Affinage

ZNF598

E3 ubiquitin-protein ligase ZNF598 · UniProt Q86UK7

Length
904 aa
Mass
98.6 kDa
Annotated
2026-06-11
17 papers in source corpus 17 papers cited in narrative 18 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ZNF598 is the primary E3 ubiquitin ligase that initiates ribosome-associated quality control (RQC) by sensing aberrant translation and marking stalled ribosomes for resolution (PMID:28132843, PMID:28685749). Acting with the E2 enzyme UBE2D3, it catalyzes regulatory ubiquitination of the small-subunit ribosomal proteins RPS10/uS10 (at K138/K139) and RPS20/uS20 (at K8) in response to ribosome stalling on poly(A) and other problematic sequences, and loss of this activity causes readthrough of stall sequences and defective stall resolution (PMID:28132843, PMID:28685749, PMID:32324387). ZNF598 is an RNA-binding protein that cross-links to tRNAs, mRNAs, and rRNA on translating ribosomes, with its yeast ortholog Hel2 using a C-terminal RNA-binding region to contact 18S rRNA in an Asc1-dependent manner required for polysome association and RQC/no-go decay function (PMID:28685749, PMID:30718516). The ubiquitin chains it deposits are read out quantitatively: chain length scales with stalling duration to distinguish transient from persistent stalls, and sufficiently long K63-linked chains on uS10 prime ribosomes for ASCC-mediated subunit dissociation, after which aberrant nascent chains are degraded by the ubiquitin-proteasome pathway (PMID:38366554, PMID:39875504, PMID:34551427). ZNF598 activity is itself regulated, being upregulated and K63-ubiquitinated in a CNOT4-dependent manner upon mitochondrial stress, and it behaves as a rate-limiting RQC factor whose recruitment to a stalled mRNA can be titrated during widespread collisions (PMID:38388640, PMID:40750700). Beyond canonical RQC, ZNF598 binds the GYF domain of GIGYF1 to link to the 4EHP–GIGYF translational repression complex and regulate cytokine mRNAs such as IL-8 and CSF2, and it binds RIG-I to promote FAT10-mediated suppression of type I interferon signaling independently of its ligase activity (PMID:30917308, PMID:31433974). An ALS-associated R69C variant is a loss-of-function mutation that impairs RQC and clearance of C9ORF72-derived poly(GR), and ZNF598 overexpression reduces poly(GR) and caspase-3 activation in patient neurons (PMID:34551427).

Mechanistic history

Synthesis pass · year-by-year structured walk · 14 steps
  1. 2017 High

    Established ZNF598 as the E3 ligase that initiates mammalian RQC, defining the enzymatic event that converts a stalled ribosome into a quality-control substrate.

    Evidence Gain/loss-of-function, ubiquitylation site mutagenesis, and poly(A) stall-readthrough reporters; parallel PAR-CLIP and E2 co-dependency in a second study

    PMID:28132843 PMID:28685749

    Open questions at the time
    • Did not define ubiquitin chain linkage type or length requirements
    • Did not identify downstream disassembly machinery
    • Mechanism of collided-ribosome recognition not structurally resolved
  2. 2017 High

    Genetic epistasis in yeast placed Hel2/Asc1 downstream of ribosome arrest but upstream of nascent-chain RQC engagement, ordering the pathway.

    Evidence Genetic epistasis with deletion combinations and nascent chain modification assays in S. cerevisiae

    PMID:28223409

    Open questions at the time
    • Did not map the molecular signal Hel2 recognizes on arrested ribosomes
    • Relationship to mammalian factors inferred by orthology
  3. 2017 Medium

    Defined the reversibility of regulatory ribosomal ubiquitination by identifying opposing deubiquitinases, framing RQC ubiquitination as a dynamic switch.

    Evidence Ubiquitination and DUB activity assays in yeast (Hel2/Ubp3) and mammalian cells

    PMID:29147007

    Open questions at the time
    • Mammalian E3/DUB assignment based on single-lab assays
    • In vivo physiological trigger for deubiquitination not established here
  4. 2019 High

    Mapped the RNA-binding determinant of the ortholog Hel2 to a C-terminal region contacting 18S rRNA, explaining how the ligase docks onto translating ribosomes.

    Evidence In vivo CRAC crosslinking/MS, C-terminal truncation mutants, polysome fractionation, and Asc1 epistasis in yeast

    PMID:30718516

    Open questions at the time
    • Structural basis of 18S contact unresolved
    • Whether the mammalian protein uses an identical RNA-binding mode not tested
  5. 2019 Medium

    Revealed a non-canonical role linking ZNF598 to translational repression of cytokine mRNAs via the GIGYF/4EHP complex, expanding its function beyond RQC.

    Evidence GYF-domain interaction assays, RNA-seq in KO cells, and RNA immunoprecipitation of IL-8/CSF2 mRNAs

    PMID:30917308

    Open questions at the time
    • Whether ligase activity is required for cytokine mRNA repression unclear
    • Mechanistic link between repression and stalling not defined
    • Single-lab, two-method support
  6. 2019 Medium

    Identified a ligase-independent innate-immunity function in which ZNF598 promotes FAT10 binding to RIG-I to dampen type I IFN signaling.

    Evidence Reciprocal Co-IP, FAT10 KO rescue, and E3-dead mutant IFN signaling assays

    PMID:31433974

    Open questions at the time
    • Structural basis of ZNF598–RIG-I–FAT10 assembly unknown
    • Physiological context distinguishing this from RQC role unclear
  7. 2020 Medium

    Showed ZNF598 is a direct chemical target of arsenite, providing a mechanistic link between an environmental proteostatic stressor and RQC inhibition.

    Evidence Direct arsenite-binding assay, site-specific ubiquitination MS, and poly(A) readthrough reporters in ZNF598 KO cells

    PMID:32324387

    Open questions at the time
    • Arsenite binding site on ZNF598 not mapped
    • Single-lab study
  8. 2021 High

    Connected ZNF598 to neurodegeneration by demonstrating co-translational titration and degradation of C9ORF72 poly(GR) and an ALS-associated loss-of-function variant.

    Evidence Reporter assays, KO/overexpression, Drosophila screen, ALS R69C mutant, and lentiviral rescue in patient-derived neurons

    PMID:34551427

    Open questions at the time
    • Causal genetic link of R69C to ALS in patient cohorts not established here
    • How poly(GR) translation triggers ZNF598 engagement unresolved
  9. 2021 Medium

    Demonstrated that Hel2 surveils secretory ribosome-nascent chain complexes and protects against organelle mistargeting, broadening the substrate range of the sensor.

    Evidence Selective ribosome profiling, SRP-deficient strains, and mitochondrial import assays in yeast

    PMID:33761353

    Open questions at the time
    • Whether mammalian ZNF598 performs equivalent secretory surveillance untested
    • Single-lab study
  10. 2024 High

    In vitro reconstitution refined the mechanism, showing collision is not strictly required for ZNF598 ubiquitination or ASCC dissociation given adequate downstream mRNA and ubiquitin chain length.

    Evidence Cell-free ubiquitination and ribosome dissociation assays with defined substrates

    PMID:38366554

    Open questions at the time
    • Reconciliation with in-cell collision-dependence not fully resolved
    • Minimal recognition determinant on the 40S not defined
  11. 2024 Medium

    Identified CNOT4-dependent K63-ubiquitination as an upstream regulatory layer that activates ZNF598 during mitochondrial stress.

    Evidence Ubiquitination assays, CNOT4 KO/KD, and Drosophila mitochondrial stress models

    PMID:38388640

    Open questions at the time
    • Ubiquitination sites on ZNF598 and their mechanistic consequence not mapped
    • Single-lab study
  12. 2025 Medium

    Established that ubiquitin chain length on uS10/uS20 encodes stalling duration, allowing ZNF598 to discriminate transient from persistent stalls.

    Evidence Quantitative in vivo Hel2-ribosome association, chain-length analysis, and Slh1/Ubp2/Ubp3 epistasis in yeast

    PMID:39875504

    Open questions at the time
    • Mechanism by which chain length is read by downstream machinery in mammals unclear
    • Single-lab study
  13. 2025 Medium

    Single-molecule imaging established ZNF598 as a rate-limiting RQC factor that multiple copies engage per stalled mRNA and that is titrated during widespread collisions.

    Evidence Single-molecule live-cell imaging with endogenous HaloTag and overexpression ribosome-clearance assays

    PMID:40750700

    Open questions at the time
    • Quantitative cellular abundance limits not defined across cell types
    • Single-lab study
  14. 2024 Medium

    Demonstrated a developmental gene-regulatory role in which Znf598 targets C2H2-zinc-finger mRNAs for no-go decay during the maternal-to-zygotic transition.

    Evidence RNA-seq of mutant embryos, disome profiling, and reporter assays in zebrafish

    PMID:39636823

    Open questions at the time
    • Whether this developmental program is conserved in mammals untested
    • Link between tandem C2H2 translation and collision not structurally defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How ZNF598 selectively recognizes the collided/40S interface at the structural level, and how cell-type-specific demand (e.g., stem cell essentiality, start-site collisions) is met by a limiting amount of the protein, remain open.
  • No structure of ZNF598 engaging collided ribosomes in the corpus
  • Cell-type essentiality data is from a preprint without biochemical reconstitution
  • Determinants of start-site collision recognition undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003723 RNA binding 3 GO:0016740 transferase activity 3 GO:0140096 catalytic activity, acting on a protein 3 GO:0016874 ligase activity 2 GO:0098772 molecular function regulator activity 2
Localization
GO:0005840 ribosome 3 GO:0005829 cytosol 2
Pathway
R-HSA-392499 Metabolism of proteins 3 R-HSA-8953854 Metabolism of RNA 3 R-HSA-168256 Immune System 2
Partners
CNOT4FAT10GIGYF1RIG-IUBE2D3

Evidence

Reading pass · 18 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2017 ZNF598 is an E3 ubiquitin ligase that mediates regulatory ubiquitylation of ribosomal proteins RPS10 and RPS20 on stalled ribosomes to initiate ribosome-associated quality control (RQC) of poly(A)-induced stalled ribosomes; loss of ZNF598 function or mutations blocking RPS10/RPS20 ubiquitylation result in defective resolution of stalled ribosomes and readthrough of poly(A)-containing stall sequences. Gain/loss-of-function experiments, ubiquitylation site mutagenesis, poly(A)-stall readthrough reporter assays Molecular cell High 28132843
2017 ZNF598 cross-links to tRNAs, mRNAs, and rRNAs on translating ribosomes (PAR-CLIP), is enriched on AAA-decoding tRNALys(UUU), triggers ubiquitination of multiple ribosomal proteins in response to translated poly(AAA) sequences, and requires the E2 ubiquitin ligase UBE2D3 to initiate RQC. PAR-CLIP, ribosomal protein ubiquitination assays, E2 ligase co-dependency experiments Nature communications High 28685749
2017 In yeast, Hel2 (ZNF598 ortholog) and Asc1 are required for RQC-mediated modification (ubiquitination/targeting) of nascent chains on arrested ribosomes; ribosome stalling itself still occurs in their absence, placing Hel2/Asc1 downstream of arrest but upstream of RQC engagement. Genetic epistasis analysis in S. cerevisiae, nascent chain modification assays RNA (New York, N.Y.) High 28223409
2017 In yeast, Hel2 E3 ligase mediates mono-ubiquitination of Rps3 (the yeast equivalent of regulatory ribosomal ubiquitination), and this is reversed by the deubiquitinase Ubp3; in mammalian cells the analogous pair is RNF123 (E3) and USP10 (DUB). Ubiquitination assays, deubiquitinase activity assays, co-fractionation Experimental & molecular medicine Medium 29147007
2019 In yeast, the C-terminal region of Hel2 is an RNA-binding domain that contacts 18S rRNA and translated mRNAs; this 18S rRNA interaction is required for Hel2 polysome association and for its function in both RQC and no-go decay (NGD). Asc1 acts upstream of Hel2 and is required for Hel2 binding to 18S rRNA. In vivo UV-crosslinking/mass spectrometry (CRAC), C-terminal truncation mutants, polysome fractionation, genetic epistasis Nature communications High 30718516
2019 ZNF598 functions as an RNA-binding protein with three proline-rich motifs that bind the GYF domain of GIGYF1, linking ZNF598 to the 4EHP-GIGYF1/2 translational repression complex; ZNF598 binds IL-8 mRNA and is required for regulation of TTP target mRNAs including IL-8 and CSF2. RNA sequencing (loss-of-function), protein interaction assays (GYF domain binding), RNA immunoprecipitation Cell reports Medium 30917308
2019 ZNF598 binds directly to RIG-I and promotes FAT10 (a ubiquitin-like protein) binding to RIG-I, thereby inhibiting RIG-I polyubiquitination required for downstream type I IFN signaling; ZNF598 ubiquitin ligase activity is dispensable for this suppression, and the effect is abrogated by FAT10 knockout. Co-immunoprecipitation, FAT10 knockout, IFN signaling assays, ubiquitination assays with E3-dead mutant Cell reports Medium 31433974
2020 Arsenite directly binds ZNF598 in cells and reduces ubiquitination of RPS10 (K138/K139) and RPS20 (K8), leading to augmented readthrough of poly(A)-containing stall sequences; this readthrough defect is abolished in ZNF598 knockout cells, placing ZNF598 as the arsenite target mediating proteostatic stress. Chemical biology (arsenite-protein interaction), ubiquitination site-specific MS, poly(A) stall-readthrough reporter in ZNF598 KO cells Chemical research in toxicology Medium 32324387
2021 ZNF598 co-translationally titrates expression of C9ORF72-derived poly(GR) protein; ZNF598 and listerin 1 promote poly(GR) degradation via the ubiquitin-proteasome pathway. An ALS-associated ZNF598 R69C mutant displays loss-of-function on poly(GR) expression and general RQC. Lentiviral ZNF598 overexpression in C9-ALS patient neurons reduces poly(GR) and suppresses caspase-3 activation. Reporter assays, ZNF598 KO/overexpression, Drosophila genetic screen, patient-derived neurons, lentiviral overexpression, ubiquitin-proteasome pathway assays Nucleic acids research High 34551427
2021 In yeast, Hel2 preferentially binds pre-engaged secretory ribosome-nascent chain complexes (RNCs) that translate upstream of signal sequences; Hel2 recruitment to secretory RNCs is elevated under SRP-deficient conditions, and hel2 deletion enhances mitochondrial mistargeting of secretory proteins. Selective ribosome profiling (genome-wide), SRP-deficient strains, mitochondrial import assays Cell reports Medium 33761353
2022 ZNF598 mediates ubiquitination and destabilization of Nrf2; 4-octyl itaconate inhibits ZNF598-dependent ubiquitination of Nrf2, thereby increasing Nrf2 protein levels. Western blotting, immunoprecipitation ubiquitination assay Osteoarthritis and cartilage Low 36270478
2024 Using in vitro reconstitution, ribosomal collision is not a strict prerequisite for ZNF598-mediated K63-polyubiquitination of uS10 (RPS10) or for ASCC-mediated ribosome dissociation; ASCC efficiently dissociates polysomes, monosomes, and reconstituted 80S elongation complexes following ZNF598 ubiquitination, provided ≥30-35 nt of mRNA extend downstream of the P site and sufficiently long ubiquitin chains are present. In vitro reconstitution, cell-free ubiquitination assays, ribosome dissociation assays with defined substrates Nucleic acids research High 38366554
2024 ZNF598 undergoes regulatory K63-linked ubiquitination in a CNOT4-dependent manner and is upregulated upon mitochondrial stress; this ZNF598 ubiquitination is required for resolution of stalled ribosomes and protection against mitochondrial stress in mammalian cells and Drosophila. Ubiquitination assays, CNOT4 KO/KD, Drosophila models, mitochondrial stress assays Nature communications Medium 38388640
2024 In zebrafish, Znf598 down-regulates mRNAs encoding C2H2-type zinc finger domains during the maternal-to-zygotic transition; ribosomes stall and collide while translating tandem C2H2-ZF sequences, triggering Znf598-dependent mRNA degradation via no-go decay. RNA-Seq of znf598 mutant embryos, reporter assays, disome profiling PLoS biology Medium 39636823
2023 During zebrafish development, Znf598 ubiquitinates ribosomal protein Rps10/eS10, and Rps10 ubiquitination-site mutations reduce the overall ubiquitination pattern of the ribosome; ribosome ubiquitination by Znf598 is dynamically regulated across developmental stages. Affinity purification of FLAG-tagged ribosomes, immunoblotting, ubiquitination-site mutant zebrafish RNA (New York, N.Y.) Medium 37751929
2025 In yeast, Hel2 occupancy on ribosomes increases progressively from monosomes to disomes to trisomes; Hel2 translates the duration of ribosome stalling into polyubiquitin chain length on Rps20/uS10 (mono/di-ubiquitinated disomes resolve independently of Slh1; tri/tetra-ubiquitinated ones do not), allowing distinction of transient from long-term stalling. Ubp2/Ubp3 deubiquitinases remove Hel2-dependent ubiquitin chains upon translational run-off. Quantitative in vivo analysis of Hel2-ribosome complexes, polysome fractionation, ubiquitination chain-length analysis, Slh1/Ubp2/Ubp3 genetic epistasis Communications biology Medium 39875504
2025 Single-protein/mRNA imaging shows that multiple ZNF598 molecules engage a single RQC reporter mRNA simultaneously (not just the leading collided ribosome); ZNF598 overexpression increases ribosomal clearance rate, establishing ZNF598 as a rate-limiting factor for RQC. Under global UV-induced RNA damage, ZNF598 recruitment to RQC reporter mRNA diminishes, consistent with ZNF598 being a limiting resource. Single-molecule live-cell imaging (HaloTag endogenous tagging), ZNF598 overexpression ribosome clearance assay The EMBO journal Medium 40750700
2025 In human iPSCs, ZNF598 is required to resolve a novel class of ribosome collisions at translation start sites on endogenous mRNAs with highly efficient initiation; CRISPRi screens show ZNF598 is selectively essential in stem cells compared to differentiated neural/cardiac cells. Comparative CRISPRi screens in hiPSC vs. differentiated cells bioRxivpreprint Low

Source papers

Stage 0 corpus · 17 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2017 ZNF598 and RACK1 Regulate Mammalian Ribosome-Associated Quality Control Function by Mediating Regulatory 40S Ribosomal Ubiquitylation. Molecular cell 308 28132843
2017 The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. Nature communications 177 28685749
2017 Asc1, Hel2, and Slh1 couple translation arrest to nascent chain degradation. RNA (New York, N.Y.) 120 28223409
2019 GIGYF1/2-Driven Cooperation between ZNF598 and TTP in Posttranscriptional Regulation of Inflammatory Signaling. Cell reports 48 30917308
2017 Modulating cellular balance of Rps3 mono-ubiquitination by both Hel2 E3 ligase and Ubp3 deubiquitinase regulates protein quality control. Experimental & molecular medicine 42 29147007
2019 Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control. Nature communications 34 30718516
2021 ZNF598 co-translationally titrates poly(GR) protein implicated in the pathogenesis of C9ORF72-associated ALS/FTD. Nucleic acids research 32 34551427
2019 Attenuation of the Innate Immune Response against Viral Infection Due to ZNF598-Promoted Binding of FAT10 to RIG-I. Cell reports 31 31433974
2022 Activation of Nrf2 signaling by 4-octyl itaconate attenuates the cartilaginous endplate degeneration by inhibiting E3 ubiquitin ligase ZNF598. Osteoarthritis and cartilage 21 36270478
2021 The ribosome collision sensor Hel2 functions as preventive quality control in the secretory pathway. Cell reports 20 33761353
2024 Ribosomal collision is not a prerequisite for ZNF598-mediated ribosome ubiquitination and disassembly of ribosomal complexes by ASCC. Nucleic acids research 17 38366554
2024 Stalled translation by mitochondrial stress upregulates a CNOT4-ZNF598 ribosomal quality control pathway important for tissue homeostasis. Nature communications 15 38388640
2020 Arsenite Binds to ZNF598 to Perturb Ribosome-Associated Protein Quality Control. Chemical research in toxicology 11 32324387
2024 Translation of zinc finger domains induces ribosome collision and Znf598-dependent mRNA decay in zebrafish. PLoS biology 6 39636823
2023 Znf598-mediated Rps10/eS10 ubiquitination contributes to the ribosome ubiquitination dynamics during zebrafish development. RNA (New York, N.Y.) 6 37751929
2025 Single-protein/RNA imaging reveals ZNF598 as a limiting factor in resolving collided ribosomes. The EMBO journal 3 40750700
2025 Stalled disomes marked by Hel2-dependent ubiquitin chains undergo Ubp2/Ubp3-mediated deubiquitination upon translational run-off. Communications biology 2 39875504

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