MUT-7 is a C. elegans 3'-5' exoribonuclease of the MUT-7/EXD3 family (RNase D-like DEDDy exonuclease domain plus a C-terminal MUT7-C domain), related to the exonuclease domain of the Werner syndrome protein and to Drosophila Nibbler. It is a core Mutator-class protein. Through its MUT7-C domain insertion it binds RDE-2/MUT-8, which links it to the scaffold MUT-16 and recruits it to perinuclear germline Mutator foci, where it supports amplification of secondary 22G siRNAs. Recombinant MUT-7 degrades single-stranded RNA 3'-to-5' in a metal-dependent way, and the MUT7-C domain contributes to RNA binding. MUT-7 is required for germline transposon silencing, exogenous RNAi and endogenous 22G and ERGO-1 class 26G siRNA pathways. Its precise substrate in the Mutator pathway is not known. MUT-7 is found in both cytosol and nucleus. In AWC olfactory neurons it acts with HPL-2 in the endogenous nuclear RNAi that mediates odor adaptation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000175 3'-5'-RNA exonuclease activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for 3'-5'-RNA exonuclease activity at the MUT-7/EXD3 node (PTN008550068), with Nibbler and EXD3 homologs among the donors. Reason: Confirmed for MUT-7 itself: recombinant MUT-7 degrades a single-stranded RNA substrate 3'-to-5', and a catalytic-site mutant is used as the inactive control (PMID:39188014). Core molecular function. Supporting Evidence: PMID:39188014 To test the exoribonuclease activity of MUT-7, we incubated recombinant MUT-7FL with a 5′-6-fluorescein amidite (5′-FAM)-labelled 28-mer ssRNA. PMID:39188014 in C. elegans and human MUT-7, the MUT7-C domain contributes to RNA binding and is thereby crucial for ribonuclease activity PMID:10535732 We found one of the mutated genes, mut-7, to encode a protein with homology to RNaseD. |
| GO:0000724 double-strand break repair via homologous recombination | IBA GO_REF:0000033 | REMOVE | Summary: PAINT IBA for homologous-recombination DSB repair at PTN008550068, with human EXD2 (Q9NVH0) as the only donor. Reason: EXD2 is a nuclear exonuclease that acts in DNA end resection; it is a paralog lineage of the MUT-7/EXD3 subfamily. MUT-7 is a single-stranded RNA exoribonuclease that acts in small-RNA pathways in germline Mutator foci (PMID:39188014, PMID:22713602). No evidence links MUT-7 to DNA repair. The function is specific to EXD2 and was over-propagated to the RNA-specialized MUT-7 branch. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008550068 · PTN008550068 SUPPORTS SOURCE BUT NOT TARGET The DNA repair assertion rests on human EXD2 alone. The MUT-7/Nibbler/EXD3 members below the node are characterized as single-stranded RNA exonucleases in small-RNA pathways. Supporting Evidence: PMID:39188014 The Nibbler EXO domain belongs to the DEDDy family of 3′-to-5′ exoribonucleases (InterPro: IPR002562) and is specific to single-stranded RNA PMID:22713602 Here we show that each of the six mutator proteins localizes to punctate foci at the periphery of germline nuclei. |
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO IEA (3'-5' exonuclease domain, RNase H-like superfamily). Reason: Correct but too general. The MUT7-C domain binds RNA and the exonuclease acts on single-stranded RNA (PMID:39188014). RNA binding is the appropriate term. Proposed replacements: RNA binding Supporting Evidence: PMID:39188014 in C. elegans and human MUT-7, the MUT7-C domain contributes to RNA binding and is thereby crucial for ribonuclease activity |
| GO:0005515 protein binding | IPI PMID:15653635 RDE-2 interacts with MUT-7 to mediate RNA interference in Ca... | REMOVE | Summary: Yeast two-hybrid and co-immunoprecipitation interaction with RDE-2/MUT-8 (Q19672) (PMID:15653635). Reason: The MUT-7-RDE-2/MUT-8 interaction is real and functionally important. It recruits MUT-7 to Mutator foci and is needed for RNAi (PMID:15653635, PMID:39188014). Removing this row does not dispute the interaction. Bare protein binding carries no functional information, and the adaptor role belongs to MUT-8, not MUT-7, so there is no informative MF replacement for MUT-7. The interaction's functional consequence is captured by the mutator focus localization and the core function. Supporting Evidence: PMID:15653635 using a yeast two-hybrid screen, we identified RDE-2/MUT-8 as one of the other components of this complex PMID:39188014 Mutations disrupting the MUT-7/MUT-8 interaction prevent MUT-7 recruitment to Mutator foci and lead to RNAi resistance. |
| GO:0005515 protein binding | IPI PMID:19123269 Empirically controlled mapping of the Caenorhabditis elegans... | REMOVE | Summary: Interaction with RDE-2/MUT-8 (Q19672) recovered in a large-scale yeast two-hybrid interactome map (PMID:19123269). Reason: An independent confirmation of the MUT-7-RDE-2 interaction (PMID:15653635, PMID:39188014). Removed as a bare protein-binding row for the same reason as above; the interaction itself is not disputed. Supporting Evidence: PMID:15653635 using a yeast two-hybrid screen, we identified RDE-2/MUT-8 as one of the other components of this complex |
| GO:0005634 nucleus | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT IBA for nuclear localization (PTN000341338). MUT-7 (WBGene00003504) is among the donors. Reason: MUT-7 is detected in nuclear extracts in a complex distinct from the cytosolic MUT-7-RDE-2 complex (PMID:15653635). The best-characterized site of action is the cytoplasmic perinuclear Mutator focus, so the nucleus is retained as a non-core location. Supporting Evidence: PMID:15653635 Here, we show that the MUT-7 protein resides in complexes of approximately 250 kDa in the nucleus and in the cytosol. |
| GO:0005634 nucleus | IDA PMID:15653635 RDE-2 interacts with MUT-7 to mediate RNA interference in Ca... | KEEP AS NON CORE | Summary: MUT-7 is detected in nuclear extracts by immunoblotting (PMID:15653635). Reason: Direct evidence. The nuclear MUT-7 complex lacks RDE-2 and its function is unclear (PMID:15653635). MUT-7 also acts in the nucleus of AWC neurons in odor adaptation (PMID:25108196). Supporting Evidence: PMID:15653635 Here, we show that the MUT-7 protein resides in complexes of approximately 250 kDa in the nucleus and in the cytosol. PMID:25108196 MUT-7, a nuclear component of the adaptation pathway that is expressed in both the cytoplasm and nucleus |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for cytoplasmic localization (PTN000341338). Reason: MUT-7 is cytosolic and concentrates in perinuclear Mutator foci in germ cells (PMID:15653635, PMID:22713602). Supporting Evidence: PMID:15653635 Here, we show that the MUT-7 protein resides in complexes of approximately 250 kDa in the nucleus and in the cytosol. PMID:22713602 Here we show that each of the six mutator proteins localizes to punctate foci at the periphery of germline nuclei. |
| GO:0005759 mitochondrial matrix | IBA GO_REF:0000033 | REMOVE | Summary: PAINT IBA for mitochondrial matrix (PTN002299009), donors human EXD2 and a Drosophila homolog. Reason: Mitochondrial matrix localization is a feature of EXD2. MUT-7 has been localized to cytosol, nucleus and Mutator foci (PMID:15653635, PMID:22713602), and no mitochondrial targeting has been reported. The location was over-propagated from the EXD2 lineage. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN002299009 · PTN002299009 SUPPORTS SOURCE BUT NOT TARGET Based on EXD2-type mitochondrial exonucleases. MUT-7 is experimentally cytosolic/nuclear and in germline Mutator foci. Supporting Evidence: PMID:15653635 Here, we show that the MUT-7 protein resides in complexes of approximately 250 kDa in the nucleus and in the cytosol. PMID:22713602 Here we show that each of the six mutator proteins localizes to punctate foci at the periphery of germline nuclei. |
| GO:0005829 cytosol | IDA PMID:15653635 RDE-2 interacts with MUT-7 to mediate RNA interference in Ca... | ACCEPT | Summary: MUT-7 is present in cytosolic (S100) extracts in a ~250 kDa complex with RDE-2 (PMID:15653635). Reason: Direct biochemical fractionation evidence. Supporting Evidence: PMID:15653635 Here, we show that the MUT-7 protein resides in complexes of approximately 250 kDa in the nucleus and in the cytosol. |
| GO:0005829 cytosol | IDA PMID:24684932 MUT-14 and SMUT-1 DEAD box RNA helicases have overlapping ro... | ACCEPT | Summary: Cytosolic MUT-7 from the Phillips et al. 2014 mutator complex study (PMID:24684932; abstract only in cache). Reason: Curator IDA from full text, consistent with the earlier fractionation (PMID:15653635) and with Mutator foci being perinuclear cytoplasmic structures. Supporting Evidence: PMID:24684932 The mutator complex localizes to Mutator foci adjacent to P granules at the nuclear periphery in germ cells. PMID:15653635 Here, we show that the MUT-7 protein resides in complexes of approximately 250 kDa in the nucleus and in the cytosol. |
| GO:0006396 RNA processing | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT IBA for RNA processing (PTN008550068). Reason: A broad but correct process term. MUT-7 is a 3'-5' exoribonuclease needed for 22G siRNA amplification (PMID:39188014). Supporting Evidence: PMID:39188014 The 3′–5′ exoribonuclease activity of MUT-7 is necessary for sRNA amplification, as mut-7 mutants show a drop in 22G RNAs |
| GO:0008306 associative learning | IMP PMID:25108196 C. elegans positive olfactory associative memory is a molecu... | KEEP AS NON CORE | Summary: mut-7 mutants have reduced learning after short-term associative memory (STAM) training (PMID:25108196). Reason: A behavioral phenotype that is a downstream consequence of MUT-7's role in small-RNA-mediated gene regulation in neurons. Not a core function. Supporting Evidence: PMID:25108196 is required for learning after STAM training, so its role in memory is not clear |
| GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: PAINT IBA for single-stranded DNA 3'-5' exonuclease activity (PTN008550068), with EXD2 and plant/fly homologs as donors. Reason: MUT-7 activity has been shown on single-stranded RNA (PMID:39188014). The family's DEDDy domain is described as specific to single-stranded RNA, and no DNA-directed role is known for MUT-7. DNase activity has not been excluded biochemically, so this is marked as over-annotation, not removed. Propagation Review Root cause: PROPAGATION BAD Failure modes: FUNCTIONAL DIVERGENCE Sources checked: PANTHER:PTN008550068 · PTN008550068 SUPPORTS SOURCE BUT NOT TARGET DNA exonuclease activity is grounded in EXD2-type members. MUT-7 and Nibbler are characterized on RNA substrates. Supporting Evidence: PMID:39188014 The Nibbler EXO domain belongs to the DEDDy family of 3′-to-5′ exoribonucleases (InterPro: IPR002562) and is specific to single-stranded RNA PMID:39188014 To test the exoribonuclease activity of MUT-7, we incubated recombinant MUT-7FL with a 5′-6-fluorescein amidite (5′-FAM)-labelled 28-mer ssRNA. |
| GO:0008355 olfactory learning | IMP PMID:23993094 Endogenous nuclear RNAi mediates behavioral adaptation to od... | KEEP AS NON CORE | Summary: mut-7 is required in AWC neurons for odor adaptation: odr-1 mRNA is not odor-responsive in mut-7 mutants, and AWC-specific MUT-7 partially restores it (PMID:23993094). Reason: A neuronal function of the endogenous nuclear RNAi pathway with HPL-2. Real but downstream of MUT-7's small-RNA role. Supporting Evidence: PMID:23993094 In mut-7(pk204) animals, odr-1 mRNA levels were not odor-responsive |
| GO:0008408 3'-5' exonuclease activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO IEA for 3'-5' exonuclease activity. Reason: Correct parent of the experimentally supported 3'-5'-RNA exonuclease activity (PMID:39188014). Supporting Evidence: PMID:39188014 To test the exoribonuclease activity of MUT-7, we incubated recombinant MUT-7FL with a 5′-6-fluorescein amidite (5′-FAM)-labelled 28-mer ssRNA. |
| GO:0016441 post-transcriptional gene silencing | IMP PMID:10535731 The rde-1 gene, RNA interference, and transposon silencing i... | ACCEPT | Summary: mut-7 mutants are RNAi-resistant and mobilize transposons in the germline (PMID:10535731, PMID:10535732). Reason: MUT-7 exonuclease activity is required for 22G siRNA amplification (PMID:39188014), so MUT-7 does part of the work of the silencing pathway. Supporting Evidence: PMID:10535732 Most of these mutants are resistant to RNA interference (RNAi). PMID:39188014 The 3′–5′ exoribonuclease activity of MUT-7 is necessary for sRNA amplification, as mut-7 mutants show a drop in 22G RNAs |
| GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing | IMP PMID:10535731 The rde-1 gene, RNA interference, and transposon silencing i... | ACCEPT | Summary: mut-7 is required for RNAi and transposon silencing (PMID:10535731). Reason: Core process, as above. MUT-7 is also required for ERGO-1 class 26G siRNAs (PMID:21245313). Supporting Evidence: PMID:10535732 Most of these mutants are resistant to RNA interference (RNAi). PMID:21245313 The results also reveal essential roles for mut-2 and mut-7 in the ERGO-1 class 26G siRNA pathway |
| GO:0044747 pre-miRNA 3'-end processing | ISS PMID:10535732 Mut-7 of C. elegans, required for transposon silencing and R... | MARK AS OVER ANNOTATED | Summary: ISS from Drosophila Nibbler (Q9VIF1), which trims the 3' ends of miRNAs. Reason: Nibbler's miRNA 3'-end trimming has not been shown for C. elegans MUT-7. In worms, MUT-7 acts in the Mutator siRNA amplification pathway (PMID:39188014), and its requirement is for siRNAs, not miRNAs (PMID:21245313). The cited paper (PMID:10535732) predates the Nibbler work and reports only RNase D homology. Not refuted, but not supported in C. elegans. Supporting Evidence: PMID:10535732 We found one of the mutated genes, mut-7, to encode a protein with homology to RNaseD. PMID:39188014 The 3′–5′ exoribonuclease activity of MUT-7 is necessary for sRNA amplification, as mut-7 mutants show a drop in 22G RNAs |
| GO:0044748 3'-5'-exoribonuclease activity involved in mature miRNA 3'-end processing | ISS PMID:10535732 Mut-7 of C. elegans, required for transposon silencing and R... | MARK AS OVER ANNOTATED | Summary: ISS from Drosophila Nibbler for 3'-5' exoribonuclease activity in mature miRNA 3'-end processing. Reason: The exoribonuclease activity itself is supported (PMID:39188014), but the miRNA-processing context comes from Drosophila Nibbler and is not supported in C. elegans. The context-free term 3'-5'-RNA exonuclease activity (GO:0000175) already captures the activity. Supporting Evidence: PMID:39188014 To test the exoribonuclease activity of MUT-7, we incubated recombinant MUT-7FL with a 5′-6-fluorescein amidite (5′-FAM)-labelled 28-mer ssRNA. |
| GO:1990633 mutator focus | IDA PMID:22713602 MUT-16 promotes formation of perinuclear mutator foci requir... | ACCEPT | Summary: MUT-7 is one of the six mutator proteins that localize to perinuclear Mutator foci (PMID:22713602). Reason: Core location. Recruitment depends on the MUT-7-MUT-8 interaction, and disrupting it causes RNAi resistance (PMID:39188014). Supporting Evidence: PMID:22713602 Here we show that each of the six mutator proteins localizes to punctate foci at the periphery of germline nuclei. PMID:39188014 Mutations disrupting the MUT-7/MUT-8 interaction prevent MUT-7 recruitment to Mutator foci and lead to RNAi resistance. |
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Download this section (compressed HTML)Q: What does MUT-7 degrade in Mutator foci: the 3' ends of target RNA fragments before or after pUGylation, abortive RdRP products, or something else? Recombinant MUT-7 trims an A-tail but cannot degrade a folded pUG unit.
Q: What is the function of the nuclear MUT-7 complex, which lacks RDE-2?
Experiment: Map MUT-7-dependent RNA 3' ends in vivo (e.g. 3'-end sequencing of pUG RNAs and RdRP products) in wild type, catalytic-dead mut-7 and mut-8 interface mutants.
Hypothesis: MUT-7 trims specific RNA intermediates in Mutator foci, and this trimming is needed for efficient RRF-1-dependent 22G-RNA synthesis.
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