Affinage

LTN1

E3 ubiquitin-protein ligase listerin · UniProt O94822

Length
1766 aa
Mass
200.6 kDa
Annotated
2026-06-10
23 papers in source corpus 21 papers cited in narrative 21 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

LTN1/Listerin is a RING-domain E3 ubiquitin ligase that serves as the central effector of ribosome-associated quality control (RQC), targeting aberrant translation products for proteasomal degradation and maintaining neuronal proteostasis (PMID:19196968, PMID:23685075). It preferentially recognizes stalled 60S-nascent chain complexes generated by Hbs1/Pelota/ABCE1-mediated ribosome splitting, rather than intact 80S ribosomes, and ubiquitinates the nascent chains exposed on these 60S subunits; this recognition depends on its conserved N-terminal domain, whose crystal structure reveals the 60S-binding surface that is separable from intrinsic ligase activity (PMID:23685075, PMID:27385828). Structurally Listerin is an elongated HEAT/ARM-repeat protein with a C-terminal RING domain and flexible hinges reminiscent of cullin-RING ligases (PMID:23319619). Within the RQC complex, the cofactor TCF25 (yeast Rqc1) binds the RING domain and orients the acceptor ubiquitin so that its K48 attacks the Ube2D-charged thioester, imposing K48 chain specificity, while Listerin recruits the Cdc48/p97 extractase (with Ufd1-Npl4) to extract ubiquitylated peptides from the 60S subunit [PMID:40169231, PMID:bio_10.1101_2025.01.03.631235, PMID:27129255]. Loss of Listerin causes aggregation of aberrant proteins in a manner dependent on Rqc2/NEMF-mediated C-terminal tailing (CAT-tails/Ala-tails), and partial reduction of NEMF Ala-tailing rescues the lister neurodegeneration phenotype, defining a genetic axis between tail addition and Listerin-dependent clearance (PMID:27129255, PMID:39229065). Beyond canonical RQC, Listerin ubiquitinates non-ribosomal substrates with non-K48 linkages to regulate diverse processes: it drives K63-linked ubiquitination of cGAS, RIG-I and MDA5 to route them for ESCRT-dependent degradation and dampen innate antiviral signaling (PMID:38109536, PMID:38060409), stabilizes ABCA1 via K63 chains to promote macrophage cholesterol efflux (PMID:40526435), directs α-synuclein to ESCRT-dependent degradation via K27 linkages in models of Parkinson's disease (PMID:39937915), and destabilizes IGF2BP1 in hepatocellular carcinoma (PMID:37708447). In yeast, Ltn1 additionally ubiquitylates the ribosomal protein Rpl25 to inhibit 60S ribophagy, an activity antagonized by the Ubp3-Bre5 deubiquitylase (PMID:24616224).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2009 High

    Established that LTN1 is an E3 ubiquitin ligase whose loss disrupts neuronal homeostasis, providing the first functional and physiological anchor for the gene.

    Evidence In vitro ligase assay plus ENU and gene-trap mouse alleles with a defined neurodegeneration phenotype

    PMID:19196968

    Open questions at the time
    • Did not define the molecular substrates or the link to translation
    • Mechanism connecting ligase activity to neurodegeneration unresolved
  2. 2013 High

    Defined the substrate context of Listerin, showing it acts on split 60S-nascent chain complexes downstream of ribosome recycling rather than on intact 80S ribosomes.

    Evidence In vitro reconstitution of nascent chain ubiquitination from aberrant mRNAs with manipulation of Hbs1/Pelota/ABCE1 recycling factors

    PMID:23685075

    Open questions at the time
    • Structural basis of 60S recognition not defined
    • Linkage type and chain-elongation machinery not yet established
  3. 2013 Medium

    Provided the first architectural view of Ltn1, revealing an elongated, conformationally flexible HEAT/ARM-repeat scaffold bridging the N-terminus and the catalytic RING.

    Evidence Single-particle negative-stain and cryo EM with 2D/3D reconstructions

    PMID:23319619

    Open questions at the time
    • Moderate resolution, no atomic model
    • No mutagenesis linking architecture to function in the same study
  4. 2014 Medium

    Dissected substrate recognition, showing in yeast that the middle domain directly binds C-terminal polylysine of nonstop proteins while Ltn1 acts upstream of ER-associated ligases for stalled and nonstop substrates.

    Evidence In vitro binding/ubiquitylation with domain mapping; comparative E3 deletion genetics with ER reporters

    PMID:25305489 PMID:26055716

    Open questions at the time
    • Direct polylysine binding shown in vitro independent of ribosome context
    • Relative contribution of context-dependent vs context-independent recognition in cells unclear
  5. 2014 Medium

    Revealed a quality-control function on intact ribosomal proteins by showing Ltn1 ubiquitylates Rpl25 to restrain 60S ribophagy, antagonized by a deubiquitylase.

    Evidence Yeast genetic epistasis, Rpl25 site mutagenesis, and ribophagy assays under starvation

    PMID:24616224

    Open questions at the time
    • Whether mammalian Listerin performs analogous ribophagy control unknown
    • Coupling to canonical RQC activity not resolved
  6. 2016 High

    Mapped the 60S-binding determinant to the conserved N-terminal domain and separated ribosome engagement from catalytic activity, and connected Listerin loss to CAT-tail-dependent aggregation and Cdc48 recruitment.

    Evidence Crystal structure of the NTD at 2.4 A with mutagenesis and reconstitution; yeast deletion combinations with aggregate proteomics and Cdc48 co-sedimentation

    PMID:27129255 PMID:27385828

    Open questions at the time
    • Full ribosome-bound complex structure not resolved
    • How Cdc48 recruitment is coordinated with ubiquitination timing unclear
  7. 2020 Low

    Implicated the Ssb/RAC chaperone system in promoting Ltn1 recruitment to ribosomes, linking co-translational chaperones to RQC ligase loading.

    Evidence Yeast overexpression rescue and ribosome fractionation in SSB deletion strains

    PMID:32957466

    Open questions at the time
    • Recruitment inferred from fractionation, no direct binding reconstitution
    • Single lab, single study
  8. 2023 Medium

    Extended Listerin function beyond RQC to innate immune regulation, showing it recruits TRIM27 to drive K63-linked ubiquitination and ESCRT-mediated degradation of cGAS, RIG-I and MDA5.

    Evidence Co-IP, K63-linkage-specific ubiquitination assays, ESCRT functional assays, and KO cell/mouse viral infection models

    PMID:38060409 PMID:38109536

    Open questions at the time
    • Direct vs TRIM27-bridged ubiquitination roles not fully separated
    • Whether Listerin acts catalytically or as a scaffold here unresolved
  9. 2023 Low

    Identified a tumor-context substrate, with Listerin ubiquitinating and destabilizing IGF2BP1 to suppress c-Myc and IGF-1R signaling in hepatocellular carcinoma.

    Evidence In vivo CRISPR KO screen, interactome MS, and ubiquitination western blots with gain/loss-of-function growth assays

    PMID:37708447

    Open questions at the time
    • No in vitro reconstitution or interface mutagenesis
    • Ubiquitin linkage type not defined
  10. 2024 Medium

    Defined the boundaries of Listerin function by uncovering a Listerin-independent mitochondrial RQC pathway (NEMF Ala-tails recognized by Pirh2/ClpXP) and a genetic Ala-tail axis where reduced NEMF tailing rescues lister neurodegeneration.

    Evidence KO cell lines with biochemical assays; mouse genetic epistasis of Nemf Ala-tailing alleles crossed with lister mice

    PMID:38412092 PMID:39229065

    Open questions at the time
    • Ala-tail epistasis reported in preprint
    • How Ala-tails switch substrates between degradation and aggregation not fully defined
  11. 2025 High

    Resolved how Listerin builds K48 chains, showing TCF25 binds the RING and orients the acceptor ubiquitin to dictate K48 specificity with Ube2D E2s, and how Cdc48 is recruited for extraction.

    Evidence In vitro ubiquitination with interface mutagenesis and AlphaFold3 modeling; cryo-EM of the yeast RQC complex with reconstitution

    PMID:40169231 PMID:bio_10.1101_2025.01.03.631235

    Open questions at the time
    • Cryo-EM complex reported in preprint
    • Mammalian RQC complex structure not solved
  12. 2025 Medium

    Expanded the non-canonical substrate repertoire and disease relevance, linking Listerin-mediated non-K48 ubiquitination and an RNA-binding activity to cholesterol efflux and neurodegeneration.

    Evidence Macrophage-specific and microglial KO/OE mouse models with K63/K27-linkage-specific ubiquitination, site mutagenesis, RIP, and disease readouts

    PMID:39937915 PMID:40448625 PMID:40526435

    Open questions at the time
    • Substrate selectivity mechanism across distinct linkage types unresolved
    • How a RING ligase achieves direct TLR4 mRNA binding not structurally defined

Open questions

Synthesis pass · forward-looking unresolved questions
  • How Listerin partitions between canonical RQC and its many non-ribosomal substrates, and what determines its choice of K48, K63 or K27 linkage in each context, remains unresolved.
  • No unifying model for substrate and linkage selection
  • Mammalian ribosome-bound holocomplex structure lacking
  • Direct vs scaffolded ligase roles in immune and metabolic contexts unseparated

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140096 catalytic activity, acting on a protein 6 GO:0016874 ligase activity 4 GO:0003723 RNA binding 1
Localization
GO:0005768 endosome 2 GO:0005829 cytosol 2 GO:0005840 ribosome 2
Pathway
R-HSA-392499 Metabolism of proteins 4 R-HSA-5357801 Programmed Cell Death 3 R-HSA-168256 Immune System 2 R-HSA-8953854 Metabolism of RNA 2
Partners
ABCA1CDC48/P97CGASIGF2BP1RPL25RQC2/NEMFTCF25TRIM27
Complex memberships
Ribosome-associated quality control (RQC) complex

Evidence

Reading pass · 21 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2009 LISTERIN (LTN1) functions as an E3 ubiquitin ligase in vitro; loss-of-function in mice (lister allele) causes progressive neurological/motor dysfunction, gliosis, dystrophic neurites, vacuolated mitochondria, and accumulation of hyperphosphorylated tau, establishing its role in neuronal homeostasis. In vitro ubiquitin ligase assay; ENU forward genetics screen; targeted gene trap mouse model Proceedings of the National Academy of Sciences of the United States of America High 19196968
2013 Listerin preferentially recognizes 60S-nascent chain complexes (not 80S ribosomes) generated by Hbs1/Pelota/ABCE1-mediated ribosome recycling, and ubiquitinates nascent chains on these 60S subunits; interfering with Hbs1 stabilizes 80S complexes, reduces Listerin recruitment, and reduces nascent chain ubiquitination. In vitro reconstitution of ubiquitination from aberrant mRNAs; ribosome fractionation; functional interference with recycling factors Molecular cell High 23685075
2013 Single-particle EM reveals Ltn1 has an elongated structure with HEAT/ARM repeats, a conserved N-terminus, and a C-terminal RING domain; the protein displays conformational variability about two flexible hinge regions, with architecture reminiscent of cullin-RING ubiquitin ligase complexes. Single-particle electron microscopy (negative stain and vitreous ice); 2D classifications and 3D reconstructions Proceedings of the National Academy of Sciences of the United States of America Medium 23319619
2014 In yeast, Ltn1/Rkr1 ubiquitylates the ribosomal protein Rpl25 and acts as an inhibitor of 60S ribosomal subunit ribophagy (selective autophagy); this activity is antagonized by the Ubp3-Bre5 deubiquitylase complex. Genetic epistasis (ltn1 and ubp3 deletions in yeast); western blotting for Rpl25 ubiquitylation; mutation of Rpl25 ubiquitylation site; ribophagy assays under nitrogen starvation The Journal of cell biology Medium 24616224
2014 The middle domain of yeast Ltn1 directly binds the C-terminal polylysine residues of nonstop proteins (affinity 2–3 μM) and efficiently ubiquitylates them, demonstrating direct substrate recognition independent of ribosome context. In vitro binding assay; ubiquitylation assay; domain mapping with Ltn1 truncations Biochemical and biophysical research communications Medium 25305489
2015 Yeast Rkr1/Ltn1 plays the primary role in proteasomal degradation of soluble and transmembrane ER-targeted nonstop and translationally stalled proteins, acting upstream of ER-associated E3 ligases Doa10 and Hrd1. Genetic deletion of candidate E3 ligases (Rkr1, Doa10, Hrd1) in yeast; reporter protein abundance assays; proteasome inhibitor experiments The Journal of biological chemistry Medium 26055716
2016 The conserved N-terminal domain (NTD) of Ltn1 is required for binding to stalled 60S ribosomal subunits; NTD mutations that impair 60S binding also reduce nonstop protein ubiquitylation without affecting intrinsic E3 ligase activity. Crystal structure of the Ltn1 NTD was solved at 2.4 Å resolution. Crystal structure determination (2.4 Å); in vitro reconstitution of nonstop protein ubiquitylation in Neurospora crassa extracts; site-directed mutagenesis; 60S binding assays Proceedings of the National Academy of Sciences of the United States of America High 27385828
2016 Absence of Rqc1 or Ltn1 in yeast leads to aggregation of aberrant proteins in a manner dependent on CAT-tail addition by Rqc2; both Rqc1 and Ltn1 are required for efficient Cdc48 recruitment to stalled 60S particles to prevent aggregate formation. Yeast genetic deletions (rqc1Δ, ltn1Δ, rqc2Δ combinations); aggregate isolation; proteasome inhibition; proteomics of aggregates; Cdc48 co-sedimentation assays The Journal of biological chemistry Medium 27129255
2020 The ribosome-associated chaperone Ssb/RAC cooperates with Ltn1 to promote ubiquitination of aberrant nascent chains on 80S ribosomes; Ssb/RAC facilitates Ltn1 recruitment to ribosomes, and deletion of Ssb genes reduces Ltn1 association with 80S and free 60S subunits. Yeast genetic overexpression rescue assays; quantitative western blot of ribosome fractions; Ltn1 association assays with 80S and 60S subunits in SSB deletion strains International journal of molecular sciences Low 32957466
2023 Listerin interacts with cGAS on endosomes and promotes K63-linked ubiquitination of cGAS through recruitment of E3 ligase TRIM27; polyubiquitinated cGAS is recognized by the ESCRT machinery and sorted into endosomes for degradation, negatively regulating cGAS-STING innate immune signaling. Co-immunoprecipitation; ubiquitination assays (K63-linkage); ESCRT pathway functional assays; Listerin KO cell and mouse experiments; HSV-1 infection model Proceedings of the National Academy of Sciences of the United States of America Medium 38109536
2023 LTN1/Listerin recruits E3 ubiquitin ligase TRIM27 to trigger K63-linked polyubiquitination of RIG-I and MDA5 (IFIH1), facilitating their sorting and degradation via the ESCRT-dependent pathway, thereby negatively regulating RLR-mediated antiviral innate immunity. Co-immunoprecipitation; K63-linkage specific ubiquitination assays; ESCRT inhibition; LTN1 KO cells; RNA virus infection models Autophagy Medium 38060409
2023 LTN1 ubiquitinates and destabilizes IGF2BP1 protein in hepatocellular carcinoma cells, inhibiting downstream c-Myc and IGF-1R signaling pathways. In vivo CRISPR KO screen; Co-IP with 2D-LC-MS/MS interactome; western blotting for ubiquitination; forced expression and knockdown with cell growth assays Hepatology communications Low 37708447
2024 A Listerin-independent mitochondrial RQC pathway exists: NEMF-mediated C-terminal poly-alanine tails on mitochondrial nascent polypeptides are recognized by cytosolic E3 ligase Pirh2 and mitochondrial protease ClpXP, working coordinately to clear stalled mitochondrial polypeptides when Listerin cannot access lysine residues inside translocons. KO cell lines; co-immunoprecipitation; proteasome and mitochondrial protease inhibition; aggregate formation assays; mitochondrial integrity assays Cell reports Medium 38412092
2024 NEMF poly-alanine (Ala-tail) tailing activity genetically interacts with Listerin function in vivo: partial reduction of NEMF Ala-tailing (heterozygous Nemf mutation) markedly improves the lister neurodegeneration phenotype, while homozygous impairment of Ala-tailing combined with lister mutation is synthetic lethal. RQC substrates that evade degradation form amyloid-like aggregates in an Ala-tail-dependent fashion. Mouse genetic epistasis (Nemf Ala-tailing mutant crossed with lister mice); lifespan and motor phenotype analysis; aggregate characterization (amyloid-like properties) bioRxivpreprint Medium 39229065
2025 TCF25 (mammalian homolog of yeast Rqc1) interacts with the RING domain of Listerin and with acceptor ubiquitin (UbA), orienting UbA such that its K48 is positioned to attack the E2~Ub thioester bond, thereby imposing K48 chain specificity on Listerin-mediated ubiquitination paired with Ube2D E2s. TCF25 itself is also K48-specifically ubiquitinated by Listerin. Functional biochemical ubiquitination assays; AlphaFold3 modeling; mutagenesis of TCF25-Listerin interface; K48-linkage specific assays Genes & development High 40169231
2025 Listerin stabilizes ABCA1 by catalyzing K63-linked polyubiquitination at residues K1884/K1957 of ABCA1, counteracting ESCRT-mediated lysosomal degradation induced by oxidized LDL, and thereby promoting macrophage cholesterol efflux. Macrophage-specific KO mice; overexpression studies; Co-IP; K63-specific ubiquitination assays; site-directed mutagenesis of ABCA1 ubiquitylation sites; ABCA1 agonist rescue; ABCA1 KO epistasis The Journal of clinical investigation Medium 40526435
2025 Listerin promotes K27-linked polyubiquitination of α-synuclein, directing it to endosomes for ESCRT-dependent degradation; Listerin gene deletion exacerbates neurodegeneration in a PD mouse model while overexpression mitigates disease progression. Co-IP; K27-linkage specific ubiquitination assays; ESCRT pathway assays; Listerin KO and overexpression in PD mouse models Science advances Medium 39937915
2025 Listerin directly binds TLR4 mRNA and facilitates IRE1α-mediated cleavage and degradation of TLR4 mRNA, reducing TLR4-induced brain inflammation and alleviating AD-related cognitive impairments in mouse models. RNA immunoprecipitation (RIP); microglial-specific KO mice; IRE1α cleavage assays; adenovirus-mediated Listerin overexpression in Aβ-neurodegeneration mouse model; cognitive behavioral testing Advanced science Medium 40448625
2025 LTN1 suppresses expression of RNF10 in a manner dependent on its RING domain, revealing crosstalk between translational quality control E3 ligases. Knockout mouse and human cell lines; western blot for RNF10 protein levels; RING domain mutant analysis FEBS letters Low 41451945
2025 Cryo-EM structure of the yeast RQC complex shows that Ltn1 recruits the Cdc48 extractase (with Ufd1-Npl4 adaptor) to extract ubiquitylated stalled peptides from the 60S ribosome; Rqc1 bridges the 60S ribosome with ubiquitin and Ltn1 to facilitate K48-linked polyubiquitin chain formation. Cryo-EM structural determination of RQC complex; functional reconstitution assays bioRxivpreprint Medium bio_10.1101_2025.01.03.631235
2025 Canonical RQC factors including LTN1/Listerin associate with ribosomes stalled at the ER; ribosome splitting is a prerequisite for UFMylation of RPL26, and UFMylation persists in the absence of late RQC components NEMF and LTN1, indicating UFMylation acts upstream of or parallel to NEMF/LTN1 in ER-stalled ribosome clearance. ER-targeted stalling reporters; functional cellular assays; UFMylation and RQC factor KO/depletion; ribosome fractionation bioRxivpreprint Low bio_10.1101_2025.01.17.633636

Source papers

Stage 0 corpus · 23 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 A mouse forward genetics screen identifies LISTERIN as an E3 ubiquitin ligase involved in neurodegeneration. Proceedings of the National Academy of Sciences of the United States of America 210 19196968
2013 Listerin-dependent nascent protein ubiquitination relies on ribosome subunit dissociation. Molecular cell 183 23685075
2014 Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy. The Journal of cell biology 82 24616224
2016 Rqc1 and Ltn1 Prevent C-terminal Alanine-Threonine Tail (CAT-tail)-induced Protein Aggregation by Efficient Recruitment of Cdc48 on Stalled 60S Subunits. The Journal of biological chemistry 77 27129255
2015 Rkr1/Ltn1 Ubiquitin Ligase-mediated Degradation of Translationally Stalled Endoplasmic Reticulum Proteins. The Journal of biological chemistry 47 26055716
2016 Structure and function of the yeast listerin (Ltn1) conserved N-terminal domain in binding to stalled 60S ribosomal subunits. Proceedings of the National Academy of Sciences of the United States of America 37 27385828
2013 Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. Proceedings of the National Academy of Sciences of the United States of America 37 23319619
2025 E3 ubiquitin ligase Listerin regulates macrophage cholesterol efflux and atherosclerosis by targeting ABCA1. The Journal of clinical investigation 16 40526435
2023 Listerin promotes cGAS protein degradation through the ESCRT pathway to negatively regulate cGAS-mediated immune response. Proceedings of the National Academy of Sciences of the United States of America 15 38109536
2024 NEMF-mediated Listerin-independent mitochondrial translational surveillance by E3 ligase Pirh2 and mitochondrial protease ClpXP. Cell reports 11 38412092
2023 LTN1 promotes RLR degradation to inhibit immune response to RNA virus through the ESCRT pathway. Autophagy 11 38060409
2025 Listerin promotes α-synuclein degradation to alleviate Parkinson's disease through the ESCRT pathway. Science advances 10 39937915
2023 In vivo CRISPR screen identifies LTN1 as a novel tumor suppressor ubiquitinating insulin-like growth factor 2 mRNA-binding protein 1 in hepatocellular carcinoma. Hepatology communications 10 37708447
2021 LISTERIN E3 Ubiquitin Ligase and Ribosome-Associated Quality Control (RQC) Mechanism. Molecular neurobiology 9 34590243
2025 The ribosome-associated quality control factor TCF25 imposes K48 specificity on Listerin-mediated ubiquitination of nascent chains by binding and specifically orienting the acceptor ubiquitin. Genes & development 7 40169231
2021 Expression Analysis of Ermin and Listerin E3 Ubiquitin Protein Ligase 1 Genes in Autistic Patients. Frontiers in molecular neuroscience 6 34349621
2020 Cooperativity between the Ribosome-Associated Chaperone Ssb/RAC and the Ubiquitin Ligase Ltn1 in Ubiquitination of Nascent Polypeptides. International journal of molecular sciences 6 32957466
2021 Expression Analysis of Ermin and Listerin E3 Ubiquitin Protein Ligase 1 Genes in the Periphery of Patients with Schizophrenia. Journal of molecular neuroscience : MN 5 34676516
2025 Listerin Alleviates Alzheimer's Disease through IRE1-mediated Decay of TLR4 mRNA. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 3 40448625
2024 The ribosome-associated quality control factor TCF25 imposes K48 specificity on Listerin-mediated ubiquitination of nascent chains by binding and specifically orienting the acceptor ubiquitin. bioRxiv : the preprint server for biology 3 39464025
2014 Direct recognition of the C-terminal polylysine residues of nonstop protein by Ltn1, an E3 ubiquitin ligase. Biochemical and biophysical research communications 3 25305489
2024 Poly-alanine-tailing is a modifier of neurodegeneration caused by Listerin mutation. bioRxiv : the preprint server for biology 2 39229065
2025 Crosstalk between the ribosome quality control-associated E3 ubiquitin ligases LTN1 and RNF10. FEBS letters 0 41451945

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