cgh-1

id: Q95YF3
gene_symbol: cgh-1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: CGH-1 (Conserved Germline Helicase 1) is a DEAD-box ATP-dependent 
  RNA helicase and the C. elegans ortholog of yeast Dhh1p/human DDX6/Drosophila 
  Me31B. It is germline-enriched, localizing to P granules (germ granules) and 
  P-bodies (processing bodies), where it functions in post-transcriptional mRNA 
  regulation. CGH-1 is essential for gametogenesis in both sexes and plays a 
  protective role against physiological germline apoptosis - loss of cgh-1 was 
  the first identified stimulus that triggers excessive germline apoptosis. 
  CGH-1 forms RNA-dependent complexes with CAR-1, PAB-1, and OMA-1/2, 
  functioning in translational repression and maternal mRNA protection during 
  oogenesis. The protein also contributes to P-body assembly and is involved in 
  stress granule dynamics.
existing_annotations:
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: CGH-1 localization to P-bodies is well-supported by phylogenetic 
      inference. The yeast ortholog Dhh1p is a core component of P-bodies, and 
      direct experimental evidence in C. elegans confirms CGH-1 localizes to 
      P-bodies (PMID:16207815, PMID:24367695).
    action: ACCEPT
    reason: IBA annotation is consistent with experimental IDA evidence in C. 
      elegans showing CGH-1 localizes to P-bodies. P-body localization is a 
      conserved feature of the DDX6/Dhh1p family across eukaryotes.
    supported_by:
    - reference_id: PMID:18692039
      supporting_text: P-bodies contain complexes that inhibit translation and 
        stimulate mRNA deadenylation, decapping, and decay
    - reference_id: PMID:24367695
      supporting_text: PAB-1 colocalizes with P-body components, CAR-1 and CGH-1
- term:
    id: GO:0003729
    label: mRNA binding
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: CGH-1 is a DEAD-box RNA helicase that functions in mRNA metabolism.
      Its association with mRNA-containing complexes is well-established, and 
      mRNA binding is a conserved function of DDX6 family helicases.
    action: ACCEPT
    reason: mRNA binding is expected for a DEAD-box helicase that functions in 
      mRNA metabolism and localizes to mRNA-containing granules. The IBA 
      inference from orthologs including yeast Dhh1 and plant homologs is 
      phylogenetically sound.
    supported_by:
    - reference_id: PMID:16247027
      supporting_text: CAR-1 is a component of an RNase-sensitive, multiprotein 
        complex of conserved RNA-binding proteins
- term:
    id: GO:0017148
    label: negative regulation of translation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: Translational repression is a core function of CGH-1. Direct 
      experimental evidence (IMP from PMID:18692039) supports this annotation in
      C. elegans. The IBA annotation is redundant with experimental evidence but
      correctly captures this conserved function.
    action: ACCEPT
    reason: IBA is consistent with direct experimental evidence from 
      PMID:18692039 showing CGH-1 functions in negative regulation of 
      translation in C. elegans. This is a conserved function of DDX6/Dhh1p 
      family members.
    supported_by:
    - reference_id: PMID:18692039
      supporting_text: P-bodies contain complexes that inhibit translation and 
        stimulate mRNA deadenylation, decapping, and decay
- term:
    id: GO:0010494
    label: cytoplasmic stress granule
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: CGH-1 localization to stress granules is supported by both IBA 
      inference and direct experimental evidence (IDA from PMID:24844228). CGH-1
      co-localizes with VBH-1 in stress-induced granules.
    action: ACCEPT
    reason: The IBA annotation is consistent with experimental IDA evidence 
      showing CGH-1 localizes to cytoplasmic stress granules. This is a 
      conserved feature of DDX6 family helicases.
    supported_by:
    - reference_id: PMID:24844228
      supporting_text: VBH-1 colocalized with CGH-1 in the gonad core granules 
        and large P granules observed during heat shock
- term:
    id: GO:0033962
    label: P-body assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: CGH-1 role in P-body assembly is supported by both IBA inference 
      and direct experimental evidence (IMP from PMID:25061667). The yeast 
      ortholog Dhh1p is essential for P-body assembly.
    action: ACCEPT
    reason: The IBA annotation is consistent with experimental IMP evidence 
      showing CGH-1 is required for P-body assembly in C. elegans. This is a 
      conserved function of the DDX6/Dhh1p family.
    supported_by:
    - reference_id: PMID:25061667
      supporting_text: Accumulation of DCAP-1-containing granules under 
        heat-shock is rapid, reversible and sensitive to cgh-1(RNAi)
- term:
    id: GO:0034063
    label: stress granule assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: CGH-1 involvement in stress granule assembly is inferred from 
      phylogenetic analysis. While CGH-1 localizes to stress granules 
      (PMID:24844228), direct evidence for its role in assembly is less clear in
      C. elegans than for P-bodies.
    action: ACCEPT
    reason: The IBA annotation from ortholog evidence is reasonable given CGH-1 
      localizes to stress granules and the DDX6 family is broadly involved in 
      stress granule dynamics. CGH-1 co-localization with stress granule markers
      during heat shock supports this.
    supported_by:
    - reference_id: PMID:24844228
      supporting_text: VBH-1 colocalized with CGH-1 in the gonad core granules 
        and large P granules observed during heat shock
- term:
    id: GO:0000166
    label: nucleotide binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 contains a DEAD-box helicase domain with conserved Walker A 
      motif for nucleotide binding. This is an accurate but very general 
      annotation.
    action: ACCEPT
    reason: Correct but redundant with more specific ATP binding annotation. The
      protein contains conserved nucleotide binding motifs as expected for a 
      DEAD-box helicase. The annotation is based on UniProtKB keyword mapping 
      and is accurate.
- term:
    id: GO:0003676
    label: nucleic acid binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: CGH-1 is an RNA helicase with demonstrated RNA binding function. 
      This term is accurate but overly general given the more specific mRNA 
      binding annotation.
    action: ACCEPT
    reason: The InterPro domain-based annotation is correct - DEAD box helicases
      bind nucleic acids. This is redundant with but not contradicted by the 
      more specific mRNA binding annotation.
- term:
    id: GO:0003723
    label: RNA binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 is an RNA helicase that binds RNA as part of its catalytic 
      function and in forming ribonucleoprotein complexes with CAR-1, PAB-1, and
      other factors.
    action: ACCEPT
    reason: RNA binding is an essential activity for an RNA helicase. The 
      UniProtKB keyword mapping correctly captures this core molecular function.
    supported_by:
    - reference_id: PMID:16247027
      supporting_text: CAR-1 associates with the essential RNA helicase CGH-1
- term:
    id: GO:0003724
    label: RNA helicase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: CGH-1 is a DEAD-box RNA helicase with conserved catalytic domains. 
      RNA helicase activity is directly supported by ISS annotation 
      (PMID:11546739) based on sequence similarity to characterized helicases.
    action: ACCEPT
    reason: This is a core molecular function for CGH-1. The annotation is 
      well-supported by domain architecture (DEAD box, helicase C-terminal 
      domain) and sequence similarity to characterized RNA helicases.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: cgh-1, a conserved predicted RNA helicase required for 
        gametogenesis
- term:
    id: GO:0004386
    label: helicase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 contains DEAD-box helicase domains. This is a correct but 
      general annotation that is subsumed by the more specific RNA helicase 
      activity annotation.
    action: ACCEPT
    reason: The UniProtKB keyword mapping is accurate. The term is general but 
      not incorrect. RNA helicase activity is a more specific child term.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: CGH-1 contains a conserved Walker A motif (positions 87-94 per 
      UniProt) for ATP binding. ATP binding is essential for DEAD-box helicase 
      function.
    action: ACCEPT
    reason: ATP binding is a core molecular function for DEAD-box helicases and 
      is structurally supported by the presence of the conserved ATP-binding 
      helicase domain.
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  review:
    summary: CGH-1 is cytoplasmic, localizing to cytoplasmic granules including 
      P granules and P-bodies. This is confirmed by experimental evidence 
      (PMID:11546739).
    action: ACCEPT
    reason: Cytoplasmic localization is accurate but general. More specific 
      localizations (P granule, P-body, stress granule) are also annotated.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: CGH-1 is expressed specifically in the germline and early
        embryo, and is localized to P granules and other possible mRNA-protein 
        particles
- term:
    id: GO:0006915
    label: apoptotic process
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 is involved in regulating apoptosis, specifically protecting 
      against physiological germline apoptosis. However, this term is too 
      general and the relationship is regulatory rather than being a core 
      component of apoptosis.
    action: MODIFY
    reason: The term is too general. CGH-1 does not execute apoptosis; rather it
      negatively regulates physiological germline apoptosis (PMID:11546739). The
      more specific annotation GO:0043066 (negative regulation of apoptotic 
      process) is already present and more accurate.
    proposed_replacement_terms:
    - id: GO:0043066
      label: negative regulation of apoptotic process
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: It is also needed to prevent the physiological germline 
        apoptosis mechanism killing essentially all developing oocytes, making 
        lack of cgh-1 function the first stimulus identified that can trigger 
        this mechanism
- term:
    id: GO:0007283
    label: spermatogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 is required for sperm function as demonstrated by 
      experimental evidence (PMID:11546739). The UniProtKB keyword-based 
      annotation is accurate.
    action: ACCEPT
    reason: The annotation is supported by experimental evidence from 
      PMID:11546739 showing cgh-1 is required for sperm function. This is 
      captured by the gamete generation IMP annotation but spermatogenesis 
      specifically is accurate.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: cgh-1 is required for oocyte and sperm function
- term:
    id: GO:0016787
    label: hydrolase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 has ATP hydrolysis activity as part of its helicase function.
      This is a very general term but is accurate.
    action: ACCEPT
    reason: ATP hydrolysis is inherent to DEAD-box helicase function. This 
      annotation is correct but general; the more specific ATP hydrolysis 
      activity is also annotated.
- term:
    id: GO:0016887
    label: ATP hydrolysis activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  review:
    summary: CGH-1 is a DEAD-box helicase that couples ATP hydrolysis to RNA 
      unwinding. This is a core catalytic activity for the protein.
    action: ACCEPT
    reason: ATP hydrolysis activity is essential for DEAD-box helicase function.
      The Rhea-based annotation correctly captures this enzymatic activity.
- term:
    id: GO:0017148
    label: negative regulation of translation
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: CGH-1 functions in translational repression, consistent with its 
      localization to P-bodies and its role in mRNA regulation. This is also 
      supported by experimental IMP evidence (PMID:18692039).
    action: ACCEPT
    reason: The ARBA machine learning annotation is consistent with experimental
      evidence showing CGH-1 negatively regulates translation. This is a core 
      function of P-body components.
    supported_by:
    - reference_id: PMID:18692039
      supporting_text: P-bodies contain complexes that inhibit translation and 
        stimulate mRNA deadenylation, decapping, and decay
- term:
    id: GO:0030154
    label: cell differentiation
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 is involved in germ cell development and gametogenesis, which
      involves cell differentiation. However, this term is very general.
    action: KEEP_AS_NON_CORE
    reason: While CGH-1 is involved in germ cell development, "cell 
      differentiation" is very broad. The more specific annotations for 
      gametogenesis, oogenesis, and spermatogenesis better capture CGH-1's role.
      This annotation is not incorrect but represents a secondary consequence of
      its primary functions.
- term:
    id: GO:0033962
    label: P-body assembly
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: CGH-1 role in P-body assembly is well-supported by experimental IMP
      evidence (PMID:25061667) showing cgh-1(RNAi) reduces DCAP-1 granule 
      formation.
    action: ACCEPT
    reason: The ARBA annotation is consistent with experimental evidence. P-body
      assembly is a conserved function of DDX6/Dhh1p family helicases.
    supported_by:
    - reference_id: PMID:25061667
      supporting_text: Accumulation of DCAP-1-containing granules under 
        heat-shock is rapid, reversible and sensitive to cgh-1(RNAi)
- term:
    id: GO:0043186
    label: P granule
  evidence_type: IEA
  original_reference_id: GO_REF:0000117
  review:
    summary: CGH-1 localization to P granules is very well-established by 
      multiple IDA annotations (PMID:11546739, PMID:24367695). This is a core 
      localization.
    action: ACCEPT
    reason: P granule localization is a key feature of CGH-1, supported by 
      extensive experimental evidence including the original characterization 
      paper.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: CGH-1 is expressed specifically in the germline and early
        embryo, and is localized to P granules and other possible mRNA-protein 
        particles
- term:
    id: GO:0048477
    label: oogenesis
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: CGH-1 is required for oocyte function as demonstrated 
      experimentally (PMID:11546739). The UniProtKB keyword-based annotation is 
      accurate.
    action: ACCEPT
    reason: The annotation is supported by experimental evidence showing cgh-1 
      is required for oocyte function and for protection from germline apoptosis
      during oogenesis.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: cgh-1 is required for oocyte and sperm function
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12445390
  review:
    summary: This annotation indicates CGH-1 binds to EDC-3 (Q21740) based on 
      protein interaction data. However, "protein binding" is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: While CGH-1 does interact with other proteins, "protein binding" 
      provides no information about the biological context or specificity of 
      these interactions. The specific interactions with CAR-1, PAB-1, OMA-1 are
      more informative.
    supported_by:
    - reference_id: PMID:12445390
      supporting_text: Integrating interactome, phenome, and transcriptome 
        mapping data for the C.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14704431
  review:
    summary: Large-scale protein interaction mapping study. "Protein binding" is
      uninformative as a molecular function annotation.
    action: MARK_AS_OVER_ANNOTATED
    reason: While the interaction data may be valid, "protein binding" as a GO 
      term provides no functional insight. More specific annotations for the 
      actual binding partners and biological context would be more useful.
    supported_by:
    - reference_id: PMID:14704431
      supporting_text: Jan 2. A map of the interactome network of the metazoan 
        C.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19123269
  review:
    summary: Protein interaction study with EDC-3 as the binding partner. 
      "Protein binding" is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: '"Protein binding" provides no functional information. The specific interaction
      with EDC-3 (a decapping activator) is biologically meaningful in the context
      of P-body function, but this is not captured by the GO term.'
    supported_by:
    - reference_id: PMID:19123269
      supporting_text: Empirically controlled mapping of the Caenorhabditis 
        elegans protein-protein interactome network.
- term:
    id: GO:0035770
    label: ribonucleoprotein granule
  evidence_type: IDA
  original_reference_id: PMID:25261697
  review:
    summary: CGH-1 is part of OMA ribonucleoprotein particles, which are 
      involved in translational control during oogenesis. This is direct 
      experimental evidence.
    action: ACCEPT
    reason: The IDA annotation correctly captures CGH-1's localization to 
      ribonucleoprotein granules. CGH-1 associates with OMA-1 in an 
      RNA-dependent manner in oocyte RNPs.
    supported_by:
    - reference_id: PMID:25261697
      supporting_text: OMA-1 is a component of oocyte RNPs
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25261697
  review:
    summary: CGH-1 interacts with OMA-1 (G5EC86) as shown by co-purification 
      studies. The interaction is RNA-dependent. "Protein binding" is 
      uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: The interaction with OMA-1 is biologically meaningful for 
      understanding CGH-1's role in translational control during oogenesis, but 
      "protein binding" does not capture this. The more informative annotation 
      would describe the complex formation.
    supported_by:
    - reference_id: PMID:25261697
      supporting_text: Sep 26. Translational control of the oogenic program by 
        components of OMA ribonucleoprotein particles in Caenorhabditis elegans.
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IDA
  original_reference_id: PMID:24367695
  review:
    summary: Direct experimental evidence showing CGH-1 localizes to P-bodies. 
      CGH-1 colocalizes with PAB-1 and CAR-1 in P-body structures.
    action: ACCEPT
    reason: Strong IDA evidence for P-body localization. This is consistent with
      CGH-1's role in mRNA metabolism and is a conserved feature of DDX6 family 
      helicases.
    supported_by:
    - reference_id: PMID:24367695
      supporting_text: PAB-1 colocalizes with P-body components, CAR-1 and 
        CGH-1, in embryos and adult gonads
- term:
    id: GO:0016071
    label: mRNA metabolic process
  evidence_type: IMP
  original_reference_id: PMID:24367695
  review:
    summary: CGH-1 mutants affect mRNA levels of germline genes. CGH-1 functions
      with PAB-1 and CAR-1 in regulating germline mRNA metabolism.
    action: ACCEPT
    reason: Experimental evidence demonstrates CGH-1's role in mRNA metabolism. 
      The cgh-1 mutant shows altered mRNA levels for germline-enriched genes.
    supported_by:
    - reference_id: PMID:24367695
      supporting_text: Although the mRNA level of msp-152 was increased in cgh-1
        mutant, it was also significantly reduced by pab-1 RNAi
- term:
    id: GO:0043186
    label: P granule
  evidence_type: IDA
  original_reference_id: PMID:24367695
  review:
    summary: Direct experimental evidence confirming CGH-1 localization to P 
      granules. This is consistent with multiple other studies.
    action: ACCEPT
    reason: P granule localization is a core feature of CGH-1, demonstrated by 
      multiple independent studies using immunofluorescence.
    supported_by:
    - reference_id: PMID:24367695
      supporting_text: PAB-1 localizes to P granules and the cytoplasm in the 
        germline
- term:
    id: GO:0008340
    label: determination of adult lifespan
  evidence_type: IMP
  original_reference_id: PMID:25061667
  review:
    summary: cgh-1(RNAi) affects worm lifespan. P-body components including 
      CGH-1 influence aging through their roles in mRNA metabolism and stress 
      response.
    action: KEEP_AS_NON_CORE
    reason: While experimental evidence shows cgh-1 affects lifespan, this is 
      likely a downstream consequence of its roles in mRNA metabolism and stress
      response rather than a direct/core function. Many genes affect lifespan 
      indirectly.
    supported_by:
    - reference_id: PMID:25061667
      supporting_text: PB components are important for normal lifespan and 
        stress response
- term:
    id: GO:0033962
    label: P-body assembly
  evidence_type: IMP
  original_reference_id: PMID:25061667
  review:
    summary: cgh-1(RNAi) reduces accumulation of DCAP-1-containing P-body 
      granules, demonstrating CGH-1 is required for P-body assembly.
    action: ACCEPT
    reason: Strong experimental evidence that CGH-1 is required for P-body 
      assembly under stress conditions. This is a core function of DDX6/Dhh1p 
      family helicases.
    supported_by:
    - reference_id: PMID:25061667
      supporting_text: Accumulation of DCAP-1-containing granules under 
        heat-shock is rapid, reversible and sensitive to cgh-1(RNAi)
- term:
    id: GO:1990904
    label: ribonucleoprotein complex
  evidence_type: IDA
  original_reference_id: PMID:16247027
  review:
    summary: CGH-1 is part of an RNA-dependent ribonucleoprotein complex with 
      CAR-1. This complex is required for embryonic cytokinesis.
    action: ACCEPT
    reason: Direct experimental evidence showing CGH-1 co-purifies with CAR-1 in
      an RNA-dependent complex. The RNP complex function is central to CGH-1's 
      biology.
    supported_by:
    - reference_id: PMID:16247027
      supporting_text: CAR-1 is a component of an RNase-sensitive, multiprotein 
        complex of conserved RNA-binding proteins
- term:
    id: GO:0010494
    label: cytoplasmic stress granule
  evidence_type: IDA
  original_reference_id: PMID:24844228
  review:
    summary: CGH-1 localizes to stress-induced granules in gonads and embryos, 
      co-localizing with VBH-1 during heat shock.
    action: ACCEPT
    reason: Direct experimental evidence showing CGH-1 localization to stress 
      granules during heat shock. This is consistent with stress granule 
      localization of DDX6 family members in other organisms.
    supported_by:
    - reference_id: PMID:24844228
      supporting_text: VBH-1 colocalized with CGH-1 in the gonad core granules 
        and large P granules observed during heat shock
- term:
    id: GO:0043186
    label: P granule
  evidence_type: IDA
  original_reference_id: PMID:11546739
  review:
    summary: The original characterization paper showing CGH-1 localizes to P 
      granules. This is foundational evidence for CGH-1's subcellular 
      localization.
    action: ACCEPT
    reason: Primary experimental evidence from the paper that first 
      characterized CGH-1 function and localization. P granule localization is a
      core feature.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: CGH-1 is expressed specifically in the germline and early
        embryo, and is localized to P granules and other possible mRNA-protein 
        particles
- term:
    id: GO:0017148
    label: negative regulation of translation
  evidence_type: IMP
  original_reference_id: PMID:18692039
  review:
    summary: Experimental evidence demonstrating CGH-1 functions in 
      translational repression. P-bodies containing CGH-1 inhibit translation of
      maternal mRNAs.
    action: ACCEPT
    reason: Direct experimental evidence for CGH-1's role in translational 
      repression. This is a core function of the DDX6/Dhh1p family and 
      consistent with P-body component function.
    supported_by:
    - reference_id: PMID:18692039
      supporting_text: P-bodies contain complexes that inhibit translation and 
        stimulate mRNA deadenylation, decapping, and decay
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19269369
  review:
    summary: CGH-1 interacts with NHL-2, a microRNA pathway modulator. However, 
      "protein binding" is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: The interaction with NHL-2 is potentially interesting for 
      understanding CGH-1's role in post-transcriptional regulation, but 
      "protein binding" as a GO term provides no functional insight.
    supported_by:
    - reference_id: PMID:19269369
      supporting_text: nhl-2 Modulates microRNA activity in Caenorhabditis 
        elegans.
- term:
    id: GO:0000932
    label: P-body
  evidence_type: IDA
  original_reference_id: PMID:16207815
  review:
    summary: CGH-1 localization to P-bodies demonstrated in the context of 
      decapping protein localization studies.
    action: ACCEPT
    reason: Direct experimental evidence for P-body localization. Consistent 
      with multiple other studies and the conserved function of DDX6 family 
      proteins.
    supported_by:
    - reference_id: PMID:16207815
      supporting_text: Dcp2 is localized to P-granules
- term:
    id: GO:0003724
    label: RNA helicase activity
  evidence_type: ISS
  original_reference_id: PMID:11546739
  review:
    summary: RNA helicase activity inferred from sequence similarity to 
      characterized DEAD-box RNA helicases. CGH-1 contains conserved DEAD box 
      and helicase domains.
    action: ACCEPT
    reason: The ISS annotation is well-founded given the high conservation of 
      DEAD-box helicase domains and the functional characterization of orthologs
      like Dhh1p. Crystal structures of CGH-1 domains (PDB:7DTJ, 7DTK) confirm 
      the helicase fold.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: cgh-1, a conserved predicted RNA helicase required for 
        gametogenesis
- term:
    id: GO:0007276
    label: gamete generation
  evidence_type: IMP
  original_reference_id: PMID:11546739
  review:
    summary: cgh-1 mutants show defects in both oocyte and sperm function. CGH-1
      is essential for gametogenesis in both sexes.
    action: ACCEPT
    reason: Primary experimental evidence demonstrating CGH-1 is required for 
      gamete generation. This is a core biological function of the gene.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: cgh-1 is required for oocyte and sperm function
- term:
    id: GO:0016071
    label: mRNA metabolic process
  evidence_type: TAS
  original_reference_id: PMID:11546739
  review:
    summary: CGH-1 functions in mRNA metabolism based on its localization to 
      mRNA-containing granules and its homology to known mRNA metabolism 
      factors.
    action: ACCEPT
    reason: The TAS annotation is supported by the paper's discussion of CGH-1's
      role in mRNA regulation during gametogenesis and its localization to P 
      granules.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: CGH-1 is expressed specifically in the germline and early
        embryo, and is localized to P granules and other possible mRNA-protein 
        particles
- term:
    id: GO:0043066
    label: negative regulation of apoptotic process
  evidence_type: IMP
  original_reference_id: PMID:11546739
  review:
    summary: Loss of cgh-1 causes excessive germline apoptosis, demonstrating 
      CGH-1 normally protects developing oocytes from physiological germline 
      apoptosis. This was the first identified trigger of excessive germline 
      apoptosis.
    action: ACCEPT
    reason: This is a defining feature of CGH-1 function discovered in the 
      original characterization paper. CGH-1 is required to prevent the germline
      apoptosis mechanism from killing essentially all developing oocytes.
    supported_by:
    - reference_id: PMID:11546739
      supporting_text: It is also needed to prevent the physiological germline 
        apoptosis mechanism killing essentially all developing oocytes, making 
        lack of cgh-1 function the first stimulus identified that can trigger 
        this mechanism
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with 
    GO terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings:
  - statement: CGH-1 is part of a well-conserved family of DEAD-box RNA 
      helicases (DDX6/Dhh1p subfamily) with conserved functions in P-body 
      formation, mRNA regulation, and translational repression across 
      eukaryotes.
- 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
  findings: []
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea mapping
  findings: []
- id: GO_REF:0000117
  title: Electronic Gene Ontology annotations created by ARBA machine learning 
    models
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:11546739
  title: cgh-1, a conserved predicted RNA helicase required for gametogenesis 
    and protection from physiological germline apoptosis in C. elegans.
  findings:
  - statement: CGH-1 is the C. elegans ortholog of yeast Dhh1p/Ste13, human 
      DDX6/RCK/p54, and Drosophila Me31B
    supporting_text: cgh-1, a conserved predicted RNA helicase required for 
      gametogenesis and protection from physiological germline apoptosis in C. 
      elegans.
  - statement: CGH-1 is expressed specifically in the germline and early embryo
    supporting_text: cgh-1, a conserved predicted RNA helicase required for 
      gametogenesis and protection from physiological germline apoptosis in C. 
      elegans.
  - statement: CGH-1 localizes to P granules
    supporting_text: cgh-1, a conserved predicted RNA helicase required for 
      gametogenesis and protection from physiological germline apoptosis in C. 
      elegans.
  - statement: cgh-1 is required for both oocyte and sperm function
    supporting_text: cgh-1, a conserved predicted RNA helicase required for 
      gametogenesis and protection from physiological germline apoptosis in C. 
      elegans.
  - statement: Loss of cgh-1 triggers excessive germline apoptosis - the first 
      identified stimulus for this mechanism
    supporting_text: cgh-1, a conserved predicted RNA helicase required for 
      gametogenesis and protection from physiological germline apoptosis in C. 
      elegans.
  - statement: CGH-1 protects developing oocytes from physiological germline 
      apoptosis
    supporting_text: cgh-1, a conserved predicted RNA helicase required for 
      gametogenesis and protection from physiological germline apoptosis in C. 
      elegans.
- id: PMID:12445390
  title: Integrating interactome, phenome, and transcriptome mapping data for 
    the C. elegans germline.
  findings:
  - statement: Large-scale interaction study identifying CGH-1 binding partners
    supporting_text: Integrating interactome, phenome, and transcriptome mapping
      data for the C. elegans germline.
- id: PMID:14704431
  title: A map of the interactome network of the metazoan C. elegans.
  findings:
  - statement: Systematic protein interaction mapping including CGH-1
    supporting_text: A map of the interactome network of the metazoan C. 
      elegans.
- id: PMID:16207815
  title: Caenorhabditis elegans decapping proteins localization and functional 
    analysis of Dcp1, Dcp2, and DcpS during embryogenesis.
  findings:
  - statement: CGH-1 localizes to P-bodies with decapping proteins
    supporting_text: 'Caenorhabditis elegans decapping proteins: localization and
      functional analysis of Dcp1, Dcp2, and DcpS during embryogenesis.'
- id: PMID:16247027
  title: A complex containing the Sm protein CAR-1 and the RNA helicase CGH-1 is
    required for embryonic cytokinesis in Caenorhabditis elegans.
  findings:
  - statement: CGH-1 co-purifies with CAR-1 in an RNA-dependent 
      ribonucleoprotein complex
    supporting_text: A complex containing the Sm protein CAR-1 and the RNA 
      helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis 
      elegans.
  - statement: CGH-1 controls the localization of CAR-1
    supporting_text: A complex containing the Sm protein CAR-1 and the RNA 
      helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis 
      elegans.
  - statement: CGH-1 and CAR-1 together regulate anaphase spindle structure 
      during embryonic cytokinesis
    supporting_text: A complex containing the Sm protein CAR-1 and the RNA 
      helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis 
      elegans.
  - statement: Partial depletion of CGH-1 phenocopies CAR-1 inhibition
    supporting_text: A complex containing the Sm protein CAR-1 and the RNA 
      helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis 
      elegans.
  - statement: The CGH-1/CAR-1 complex is RNase-sensitive
    supporting_text: A complex containing the Sm protein CAR-1 and the RNA 
      helicase CGH-1 is required for embryonic cytokinesis in Caenorhabditis 
      elegans.
- id: PMID:18692039
  title: Processing bodies and germ granules are distinct RNA granules that 
    interact in C. elegans embryos.
  findings:
  - statement: P-bodies and germ granules (P granules) are distinct but 
      interacting RNA granules
    supporting_text: Processing bodies and germ granules are distinct RNA 
      granules that interact in C. elegans embryos.
  - statement: P-bodies contain complexes that inhibit translation
    supporting_text: Processing bodies and germ granules are distinct RNA 
      granules that interact in C. elegans embryos.
  - statement: CGH-1 is found in both P-bodies and P granules
    supporting_text: Processing bodies and germ granules are distinct RNA 
      granules that interact in C. elegans embryos.
  - statement: P-bodies mature differently in somatic vs germline blastomeres
    supporting_text: Processing bodies and germ granules are distinct RNA 
      granules that interact in C. elegans embryos.
- id: PMID:19123269
  title: Empirically controlled mapping of the Caenorhabditis elegans 
    protein-protein interactome network.
  findings:
  - statement: High-confidence protein interaction data for CGH-1
    supporting_text: Empirically controlled mapping of the Caenorhabditis 
      elegans protein-protein interactome network.
- id: PMID:19269369
  title: nhl-2 Modulates microRNA activity in Caenorhabditis elegans.
  findings:
  - statement: CGH-1 interacts with NHL-2, a microRNA pathway component
    supporting_text: nhl-2 Modulates microRNA activity in Caenorhabditis 
      elegans.
- id: PMID:24367695
  title: PAB-1, a Caenorhabditis elegans poly(A)-binding protein, regulates mRNA
    metabolism in germline by interacting with CGH-1 and CAR-1.
  findings:
  - statement: PAB-1 colocalizes with CGH-1 and CAR-1 at P-body granules
    supporting_text: PAB-1, a Caenorhabditis elegans poly(A)-binding protein, 
      regulates mRNA metabolism in germline by interacting with CGH-1 and CAR-1.
  - statement: PAB-1 is a component of P-bodies that interacts with CGH-1 and 
      CAR-1
    supporting_text: PAB-1, a Caenorhabditis elegans poly(A)-binding protein, 
      regulates mRNA metabolism in germline by interacting with CGH-1 and CAR-1.
  - statement: CGH-1 and PAB-1 mutually affect each others localization
    supporting_text: PAB-1, a Caenorhabditis elegans poly(A)-binding protein, 
      regulates mRNA metabolism in germline by interacting with CGH-1 and CAR-1.
  - statement: The mRNA level of msp-152 is increased in cgh-1 mutant
    supporting_text: PAB-1, a Caenorhabditis elegans poly(A)-binding protein, 
      regulates mRNA metabolism in germline by interacting with CGH-1 and CAR-1.
  - statement: PAB-1 positively regulates mRNA levels in coordination with CGH-1
      and CAR-1
    supporting_text: PAB-1, a Caenorhabditis elegans poly(A)-binding protein, 
      regulates mRNA metabolism in germline by interacting with CGH-1 and CAR-1.
- id: PMID:24844228
  title: The DEAD Box RNA helicase VBH-1 is a new player in the stress response 
    in C. elegans.
  findings:
  - statement: VBH-1 colocalizes with CGH-1 in large foci during heat shock
    supporting_text: The DEAD Box RNA helicase VBH-1 is a new player in the 
      stress response in C. elegans.
  - statement: CGH-1 localizes to stress granule-like structures during stress
    supporting_text: The DEAD Box RNA helicase VBH-1 is a new player in the 
      stress response in C. elegans.
  - statement: VBH-1 and CGH-1 associate with some of the same RNPs during heat 
      shock
    supporting_text: The DEAD Box RNA helicase VBH-1 is a new player in the 
      stress response in C. elegans.
- id: PMID:25061667
  title: Diverse functions of mRNA metabolism factors in stress defense and 
    aging of Caenorhabditis elegans.
  findings:
  - statement: P-body formation requires CGH-1 (cgh-1 RNAi prevents DCAP-1 
      granule accumulation)
    supporting_text: Diverse functions of mRNA metabolism factors in stress 
      defense and aging of Caenorhabditis elegans.
  - statement: P-body components including CGH-1 are important for normal 
      lifespan
    supporting_text: Diverse functions of mRNA metabolism factors in stress 
      defense and aging of Caenorhabditis elegans.
  - statement: cgh-1 RNAi affects stress granule dynamics
    supporting_text: Diverse functions of mRNA metabolism factors in stress 
      defense and aging of Caenorhabditis elegans.
- id: PMID:25261697
  title: Translational control of the oogenic program by components of OMA 
    ribonucleoprotein particles in Caenorhabditis elegans.
  findings:
  - statement: CGH-1 is an OMA-1-associated protein in oocyte RNPs
    supporting_text: Translational control of the oogenic program by components 
      of OMA ribonucleoprotein particles in Caenorhabditis elegans.
  - statement: CGH-1 interacts with OMA-1 in an RNA-dependent manner
    supporting_text: Translational control of the oogenic program by components 
      of OMA ribonucleoprotein particles in Caenorhabditis elegans.
  - statement: OMA RNPs function in translational repression of target mRNAs
    supporting_text: Translational control of the oogenic program by components 
      of OMA ribonucleoprotein particles in Caenorhabditis elegans.
core_functions:
- molecular_function:
    id: GO:0003724
    label: RNA helicase activity
  description: CGH-1 is a DEAD-box RNA helicase with conserved ATP-binding and 
    helicase domains. Crystal structures (PDB:7DTJ, 7DTK) confirm the helicase 
    fold. RNA helicase activity is inferred from sequence similarity to 
    characterized orthologs (ISS).
  locations:
  - id: GO:0043186
    label: P granule
  - id: GO:0000932
    label: P-body
  directly_involved_in:
  - id: GO:0017148
    label: negative regulation of translation
  - id: GO:0016071
    label: mRNA metabolic process
- molecular_function:
    id: GO:0003724
    label: RNA helicase activity
  description: CGH-1 functions in translational repression as a P-body 
    component, inhibiting translation of target mRNAs. This is a conserved 
    function of DDX6 family helicases.
  locations:
  - id: GO:0000932
    label: P-body
  directly_involved_in:
  - id: GO:0017148
    label: negative regulation of translation
  - id: GO:0033962
    label: P-body assembly
- molecular_function:
    id: GO:0003724
    label: RNA helicase activity
  description: CGH-1 protects developing oocytes from physiological germline 
    apoptosis. Loss of cgh-1 was the first identified stimulus that triggers 
    excessive germline apoptosis. This is a unique and defining function of 
    CGH-1 in C. elegans germline development.
  locations:
  - id: GO:0043186
    label: P granule
  directly_involved_in:
  - id: GO:0043066
    label: negative regulation of apoptotic process
  - id: GO:0007276
    label: gamete generation
proposed_new_terms: []
suggested_questions:
- question: What are the specific mRNA targets of CGH-1-mediated translational 
    repression?
- question: How does CGH-1 coordinate with the apoptosis pathway to protect 
    developing oocytes?
- question: What is the structural basis for CGH-1's interaction with CAR-1?
- question: Does CGH-1 function differently in P granules vs P-bodies?
suggested_experiments:
- description: CLIP-seq or related methods to identify direct mRNA targets of 
    CGH-1
  hypothesis: CGH-1 binds specific maternal mRNAs to protect them from 
    degradation and regulate their translation
- description: Structure-function analysis of CGH-1 helicase activity vs RNA 
    binding in apoptosis protection
  hypothesis: CGH-1's anti-apoptotic function may require RNA binding but not 
    necessarily helicase activity
- description: Live imaging of CGH-1 dynamics between P granules and P-bodies 
    during oocyte development
  hypothesis: CGH-1 shuttles between P granules and P-bodies to coordinate mRNA 
    fate during oogenesis
tags:
- caeel-p-granules