{"gene":"IFT54","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":2000,"finding":"MIP-T3 (IFT54) binds to Taxol-stabilized microtubules and to tubulin in vitro, and recruits TRAF3 to microtubules when both proteins are overexpressed in HeLa cells. The MIP-T3–TRAF3 interaction requires the coiled-coil TRAF-N domain of TRAF3. Upon CD40 ligand stimulation, TRAF3 is released from the TRAF3·MIP-T3 complex and recruited to the CD40 receptor, suggesting MIP-T3 sequesters TRAF3 on the cytoskeletal network.","method":"In vitro microtubule-binding assay with Taxol-stabilized microtubules, co-immunoprecipitation, overexpression in HeLa and 293 cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro binding assay plus co-IP in cells, single lab, two orthogonal methods","pmids":["10791955"],"is_preprint":false},{"year":2003,"finding":"DISC1 interacts with MIPT3 (IFT54) via the central coiled-coil domain of DISC1; MIPT3 binds via its C-terminal domain. DISC1 associates with microtubules in a MIPT3-dependent fashion stabilized by taxol, indicating DISC1 itself does not bind microtubules directly but does so through IFT54/MIPT3.","method":"Yeast two-hybrid, mammalian two-hybrid, co-immunoprecipitation, deletion mapping, microtubule fractionation assay","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple interaction assays (Y2H, mammalian 2H, Co-IP) plus deletion mapping, single lab","pmids":["12812986"],"is_preprint":false},{"year":2003,"finding":"MIP-T3 (IFT54) constitutively associates with IL-13Rα1 and suppresses IL-4/IL-13-induced STAT6 phosphorylation and transcriptional activation, identified via yeast tri-hybrid screening.","method":"Yeast tri-hybrid screen, co-immunoprecipitation, dual luciferase assay, EMSA","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — interaction identified by Y3H with functional follow-up (STAT6 phosphorylation, reporter assay), single lab","pmids":["12935900"],"is_preprint":false},{"year":2008,"finding":"C. elegans DYF-11 (ortholog of MIP-T3/IFT54) is an IFT-B subcomplex component required for assembling functional kinesin motor–IFT particle complexes; loss of DYF-11 causes kinesin-II, IFT-A, and IFT-B proteins to fail to enter ciliary axonemes. Mammalian MIP-T3 localizes to basal bodies and cilia, and zebrafish mipt3 functions synergistically with Bbs4 in gastrulation.","method":"C. elegans genetics (loss-of-function mutant), fluorescence microscopy of IFT component localization, ciliary dye-filling assay, zebrafish morpholino knockdown epistasis with bbs4","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic loss-of-function in C. elegans with defined IFT assembly phenotype, localization in mammalian cells and zebrafish epistasis, replicated across two model systems","pmids":["18369462"],"is_preprint":false},{"year":2008,"finding":"C. elegans DYF-11 (IFT54 ortholog) localizes to cilia and moves anterogradely and retrogradely via IFT; movement analysis in bbs mutants indicates DYF-11 is associated with IFT complex B. The coiled-coil region of DYF-11 is required for proper cilia localization and ciliogenesis. Mammalian Traf3ip1/MIP-T3 localizes to cilia in MDCK renal epithelial cells.","method":"Fluorescence live imaging of GFP-tagged DYF-11 in C. elegans cilia, IFT velocity analysis, deletion construct domain analysis, double-mutant (bbs) epistasis, immunofluorescence in MDCK cells","journal":"Genes to cells","confidence":"High","confidence_rationale":"Tier 2 / Strong — live IFT movement imaging with domain mapping and genetic epistasis, independently consistent with PMID 18369462","pmids":["18173744"],"is_preprint":false},{"year":2010,"finding":"MIP-T3 (IFT54) interacts with actin, HSPA8, and tubulin in human embryonic kidney 293 cells, confirmed by reciprocal co-immunoprecipitation and colocalization; this suggests IFT54 may play a role in regulation of both actin filament and microtubule dynamics.","method":"Immunoprecipitation followed by mass spectrometry, reciprocal co-immunoprecipitation, colocalization microscopy","journal":"Proteomics","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reciprocal Co-IP confirms interaction with actin and tubulin, single lab, no direct functional assay","pmids":["20391533"],"is_preprint":false},{"year":2011,"finding":"MIP-T3 (IFT54) acts as a negative regulator of innate type I IFN production by interacting with TRAF3 and disrupting formation of TRAF3 complexes with VISA, TBK1, IKKε, and IRF3, thereby reducing IRF3 phosphorylation. MIP-T3 dissociates from TRAF3 during Sendai virus infection. Depletion of MIP-T3 enhances IFN production and reduces VSV replication.","method":"Overexpression/knockdown in cell lines, luciferase reporter assays (ISRE and IFN-β promoter), co-immunoprecipitation, IRF3 phosphorylation western blot, viral replication assay","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP of TRAF3 complexes plus loss-of-function (depletion) with functional readout (IRF3 phosphorylation, viral replication), single lab","pmids":["22079989"],"is_preprint":false},{"year":2011,"finding":"The C-terminus of MIP-T3 (IFT54) is required for its ubiquitination and proteasome-mediated degradation in human cells; deletion of the C-terminus stabilizes the protein.","method":"C-terminal deletion constructs expressed in human cell lines, proteasome inhibitor treatment, ubiquitination assay","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — domain deletion with proteasome inhibitor and ubiquitination assay, single lab, single study","pmids":["21510943"],"is_preprint":false},{"year":2015,"finding":"IFT54 (TRAF3IP1) is a subunit of the IFT-B complex required for ciliogenesis; patient-identified mutations cause mild ciliary defects. IFT54 also acts as a negative regulator of cytoplasmic microtubule stability via MAP4 (microtubule-associated protein 4). Loss of IFT54 leads to altered epithelialization/polarity in renal cells and pronephric cysts and microphthalmia in zebrafish.","method":"Patient mutation identification, zebrafish morpholino knockdown, renal cell knockdown with microtubule dynamics assay, MAP4 interaction analysis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — patient mutations linked to IFT-B complex defects, zebrafish loss-of-function with organogenesis phenotype, microtubule dynamics assay identifying MAP4 as effector, multiple orthogonal methods","pmids":["26487268"],"is_preprint":false},{"year":2017,"finding":"In Chlamydomonas, IFT54's N-terminal calponin homology (CH) domain is required for association with the axoneme and for regulating flagellar import of IFT54 itself (but not IFT81 or IFT46), while the C-terminal coiled-coil (CC) domain is essential for binding IFT20, for recruitment to the basal body, and for incorporation into IFT complexes. Loss of the CC domain (or complete loss of IFT54) destabilizes IFT20. The CH domain is dispensable for flagellar assembly. IFT54 also functions in IFT turnaround at the flagellar tip.","method":"Chlamydomonas ift54 null mutant rescue with domain deletion constructs, co-immunoprecipitation, immunofluorescence, IFT motility analysis","journal":"Cellular and molecular life sciences","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — domain-specific rescue in null mutant, co-IP of IFT20 interaction, multiple deletion constructs with defined phenotypes, single lab but multiple orthogonal methods","pmids":["28417161"],"is_preprint":false},{"year":2020,"finding":"IFT54 directly interacts with kinesin-II (anterograde motor) and IFT dynein subunit D1bLIC (retrograde motor) via distinct regions (residues 342–356 and 261–275, respectively). Deletion of residues 342–356 causes diminished anterograde IFT traffic and accumulation of IFT motors and complexes in the proximal cilium; this deletion also strengthens IFT54–kinesin-II interaction in vitro and in vivo. Deletion of residues 261–275 reduces ciliary entry and anterograde traffic of IFT dynein with tip accumulation of IFT complexes. These interactions were also observed in mammalian cells.","method":"Chlamydomonas deletion mutant analysis, in vitro pull-down assays, co-immunoprecipitation in Chlamydomonas and mammalian cells, quantitative IFT motility analysis by live imaging","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro direct interaction assays plus mutagenesis in Chlamydomonas null background, replicated in mammalian cells, quantitative IFT analysis, multiple orthogonal methods","pmids":["33368450"],"is_preprint":false}],"current_model":"IFT54 (MIP-T3/TRAF3IP1) is an IFT-B complex subunit whose C-terminal coiled-coil domain anchors IFT20 stability and basal-body recruitment while distinct central regions directly bind kinesin-II and IFT dynein subunit D1bLIC to coordinate anterograde intraflagellar transport; its N-terminal calponin homology domain associates with tubulin/microtubules and the axoneme; beyond the cilium, IFT54 negatively regulates cytoplasmic microtubule stability via MAP4 and sequesters TRAF3 on microtubules to suppress innate type I IFN signaling, with IFT54 protein stability itself controlled by C-terminus-dependent ubiquitin–proteasome degradation."},"narrative":{"mechanistic_narrative":"IFT54 (MIP-T3/TRAF3IP1) is a subunit of the intraflagellar transport B (IFT-B) complex that organizes anterograde and retrograde transport along the ciliary axoneme and is required for ciliogenesis [PMID:18369462, PMID:26487268]. Its modular architecture partitions these functions: the C-terminal coiled-coil domain mediates basal-body recruitment, incorporation into IFT complexes, and binding to IFT20, whose stability depends on this interaction, while the N-terminal calponin homology domain associates with the axoneme and microtubules and governs IFT54's own flagellar import [PMID:28417161]. Distinct central regions directly bind the anterograde motor kinesin-II (residues 342–356) and the retrograde IFT dynein subunit D1bLIC (residues 261–275), coordinating bidirectional motor traffic and IFT turnaround at the ciliary tip [PMID:28417161, PMID:33368450]. Loss of IFT54 disrupts entry of kinesin-II, IFT-A, and IFT-B components into the axoneme [PMID:18369462], and patient mutations produce ciliary defects with renal and ocular phenotypes [PMID:26487268]. Beyond the cilium, IFT54 binds tubulin and microtubules and negatively regulates cytoplasmic microtubule stability through MAP4 [PMID:10791955, PMID:26487268], and it sequesters TRAF3 on the cytoskeleton to suppress innate type I interferon signaling, releasing TRAF3 upon receptor or viral stimulation [PMID:10791955, PMID:22079989]. IFT54 protein abundance is itself controlled by C-terminus-dependent ubiquitin–proteasome degradation [PMID:21510943].","teleology":[{"year":2000,"claim":"Established IFT54/MIP-T3 as a microtubule- and tubulin-binding protein that physically tethers TRAF3 to the cytoskeleton, defining its first molecular activity before any ciliary role was known.","evidence":"In vitro microtubule-binding assay and co-immunoprecipitation in HeLa/293 cells","pmids":["10791955"],"confidence":"Medium","gaps":["Functional consequence of TRAF3 sequestration in signaling not yet defined","Binding mapped by overexpression rather than endogenous interaction"]},{"year":2003,"claim":"Showed IFT54 acts as an adaptor linking partner proteins to microtubules, recruiting DISC1 to the cytoskeleton it does not bind directly, broadening its scaffolding role.","evidence":"Yeast two-hybrid, mammalian two-hybrid, co-IP and deletion mapping with microtubule fractionation","pmids":["12812986"],"confidence":"Medium","gaps":["Physiological context of DISC1–IFT54 association unresolved","No in vivo phenotype tied to the interaction"]},{"year":2003,"claim":"Implicated IFT54 as a negative regulator of cytokine signaling by constitutively associating with IL-13Rα1 and dampening STAT6 activation.","evidence":"Yeast tri-hybrid screen, co-IP, luciferase reporter and EMSA","pmids":["12935900"],"confidence":"Medium","gaps":["Mechanism of STAT6 suppression not established","Single-lab functional readout"]},{"year":2008,"claim":"Reassigned IFT54 to the cilium by identifying its ortholog as an IFT-B subunit essential for assembling kinesin motor–IFT particle complexes and for ciliary entry of IFT machinery.","evidence":"C. elegans loss-of-function genetics, live IFT imaging with domain analysis, zebrafish bbs4 epistasis, MDCK localization","pmids":["18369462","18173744"],"confidence":"High","gaps":["Direct motor-binding regions not yet mapped","Mammalian ciliary function inferred from localization"]},{"year":2010,"claim":"Expanded the cytoskeletal interactome of IFT54 to include actin and the chaperone HSPA8 alongside tubulin, hinting at dual microtubule/actin regulation.","evidence":"IP-mass spectrometry and reciprocal co-IP with colocalization in 293 cells","pmids":["20391533"],"confidence":"Medium","gaps":["No functional assay linking IFT54 to actin dynamics","Interactions not validated in ciliated cells"]},{"year":2011,"claim":"Defined a mechanism for IFT54's interferon suppression: it disrupts assembly of TRAF3 with VISA, TBK1, IKKε and IRF3, and dissociates upon viral infection to permit IRF3 activation.","evidence":"Overexpression/knockdown, luciferase reporters, co-IP of TRAF3 complexes, IRF3 phosphorylation blots and viral replication assay","pmids":["22079989"],"confidence":"Medium","gaps":["Whether microtubule tethering is required for IFN suppression unresolved","Single-lab functional study"]},{"year":2011,"claim":"Identified the C-terminus as the determinant of IFT54's own turnover, establishing ubiquitin–proteasome control of its abundance.","evidence":"C-terminal deletion constructs, proteasome inhibitor treatment and ubiquitination assay in human cells","pmids":["21510943"],"confidence":"Medium","gaps":["Responsible E3 ligase not identified","Degron sequence not mapped"]},{"year":2015,"claim":"Linked IFT54 to human ciliopathy and uncovered a non-ciliary role: it destabilizes cytoplasmic microtubules via MAP4 and is required for renal epithelial polarity.","evidence":"Patient mutation identification, zebrafish knockdown with organogenesis phenotypes, renal cell microtubule dynamics assay and MAP4 interaction analysis","pmids":["26487268"],"confidence":"High","gaps":["How MAP4 effector activity is regulated unresolved","Genotype–phenotype relationship of patient mutations incomplete"]},{"year":2017,"claim":"Dissected the domain architecture: the C-terminal coiled-coil drives basal-body recruitment, IFT incorporation and IFT20 stabilization, while the N-terminal CH domain controls axonemal association and IFT54 self-import but is dispensable for assembly.","evidence":"Chlamydomonas ift54 null rescue with domain-deletion constructs, co-IP, immunofluorescence and IFT motility analysis","pmids":["28417161"],"confidence":"High","gaps":["Molecular basis of CH-domain–dependent import unclear","Role in tip turnaround mechanistically undefined"]},{"year":2020,"claim":"Resolved how a single IFT-B subunit coordinates both motors, showing IFT54 directly binds kinesin-II and IFT dynein D1bLIC through distinct short regions that balance anterograde and retrograde traffic.","evidence":"Chlamydomonas deletion mutagenesis in null background, in vitro pull-downs, co-IP in Chlamydomonas and mammalian cells, quantitative live IFT imaging","pmids":["33368450"],"confidence":"High","gaps":["Structural basis of dual motor binding not determined","Regulation switching between motor interactions unknown"]},{"year":null,"claim":"How IFT54's ciliary transport function is mechanistically coupled to its cytoplasmic microtubule and innate-immune roles remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model integrating motor- and IFT20-binding regions","Identity of the E3 ligase controlling IFT54 turnover unknown","Whether non-ciliary TRAF3/MAP4 roles share the cilium-relevant binding surfaces is untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,5,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,9,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[6,8]}],"localization":[{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[3,4,8]},{"term_id":"GO:0005815","term_label":"microtubule organizing center","supporting_discovery_ids":[3,9]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,9]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,6]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3,8,9]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[3,10]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[6]}],"complexes":["IFT-B complex"],"partners":["IFT20","TRAF3","MAP4","DISC1","IL13RA1","HSPA8","D1BLIC"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8TDR0","full_name":"TRAF3-interacting protein 1","aliases":["Interleukin-13 receptor alpha 1-binding protein 1","Intraflagellar transport protein 54 homolog","Microtubule-interacting protein associated with TRAF3","MIP-T3"],"length_aa":691,"mass_kda":78.6,"function":"Plays an inhibitory role on IL13 signaling by binding to IL13RA1. Involved in suppression of IL13-induced STAT6 phosphorylation, transcriptional activity and DNA-binding. Recruits TRAF3 and DISC1 to the microtubules. Involved in kidney development and epithelial morphogenesis. Involved in the regulation of microtubule cytoskeleton organization. Is a negative regulator of microtubule stability, acting through the control of MAP4 levels (PubMed:26487268). Involved in ciliogenesis (By similarity)","subcellular_location":"Cytoplasm, cytoskeleton; Cell projection, cilium; Cytoplasm, cytoskeleton, cilium axoneme; Cytoplasm, cytoskeleton, cilium basal body","url":"https://www.uniprot.org/uniprotkb/Q8TDR0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"TRAF3IP1","url":"https://depmap.org/portal/gene/TRAF3IP1","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":"HSPB11","stoichiometry":4.0}],"url":"https://opencell.sf.czbiohub.org/search/IFT54","total_profiled":1310},"omim":[{"mim_id":"616629","title":"SENIOR-LOKEN SYNDROME 9; SLSN9","url":"https://www.omim.org/entry/616629"},{"mim_id":"607380","title":"TNF RECEPTOR-ASSOCIATED FACTOR 3-INTERACTING PROTEIN 1; TRAF3IP1","url":"https://www.omim.org/entry/607380"}],"hpa":{"profiled":true,"resolved_as":"TRAF3IP1","reliability":"Approved","locations":[{"location":"Nuclear bodies","reliability":"Approved"},{"location":"Primary cilium transition zone","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Nucleoli fibrillar center","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRAF3IP1"},"hgnc":{"alias_symbol":["MIP-T3","DKFZP434F124","MIPT3","FAP116","CFAP116"],"prev_symbol":["TRAF3IP1"]},"alphafold":{"accession":"Q8TDR0","domains":[{"cath_id":"1.10.418.50","chopping":"4-131","consensus_level":"high","plddt":92.1625,"start":4,"end":131}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TDR0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TDR0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8TDR0-F1-predicted_aligned_error_v6.png","plddt_mean":61.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=IFT54","jax_strain_url":"https://www.jax.org/strain/search?query=IFT54"},"sequence":{"accession":"Q8TDR0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8TDR0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8TDR0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8TDR0"}},"corpus_meta":[{"pmid":"12812986","id":"PMC_12812986","title":"DISC1 (Disrupted-In-Schizophrenia 1) is a centrosome-associated protein that interacts with MAP1A, MIPT3, ATF4/5 and NUDEL: regulation and loss of interaction with mutation.","date":"2003","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12812986","citation_count":314,"is_preprint":false},{"pmid":"26487268","id":"PMC_26487268","title":"Mutations in TRAF3IP1/IFT54 reveal a new role for IFT proteins in microtubule stabilization.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/26487268","citation_count":85,"is_preprint":false},{"pmid":"10791955","id":"PMC_10791955","title":"MIP-T3, a novel protein linking tumor necrosis factor receptor-associated factor 3 to the microtubule network.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10791955","citation_count":57,"is_preprint":false},{"pmid":"18369462","id":"PMC_18369462","title":"An essential role for DYF-11/MIP-T3 in assembling functional intraflagellar transport complexes.","date":"2008","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/18369462","citation_count":48,"is_preprint":false},{"pmid":"22079989","id":"PMC_22079989","title":"MIP-T3 is a negative regulator of innate type I IFN response.","date":"2011","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/22079989","citation_count":41,"is_preprint":false},{"pmid":"18173744","id":"PMC_18173744","title":"Caenorhabditis elegans DYF-11, an orthologue of mammalian Traf3ip1/MIP-T3, is required for sensory cilia formation.","date":"2008","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/18173744","citation_count":40,"is_preprint":false},{"pmid":"28417161","id":"PMC_28417161","title":"IFT54 regulates IFT20 stability but is not essential for tubulin transport during ciliogenesis.","date":"2017","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/28417161","citation_count":35,"is_preprint":false},{"pmid":"33368450","id":"PMC_33368450","title":"IFT54 directly interacts with kinesin-II and IFT dynein to regulate anterograde intraflagellar transport.","date":"2020","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/33368450","citation_count":33,"is_preprint":false},{"pmid":"12935900","id":"PMC_12935900","title":"MIP-T3 associates with IL-13Ralpha1 and suppresses STAT6 activation in response to IL-13 stimulation.","date":"2003","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/12935900","citation_count":16,"is_preprint":false},{"pmid":"20391533","id":"PMC_20391533","title":"Proteomic analysis reveals novel binding partners of MIP-T3 in human cells.","date":"2010","source":"Proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/20391533","citation_count":14,"is_preprint":false},{"pmid":"35697271","id":"PMC_35697271","title":"The MIP-T3 from shrimp Litopenaeus vannamei restricts white spot syndrome virus infection via regulating NF-κB activation.","date":"2022","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/35697271","citation_count":6,"is_preprint":false},{"pmid":"21510943","id":"PMC_21510943","title":"The C-terminus of MIP-T3 protein is required for ubiquitin-proteasome-mediated degradation in human cells.","date":"2011","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/21510943","citation_count":4,"is_preprint":false},{"pmid":"32104517","id":"PMC_32104517","title":"MIP-T3 Expression Associated with Defects of Ciliogenesis in Airway of COPD Patients.","date":"2020","source":"Canadian respiratory journal","url":"https://pubmed.ncbi.nlm.nih.gov/32104517","citation_count":2,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.01.15.633139","title":"Evaluation of Prostaglandin Receptor Agonists and Eupatilin in the Context of Nephronophthisis","date":"2025-01-15","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.15.633139","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8842,"output_tokens":3237,"usd":0.03754,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10575,"output_tokens":3462,"usd":0.069712,"stage2_stop_reason":"end_turn"},"total_usd":0.107252,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"MIP-T3 (IFT54) binds to Taxol-stabilized microtubules and to tubulin in vitro, and recruits TRAF3 to microtubules when both proteins are overexpressed in HeLa cells. The MIP-T3–TRAF3 interaction requires the coiled-coil TRAF-N domain of TRAF3. Upon CD40 ligand stimulation, TRAF3 is released from the TRAF3·MIP-T3 complex and recruited to the CD40 receptor, suggesting MIP-T3 sequesters TRAF3 on the cytoskeletal network.\",\n      \"method\": \"In vitro microtubule-binding assay with Taxol-stabilized microtubules, co-immunoprecipitation, overexpression in HeLa and 293 cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro binding assay plus co-IP in cells, single lab, two orthogonal methods\",\n      \"pmids\": [\"10791955\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"DISC1 interacts with MIPT3 (IFT54) via the central coiled-coil domain of DISC1; MIPT3 binds via its C-terminal domain. DISC1 associates with microtubules in a MIPT3-dependent fashion stabilized by taxol, indicating DISC1 itself does not bind microtubules directly but does so through IFT54/MIPT3.\",\n      \"method\": \"Yeast two-hybrid, mammalian two-hybrid, co-immunoprecipitation, deletion mapping, microtubule fractionation assay\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple interaction assays (Y2H, mammalian 2H, Co-IP) plus deletion mapping, single lab\",\n      \"pmids\": [\"12812986\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"MIP-T3 (IFT54) constitutively associates with IL-13Rα1 and suppresses IL-4/IL-13-induced STAT6 phosphorylation and transcriptional activation, identified via yeast tri-hybrid screening.\",\n      \"method\": \"Yeast tri-hybrid screen, co-immunoprecipitation, dual luciferase assay, EMSA\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — interaction identified by Y3H with functional follow-up (STAT6 phosphorylation, reporter assay), single lab\",\n      \"pmids\": [\"12935900\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"C. elegans DYF-11 (ortholog of MIP-T3/IFT54) is an IFT-B subcomplex component required for assembling functional kinesin motor–IFT particle complexes; loss of DYF-11 causes kinesin-II, IFT-A, and IFT-B proteins to fail to enter ciliary axonemes. Mammalian MIP-T3 localizes to basal bodies and cilia, and zebrafish mipt3 functions synergistically with Bbs4 in gastrulation.\",\n      \"method\": \"C. elegans genetics (loss-of-function mutant), fluorescence microscopy of IFT component localization, ciliary dye-filling assay, zebrafish morpholino knockdown epistasis with bbs4\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic loss-of-function in C. elegans with defined IFT assembly phenotype, localization in mammalian cells and zebrafish epistasis, replicated across two model systems\",\n      \"pmids\": [\"18369462\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"C. elegans DYF-11 (IFT54 ortholog) localizes to cilia and moves anterogradely and retrogradely via IFT; movement analysis in bbs mutants indicates DYF-11 is associated with IFT complex B. The coiled-coil region of DYF-11 is required for proper cilia localization and ciliogenesis. Mammalian Traf3ip1/MIP-T3 localizes to cilia in MDCK renal epithelial cells.\",\n      \"method\": \"Fluorescence live imaging of GFP-tagged DYF-11 in C. elegans cilia, IFT velocity analysis, deletion construct domain analysis, double-mutant (bbs) epistasis, immunofluorescence in MDCK cells\",\n      \"journal\": \"Genes to cells\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — live IFT movement imaging with domain mapping and genetic epistasis, independently consistent with PMID 18369462\",\n      \"pmids\": [\"18173744\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"MIP-T3 (IFT54) interacts with actin, HSPA8, and tubulin in human embryonic kidney 293 cells, confirmed by reciprocal co-immunoprecipitation and colocalization; this suggests IFT54 may play a role in regulation of both actin filament and microtubule dynamics.\",\n      \"method\": \"Immunoprecipitation followed by mass spectrometry, reciprocal co-immunoprecipitation, colocalization microscopy\",\n      \"journal\": \"Proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reciprocal Co-IP confirms interaction with actin and tubulin, single lab, no direct functional assay\",\n      \"pmids\": [\"20391533\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"MIP-T3 (IFT54) acts as a negative regulator of innate type I IFN production by interacting with TRAF3 and disrupting formation of TRAF3 complexes with VISA, TBK1, IKKε, and IRF3, thereby reducing IRF3 phosphorylation. MIP-T3 dissociates from TRAF3 during Sendai virus infection. Depletion of MIP-T3 enhances IFN production and reduces VSV replication.\",\n      \"method\": \"Overexpression/knockdown in cell lines, luciferase reporter assays (ISRE and IFN-β promoter), co-immunoprecipitation, IRF3 phosphorylation western blot, viral replication assay\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP of TRAF3 complexes plus loss-of-function (depletion) with functional readout (IRF3 phosphorylation, viral replication), single lab\",\n      \"pmids\": [\"22079989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"The C-terminus of MIP-T3 (IFT54) is required for its ubiquitination and proteasome-mediated degradation in human cells; deletion of the C-terminus stabilizes the protein.\",\n      \"method\": \"C-terminal deletion constructs expressed in human cell lines, proteasome inhibitor treatment, ubiquitination assay\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — domain deletion with proteasome inhibitor and ubiquitination assay, single lab, single study\",\n      \"pmids\": [\"21510943\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"IFT54 (TRAF3IP1) is a subunit of the IFT-B complex required for ciliogenesis; patient-identified mutations cause mild ciliary defects. IFT54 also acts as a negative regulator of cytoplasmic microtubule stability via MAP4 (microtubule-associated protein 4). Loss of IFT54 leads to altered epithelialization/polarity in renal cells and pronephric cysts and microphthalmia in zebrafish.\",\n      \"method\": \"Patient mutation identification, zebrafish morpholino knockdown, renal cell knockdown with microtubule dynamics assay, MAP4 interaction analysis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — patient mutations linked to IFT-B complex defects, zebrafish loss-of-function with organogenesis phenotype, microtubule dynamics assay identifying MAP4 as effector, multiple orthogonal methods\",\n      \"pmids\": [\"26487268\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"In Chlamydomonas, IFT54's N-terminal calponin homology (CH) domain is required for association with the axoneme and for regulating flagellar import of IFT54 itself (but not IFT81 or IFT46), while the C-terminal coiled-coil (CC) domain is essential for binding IFT20, for recruitment to the basal body, and for incorporation into IFT complexes. Loss of the CC domain (or complete loss of IFT54) destabilizes IFT20. The CH domain is dispensable for flagellar assembly. IFT54 also functions in IFT turnaround at the flagellar tip.\",\n      \"method\": \"Chlamydomonas ift54 null mutant rescue with domain deletion constructs, co-immunoprecipitation, immunofluorescence, IFT motility analysis\",\n      \"journal\": \"Cellular and molecular life sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — domain-specific rescue in null mutant, co-IP of IFT20 interaction, multiple deletion constructs with defined phenotypes, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"28417161\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"IFT54 directly interacts with kinesin-II (anterograde motor) and IFT dynein subunit D1bLIC (retrograde motor) via distinct regions (residues 342–356 and 261–275, respectively). Deletion of residues 342–356 causes diminished anterograde IFT traffic and accumulation of IFT motors and complexes in the proximal cilium; this deletion also strengthens IFT54–kinesin-II interaction in vitro and in vivo. Deletion of residues 261–275 reduces ciliary entry and anterograde traffic of IFT dynein with tip accumulation of IFT complexes. These interactions were also observed in mammalian cells.\",\n      \"method\": \"Chlamydomonas deletion mutant analysis, in vitro pull-down assays, co-immunoprecipitation in Chlamydomonas and mammalian cells, quantitative IFT motility analysis by live imaging\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro direct interaction assays plus mutagenesis in Chlamydomonas null background, replicated in mammalian cells, quantitative IFT analysis, multiple orthogonal methods\",\n      \"pmids\": [\"33368450\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"IFT54 (MIP-T3/TRAF3IP1) is an IFT-B complex subunit whose C-terminal coiled-coil domain anchors IFT20 stability and basal-body recruitment while distinct central regions directly bind kinesin-II and IFT dynein subunit D1bLIC to coordinate anterograde intraflagellar transport; its N-terminal calponin homology domain associates with tubulin/microtubules and the axoneme; beyond the cilium, IFT54 negatively regulates cytoplasmic microtubule stability via MAP4 and sequesters TRAF3 on microtubules to suppress innate type I IFN signaling, with IFT54 protein stability itself controlled by C-terminus-dependent ubiquitin–proteasome degradation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"IFT54 (MIP-T3/TRAF3IP1) is a subunit of the intraflagellar transport B (IFT-B) complex that organizes anterograde and retrograde transport along the ciliary axoneme and is required for ciliogenesis [#3, #8]. Its modular architecture partitions these functions: the C-terminal coiled-coil domain mediates basal-body recruitment, incorporation into IFT complexes, and binding to IFT20, whose stability depends on this interaction, while the N-terminal calponin homology domain associates with the axoneme and microtubules and governs IFT54's own flagellar import [#9]. Distinct central regions directly bind the anterograde motor kinesin-II (residues 342–356) and the retrograde IFT dynein subunit D1bLIC (residues 261–275), coordinating bidirectional motor traffic and IFT turnaround at the ciliary tip [#9, #10]. Loss of IFT54 disrupts entry of kinesin-II, IFT-A, and IFT-B components into the axoneme [#3], and patient mutations produce ciliary defects with renal and ocular phenotypes [#8]. Beyond the cilium, IFT54 binds tubulin and microtubules and negatively regulates cytoplasmic microtubule stability through MAP4 [#0, #8], and it sequesters TRAF3 on the cytoskeleton to suppress innate type I interferon signaling, releasing TRAF3 upon receptor or viral stimulation [#0, #6]. IFT54 protein abundance is itself controlled by C-terminus-dependent ubiquitin–proteasome degradation [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established IFT54/MIP-T3 as a microtubule- and tubulin-binding protein that physically tethers TRAF3 to the cytoskeleton, defining its first molecular activity before any ciliary role was known.\",\n      \"evidence\": \"In vitro microtubule-binding assay and co-immunoprecipitation in HeLa/293 cells\",\n      \"pmids\": [\"10791955\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of TRAF3 sequestration in signaling not yet defined\", \"Binding mapped by overexpression rather than endogenous interaction\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Showed IFT54 acts as an adaptor linking partner proteins to microtubules, recruiting DISC1 to the cytoskeleton it does not bind directly, broadening its scaffolding role.\",\n      \"evidence\": \"Yeast two-hybrid, mammalian two-hybrid, co-IP and deletion mapping with microtubule fractionation\",\n      \"pmids\": [\"12812986\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological context of DISC1–IFT54 association unresolved\", \"No in vivo phenotype tied to the interaction\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Implicated IFT54 as a negative regulator of cytokine signaling by constitutively associating with IL-13Rα1 and dampening STAT6 activation.\",\n      \"evidence\": \"Yeast tri-hybrid screen, co-IP, luciferase reporter and EMSA\",\n      \"pmids\": [\"12935900\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of STAT6 suppression not established\", \"Single-lab functional readout\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Reassigned IFT54 to the cilium by identifying its ortholog as an IFT-B subunit essential for assembling kinesin motor–IFT particle complexes and for ciliary entry of IFT machinery.\",\n      \"evidence\": \"C. elegans loss-of-function genetics, live IFT imaging with domain analysis, zebrafish bbs4 epistasis, MDCK localization\",\n      \"pmids\": [\"18369462\", \"18173744\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct motor-binding regions not yet mapped\", \"Mammalian ciliary function inferred from localization\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Expanded the cytoskeletal interactome of IFT54 to include actin and the chaperone HSPA8 alongside tubulin, hinting at dual microtubule/actin regulation.\",\n      \"evidence\": \"IP-mass spectrometry and reciprocal co-IP with colocalization in 293 cells\",\n      \"pmids\": [\"20391533\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No functional assay linking IFT54 to actin dynamics\", \"Interactions not validated in ciliated cells\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Defined a mechanism for IFT54's interferon suppression: it disrupts assembly of TRAF3 with VISA, TBK1, IKKε and IRF3, and dissociates upon viral infection to permit IRF3 activation.\",\n      \"evidence\": \"Overexpression/knockdown, luciferase reporters, co-IP of TRAF3 complexes, IRF3 phosphorylation blots and viral replication assay\",\n      \"pmids\": [\"22079989\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether microtubule tethering is required for IFN suppression unresolved\", \"Single-lab functional study\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified the C-terminus as the determinant of IFT54's own turnover, establishing ubiquitin–proteasome control of its abundance.\",\n      \"evidence\": \"C-terminal deletion constructs, proteasome inhibitor treatment and ubiquitination assay in human cells\",\n      \"pmids\": [\"21510943\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Responsible E3 ligase not identified\", \"Degron sequence not mapped\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Linked IFT54 to human ciliopathy and uncovered a non-ciliary role: it destabilizes cytoplasmic microtubules via MAP4 and is required for renal epithelial polarity.\",\n      \"evidence\": \"Patient mutation identification, zebrafish knockdown with organogenesis phenotypes, renal cell microtubule dynamics assay and MAP4 interaction analysis\",\n      \"pmids\": [\"26487268\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How MAP4 effector activity is regulated unresolved\", \"Genotype–phenotype relationship of patient mutations incomplete\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Dissected the domain architecture: the C-terminal coiled-coil drives basal-body recruitment, IFT incorporation and IFT20 stabilization, while the N-terminal CH domain controls axonemal association and IFT54 self-import but is dispensable for assembly.\",\n      \"evidence\": \"Chlamydomonas ift54 null rescue with domain-deletion constructs, co-IP, immunofluorescence and IFT motility analysis\",\n      \"pmids\": [\"28417161\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of CH-domain–dependent import unclear\", \"Role in tip turnaround mechanistically undefined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Resolved how a single IFT-B subunit coordinates both motors, showing IFT54 directly binds kinesin-II and IFT dynein D1bLIC through distinct short regions that balance anterograde and retrograde traffic.\",\n      \"evidence\": \"Chlamydomonas deletion mutagenesis in null background, in vitro pull-downs, co-IP in Chlamydomonas and mammalian cells, quantitative live IFT imaging\",\n      \"pmids\": [\"33368450\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of dual motor binding not determined\", \"Regulation switching between motor interactions unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How IFT54's ciliary transport function is mechanistically coupled to its cytoplasmic microtubule and innate-immune roles remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model integrating motor- and IFT20-binding regions\", \"Identity of the E3 ligase controlling IFT54 turnover unknown\", \"Whether non-ciliary TRAF3/MAP4 roles share the cilium-relevant binding surfaces is untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 5, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 9, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [6, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [3, 4, 8]},\n      {\"term_id\": \"GO:0005815\", \"supporting_discovery_ids\": [3, 9]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3, 8, 9]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [3, 10]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"IFT-B complex\"],\n    \"partners\": [\"IFT20\", \"TRAF3\", \"MAP4\", \"DISC1\", \"IL13RA1\", \"HSPA8\", \"D1bLIC\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}