NEMF (Nuclear Export Mediator Factor; also called RQC2, the mammalian ortholog of yeast Rqc2/Tae2 and bacterial RqcH) is a core subunit of the ribosome-associated quality control (RQC) complex that acts on stalled 60S large ribosomal subunits. After an aberrant ribosome stalls and is split, NEMF recognizes the exposed nascent-chain-conjugated (peptidyl) tRNA in the 60S subunit, which allows it to discriminate occupied from empty 60S, and it recruits and stabilizes the E3 ubiquitin ligase LTN1/Listerin. NEMF additionally catalyzes CAT tailing, in which (in an mRNA- and 40S-independent manner) it delivers mainly alanine-charged tRNA (and other aminoacyl-tRNAs) to the ribosomal A site and directs non-templated C-terminal elongation of the stalled nascent chain, generating C-terminal alanine/threonine (CAT) tails. These tails promote degradation of the stalled chain by two routes. In the canonical RQC-L pathway they expose buried lysines for LTN1-dependent ubiquitination, and in the alternative RQC-C pathway they form a C-terminal alanine degron recognized by C-end-rule E3 ligases (CRL2-KLHDC10 and RCHY1/PIRH2). NEMF acts in the cytosol on cytosolic ribosomes; loss of NEMF function causes accumulation of toxic, aggregation-prone nascent chains, and biallelic NEMF variants cause an autosomal-recessive neurodevelopmental disorder with peripheral neuropathy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000049 tRNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: NEMF binds tRNA - both the nascent-chain-conjugated peptidyl-tRNA it uses to sense stalled 60S and the aminoacyl-tRNA it delivers for CAT tailing. tRNA binding is conserved across the NEMF/Rqc2 family. Reason: Well supported; the more specific alpha-aminoacyl-tRNA binding (GO:1904678) is also annotated. tRNA binding is integral to NEMF's 60S sensing and CAT-tailing activities. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF specifically binds stalled 60S ribosomal subunits by recognizing an exposed, nascent chain-conjugated tRNA moiety |
| GO:0043023 ribosomal large subunit binding | IBA GO_REF:0000033 | ACCEPT | Summary: NEMF binds the stalled 60S large ribosomal subunit, making multiple contacts with 60S and the P-site tRNA. This is core to its RQC function. Reason: Directly demonstrated structurally and biochemically; binding 60S is the basis for NEMF's nascent-chain sensing. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF specifically binds stalled 60S ribosomal subunits |
| GO:1990112 RQC complex | IBA GO_REF:0000033 | ACCEPT | Summary: NEMF is one of the three defining subunits of the RQC complex (LTN1, TCF25, NEMF) on the 60S subunit. Reason: Directly demonstrated; conserved RQC complex membership. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt Component of the ribosome quality control complex (RQC), composed of the E3 ubiquitin ligase LTN1, TCF25 and NEMF associated with the 60S ribosomal subunit |
| GO:0072344 rescue of stalled cytosolic ribosome | IBA GO_REF:0000033 | ACCEPT | Summary: NEMF participates in resolving stalled ribosomes by sensing 60S-nascent chain complexes and triggering downstream degradation/CAT-tailing. Reason: Conserved and experimentally supported RQC role. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt frees 60S subunit ribosomes from the stalled translation complex |
| GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: By recruiting LTN1 and CAT-tailing nascent chains to promote their ubiquitination, NEMF is integral to ribosome-associated ubiquitin-dependent degradation. Reason: Conserved and experimentally supported; NEMF promotes degradation of stalled nascent chains. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt as well as their ubiquitin-mediated proteasomal degradation |
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Nuclear localization derives from the legacy nuclear-export-mediator-factor role (PubMed:16103875), predating NEMF's characterization as an RQC factor. The predominant, well-supported localization is cytosolic. Reason: UniProt lists Nucleus by ECO:0000305 based on the older nuclear-export role, but the core, extensively documented function of NEMF is cytoplasmic RQC; nuclear localization is peripheral. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF may also indirectly play a role in nuclear export |
| GO:0005829 cytosol | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic transfer of cytosolic localization, consistent with the experimentally documented site of NEMF action. Reason: Correct compartment; redundant with IDA cytosol evidence. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0140708 CAT tailing | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic (ARBA, ortholog) assignment of CAT tailing, the signature catalytic activity of NEMF, consistent with direct experimental IDA evidence. Reason: Correct core process; NEMF is the mammalian enzyme that adds C-terminal alanine (CAT) tails to stalled nascent chains. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF mediates CAT tailing by recruiting alanine-charged tRNA to the A- site |
| GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process | IEA GO_REF:0000107 | ACCEPT | Summary: Ortholog-based electronic assignment of the RQC ubiquitin-dependent catabolic process, consistent with experimental evidence. Reason: Correct core process; redundant with IDA evidence. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt as well as their ubiquitin-mediated proteasomal degradation |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9948318 | ACCEPT | Summary: Reactome curation of NEMF cytosolic localization. Reason: Correct compartment; redundant with experimental cytosol annotations. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9948360 | ACCEPT | Summary: Reactome curation of NEMF cytosolic localization. Reason: Correct compartment; redundant with experimental cytosol annotations. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9948362 | ACCEPT | Summary: Reactome curation of NEMF cytosolic localization. Reason: Correct compartment; redundant with experimental cytosol annotations. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9948427 | ACCEPT | Summary: Reactome curation of NEMF cytosolic localization. Reason: Correct compartment; redundant with experimental cytosol annotations. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9948458 | ACCEPT | Summary: Reactome curation of NEMF cytosolic localization. Reason: Correct compartment; redundant with experimental cytosol annotations. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9954723 | ACCEPT | Summary: Reactome curation of NEMF cytosolic localization. Reason: Correct compartment; redundant with experimental cytosol annotations. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9954727 | ACCEPT | Summary: Reactome curation of NEMF cytosolic localization. Reason: Correct compartment; redundant with experimental cytosol annotations. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:0072344 rescue of stalled cytosolic ribosome | NAS PMID:35452614 Ribosome-associated quality-control mechanisms from bacteria... | ACCEPT | Summary: Review-based (ComplexPortal NAS) assertion of NEMF's RQC rescue role. Reason: Consistent with experimentally supported RQC function. Supporting Evidence: PMID:35452614 Ribosome-associated quality-control mechanisms from bacteria to humans |
| GO:1990112 RQC complex | NAS PMID:35452614 Ribosome-associated quality-control mechanisms from bacteria... | ACCEPT | Summary: Review-based (ComplexPortal NAS) assertion of NEMF as an RQC complex subunit. Reason: Consistent with experimentally demonstrated RQC complex membership. Supporting Evidence: PMID:35452614 Ribosome-associated quality-control mechanisms from bacteria to humans |
| GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process | NAS PMID:35452614 Ribosome-associated quality-control mechanisms from bacteria... | ACCEPT | Summary: Review-based (ComplexPortal NAS) assertion of NEMF's RQC catabolic role. Reason: Consistent with the experimentally supported process. Supporting Evidence: PMID:35452614 Ribosome-associated quality-control mechanisms from bacteria to humans |
| GO:0022626 cytosolic ribosome | IDA PMID:25578875 Structure and assembly pathway of the ribosome quality contr... | ACCEPT | Summary: NEMF acts on the cytosolic 60S ribosome; the cryo-EM RQC structure places NEMF on the 60S subunit contacting the P-site tRNA. Reason: Directly demonstrated; NEMF functions while bound to the cytosolic ribosome. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF specifically binds stalled 60S ribosomal subunits |
| GO:0022626 cytosolic ribosome | IDA PMID:33909987 Convergence of mammalian RQC and C-end rule proteolytic path... | ACCEPT | Summary: NEMF acts on the cytosolic ribosome during alanine tailing of stalled nascent chains. Reason: Directly demonstrated; NEMF's Ala-tailing activity occurs on 60S-nascent chain complexes. Supporting Evidence: PMID:33909987 mediated by tRNA-Ala binding and Ala tailing |
| GO:0043023 ribosomal large subunit binding | IDA PMID:25578875 Structure and assembly pathway of the ribosome quality contr... | ACCEPT | Summary: Direct evidence that NEMF binds the 60S large subunit, making simultaneous contacts with 60S and the peptidyl-tRNA. Reason: Core; experimentally demonstrated 60S binding underlies NEMF's nascent-chain sensing. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF specifically binds stalled 60S ribosomal subunits |
| GO:0072344 rescue of stalled cytosolic ribosome | IDA PMID:25578875 Structure and assembly pathway of the ribosome quality contr... | ACCEPT | Summary: Direct experimental evidence for NEMF's role in resolving stalled 60S-nascent chain complexes within RQC. Reason: Core, experimentally supported RQC/rescue function. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt frees 60S subunit ribosomes from the stalled translation complex |
| GO:0140708 CAT tailing | IDA PMID:33406423 Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Mor... | ACCEPT | Summary: Direct evidence that mammalian NEMF modifies stalled (nonstop) translation products with non-templated C-terminal alanine-rich (CAT) tails. This is NEMF's signature catalytic activity. Reason: Core molecular activity demonstrated directly in mammalian cells; NEMF is the CAT- tailing enzyme. Supporting Evidence: PMID:33406423 NEMF, a mammalian RQC2 homolog, modifies translation products of nonstop mRNAs, major erroneous mRNAs in mammals, with a C-terminal tail mainly composed of alanine with several other amino acids |
| GO:0140708 CAT tailing | IDA PMID:33909987 Convergence of mammalian RQC and C-end rule proteolytic path... | ACCEPT | Summary: Direct evidence that NEMF performs alanine tailing of stalled nascent chains via tRNA-Ala binding, in both Listerin-dependent and Listerin-independent routes. Reason: Core; experimentally demonstrated CAT/Ala tailing activity. Supporting Evidence: PMID:33909987 mammalian NEMF has an additional, Listerin-independent proteolytic role, which, as in bacteria, is mediated by tRNA-Ala binding and Ala tailing |
| GO:1904678 alpha-aminoacyl-tRNA binding | IDA PMID:33406423 Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Mor... | ACCEPT | Summary: NEMF binds aminoacyl-tRNA (mainly Ala-charged) to deliver it to the A site during CAT tailing. This is the molecular function underlying its tailing activity. Reason: Core molecular function; directly supports the CAT-tailing mechanism. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF mediates CAT tailing by recruiting alanine-charged tRNA to the A- site |
| GO:1904678 alpha-aminoacyl-tRNA binding | IDA PMID:33909987 Convergence of mammalian RQC and C-end rule proteolytic path... | ACCEPT | Summary: NEMF binds Ala-charged tRNA, the molecular basis for alanine tailing of stalled nascent chains. Reason: Core molecular function; directly demonstrated tRNA-Ala binding. Supporting Evidence: PMID:33909987 mediated by tRNA-Ala binding and Ala tailing |
| GO:1990112 RQC complex | IDA PMID:33909987 Convergence of mammalian RQC and C-end rule proteolytic path... | ACCEPT | Summary: Direct evidence for NEMF as an RQC complex component in mammalian cells. Reason: Core; experimentally demonstrated RQC complex membership. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt Component of the ribosome quality control complex (RQC) |
| GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process | IDA PMID:33406423 Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Mor... | ACCEPT | Summary: NEMF-mediated CAT tailing promotes ubiquitination and proteasomal degradation of stalled nascent chains. Reason: Core; CAT tailing facilitates ubiquitin-dependent degradation of stalled chains. Supporting Evidence: PMID:33406423 CAT tailing promotes ubiquitination of NCs for proteasomal degradation |
| GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process | IDA PMID:33909987 Convergence of mammalian RQC and C-end rule proteolytic path... | ACCEPT | Summary: NEMF directs Ala-tailed stalled chains to ubiquitin-dependent degradation via Listerin and via C-end-rule E3 ligases. Reason: Core; experimentally supported role in ribosome-associated ubiquitin-dependent catabolism. Supporting Evidence: PMID:33909987 target them for degradation |
| GO:0065003 protein-containing complex assembly | IMP PMID:25578875 Structure and assembly pathway of the ribosome quality contr... | KEEP AS NON CORE | Summary: NEMF promotes assembly of the RQC complex by recruiting and stabilizing LTN1 on the stalled 60S. This is the complex-assembly aspect of its RQC role rather than an independent function. Reason: Supported by IMP, but it describes NEMF's contribution to RQC assembly (LTN1 recruitment); the informative core functions are 60S sensing, CAT tailing and tRNA binding. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt promotes the recruitment of LTN1 to stalled 60S subunits |
| GO:0005829 cytosol | IDA PMID:25578875 Structure and assembly pathway of the ribosome quality contr... | ACCEPT | Summary: Direct evidence for cytosolic localization of NEMF. Reason: Correct compartment; NEMF acts in the cytosol on ribosomes. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm, cytosol |
| GO:1990112 RQC complex | IDA PMID:25578875 Structure and assembly pathway of the ribosome quality contr... | ACCEPT | Summary: The cryo-EM structure resolves NEMF as part of the RQC complex bridging 60S, the P-site tRNA and LTN1. Reason: Core; directly demonstrated structurally. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt Component of the ribosome quality control complex (RQC) |
| GO:1990116 ribosome-associated ubiquitin-dependent protein catabolic process | IDA PMID:25578875 Structure and assembly pathway of the ribosome quality contr... | ACCEPT | Summary: NEMF promotes ubiquitin-dependent degradation of stalled nascent chains by recruiting LTN1 to the 60S. Reason: Core, experimentally supported defining biological process. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt as well as their ubiquitin-mediated proteasomal degradation |
| GO:0051168 nuclear export | IMP PMID:16103875 Drosophila caliban, a nuclear export mediator, can function ... | KEEP AS NON CORE | Summary: An older study (the source of the nuclear-export-mediator-factor name) implicated NEMF/Caliban in nuclear export and tumor suppression. UniProt records only an indirect role. This predates and is peripheral to NEMF's central RQC function. Reason: Legacy/indirect role recorded by UniProt as an indirect role in nuclear export; not the core, extensively characterized RQC function. Full text not available for independent verification beyond the UniProt summary. Supporting Evidence: file:human/NEMF/NEMF-uniprot.txt NEMF may also indirectly play a role in nuclear export |
| GO:0140708 CAT tailing | IDA PMID:33909987 Convergence of mammalian RQC and C-end rule proteolytic path... | ACCEPT | Summary: Additional direct annotation of CAT tailing; NEMF adds non-templated alanine tails to stalled nascent chains. Reason: Core catalytic activity of NEMF, directly demonstrated. Supporting Evidence: PMID:33909987 mediated by tRNA-Ala binding and Ala tailing |
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Download this section (compressed HTML)Q: What determines the choice between the LTN1-dependent (RQC-L) and C-end-rule (RQC-C) degradation routes downstream of NEMF Ala tailing in mammalian cells?
Q: How do the disease-causing NEMF variants (IDDSAPN) mechanistically impair 60S sensing, LTN1 recruitment, or CAT tailing, and which deficit drives the neuropathy?
Experiment: Reconstitute CAT tailing in vitro with purified human NEMF, 60S-nascent chain complexes, and charged tRNAs to quantify amino-acid selectivity (Ala vs Thr vs others) and its dependence on 40S/mRNA.
Experiment: Introduce patient-derived NEMF missense variants into cells and assay 60S binding, LTN1 recruitment, CAT-tail length/composition, and nascent-chain degradation to map genotype to molecular defect.
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