{"gene":"RIOK3","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":2010,"finding":"Riok3 is required for erythroblast chromatin condensation and enucleation; knockdown of Riok3 blocks both chromatin condensation and enucleation in terminal erythroid differentiation, and Riok3 mRNA is a direct target repressed by miR-191.","method":"RNA interference (Riok3 knockdown), miR-191 overexpression, erythroblast differentiation assays; miR-191 target site validation","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal loss-of-function approaches with specific phenotypic readout, replicated across miR-191 OE and direct Riok3 KD","pmids":["21196494"],"is_preprint":false},{"year":2012,"finding":"Human RioK3 is a cytoplasmic protein that associates with pre-40S ribosomal particles, co-sediments with 40S particles in sucrose gradients, interacts with pre-40S components hLtv1 and hEnp1 and with 18S-E pre-rRNA, and its depletion causes accumulation of 21S pre-rRNA, indicating a role in cytoplasmic 18S-E pre-rRNA processing.","method":"Sucrose gradient sedimentation, co-immunoprecipitation with hLtv1/hEnp1, Northern blot for pre-rRNA intermediates, siRNA knockdown","journal":"RNA biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (sedimentation, Co-IP, Northern blot) in a single study with functional readout","pmids":["22418843"],"is_preprint":false},{"year":2014,"finding":"RIOK3 acts as an adaptor protein downstream of TBK1 and upstream of IRF3 in the cytosolic nucleic acid-sensing pathway; RIOK3 physically interacts with both TBK1 and IRF3 and is required for the TBK1–IRF3 interaction, leading to IRF3 activation and IFN-β production.","method":"Kinome-wide RNAi screens, co-immunoprecipitation (RIOK3–TBK1, RIOK3–IRF3), RIOK3 overexpression/knockdown with IRF3 phosphorylation and IFN-β reporter assays, transcriptome analysis","journal":"Journal of virology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP for both interactors, epistasis established by bridging requirement, replicated with genome-wide screens","pmids":["24807708"],"is_preprint":false},{"year":2014,"finding":"RIOK3 expression is induced by hypoxia in an HIF1α-dependent manner; under hypoxia, RIOK3 redistributes from cytoplasmic aggregates to the leading edge of the cell with reorganization of the actin cytoskeleton. RIOK3 interacts with actin and actin-binding proteins tropomyosins (TPM3, TPM4) and tropomodulin 3, and is required for actin filament organization and TPM3 association with filaments, thereby driving cell migration and invasion.","method":"HIF1α-dependent reporter assays, siRNA knockdown with live-cell imaging and morphology analysis, proteomics (Co-IP/MS for interactors), wound-healing and 3D invasion assays, zebrafish and mouse metastasis models, immunofluorescence for actin/TPM3","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (proteomics, imaging, KD with in vivo models), strong mechanistic evidence across cell and animal models","pmids":["25486436"],"is_preprint":false},{"year":2015,"finding":"RIOK3 is a protein kinase that phosphorylates the C-terminal region of MDA5 (at S828), impairing MDA5 multimer/filament formation on dsRNA and thereby attenuating MDA5-mediated type I IFN signaling. RIOK3 knockout strongly enhances IFN responses to measles virus, and phosphomimetic MDA5-S828D recapitulates the inhibitory effect.","method":"RIOK3 knockout cells, in vitro kinase assay (RIOK3 phosphorylates MDA5 C-terminus), phosphomimetic mutation (S828D), MDA5 multimerization assay (native PAGE), IFN reporter and gene expression assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 — in vitro kinase assay with mutagenesis (S828D), KO cells, and multimerization functional readout","pmids":["25865883"],"is_preprint":false},{"year":2009,"finding":"RIOK3 interacts with caspase-10 via its RIO domain binding to the death effector domains of caspase-10, and negatively regulates NF-κB signaling; it suppresses caspase-10-mediated NF-κB activation by competing with RIP1 and NIK for binding to caspase-10. RIOK3 kinase activity is required for its effect on TNFα-induced NF-κB but not for the caspase-10-mediated branch.","method":"Yeast two-hybrid, GST pull-down, endogenous co-immunoprecipitation, siRNA knockdown, NF-κB reporter assays, kinase-dead mutant analysis","journal":"Molecular and cellular biochemistry","confidence":"High","confidence_rationale":"Tier 1–2 — yeast two-hybrid confirmed by GST pull-down and endogenous Co-IP, kinase-dead mutant used to dissect mechanism","pmids":["19557502"],"is_preprint":false},{"year":2021,"finding":"Riok3 recruits the E3 ubiquitin ligase TRIM40, which catalyzes K48- and K27-linked ubiquitination of RIG-I and MDA5, leading to their proteasomal degradation, thereby negatively regulating antiviral type I IFN signaling. Myeloid-specific Riok3 knockout mice show enhanced IFN induction and resistance to RNA virus pathogenesis.","method":"Co-immunoprecipitation (Riok3–TRIM40, Riok3–RIG-I/MDA5), ubiquitination assays (K48/K27 linkage-specific), myeloid-specific Riok3 KO mice, in vitro and in vivo viral infection assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IPs, linkage-specific ubiquitination assays, in vivo KO validation","pmids":["34161773"],"is_preprint":false},{"year":2021,"finding":"RIOK3 mRNA is alternatively spliced during RVFV infection to produce isoforms with premature termination codons that dampen IFN production; the full-length RIOK3 is required for IFN induction, while the dominant alternatively spliced isoform (RIOK3 X2) inhibits IFN responses. Forcing alternative splicing with a morpholino oligonucleotide reduces IFN expression.","method":"Transcriptome profiling, morpholino-mediated splice-site blocking, RIOK3 isoform overexpression, IFN reporter assays, siRNA knockdown","journal":"Viruses","confidence":"Medium","confidence_rationale":"Tier 2 — morpholino functional experiment plus isoform overexpression, single lab","pmids":["33652597"],"is_preprint":false},{"year":2022,"finding":"RIOK3 promotes PDAC cell invasion and metastasis by physically interacting with focal adhesion kinase (FAK) and stabilizing FAK protein, increasing FAK phosphorylation at Tyr397 and Tyr925; the pro-invasive function of RIOK3 depends on FAK activation.","method":"Co-immunoprecipitation (RIOK3–FAK), siRNA knockdown, Western blot for FAK protein stability and phosphorylation, FAK-Y925F mutant, invasion/migration assays","journal":"Heliyon","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, Co-IP plus functional rescue, moderate mechanistic depth","pmids":["35982848"],"is_preprint":false},{"year":2022,"finding":"Wild-type but not kinase-dead RIOK3 mediates Akt phosphorylation and promotes synergistic replication of MDV and REV, defining a RIOK3–Akt signaling axis that is PI3K-independent.","method":"Kinase-dead RIOK3 mutant, Akt phosphorylation assays, PI3K inhibitor controls, viral titer assays, mass spectrometry (TMT-LC/MS)","journal":"Virulence","confidence":"Medium","confidence_rationale":"Tier 2 — kinase-dead mutant demonstrates kinase activity requirement, PI3K independence established by inhibitor","pmids":["35795905"],"is_preprint":false},{"year":2023,"finding":"RIOK3 promotes arginine uptake in pancreatic ductal adenocarcinoma cells by upregulating the arginine transporter SLC7A2, leading to mTORC1 activation, cell invasion and metastasis.","method":"RIOK3 stable knockdown, RNA-seq, LC-MS metabolomics, Western blot for SLC7A2 and mTORC1 pathway components, invasion assays","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2 — multiple omics methods plus functional KD phenotype, single lab","pmids":["36880835"],"is_preprint":false},{"year":2024,"finding":"RIOK3 interacts with HSP90α and facilitates its binding to IDH1, upregulating IDH1 expression and thereby increasing NADPH production to maintain redox balance and cancer cell survival during glucose deprivation; RIOK3 inhibition has no effect on NADPH levels when HSP90α is knocked down, confirming pathway dependence.","method":"Co-immunoprecipitation (RIOK3–HSP90α, HSP90α–IDH1), RIOK3 and HSP90α knockout/knockdown, NADPH measurement, cell viability assays","journal":"Oncogenesis","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis by double KD, Co-IP of relevant interactors, metabolite readout; single lab","pmids":["38453884"],"is_preprint":false},{"year":2025,"finding":"RIOK3 specifically recognizes RNF10-ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif (UIM) and induces their degradation via progressive 3′-to-5′ decay of 18S rRNA during starvation; cryo-EM structures of RIOK3 bound to ubiquitylated 40S and of degradation intermediates define the molecular mechanism.","method":"Cryo-EM structure determination, in vitro ubiquitylation assays (RNF10), UIM mutagenesis, starvation-induced 40S degradation assays, rRNA decay analysis","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structures with mutagenesis and in vitro reconstitution, multiple mechanistic readouts","pmids":["39947183"],"is_preprint":false},{"year":2025,"finding":"RIOK3 interacts with RNF10-ubiquitylated 40S subunits (ubiquitylated at uS3 and uS5) as part of the initiation-specific ribosome-associated quality control (iRQC) pathway; RIOK3 and RNF10 protein levels increase upon iRQC activation, establishing a feedforward mechanism for 40S decay. mRNA engagement via eIF4A1 is required upstream of ubiquitylation and RIOK3 action.","method":"siRNA/shRNA depletion, co-immunoprecipitation (RIOK3–ubiquitylated 40S), polysome profiling, rRNA quantification, eIF4A1 depletion epistasis","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods, epistasis with eIF4A1, replicated key findings from parallel study (PMID:39947183)","pmids":["40022732"],"is_preprint":false},{"year":2025,"finding":"RIOK3 modulates the JAK1/STAT1 signaling pathway in macrophages during RSV infection; RIOK3 knockout enhances viral replication and disrupts type I interferon balance, demonstrating that RIOK3 normally promotes antiviral JAK1/STAT1 signaling.","method":"RIOK3 KO mice (bone marrow-derived macrophages), in vitro and in vivo RSV infection, JAK1/STAT1 pathway analysis","journal":"Frontiers in microbiology","confidence":"Low","confidence_rationale":"Tier 3 — KO phenotype with pathway inference, single lab, limited mechanistic depth on direct RIOK3–JAK1 interaction","pmids":["40371100"],"is_preprint":false},{"year":2025,"finding":"METTL3-mediated m6A modification of RIOK3 mRNA enhances RIOK3 expression during Coxsackievirus B3 (CVB3) infection; elevated RIOK3 suppresses CDC42, a Rho-family GTPase, thereby activating NF-κB signaling and promoting viral replication.","method":"m6A-seq/MeRIP, METTL3 knockdown, RIOK3 overexpression/knockdown, CDC42 rescue experiments, NF-κB reporter assays, in vivo CVB3 infection model","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal methods including m6A mapping and epistasis rescue, single lab","pmids":["39961559"],"is_preprint":false}],"current_model":"RIOK3 is an atypical serine-threonine kinase that functions in multiple cellular contexts: (1) in ribosome biology, it is a cytoplasmic component of pre-40S particles required for 18S-E pre-rRNA processing, and during starvation it recognizes RNF10-ubiquitylated 40S ribosomes via a ubiquitin-interacting motif to drive their degradation through 3′-end 18S rRNA decay; (2) in innate immunity, it both promotes antiviral IFN responses by bridging TBK1 and IRF3 and negatively regulates them by phosphorylating MDA5-S828 to disrupt filament formation and by recruiting TRIM40 to ubiquitinate and degrade RIG-I/MDA5; (3) it regulates NF-κB signaling by interacting with caspase-10 and competing with RIP1/NIK; and (4) in cancer cells, it promotes migration/invasion via actin cytoskeletal reorganization, FAK stabilization, and SLC7A2-mediated arginine uptake/mTORC1 activation, and supports metabolic survival by facilitating an HSP90α–IDH1 axis for NADPH production."},"narrative":{"teleology":[{"year":2009,"claim":"Establishing that RIOK3 functions beyond ribosome biology as a regulator of NF-κB signaling answered how an atypical kinase intersects with inflammatory pathways: RIOK3 binds caspase-10 death effector domains and competes with RIP1/NIK to suppress caspase-10-mediated NF-κB activation.","evidence":"Yeast two-hybrid, GST pull-down, endogenous Co-IP, NF-κB reporter assays, and kinase-dead mutant analysis in human cells","pmids":["19557502"],"confidence":"High","gaps":["Whether RIOK3–caspase-10 interaction occurs in primary immune cells","Substrates of RIOK3 kinase activity relevant to TNFα-induced NF-κB","Relationship to RIOK3's ribosomal function"]},{"year":2010,"claim":"Identifying RIOK3 as essential for erythroblast chromatin condensation and enucleation revealed a developmental role, showing that miR-191 represses RIOK3 to control terminal erythroid differentiation.","evidence":"siRNA knockdown of Riok3, miR-191 overexpression, and erythroblast differentiation assays in murine fetal liver cells","pmids":["21196494"],"confidence":"High","gaps":["Mechanistic link between RIOK3 and chromatin condensation machinery","Whether the effect is kinase-activity-dependent","Whether ribosome maturation defects underlie the differentiation block"]},{"year":2012,"claim":"Demonstrating that RIOK3 is a cytoplasmic component of pre-40S ribosomal particles required for 18S-E pre-rRNA processing established its conserved role in ribosome biogenesis.","evidence":"Sucrose gradient sedimentation, Co-IP with hLtv1/hEnp1, Northern blot for pre-rRNA intermediates, and siRNA knockdown in human cells","pmids":["22418843"],"confidence":"High","gaps":["Whether RIOK3 kinase activity is needed for rRNA processing","Identity of the endonuclease acting downstream","Structural basis of RIOK3 on the pre-40S particle"]},{"year":2014,"claim":"Two studies resolved opposing roles of RIOK3 in innate immunity: it bridges TBK1–IRF3 to promote IFN-β induction, yet also directly phosphorylates MDA5 at S828 to prevent filament formation and limit signaling, revealing RIOK3 as a dual-function regulator operating at different pathway nodes.","evidence":"Kinome-wide RNAi screen, reciprocal Co-IPs (RIOK3–TBK1, RIOK3–IRF3), in vitro kinase assays, phosphomimetic MDA5-S828D, native PAGE multimerization assays, and RIOK3 KO cells","pmids":["24807708","25865883"],"confidence":"High","gaps":["How the cell partitions RIOK3 between its adaptor and kinase functions","Whether additional MDA5 phospho-sites are RIOK3 substrates","Relevance to bacterial vs. viral PAMPs"]},{"year":2014,"claim":"Showing that hypoxia-induced RIOK3 relocalizes to the leading edge and interacts with actin/tropomyosins to drive cytoskeletal reorganization, migration, and invasion explained how RIOK3 contributes to cancer metastasis.","evidence":"HIF1α reporter assays, siRNA knockdown with live-cell imaging, Co-IP/MS proteomics, wound-healing and 3D invasion assays, zebrafish and mouse metastasis models","pmids":["25486436"],"confidence":"High","gaps":["Whether RIOK3 kinase activity is required for actin remodeling","Direct phosphorylation substrates at the leading edge","How RIOK3's ribosomal and cytoskeletal pools are regulated"]},{"year":2021,"claim":"Identifying RIOK3 as a recruiter of E3 ligase TRIM40 to ubiquitinate and degrade RIG-I/MDA5 via K48/K27-linked chains resolved a second negative-regulatory mechanism in innate immunity, validated by enhanced antiviral resistance in myeloid-specific Riok3 KO mice.","evidence":"Reciprocal Co-IPs, linkage-specific ubiquitination assays, myeloid-specific Riok3 KO mice with in vivo viral challenge","pmids":["34161773"],"confidence":"High","gaps":["Whether RIOK3 kinase activity is required for TRIM40 recruitment","Structural basis of the RIOK3–TRIM40 interaction","Interplay between MDA5 phosphorylation (S828) and TRIM40-mediated degradation"]},{"year":2022,"claim":"Demonstrating that RIOK3 stabilizes FAK and promotes its phosphorylation extended the pro-invasive mechanism in pancreatic cancer beyond actin reorganization to focal adhesion signaling.","evidence":"Co-IP of RIOK3–FAK, siRNA knockdown, FAK-Y925F mutant rescue, invasion assays in PDAC cells","pmids":["35982848"],"confidence":"Medium","gaps":["Whether RIOK3 directly phosphorylates FAK or acts as a scaffold","In vivo validation of FAK dependence","Relationship to tropomyosin-dependent actin remodeling"]},{"year":2023,"claim":"Linking RIOK3 to SLC7A2-mediated arginine uptake and mTORC1 activation in PDAC revealed a metabolic axis through which RIOK3 supports cancer cell invasion and growth.","evidence":"RIOK3 stable knockdown, RNA-seq, LC-MS metabolomics, Western blot for SLC7A2 and mTORC1 pathway components","pmids":["36880835"],"confidence":"Medium","gaps":["Mechanism by which RIOK3 upregulates SLC7A2","Whether kinase activity is required","Generalizability beyond PDAC"]},{"year":2024,"claim":"Showing that RIOK3 facilitates HSP90α binding to IDH1 to sustain NADPH production during glucose deprivation revealed a metabolic scaffolding function essential for cancer cell redox homeostasis.","evidence":"Co-IP (RIOK3–HSP90α, HSP90α–IDH1), epistasis by combined RIOK3/HSP90α knockdown, NADPH and viability measurements","pmids":["38453884"],"confidence":"Medium","gaps":["Whether RIOK3 directly binds IDH1 or only acts through HSP90α","Structural basis of the RIOK3–HSP90α complex","Relevance to non-cancer cell metabolism"]},{"year":2025,"claim":"Cryo-EM structures of RIOK3 bound to RNF10-ubiquitylated 40S subunits and rRNA degradation intermediates defined the molecular mechanism of initiation-specific ribosome quality control (iRQC), establishing RIOK3's UIM as the ubiquitin sensor that initiates 3′-to-5′ 18S rRNA decay during starvation.","evidence":"Cryo-EM structure determination, in vitro RNF10 ubiquitylation, UIM mutagenesis, starvation-induced 40S degradation assays, rRNA decay analysis; corroborated by parallel study using siRNA/shRNA depletion and polysome profiling with eIF4A1 epistasis","pmids":["39947183","40022732"],"confidence":"High","gaps":["Identity of the nuclease(s) executing 18S rRNA 3′ decay downstream of RIOK3","Whether RIOK3 kinase activity contributes to iRQC beyond UIM-mediated recognition","How iRQC and pre-40S maturation functions of RIOK3 are coordinated"]},{"year":null,"claim":"How the cell partitions RIOK3 among its ribosomal, innate-immune, and cytoskeletal functions remains unknown; whether context-dependent post-translational modifications, interacting partners, or subcellular relocalization direct RIOK3 to distinct pathways has not been determined.","evidence":"","pmids":[],"confidence":"Low","gaps":["No systematic structure–function study dissecting which RIOK3 domains are required for each pathway","No identified upstream signal that switches RIOK3 between kinase and adaptor/UIM modes","No conditional knockout phenotyping across tissues beyond myeloid cells"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,5,9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,6,11]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[3]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4,5,6]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1,3]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[1,12,13]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,12,13]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[2,4,5,6,14,15]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,12,13]}],"complexes":["pre-40S ribosomal particle","RNF10–ubiquitylated 40S (iRQC complex)"],"partners":["TBK1","IRF3","MDA5","TRIM40","FAK","HSP90AA1","CASP10","RNF10"],"other_free_text":[]},"mechanistic_narrative":"RIOK3 is an atypical serine/threonine kinase that functions as a central regulatory node in ribosome quality control, innate immune signaling, and cancer cell migration. In ribosome biology, RIOK3 associates with cytoplasmic pre-40S particles to promote 18S-E pre-rRNA processing and, during starvation, recognizes RNF10-ubiquitylated 40S subunits via a ubiquitin-interacting motif to drive their degradation through 3′-to-5′ 18S rRNA decay as part of the initiation-specific ribosome-associated quality control (iRQC) pathway [PMID:22418843, PMID:39947183, PMID:40022732]. In innate immunity, RIOK3 bridges TBK1 and IRF3 to promote IFN-β production, but also negatively regulates cytosolic RNA sensing by phosphorylating MDA5 at S828 to disrupt filament formation and by recruiting TRIM40 to ubiquitinate RIG-I and MDA5 for proteasomal degradation [PMID:24807708, PMID:25865883, PMID:34161773]. RIOK3 additionally promotes cancer cell invasion by reorganizing the actin cytoskeleton through interactions with tropomyosins and FAK stabilization, and supports metabolic adaptation by facilitating HSP90α-dependent IDH1 expression for NADPH production and SLC7A2-mediated arginine uptake for mTORC1 activation [PMID:25486436, PMID:35982848, PMID:38453884, PMID:36880835]."},"prefetch_data":{"uniprot":{"accession":"O14730","full_name":"Serine/threonine-protein kinase RIO3","aliases":["RIO kinase 3","sudD homolog"],"length_aa":519,"mass_kda":59.1,"function":"Serine/threonine-protein kinase involved in a ribosome quality control that takes place when ribosomes have stalled, leading to 18S non-functional rRNA decay and degradation of the 40S ribosomal subunit (PubMed:39947182, PubMed:39947183, PubMed:40022732). Acts downstream of RNF10: specifically recognizes and binds RPS2/us5 and RPS3/us3 monoubiquitinated by RNF10, promoting degradation of the 40S ribosomal subunit in a kinase-dependent manner (PubMed:39947182, PubMed:39947183, PubMed:40022732). The RNF10-RIOK3 ribosome quality control takes place in response to ribosome subunit imbalance or downstream the EIF2AK4/GCN2-mediated integrated stress response (ISR) (PubMed:39947182, PubMed:39947183, PubMed:40022732). Also involved in regulation of type I interferon (IFN)-dependent immune response, possibly by acting as an adapter protein essential for the recruitment of TBK1 to IRF3 (PubMed:24807708). Phosphorylates IFIH1 on 'Ser-828' interfering with IFIH1 filament assembly on long dsRNA and resulting in attenuated IFIH1-signaling (PubMed:25865883). Can inhibit CASP10 isoform 7-mediated activation of the NF-kappa-B signaling pathway (PubMed:19557502)","subcellular_location":"Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/O14730/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RIOK3","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000101782","cell_line_id":"CID001258","localizations":[{"compartment":"cytoplasmic","grade":3}],"interactors":[{"gene":"LTV1","stoichiometry":10.0},{"gene":"TSR1","stoichiometry":4.0},{"gene":"BYSL","stoichiometry":4.0},{"gene":"NOB1","stoichiometry":4.0},{"gene":"RACK1","stoichiometry":0.2},{"gene":"ASCC3","stoichiometry":0.2},{"gene":"RPS27A","stoichiometry":0.2},{"gene":"GNB2L1","stoichiometry":0.2},{"gene":"RPS20","stoichiometry":0.2},{"gene":"RPS11","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001258","total_profiled":1310},"omim":[{"mim_id":"603579","title":"RIO KINASE 3; RIOK3","url":"https://www.omim.org/entry/603579"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Golgi apparatus","reliability":"Additional"},{"location":"Centriolar satellite","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"bone marrow","ntpm":164.5}],"url":"https://www.proteinatlas.org/search/RIOK3"},"hgnc":{"alias_symbol":[],"prev_symbol":["SUDD"]},"alphafold":{"accession":"O14730","domains":[{"cath_id":"-","chopping":"154-224","consensus_level":"high","plddt":72.2151,"start":154,"end":224},{"cath_id":"3.30.200.20","chopping":"232-368","consensus_level":"medium","plddt":82.565,"start":232,"end":368},{"cath_id":"1.10.510.10","chopping":"370-505","consensus_level":"medium","plddt":89.448,"start":370,"end":505}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O14730","model_url":"https://alphafold.ebi.ac.uk/files/AF-O14730-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O14730-F1-predicted_aligned_error_v6.png","plddt_mean":74.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RIOK3","jax_strain_url":"https://www.jax.org/strain/search?query=RIOK3"},"sequence":{"accession":"O14730","fasta_url":"https://rest.uniprot.org/uniprotkb/O14730.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O14730/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O14730"}},"corpus_meta":[{"pmid":"21196494","id":"PMC_21196494","title":"miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1.","date":"2010","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/21196494","citation_count":102,"is_preprint":false},{"pmid":"25865883","id":"PMC_25865883","title":"RIOK3-mediated phosphorylation of MDA5 interferes with its assembly and attenuates the innate immune response.","date":"2015","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/25865883","citation_count":72,"is_preprint":false},{"pmid":"29233656","id":"PMC_29233656","title":"The atypical protein kinase RIOK3 contributes to glioma cell proliferation/survival, migration/invasion and the AKT/mTOR signaling pathway.","date":"2017","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/29233656","citation_count":47,"is_preprint":false},{"pmid":"34161773","id":"PMC_34161773","title":"Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation.","date":"2021","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/34161773","citation_count":45,"is_preprint":false},{"pmid":"25486436","id":"PMC_25486436","title":"Hypoxic regulation of RIOK3 is a major mechanism for cancer cell invasion and metastasis.","date":"2014","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/25486436","citation_count":45,"is_preprint":false},{"pmid":"22418843","id":"PMC_22418843","title":"Human RioK3 is a novel component of cytoplasmic pre-40S pre-ribosomal particles.","date":"2012","source":"RNA biology","url":"https://pubmed.ncbi.nlm.nih.gov/22418843","citation_count":45,"is_preprint":false},{"pmid":"24807708","id":"PMC_24807708","title":"RIOK3 is an adaptor protein required for IRF3-mediated antiviral type I interferon production.","date":"2014","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/24807708","citation_count":40,"is_preprint":false},{"pmid":"19557502","id":"PMC_19557502","title":"RIOK3 interacts with caspase-10 and negatively regulates the NF-kappaB signaling pathway.","date":"2009","source":"Molecular and cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19557502","citation_count":34,"is_preprint":false},{"pmid":"9602165","id":"PMC_9602165","title":"Isolation of the Aspergillus nidulans sudD gene and its human homologue.","date":"1998","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/9602165","citation_count":21,"is_preprint":false},{"pmid":"39947183","id":"PMC_39947183","title":"RIOK3 mediates the degradation of 40S ribosomes.","date":"2025","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/39947183","citation_count":14,"is_preprint":false},{"pmid":"40022732","id":"PMC_40022732","title":"RNF10 and RIOK3 facilitate 40S ribosomal subunit degradation upon 60S biogenesis disruption or amino acid starvation.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/40022732","citation_count":11,"is_preprint":false},{"pmid":"36880835","id":"PMC_36880835","title":"RIOK3 promotes mTORC1 activation by facilitating SLC7A2-mediated arginine uptake in pancreatic ductal adenocarcinoma.","date":"2023","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/36880835","citation_count":11,"is_preprint":false},{"pmid":"33652597","id":"PMC_33652597","title":"The Atypical Kinase RIOK3 Limits RVFV Propagation and Is Regulated by Alternative Splicing.","date":"2021","source":"Viruses","url":"https://pubmed.ncbi.nlm.nih.gov/33652597","citation_count":9,"is_preprint":false},{"pmid":"36146870","id":"PMC_36146870","title":"RIOK3 and Its Alternatively Spliced Isoform Have Disparate Roles in the Innate Immune Response to Rift Valley Fever Virus (MP12) 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macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/39961559","citation_count":5,"is_preprint":false},{"pmid":"35795905","id":"PMC_35795905","title":"RIOK3-Mediated Akt phosphorylation facilitates synergistic replication of Marek's disease and reticuloendotheliosis viruses.","date":"2022","source":"Virulence","url":"https://pubmed.ncbi.nlm.nih.gov/35795905","citation_count":5,"is_preprint":false},{"pmid":"37866658","id":"PMC_37866658","title":"RIOK3 potentially regulates osteogenesis-related pathways in ankylosing spondylitis and the differentiation of bone marrow mesenchymal stem cells.","date":"2023","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/37866658","citation_count":3,"is_preprint":false},{"pmid":"38453884","id":"PMC_38453884","title":"RIOK3 sustains colorectal cancer cell survival under glucose deprivation via an HSP90α-dependent 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potential.","date":"2025","source":"Frontiers in microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/40371100","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11682,"output_tokens":4345,"usd":0.050111},"stage2":{"model":"claude-opus-4-6","input_tokens":7877,"output_tokens":3288,"usd":0.182377},"total_usd":0.232488,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"Riok3 is required for erythroblast chromatin condensation and enucleation; knockdown of Riok3 blocks both chromatin condensation and enucleation in terminal erythroid differentiation, and Riok3 mRNA is a direct target repressed by miR-191.\",\n      \"method\": \"RNA interference (Riok3 knockdown), miR-191 overexpression, erythroblast differentiation assays; miR-191 target site validation\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal loss-of-function approaches with specific phenotypic readout, replicated across miR-191 OE and direct Riok3 KD\",\n      \"pmids\": [\"21196494\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Human RioK3 is a cytoplasmic protein that associates with pre-40S ribosomal particles, co-sediments with 40S particles in sucrose gradients, interacts with pre-40S components hLtv1 and hEnp1 and with 18S-E pre-rRNA, and its depletion causes accumulation of 21S pre-rRNA, indicating a role in cytoplasmic 18S-E pre-rRNA processing.\",\n      \"method\": \"Sucrose gradient sedimentation, co-immunoprecipitation with hLtv1/hEnp1, Northern blot for pre-rRNA intermediates, siRNA knockdown\",\n      \"journal\": \"RNA biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (sedimentation, Co-IP, Northern blot) in a single study with functional readout\",\n      \"pmids\": [\"22418843\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"RIOK3 acts as an adaptor protein downstream of TBK1 and upstream of IRF3 in the cytosolic nucleic acid-sensing pathway; RIOK3 physically interacts with both TBK1 and IRF3 and is required for the TBK1–IRF3 interaction, leading to IRF3 activation and IFN-β production.\",\n      \"method\": \"Kinome-wide RNAi screens, co-immunoprecipitation (RIOK3–TBK1, RIOK3–IRF3), RIOK3 overexpression/knockdown with IRF3 phosphorylation and IFN-β reporter assays, transcriptome analysis\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP for both interactors, epistasis established by bridging requirement, replicated with genome-wide screens\",\n      \"pmids\": [\"24807708\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"RIOK3 expression is induced by hypoxia in an HIF1α-dependent manner; under hypoxia, RIOK3 redistributes from cytoplasmic aggregates to the leading edge of the cell with reorganization of the actin cytoskeleton. RIOK3 interacts with actin and actin-binding proteins tropomyosins (TPM3, TPM4) and tropomodulin 3, and is required for actin filament organization and TPM3 association with filaments, thereby driving cell migration and invasion.\",\n      \"method\": \"HIF1α-dependent reporter assays, siRNA knockdown with live-cell imaging and morphology analysis, proteomics (Co-IP/MS for interactors), wound-healing and 3D invasion assays, zebrafish and mouse metastasis models, immunofluorescence for actin/TPM3\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (proteomics, imaging, KD with in vivo models), strong mechanistic evidence across cell and animal models\",\n      \"pmids\": [\"25486436\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RIOK3 is a protein kinase that phosphorylates the C-terminal region of MDA5 (at S828), impairing MDA5 multimer/filament formation on dsRNA and thereby attenuating MDA5-mediated type I IFN signaling. RIOK3 knockout strongly enhances IFN responses to measles virus, and phosphomimetic MDA5-S828D recapitulates the inhibitory effect.\",\n      \"method\": \"RIOK3 knockout cells, in vitro kinase assay (RIOK3 phosphorylates MDA5 C-terminus), phosphomimetic mutation (S828D), MDA5 multimerization assay (native PAGE), IFN reporter and gene expression assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro kinase assay with mutagenesis (S828D), KO cells, and multimerization functional readout\",\n      \"pmids\": [\"25865883\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"RIOK3 interacts with caspase-10 via its RIO domain binding to the death effector domains of caspase-10, and negatively regulates NF-κB signaling; it suppresses caspase-10-mediated NF-κB activation by competing with RIP1 and NIK for binding to caspase-10. RIOK3 kinase activity is required for its effect on TNFα-induced NF-κB but not for the caspase-10-mediated branch.\",\n      \"method\": \"Yeast two-hybrid, GST pull-down, endogenous co-immunoprecipitation, siRNA knockdown, NF-κB reporter assays, kinase-dead mutant analysis\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — yeast two-hybrid confirmed by GST pull-down and endogenous Co-IP, kinase-dead mutant used to dissect mechanism\",\n      \"pmids\": [\"19557502\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Riok3 recruits the E3 ubiquitin ligase TRIM40, which catalyzes K48- and K27-linked ubiquitination of RIG-I and MDA5, leading to their proteasomal degradation, thereby negatively regulating antiviral type I IFN signaling. Myeloid-specific Riok3 knockout mice show enhanced IFN induction and resistance to RNA virus pathogenesis.\",\n      \"method\": \"Co-immunoprecipitation (Riok3–TRIM40, Riok3–RIG-I/MDA5), ubiquitination assays (K48/K27 linkage-specific), myeloid-specific Riok3 KO mice, in vitro and in vivo viral infection assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IPs, linkage-specific ubiquitination assays, in vivo KO validation\",\n      \"pmids\": [\"34161773\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RIOK3 mRNA is alternatively spliced during RVFV infection to produce isoforms with premature termination codons that dampen IFN production; the full-length RIOK3 is required for IFN induction, while the dominant alternatively spliced isoform (RIOK3 X2) inhibits IFN responses. Forcing alternative splicing with a morpholino oligonucleotide reduces IFN expression.\",\n      \"method\": \"Transcriptome profiling, morpholino-mediated splice-site blocking, RIOK3 isoform overexpression, IFN reporter assays, siRNA knockdown\",\n      \"journal\": \"Viruses\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — morpholino functional experiment plus isoform overexpression, single lab\",\n      \"pmids\": [\"33652597\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RIOK3 promotes PDAC cell invasion and metastasis by physically interacting with focal adhesion kinase (FAK) and stabilizing FAK protein, increasing FAK phosphorylation at Tyr397 and Tyr925; the pro-invasive function of RIOK3 depends on FAK activation.\",\n      \"method\": \"Co-immunoprecipitation (RIOK3–FAK), siRNA knockdown, Western blot for FAK protein stability and phosphorylation, FAK-Y925F mutant, invasion/migration assays\",\n      \"journal\": \"Heliyon\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, Co-IP plus functional rescue, moderate mechanistic depth\",\n      \"pmids\": [\"35982848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Wild-type but not kinase-dead RIOK3 mediates Akt phosphorylation and promotes synergistic replication of MDV and REV, defining a RIOK3–Akt signaling axis that is PI3K-independent.\",\n      \"method\": \"Kinase-dead RIOK3 mutant, Akt phosphorylation assays, PI3K inhibitor controls, viral titer assays, mass spectrometry (TMT-LC/MS)\",\n      \"journal\": \"Virulence\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — kinase-dead mutant demonstrates kinase activity requirement, PI3K independence established by inhibitor\",\n      \"pmids\": [\"35795905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RIOK3 promotes arginine uptake in pancreatic ductal adenocarcinoma cells by upregulating the arginine transporter SLC7A2, leading to mTORC1 activation, cell invasion and metastasis.\",\n      \"method\": \"RIOK3 stable knockdown, RNA-seq, LC-MS metabolomics, Western blot for SLC7A2 and mTORC1 pathway components, invasion assays\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple omics methods plus functional KD phenotype, single lab\",\n      \"pmids\": [\"36880835\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RIOK3 interacts with HSP90α and facilitates its binding to IDH1, upregulating IDH1 expression and thereby increasing NADPH production to maintain redox balance and cancer cell survival during glucose deprivation; RIOK3 inhibition has no effect on NADPH levels when HSP90α is knocked down, confirming pathway dependence.\",\n      \"method\": \"Co-immunoprecipitation (RIOK3–HSP90α, HSP90α–IDH1), RIOK3 and HSP90α knockout/knockdown, NADPH measurement, cell viability assays\",\n      \"journal\": \"Oncogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis by double KD, Co-IP of relevant interactors, metabolite readout; single lab\",\n      \"pmids\": [\"38453884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RIOK3 specifically recognizes RNF10-ubiquitylated 40S ribosomes through a unique ubiquitin-interacting motif (UIM) and induces their degradation via progressive 3′-to-5′ decay of 18S rRNA during starvation; cryo-EM structures of RIOK3 bound to ubiquitylated 40S and of degradation intermediates define the molecular mechanism.\",\n      \"method\": \"Cryo-EM structure determination, in vitro ubiquitylation assays (RNF10), UIM mutagenesis, starvation-induced 40S degradation assays, rRNA decay analysis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structures with mutagenesis and in vitro reconstitution, multiple mechanistic readouts\",\n      \"pmids\": [\"39947183\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RIOK3 interacts with RNF10-ubiquitylated 40S subunits (ubiquitylated at uS3 and uS5) as part of the initiation-specific ribosome-associated quality control (iRQC) pathway; RIOK3 and RNF10 protein levels increase upon iRQC activation, establishing a feedforward mechanism for 40S decay. mRNA engagement via eIF4A1 is required upstream of ubiquitylation and RIOK3 action.\",\n      \"method\": \"siRNA/shRNA depletion, co-immunoprecipitation (RIOK3–ubiquitylated 40S), polysome profiling, rRNA quantification, eIF4A1 depletion epistasis\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods, epistasis with eIF4A1, replicated key findings from parallel study (PMID:39947183)\",\n      \"pmids\": [\"40022732\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RIOK3 modulates the JAK1/STAT1 signaling pathway in macrophages during RSV infection; RIOK3 knockout enhances viral replication and disrupts type I interferon balance, demonstrating that RIOK3 normally promotes antiviral JAK1/STAT1 signaling.\",\n      \"method\": \"RIOK3 KO mice (bone marrow-derived macrophages), in vitro and in vivo RSV infection, JAK1/STAT1 pathway analysis\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — KO phenotype with pathway inference, single lab, limited mechanistic depth on direct RIOK3–JAK1 interaction\",\n      \"pmids\": [\"40371100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"METTL3-mediated m6A modification of RIOK3 mRNA enhances RIOK3 expression during Coxsackievirus B3 (CVB3) infection; elevated RIOK3 suppresses CDC42, a Rho-family GTPase, thereby activating NF-κB signaling and promoting viral replication.\",\n      \"method\": \"m6A-seq/MeRIP, METTL3 knockdown, RIOK3 overexpression/knockdown, CDC42 rescue experiments, NF-κB reporter assays, in vivo CVB3 infection model\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods including m6A mapping and epistasis rescue, single lab\",\n      \"pmids\": [\"39961559\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RIOK3 is an atypical serine-threonine kinase that functions in multiple cellular contexts: (1) in ribosome biology, it is a cytoplasmic component of pre-40S particles required for 18S-E pre-rRNA processing, and during starvation it recognizes RNF10-ubiquitylated 40S ribosomes via a ubiquitin-interacting motif to drive their degradation through 3′-end 18S rRNA decay; (2) in innate immunity, it both promotes antiviral IFN responses by bridging TBK1 and IRF3 and negatively regulates them by phosphorylating MDA5-S828 to disrupt filament formation and by recruiting TRIM40 to ubiquitinate and degrade RIG-I/MDA5; (3) it regulates NF-κB signaling by interacting with caspase-10 and competing with RIP1/NIK; and (4) in cancer cells, it promotes migration/invasion via actin cytoskeletal reorganization, FAK stabilization, and SLC7A2-mediated arginine uptake/mTORC1 activation, and supports metabolic survival by facilitating an HSP90α–IDH1 axis for NADPH production.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RIOK3 is an atypical serine/threonine kinase that functions as a central regulatory node in ribosome quality control, innate immune signaling, and cancer cell migration. In ribosome biology, RIOK3 associates with cytoplasmic pre-40S particles to promote 18S-E pre-rRNA processing and, during starvation, recognizes RNF10-ubiquitylated 40S subunits via a ubiquitin-interacting motif to drive their degradation through 3′-to-5′ 18S rRNA decay as part of the initiation-specific ribosome-associated quality control (iRQC) pathway [PMID:22418843, PMID:39947183, PMID:40022732]. In innate immunity, RIOK3 bridges TBK1 and IRF3 to promote IFN-β production, but also negatively regulates cytosolic RNA sensing by phosphorylating MDA5 at S828 to disrupt filament formation and by recruiting TRIM40 to ubiquitinate RIG-I and MDA5 for proteasomal degradation [PMID:24807708, PMID:25865883, PMID:34161773]. RIOK3 additionally promotes cancer cell invasion by reorganizing the actin cytoskeleton through interactions with tropomyosins and FAK stabilization, and supports metabolic adaptation by facilitating HSP90α-dependent IDH1 expression for NADPH production and SLC7A2-mediated arginine uptake for mTORC1 activation [PMID:25486436, PMID:35982848, PMID:38453884, PMID:36880835].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Establishing that RIOK3 functions beyond ribosome biology as a regulator of NF-κB signaling answered how an atypical kinase intersects with inflammatory pathways: RIOK3 binds caspase-10 death effector domains and competes with RIP1/NIK to suppress caspase-10-mediated NF-κB activation.\",\n      \"evidence\": \"Yeast two-hybrid, GST pull-down, endogenous Co-IP, NF-κB reporter assays, and kinase-dead mutant analysis in human cells\",\n      \"pmids\": [\"19557502\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RIOK3–caspase-10 interaction occurs in primary immune cells\", \"Substrates of RIOK3 kinase activity relevant to TNFα-induced NF-κB\", \"Relationship to RIOK3's ribosomal function\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identifying RIOK3 as essential for erythroblast chromatin condensation and enucleation revealed a developmental role, showing that miR-191 represses RIOK3 to control terminal erythroid differentiation.\",\n      \"evidence\": \"siRNA knockdown of Riok3, miR-191 overexpression, and erythroblast differentiation assays in murine fetal liver cells\",\n      \"pmids\": [\"21196494\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link between RIOK3 and chromatin condensation machinery\", \"Whether the effect is kinase-activity-dependent\", \"Whether ribosome maturation defects underlie the differentiation block\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrating that RIOK3 is a cytoplasmic component of pre-40S ribosomal particles required for 18S-E pre-rRNA processing established its conserved role in ribosome biogenesis.\",\n      \"evidence\": \"Sucrose gradient sedimentation, Co-IP with hLtv1/hEnp1, Northern blot for pre-rRNA intermediates, and siRNA knockdown in human cells\",\n      \"pmids\": [\"22418843\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RIOK3 kinase activity is needed for rRNA processing\", \"Identity of the endonuclease acting downstream\", \"Structural basis of RIOK3 on the pre-40S particle\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Two studies resolved opposing roles of RIOK3 in innate immunity: it bridges TBK1–IRF3 to promote IFN-β induction, yet also directly phosphorylates MDA5 at S828 to prevent filament formation and limit signaling, revealing RIOK3 as a dual-function regulator operating at different pathway nodes.\",\n      \"evidence\": \"Kinome-wide RNAi screen, reciprocal Co-IPs (RIOK3–TBK1, RIOK3–IRF3), in vitro kinase assays, phosphomimetic MDA5-S828D, native PAGE multimerization assays, and RIOK3 KO cells\",\n      \"pmids\": [\"24807708\", \"25865883\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the cell partitions RIOK3 between its adaptor and kinase functions\", \"Whether additional MDA5 phospho-sites are RIOK3 substrates\", \"Relevance to bacterial vs. viral PAMPs\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showing that hypoxia-induced RIOK3 relocalizes to the leading edge and interacts with actin/tropomyosins to drive cytoskeletal reorganization, migration, and invasion explained how RIOK3 contributes to cancer metastasis.\",\n      \"evidence\": \"HIF1α reporter assays, siRNA knockdown with live-cell imaging, Co-IP/MS proteomics, wound-healing and 3D invasion assays, zebrafish and mouse metastasis models\",\n      \"pmids\": [\"25486436\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RIOK3 kinase activity is required for actin remodeling\", \"Direct phosphorylation substrates at the leading edge\", \"How RIOK3's ribosomal and cytoskeletal pools are regulated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Identifying RIOK3 as a recruiter of E3 ligase TRIM40 to ubiquitinate and degrade RIG-I/MDA5 via K48/K27-linked chains resolved a second negative-regulatory mechanism in innate immunity, validated by enhanced antiviral resistance in myeloid-specific Riok3 KO mice.\",\n      \"evidence\": \"Reciprocal Co-IPs, linkage-specific ubiquitination assays, myeloid-specific Riok3 KO mice with in vivo viral challenge\",\n      \"pmids\": [\"34161773\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RIOK3 kinase activity is required for TRIM40 recruitment\", \"Structural basis of the RIOK3–TRIM40 interaction\", \"Interplay between MDA5 phosphorylation (S828) and TRIM40-mediated degradation\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrating that RIOK3 stabilizes FAK and promotes its phosphorylation extended the pro-invasive mechanism in pancreatic cancer beyond actin reorganization to focal adhesion signaling.\",\n      \"evidence\": \"Co-IP of RIOK3–FAK, siRNA knockdown, FAK-Y925F mutant rescue, invasion assays in PDAC cells\",\n      \"pmids\": [\"35982848\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether RIOK3 directly phosphorylates FAK or acts as a scaffold\", \"In vivo validation of FAK dependence\", \"Relationship to tropomyosin-dependent actin remodeling\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Linking RIOK3 to SLC7A2-mediated arginine uptake and mTORC1 activation in PDAC revealed a metabolic axis through which RIOK3 supports cancer cell invasion and growth.\",\n      \"evidence\": \"RIOK3 stable knockdown, RNA-seq, LC-MS metabolomics, Western blot for SLC7A2 and mTORC1 pathway components\",\n      \"pmids\": [\"36880835\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which RIOK3 upregulates SLC7A2\", \"Whether kinase activity is required\", \"Generalizability beyond PDAC\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showing that RIOK3 facilitates HSP90α binding to IDH1 to sustain NADPH production during glucose deprivation revealed a metabolic scaffolding function essential for cancer cell redox homeostasis.\",\n      \"evidence\": \"Co-IP (RIOK3–HSP90α, HSP90α–IDH1), epistasis by combined RIOK3/HSP90α knockdown, NADPH and viability measurements\",\n      \"pmids\": [\"38453884\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether RIOK3 directly binds IDH1 or only acts through HSP90α\", \"Structural basis of the RIOK3–HSP90α complex\", \"Relevance to non-cancer cell metabolism\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cryo-EM structures of RIOK3 bound to RNF10-ubiquitylated 40S subunits and rRNA degradation intermediates defined the molecular mechanism of initiation-specific ribosome quality control (iRQC), establishing RIOK3's UIM as the ubiquitin sensor that initiates 3′-to-5′ 18S rRNA decay during starvation.\",\n      \"evidence\": \"Cryo-EM structure determination, in vitro RNF10 ubiquitylation, UIM mutagenesis, starvation-induced 40S degradation assays, rRNA decay analysis; corroborated by parallel study using siRNA/shRNA depletion and polysome profiling with eIF4A1 epistasis\",\n      \"pmids\": [\"39947183\", \"40022732\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the nuclease(s) executing 18S rRNA 3′ decay downstream of RIOK3\", \"Whether RIOK3 kinase activity contributes to iRQC beyond UIM-mediated recognition\", \"How iRQC and pre-40S maturation functions of RIOK3 are coordinated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the cell partitions RIOK3 among its ribosomal, innate-immune, and cytoskeletal functions remains unknown; whether context-dependent post-translational modifications, interacting partners, or subcellular relocalization direct RIOK3 to distinct pathways has not been determined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No systematic structure–function study dissecting which RIOK3 domains are required for each pathway\", \"No identified upstream signal that switches RIOK3 between kinase and adaptor/UIM modes\", \"No conditional knockout phenotyping across tissues beyond myeloid cells\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 5, 9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 6, 11]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4, 5, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1, 3]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [1, 12, 13]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0168256\", \"supporting_discovery_ids\": [2, 4, 5, 6, 14, 15]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 12, 13]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [2, 4, 5, 6, 14, 15]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 12, 13]}\n    ],\n    \"complexes\": [\n      \"pre-40S ribosomal particle\",\n      \"RNF10–ubiquitylated 40S (iRQC complex)\"\n    ],\n    \"partners\": [\n      \"TBK1\",\n      \"IRF3\",\n      \"MDA5\",\n      \"TRIM40\",\n      \"FAK\",\n      \"HSP90AA1\",\n      \"CASP10\",\n      \"RNF10\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}