meg-4

id: Q9TZK8
gene_symbol: meg-4
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:6239
  label: Caenorhabditis elegans
description: MEG-4 (maternal-effect germline defective 4) is an intrinsically disordered
  protein (IDP) that functions redundantly with its homolog MEG-3 in P granule assembly
  and segregation in C. elegans embryos. MEG-4 contains multiple disordered regions
  enriched in polar and low-complexity sequences, consistent with its role as a scaffold
  for biomolecular condensates. MEG-4 localizes to P granules and is regulated by
  MBK-2/DYRK phosphorylation, which controls P granule dynamics through phase separation.
  While meg-4 single mutants have mild phenotypes, meg-3 meg-4 double mutants fail
  to segregate P granules to the posterior of the zygote, and meg-1 meg-3 meg-4 triple
  mutants are 100% sterile. MEG-4 is essential for RNA recruitment to germ granules
  and proper small RNA homeostasis.
existing_annotations:
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12445390
  review:
    summary: High-throughput yeast two-hybrid screen identified interactions with
      atz-1 and klc-1. The PMID:12445390 publication describes an integrated interactome
      mapping approach for C. elegans germline proteins. While the interaction data
      is valid, the generic term "protein binding" does not provide functional insight
      for a scaffold protein whose core function is phase separation-mediated granule
      assembly.
    action: MARK_AS_OVER_ANNOTATED
    reason: The protein binding annotation from high-throughput Y2H screening is technically
      correct but uninformative. MEG-4 functions as a scaffold protein for P granule
      assembly through phase separation, and its biologically relevant interactions
      (e.g., with MEG-3) involve molecular condensate scaffold activity. Generic "protein
      binding" does not capture this functional context. The specific interactors
      (atz-1, klc-1) from this screen have not been validated for functional relevance
      to P granule biology.
    supported_by:
    - reference_id: PMID:12445390
      supporting_text: we generated a two-hybrid interactome map of the Caenorhabditis
        elegans germline by using 600 transcripts enriched in this tissue
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:14704431
  review:
    summary: Large-scale worm interactome mapping study identified MEG-4 interaction
      with ikb-1. This is a high-throughput Y2H screen with independent co-affinity
      purification validation.
    action: MARK_AS_OVER_ANNOTATED
    reason: While the Y2H interaction is experimentally supported, the generic "protein
      binding" term lacks functional specificity. MEG-4 is an IDP scaffold protein
      whose meaningful interactions involve condensate assembly. The interaction with
      ikb-1 (IKK binding protein) has not been shown to be relevant to MEG-4's core
      function in P granule biology. A more informative MF annotation would capture
      the molecular condensate scaffold activity.
    supported_by:
    - reference_id: PMID:14704431
      supporting_text: more than 4000 interactions were identified from high-throughput,
        yeast two-hybrid (HT=Y2H) screens
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19123269
  review:
    summary: Empirically controlled C. elegans interactome study (WI-2007) with quality
      control framework showing interaction data similar in quality to low-throughput
      literature-curated data.
    action: MARK_AS_OVER_ANNOTATED
    reason: This annotation comes from a rigorous high-throughput Y2H study with empirical
      quality control. However, "protein binding" remains an uninformative term for
      MEG-4, whose function depends on its ability to scaffold molecular condensates
      through multivalent interactions mediated by its intrinsically disordered regions.
      The annotation does not capture the functional significance of MEG-4's protein
      interactions.
    supported_by:
    - reference_id: PMID:19123269
      supporting_text: the resulting dataset (Worm Interactome 2007 or WI-2007) is
        similar in quality to low-throughput data curated from the literature
- term:
    id: GO:0051640
    label: organelle localization
  evidence_type: IMP
  original_reference_id: PMID:25535836
  review:
    summary: Wang et al. (2014) demonstrated that MEG proteins regulate P granule
      dynamics through phosphorylation-controlled phase separation. MEG-4 functions
      redundantly with MEG-3 in localizing P granules to the posterior of the embryo
      (PMID:25535836).
    action: ACCEPT
    reason: 'This annotation accurately captures MEG-4''s role in P granule localization.
      The Wang et al. study provides direct mutant phenotype evidence that MEG proteins
      are required for proper organelle localization: "MEG (maternal-effect germline
      defective) proteins are germ plasm components that are required redundantly
      for fertility." P granule segregation to the posterior involves MEG-regulated
      condensation/dissolution dynamics controlled by MBK-2/DYRK kinase and PP2A phosphatase.'
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
        dephosphorylation promotes granule assembly
- term:
    id: GO:1903863
    label: P granule assembly
  evidence_type: IGI
  original_reference_id: PMID:25535836
  review:
    summary: MEG-3 and MEG-4 are required together (genetic interaction) for proper
      P granule assembly. The Wang et al. study shows MEGs stabilize the condensed
      phase of P granules through regulated phase separation.
    action: ACCEPT
    reason: This is a core annotation for MEG-4 function. The IGI evidence code is
      appropriate as meg-3 meg-4 double mutants show synergistic defects in P granule
      assembly not seen in single mutants. MEG proteins localize to a dynamic domain
      surrounding P granules and are direct regulators of granule condensation dynamics
      through their intrinsically disordered, serine-rich regions that undergo phosphorylation-dependent
      phase transitions.
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: GFP-tagged MEG-3 localizes to a dynamic domain that surrounds
        and penetrates each granule
    - reference_id: PMID:25535836
      supporting_text: despite their liquid-like behavior, P granules are non-homogeneous
        structures whose assembly in embryos is regulated by phosphorylation
- term:
    id: GO:0036093
    label: germ cell proliferation
  evidence_type: IGI
  original_reference_id: PMID:25535836
  review:
    summary: MEG proteins are required for germ cell viability and proliferation.
      The meg-1 meg-3 meg-4 triple mutant is 100% sterile, indicating MEGs contribute
      redundantly to germline function.
    action: KEEP_AS_NON_CORE
    reason: While MEG-4 is involved in germ cell proliferation, this represents a
      downstream consequence of its primary function in P granule assembly rather
      than a direct mechanistic role in cell proliferation. The sterility phenotype
      of triple mutants reflects failed germline development due to defective P granule
      function. This is a valid annotation but should be considered non-core compared
      to the direct molecular function in granule assembly.
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: The MEG (maternal-effect germline defective) proteins are germ
        plasm components that are required redundantly for fertility
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25535836
  review:
    summary: Wang et al. identified specific protein interactions for MEG-4 in the
      context of P granule biology, including interactions with MEG-3 and phosphoregulators
      MBK-2 and PP2A(PPTR-1/2).
    action: MODIFY
    reason: While the IPI evidence from PMID:25535836 is more functionally relevant
      than the high-throughput Y2H studies (demonstrating interactions with MEG-3
      and kinase/phosphatase regulators), "protein binding" still fails to capture
      MEG-4's molecular function. MEG-4 functions as a scaffold for molecular condensate
      assembly through its intrinsically disordered regions. The term GO:0140693 "molecular
      condensate scaffold activity" would more accurately describe MEG-4's molecular
      function.
    proposed_replacement_terms:
    - id: GO:0140693
      label: molecular condensate scaffold activity
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: we present evidence that a group of intrinsically disordered,
        serine-rich proteins regulate the dynamics of P granules
    - reference_id: PMID:25535836
      supporting_text: "We demonstrate that MEG-1 and MEG-3 are substrates of the\
        \ kinase MBK-2/DYRK and the phosphatase PP2A(PPTR-\xBD)"
- term:
    id: GO:0043186
    label: P granule
  evidence_type: IDA
  original_reference_id: PMID:25535836
  review:
    summary: Direct experimental observation showing MEG-4 localizes to P granules.
      Wang et al. used GFP-tagged MEG proteins and lattice light sheet microscopy
      to demonstrate localization to a dynamic domain surrounding and penetrating
      P granules.
    action: ACCEPT
    reason: This is a well-supported cellular component annotation. IDA evidence from
      imaging studies directly demonstrates MEG-4 localization to P granules. The
      study further characterizes MEG proteins as localizing to a dynamic peripheral
      domain of P granules that regulates condensate assembly/disassembly.
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: GFP-tagged MEG-3 localizes to a dynamic domain that surrounds
        and penetrates each granule
- term:
    id: GO:0140693
    label: molecular condensate scaffold activity
  evidence_type: IDA
  original_reference_id: PMID:25535836
  review:
    summary: MEG-4 is an intrinsically disordered protein that functions as a scaffold
      for P granule condensate assembly. Wang et al. demonstrate that MEG proteins
      regulate granule dynamics through phase separation controlled by phosphorylation.
    action: NEW
    reason: This annotation captures MEG-4's core molecular function as a scaffold
      that promotes the assembly of molecular condensates (P granules) through phase
      separation. MEG-4's long N-terminal intrinsically disordered region with serine-rich,
      polar residue composition (as documented in UniProt features) is characteristic
      of condensate scaffold proteins. The Wang et al. study demonstrates that MEG
      proteins directly regulate P granule condensation/dissolution dynamics through
      phosphorylation-dependent phase transitions.
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: we present evidence that a group of intrinsically disordered,
        serine-rich proteins regulate the dynamics of P granules in C. elegans embryos
    - reference_id: PMID:25535836
      supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
        dephosphorylation promotes granule assembly
- term:
    id: GO:0060293
    label: germ plasm
  evidence_type: IDA
  original_reference_id: PMID:25535836
  review:
    summary: MEG-4 is a germ plasm component that localizes to P granules in the posterior
      cytoplasm of early embryos.
    action: NEW
    reason: MEG-4 is explicitly described as a germ plasm component. The germ plasm
      is the specialized cytoplasm inherited by germline precursor cells, and P granules
      are the defining feature of C. elegans germ plasm. This cellular component annotation
      complements the P granule annotation by placing MEG-4 in the broader context
      of germline specification.
    supported_by:
    - reference_id: PMID:25535836
      supporting_text: The MEG (maternal-effect germline defective) proteins are germ
        plasm components that are required redundantly for fertility
references:
- id: PMID:12445390
  title: Integrating interactome, phenome, and transcriptome mapping data for the
    C. elegans germline.
  findings:
  - statement: MEG-4 identified in germline-enriched Y2H interactome screen
    supporting_text: we generated a two-hybrid interactome map of the Caenorhabditis
      elegans germline by using 600 transcripts enriched in this tissue
  - statement: Interactions detected with atz-1 and klc-1
    supporting_text: we find that essential proteins have a tendency to interact with
      each other
- id: PMID:14704431
  title: A map of the interactome network of the metazoan C. elegans.
  findings:
  - statement: Large-scale Y2H interactome mapping
    supporting_text: more than 4000 interactions were identified from high-throughput,
      yeast two-hybrid (HT=Y2H) screens
  - statement: MEG-4 interaction with ikb-1 identified
    supporting_text: Independent coaffinity purification assays experimentally validated
      the overall quality of this Y2H data set
- id: PMID:19123269
  title: Empirically controlled mapping of the Caenorhabditis elegans protein-protein
    interactome network.
  findings:
  - statement: High-confidence interactome data (WI-2007)
    supporting_text: the resulting dataset (Worm Interactome 2007 or WI-2007) is similar
      in quality to low-throughput data curated from the literature
  - statement: Quality control framework validates Y2H data quality
    supporting_text: Through a new quality control empirical framework
- id: PMID:25535836
  title: Regulation of RNA granule dynamics by phosphorylation of serine-rich, intrinsically
    disordered proteins in C. elegans.
  findings:
  - statement: MEG proteins (MEG-1, MEG-3, MEG-4) are IDPs that regulate P granule
      dynamics
    supporting_text: we present evidence that a group of intrinsically disordered,
      serine-rich proteins regulate the dynamics of P granules in C. elegans embryos
  - statement: MEGs are substrates of MBK-2/DYRK kinase and PP2A phosphatase
    supporting_text: "We demonstrate that MEG-1 and MEG-3 are substrates of the kinase\
      \ MBK-2/DYRK and the phosphatase PP2A(PPTR-\xBD)"
  - statement: Phosphorylation promotes granule disassembly, dephosphorylation promotes
      assembly
    supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
      dephosphorylation promotes granule assembly
  - statement: GFP-MEG-3 localizes to dynamic domain surrounding P granules
    supporting_text: GFP-tagged MEG-3 localizes to a dynamic domain that surrounds
      and penetrates each granule
  - statement: MEG proteins function redundantly for fertility
    supporting_text: The MEG (maternal-effect germline defective) proteins are germ
      plasm components that are required redundantly for fertility
core_functions:
- description: MEG-4 functions as an intrinsically disordered scaffold protein that
    promotes P granule assembly through phase separation. Its long disordered N-terminal
    region with serine-rich, polar residue composition enables multivalent interactions
    required for condensate formation. This is MEG-4's primary molecular function.
  molecular_function:
    id: GO:0140693
    label: molecular condensate scaffold activity
  directly_involved_in:
  - id: GO:1903863
    label: P granule assembly
  locations:
  - id: GO:0043186
    label: P granule
  - id: GO:0060293
    label: germ plasm
  supported_by:
  - reference_id: PMID:25535836
    supporting_text: we present evidence that a group of intrinsically disordered,
      serine-rich proteins regulate the dynamics of P granules in C. elegans embryos
  - reference_id: PMID:25535836
    supporting_text: Phosphorylation of the MEGs promotes granule disassembly and
      dephosphorylation promotes granule assembly
proposed_new_terms: []
suggested_questions:
- question: Does MEG-4 bind RNA directly, or does it primarily function through protein-protein
    interactions?
- question: What is the precise molecular mechanism by which phosphorylation of MEG-4
    promotes granule disassembly?
- question: Are there MEG-4-specific functions that are distinct from MEG-3, or are
    they fully redundant?
suggested_experiments:
- description: In vitro phase separation assays with purified MEG-4 to characterize
    its intrinsic condensation properties
  hypothesis: MEG-4 can undergo liquid-liquid phase separation in vitro dependent
    on protein concentration and phosphorylation state
  experiment_type: biochemical reconstitution
- description: Phosphomimetic and phospho-null mutations in MEG-4 to map critical
    phosphorylation sites for granule dynamics
  hypothesis: Specific serine residues in MEG-4 are required for MBK-2-dependent regulation
    of P granule assembly
  experiment_type: mutagenesis
- description: CLIP-seq to identify direct RNA targets of MEG-4
  hypothesis: MEG-4 directly binds specific mRNA populations that are recruited to
    P granules
  experiment_type: RNA-protein interaction
- description: Cryo-ET of P granules in wild-type vs meg-4 mutants to characterize
    granule ultrastructure
  hypothesis: MEG-4 contributes to the non-homogeneous internal structure of P granules
  experiment_type: structural biology
tags:
- caeel-p-granules