Affinage

RIOK3

Serine/threonine-protein kinase RIO3 · UniProt O14730

Length
519 aa
Mass
59.1 kDa
Annotated
2026-04-28
23 papers in source corpus 16 papers cited in narrative 16 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

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).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2009 High

    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

    PMID:19557502

    Open questions at the time
    • 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
  2. 2010 High

    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

    PMID:21196494

    Open questions at the time
    • Mechanistic link between RIOK3 and chromatin condensation machinery
    • Whether the effect is kinase-activity-dependent
    • Whether ribosome maturation defects underlie the differentiation block
  3. 2012 High

    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

    PMID:22418843

    Open questions at the time
    • Whether RIOK3 kinase activity is needed for rRNA processing
    • Identity of the endonuclease acting downstream
    • Structural basis of RIOK3 on the pre-40S particle
  4. 2014 High

    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

    PMID:24807708 PMID:25865883

    Open questions at the time
    • 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
  5. 2014 High

    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

    PMID:25486436

    Open questions at the time
    • 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
  6. 2021 High

    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

    PMID:34161773

    Open questions at the time
    • 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
  7. 2022 Medium

    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

    PMID:35982848

    Open questions at the time
    • Whether RIOK3 directly phosphorylates FAK or acts as a scaffold
    • In vivo validation of FAK dependence
    • Relationship to tropomyosin-dependent actin remodeling
  8. 2023 Medium

    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

    PMID:36880835

    Open questions at the time
    • Mechanism by which RIOK3 upregulates SLC7A2
    • Whether kinase activity is required
    • Generalizability beyond PDAC
  9. 2024 Medium

    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

    PMID:38453884

    Open questions at the time
    • Whether RIOK3 directly binds IDH1 or only acts through HSP90α
    • Structural basis of the RIOK3–HSP90α complex
    • Relevance to non-cancer cell metabolism
  10. 2025 High

    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

    PMID:39947183 PMID:40022732

    Open questions at the time
    • 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

Open questions

Synthesis pass · forward-looking unresolved questions
  • 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.
  • 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

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0060090 molecular adaptor activity 3 GO:0098772 molecular function regulator activity 3 GO:0140096 catalytic activity, acting on a protein 3 GO:0008092 cytoskeletal protein binding 1
Localization
GO:0005840 ribosome 3 GO:0005829 cytosol 2
Pathway
R-HSA-168256 Immune System 6 R-HSA-392499 Metabolism of proteins 3 R-HSA-8953854 Metabolism of RNA 3
Partners
CASP10FAKHSP90AA1IRF3MDA5RNF10TBK1TRIM40
Complex memberships
RNF10–ubiquitylated 40S (iRQC complex)pre-40S ribosomal particle

Evidence

Reading pass · 16 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2010 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. RNA interference (Riok3 knockdown), miR-191 overexpression, erythroblast differentiation assays; miR-191 target site validation Genes & development High 21196494
2012 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. Sucrose gradient sedimentation, co-immunoprecipitation with hLtv1/hEnp1, Northern blot for pre-rRNA intermediates, siRNA knockdown RNA biology High 22418843
2014 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. Kinome-wide RNAi screens, co-immunoprecipitation (RIOK3–TBK1, RIOK3–IRF3), RIOK3 overexpression/knockdown with IRF3 phosphorylation and IFN-β reporter assays, transcriptome analysis Journal of virology High 24807708
2014 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. 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 Oncogene High 25486436
2015 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. 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 Cell reports High 25865883
2009 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. Yeast two-hybrid, GST pull-down, endogenous co-immunoprecipitation, siRNA knockdown, NF-κB reporter assays, kinase-dead mutant analysis Molecular and cellular biochemistry High 19557502
2021 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. 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 Cell reports High 34161773
2021 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. Transcriptome profiling, morpholino-mediated splice-site blocking, RIOK3 isoform overexpression, IFN reporter assays, siRNA knockdown Viruses Medium 33652597
2022 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. Co-immunoprecipitation (RIOK3–FAK), siRNA knockdown, Western blot for FAK protein stability and phosphorylation, FAK-Y925F mutant, invasion/migration assays Heliyon Medium 35982848
2022 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. Kinase-dead RIOK3 mutant, Akt phosphorylation assays, PI3K inhibitor controls, viral titer assays, mass spectrometry (TMT-LC/MS) Virulence Medium 35795905
2023 RIOK3 promotes arginine uptake in pancreatic ductal adenocarcinoma cells by upregulating the arginine transporter SLC7A2, leading to mTORC1 activation, cell invasion and metastasis. RIOK3 stable knockdown, RNA-seq, LC-MS metabolomics, Western blot for SLC7A2 and mTORC1 pathway components, invasion assays Aging Medium 36880835
2024 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. Co-immunoprecipitation (RIOK3–HSP90α, HSP90α–IDH1), RIOK3 and HSP90α knockout/knockdown, NADPH measurement, cell viability assays Oncogenesis Medium 38453884
2025 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. Cryo-EM structure determination, in vitro ubiquitylation assays (RNF10), UIM mutagenesis, starvation-induced 40S degradation assays, rRNA decay analysis Molecular cell High 39947183
2025 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. siRNA/shRNA depletion, co-immunoprecipitation (RIOK3–ubiquitylated 40S), polysome profiling, rRNA quantification, eIF4A1 depletion epistasis Cell reports High 40022732
2025 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. RIOK3 KO mice (bone marrow-derived macrophages), in vitro and in vivo RSV infection, JAK1/STAT1 pathway analysis Frontiers in microbiology Low 40371100
2025 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. m6A-seq/MeRIP, METTL3 knockdown, RIOK3 overexpression/knockdown, CDC42 rescue experiments, NF-κB reporter assays, in vivo CVB3 infection model International journal of biological macromolecules Medium 39961559

Source papers

Stage 0 corpus · 23 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2010 miR-191 regulates mouse erythroblast enucleation by down-regulating Riok3 and Mxi1. Genes & development 102 21196494
2015 RIOK3-mediated phosphorylation of MDA5 interferes with its assembly and attenuates the innate immune response. Cell reports 72 25865883
2017 The atypical protein kinase RIOK3 contributes to glioma cell proliferation/survival, migration/invasion and the AKT/mTOR signaling pathway. Cancer letters 47 29233656
2021 Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation. Cell reports 45 34161773
2014 Hypoxic regulation of RIOK3 is a major mechanism for cancer cell invasion and metastasis. Oncogene 45 25486436
2012 Human RioK3 is a novel component of cytoplasmic pre-40S pre-ribosomal particles. RNA biology 45 22418843
2014 RIOK3 is an adaptor protein required for IRF3-mediated antiviral type I interferon production. Journal of virology 40 24807708
2009 RIOK3 interacts with caspase-10 and negatively regulates the NF-kappaB signaling pathway. Molecular and cellular biochemistry 34 19557502
1998 Isolation of the Aspergillus nidulans sudD gene and its human homologue. Gene 21 9602165
2025 RIOK3 mediates the degradation of 40S ribosomes. Molecular cell 14 39947183
2025 RNF10 and RIOK3 facilitate 40S ribosomal subunit degradation upon 60S biogenesis disruption or amino acid starvation. Cell reports 11 40022732
2023 RIOK3 promotes mTORC1 activation by facilitating SLC7A2-mediated arginine uptake in pancreatic ductal adenocarcinoma. Aging 11 36880835
2022 RIOK3 and Its Alternatively Spliced Isoform Have Disparate Roles in the Innate Immune Response to Rift Valley Fever Virus (MP12) Infection. Viruses 9 36146870
2021 The Atypical Kinase RIOK3 Limits RVFV Propagation and Is Regulated by Alternative Splicing. Viruses 9 33652597
2023 Alternative Splicing of RIOK3 Engages the Noncanonical NFκB Pathway during Rift Valley Fever Virus Infection. Viruses 6 37515252
2025 m6A-modified RIOK3 activated the NF-κB-signaling pathway by CDC42, promoting the replication and proliferation of enterovirus. International journal of biological macromolecules 5 39961559
2022 RIOK3-Mediated Akt phosphorylation facilitates synergistic replication of Marek's disease and reticuloendotheliosis viruses. Virulence 5 35795905
2022 RIOK3 promotes pancreatic ductal adenocarcinoma cell invasion and metastasis by stabilizing FAK. Heliyon 5 35982848
2023 RIOK3 potentially regulates osteogenesis-related pathways in ankylosing spondylitis and the differentiation of bone marrow mesenchymal stem cells. Genomics 3 37866658
2024 RIOK3 sustains colorectal cancer cell survival under glucose deprivation via an HSP90α-dependent pathway. Oncogenesis 2 38453884
2025 The economical role of RIOK3 in modulating the Jak1/STAT1 pathway and antiviral immunity against respiratory syncytial virus infection in macrophages: implications for therapeutic potential. Frontiers in microbiology 0 40371100
2023 Black carp RIOK3 suppresses MDA5-mediated IFN signaling in the antiviral innate immunity. Developmental and comparative immunology 0 37722630
2021 Induction of right open reading frame kinase 3 (RIOK3) during ovulation and luteinisation in rat ovary. Reproduction, fertility, and development 0 34758896