deps-1

id: Q9N303
gene_symbol: deps-1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: 'DEPS-1 (DEfective P granules and Sterile) is a scaffold protein essential
  for P granule assembly and integrity in C. elegans germ cells. It functions as a
  key component of the P-granule assembly pathway, required for proper localization
  of PGL-1 and accumulation of GLH-1. DEPS-1 is also essential for RNA interference
  (RNAi) in the germline, particularly for piRNA-mediated gene silencing, where it
  directly interacts with the Argonaute protein PRG-1 and promotes formation of secondary
  22G-RNAs (endo-siRNAs). The protein plays roles in germ cell proliferation, fertility,
  and small RNA-directed transgenerational epigenetic inheritance.

  '
existing_annotations:
  - term:
      id: GO:0031047
      label: regulatory ncRNA-mediated gene silencing
    evidence_type: IEA
    original_reference_id: GO_REF:0000043
    review:
      summary: 'DEPS-1 is involved in multiple ncRNA-mediated gene silencing pathways.
        It is required for RNAi of germline-expressed genes and specifically for piRNA
        gene silencing (PMID:18234720, PMID:32843637). DEPS-1 promotes accumulation
        of RDE-4 (a dsRNA-binding protein required for RNAi) and positively regulates
        formation of secondary 22G-RNAs, which are endo-siRNAs.

        '
      action: ACCEPT
      reason: 'This annotation correctly captures a core function of DEPS-1. The gene
        is required for RNA interference in the germline, promoting accumulation of
        RDE-4 and regulating endo-siRNA production (PMID:18234720). Additionally,
        DEPS-1 is essential for piRNA-mediated silencing through its interaction with
        PRG-1 (PMID:32843637). While GO:0031047 is a broad term, it accurately encompasses
        DEPS-1''s role in both RNAi and piRNA pathways.

        '
      supported_by:
        - reference_id: PMID:18234720
          supporting_text: DEPS-1 is required for RNA interference (RNAi) of 
            germline-expressed genes, possibly because DEPS-1 promotes the 
            accumulation of RDE-4, a dsRNA-binding protein required for RNAi.
  - term:
      id: GO:0048471
      label: perinuclear region of cytoplasm
    evidence_type: IEA
    original_reference_id: GO_REF:0000044
    review:
      summary: 'DEPS-1 localizes to the perinuclear region of cytoplasm where P granules
        are found. It co-localizes with PRG-1 at peri-nuclear P-granules in the proliferative
        zone, transition zone, at pachytene, in oocytes and in embryos (PMID:32843637).

        '
      action: ACCEPT
      reason: 'This annotation is correct but less specific than GO:0043186 (P granule).
        P granules are located at the perinuclear region of the cytoplasm, so this
        annotation is technically correct. However, the IDA annotation to GO:0043186
        provides more specific localization information. This IEA annotation can be
        retained as it accurately reflects the general subcellular localization derived
        from UniProt annotation.

        '
      supported_by:
        - reference_id: PMID:18234720
          supporting_text: We have identified a new P-granule-associated 
            protein, DEPS-1
  - term:
      id: GO:0043186
      label: P granule
    evidence_type: IDA
    original_reference_id: PMID:18234720
    review:
      summary: 'DEPS-1 localizes to P granules in germ cells at all stages of development.
        Direct experimental evidence from immunofluorescence studies demonstrates
        DEPS-1 localization to P granules (PMID:18234720). Additional studies confirm
        co-localization with PRG-1 at peri-nuclear P-granules and with PGL-1 in the
        pachytene region (PMID:32843637).

        '
      action: ACCEPT
      reason: 'This is a well-supported IDA annotation based on direct localization
        studies. PMID:18234720 identified DEPS-1 as a P-granule-associated protein
        through immunofluorescence experiments. This is a core annotation for the
        gene, as P granule localization is essential for DEPS-1 function.

        '
      supported_by:
        - reference_id: PMID:18234720
          supporting_text: We have identified a new P-granule-associated 
            protein, DEPS-1
  - term:
      id: GO:1903863
      label: P granule assembly
    evidence_type: IMP
    original_reference_id: PMID:18234720
    review:
      summary: 'DEPS-1 is required for P granule assembly and integrity. Loss of DEPS-1
        disrupts P-granule structure, prevents proper PGL-1 localization to P granules,
        and reduces GLH-1 accumulation (PMID:18234720). DEPS-1 acts as a scaffold
        protein in the P-granule assembly pathway.

        '
      action: NEW
      reason: 'This annotation should be added based on functional evidence from PMID:18234720.
        The publication demonstrates that DEPS-1 loss-of-function disrupts P granule
        structure and composition, indicating a direct role in P granule assembly.
        This is a core function of the gene.

        '
      supported_by:
        - reference_id: PMID:18234720
          supporting_text: DEPS-1 promotes P-granule assembly... the loss of 
            which disrupts P-granule structure and function. DEPS-1 is required 
            for the proper localization of PGL-1 to P granules, the accumulation
            of glh-1 mRNA and protein
  - term:
      id: GO:0036093
      label: germ cell proliferation
    evidence_type: IMP
    original_reference_id: PMID:18234720
    review:
      summary: 'deps-1 mutants show underproliferated germlines and fail to produce
        oocytes and sperm at restrictive temperatures, indicating a role in germ cell
        proliferation (PMID:18234720).

        '
      action: NEW
      reason: 'This annotation should be added as DEPS-1 is required for germ cell
        proliferation. The deps-1 mutant phenotype includes underproliferated germlines
        and sterility at elevated temperatures, demonstrating involvement in this
        biological process.

        '
      supported_by:
        - reference_id: PMID:18234720
          supporting_text: DEPS-1 is required for... germ cell proliferation and
            fertility at elevated temperatures.
  - term:
      id: GO:0140693
      label: molecular condensate scaffold activity
    evidence_type: NAS
    review:
      summary: Added to align core_functions with existing annotations.
      action: NEW
      reason: Core function term not present in existing_annotations.
references:
  - id: GO_REF:0000043
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword 
      mapping
    findings: []
  - id: GO_REF:0000044
    title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular 
      Location vocabulary mapping, accompanied by conservative changes to GO 
      terms applied by UniProt
    findings: []
  - id: PMID:18234720
    title: DEPS-1 promotes P-granule assembly and RNA interference in C. elegans
      germ cells.
    findings:
      - statement: DEPS-1 is a novel P-granule-associated protein required for P
          granule structure and function
        supporting_text: We have identified a new P-granule-associated protein, 
          DEPS-1, the loss of which disrupts P-granule structure and function.
      - statement: DEPS-1 is required for proper localization of PGL-1 to P 
          granules
        supporting_text: DEPS-1 is required for the proper localization of PGL-1
          to P granules
      - statement: DEPS-1 promotes accumulation of glh-1 mRNA and protein
        supporting_text: DEPS-1 is required for... the accumulation of glh-1 
          mRNA and protein
      - statement: DEPS-1 is required for germ cell proliferation and fertility 
          at elevated temperatures
        supporting_text: DEPS-1 is required for... germ cell proliferation and 
          fertility at elevated temperatures
      - statement: DEPS-1 is required for RNAi of germline-expressed genes
        supporting_text: DEPS-1 is required for RNA interference (RNAi) of 
          germline-expressed genes
      - statement: DEPS-1 promotes accumulation of RDE-4, a dsRNA-binding 
          protein required for RNAi
        supporting_text: DEPS-1 promotes the accumulation of RDE-4, a 
          dsRNA-binding protein required for RNAi
  - id: PMID:32843637
    title: DEPS-1 is required for piRNA-dependent silencing and PIWI condensate 
      organisation in Caenorhabditis elegans.
    findings:
      - statement: DEPS-1 directly interacts with PRG-1 (Piwi Argonaute) via its
          N-terminus
      - statement: DEPS-1 is required for piRNA-mediated gene silencing
      - statement: DEPS-1 positively regulates formation of secondary 22G-RNAs 
          (endo-siRNAs)
      - statement: DEPS-1 co-localizes with PRG-1 at peri-nuclear P-granules
  - id: PMID:27015309
    title: A Tunable Mechanism Determines the Duration of the Transgenerational 
      Small RNA Inheritance in C. elegans.
    findings:
      - statement: DEPS-1 plays a role in small RNA-directed transgenerational 
          epigenetic inheritance
  - id: PMID:29769721
    title: Spatiotemporal regulation of liquid-like condensates in epigenetic 
      inheritance.
    findings:
      - statement: deps-1 mutants have smaller Z granules (liquid-like 
          condensates)
      - statement: DEPS-1 is required for proper binding of ZNFX-1 to RNA
core_functions:
  - molecular_function:
      id: GO:0140693
      label: molecular condensate scaffold activity
    description: DEPS-1 functions as a scaffold protein for P granule assembly, 
      organizing the liquid-like condensate structure of P granules in C. 
      elegans germ cells. It is required for proper localization of PGL-1 and 
      accumulation of GLH-1, acting as a core structural component of these 
      ribonucleoprotein granules.
    directly_involved_in:
      - id: GO:1903863
        label: P granule assembly
      - id: GO:0031047
        label: regulatory ncRNA-mediated gene silencing
    locations:
      - id: GO:0043186
        label: P granule
      - id: GO:0048471
        label: perinuclear region of cytoplasm
    supported_by:
      - reference_id: PMID:18234720
        supporting_text: We have identified a new P-granule-associated protein, 
          DEPS-1, the loss of which disrupts P-granule structure and function. 
          DEPS-1 is required for the proper localization of PGL-1 to P granules,
          the accumulation of glh-1 mRNA and protein.
tags:
  - caeel-p-granules