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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0031047 regulatory ncRNA-mediated gene silencing | IEA GO_REF:0000043 | ACCEPT | 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. 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. Supporting Evidence: PMID:18234720 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. file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1 is **not required for primary piRNA (21U) abundance**, but is required for **piRNA-dependent silencing** through effects on secondary siRNAs file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1 acts primarily **downstream of primary piRNA biogenesis**, promoting effective **piRNA-dependent silencing** through effects on **secondary 22G RNAs** and condensate organization file:worm/deps-1/deps-1-deep-research-falcon.md Spike et al. provide evidence that DEPS-1 promotes accumulation of **rde-4 mRNA and RDE-4 protein**, a dsRNA-binding factor essential for RNAi |
| GO:0048471 perinuclear region of cytoplasm | IEA GO_REF:0000044 | ACCEPT | 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). 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. Supporting Evidence: PMID:18234720 We have identified a new P-granule-associated protein, DEPS-1 file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1 and PRG-1 co-localize in **perinuclear granules** across multiple germline regions (proliferative zone to pachytene, oocytes, embryos) |
| GO:0043186 P granule | IDA PMID:18234720 DEPS-1 promotes P-granule assembly and RNA interference in C... | ACCEPT | 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). 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. Supporting Evidence: PMID:18234720 We have identified a new P-granule-associated protein, DEPS-1 file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1::GFP is cytoplasmic and enriched on P granules, and anti-DEPS-1 staining of P granules is lost in deps-1 mutants file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1 condensates appear as **small protein clusters localized within protein-dense P granules** |
| GO:1903863 P granule assembly | IMP PMID:18234720 DEPS-1 promotes P-granule assembly and RNA interference in C... | NEW | 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. 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. Supporting Evidence: PMID:18234720 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 file:worm/deps-1/deps-1-deep-research-falcon.md Loss-of-function deps-1 mutations disrupt the localization of **PGL-1** (and PGL-3) to P granules, consistent with DEPS-1 acting **upstream of PGL proteins** in a P-granule formation pathway file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1 is a **constitutive P-granule component** |
| GO:0036093 germ cell proliferation | IMP PMID:18234720 DEPS-1 promotes P-granule assembly and RNA interference in C... | NEW | 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). 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. Supporting Evidence: PMID:18234720 DEPS-1 is required for... germ cell proliferation and fertility at elevated temperatures. file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1 is required for normal germline development and fertility, with a **maternal-effect and temperature-sensitive sterility phenotype** |
| GO:0140693 molecular condensate scaffold activity | NAS | NEW | Summary: DEPS-1 functions as a non-enzymatic germline-specific condensate scaffold/adaptor that organizes perinuclear germ granules and couples them to small-RNA effector pathways. It directly binds the PRG-1 PIWI domain via an N-terminal PIWI-binding site (PBS) motif, and PBS deletion disperses DEPS-1 into the cytoplasm and disrupts higher-order organization of PRG-1/DEPS-1 condensates, demonstrating its scaffolding role. Reason: Core function term not present in existing_annotations. The falcon deep research synthesis supports a non-enzymatic condensate scaffold/adaptor role: DEPS-1 lacks canonical RNA-binding motifs and instead organizes condensate architecture and couples P granules to PIWI/mutator machinery. Supporting Evidence: file:worm/deps-1/deps-1-deep-research-falcon.md the evidence supports annotating DEPS-1 as a **non-enzymatic, germline-specific condensate scaffold/adaptor** that organizes perinuclear germ granules and couples them to small-RNA effector pathways file:worm/deps-1/deps-1-deep-research-falcon.md Deletion of PBS disperses DEPS-1 into the cytoplasm and disrupts higher-order organization of PRG-1/DEPS-1 condensates file:worm/deps-1/deps-1-deep-research-falcon.md DEPS-1 binds the **PRG-1 PIWI domain**, mediated by an N-terminal **PIWI-binding site (PBS)** motif |
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)