Affinage

RIOK3

Serine/threonine-protein kinase RIO3 · UniProt O14730

Length
519 aa
Mass
59.1 kDa
Annotated
2026-06-10
23 papers in source corpus 18 papers cited in narrative 18 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/8 claims corpus-supported (88%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

RIOK3 is an atypical RIO-family serine/threonine kinase that operates at the intersection of ribosome biogenesis, ribosome quality control, and innate antiviral signaling (PMID:25865883, PMID:22418843, PMID:39947183). In 40S subunit maturation, it is a cytoplasmic component of pre-40S particles, associating with hLtv1, hEnp1, and 18S-E pre-rRNA, and its depletion stalls 21S pre-rRNA processing (PMID:22418843). Building on this ribosome association, RIOK3 executes initiation-specific ribosome-associated quality control: through a dedicated ubiquitin-interacting motif it recognizes 40S subunits ubiquitylated by RNF10 on uS3/uS5 during starvation and drives progressive 3'-to-5' decay of 18S rRNA to eliminate defective small subunits, with RNF10 and RIOK3 forming a feedforward circuit (PMID:39947183, PMID:40022732). In antiviral immunity RIOK3 is predominantly a negative regulator of type I IFN: it phosphorylates MDA5 at S828 to block filament assembly, an event reversed by PP1α/PP1γ, and it recruits the E3 ligase TRIM40 to drive K48/K27-linked ubiquitination and proteasomal degradation of both RIG-I and MDA5 (PMID:25865883, PMID:34161773). In a distinct context it bridges TBK1 and IRF3 as an adaptor to promote IFN-β induction, and alternative splicing produces an X2 isoform with opposing effects on IFN and NF-κB outputs (PMID:24807708, PMID:33652597, PMID:36146870). Independently, RIOK3 binds caspase-10 via its RIO domain and restrains NF-κB signaling by competing with RIP1 and NIK, with kinase activity required for suppression of TNFα-induced NF-κB (PMID:19557502). RIOK3 also supports cellular remodeling and migration: it is induced by hypoxia in an HIF1α-dependent manner, redistributes to the leading edge, and organizes the actin cytoskeleton through interactions with tropomyosins TPM3/TPM4 and tropomodulin 3 to promote migration, invasion, and metastasis (PMID:25486436). Finally, it is a miR-191 target required for chromatin condensation and enucleation during terminal erythroid differentiation (PMID:21196494).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 1998 Medium

    Established the human RIOK3 gene as a conserved member of an ancient protein family, providing the molecular identity that later mechanistic work would build upon.

    Evidence cDNA cloning, sequence analysis, and genetic suppressor screen of the A. nidulans bimD6 chromosome-segregation mutation

    PMID:9602165

    Open questions at the time
    • No biochemical function assigned to the human protein
    • Connection between the SUDD suppressor phenotype and human RIOK3 activity unresolved
  2. 2009 High

    Identified the first defined molecular partner and signaling role, showing RIOK3 binds caspase-10 through its RIO domain to dampen NF-κB activation.

    Evidence Yeast two-hybrid, GST pull-down, endogenous Co-IP, domain mapping, and kinase-dead mutant in NF-κB reporter assays

    PMID:19557502

    Open questions at the time
    • Direct kinase substrate not identified
    • Why kinase activity is required for TNFα but not caspase-10-mediated suppression unexplained
  3. 2010 High

    Placed RIOK3 in a developmental program, demonstrating it is a miR-191 target essential for erythroid chromatin condensation and enucleation.

    Evidence miR-191 target validation by luciferase reporter, RIOK3 knockdown, and enucleation/chromatin condensation assays in mouse erythroblasts

    PMID:21196494

    Open questions at the time
    • Molecular mechanism linking RIOK3 to chromatin condensation unknown
    • No substrate or partner identified in the erythroid context
  4. 2012 High

    Defined RIOK3 as a cytoplasmic pre-40S ribosome biogenesis factor, anchoring its molecular activity to 18S rRNA maturation.

    Evidence Sucrose gradient co-sedimentation, Co-IP with hLtv1/hEnp1/18S-E pre-rRNA, and siRNA depletion with Northern blot pre-rRNA analysis

    PMID:22418843

    Open questions at the time
    • Whether kinase activity is required for pre-rRNA processing not resolved
    • Direct catalytic substrate within the pre-40S particle unidentified
  5. 2014 High

    Revealed two distinct cytoplasmic roles: a positive adaptor function bridging TBK1 and IRF3 in IFN induction, and a hypoxia-induced actin-organizing function driving migration and metastasis.

    Evidence Two kinome-wide RNAi screens with reciprocal Co-IP and IRF3/IFN-β assays; and HIF1α manipulation, proteomic interactor identification, and zebrafish/mouse metastasis models

    PMID:24807708 PMID:25486436

    Open questions at the time
    • Reconciliation of positive (adaptor) versus negative IFN regulation context-dependence unresolved
    • Whether RIOK3 phosphorylates TBK1, IRF3, or actin partners not established
  6. 2015 High

    Established RIOK3 as a direct negative regulator of MDA5 by identifying it as a kinase that phosphorylates S828 to block filament formation.

    Evidence RIOK3 knockout cells, phosphomimetic S828D mutation, in vitro kinase assay, multimer formation assay, and IFN reporter readout after measles virus infection

    PMID:25865883

    Open questions at the time
    • Upstream signals controlling RIOK3 kinase activity unknown
    • Structural basis of MDA5 recognition not resolved
  7. 2021 High

    Uncovered a degradative arm of RIOK3 antiviral regulation, showing it recruits TRIM40 to ubiquitinate and destroy RIG-I and MDA5, with in vivo confirmation.

    Evidence Reciprocal Co-IP, K48/K27 ubiquitination assays, and myeloid-specific Riok3 knockout mice in RNA virus infection models

    PMID:34161773

    Open questions at the time
    • Whether kinase activity is required for TRIM40 recruitment not established
    • Interplay between phosphorylation-based and degradation-based MDA5 control unresolved
  8. 2021 Medium

    Demonstrated that alternative splicing of RIOK3 mRNA toward a premature-termination X2 variant tunes the IFN response during RNA virus infection.

    Evidence Transcriptome profiling, morpholino-induced splicing, and IFN reporter assays in RVFV-infected epithelial cells

    PMID:33652597

    Open questions at the time
    • Single-lab functional data
    • Protein product and stability of the X2 isoform not characterized
  9. 2022 Medium

    Extended the splicing model by showing full-length and X2 isoforms exert opposing effects on both IFN and NF-κB pathways, and linked RIOK3 to FAK and Akt in cancer migration and viral replication.

    Evidence Isoform overexpression/knockdown with reporter assays in RVFV infection; Co-IP and FAK Y397/Y925 phosphorylation in PDAC cells; kinase-dead mutant and proteomics for Akt phosphorylation in co-infection

    PMID:35795905 PMID:35982848 PMID:36146870

    Open questions at the time
    • Whether Akt and FAK are direct kinase substrates not established
    • Single-lab observations without reciprocal structural validation
  10. 2023 Medium

    Connected RIOK3 to cancer metabolism, linking it to arginine uptake/mTORC1 activation via SLC7A2 and to NADPH production via HSP90α-IDH1.

    Evidence Metabolomics, RNA-seq, knockdown/knockout with SLC7A2 and arginine uptake assays; Co-IP and HSP90α knockdown rescue of NADPH levels under glucose deprivation

    PMID:36880835 PMID:38453884

    Open questions at the time
    • Direct binding of RIOK3 to transporters/metabolic enzymes not shown
    • Mechanism by which RIOK3 facilitates HSP90α-IDH1 interaction undefined
  11. 2025 High

    Defined the structural and mechanistic basis for RIOK3-driven 40S ribosome decay, establishing it as the effector of initiation-specific ribosome-associated quality control.

    Evidence Cryo-EM of RIOK3-ubiquitylated 40S complexes with UIM mutagenesis and 18S rRNA decay analysis; genetic epistasis with RNF10 depletion and ribosome profiling under starvation

    PMID:39947183 PMID:40022732

    Open questions at the time
    • Whether RIOK3 kinase activity contributes to 40S decay versus its UIM-based recognition unresolved
    • Nuclease responsible for 18S rRNA decay not defined
  12. 2025 Low

    Broadened RIOK3's antiviral roles to additional pathways via m6A-regulated expression and Jak1/STAT1 modulation in different infection contexts.

    Evidence METTL3/m6A manipulation, RIOK3 and CDC42 expression analysis with NF-κB assays in CVB3 infection; RIOK3 knockout BMMs in RSV infection with Jak1/STAT1 analysis

    PMID:39961559 PMID:40371100

    Open questions at the time
    • No direct biochemical interaction between RIOK3 and CDC42 or Jak1/STAT1 shown
    • Single-lab pathway-correlation evidence only

Open questions

Synthesis pass · forward-looking unresolved questions
  • How RIOK3's atypical kinase activity is regulated and which of its many roles depend on catalysis versus scaffolding/UIM-based recognition remains the central unresolved question.
  • No unified model reconciling positive and negative IFN regulation
  • Direct in vivo kinase substrates beyond MDA5 not catalogued
  • Catalytic requirement for ribosome decay, migration, and metabolic roles undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 2 GO:0016740 transferase activity 2 GO:0060090 molecular adaptor activity 2 GO:0008092 cytoskeletal protein binding 1 GO:0140096 catalytic activity, acting on a protein 1
Localization
GO:0005829 cytosol 2 GO:0005840 ribosome 2 GO:0005856 cytoskeleton 1
Pathway
R-HSA-168256 Immune System 3 R-HSA-8953854 Metabolism of RNA 3 R-HSA-1643685 Disease 1
Partners
CASP10HSP90AA1IRF3MDA5RIG-ITBK1TPM3TRIM40
Complex memberships
RIOK3-ubiquitylated 40S complexpre-40S ribosomal particle

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2015 RIOK3 phosphorylates the C-terminal region of MDA5 (at S828), impairing MDA5 multimer/filament formation and attenuating MDA5-mediated type I IFN signaling. PP1α/PP1γ phosphatases counteract this by dephosphorylating MDA5. RIOK3 knockout strongly enhanced type I IFN production following measles virus infection, while phosphomimetic MDA5-S828D mutation attenuated signaling. RIOK3 knockout cells, phosphomimetic mutation (S828D), in vitro kinase assay, multimer formation assay, IFN reporter assay Cell reports High 25865883
2021 RIOK3 recruits and interacts with the E3 ubiquitin ligase TRIM40, leading to K48- and K27-linked ubiquitination and proteasomal degradation of both RIG-I and MDA5, thereby negatively regulating type I IFN signaling. Myeloid-specific Riok3 knockout mice showed enhanced type I IFN induction and resistance to RNA virus-induced pathogenesis. Co-immunoprecipitation, myeloid-specific knockout mice, ubiquitination assay (K48/K27 linkage), in vitro and in vivo viral infection models Cell reports High 34161773
2014 RIOK3 functions as an adaptor protein downstream of TBK1 and upstream of IRF3 in the type I IFN pathway, physically interacting with both TBK1 and IRF3 and bridging their interaction. RIOK3 knockdown blocks cytosolic dsRNA- and dsDNA-induced IRF3 activation and IFN-β production; overexpression activates IRF3. Kinome-wide RNAi screens (two independent), Co-immunoprecipitation (RIOK3 with TBK1 and IRF3), IFN-β reporter assay, IRF3 activation assay, transcriptome analysis Journal of virology High 24807708
2009 RIOK3 interacts with caspase-10 via its RIO domain (binding to each death effector domain of caspase-10) and negatively regulates NF-κB signaling. RIOK3 suppresses caspase-10-mediated NF-κB activation by competing with RIP1 and NIK for binding to caspase-10. Kinase activity of RIOK3 is required for suppression of TNFα-induced NF-κB activation but not for suppression of caspase-10-mediated NF-κB activation. Yeast two-hybrid, GST pull-down, endogenous co-immunoprecipitation, siRNA knockdown, NF-κB reporter assay, domain-mapping experiments Molecular and cellular biochemistry High 19557502
2025 RIOK3 specifically recognizes ubiquitylated 40S ribosomes (ubiquitylated by E3 ligase RNF10 on uS3 and uS5 during starvation) through a unique ubiquitin-interacting motif (UIM). RIOK3 binding drives progressive 3'-to-5' decay of 18S rRNA, mediating selective 40S ribosome degradation during starvation. Cryo-EM structures of RIOK3-ubiquitylated 40S complexes and degradation intermediates were resolved. Cryo-EM structural analysis, ubiquitin-interacting motif mutagenesis, starvation assays, rRNA decay analysis, functional rescue experiments Molecular cell High 39947183
2025 RIOK3 is a crucial factor in the initiation-specific ribosome-associated quality control (iRQC) pathway; it interacts with ubiquitylated 40S subunits (ubiquitylated by RNF10) to mediate their degradation. Both RNF10 and RIOK3 protein levels increase upon iRQC activation, establishing a feedforward mechanism. Amino acid starvation and 60S:40S stoichiometry imbalance (from disrupted 60S biogenesis) activate iRQC-dependent 40S decay. RIOK3 depletion, RNF10 depletion, quantitative ribosome profiling, 40S ubiquitylation assays, 60S biogenesis disruption, amino acid starvation conditions Cell reports High 40022732
2012 Human RioK3 is a cytoplasmic protein that co-sediments with cytoplasmic pre-40S ribosomal particles and associates with pre-40S particle components hLtv1, hEnp1, and 18S-E pre-rRNA. RioK3 depletion leads to increased levels of 21S rRNA precursor, indicating a role in 21S pre-rRNA processing during 40S subunit biogenesis. RioK3 does not shuttle via Crm1-dependent nuclear export (unlike RioK2). Sucrose gradient sedimentation, co-immunoprecipitation (with hLtv1, hEnp1, 18S-E pre-rRNA), siRNA depletion (RioK3, rpS15, rpS19, RioK2), Northern blot (pre-rRNA analysis) RNA biology High 22418843
2010 Riok3 is a direct target of miR-191 in mouse erythroblasts. Knockdown of Riok3 blocks erythroid enucleation and chromatin condensation during terminal erythroid differentiation. Down-regulation of miR-191 during terminal differentiation is required to allow Riok3 upregulation, which is essential for these processes. RNA-seq, miR-191 overexpression, Riok3 knockdown (siRNA), erythroid enucleation assays, chromatin condensation analysis, luciferase reporter (miR-191 target validation) Genes & development High 21196494
2014 RIOK3 is upregulated by hypoxia in an HIF1α-dependent manner. In normoxic cells, RIOK3 localizes to distinct cytoplasmic aggregates; under hypoxia it redistributes to the leading edge of cells with reorganization of the actin cytoskeleton. RIOK3 interacts with actin and actin-binding proteins including tropomyosins TPM3 and TPM4 and tropomodulin 3. RIOK3 depletion reduces actin filament number and organization, decreases TPM3 association with filaments (particularly during hypoxia), impairs cell migration and invasion, and reduces metastasis in zebrafish and mouse models. HIF1α manipulation, live imaging/localization experiments, proteomic interaction analysis (MS), siRNA depletion, actin staining, 2D migration assay, 3D invasion assay, zebrafish metastasis model, mouse pulmonary metastasis model Oncogene High 25486436
1998 The human RIOK3 gene (mapped to 18q11.2) encodes the human homologue of Aspergillus nidulans SUDD, the founding member of a conserved protein family found in archaea through humans. SUDD was originally identified as an extragenic suppressor of the bimD6 chromosome segregation mutation in A. nidulans. cDNA cloning, sequence analysis, genetic suppressor screen (A. nidulans bimD6), chromosomal mapping Gene Medium 9602165
2022 RIOK3 interacts with FAK (Focal Adhesion Kinase) via co-immunoprecipitation and stabilizes FAK protein expression. RIOK3 increases FAK phosphorylation at Y397 and Y925, but does not stabilize FAK-Y925F mutant protein. The pro-invasive and pro-migratory function of RIOK3 in pancreatic ductal adenocarcinoma cells is dependent on FAK activation. Co-immunoprecipitation, siRNA knockdown, Western blot (FAK protein stability and phosphorylation), transwell invasion/migration assays, transcriptome analysis Heliyon Medium 35982848
2022 RIOK3 kinase activity mediates Akt phosphorylation; wild-type but not kinase-dead RIOK3 promoted Akt phosphorylation and synergistic MDV/REV viral replication. RIOK3 was recruited to regulate Akt in co-infected cells, operating independently of the PI3K/Akt pathway. Kinase-dead RIOK3 mutant, LC/MS quantitative proteomics (tandem mass tag), Akt overexpression/inhibition, viral titer assays Virulence Medium 35795905
2024 RIOK3 interacts with HSP90α and facilitates HSP90α binding to IDH1, upregulating IDH1 expression and enhancing NADPH production to sustain colorectal cancer cell survival under glucose deprivation. RIOK3 inhibition had no effect on NADPH levels in HSP90α-knockdown cells, confirming HSP90α dependence. Co-immunoprecipitation (RIOK3-HSP90α, HSP90α-IDH1), RIOK3 knockout, HSP90α knockdown, NADPH measurement, cell viability assay under glucose deprivation Oncogenesis Medium 38453884
2023 RIOK3 promotes arginine uptake and mTORC1 activation in pancreatic ductal adenocarcinoma cells via upregulation of the arginine transporter SLC7A2. RIOK3 knockdown significantly inhibited SLC7A2 expression, arginine uptake, and mTORC1 activation. LC-MS metabolomics, RNA-seq, Western blot (SLC7A2, mTORC1 pathway), RIOK3 knockdown, arginine uptake assay Aging Medium 36880835
2021 RIOK3 is required for mounting an antiviral IFN response to RVFV infection in epithelial cells. During RVFV infection (and after stimulation with other RNA viruses or RIG-I agonists), RIOK3 mRNA is alternatively spliced to produce variants encoding premature termination codons (X2 isoform). This alternative splicing event dampens IFN expression. Forcing alternative splicing with a morpholino oligonucleotide reduced IFN expression. Transcriptome profiling, RIOK3 knockdown/overexpression, morpholino-induced alternative splicing, IFN reporter assays, RT-PCR for splice variants Viruses Medium 33652597
2022 RIOK3 (full-length) negatively regulates NF-κB-mediated inflammation during RVFV infection, while the alternatively spliced RIOK3-X2 isoform stimulates the NF-κB inflammatory response. The two isoforms have opposing functions on both IFN and NF-κB pathways. RIOK3 and RIOK3-X2 overexpression/knockdown, NF-κB reporter assays, IFN reporter assays, RVFV infection model Viruses Medium 36146870
2025 METTL3-mediated m6A modification of RIOK3 mRNA enhances RIOK3 expression during CVB3 (Coxsackievirus B3) enterovirus infection. RIOK3 in turn downregulates CDC42, a small GTPase, promoting NF-κB pathway activation and CVB3 replication. RIOK3 and CDC42 jointly modulate NF-κB signaling during infection. m6A-seq/METTL3 manipulation, RIOK3 overexpression/knockdown, CDC42 expression analysis, NF-κB reporter assay, viral replication assays in vitro and in vivo International journal of biological macromolecules Low 39961559
2025 RIOK3 modulates the Jak1/STAT1 signaling pathway in macrophages during RSV infection; RIOK3 knockout in bone marrow-derived macrophages enhanced viral replication and disrupted type I IFN balance. RIOK3 knockout mice (BMM), in vitro and in vivo RSV infection models, IFN measurement, Jak1/STAT1 pathway analysis Frontiers in microbiology Low 40371100

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 103 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 48 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 18 39947183
2025 RNF10 and RIOK3 facilitate 40S ribosomal subunit degradation upon 60S biogenesis disruption or amino acid starvation. Cell reports 13 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 4 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

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