wago-1

id: Q21770
gene_symbol: wago-1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: WAGO-1 (Worm-specific Argonaute 1) is a member of the WAGO subfamily
  of Argonaute proteins that functions as a key effector in the endogenous small interfering
  RNA (endo-siRNA) pathway in the C. elegans germline. WAGO-1 binds 22G-RNAs, which
  are RNA-dependent RNA polymerase-derived secondary siRNAs characterized by their
  22-nucleotide length and 5'-guanosine. Unlike canonical Argonaute proteins, WAGO
  subfamily members lack conserved metal-binding residues required for catalytic slicer
  activity and likely function through recruitment of other nucleases for target degradation.
  WAGO-1 localizes to P granules (germline nuage structures) where it functions in
  a genome surveillance system to silence transposons, pseudogenes, and cryptic loci.
  WAGO-1 acts downstream of the primary Argonaute PRG-1 in the piRNA pathway, where
  piRNA-triggered 22G-RNA production leads to loading of these secondary siRNAs into
  WAGO-1 and HRDE-1. WAGO-1 interacts with the Vasa homolog RDE-12 and the zinc-finger
  helicase ZNFX-1 as part of the RNA silencing machinery. The protein is enriched
  in sperm and oocytes and is essential for germline integrity and transposon control.
existing_annotations:
- term:
    id: GO:0005634
    label: nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA annotation based on phylogenetic inference from other Argonaute family
      members. While some Argonaute proteins do localize to the nucleus, the primary
      literature for WAGO-1 specifically demonstrates cytoplasmic P granule localization
      in the germline (PMID:19800275, PMID:24684931). UniProt annotation describes
      WAGO-1 subcellular location as "Cytoplasmic granule" with no nuclear localization
      reported.
    action: REMOVE
    reason: WAGO-1 has been experimentally characterized as localizing to cytoplasmic
      P granules (PMID:19800275). The nuclear annotation appears to be an over-generalization
      from other Argonaute family members. WAGO-1 functions in cytoplasmic post-transcriptional
      gene silencing and there is no direct evidence for nuclear localization in C.
      elegans.
    supported_by:
    - reference_id: PMID:19800275
      supporting_text: We show that, in the germline, one system is dependent on worm-specific
        AGOs, including WAGO-1, which localizes to germline nuage structures called
        P granules
    - reference_id: PMID:24684931
      supporting_text: RDE-12 colocalizes with WAGO-1 in germline P granules and in
        cytoplasmic and perinuclear foci in somatic cells
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: IBA annotation for cytoplasmic localization is broadly consistent with
      experimental evidence showing WAGO-1 in cytoplasmic P granules. However, the
      more specific term GO:0043186 (P granule) is preferable as it captures the precise
      subcellular localization.
    action: ACCEPT
    reason: Cytoplasmic localization is accurate - WAGO-1 localizes to cytoplasmic
      P granules (PMID:19800275, PMID:24684931). This is a valid parent term for the
      more specific P granule localization. Retaining as it provides broader context.
    supported_by:
    - reference_id: PMID:19800275
      supporting_text: We show that, in the germline, one system is dependent on worm-specific
        AGOs, including WAGO-1, which localizes to germline nuage structures called
        P granules
- term:
    id: GO:0004521
    label: RNA endonuclease activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: This annotation is phylogenetically inferred from slicer-competent Argonaute
      proteins. However, WAGO subfamily Argonautes specifically lack the conserved
      metal-binding residues (DDH/DDX catalytic tetrad) required for endonuclease
      activity. UniProt explicitly notes that WAGO subfamily members lack conserved
      metal-binding residues and probably do not cleave target mRNAs directly (PMID:17110334).
    action: REMOVE
    reason: WAGO-1 lacks the catalytic tetrad required for RNA endonuclease (slicer)
      activity. This is a known distinguishing feature of the WAGO subfamily. The
      protein likely recruits other endonucleases for target degradation rather than
      performing cleavage itself. This annotation is an over-annotation based on ancestral
      function that has been lost in this subfamily.
    supported_by:
    - reference_id: PMID:17110334
      supporting_text: these AGO proteins lack key residues required for mRNA cleavage
- term:
    id: GO:0035194
    label: regulatory ncRNA-mediated post-transcriptional gene silencing
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: WAGO-1 is a central effector in the 22G-RNA pathway, which is a form
      of endo-siRNA-mediated gene silencing. The protein binds 22G-RNAs and mediates
      silencing of transposons, pseudogenes, and aberrant transcripts in the germline
      (PMID:19800275). This is a core function of WAGO-1.
    action: ACCEPT
    reason: This annotation accurately captures WAGO-1's primary biological function.
      WAGO-1 participates in a regulatory ncRNA-mediated silencing pathway using endogenous
      22G-RNAs. Experimental evidence from PMID:19800275 demonstrates this function
      directly.
    supported_by:
    - reference_id: PMID:19800275
      supporting_text: WAGO-1 silences certain genes, transposons, pseudogenes, and
        cryptic loci
- term:
    id: GO:0016442
    label: RISC complex
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: As an Argonaute protein that binds small RNAs and mediates gene silencing,
      WAGO-1 functions as part of an RNA-induced silencing complex. While the worm-specific
      WAGO-1-containing complex may have distinct features, RISC complex is an appropriate
      general term for Argonaute-containing silencing effector complexes.
    action: ACCEPT
    reason: WAGO-1 is the core Argonaute component of a small RNA-mediated silencing
      complex. It associates with 22G-RNAs and interacts with RDE-12 (PMID:24684931)
      and ZNFX-1 (PMID:29775580) as part of the silencing machinery. RISC complex
      appropriately describes this functional complex.
    supported_by:
    - reference_id: PMID:24684931
      supporting_text: RDE-12 forms an RNase-resistant (target mRNA-independent) complex
        with WAGO-1
    - reference_id: PMID:17110334
      supporting_text: several other AGO proteins interact with amplified siRNAs to
        mediate downstream silencing
- term:
    id: GO:0036464
    label: cytoplasmic ribonucleoprotein granule
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: P granules are a type of cytoplasmic ribonucleoprotein granule. WAGO-1
      has been directly demonstrated to localize to P granules (PMID:19800275). This
      term is appropriate as a parent term, though the more specific GO:0043186 (P
      granule) is also annotated with experimental evidence.
    action: ACCEPT
    reason: This is a valid broader annotation. P granules are cytoplasmic ribonucleoprotein
      granules, and WAGO-1 localizes to P granules (PMID:19800275, PMID:24684931).
      The IBA annotation is consistent with experimental data.
    supported_by:
    - reference_id: PMID:19800275
      supporting_text: We show that, in the germline, one system is dependent on worm-specific
        AGOs, including WAGO-1, which localizes to germline nuage structures called
        P granules
- term:
    id: GO:0035198
    label: miRNA binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: This annotation is phylogenetically inferred from miRNA-binding Argonautes.
      However, WAGO-1 specifically binds 22G-RNAs (endogenous siRNAs), not miRNAs.
      The 22G-RNA pathway is distinct from the miRNA pathway in C. elegans. WAGO-1
      binds secondary siRNAs produced by RNA-dependent RNA polymerases, which are
      structurally and functionally distinct from miRNAs.
    action: MODIFY
    reason: WAGO-1 binds 22G-RNAs (endogenous siRNAs), not miRNAs. The miRNA binding
      annotation is an over-generalization from other Argonaute family members. The
      appropriate term is siRNA binding (GO:0035197), which accurately describes binding
      to the 21-23 nt small interfering RNAs that WAGO-1 associates with.
    proposed_replacement_terms:
    - id: GO:0035197
      label: siRNA binding
    supported_by:
    - reference_id: PMID:17110334
      supporting_text: several other AGO proteins interact with amplified siRNAs to
        mediate downstream silencing
- term:
    id: GO:0003727
    label: single-stranded RNA binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Argonaute proteins bind single-stranded guide RNAs. WAGO-1 binds 22G-RNAs
      in their single-stranded form after processing. This is a valid general molecular
      function annotation for an Argonaute protein.
    action: ACCEPT
    reason: WAGO-1 binds single-stranded 22G-RNAs as guide RNAs for target recognition.
      This is a core molecular function of Argonaute proteins. The annotation is appropriate
      though more specific terms like siRNA binding would also be accurate.
    supported_by:
    - reference_id: PMID:17110334
      supporting_text: Argonaute (AGO) proteins interact with small RNAs to mediate
        gene silencing
- term:
    id: GO:0003676
    label: nucleic acid binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: IEA annotation based on InterPro domains (PAZ and Piwi domains). This
      is a very broad term that is subsumed by more specific RNA binding annotations.
      While technically correct, it provides little informative value given the more
      specific annotations.
    action: ACCEPT
    reason: This is a valid but very general annotation based on domain composition.
      The PAZ and Piwi domains are nucleic acid binding domains. More specific annotations
      (RNA binding, siRNA binding) are also present and more informative.
- term:
    id: GO:0003723
    label: RNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: IEA annotation based on InterPro PAZ domain (IPR003100). WAGO-1 contains
      PAZ and Piwi domains characteristic of Argonaute proteins that bind small RNAs.
      This is a valid general annotation.
    action: ACCEPT
    reason: WAGO-1 binds 22G-RNAs through its PAZ and Piwi domains. RNA binding is
      a core molecular function. This annotation is appropriate as a broader classification
      of the siRNA binding activity.
- term:
    id: GO:0031047
    label: regulatory ncRNA-mediated gene silencing
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: IEA annotation based on UniProtKB keyword mapping (RNA-mediated gene
      silencing). This term encompasses both transcriptional and post-transcriptional
      silencing. WAGO-1 primarily functions in post-transcriptional silencing (GO:0035194),
      which is a child term already annotated.
    action: ACCEPT
    reason: This is a valid parent term for the more specific post-transcriptional
      silencing annotation. WAGO-1 is involved in regulatory ncRNA-mediated gene silencing
      using 22G-RNAs. Both this term and the more specific GO:0035194 are appropriate.
- term:
    id: GO:0017151
    label: DEAD/H-box RNA helicase binding
  evidence_type: IPI
  original_reference_id: PMID:24684931
  review:
    summary: This annotation is based on the physical interaction between WAGO-1 and
      RDE-12, a Vasa homolog DEAD-box RNA helicase. PMID:24684931 identified RDE-12
      as a robust interaction partner of WAGO-1 through immunoprecipitation studies.
      RDE-12 is required for secondary siRNA production and colocalizes with WAGO-1
      in P granules.
    action: ACCEPT
    reason: This is a well-supported experimental annotation. PMID:24684931 directly
      demonstrated physical interaction between WAGO-1 and RDE-12 (P90897), a DEAD-box
      RNA helicase. This interaction is functionally important for RNAi and endo-siRNA
      pathways.
    supported_by:
    - reference_id: PMID:24684931
      supporting_text: These studies identified a robust association between WAGO-1
        and a conserved Vasa ATPase-related protein RDE-12
    - reference_id: PMID:24684931
      supporting_text: RDE-12 colocalizes with WAGO-1 in germline P granules and in
        cytoplasmic and perinuclear foci in somatic cells
- term:
    id: GO:0043186
    label: P granule
  evidence_type: IDA
  original_reference_id: PMID:19800275
  review:
    summary: This is a direct experimental annotation showing WAGO-1 localization
      to P granules. PMID:19800275 demonstrated that WAGO-1 localizes to germline
      nuage structures called P granules. This is a key finding that establishes the
      subcellular context for WAGO-1 function in germline gene silencing.
    action: ACCEPT
    reason: Direct experimental evidence (IDA) demonstrating P granule localization.
      This is a core cellular component annotation supported by primary literature.
      P granule localization is essential for WAGO-1's function in germline surveillance.
    supported_by:
    - reference_id: PMID:19800275
      supporting_text: We show that, in the germline, one system is dependent on worm-specific
        AGOs, including WAGO-1, which localizes to germline nuage structures called
        P granules
    - reference_id: PMID:24684931
      supporting_text: RDE-12 colocalizes with WAGO-1 in germline P granules and in
        cytoplasmic and perinuclear foci in somatic cells
- term:
    id: GO:0035197
    label: siRNA binding
  evidence_type: IDA
  original_reference_id: PMID:19800275
  review:
    summary: WAGO-1 specifically binds 22G-RNAs, which are endogenous siRNAs. This
      binding activity is central to WAGO-1's function and is directly demonstrated
      in PMID:19800275.
    action: NEW
    reason: WAGO-1 binds 22G-RNAs (endogenous siRNAs). This is a more accurate molecular
      function annotation than miRNA binding, which was incorrectly inferred phylogenetically.
      22G-RNAs are siRNAs by definition - 22 nucleotide small RNAs processed by RdRP.
    supported_by:
    - reference_id: PMID:17110334
      supporting_text: several other AGO proteins interact with amplified siRNAs to
        mediate downstream silencing
- term:
    id: GO:0010526
    label: transposable element silencing
  evidence_type: IMP
  original_reference_id: PMID:19800275
  review:
    summary: WAGO-1 functions in silencing transposons as part of the germline genome
      surveillance system. This is a key biological process function demonstrated
      in PMID:19800275.
    action: NEW
    reason: Transposon silencing is a primary function of the WAGO-1 22G-RNA pathway
      in the germline. This should be annotated as a core biological process function.
    supported_by:
    - reference_id: PMID:19800275
      supporting_text: WAGO-1 silences certain genes, transposons, pseudogenes, and
        cryptic loci
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings:
  - statement: InterPro PAZ domain (IPR003100) predicts RNA binding
  - statement: InterPro Piwi domain (IPR003165) predicts nucleic acid binding
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: Phylogenetic inference from Argonaute family members
  - statement: Some inferred functions may not apply to WAGO subfamily due to loss
      of catalytic residues
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings:
  - statement: RNA-mediated gene silencing keyword mapped to GO terms
- id: PMID:19800275
  title: Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in
    the C. elegans germline.
  findings:
  - statement: WAGO-1 localizes to P granules in the germline
    supporting_text: We show that, in the germline, one system is dependent on worm-specific
      AGOs, including WAGO-1, which localizes to germline nuage structures called
      P granules
  - statement: WAGO-1 binds 22G-RNAs (secondary siRNAs)
    supporting_text: Endogenous small RNAs (endo-siRNAs) interact with Argonaute (AGO)
      proteins to mediate sequence-specific regulation of diverse biological processes
  - statement: WAGO-1 silences transposons, pseudogenes, and cryptic loci
    supporting_text: WAGO-1 silences certain genes, transposons, pseudogenes, and
      cryptic loci
  - statement: WAGO-1 is part of a genome surveillance system distinct from CSR-1
      pathway
    supporting_text: We show that, in the germline, one system is dependent on worm-specific
      AGOs, including WAGO-1
  - statement: DRH-3 is required for 22G-RNA biogenesis
    supporting_text: DRH-3 is a core component of RNA-dependent RNA polymerase (RdRP)
      complexes essential for several distinct 22G-RNA systems
- id: PMID:24684931
  title: The Vasa Homolog RDE-12 engages target mRNA and multiple argonaute proteins
    to promote RNAi in C. elegans.
  findings:
  - statement: WAGO-1 physically interacts with RDE-12 (Vasa homolog DEAD-box helicase)
    supporting_text: These studies identified a robust association between WAGO-1
      and a conserved Vasa ATPase-related protein RDE-12
  - statement: RDE-12 colocalizes with WAGO-1 in P granules
    supporting_text: RDE-12 colocalizes with WAGO-1 in germline P granules and in
      cytoplasmic and perinuclear foci in somatic cells
  - statement: RDE-12 is required for secondary siRNA production
    supporting_text: rde-12 mutants are deficient in RNAi, including viral suppression,
      and fail to produce amplified secondary siRNAs and certain endogenous siRNAs
      (endo-siRNAs)
  - statement: RDE-12 forms RNase-resistant complex with WAGO-1
    supporting_text: RDE-12 forms an RNase-resistant (target mRNA-independent) complex
      with WAGO-1
- id: PMID:17110334
  title: Analysis of the C. elegans Argonaute family reveals that distinct Argonautes
    act sequentially during RNAi.
  findings:
  - statement: WAGO subfamily Argonautes lack conserved metal-binding residues
    supporting_text: these AGO proteins lack key residues required for mRNA cleavage
  - statement: WAGO proteins probably do not cleave target mRNAs directly
    supporting_text: these AGO proteins lack key residues required for mRNA cleavage
  - statement: Distinct Argonautes act sequentially in RNAi pathway
    supporting_text: functionally and structurally distinct AGOs act sequentially
      to direct gene silencing
- id: PMID:29775580
  title: ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals.
  full_text_unavailable: true
  findings:
  - statement: WAGO-1 interacts with ZNFX-1
  - statement: ZNFX-1 functions in perinuclear nuage for epigenetic regulation
core_functions:
- description: WAGO-1 binds 22G-RNAs (endogenous siRNAs) and functions as a core effector
    in post-transcriptional gene silencing of transposons and aberrant transcripts
    in the C. elegans germline.
  molecular_function:
    id: GO:0035197
    label: siRNA binding
  directly_involved_in:
  - id: GO:0035194
    label: regulatory ncRNA-mediated post-transcriptional gene silencing
  - id: GO:0010526
    label: transposable element silencing
  locations:
  - id: GO:0043186
    label: P granule
  in_complex:
    id: GO:0016442
    label: RISC complex
  supported_by:
  - reference_id: PMID:19800275
    supporting_text: WAGO-1 silences certain genes, transposons, pseudogenes, and
      cryptic loci
proposed_new_terms: []
suggested_questions:
- question: What is the mechanism by which WAGO-1, lacking endonuclease activity,
    achieves target mRNA degradation? Does it recruit specific nucleases?
- question: How is the balance between WAGO-1 (silencing) and CSR-1 (protecting) pathways
    maintained for genome surveillance in the germline?
- question: Does WAGO-1 have any transcriptional silencing functions in addition to
    post-transcriptional silencing?
suggested_experiments:
- description: Identify nucleases recruited by WAGO-1 for target degradation using
    proximity labeling or co-IP followed by mass spectrometry
  hypothesis: WAGO-1 recruits specific endonucleases to P granules for target mRNA
    cleavage since it lacks intrinsic slicer activity
- description: Determine the complete catalog of WAGO-1 22G-RNA targets using CLIP-seq
    or similar approaches
  hypothesis: WAGO-1 targets a defined set of transposons, pseudogenes, and cryptic
    loci distinct from CSR-1 targets
- description: Test whether WAGO-1 has any role in chromatin-level silencing using
    ChIP-seq for silencing-associated histone marks in wago-1 mutants
  hypothesis: WAGO-1 may indirectly influence heterochromatin formation through its
    interaction with ZNFX-1 and nuclear Argonautes like HRDE-1
tags:
- caeel-p-granules