIRT1 and SIRT2","date":"2024-12-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.23.630205","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":15204,"output_tokens":3408,"usd":0.048366},"stage2":{"model":"claude-opus-4-6","input_tokens":6859,"output_tokens":6043,"usd":0.278055},"total_usd":0.326421,"stage1_batch_id":"msgbatch_01RPbVc9PDH9zQmYK5Hs6srm","stage2_batch_id":"msgbatch_01JVbVLzeKN2yVrsGp3zC8aM","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"TULP3 directly binds to the IFT-A complex, and this interaction is required for ciliary entry of TULP3 itself and for trafficking of a subset of GPCRs (but not Smoothened) into primary cilia. Both IFT-A binding and phosphoinositide-binding properties of the TULP3 tubby domain are required for ciliary GPCR localization.\",\n      \"method\": \"Co-immunoprecipitation, phosphoinositide-binding assays, genetic epistasis in mouse embryo, loss-of-function ciliary trafficking assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — multiple orthogonal methods (Co-IP, lipid binding, mouse genetics, ciliary trafficking assays), foundational paper with 358 citations, replicated by subsequent studies\",\n      \"pmids\": [\"20889716\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"TULP3 acts as a negative regulator of Sonic Hedgehog (Shh) signaling downstream of Shh and Smoothened but upstream of Gli2, as established by genetic epistasis in mouse neural tube; TULP3 localizes to the tips of primary cilia.\",\n      \"method\": \"Genetic epistasis (Tulp3−/−, Tulp3−/−/Shh−/−, Tulp3−/−/Smo compound mutants), immunofluorescence localization\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — epistasis with multiple compound mutants, independently replicated by three labs in the same year (PMIDs 19286674, 19223390, 19334287)\",\n      \"pmids\": [\"19286674\", \"19223390\", \"19334287\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Tulp3 acts genetically downstream of Shh and Smo in neural tube patterning and exhibits a genetic interaction with Gli3 in limb development, without affecting Gli3 expression or processing.\",\n      \"method\": \"Genetic epistasis with Shh, Smo, and Gli3 mutants; immunofluorescence; in situ hybridization\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean genetic epistasis with multiple alleles, replicated across labs\",\n      \"pmids\": [\"19223390\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Tulp3 knockout in mice causes failure of neural tube closure and increased neuroepithelial apoptosis specifically in the hindbrain and caudal neural tube, demonstrating an essential role in neural development.\",\n      \"method\": \"Homologous recombination knockout in mouse, TUNEL apoptosis assay, immunohistochemistry\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean germline KO with specific cellular phenotype, foundational paper\",\n      \"pmids\": [\"11406614\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TULP3 is required for ciliary trafficking of polycystin-1, polycystin-2, and Arl13b in kidney collecting duct cells without affecting ciliogenesis; nephron-specific Tulp3 knockout causes renal cystogenesis with increased MAPK/ERK, mTOR, and cAMP signaling.\",\n      \"method\": \"Conditional knockout mouse model, immunofluorescence, co-immunoprecipitation, signaling pathway analysis\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — tissue-specific KO with defined molecular phenotype, independently replicated by two concurrent papers (PMIDs 30799239, 30799240)\",\n      \"pmids\": [\"30799239\", \"30799240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"A hypomorphic missense mutation in the conserved Tubby domain of Tulp3 abolishes trafficking of Arl13b into kidney cilia without affecting ciliogenesis, causing renal cystic disease; simultaneous Tulp3 loss ameliorates cystic disease in adult inducible Pkd1 knockout mice.\",\n      \"method\": \"Forward genetic screen in mouse, conditional knockout, immunofluorescence, genetic interaction with Pkd1\",\n      \"journal\": \"Current biology : CB\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — forward genetic screen plus conditional KO with defined ciliary trafficking phenotype\",\n      \"pmids\": [\"30799240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TULP3 is required for localization of membrane-associated proteins ARL13B and INPP5E to primary cilia; a TULP3 mutant lacking IFT-A binding fails to rescue these defects in TULP3-KO cells, indicating IFT-A interaction is essential for this function.\",\n      \"method\": \"TULP3 knockout in hTERT RPE-1 cells by gene editing, immunofluorescence, rescue with wild-type vs. IFT-A-binding-deficient mutant TULP3\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — KO plus structure-function mutagenesis rescue experiments with orthogonal readouts\",\n      \"pmids\": [\"30583862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TULP3 transports the palmitoylated GTPase ARL13B into cilia via a ciliary localization sequence (CLS); an N-terminal amphipathic helix of ARL13B interacts with the TULP3 tubby domain for ciliary trafficking, independently of palmitoylation; this trafficking requires TULP3 binding to IFT-A but not to phosphoinositides.\",\n      \"method\": \"Mutational analysis of ARL13B and TULP3, co-immunoprecipitation, immunofluorescence in knockout cells, rescue experiments\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — structure-function mutagenesis combined with multiple biochemical and cell biological assays\",\n      \"pmids\": [\"36652335\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"A specific surface region on one side of the TULP3 tubby domain β-barrel (overlooking β-strands 8–12), distinct from the phosphoinositide binding site, mediates ciliary trafficking of both lipidated and transmembrane cargoes and determines proximity to diverse cargoes in vivo without affecting TULP3 ciliary localization or phosphoinositide binding.\",\n      \"method\": \"Proximity biotinylation-mass spectrometry, structural analysis, mutagenesis, functional rescue in ciliary trafficking assays\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — proximity labeling MS combined with structural analysis and mutagenesis\",\n      \"pmids\": [\"39565681\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TULP3 is a direct receptor for lithocholic acid (LCA); LCA-bound TULP3 allosterically activates sirtuins (SIRT1), which then deacetylate the V1E1 subunit of v-ATPase, leading to AMPK activation through the lysosomal glucose-sensing pathway.\",\n      \"method\": \"Co-immunoprecipitation proteomics, biochemical binding assays, in vitro deacetylation assays, mutagenesis, in vivo mouse muscle-specific expression, genetic experiments in C. elegans (tub-1) and Drosophila (ktub)\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — multiple orthogonal methods including proteomics, biochemical assays, mutagenesis, and in vivo validation across species\",\n      \"pmids\": [\"39695235\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TULP3 interacts with the nuclear deacetylase SIRT1; patient-derived cells with TULP3 mutations show increased DNA damage, implicating the TULP3-SIRT1 interaction in DNA damage repair.\",\n      \"method\": \"Co-immunoprecipitation in primary cells from affected individuals, ex vivo DNA damage assays, transcriptomic analysis\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP with functional correlate in patient cells, single lab\",\n      \"pmids\": [\"35397207\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The TULP3 R382W patient missense variant within the Tubby domain severely reduces the ability to localize ARL13b, INPP5E, and GPR161 to the cilium, establishing Arg382 as a critical residue for TULP3-mediated phosphoinositide binding and ciliary protein trafficking.\",\n      \"method\": \"Expression of patient variant in IMCD-3 cells, immunofluorescence for ciliary cargo localization\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — structure-function mutation in cellular assay, single lab, single paper\",\n      \"pmids\": [\"36276950\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"TULP3 facilitates ACE2 localization to the primary cilium through physical association with ACE2; TULP3 depletion removes ACE2 from ciliary axonemes and impairs SARS-CoV-2 pseudovirus entry; ciliary localization of ACE2 is partially dependent on TULP3's IFT-A interaction.\",\n      \"method\": \"Co-immunoprecipitation, co-immunofluorescence/confocal microscopy, siRNA knockdown, IFT-A-binding-deficient TULP3 mutant rescue, pseudovirus infection assay\",\n      \"journal\": \"Cell communication and signaling : CCS\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus functional pseudovirus assay and mutagenesis, but single lab\",\n      \"pmids\": [\"41316318\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Both the N- and C-terminal domains of TULP3 are necessary for interaction with SIRT1 and SIRT2; TULP3 is not a deacetylation substrate for SIRT1.\",\n      \"method\": \"Biochemical and biophysical binding assays (in vitro interaction experiments with domain deletion constructs, in vitro deacetylation assay)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — biochemical domain mapping with in vitro deacetylation assay, but preprint only\",\n      \"pmids\": [\"bio_10.1101_2024.12.23.630205\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TULP3 localizes to kinocilia of cochlear and vestibular hair cells during early postnatal development and subsequently redistributes to microtubule bundles in non-sensory Pillar and Deiters cells, suggesting distinct functional roles at different developmental stages.\",\n      \"method\": \"Immunofluorescence microscopy in mouse inner ear\",\n      \"journal\": \"Frontiers in neuroscience\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — localization data only, no direct functional consequence demonstrated\",\n      \"pmids\": [\"37144094\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TULP3 is a ciliary trafficking adaptor that binds the IFT-A complex via its N-terminal region and membrane phosphoinositides via its C-terminal tubby domain β-barrel; together, a specific β-barrel surface region of the tubby domain captures diverse cargoes—including GPCRs, polycystins, ARL13B (via its amphipathic helix), INPP5E, and ACE2—for transport into primary cilia, thereby controlling Hedgehog signaling, renal cystic disease, and SARS-CoV-2 tropism; additionally, TULP3 functions outside cilia as a receptor for lithocholic acid that allosterically activates SIRT1 to deacetylate v-ATPase and activate AMPK, linking it to caloric-restriction-mimetic aging pathways.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"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].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"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.\",\n      \"evidence\": \"Germline knockout in mouse with TUNEL apoptosis and histological analysis\",\n      \"pmids\": [\"11406614\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism linking TULP3 loss to neuroepithelial apoptosis was unknown\",\n        \"No connection to cilia or signaling pathways had been made\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"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.\",\n      \"evidence\": \"Compound mutant analysis (Tulp3/Shh, Tulp3/Smo, Tulp3/Gli3) in mouse neural tube and limb, immunofluorescence\",\n      \"pmids\": [\"19286674\", \"19223390\", \"19334287\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TULP3 reached cilia and whether it trafficked other proteins was unknown\",\n        \"Whether TULP3 regulated Gli processing or just Gli activity was unclear\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"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.\",\n      \"evidence\": \"Co-immunoprecipitation, phosphoinositide-binding assays, domain mutagenesis, ciliary trafficking assays in mouse embryonic cells\",\n      \"pmids\": [\"20889716\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Full cargo repertoire beyond a subset of GPCRs was undefined\",\n        \"Whether TULP3 directly contacts cargo or acts indirectly was unknown\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"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.\",\n      \"evidence\": \"TULP3 knockout in hTERT RPE-1 cells, rescue with wild-type vs. IFT-A-binding-deficient mutant\",\n      \"pmids\": [\"30583862\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TULP3 recognizes such structurally diverse cargoes was not resolved\",\n        \"Whether phosphoinositide binding was always required for all cargo classes was unclear\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"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.\",\n      \"evidence\": \"Nephron-specific conditional knockout, forward genetic screen in mouse, genetic interaction with Pkd1\",\n      \"pmids\": [\"30799239\", \"30799240\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TULP3 dysfunction contributes to human polycystic kidney disease was untested\",\n        \"Relative contributions of individual mislocalized cargoes to cystogenesis were not separated\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"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.\",\n      \"evidence\": \"Patient-derived cell Co-IP, DNA damage assays, functional expression of R382W variant in IMCD-3 cells\",\n      \"pmids\": [\"35397207\", \"36276950\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The TULP3–SIRT1 interaction's mechanism and whether it is direct awaited biochemical dissection\",\n        \"Whether the DNA damage phenotype is a direct consequence of SIRT1 modulation or ciliary dysfunction was not distinguished\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"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.\",\n      \"evidence\": \"Mutational analysis of ARL13B and TULP3, Co-IP, rescue in knockout cells\",\n      \"pmids\": [\"36652335\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether other cargoes use analogous amphipathic helices for TULP3 recognition was untested\",\n        \"Structural basis of the ARL13B helix–tubby domain interface was not determined\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"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.\",\n      \"evidence\": \"Proximity biotinylation-mass spectrometry, structural analysis, mutagenesis, ciliary trafficking rescue assays\",\n      \"pmids\": [\"39565681\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic-resolution structure of cargo–tubby domain complexes is lacking\",\n        \"How cargo selectivity is achieved given a shared binding surface is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"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.\",\n      \"evidence\": \"Biochemical binding assays, in vitro deacetylation, proteomics, mouse muscle-specific expression, genetic experiments in C. elegans (tub-1) and Drosophila (ktub)\",\n      \"pmids\": [\"39695235\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TULP3's ciliary trafficking and SIRT1-activating functions are coordinated or segregated in the same cell is unknown\",\n        \"Whether other bile acids or endogenous ligands also bind TULP3 is untested\",\n        \"Structural basis of the LCA-TULP3-SIRT1 ternary complex is not resolved\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"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.\",\n      \"evidence\": \"Co-immunoprecipitation, confocal microscopy, siRNA knockdown, IFT-A-binding-deficient TULP3 mutant rescue, pseudovirus infection assay\",\n      \"pmids\": [\"41316318\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Relevance to authentic SARS-CoV-2 infection in vivo is not established\",\n        \"Whether ciliary versus apical membrane ACE2 is the relevant pool for viral entry is not distinguished\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"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.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No atomic-resolution structure of TULP3 in complex with any cargo or SIRT1 exists\",\n        \"Genotype-phenotype correlation for human TULP3 mutations across ciliary and metabolic phenotypes is incomplete\",\n        \"Whether TULP3-SIRT1-AMPK axis is druggable or relevant to human aging remains untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 8, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 6, 7, 8]},\n      {\"term_id\": \"GO:0038024\", \"supporting_discovery_ids\": [0, 7, 8, 12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 6, 7, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\n      \"IFT-A complex\"\n    ],\n    \"partners\": [\n      \"IFT140\",\n      \"ARL13B\",\n      \"INPP5E\",\n      \"GPR161\",\n      \"SIRT1\",\n      \"PKD1\",\n      \"PKD2\",\n      \"ACE2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\nWait, I need to correct the pathway entries. The pathway slot uses Reactome IDs, not GO IDs. Let me fix that.\n\n```json\n{\n  \"mechanistic_narrative\": \"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].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"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.\",\n      \"evidence\": \"Germline knockout in mouse with TUNEL apoptosis and histological analysis\",\n      \"pmids\": [\"11406614\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular mechanism linking TULP3 loss to neuroepithelial apoptosis was unknown\",\n        \"No connection to cilia or signaling pathways had been made\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"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.\",\n      \"evidence\": \"Compound mutant analysis (Tulp3/Shh, Tulp3/Smo, Tulp3/Gli3) in mouse neural tube and limb, immunofluorescence\",\n      \"pmids\": [\"19286674\", \"19223390\", \"19334287\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TULP3 reached cilia and whether it trafficked other proteins was unknown\",\n        \"Whether TULP3 regulated Gli processing or just Gli activity was unclear\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"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.\",\n      \"evidence\": \"Co-immunoprecipitation, phosphoinositide-binding assays, domain mutagenesis, ciliary trafficking assays in mouse embryonic cells\",\n      \"pmids\": [\"20889716\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Full cargo repertoire beyond a subset of GPCRs was undefined\",\n        \"Whether TULP3 directly contacts cargo or acts indirectly was unknown\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"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.\",\n      \"evidence\": \"TULP3 knockout in hTERT RPE-1 cells, rescue with wild-type vs. IFT-A-binding-deficient mutant\",\n      \"pmids\": [\"30583862\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TULP3 recognizes such structurally diverse cargoes was not resolved\",\n        \"Whether phosphoinositide binding was always required for all cargo classes was unclear\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"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.\",\n      \"evidence\": \"Nephron-specific conditional knockout, forward genetic screen in mouse, genetic interaction with Pkd1\",\n      \"pmids\": [\"30799239\", \"30799240\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether TULP3 dysfunction contributes to human polycystic kidney disease was untested\",\n        \"Relative contributions of individual mislocalized cargoes to cystogenesis were not separated\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"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.\",\n      \"evidence\": \"Patient-derived cell Co-IP, DNA damage assays, functional expression of R382W variant in IMCD-3 cells\",\n      \"pmids\": [\"35397207\", \"36276950\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The TULP3–SIRT1 interaction's mechanism and whether it is direct awaited biochemical dissection\",\n        \"Whether the DNA damage phenotype is a direct consequence of SIRT1 modulation or ciliary dysfunction was not distinguished\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"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.\",\n      \"evidence\": \"Mutational analysis of ARL13B and TULP3, Co-IP, rescue in knockout cells\",\n      \"pmids\": [\"36652335\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether other cargoes use analogous amphipathic helices for TULP3 recognition was untested\",\n        \"Structural basis of the ARL13B helix–tubby domain interface was not determined\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"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.\",\n      \"evidence\": \"Proximity biotinylation-mass spectrometry, structural analysis, mutagenesis, ciliary trafficking rescue assays\",\n      \"pmids\": [\"39565681\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Atomic-resolution structure of cargo–tubby domain complexes is lacking\",\n        \"How cargo selectivity is achieved given a shared binding surface is unresolved\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"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.\",\n      \"evidence\": \"Biochemical binding assays, in vitro deacetylation, proteomics, mouse muscle-specific expression, genetic experiments in C. elegans (tub-1) and Drosophila (ktub)\",\n      \"pmids\": [\"39695235\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How TULP3's ciliary trafficking and SIRT1-activating functions are coordinated or segregated in the same cell is unknown\",\n        \"Whether other bile acids or endogenous ligands also bind TULP3 is untested\",\n        \"Structural basis of the LCA-TULP3-SIRT1 ternary complex is not resolved\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"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.\",\n      \"evidence\": \"Co-immunoprecipitation, confocal microscopy, siRNA knockdown, IFT-A-binding-deficient TULP3 mutant rescue, pseudovirus infection assay\",\n      \"pmids\": [\"41316318\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Relevance to authentic SARS-CoV-2 infection in vivo is not established\",\n        \"Whether ciliary versus apical membrane ACE2 is the relevant pool for viral entry is not distinguished\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"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.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No atomic-resolution structure of TULP3 in complex with any cargo or SIRT1 exists\",\n        \"Genotype-phenotype correlation for human TULP3 mutations across ciliary and metabolic phenotypes is incomplete\",\n        \"Whether TULP3-SIRT1-AMPK axis is druggable or relevant to human aging remains untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 8, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 6, 7, 8]},\n      {\"term_id\": \"GO:0038024\", \"supporting_discovery_ids\": [0, 7, 8, 12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [0, 1, 6, 7, 8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 6, 7, 8, 12]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1, 2, 4, 9]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 2, 3]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 4, 6]}\n    ],\n    \"complexes\": [\n      \"IFT-A complex\"\n    ],\n    \"partners\": [\n      \"IFT140\",\n      \"ARL13B\",\n      \"INPP5E\",\n      \"GPR161\",\n      \"SIRT1\",\n      \"PKD1\",\n      \"PKD2\",\n      \"ACE2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}