{"gene":"NEMF","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2016,"finding":"Rqc2/NEMF marks ribosome-stalled nascent polypeptide chains (NCs) for aggregation by appending a carboxy-terminal Ala- and Thr-containing extension ('CAT tail'), and CATylation mediates formation of detergent-insoluble NC aggregates; CATylation is favored when Ltn1/Listerin-mediated ubiquitination is inefficient.","method":"Yeast genetic and biochemical assays; Ltn1 inactivation; detergent-solubility fractionation of CATylated nascent chains; mutagenesis of ubiquitylation-target lysines","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (genetics, biochemistry, fractionation) in a focused mechanistic study; replicated conceptually across multiple subsequent studies","pmids":["26943317"],"is_preprint":false},{"year":2016,"finding":"Rqc2/NEMF stabilizes binding of the E3 ligase Listerin/Ltn1 to the 60S subunit containing stalled nascent polypeptide chains, thereby facilitating their ubiquitylation and proteasomal targeting in the RQC pathway.","method":"Yeast genetic and biochemical studies; Rqc2 mutant analysis showing loss of Ltn1 stabilization","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — functionally validated in yeast RQC system, replicated across multiple subsequent studies","pmids":["26943317"],"is_preprint":false},{"year":2020,"finding":"Mouse NEMF/Rqc2 mutations that selectively interfere with C-terminal tail addition to stalled translation products (without abolishing Listerin recruitment) cause progressive motor neuron degeneration, establishing that NEMF's CAT-tailing activity is required for RQC-mediated protein degradation and neuronal homeostasis.","method":"Three independently-generated mouse models carrying NEMF mutations; yeast Rqc2 equivalent mutations tested for CAT-tailing defect; human genetic identification of NEMF loss-of-function variants in juvenile neuromuscular disease patients","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — three independent mouse models plus yeast functional assays plus human genetics, replicated mechanistic inference","pmids":["32934225"],"is_preprint":false},{"year":2020,"finding":"Knockdown of Nemf in cultured mouse primary cortical neurons impairs axonal outgrowth and synapse development, demonstrating a role for NEMF in mammalian neuron development.","method":"Immunofluorescence and morphological analysis of Nemf-knockdown mouse primary cortical neurons","journal":"Human genetics","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, single knockdown assay with morphological readout, no pathway placement","pmids":["33048237"],"is_preprint":false},{"year":2021,"finding":"CAT-tailing by Rqc2/NEMF in the 60S subunit can be modulated (inhibited) by the identity of the polypeptide in the ribosome exit tunnel; poly-tryptophan sequences (≥8 residues proximal to the peptidyl transferase center) block CAT-tailing, enabling Rqc2-independent RQC in which Ltn1-dependent degradation proceeds without Rqc2.","method":"Yeast genetics; CAT-tail reporter assays with poly-tryptophan, poly-CGA, and poly-A stalling sequences; Rqc2 deletion analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical assays in yeast, single lab, two orthogonal methods","pmids":["33511411"],"is_preprint":false},{"year":2024,"finding":"In mammalian cells, NEMF mediates a Listerin-independent mitochondrial RQC pathway: NEMF appends C-terminal poly-alanine tails to ribosome-stalled nuclear-encoded mitochondrial nascent polypeptides that are partially imported through translocons (restricting lysine access for Listerin). These poly-Ala-tailed proteins are then recognized by cytosolic E3 ligase Pirh2 and mitochondrial protease ClpXP for degradation. Defects in this pathway cause NEMF-mediated aggregates and mitochondrial integrity failure.","method":"Cell-based RQC reporter assays for mitochondrial substrates; Co-IP identifying Pirh2 and ClpXP as NEMF-pathway components; loss-of-function analysis of pathway components; mitochondrial integrity assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, multiple orthogonal methods (reporters, Co-IP, functional knockdown), no independent replication yet","pmids":["38412092"],"is_preprint":false},{"year":2024,"finding":"In two novel NEMF neurodegeneration mouse models (NemfR86S and NemfR487G), mutant NEMF protein causes an Importin-β-specific nuclear import block, cytoplasmic mis-localization and aggregation of TDP43, Importin-β, RanGAP1, and Ran, and a pathological interaction between Importin-β and mutant NEMFR86S protein in cytoplasmic accumulations.","method":"Mouse models; nuclear import assays; immunofluorescence and co-localization; Co-IP of Importin-β with mutant NEMF; pharmacological inhibition of Importin-β in mouse and human neuronal cells","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two mouse models plus cellular assays plus Co-IP, single lab, multiple orthogonal methods","pmids":["39312574"],"is_preprint":false},{"year":2025,"finding":"NEMF-mediated CAT-tailing directs the degradation of a subset of ER translocation-associated quality control (TAQC) substrates: nonstop mRNA-encoded stalled nascent chains at the ER are modified by NEMF and cleared via an unconventional ERAD mechanism requiring ER-to-Golgi trafficking and KDEL-mediated Golgi retrieval, distinct from poly(A)-stalling substrates that are degraded by lysosomes/proteasome. The composition of the CAT tail (AT-rich vs. AG-rich) determines whether the substrate is routed to ERAD or lysosome.","method":"Genome-wide CRISPR screen; live-cell imaging; nonstop and poly(A) stalling reporters at the ER; NEMF loss-of-function; characterization of CAT-tail mimetics","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide CRISPR screen plus live-cell imaging plus multiple reporter systems plus NEMF KO, single lab but multiple highly orthogonal methods in one rigorous study","pmids":["40257401"],"is_preprint":false},{"year":2025,"finding":"A cryo-EM structure of the RQC complex reveals that the Rqc2 (NEMF ortholog) F340I mutation alters binding of Rqc2 to the 60S subunit, disrupts the A-site's ability to bind tRNA in the presence of Ltn1, and thereby limits CAT-tailing and contributes to peptide release from stalled ribosomes.","method":"Cryo-EM structure of RQC complex; genetic screen identifying RQC2 F340I mutant allele; functional CAT-tailing assays with mutant","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cryo-EM structure with mutagenesis and functional validation, single lab","pmids":["40187343"],"is_preprint":false},{"year":2024,"finding":"In canonical mammalian RQC, NEMF binds to the large ribosomal subunit and recruits E3 ubiquitin ligase Listerin, which marks nascent chains for proteasomal degradation; additionally, NEMF extends the nascent chain C-terminus with poly-alanine ('Ala-tail') to expose lysines in the ribosomal exit tunnel for ubiquitination. RQC substrates that evade degradation form amyloid-like aggregates in an Ala-tail-dependent fashion.","method":"Mouse genetic models with selective impairment of NEMF Ala-tailing; genetic interaction (synthetic lethality with lister mutation); aggregate analysis of RQC substrates","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mouse genetics with selective Ala-tailing mutation plus genetic epistasis plus aggregate assays, single lab, preprint","pmids":["bio_10.1101_2024.08.24.608776"],"is_preprint":true},{"year":2024,"finding":"60S ribosomal nascent chain complexes (60S RNCs) associate with NEMF, which promotes recruitment of the RING-type E3 ubiquitin ligase Listerin to ubiquitinate nascent chains in the RQC pathway.","method":"Functional biochemical reconstitution assays; AlphaFold3 modeling of complex interactions","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical reconstitution supporting NEMF-Listerin recruitment, single lab, preprint","pmids":["bio_10.1101_2024.10.17.618946"],"is_preprint":true},{"year":2025,"finding":"UFMylation of RPL26 on ER-stalled ribosomes persists in the absence of late RQC components NEMF and LTN1, indicating that UFMylation marks the 60S-peptidyl-tRNA complex independently of NEMF/Listerin-mediated nascent chain clearance steps, though UFMylation and the canonical RQC pathway act in concert to facilitate clearance of arrested polypeptides at the ER.","method":"Functional cellular assays with ER-targeted stalling reporters; NEMF and LTN1 loss-of-function combined with UFMylation analysis","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, genetic knockouts with reporter assay but no structural or biochemical reconstitution of the specific NEMF relationship","pmids":["bio_10.1101_2025.01.17.633636"],"is_preprint":true}],"current_model":"NEMF (RQC2) is a core subunit of the ribosome-associated quality control (RQC) complex that binds to 60S ribosomal subunits bearing stalled nascent polypeptide chains, where it (1) stabilizes/recruits the E3 ubiquitin ligase Listerin to promote K48-linked ubiquitination and proteasomal degradation of the stalled chains, and (2) appends non-templated C-terminal poly-alanine/threonine ('CAT') tails to stalled nascent chains using tRNA as a substrate, which exposes buried lysines for ubiquitination, can route substrates to aggregation when ubiquitination is inefficient, and directs context-specific degradation routes including a Listerin-independent mitochondrial pathway (via Pirh2/ClpXP) and ER translocation-associated quality control via Golgi retrieval; mutations impairing NEMF's CAT-tailing activity cause progressive motor neuron degeneration in mice and humans."},"narrative":{"mechanistic_narrative":"NEMF (RQC2) is a core subunit of the ribosome-associated quality control (RQC) machinery that recognizes 60S large ribosomal subunits carrying stalled nascent polypeptide chains and commits those chains to degradation [PMID:26943317, PMID:bio_10.1101_2024.08.24.608776]. On the stalled 60S, NEMF performs two coupled functions: it stabilizes recruitment of the RING E3 ubiquitin ligase Listerin/Ltn1 to promote ubiquitination and proteasomal targeting of the nascent chain [PMID:26943317, PMID:bio_10.1101_2024.10.17.618946], and it appends non-templated C-terminal Ala/Thr ('CAT') tails to the chain, which extrude buried lysines from the exit tunnel to enable ubiquitination [PMID:26943317, PMID:bio_10.1101_2024.08.24.608776]. A cryo-EM structure of the RQC complex shows that CAT-tailing depends on Rqc2/NEMF positioning tRNA at the ribosomal A site, and a mutation in this interface limits CAT-tailing while promoting peptide release [PMID:40187343]. CAT-tailing is context-dependent: when ubiquitination is inefficient, CATylated chains are routed to detergent-insoluble, amyloid-like aggregates [PMID:26943317, PMID:bio_10.1101_2024.08.24.608776], and exit-tunnel sequence features such as poly-tryptophan tracts block CAT-tailing to permit Rqc2-independent clearance [PMID:33511411]. NEMF also directs substrate-specific degradation routes beyond the canonical cytosolic pathway, including a Listerin-independent mitochondrial route in which poly-Ala-tailed nuclear-encoded mitochondrial substrates are handed to the E3 ligase Pirh2 and the protease ClpXP [PMID:38412092], and an ER translocation-associated quality control route in which CAT-tail composition determines clearance via unconventional ERAD with Golgi retrieval versus lysosomal degradation [PMID:40257401]. Mutations that selectively impair NEMF CAT-tailing cause progressive motor neuron degeneration in mice and juvenile neuromuscular disease in humans [PMID:32934225].","teleology":[{"year":2016,"claim":"Established the dual molecular function of NEMF on stalled 60S subunits—both stabilizing Listerin and adding a non-templated C-terminal tail—answering how a stalled nascent chain is marked for clearance versus aggregation.","evidence":"Yeast genetics and biochemistry with Ltn1 inactivation, detergent-solubility fractionation, and ubiquitylation-lysine mutagenesis","pmids":["26943317"],"confidence":"High","gaps":["Did not resolve the structural basis of tRNA-dependent tail addition","Mammalian relevance not directly tested"]},{"year":2020,"claim":"Separated NEMF's two activities in vivo by showing that CAT-tailing—not Listerin recruitment—is the activity whose loss drives neurodegeneration, linking RQC tail-addition to mammalian neuronal homeostasis and human disease.","evidence":"Three independent mouse models, yeast equivalent mutations for CAT-tailing defect, and human loss-of-function variant identification","pmids":["32934225"],"confidence":"High","gaps":["Did not define which neuronal substrates are CAT-tailed","Mechanism linking aggregation to neuronal death not established"]},{"year":2020,"claim":"Provided cellular evidence that NEMF supports neuron development beyond degradation, showing knockdown impairs axon outgrowth and synapse formation.","evidence":"Immunofluorescence and morphology of Nemf-knockdown mouse primary cortical neurons","pmids":["33048237"],"confidence":"Medium","gaps":["Single knockdown assay with morphological readout only","No connection to RQC pathway placement","No rescue with CAT-tailing-dead mutant"]},{"year":2021,"claim":"Showed CAT-tailing is gated by nascent-chain identity in the exit tunnel, with poly-tryptophan blocking tail addition and enabling Rqc2-independent Listerin-driven clearance.","evidence":"Yeast CAT-tail reporter assays with distinct stalling sequences and Rqc2 deletion analysis","pmids":["33511411"],"confidence":"Medium","gaps":["Mechanism by which exit-tunnel sequence blocks tail addition unresolved","Not tested in mammalian system"]},{"year":2024,"claim":"Defined a Listerin-independent mitochondrial RQC branch in which NEMF poly-Ala-tails partially imported mitochondrial nascent chains for Pirh2/ClpXP-mediated degradation, explaining how RQC operates when lysine access is restricted by the translocon.","evidence":"Mammalian mitochondrial RQC reporters, Co-IP of Pirh2 and ClpXP, loss-of-function and mitochondrial integrity assays","pmids":["38412092"],"confidence":"Medium","gaps":["Single lab without independent replication","Direct NEMF–Pirh2 interaction interface not mapped","Co-IP not reciprocally validated"]},{"year":2024,"claim":"Linked NEMF mutant protein to a nucleocytoplasmic transport defect, showing mutant NEMF traps Importin-β and disrupts TDP43/RanGAP1/Ran localization, suggesting a gain-of-function pathology distinct from RQC loss.","evidence":"Two mouse models, nuclear import assays, co-localization, Co-IP of Importin-β with mutant NEMF, and pharmacological Importin-β inhibition","pmids":["39312574"],"confidence":"Medium","gaps":["Relationship to CAT-tailing activity unresolved","Whether transport defect is cause or consequence of aggregation unclear","Single lab"]},{"year":2025,"claim":"Resolved the structural basis of CAT-tailing, showing Rqc2/NEMF positions A-site tRNA on the 60S and that a point mutation at this interface limits tail addition and favors peptide release.","evidence":"Cryo-EM structure of the RQC complex with genetic screen and functional CAT-tailing assays of the F340I allele","pmids":["40187343"],"confidence":"High","gaps":["Mammalian structural conservation not directly addressed","Dynamics of repeated tRNA loading during tail elongation not captured"]},{"year":2025,"claim":"Showed NEMF CAT-tailing directs ER translocation-associated QC substrates, with CAT-tail composition (AT- vs AG-rich) determining routing to unconventional ERAD with Golgi retrieval versus lysosomal degradation.","evidence":"Genome-wide CRISPR screen, live-cell imaging, ER nonstop and poly(A) stalling reporters, NEMF KO, and CAT-tail mimetics","pmids":["40257401"],"confidence":"High","gaps":["Reader that decodes CAT-tail composition into routing not identified","Generality across endogenous substrates not established"]},{"year":2025,"claim":"Placed RPL26 UFMylation upstream of and independent from NEMF/Listerin at ER-stalled ribosomes, indicating UFMylation marks the 60S-peptidyl-tRNA complex separately from NEMF-dependent chain clearance.","evidence":"ER-targeted stalling reporters with combined NEMF/LTN1 loss-of-function and UFMylation analysis (preprint)","pmids":["bio_10.1101_2025.01.17.633636"],"confidence":"Low","gaps":["Preprint, single lab, not independently confirmed","No biochemical reconstitution of the NEMF–UFMylation relationship","Functional consequence of coordination not defined"]},{"year":null,"claim":"How CAT-tail composition is read by downstream machinery to select among aggregation, proteasomal, mitochondrial, ERAD, and lysosomal fates, and how this decoding fails in NEMF-driven neurodegeneration, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No identified CAT-tail reader or sensor","Causal link between CAT-tail defects and specific neuronal substrate aggregation unmapped"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,9,7]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[8]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[1,9]}],"localization":[{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[1,8,10]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,9]},{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[7,11]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,9]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-8953897","term_label":"Cellular responses to stimuli","supporting_discovery_ids":[5,7]}],"complexes":["Ribosome-associated quality control (RQC) complex","60S ribosomal subunit nascent chain complex"],"partners":["LTN1","PIRH2","CLPX","IPO/IMPORTIN-Β"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O60524","full_name":"Ribosome quality control complex subunit NEMF","aliases":["Antigen NY-CO-1","Nuclear export mediator factor","Serologically defined colon cancer antigen 1"],"length_aa":1076,"mass_kda":123.0,"function":"Key component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates the extraction of incompletely synthesized nascent chains from stalled ribosomes as well as their ubiquitin-mediated proteasomal degradation (PubMed:25578875, PubMed:32726578, PubMed:33406423, PubMed:33909987). Thereby, frees 60S subunit ribosomes from the stalled translation complex and prevents the accumulation of nascent polypeptide chains that are potentially toxic for the cell (PubMed:25578875, PubMed:33406423, PubMed:33909987). Within the RQC complex, NEMF specifically binds stalled 60S ribosomal subunits by recognizing an exposed, nascent chain-conjugated tRNA moiety and promotes the recruitment of LTN1 to stalled 60S subunits (PubMed:25578875). Following binding to stalled 60S ribosomal subunits, NEMF mediates CAT tailing by recruiting alanine-charged tRNA to the A-site and directing the elongation of stalled nascent chains independently of mRNA or 40S subunits, leading to non-templated C-terminal alanine extensions (CAT tails) (PubMed:33406423, PubMed:33909987). Mainly recruits alanine-charged tRNAs, but can also other amino acid-charged tRNAs (PubMed:33406423, PubMed:33909987). CAT tailing is required to promote ubiquitination of stalled nascent chains by different E3 ubiquitin-protein ligases (PubMed:33909987). In the canonical RQC pathway (RQC-L), CAT tailing facilitates LTN1-dependent ubiquitination by exposing lysine residues that would otherwise remain buried in the ribosomal exit tunnel (By similarity). In the alternative RQC pathway (RQC-C) CAT tailing creates an C-degron mainly composed of alanine that is recognized by the CRL2(KLHDC10) and RCHY1/PIRH2 E3 ligases, leading to ubiquitination and degradation of stalled nascent chains (PubMed:33909987). NEMF may also indirectly play a role in nuclear export (PubMed:16103875)","subcellular_location":"Cytoplasm, cytosol; Nucleus","url":"https://www.uniprot.org/uniprotkb/O60524/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NEMF","classification":"Not Classified","n_dependent_lines":145,"n_total_lines":1208,"dependency_fraction":0.12003311258278146},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000165525","cell_line_id":"CID001825","localizations":[{"compartment":"cytoplasmic","grade":3}],"interactors":[{"gene":"EZR","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001825","total_profiled":1310},"omim":[{"mim_id":"619099","title":"INTELLECTUAL DEVELOPMENTAL DISORDER WITH SPEECH DELAY AND AXONAL PERIPHERAL NEUROPATHY; IDDSAPN","url":"https://www.omim.org/entry/619099"},{"mim_id":"608378","title":"NUCLEAR EXPORT MEDIATOR FACTOR; NEMF","url":"https://www.omim.org/entry/608378"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NEMF"},"hgnc":{"alias_symbol":["NY-CO-1","FLJ10051","RQC2"],"prev_symbol":["SDCCAG1"]},"alphafold":{"accession":"O60524","domains":[{"cath_id":"2.30.310.10","chopping":"8-158","consensus_level":"high","plddt":88.0572,"start":8,"end":158},{"cath_id":"-","chopping":"247-307","consensus_level":"medium","plddt":81.5751,"start":247,"end":307},{"cath_id":"-","chopping":"528-649","consensus_level":"medium","plddt":90.062,"start":528,"end":649},{"cath_id":"-","chopping":"651-673_979-1076","consensus_level":"medium","plddt":85.5187,"start":651,"end":1076},{"cath_id":"1.10.238","chopping":"168-242","consensus_level":"high","plddt":79.6495,"start":168,"end":242},{"cath_id":"1.10.287","chopping":"308-415_452-522","consensus_level":"medium","plddt":87.2554,"start":308,"end":522}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O60524","model_url":"https://alphafold.ebi.ac.uk/files/AF-O60524-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O60524-F1-predicted_aligned_error_v6.png","plddt_mean":69.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NEMF","jax_strain_url":"https://www.jax.org/strain/search?query=NEMF"},"sequence":{"accession":"O60524","fasta_url":"https://rest.uniprot.org/uniprotkb/O60524.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O60524/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O60524"}},"corpus_meta":[{"pmid":"26943317","id":"PMC_26943317","title":"The Rqc2/Tae2 subunit of the ribosome-associated quality control (RQC) complex marks ribosome-stalled nascent polypeptide chains for aggregation.","date":"2016","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/26943317","citation_count":122,"is_preprint":false},{"pmid":"32934225","id":"PMC_32934225","title":"NEMF mutations that impair ribosome-associated quality control are associated with neuromuscular disease.","date":"2020","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/32934225","citation_count":86,"is_preprint":false},{"pmid":"33048237","id":"PMC_33048237","title":"Biallelic loss-of-function variants in NEMF cause central nervous system impairment and axonal polyneuropathy.","date":"2020","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33048237","citation_count":22,"is_preprint":false},{"pmid":"33511411","id":"PMC_33511411","title":"The nascent polypeptide in the 60S subunit determines the Rqc2-dependency of ribosomal quality control.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/33511411","citation_count":18,"is_preprint":false},{"pmid":"38412092","id":"PMC_38412092","title":"NEMF-mediated Listerin-independent mitochondrial translational surveillance by E3 ligase Pirh2 and mitochondrial protease ClpXP.","date":"2024","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/38412092","citation_count":11,"is_preprint":false},{"pmid":"11291076","id":"PMC_11291076","title":"Up-regulation of a novel mRNA (NY-CO-1) involved in the methyl 4-methoxy-3-(3-methyl-2-butenoyl) benzoate (VT1)-induced proliferation arrest of a non-small-cell lung carcinoma cell line (NSCLC-N6).","date":"2001","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/11291076","citation_count":11,"is_preprint":false},{"pmid":"39312574","id":"PMC_39312574","title":"NEMF mutations in mice illustrate how Importin-β specific nuclear transport defects recapitulate neurodegenerative disease hallmarks.","date":"2024","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/39312574","citation_count":4,"is_preprint":false},{"pmid":"40257401","id":"PMC_40257401","title":"NEMF-mediated CAT tailing facilitates translocation-associated quality control.","date":"2025","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/40257401","citation_count":2,"is_preprint":false},{"pmid":"41011373","id":"PMC_41011373","title":"Ribosome-Associated Quality Control Mediated by Rqc2 Contributes to the Lytic Cycle and Stage Conversion of Toxoplasma gondii.","date":"2025","source":"Microorganisms","url":"https://pubmed.ncbi.nlm.nih.gov/41011373","citation_count":1,"is_preprint":false},{"pmid":"39253483","id":"PMC_39253483","title":"NEMF-mediated CAT-tailing defines distinct branches of translocation-associated quality control.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39253483","citation_count":1,"is_preprint":false},{"pmid":"40187343","id":"PMC_40187343","title":"RQC2 is a major player in peptide release from stalled ribosomes.","date":"2025","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/40187343","citation_count":0,"is_preprint":false},{"pmid":"39395174","id":"PMC_39395174","title":"Protocol for identification of NEMF-mediated C-terminal extensions on mitochondrial nonstop proteins via customized MS/MS spectra database searching.","date":"2024","source":"STAR protocols","url":"https://pubmed.ncbi.nlm.nih.gov/39395174","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.04.673968","title":"Jlp2 is an RQC complex-independent release factor acting on aberrant peptidyl-tRNA, protecting cells against translation elongation stress","date":"2025-09-06","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.04.673968","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.01.17.633636","title":"The coordinated action of UFMylation and ribosome-associated quality control pathway clears arrested nascent chains at the endoplasmic reticulum","date":"2025-01-18","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.17.633636","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.11.20.624445","title":"NEMF inhibits proliferation and migration of ovarian cancer cells by blocking the PI3K/mTOR pathway","date":"2024-11-22","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.20.624445","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.01.28.635269","title":"Nuclear Import Defects Drive Cell Cycle Dysregulation in Neurodegeneration","date":"2025-01-31","source":"bioRxiv","url":"https://doi.org/10.1101/2025.01.28.635269","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.24.608776","title":"Poly-alanine-tailing is a modifier of neurodegeneration caused by Listerin mutation","date":"2024-08-24","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.24.608776","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.10.17.618946","title":"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","date":"2024-10-18","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.17.618946","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10536,"output_tokens":3269,"usd":0.040322,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10748,"output_tokens":3607,"usd":0.071957,"stage2_stop_reason":"end_turn"},"total_usd":0.112279,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"Rqc2/NEMF marks ribosome-stalled nascent polypeptide chains (NCs) for aggregation by appending a carboxy-terminal Ala- and Thr-containing extension ('CAT tail'), and CATylation mediates formation of detergent-insoluble NC aggregates; CATylation is favored when Ltn1/Listerin-mediated ubiquitination is inefficient.\",\n      \"method\": \"Yeast genetic and biochemical assays; Ltn1 inactivation; detergent-solubility fractionation of CATylated nascent chains; mutagenesis of ubiquitylation-target lysines\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (genetics, biochemistry, fractionation) in a focused mechanistic study; replicated conceptually across multiple subsequent studies\",\n      \"pmids\": [\"26943317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Rqc2/NEMF stabilizes binding of the E3 ligase Listerin/Ltn1 to the 60S subunit containing stalled nascent polypeptide chains, thereby facilitating their ubiquitylation and proteasomal targeting in the RQC pathway.\",\n      \"method\": \"Yeast genetic and biochemical studies; Rqc2 mutant analysis showing loss of Ltn1 stabilization\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — functionally validated in yeast RQC system, replicated across multiple subsequent studies\",\n      \"pmids\": [\"26943317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Mouse NEMF/Rqc2 mutations that selectively interfere with C-terminal tail addition to stalled translation products (without abolishing Listerin recruitment) cause progressive motor neuron degeneration, establishing that NEMF's CAT-tailing activity is required for RQC-mediated protein degradation and neuronal homeostasis.\",\n      \"method\": \"Three independently-generated mouse models carrying NEMF mutations; yeast Rqc2 equivalent mutations tested for CAT-tailing defect; human genetic identification of NEMF loss-of-function variants in juvenile neuromuscular disease patients\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — three independent mouse models plus yeast functional assays plus human genetics, replicated mechanistic inference\",\n      \"pmids\": [\"32934225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Knockdown of Nemf in cultured mouse primary cortical neurons impairs axonal outgrowth and synapse development, demonstrating a role for NEMF in mammalian neuron development.\",\n      \"method\": \"Immunofluorescence and morphological analysis of Nemf-knockdown mouse primary cortical neurons\",\n      \"journal\": \"Human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single knockdown assay with morphological readout, no pathway placement\",\n      \"pmids\": [\"33048237\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CAT-tailing by Rqc2/NEMF in the 60S subunit can be modulated (inhibited) by the identity of the polypeptide in the ribosome exit tunnel; poly-tryptophan sequences (≥8 residues proximal to the peptidyl transferase center) block CAT-tailing, enabling Rqc2-independent RQC in which Ltn1-dependent degradation proceeds without Rqc2.\",\n      \"method\": \"Yeast genetics; CAT-tail reporter assays with poly-tryptophan, poly-CGA, and poly-A stalling sequences; Rqc2 deletion analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical assays in yeast, single lab, two orthogonal methods\",\n      \"pmids\": [\"33511411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In mammalian cells, NEMF mediates a Listerin-independent mitochondrial RQC pathway: NEMF appends C-terminal poly-alanine tails to ribosome-stalled nuclear-encoded mitochondrial nascent polypeptides that are partially imported through translocons (restricting lysine access for Listerin). These poly-Ala-tailed proteins are then recognized by cytosolic E3 ligase Pirh2 and mitochondrial protease ClpXP for degradation. Defects in this pathway cause NEMF-mediated aggregates and mitochondrial integrity failure.\",\n      \"method\": \"Cell-based RQC reporter assays for mitochondrial substrates; Co-IP identifying Pirh2 and ClpXP as NEMF-pathway components; loss-of-function analysis of pathway components; mitochondrial integrity assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, multiple orthogonal methods (reporters, Co-IP, functional knockdown), no independent replication yet\",\n      \"pmids\": [\"38412092\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In two novel NEMF neurodegeneration mouse models (NemfR86S and NemfR487G), mutant NEMF protein causes an Importin-β-specific nuclear import block, cytoplasmic mis-localization and aggregation of TDP43, Importin-β, RanGAP1, and Ran, and a pathological interaction between Importin-β and mutant NEMFR86S protein in cytoplasmic accumulations.\",\n      \"method\": \"Mouse models; nuclear import assays; immunofluorescence and co-localization; Co-IP of Importin-β with mutant NEMF; pharmacological inhibition of Importin-β in mouse and human neuronal cells\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two mouse models plus cellular assays plus Co-IP, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"39312574\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NEMF-mediated CAT-tailing directs the degradation of a subset of ER translocation-associated quality control (TAQC) substrates: nonstop mRNA-encoded stalled nascent chains at the ER are modified by NEMF and cleared via an unconventional ERAD mechanism requiring ER-to-Golgi trafficking and KDEL-mediated Golgi retrieval, distinct from poly(A)-stalling substrates that are degraded by lysosomes/proteasome. The composition of the CAT tail (AT-rich vs. AG-rich) determines whether the substrate is routed to ERAD or lysosome.\",\n      \"method\": \"Genome-wide CRISPR screen; live-cell imaging; nonstop and poly(A) stalling reporters at the ER; NEMF loss-of-function; characterization of CAT-tail mimetics\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide CRISPR screen plus live-cell imaging plus multiple reporter systems plus NEMF KO, single lab but multiple highly orthogonal methods in one rigorous study\",\n      \"pmids\": [\"40257401\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"A cryo-EM structure of the RQC complex reveals that the Rqc2 (NEMF ortholog) F340I mutation alters binding of Rqc2 to the 60S subunit, disrupts the A-site's ability to bind tRNA in the presence of Ltn1, and thereby limits CAT-tailing and contributes to peptide release from stalled ribosomes.\",\n      \"method\": \"Cryo-EM structure of RQC complex; genetic screen identifying RQC2 F340I mutant allele; functional CAT-tailing assays with mutant\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cryo-EM structure with mutagenesis and functional validation, single lab\",\n      \"pmids\": [\"40187343\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In canonical mammalian RQC, NEMF binds to the large ribosomal subunit and recruits E3 ubiquitin ligase Listerin, which marks nascent chains for proteasomal degradation; additionally, NEMF extends the nascent chain C-terminus with poly-alanine ('Ala-tail') to expose lysines in the ribosomal exit tunnel for ubiquitination. RQC substrates that evade degradation form amyloid-like aggregates in an Ala-tail-dependent fashion.\",\n      \"method\": \"Mouse genetic models with selective impairment of NEMF Ala-tailing; genetic interaction (synthetic lethality with lister mutation); aggregate analysis of RQC substrates\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mouse genetics with selective Ala-tailing mutation plus genetic epistasis plus aggregate assays, single lab, preprint\",\n      \"pmids\": [\"bio_10.1101_2024.08.24.608776\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"60S ribosomal nascent chain complexes (60S RNCs) associate with NEMF, which promotes recruitment of the RING-type E3 ubiquitin ligase Listerin to ubiquitinate nascent chains in the RQC pathway.\",\n      \"method\": \"Functional biochemical reconstitution assays; AlphaFold3 modeling of complex interactions\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical reconstitution supporting NEMF-Listerin recruitment, single lab, preprint\",\n      \"pmids\": [\"bio_10.1101_2024.10.17.618946\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"UFMylation of RPL26 on ER-stalled ribosomes persists in the absence of late RQC components NEMF and LTN1, indicating that UFMylation marks the 60S-peptidyl-tRNA complex independently of NEMF/Listerin-mediated nascent chain clearance steps, though UFMylation and the canonical RQC pathway act in concert to facilitate clearance of arrested polypeptides at the ER.\",\n      \"method\": \"Functional cellular assays with ER-targeted stalling reporters; NEMF and LTN1 loss-of-function combined with UFMylation analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, genetic knockouts with reporter assay but no structural or biochemical reconstitution of the specific NEMF relationship\",\n      \"pmids\": [\"bio_10.1101_2025.01.17.633636\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"NEMF (RQC2) is a core subunit of the ribosome-associated quality control (RQC) complex that binds to 60S ribosomal subunits bearing stalled nascent polypeptide chains, where it (1) stabilizes/recruits the E3 ubiquitin ligase Listerin to promote K48-linked ubiquitination and proteasomal degradation of the stalled chains, and (2) appends non-templated C-terminal poly-alanine/threonine ('CAT') tails to stalled nascent chains using tRNA as a substrate, which exposes buried lysines for ubiquitination, can route substrates to aggregation when ubiquitination is inefficient, and directs context-specific degradation routes including a Listerin-independent mitochondrial pathway (via Pirh2/ClpXP) and ER translocation-associated quality control via Golgi retrieval; mutations impairing NEMF's CAT-tailing activity cause progressive motor neuron degeneration in mice and humans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NEMF (RQC2) is a core subunit of the ribosome-associated quality control (RQC) machinery that recognizes 60S large ribosomal subunits carrying stalled nascent polypeptide chains and commits those chains to degradation [#1, #9]. On the stalled 60S, NEMF performs two coupled functions: it stabilizes recruitment of the RING E3 ubiquitin ligase Listerin/Ltn1 to promote ubiquitination and proteasomal targeting of the nascent chain [#1, #10], and it appends non-templated C-terminal Ala/Thr ('CAT') tails to the chain, which extrude buried lysines from the exit tunnel to enable ubiquitination [#0, #9]. A cryo-EM structure of the RQC complex shows that CAT-tailing depends on Rqc2/NEMF positioning tRNA at the ribosomal A site, and a mutation in this interface limits CAT-tailing while promoting peptide release [#8]. CAT-tailing is context-dependent: when ubiquitination is inefficient, CATylated chains are routed to detergent-insoluble, amyloid-like aggregates [#0, #9], and exit-tunnel sequence features such as poly-tryptophan tracts block CAT-tailing to permit Rqc2-independent clearance [#4]. NEMF also directs substrate-specific degradation routes beyond the canonical cytosolic pathway, including a Listerin-independent mitochondrial route in which poly-Ala-tailed nuclear-encoded mitochondrial substrates are handed to the E3 ligase Pirh2 and the protease ClpXP [#5], and an ER translocation-associated quality control route in which CAT-tail composition determines clearance via unconventional ERAD with Golgi retrieval versus lysosomal degradation [#7]. Mutations that selectively impair NEMF CAT-tailing cause progressive motor neuron degeneration in mice and juvenile neuromuscular disease in humans [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established the dual molecular function of NEMF on stalled 60S subunits—both stabilizing Listerin and adding a non-templated C-terminal tail—answering how a stalled nascent chain is marked for clearance versus aggregation.\",\n      \"evidence\": \"Yeast genetics and biochemistry with Ltn1 inactivation, detergent-solubility fractionation, and ubiquitylation-lysine mutagenesis\",\n      \"pmids\": [\"26943317\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the structural basis of tRNA-dependent tail addition\", \"Mammalian relevance not directly tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Separated NEMF's two activities in vivo by showing that CAT-tailing—not Listerin recruitment—is the activity whose loss drives neurodegeneration, linking RQC tail-addition to mammalian neuronal homeostasis and human disease.\",\n      \"evidence\": \"Three independent mouse models, yeast equivalent mutations for CAT-tailing defect, and human loss-of-function variant identification\",\n      \"pmids\": [\"32934225\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which neuronal substrates are CAT-tailed\", \"Mechanism linking aggregation to neuronal death not established\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Provided cellular evidence that NEMF supports neuron development beyond degradation, showing knockdown impairs axon outgrowth and synapse formation.\",\n      \"evidence\": \"Immunofluorescence and morphology of Nemf-knockdown mouse primary cortical neurons\",\n      \"pmids\": [\"33048237\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single knockdown assay with morphological readout only\", \"No connection to RQC pathway placement\", \"No rescue with CAT-tailing-dead mutant\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed CAT-tailing is gated by nascent-chain identity in the exit tunnel, with poly-tryptophan blocking tail addition and enabling Rqc2-independent Listerin-driven clearance.\",\n      \"evidence\": \"Yeast CAT-tail reporter assays with distinct stalling sequences and Rqc2 deletion analysis\",\n      \"pmids\": [\"33511411\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which exit-tunnel sequence blocks tail addition unresolved\", \"Not tested in mammalian system\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined a Listerin-independent mitochondrial RQC branch in which NEMF poly-Ala-tails partially imported mitochondrial nascent chains for Pirh2/ClpXP-mediated degradation, explaining how RQC operates when lysine access is restricted by the translocon.\",\n      \"evidence\": \"Mammalian mitochondrial RQC reporters, Co-IP of Pirh2 and ClpXP, loss-of-function and mitochondrial integrity assays\",\n      \"pmids\": [\"38412092\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab without independent replication\", \"Direct NEMF–Pirh2 interaction interface not mapped\", \"Co-IP not reciprocally validated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked NEMF mutant protein to a nucleocytoplasmic transport defect, showing mutant NEMF traps Importin-β and disrupts TDP43/RanGAP1/Ran localization, suggesting a gain-of-function pathology distinct from RQC loss.\",\n      \"evidence\": \"Two mouse models, nuclear import assays, co-localization, Co-IP of Importin-β with mutant NEMF, and pharmacological Importin-β inhibition\",\n      \"pmids\": [\"39312574\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relationship to CAT-tailing activity unresolved\", \"Whether transport defect is cause or consequence of aggregation unclear\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Resolved the structural basis of CAT-tailing, showing Rqc2/NEMF positions A-site tRNA on the 60S and that a point mutation at this interface limits tail addition and favors peptide release.\",\n      \"evidence\": \"Cryo-EM structure of the RQC complex with genetic screen and functional CAT-tailing assays of the F340I allele\",\n      \"pmids\": [\"40187343\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mammalian structural conservation not directly addressed\", \"Dynamics of repeated tRNA loading during tail elongation not captured\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed NEMF CAT-tailing directs ER translocation-associated QC substrates, with CAT-tail composition (AT- vs AG-rich) determining routing to unconventional ERAD with Golgi retrieval versus lysosomal degradation.\",\n      \"evidence\": \"Genome-wide CRISPR screen, live-cell imaging, ER nonstop and poly(A) stalling reporters, NEMF KO, and CAT-tail mimetics\",\n      \"pmids\": [\"40257401\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Reader that decodes CAT-tail composition into routing not identified\", \"Generality across endogenous substrates not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed RPL26 UFMylation upstream of and independent from NEMF/Listerin at ER-stalled ribosomes, indicating UFMylation marks the 60S-peptidyl-tRNA complex separately from NEMF-dependent chain clearance.\",\n      \"evidence\": \"ER-targeted stalling reporters with combined NEMF/LTN1 loss-of-function and UFMylation analysis (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.01.17.633636\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint, single lab, not independently confirmed\", \"No biochemical reconstitution of the NEMF–UFMylation relationship\", \"Functional consequence of coordination not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How CAT-tail composition is read by downstream machinery to select among aggregation, proteasomal, mitochondrial, ERAD, and lysosomal fates, and how this decoding fails in NEMF-driven neurodegeneration, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No identified CAT-tail reader or sensor\", \"Causal link between CAT-tail defects and specific neuronal substrate aggregation unmapped\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 9, 7]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [1, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [1, 8, 10]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [7, 11]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 9]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-8953897\", \"supporting_discovery_ids\": [5, 7]}\n    ],\n    \"complexes\": [\"Ribosome-associated quality control (RQC) complex\", \"60S ribosomal subunit nascent chain complex\"],\n    \"partners\": [\"LTN1\", \"PIRH2\", \"CLPX\", \"IPO/Importin-β\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}