RDE-2 (also known as MUT-8) is an intrinsically disordered bridging adaptor protein of the C. elegans Mutator complex, the germline machinery that amplifies secondary small interfering RNAs (22G-RNAs) for RNA-mediated silencing. RDE-2 has no catalytic activity and no canonical folded domain; its structured C-terminal domain binds the C-terminal domain of the 3'-5' exoribonuclease MUT-7, while its partially structured N-terminal region contacts the intrinsically disordered scaffold MUT-16. By physically linking MUT-7 to MUT-16, RDE-2 recruits the MUT-7 exoribonuclease into perinuclear Mutator foci, the phase-separated condensates (adjacent to but distinct from P granules) in which the RNA-dependent RNA polymerase RRF-1 synthesizes secondary siRNAs. This function is required for exogenous and endogenous RNAi, transposon silencing, and germline genome surveillance; loss of rde-2 abolishes secondary siRNA accumulation and causes RNAi resistance, transposon mobilization and an X-chromosome non-disjunction (high-incidence-of-males) phenotype. RDE-2 and its MUT-7 interaction are restricted to the Caenorhabditis lineage.
Definition: The RNA-dependent RNA polymerase (RdRP)-mediated de novo synthesis of secondary small interfering RNAs (e.g. C. elegans 22G-RNAs) templated on target mRNAs recognized by primary small RNAs, occurring within a specialized RNA-processing compartment (Mutator focus). Distinguished from siRNA processing/Dicer-dependent primary siRNA generation.
Justification: RDE-2 and the Mutator complex act specifically in RdRP-dependent secondary siRNA amplification, a step for which no dedicated GO term exists; siRNA processing (GO:0030422) conflates Dicer-dependent primary siRNA generation with amplification.
Definition: A molecular function in which a protein provides a structural/organizational role as a subunit of the C. elegans Mutator complex, contributing to assembly of the siRNA-amplification compartment rather than catalysis.
Justification: RDE-2 is an obligate structural adaptor subunit with no catalytic activity; molecular adaptor activity (GO:0060090) captures the bridging aspect, but a complex-specific structural-constituent term would more precisely express its 'be part of the machine' role.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
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GO:0005515
protein binding
|
IPI
PMID:15653635 RDE-2 interacts with MUT-7 to mediate RNA interference in Ca... |
MODIFY |
Summary: The IPI interaction with MUT-7 (P34607) is real and central, but 'protein binding' is uninformative. RDE-2's molecular function is to bridge the MUT-7 exoribonuclease to the MUT-16 scaffold, i.e. a molecular adaptor activity; this is the core molecular function of the protein.
Reason: Replace the uninformative 'protein binding' with the more specific molecular adaptor activity. RDE-2 binds MUT-7 via its CTD and MUT-16 via its NTD, physically linking the two so that MUT-7 is recruited into Mutator foci (PMID:15653635, PMID:39188014).
Proposed replacements:
molecular adaptor activity
Supporting Evidence:
PMID:39188014
Caenorhabditis elegans MUT-7 contains a specific insertion within MUT7-C, which allows binding to MUT-8 and, consequently, MUT-7 recruitment to germ granules
|
|
GO:0005515
protein binding
|
IPI
PMID:19123269 Empirically controlled mapping of the Caenorhabditis elegans... |
MARK AS OVER ANNOTATED |
Summary: A second IPI 'protein binding' annotation from a high-throughput interactome dataset recording the RDE-2/MUT-7 interaction. The interaction is genuine and corroborates the adaptor role, but the term itself is uninformative.
Reason: 'protein binding' conveys no functional specificity; the informative molecular function (molecular adaptor activity) is captured from the dedicated interaction studies. Retained as supporting evidence for the MUT-7 interaction but not as a core function.
Supporting Evidence:
PMID:30036386
two proteins of unknown function, RDE-2 and MUT-15
|
|
GO:0030422
siRNA processing
|
IDA
PMID:15653635 RDE-2 interacts with MUT-7 to mediate RNA interference in Ca... |
ACCEPT |
Summary: RDE-2 is required for accumulation of siRNAs in vivo; the MUT-7/RDE-2 complex acts in the RdRP-dependent siRNA amplification step. GO:0030422 explicitly includes amplification of siRNA by RNA-directed RNA polymerase, so this is an appropriate core biological-process term.
Reason: rde-2 mutants do not produce detectable siRNAs in vivo, and the complex functions downstream of primary siRNA production in amplification, consistent with the siRNA-processing term definition.
Supporting Evidence:
PMID:15653635
Together these data hint at a role for the MUT-7/RDE-2 complex in the amplification step of the RNAi pathway in C.elegans.
|
|
GO:1990633
mutator focus
|
IDA
PMID:22713602 MUT-16 promotes formation of perinuclear mutator foci requir... |
ACCEPT |
Summary: RDE-2 is one of the six mutator proteins that localize to perinuclear Mutator foci in the germline, the siRNA-amplification compartment. This is the informative, species-appropriate cellular-component annotation and represents where RDE-2 carries out its function.
Reason: Direct localization of the mutator proteins (including RDE-2) to perinuclear Mutator foci; RDE-2 localization to these foci depends on MUT-16 (PMID:30036386).
Supporting Evidence:
PMID:22713602
each of the six mutator proteins localizes to punctate foci at the periphery of germline nuclei. The Mutator foci are adjacent to P granules
|
|
GO:0016441
post-transcriptional gene silencing
|
IMP
PMID:10535731 The rde-1 gene, RNA interference, and transposon silencing i... |
KEEP AS NON CORE |
Summary: Loss of rde-2 causes RNAi resistance and transposon de-silencing, i.e. defective post-transcriptional gene silencing. This is a defining phenotype of the gene, though it is a parent of the more specific regulatory-ncRNA-mediated PTGS term.
Reason: Correct but general; the more specific GO:0035194 (regulatory ncRNA-mediated post-transcriptional gene silencing) better captures the mechanism and is retained as core. Kept as valid non-core context.
Supporting Evidence:
PMID:15653635
This allele, removing the last three-quarters of the gene, is viable and is RNAi resistant
|
|
GO:0045132
meiotic chromosome segregation
|
IMP
PMID:10535731 The rde-1 gene, RNA interference, and transposon silencing i... |
KEEP AS NON CORE |
Summary: rde-2 mutants show a high-incidence-of-males (Him) phenotype caused by X-chromosome non-disjunction. This is a downstream, pleiotropic consequence of losing germline small-RNA silencing rather than evidence that RDE-2 acts directly in the meiotic chromosome-segregation machinery.
Reason: The segregation defect is an indirect consequence of the RNAi/silencing deficiency (shared with mut-7), not a direct molecular role of RDE-2 in meiosis. Retained as a non-core phenotype-based annotation.
Supporting Evidence:
PMID:15653635
both mut-7 and rde-2 mutants show a high incidence of males (him) phenotype
|
|
GO:0035194
regulatory ncRNA-mediated post-transcriptional gene silencing
|
IMP
PMID:10535731 The rde-1 gene, RNA interference, and transposon silencing i... |
ACCEPT |
Summary: RDE-2 is required for small-RNA (siRNA/22G-RNA)-guided silencing of endogenous and exogenous targets and of transposons; this term captures the specific mechanism of RDE-2's biological role and is a core process annotation.
Reason: Loss of rde-2 abolishes RdRP-dependent secondary siRNA accumulation and silencing, the defining regulatory-ncRNA-mediated PTGS function.
Supporting Evidence:
PMID:30036386
mut-15, rde-2, rde-8, or rrf-1) result in a substantial loss of the RdRP-dependent secondary siRNAs
|
|
GO:0005829
cytosol
|
IDA
PMID:15653635 RDE-2 interacts with MUT-7 to mediate RNA interference in Ca... |
KEEP AS NON CORE |
Summary: Biochemical fractionation placed the MUT-7/RDE-2 complex in the cytosolic (S100) fraction. This is correct but generic; the informative, function-relevant localization is the perinuclear Mutator focus (GO:1990633), which is a specialized cytoplasmic compartment.
Reason: Valid subcellular fraction data, but subsumed functionally by the Mutator-focus annotation. Kept as non-core supporting localization.
Supporting Evidence:
PMID:15653635
the MUT-7 and RDE-2 proteins are associated with each other in the cytosol, but not in the nucleus
|
Q: Does RDE-2/MUT-8 possess any activity beyond bridging MUT-7 and MUT-16 - for example intrinsic RNA binding or a role in nucleating Mutator-focus condensation?
Suggested experts: René F. Ketting, Sebastian Falk, Carolyn M. Phillips
Experiment: Generate separation-of-function rde-2 alleles that retain MUT-16 binding but disrupt the MUT-7 CTD interface (guided by the PDB 8Q66 interface), assay MUT-7 focus localization, secondary 22G-RNA levels, and RNAi/transposon-silencing competence.
Hypothesis: RDE-2 acts purely as a structural adaptor whose sole essential role is to recruit and position MUT-7 within Mutator foci.
Type: structure-guided mutagenesis with small-RNA sequencing and localization
Experiment: Reconstitute recombinant RDE-2 with each mutator component and RRF-1 and test for direct binary interactions by pulldown/SEC and crosslinking mass spectrometry, and attempt cryo-EM of the assembled complex.
Hypothesis: RDE-2 directly contacts additional mutator components beyond MUT-7 and MUT-16.
Type: in vitro interaction mapping / structural biology
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Beyond acting as a passive structural bridge between MUT-7 and MUT-16, it is unknown whether the intrinsically disordered regions of RDE-2/MUT-8 have any additional molecular activity (e.g. RNA binding, condensate nucleation, or allosteric regulation of MUT-7 nuclease activity). RDE-2 has no catalytic activity and no canonical folded domain, so its full biochemical contribution to the complex is undefined.
OPEN BIOLOGY MF_DARK
What is known: It is firmly established that RDE-2's structured C-terminal domain binds the MUT-7 CTD (crystal structure PDB 8Q66) and that its partially structured N-terminal region contacts the MUT-16 scaffold, recruiting MUT-7 to Mutator foci. What is unknown is whether RDE-2 does anything mechanistically beyond this bridging.
Significance: Because RDE-2 is essential for secondary siRNA amplification but is not itself an enzyme, distinguishing 'pure scaffold/recruiter' from 'active participant' would determine whether the amplification defect in rde-2 mutants is purely a mislocalization/assembly failure or also a loss of a direct biochemical step.
What would resolve it: In vitro reconstitution of the MUT-16/RDE-2/MUT-7 module with siRNA-amplification assays, RNA-binding assays on isolated RDE-2 domains, and separation-of-function RDE-2 alleles that retain MUT-7/MUT-16 binding but disrupt any additional activity would resolve this.
Provenance (the field's own admissions):
Gap: The complete set of RDE-2 direct binding partners within the Mutator complex is unresolved. Direct interactions are established only with MUT-7 (CTD-CTD) and MUT-16 (via the RDE-2 N-terminal region); whether RDE-2 directly contacts other mutator components (MUT-2/RDE-3, MUT-14, MUT-15, NYN-1/2, RDE-8) or the RdRP RRF-1, or merely co-resides with them in the focus, has not been tested biochemically.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: RDE-2 localization to Mutator foci depends on MUT-16, and RDE-2 is in turn required for MUT-7 localization (a MUT-16 -> RDE-2 -> MUT-7 recruitment axis). Other mutator components localize via separate MUT-16 branches, but their direct/indirect relationship to RDE-2 is inferred from localization dependencies, not from binary interaction data.
Significance: Knowing which contacts are direct defines the true architecture of the amplification compartment and whether RDE-2 is a dedicated MUT-7 adaptor or a more central hub.
What would resolve it: Systematic binary interaction mapping (e.g. reconstituted pulldowns, crosslinking mass spectrometry, or cryo-EM of the assembled complex) of RDE-2 against each mutator component.
Provenance (the field's own admissions):
Gap: How RDE-2 mechanistically contributes to the secondary siRNA (22G-RNA) amplification reaction itself is unknown. It is established that rde-2 loss abolishes RdRP-dependent secondary siRNA accumulation, but whether RDE-2's only role is to recruit and position MUT-7, or whether it also participates in target-mRNA capture or templating for RRF-1, is undetermined.
OPEN BIOLOGYONTOLOGY MF_DARK
What is known: The genetic requirement is clear (no detectable secondary siRNAs without rde-2) and the focus-assembly role is structurally defined, but the biochemical step at which RDE-2 acts within amplification is not.
Significance: Secondary siRNA amplification is the amplifying core of C. elegans RNA silencing and heritable epigenetic inheritance; resolving RDE-2's step would clarify a rate-limiting node. There is also no GO term for 'secondary siRNA amplification' as a distinct process or for a 'structural constituent of the Mutator complex', so RDE-2's specific contribution cannot currently be expressed precisely.
What would resolve it: Mechanistic in vitro amplification assays with defined mutator subcomplexes, plus ontology development for a secondary-siRNA-amplification process term and/or a Mutator-complex structural-constituent term.
Provenance (the field's own admissions):
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The gene rde-2 (RNAi Deficient-2) in Caenorhabditis elegans encodes the protein RDE-2, which is also known as MUT-8 (Mutator-8). The gene is located at locus F21C3.4 on the C. elegans genome (UniProt accession Q19672). The dual nomenclature reflects its independent identification in two distinct genetic screens: rde-2 was identified as a gene required for exogenous RNA interference (RNAi), while mut-8 was identified in screens for mutator-class genes required for transposon silencing (phillips2012mut16promotesformation pages 2-4). The protein is annotated in UniProt as containing an SH2 domain, though the functional literature characterizes RDE-2/MUT-8 as a largely intrinsically disordered adaptor protein with a partially structured N-terminal domain (NTD) and a structured C-terminal domain (CTD) connected by a long flexible linker (busetto2024mut7exoribonucleaseactivity pages 4-5).
RDE-2/MUT-8 functions as a bridging adaptor protein within the Mutator complex, a multi-protein assembly essential for small RNA amplification in the C. elegans germline. Its primary role is to physically connect the 3′–5′ exoribonuclease MUT-7 to the scaffolding protein MUT-16, thereby recruiting MUT-7 to Mutator foci and enabling its participation in RNA silencing (busetto2024mut7exoribonucleaseactivity pages 7-9, busetto2024mut7exoribonucleaseactivity pages 5-7).
The key structural finding from Busetto et al. (2024) is summarized below:
RDE-2/MUT-8 functions as a bridging adaptor in the C. elegans Mutator complex: its N-terminal domain (aa 36-235) contacts the MUT-16 scaffold at residues 584-724, while its C-terminal domain binds the MUT-7 C-terminal domain through an extended ~2140 Ų interface. This architecture links the MUT-7 exoribonuclease to the MUT-16 scaffold, enabling MUT-7 recruitment to Mutator foci and supporting RNAi function; disrupting the MUT-7–MUT-8 interaction causes RNAi-resistant phenotypes. (busetto2024mut7exoribonucleaseactivity pages 5-7, busetto2024mut7exoribonucleaseactivity pages 9-11)
Blockquote: This blockquote summarizes the central mechanistic finding from Busetto et al. 2024 on how RDE-2/MUT-8 physically connects MUT-7 to the MUT-16 scaffold. It is useful for clearly stating the current best-supported molecular role of RDE-2 in Mutator complex assembly.
Specifically, the C-terminal domain (CTD) of MUT-8/RDE-2 directly binds the MUT-7 CTD, forming an extensive protein–protein interaction interface of approximately 2,140 Ų (busetto2024mut7exoribonucleaseactivity pages 5-7, busetto2024mut7exoribonucleaseactivity pages 4-5). Both the CTD-N and CTD-C subdomains of MUT-7 contribute to this complex formation, with MUT-7 residues Arg853 and Thr855 playing critical roles at the interface (busetto2024mut7exoribonucleaseactivity pages 4-5). The N-terminal domain (NTD) of MUT-8 (amino acids 36–235), which is partially structured, directly contacts MUT-16 at residues 584–724, a region that is intrinsically disordered but both necessary and sufficient for binding (busetto2024mut7exoribonucleaseactivity pages 5-7). Crucially, MUT-7 alone cannot bind MUT-16 without MUT-8, and MUT-8's CTD alone is insufficient for MUT-16 binding, demonstrating that both interaction interfaces of MUT-8 are essential for linking the catalytic exoribonuclease to the scaffolding platform (busetto2024mut7exoribonucleaseactivity pages 5-7).
RDE-2/MUT-8 is not an enzyme itself; rather, it serves a structural/adapter role, enabling the assembly of a functional small RNA amplification complex. Disruption of the MUT-7/MUT-8 interaction (e.g., via point mutations R853E, T855E in MUT-7) prevents MUT-7 localization to Mutator foci and causes RNAi-resistant phenotypes (busetto2024mut7exoribonucleaseactivity pages 9-11).
RDE-2/MUT-8 localizes to perinuclear punctate structures termed Mutator foci in the C. elegans germline (phillips2012mut16promotesformation pages 2-4, phillips2012mut16promotesformation pages 4-5). These foci are present in both hermaphrodite and male germlines during larval and adult stages, with brightest concentrations in the mitotic proliferation region and transition zone (leptotene/zygotene) of the germline, persisting through the pachytene stage (phillips2012mut16promotesformation pages 2-4). In embryos, Mutator foci remain diffuse in the cytoplasm until approximately the 100-cell stage, when they associate with nuclear structures (sundby2021connectingthedots pages 4-6, phillips2022germgranulesand pages 8-9).
Mutator foci are positioned adjacent to P granules (nuclear pore-associated ribonucleoprotein structures) but are distinct from them; they rarely overlap completely with P-granule markers such as PGL-1 and DRH-3 (phillips2012mut16promotesformation pages 4-5, phillips2012mut16promotesformation pages 1-2). Mutator foci form independently of core P-granule components, although simultaneous depletion of multiple P-granule proteins can disrupt Mutator foci formation (phillips2012mut16promotesformation pages 1-2, phillips2022germgranulesand pages 8-9). Z granules appear to bridge the region between P granules and Mutator foci, suggesting a spatial organization of these perinuclear compartments (sundby2021connectingthedots pages 6-7).
Mutator foci exhibit liquid-like properties consistent with phase-separated condensates, including spherical shape, internal flow, component diffusion, and sensitivity to aliphatic alcohols (sundby2021connectingthedots pages 6-7, uebel2018distinctregionsof pages 1-2). MUT-16 nucleates Mutator foci formation through its intrinsically disordered C-terminal region, and the ternary MUT-7/MUT-8/MUT-16 complex promotes condensate formation (busetto2024mut7exoribonucleaseactivity pages 7-9, uebel2018distinctregionsof pages 1-2).
RDE-2/MUT-8 functions within the WAGO-class 22G-RNA biogenesis pathway, which is central to multiple RNA silencing processes in C. elegans. The Mutator complex, in which RDE-2 is a core component, serves as the platform for amplification of secondary small interfering RNAs (siRNAs) called 22G-RNAs. These 22G-RNAs are synthesized by the RNA-dependent RNA polymerase (RdRP) RRF-1, which also localizes to Mutator foci (sundby2021connectingthedots pages 6-7, phillips2012mut16promotesformation pages 1-2). The Mutator complex captures recently transcribed target mRNAs at Mutator foci for small RNA amplification (phillips2022germgranulesand pages 8-9).
Within this pathway, RDE-2/MUT-8 contributes to multiple silencing processes:
Exogenous RNAi (exo-RNAi): RDE-2 is required for effective responses to exogenously introduced double-stranded RNA. Loss of rde-2 causes defects in both germline and somatic RNAi, which can be rescued by RDE-2::GFP fusion transgenes (phillips2012mut16promotesformation pages 2-4).
Transposon silencing: rde-2/mut-8 mutants exhibit active transposons due to defective transposon silencing, including Tc1 DNA transposons (phillips2012mut16promotesformation pages 2-4). The mutator class genes, including rde-2, were originally identified through their role in preventing Tc1 transposition in the germline.
Endogenous siRNA production: RDE-2 is required for accumulation of WAGO-class 22G siRNAs, including the abundant X-cluster siRNA 22G siR-1. Loss of rde-2 substantially reduces 22G siR-1 levels (phillips2012mut16promotesformation pages 2-4).
piRNA-initiated silencing: The Mutator complex amplifies 22G-RNAs downstream of piRNA (21U-RNA) triggers. piRNA targets are shuttled to Mutator foci where the Mutator complex, including RDE-2, mediates secondary siRNA amplification (sundby2021connectingthedots pages 6-7).
Transgene silencing: The endo-RNAi pathway involving mutator complex components mediates tissue-specific silencing of integrated transgenes, particularly in the intestine (chen2024tissuespecificsilencingof pages 4-5, chen2024tissuespecificsilencingof pages 1-2). MUT-16 recruits the complex including MUT-8/RDE-2, which further recruits MUT-7 to assemble the functional mutator focus (chen2024tissuespecificsilencingof pages 4-5).
Antiviral defense and heritable RNAi: RDE-2 is involved in heritable silencing of RNA and functions after initiation of the original RNAi response, working in concert with MUT-7 (sterken2014aheritableantiviral pages 4-5). In experiments with Orsay virus (OrV), rde-2 mutants failed to mount a trans-generational antiviral response; pre-exposed rde-2 mutants did not show decreased viral replication in their offspring, unlike wild-type N2 animals (sterken2014aheritableantiviral pages 4-5).
The Mutator complex assembles through hierarchical recruitment mediated by distinct regions of the MUT-16 scaffold protein. RDE-2/MUT-8 is recruited to Mutator foci by the H-I region of MUT-16; deletion of this region causes RDE-2 to fail to localize (uebel2018distinctregionsof pages 5-7, uebel2018distinctregionsof pages 4-5). Once recruited, RDE-2 in turn recruits MUT-7 through their CTD–CTD interaction (busetto2024mut7exoribonucleaseactivity pages 5-7, uebel2018distinctregionsof pages 11-13). This places RDE-2 as a critical intermediate in a MUT-16 → RDE-2 → MUT-7 recruitment axis, which operates in parallel to other recruitment branches: the B-C region of MUT-16 recruits MUT-2, MUT-14, and MUT-15, with MUT-15 subsequently recruiting NYN-1/2 and RDE-8 (uebel2018distinctregionsof pages 11-13, uebel2018distinctregionsof pages 5-7). The RdRP RRF-1 is recruited through the F region of MUT-16 (uebel2018distinctregionsof pages 11-13).
The following table summarizes the major components of the Mutator complex and their relationships:
| Protein Name | Known Function/Activity | Relationship to RDE-2/MUT-8 | MUT-16 Recruitment Region | Key References |
|---|---|---|---|---|
| MUT-16 | Core scaffold of Mutator foci; Q/N-rich, intrinsically disordered protein that nucleates Mutator complex assembly and promotes phase-separated condensates required for small-RNA amplification | RDE-2/MUT-8 is recruited to Mutator foci by MUT-16; RDE-2 then links MUT-16 to MUT-7. A defined MUT-16 segment (aa 584-724; within H-I region) binds the RDE-2/MUT-7 module (uebel2018distinctregionsof pages 1-2, busetto2024mut7exoribonucleaseactivity pages 5-7, uebel2018distinctregionsof pages 2-4) | Not applicable; scaffold itself | (uebel2018distinctregionsof pages 1-2, busetto2024mut7exoribonucleaseactivity pages 5-7, uebel2018distinctregionsof pages 11-13, uebel2018distinctregionsof pages 2-4) |
| MUT-2 / RDE-3 | Nucleotidyltransferase; mutator component required for RNA silencing and transposon control; localizes to Mutator foci | Co-localizes with RDE-2 in Mutator foci; recruited independently of RDE-2 via MUT-16 scaffold, in a branch distinct from the RDE-2→MUT-7 linkage (phillips2012mut16promotesformation pages 4-5, uebel2018distinctregionsof pages 11-13) | B-C region of MUT-16 (uebel2018distinctregionsof pages 11-13, uebel2018distinctregionsof pages 5-7) | (phillips2012mut16promotesformation pages 4-5, uebel2018distinctregionsof pages 11-13) |
| MUT-7 | 3′-5′ exoribonuclease with MUT7-C domain; essential for RNA silencing and small-RNA production | Direct binding partner of RDE-2/MUT-8: MUT-7 CTD binds MUT-8 CTD, and this interaction recruits MUT-7 to Mutator foci; disrupting the interface causes RNAi resistance (busetto2024mut7exoribonucleaseactivity pages 7-9, busetto2024mut7exoribonucleaseactivity pages 5-7, busetto2024mut7exoribonucleaseactivity pages 9-11, busetto2024mut7exoribonucleaseactivity pages 4-5) | H-I region, indirectly via RDE-2/MUT-8 bridge (uebel2018distinctregionsof pages 11-13, uebel2018distinctregionsof pages 4-5) | (busetto2024mut7exoribonucleaseactivity pages 7-9, busetto2024mut7exoribonucleaseactivity pages 5-7, busetto2024mut7exoribonucleaseactivity pages 9-11, uebel2018distinctregionsof pages 11-13) |
| MUT-8 / RDE-2 | Adaptor/bridging protein in Mutator complex; required for exogenous RNAi, endogenous silencing, transposon repression, fertility, and WAGO-class 22G-RNA accumulation | Central reference protein: bridges MUT-7 to MUT-16 using distinct domains; NTD contacts MUT-16, CTD binds MUT-7 CTD (phillips2012mut16promotesformation pages 2-4, busetto2024mut7exoribonucleaseactivity pages 5-7) | H-I region; RDE-2 fails to localize when H-I is deleted (uebel2018distinctregionsof pages 5-7, uebel2018distinctregionsof pages 4-5) | (phillips2012mut16promotesformation pages 2-4, busetto2024mut7exoribonucleaseactivity pages 5-7, uebel2018distinctregionsof pages 5-7) |
| MUT-14 | RNA helicase mutator component involved in RNA silencing; localizes to Mutator foci | Co-localizes with RDE-2 in the same perinuclear compartment; recruited in a branch separate from the RDE-2→MUT-7 arm (phillips2012mut16promotesformation pages 4-5, uebel2018distinctregionsof pages 11-13) | B-C region of MUT-16 (uebel2018distinctregionsof pages 11-13, uebel2018distinctregionsof pages 5-7) | (phillips2012mut16promotesformation pages 4-5, uebel2018distinctregionsof pages 11-13) |
| MUT-15 | Mutator component needed for RNA silencing; also recruits downstream effectors | Co-localizes with RDE-2; recruited independently of RDE-2 by MUT-16 and then helps recruit NYN-1/2 and RDE-8, placing it in a parallel branch to the RDE-2→MUT-7 linkage (phillips2012mut16promotesformation pages 4-5, uebel2018distinctregionsof pages 11-13) | B-C region of MUT-16 (uebel2018distinctregionsof pages 11-13) | (phillips2012mut16promotesformation pages 4-5, uebel2018distinctregionsof pages 11-13) |
| RRF-1 | RNA-dependent RNA polymerase (RdRP) that synthesizes secondary WAGO-class 22G-RNAs in Mutator foci | Works in the same amplification compartment as RDE-2; RDE-2 helps organize the Mutator complex that supports RRF-1-dependent 22G-RNA biogenesis, but no direct RDE-2–RRF-1 interaction is established in the cited evidence (sundby2021connectingthedots pages 6-7, phillips2012mut16promotesformation pages 1-2, phillips2012mut16promotesformation pages 5-7) | F region of MUT-16 (with partial effects from other regions) (uebel2018distinctregionsof pages 11-13, uebel2018distinctregionsof pages 5-7) | (uebel2018distinctregionsof pages 11-13, sundby2021connectingthedots pages 6-7, phillips2012mut16promotesformation pages 1-2, phillips2012mut16promotesformation pages 5-7) |
| RDE-8 | NYN-domain endoribonuclease implicated in small-RNA amplification/silencing | In the same Mutator amplification system as RDE-2, but recruited through the MUT-15 branch rather than through the RDE-2→MUT-7 bridge (uebel2018distinctregionsof pages 11-13, sundby2021connectingthedots pages 4-6) | Indirect via B-C → MUT-15 branch (uebel2018distinctregionsof pages 11-13, uebel2018distinctregionsof pages 5-7) | (uebel2018distinctregionsof pages 11-13, sundby2021connectingthedots pages 4-6) |
| NYN-1 / NYN-2 | NYN-domain proteins associated with Mutator foci and small-RNA pathway assembly | Parallel to RDE-2 branch: recruited downstream of MUT-15 rather than through RDE-2, but part of the same amplification compartment (uebel2018distinctregionsof pages 11-13, sundby2021connectingthedots pages 4-6) | Indirect via B-C → MUT-15 branch (uebel2018distinctregionsof pages 11-13) | (uebel2018distinctregionsof pages 11-13, sundby2021connectingthedots pages 4-6) |
| SMUT-1 | RNA helicase-like mutator component of Mutator foci | Co-recruited to Mutator foci with RDE-2 as part of the broader MUT-16-dependent complex; specific direct interaction with RDE-2 not defined in cited evidence (uebel2018distinctregionsof pages 1-2, uebel2018distinctregionsof pages 2-4) | Specific MUT-16 subregion not resolved in the cited excerpts | (uebel2018distinctregionsof pages 1-2, uebel2018distinctregionsof pages 2-4) |
Table: This table summarizes major C. elegans Mutator complex components, emphasizing how RDE-2/MUT-8 fits into assembly of the small-RNA amplification machinery. It is useful for quickly mapping protein function, recruitment logic, and the specific MUT-16 scaffold regions implicated by current evidence.
Loss-of-function mutations in rde-2/mut-8 produce a constellation of phenotypes reflecting its broad role in RNA silencing:
MUT-8/RDE-2 and its interaction with MUT-7 appear to be restricted to the genus Caenorhabditis. The Mutator complex as a whole is not present in animals outside Caenorhabditis (busetto2024mut7exoribonucleaseactivity pages 11-12, busetto2024mut7exoribonucleaseactivity pages 9-11). While the MUT-7 exoribonuclease is evolutionarily conserved (with orthologs such as EXD3 in humans and zebrafish), the specific insertion in MUT-7's MUT7-C domain that serves as the MUT-8 binding platform is a Caenorhabditis-specific adaptation. Co-expression experiments demonstrate that the MUT-8 CTD does not interact with human EXD3 or Danio rerio EXD3, confirming that the MUT-8 interaction is not conserved outside nematodes (busetto2024mut7exoribonucleaseactivity pages 11-12). Within Caenorhabditis, both MUT-8 and MUT-16 homologs are conserved, and the MUT-7 CTD function in establishing localization via MUT-8 is likely extended to other species in the genus (busetto2024mut7exoribonucleaseactivity pages 9-11).
RDE-2/MUT-8 is a C. elegans adaptor protein that plays an essential structural role in the Mutator complex, a perinuclear, phase-separated condensate in the germline dedicated to small RNA amplification. Its primary molecular function is to bridge the 3′–5′ exoribonuclease MUT-7 to the scaffolding protein MUT-16, using distinct N-terminal and C-terminal protein interaction domains. Through this bridging function, RDE-2 enables the assembly of a functional small RNA amplification compartment that is required for WAGO-class 22G-RNA biogenesis, transposon silencing, exogenous and endogenous RNAi, antiviral defense, and transgenerational epigenetic inheritance. The protein localizes to perinuclear Mutator foci in the germline, adjacent to but distinct from P granules. RDE-2/MUT-8 and its interaction with MUT-7 appear to be specific to the Caenorhabditis genus, representing a lineage-specific adaptation of the small RNA silencing machinery.
References
(phillips2012mut16promotesformation pages 2-4): Carolyn M. Phillips, Taiowa A. Montgomery, Peter C. Breen, and Gary Ruvkun. Mut-16 promotes formation of perinuclear mutator foci required for rna silencing in the c. elegans germline. Genes & development, 26 13:1433-44, Jul 2012. URL: https://doi.org/10.1101/gad.193904.112, doi:10.1101/gad.193904.112. This article has 242 citations and is from a highest quality peer-reviewed journal.
(busetto2024mut7exoribonucleaseactivity pages 4-5): Virginia Busetto, Lizaveta Pshanichnaya, Raffael Lichtenberger, Stephan Hann, René F Ketting, and Sebastian Falk. Mut-7 exoribonuclease activity and localization are mediated by an ancient domain. Nucleic Acids Research, 52:9076-9091, Jul 2024. URL: https://doi.org/10.1093/nar/gkae610, doi:10.1093/nar/gkae610. This article has 6 citations and is from a highest quality peer-reviewed journal.
(busetto2024mut7exoribonucleaseactivity pages 7-9): Virginia Busetto, Lizaveta Pshanichnaya, Raffael Lichtenberger, Stephan Hann, René F Ketting, and Sebastian Falk. Mut-7 exoribonuclease activity and localization are mediated by an ancient domain. Nucleic Acids Research, 52:9076-9091, Jul 2024. URL: https://doi.org/10.1093/nar/gkae610, doi:10.1093/nar/gkae610. This article has 6 citations and is from a highest quality peer-reviewed journal.
(busetto2024mut7exoribonucleaseactivity pages 5-7): Virginia Busetto, Lizaveta Pshanichnaya, Raffael Lichtenberger, Stephan Hann, René F Ketting, and Sebastian Falk. Mut-7 exoribonuclease activity and localization are mediated by an ancient domain. Nucleic Acids Research, 52:9076-9091, Jul 2024. URL: https://doi.org/10.1093/nar/gkae610, doi:10.1093/nar/gkae610. This article has 6 citations and is from a highest quality peer-reviewed journal.
(busetto2024mut7exoribonucleaseactivity pages 9-11): Virginia Busetto, Lizaveta Pshanichnaya, Raffael Lichtenberger, Stephan Hann, René F Ketting, and Sebastian Falk. Mut-7 exoribonuclease activity and localization are mediated by an ancient domain. Nucleic Acids Research, 52:9076-9091, Jul 2024. URL: https://doi.org/10.1093/nar/gkae610, doi:10.1093/nar/gkae610. This article has 6 citations and is from a highest quality peer-reviewed journal.
(phillips2012mut16promotesformation pages 4-5): Carolyn M. Phillips, Taiowa A. Montgomery, Peter C. Breen, and Gary Ruvkun. Mut-16 promotes formation of perinuclear mutator foci required for rna silencing in the c. elegans germline. Genes & development, 26 13:1433-44, Jul 2012. URL: https://doi.org/10.1101/gad.193904.112, doi:10.1101/gad.193904.112. This article has 242 citations and is from a highest quality peer-reviewed journal.
(sundby2021connectingthedots pages 4-6): Adam E. Sundby, Ruxandra I. Molnar, and Julie M. Claycomb. Connecting the dots: linking caenorhabditis elegans small rna pathways and germ granules. May 2021. URL: https://doi.org/10.1016/j.tcb.2020.12.012, doi:10.1016/j.tcb.2020.12.012. This article has 74 citations and is from a domain leading peer-reviewed journal.
(phillips2022germgranulesand pages 8-9): Carolyn M Phillips and Dustin L Updike. Germ granules and gene regulation in the caenorhabditis elegans germline. Genetics, Mar 2022. URL: https://doi.org/10.1093/genetics/iyab195, doi:10.1093/genetics/iyab195. This article has 79 citations and is from a domain leading peer-reviewed journal.
(phillips2012mut16promotesformation pages 1-2): Carolyn M. Phillips, Taiowa A. Montgomery, Peter C. Breen, and Gary Ruvkun. Mut-16 promotes formation of perinuclear mutator foci required for rna silencing in the c. elegans germline. Genes & development, 26 13:1433-44, Jul 2012. URL: https://doi.org/10.1101/gad.193904.112, doi:10.1101/gad.193904.112. This article has 242 citations and is from a highest quality peer-reviewed journal.
(sundby2021connectingthedots pages 6-7): Adam E. Sundby, Ruxandra I. Molnar, and Julie M. Claycomb. Connecting the dots: linking caenorhabditis elegans small rna pathways and germ granules. May 2021. URL: https://doi.org/10.1016/j.tcb.2020.12.012, doi:10.1016/j.tcb.2020.12.012. This article has 74 citations and is from a domain leading peer-reviewed journal.
(uebel2018distinctregionsof pages 1-2): Celja J. Uebel, Dorian C. Anderson, Lisa M. Mandarino, Kevin I. Manage, Stephan Aynaszyan, and Carolyn M. Phillips. Distinct regions of the intrinsically disordered protein mut-16 mediate assembly of a small rna amplification complex and promote phase separation of mutator foci. PLOS Genetics, 14:e1007542, Jul 2018. URL: https://doi.org/10.1371/journal.pgen.1007542, doi:10.1371/journal.pgen.1007542. This article has 67 citations and is from a domain leading peer-reviewed journal.
(chen2024tissuespecificsilencingof pages 4-5): Siyu Chen, Weihong Liu, Lei Xiong, Zhiju Tao, and Di Zhao. Tissue-specific silencing of integrated transgenes achieved through endogenous rna interference in caenorhabditis elegans. RNA Biology, 21:449-458, Mar 2024. URL: https://doi.org/10.1080/15476286.2024.2332856, doi:10.1080/15476286.2024.2332856. This article has 3 citations and is from a peer-reviewed journal.
(chen2024tissuespecificsilencingof pages 1-2): Siyu Chen, Weihong Liu, Lei Xiong, Zhiju Tao, and Di Zhao. Tissue-specific silencing of integrated transgenes achieved through endogenous rna interference in caenorhabditis elegans. RNA Biology, 21:449-458, Mar 2024. URL: https://doi.org/10.1080/15476286.2024.2332856, doi:10.1080/15476286.2024.2332856. This article has 3 citations and is from a peer-reviewed journal.
(sterken2014aheritableantiviral pages 4-5): Mark G. Sterken, L. Basten Snoek, Kobus J. Bosman, Jikke Daamen, Joost A. G. Riksen, Jaap Bakker, Gorben P. Pijlman, and Jan E. Kammenga. A heritable antiviral rnai response limits orsay virus infection in caenorhabditis elegans n2. PLoS ONE, 9:e89760, Feb 2014. URL: https://doi.org/10.1371/journal.pone.0089760, doi:10.1371/journal.pone.0089760. This article has 61 citations and is from a peer-reviewed journal.
(uebel2018distinctregionsof pages 5-7): Celja J. Uebel, Dorian C. Anderson, Lisa M. Mandarino, Kevin I. Manage, Stephan Aynaszyan, and Carolyn M. Phillips. Distinct regions of the intrinsically disordered protein mut-16 mediate assembly of a small rna amplification complex and promote phase separation of mutator foci. PLOS Genetics, 14:e1007542, Jul 2018. URL: https://doi.org/10.1371/journal.pgen.1007542, doi:10.1371/journal.pgen.1007542. This article has 67 citations and is from a domain leading peer-reviewed journal.
(uebel2018distinctregionsof pages 4-5): Celja J. Uebel, Dorian C. Anderson, Lisa M. Mandarino, Kevin I. Manage, Stephan Aynaszyan, and Carolyn M. Phillips. Distinct regions of the intrinsically disordered protein mut-16 mediate assembly of a small rna amplification complex and promote phase separation of mutator foci. PLOS Genetics, 14:e1007542, Jul 2018. URL: https://doi.org/10.1371/journal.pgen.1007542, doi:10.1371/journal.pgen.1007542. This article has 67 citations and is from a domain leading peer-reviewed journal.
(uebel2018distinctregionsof pages 11-13): Celja J. Uebel, Dorian C. Anderson, Lisa M. Mandarino, Kevin I. Manage, Stephan Aynaszyan, and Carolyn M. Phillips. Distinct regions of the intrinsically disordered protein mut-16 mediate assembly of a small rna amplification complex and promote phase separation of mutator foci. PLOS Genetics, 14:e1007542, Jul 2018. URL: https://doi.org/10.1371/journal.pgen.1007542, doi:10.1371/journal.pgen.1007542. This article has 67 citations and is from a domain leading peer-reviewed journal.
(uebel2018distinctregionsof pages 2-4): Celja J. Uebel, Dorian C. Anderson, Lisa M. Mandarino, Kevin I. Manage, Stephan Aynaszyan, and Carolyn M. Phillips. Distinct regions of the intrinsically disordered protein mut-16 mediate assembly of a small rna amplification complex and promote phase separation of mutator foci. PLOS Genetics, 14:e1007542, Jul 2018. URL: https://doi.org/10.1371/journal.pgen.1007542, doi:10.1371/journal.pgen.1007542. This article has 67 citations and is from a domain leading peer-reviewed journal.
(phillips2012mut16promotesformation pages 5-7): Carolyn M. Phillips, Taiowa A. Montgomery, Peter C. Breen, and Gary Ruvkun. Mut-16 promotes formation of perinuclear mutator foci required for rna silencing in the c. elegans germline. Genes & development, 26 13:1433-44, Jul 2012. URL: https://doi.org/10.1101/gad.193904.112, doi:10.1101/gad.193904.112. This article has 242 citations and is from a highest quality peer-reviewed journal.
(busetto2024mut7exoribonucleaseactivity pages 11-12): Virginia Busetto, Lizaveta Pshanichnaya, Raffael Lichtenberger, Stephan Hann, René F Ketting, and Sebastian Falk. Mut-7 exoribonuclease activity and localization are mediated by an ancient domain. Nucleic Acids Research, 52:9076-9091, Jul 2024. URL: https://doi.org/10.1093/nar/gkae610, doi:10.1093/nar/gkae610. This article has 6 citations and is from a highest quality peer-reviewed journal.
Gene: rde-2 = mut-8 ; ORF F21C3.4 ; UniProt Q19672 ; WormBase WBGene00004324
Organism: Caenorhabditis elegans (NCBITaxon:6239). Chromosome I.
id: Q19672
gene_symbol: rde-2
aliases:
- mut-8
- F21C3.4
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:6239
label: Caenorhabditis elegans
description: >-
RDE-2 (also known as MUT-8) is an intrinsically disordered bridging adaptor protein
of the C. elegans Mutator complex, the germline machinery that amplifies secondary
small interfering RNAs (22G-RNAs) for RNA-mediated silencing. RDE-2 has no catalytic
activity and no canonical folded domain; its structured C-terminal domain binds the
C-terminal domain of the 3'-5' exoribonuclease MUT-7, while its partially structured
N-terminal region contacts the intrinsically disordered scaffold MUT-16. By physically
linking MUT-7 to MUT-16, RDE-2 recruits the MUT-7 exoribonuclease into perinuclear
Mutator foci, the phase-separated condensates (adjacent to but distinct from P granules)
in which the RNA-dependent RNA polymerase RRF-1 synthesizes secondary siRNAs. This
function is required for exogenous and endogenous RNAi, transposon silencing, and
germline genome surveillance; loss of rde-2 abolishes secondary siRNA accumulation and
causes RNAi resistance, transposon mobilization and an X-chromosome non-disjunction
(high-incidence-of-males) phenotype. RDE-2 and its MUT-7 interaction are restricted to
the Caenorhabditis lineage.
references:
- id: PMID:10535731
title: The rde-1 gene, RNA interference, and transposon silencing in C. elegans.
findings:
- statement: >-
Forward genetic screens for mutants resistant to double-stranded-RNA-mediated
interference defined the RNAi-deficient (rde) complementation groups in C. elegans,
the screen that isolated rde-2 alongside rde-1 and rde-4.
reference_section_type: ABSTRACT
supporting_text: >-
In order to study the interference process, we have selected C. elegans mutants
resistant to dsRNA-mediated interference (RNAi).
reference_review:
relevance: MEDIUM
correctness: VERIFIED
review_notes: >-
Abstract-only in cache and foregrounds rde-1/rde-4 (rde-2 is not named in the
abstract), but this is the foundational rde screen that defined the rde-2
complementation group and is the reference WormBase cites for the rde-2 IMP
silencing/segregation annotations (with WB:WBVar00090964). Not removed on the basis
of abstract framing per curation guidance; specific rde-2 phenotypes are documented
in PMID:15653635.
- id: PMID:15653635
title: RDE-2 interacts with MUT-7 to mediate RNA interference in Caenorhabditis elegans.
findings:
- statement: >-
RDE-2 (F21C3.4 = rde-2/mut-8) was identified as a MUT-7-interacting protein by yeast
two-hybrid, co-immunoprecipitation and re-localization; the MUT-7/RDE-2 complex acts
downstream of primary siRNA production and upstream of target recognition, in the
amplification step of RNAi.
reference_section_type: RESULTS
supporting_text: >-
Together these data hint at a role for the MUT-7/RDE-2 complex in the amplification
step of the RNAi pathway in C.elegans.
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text (PMC546165) directly assays RDE-2/Q19672: establishes the direct MUT-7
interaction, cytosolic complex, RNAi requirement, gene identity (F21C3.4 =
rde-2/mut-8), and the Him phenotype. Primary reference for the molecular function,
cytosol localization and siRNA-amplification role.
- id: PMID:19123269
title: Empirically controlled mapping of the Caenorhabditis elegans protein-protein interactome network.
findings:
- statement: >-
High-throughput yeast two-hybrid interactome mapping reported an RDE-2 (Q19672)
protein-protein interaction with MUT-7 (P34607).
reference_section_type: ABSTRACT
supporting_text: >-
Empirically controlled mapping of the Caenorhabditis elegans protein-protein
interactome network.
reference_review:
relevance: LOW
correctness: VERIFIED
review_notes: >-
Systematic Y2H network study; source of a second IPI 'protein binding' annotation
for the RDE-2/MUT-7 interaction. Corroborates, but is less informative than, the
dedicated MUT-7/RDE-2 studies (PMID:15653635, PMID:39188014).
- id: PMID:22713602
title: MUT-16 promotes formation of perinuclear mutator foci required for RNA silencing in the C. elegans germline.
findings:
- statement: >-
Each of the six mutator proteins (including RDE-2) localizes to perinuclear Mutator
foci, punctate germline structures adjacent to but distinct from P granules that
constitute an RNA-processing compartment for siRNA amplification with the RdRP RRF-1.
reference_section_type: ABSTRACT
supporting_text: >-
each of the six mutator proteins localizes to punctate foci at the periphery of
germline nuclei. The Mutator foci are adjacent to P granules
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Abstract-only in cache but is the origin reference for the GO:1990633 mutator focus
localization of RDE-2; defines Mutator foci as the siRNA-amplification compartment.
- id: PMID:39188014
title: MUT-7 exoribonuclease activity and localization are mediated by an ancient domain.
findings:
- statement: >-
Structural and biochemical study (crystal structure PDB 8Q66 of the MUT-7 CTD /
MUT-8 CTD complex) showing RDE-2/MUT-8 binds the MUT-7 exoribonuclease via a
worm-specific insertion in MUT7-C and thereby mediates MUT-7 recruitment to germ
granules / Mutator foci.
reference_section_type: ABSTRACT
supporting_text: >-
Caenorhabditis elegans MUT-7 contains a specific insertion within MUT7-C, which
allows binding to MUT-8 and, consequently, MUT-7 recruitment to germ granules
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
PubMed/PMC-verified (PMC11347159); full text directly characterizes CeMUT-8 (Q19672)
as a mostly disordered adaptor with no annotated domains that bridges MUT-7 to the
MUT-16 scaffold, contradicting the automated UniProt 'SH2 domain' name. Referenced by
UniProt as the source of PDB 8Q66.
- id: PMID:30036386
title: Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of mutator foci.
findings:
- statement: >-
MUT-16 is required for localization of RDE-2 (and other mutator proteins) to Mutator
foci; RDE-2 in turn is required for MUT-7 localization, placing RDE-2 in a
MUT-16 -> RDE-2 -> MUT-7 recruitment axis. Loss of any mutator complex protein
abolishes RdRP-dependent secondary siRNAs.
reference_section_type: RESULTS
supporting_text: >-
MUT-16 is required for localization of MUT-2, MUT-7, RDE-2, MUT-14, and MUT-15, all
of which localize independently of one another except for MUT-7, which requires RDE-2
for localization
reference_review:
relevance: HIGH
correctness: VERIFIED
review_notes: >-
Full text (PMC6072111) directly assays RDE-2 localization dependence and calls RDE-2
a protein of previously unknown function; supports the adaptor/recruitment role and
the requirement of the whole complex for secondary siRNA accumulation.
existing_annotations:
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:15653635
qualifier: enables
review:
summary: >-
The IPI interaction with MUT-7 (P34607) is real and central, but 'protein binding'
is uninformative. RDE-2's molecular function is to bridge the MUT-7 exoribonuclease
to the MUT-16 scaffold, i.e. a molecular adaptor activity; this is the core molecular
function of the protein.
action: MODIFY
reason: >-
Replace the uninformative 'protein binding' with the more specific molecular adaptor
activity. RDE-2 binds MUT-7 via its CTD and MUT-16 via its NTD, physically linking
the two so that MUT-7 is recruited into Mutator foci (PMID:15653635, PMID:39188014).
proposed_replacement_terms:
- id: GO:0060090
label: molecular adaptor activity
supported_by:
- reference_id: PMID:39188014
supporting_text: >-
Caenorhabditis elegans MUT-7 contains a specific insertion within MUT7-C, which
allows binding to MUT-8 and, consequently, MUT-7 recruitment to germ granules
- term:
id: GO:0005515
label: protein binding
evidence_type: IPI
original_reference_id: PMID:19123269
qualifier: enables
review:
summary: >-
A second IPI 'protein binding' annotation from a high-throughput interactome dataset
recording the RDE-2/MUT-7 interaction. The interaction is genuine and corroborates
the adaptor role, but the term itself is uninformative.
action: MARK_AS_OVER_ANNOTATED
reason: >-
'protein binding' conveys no functional specificity; the informative molecular
function (molecular adaptor activity) is captured from the dedicated interaction
studies. Retained as supporting evidence for the MUT-7 interaction but not as a core
function.
supported_by:
- reference_id: PMID:30036386
supporting_text: >-
two proteins of unknown function, RDE-2 and MUT-15
- term:
id: GO:0030422
label: siRNA processing
evidence_type: IDA
original_reference_id: PMID:15653635
qualifier: involved_in
review:
summary: >-
RDE-2 is required for accumulation of siRNAs in vivo; the MUT-7/RDE-2 complex acts in
the RdRP-dependent siRNA amplification step. GO:0030422 explicitly includes
amplification of siRNA by RNA-directed RNA polymerase, so this is an appropriate core
biological-process term.
action: ACCEPT
reason: >-
rde-2 mutants do not produce detectable siRNAs in vivo, and the complex functions
downstream of primary siRNA production in amplification, consistent with the
siRNA-processing term definition.
supported_by:
- reference_id: PMID:15653635
supporting_text: >-
Together these data hint at a role for the MUT-7/RDE-2 complex in the amplification
step of the RNAi pathway in C.elegans.
- term:
id: GO:1990633
label: mutator focus
evidence_type: IDA
original_reference_id: PMID:22713602
qualifier: located_in
review:
summary: >-
RDE-2 is one of the six mutator proteins that localize to perinuclear Mutator foci in
the germline, the siRNA-amplification compartment. This is the informative,
species-appropriate cellular-component annotation and represents where RDE-2 carries
out its function.
action: ACCEPT
reason: >-
Direct localization of the mutator proteins (including RDE-2) to perinuclear Mutator
foci; RDE-2 localization to these foci depends on MUT-16 (PMID:30036386).
supported_by:
- reference_id: PMID:22713602
supporting_text: >-
each of the six mutator proteins localizes to punctate foci at the periphery of
germline nuclei. The Mutator foci are adjacent to P granules
- term:
id: GO:0016441
label: post-transcriptional gene silencing
evidence_type: IMP
original_reference_id: PMID:10535731
qualifier: involved_in
review:
summary: >-
Loss of rde-2 causes RNAi resistance and transposon de-silencing, i.e. defective
post-transcriptional gene silencing. This is a defining phenotype of the gene, though
it is a parent of the more specific regulatory-ncRNA-mediated PTGS term.
action: KEEP_AS_NON_CORE
reason: >-
Correct but general; the more specific GO:0035194 (regulatory ncRNA-mediated
post-transcriptional gene silencing) better captures the mechanism and is retained as
core. Kept as valid non-core context.
supported_by:
- reference_id: PMID:15653635
supporting_text: >-
This allele, removing the last three-quarters of the gene, is viable and is RNAi
resistant
- term:
id: GO:0045132
label: meiotic chromosome segregation
evidence_type: IMP
original_reference_id: PMID:10535731
qualifier: involved_in
review:
summary: >-
rde-2 mutants show a high-incidence-of-males (Him) phenotype caused by X-chromosome
non-disjunction. This is a downstream, pleiotropic consequence of losing germline
small-RNA silencing rather than evidence that RDE-2 acts directly in the meiotic
chromosome-segregation machinery.
action: KEEP_AS_NON_CORE
reason: >-
The segregation defect is an indirect consequence of the RNAi/silencing deficiency
(shared with mut-7), not a direct molecular role of RDE-2 in meiosis. Retained as a
non-core phenotype-based annotation.
supported_by:
- reference_id: PMID:15653635
supporting_text: >-
both mut-7 and rde-2 mutants show a high incidence of males (him) phenotype
- term:
id: GO:0035194
label: regulatory ncRNA-mediated post-transcriptional gene silencing
evidence_type: IMP
original_reference_id: PMID:10535731
qualifier: involved_in
review:
summary: >-
RDE-2 is required for small-RNA (siRNA/22G-RNA)-guided silencing of endogenous and
exogenous targets and of transposons; this term captures the specific mechanism of
RDE-2's biological role and is a core process annotation.
action: ACCEPT
reason: >-
Loss of rde-2 abolishes RdRP-dependent secondary siRNA accumulation and silencing,
the defining regulatory-ncRNA-mediated PTGS function.
supported_by:
- reference_id: PMID:30036386
supporting_text: >-
mut-15, rde-2, rde-8, or rrf-1) result in a substantial loss of the RdRP-dependent
secondary siRNAs
- term:
id: GO:0005829
label: cytosol
evidence_type: IDA
original_reference_id: PMID:15653635
qualifier: located_in
review:
summary: >-
Biochemical fractionation placed the MUT-7/RDE-2 complex in the cytosolic (S100)
fraction. This is correct but generic; the informative, function-relevant localization
is the perinuclear Mutator focus (GO:1990633), which is a specialized cytoplasmic
compartment.
action: KEEP_AS_NON_CORE
reason: >-
Valid subcellular fraction data, but subsumed functionally by the Mutator-focus
annotation. Kept as non-core supporting localization.
supported_by:
- reference_id: PMID:15653635
supporting_text: >-
the MUT-7 and RDE-2 proteins are associated with each other in the cytosol, but not
in the nucleus
core_functions:
- description: >-
Molecular adaptor that bridges the MUT-7 3'-5' exoribonuclease to the MUT-16 scaffold,
recruiting MUT-7 into perinuclear Mutator foci for secondary siRNA amplification.
molecular_function:
id: GO:0060090
label: molecular adaptor activity
directly_involved_in:
- id: GO:0035194
label: regulatory ncRNA-mediated post-transcriptional gene silencing
locations:
- id: GO:1990633
label: mutator focus
supported_by:
- reference_id: PMID:39188014
supporting_text: >-
Caenorhabditis elegans MUT-7 contains a specific insertion within MUT7-C, which
allows binding to MUT-8 and, consequently, MUT-7 recruitment to germ granules
- reference_id: PMID:15653635
supporting_text: >-
Together these data hint at a role for the MUT-7/RDE-2 complex in the amplification
step of the RNAi pathway in C.elegans.
- reference_id: file:worm/rde-2/rde-2-deep-research-falcon.md
supporting_text: >-
RDE-2/MUT-8 is not an enzyme itself; rather, it serves a structural/adapter role
- description: >-
Required for RdRP (RRF-1)-dependent secondary siRNA (22G-RNA) amplification underlying
RNA interference and transposon silencing in the germline.
molecular_function:
id: GO:0060090
label: molecular adaptor activity
directly_involved_in:
- id: GO:0030422
label: siRNA processing
locations:
- id: GO:1990633
label: mutator focus
supported_by:
- reference_id: PMID:30036386
supporting_text: >-
mut-15, rde-2, rde-8, or rrf-1) result in a substantial loss of the RdRP-dependent
secondary siRNAs
knowledge_gaps:
- gap_statement: >-
Beyond acting as a passive structural bridge between MUT-7 and MUT-16, it is unknown
whether the intrinsically disordered regions of RDE-2/MUT-8 have any additional
molecular activity (e.g. RNA binding, condensate nucleation, or allosteric regulation
of MUT-7 nuclease activity). RDE-2 has no catalytic activity and no canonical folded
domain, so its full biochemical contribution to the complex is undefined.
boundary: >-
It is firmly established that RDE-2's structured C-terminal domain binds the MUT-7 CTD
(crystal structure PDB 8Q66) and that its partially structured N-terminal region
contacts the MUT-16 scaffold, recruiting MUT-7 to Mutator foci. What is unknown is
whether RDE-2 does anything mechanistically beyond this bridging.
gap_kind:
- BIOLOGY
dark_aspect: MF_DARK
status: OPEN
significance: >-
Because RDE-2 is essential for secondary siRNA amplification but is not itself an
enzyme, distinguishing 'pure scaffold/recruiter' from 'active participant' would
determine whether the amplification defect in rde-2 mutants is purely a
mislocalization/assembly failure or also a loss of a direct biochemical step.
resolution: >-
In vitro reconstitution of the MUT-16/RDE-2/MUT-7 module with siRNA-amplification
assays, RNA-binding assays on isolated RDE-2 domains, and separation-of-function RDE-2
alleles that retain MUT-7/MUT-16 binding but disrupt any additional activity would
resolve this.
provenance:
- reference_id: PMID:30036386
supporting_text: >-
two proteins of unknown function, RDE-2 and MUT-15
- gap_statement: >-
The complete set of RDE-2 direct binding partners within the Mutator complex is
unresolved. Direct interactions are established only with MUT-7 (CTD-CTD) and MUT-16
(via the RDE-2 N-terminal region); whether RDE-2 directly contacts other mutator
components (MUT-2/RDE-3, MUT-14, MUT-15, NYN-1/2, RDE-8) or the RdRP RRF-1, or merely
co-resides with them in the focus, has not been tested biochemically.
boundary: >-
RDE-2 localization to Mutator foci depends on MUT-16, and RDE-2 is in turn required for
MUT-7 localization (a MUT-16 -> RDE-2 -> MUT-7 recruitment axis). Other mutator
components localize via separate MUT-16 branches, but their direct/indirect relationship
to RDE-2 is inferred from localization dependencies, not from binary interaction data.
gap_kind:
- BIOLOGY
dark_aspect: RESIDUAL_SUBGAP
status: OPEN
significance: >-
Knowing which contacts are direct defines the true architecture of the amplification
compartment and whether RDE-2 is a dedicated MUT-7 adaptor or a more central hub.
resolution: >-
Systematic binary interaction mapping (e.g. reconstituted pulldowns, crosslinking mass
spectrometry, or cryo-EM of the assembled complex) of RDE-2 against each mutator
component.
provenance:
- reference_id: PMID:30036386
supporting_text: >-
MUT-16 is required for localization of MUT-2, MUT-7, RDE-2, MUT-14, and MUT-15, all
of which localize independently of one another except for MUT-7, which requires RDE-2
for localization
- gap_statement: >-
How RDE-2 mechanistically contributes to the secondary siRNA (22G-RNA) amplification
reaction itself is unknown. It is established that rde-2 loss abolishes RdRP-dependent
secondary siRNA accumulation, but whether RDE-2's only role is to recruit and position
MUT-7, or whether it also participates in target-mRNA capture or templating for RRF-1,
is undetermined.
boundary: >-
The genetic requirement is clear (no detectable secondary siRNAs without rde-2) and the
focus-assembly role is structurally defined, but the biochemical step at which RDE-2 acts
within amplification is not.
gap_kind:
- BIOLOGY
- ONTOLOGY
dark_aspect: MF_DARK
status: OPEN
significance: >-
Secondary siRNA amplification is the amplifying core of C. elegans RNA silencing and
heritable epigenetic inheritance; resolving RDE-2's step would clarify a rate-limiting
node. There is also no GO term for 'secondary siRNA amplification' as a distinct process
or for a 'structural constituent of the Mutator complex', so RDE-2's specific
contribution cannot currently be expressed precisely.
resolution: >-
Mechanistic in vitro amplification assays with defined mutator subcomplexes, plus
ontology development for a secondary-siRNA-amplification process term and/or a
Mutator-complex structural-constituent term.
provenance:
- reference_id: PMID:22713602
supporting_text: >-
We propose that the mutator proteins and RRF-1 constitute an RNA processing
compartment required for siRNA amplification and RNA silencing
proposed_new_terms:
- proposed_name: secondary siRNA amplification
proposed_definition: >-
The RNA-dependent RNA polymerase (RdRP)-mediated de novo synthesis of secondary small
interfering RNAs (e.g. C. elegans 22G-RNAs) templated on target mRNAs recognized by
primary small RNAs, occurring within a specialized RNA-processing compartment (Mutator
focus). Distinguished from siRNA processing/Dicer-dependent primary siRNA generation.
justification: >-
RDE-2 and the Mutator complex act specifically in RdRP-dependent secondary siRNA
amplification, a step for which no dedicated GO term exists; siRNA processing (GO:0030422)
conflates Dicer-dependent primary siRNA generation with amplification.
- proposed_name: structural constituent of Mutator complex
proposed_definition: >-
A molecular function in which a protein provides a structural/organizational role as a
subunit of the C. elegans Mutator complex, contributing to assembly of the
siRNA-amplification compartment rather than catalysis.
justification: >-
RDE-2 is an obligate structural adaptor subunit with no catalytic activity; molecular
adaptor activity (GO:0060090) captures the bridging aspect, but a complex-specific
structural-constituent term would more precisely express its 'be part of the machine'
role.
suggested_questions:
- question: >-
Does RDE-2/MUT-8 possess any activity beyond bridging MUT-7 and MUT-16 - for example
intrinsic RNA binding or a role in nucleating Mutator-focus condensation?
experts:
- René F. Ketting
- Sebastian Falk
- Carolyn M. Phillips
suggested_experiments:
- hypothesis: >-
RDE-2 acts purely as a structural adaptor whose sole essential role is to recruit and
position MUT-7 within Mutator foci.
description: >-
Generate separation-of-function rde-2 alleles that retain MUT-16 binding but disrupt
the MUT-7 CTD interface (guided by the PDB 8Q66 interface), assay MUT-7 focus
localization, secondary 22G-RNA levels, and RNAi/transposon-silencing competence.
experiment_type: structure-guided mutagenesis with small-RNA sequencing and localization
- hypothesis: >-
RDE-2 directly contacts additional mutator components beyond MUT-7 and MUT-16.
description: >-
Reconstitute recombinant RDE-2 with each mutator component and RRF-1 and test for
direct binary interactions by pulldown/SEC and crosslinking mass spectrometry, and
attempt cryo-EM of the assembled complex.
experiment_type: in vitro interaction mapping / structural biology