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. Falcon deep research confirms MEG-4 (~71% identical to MEG-3, ~69% predicted disorder) is specifically required for cytoplasmic (embryonic) P granule assembly but not perinuclear germ granules, which reappear later (L1/L4), indicating a stage-specific requirement; in meg-3 meg-4 zygotes total P granules drop to ~11% of wild-type and nos-2 mRNA segregates symmetrically. The UniProt name "J domain-containing protein" is not supported by the primary literature, which describes MEG-4 as an intrinsically disordered MEG-family germ-plasm protein with no Hsp40/J-domain co-chaperone activity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005515 protein binding | IPI PMID:12445390 Integrating interactome, phenome, and transcriptome mapping ... | MARK AS OVER ANNOTATED | 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. 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. Supporting Evidence: PMID:12445390 we generated a two-hybrid interactome map of the Caenorhabditis elegans germline by using 600 transcripts enriched in this tissue |
| GO:0005515 protein binding | IPI PMID:14704431 A map of the interactome network of the metazoan C. elegans. | MARK AS OVER ANNOTATED | 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. 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. Supporting Evidence: PMID:14704431 more than 4000 interactions were identified from high-throughput, yeast two-hybrid (HT=Y2H) screens |
| GO:0005515 protein binding | IPI PMID:19123269 Empirically controlled mapping of the Caenorhabditis elegans... | MARK AS OVER ANNOTATED | 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. 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. Supporting Evidence: PMID:19123269 the resulting dataset (Worm Interactome 2007 or WI-2007) is similar in quality to low-throughput data curated from the literature |
| GO:0051640 organelle localization | IMP PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser... | ACCEPT | 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). 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. Supporting Evidence: PMID:25535836 Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly file:worm/meg-4/meg-4-deep-research-falcon.md MEG-4 is maternally provided and associates with embryonic P granules from the **1-cell through ~100-cell stage**, segregating with the P lineage. |
| GO:1903863 P granule assembly | IGI PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser... | ACCEPT | 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. 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. Supporting Evidence: PMID:25535836 GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule PMID:25535836 despite their liquid-like behavior, P granules are non-homogeneous structures whose assembly in embryos is regulated by phosphorylation file:worm/meg-4/meg-4-deep-research-falcon.md total P granules in meg-3 meg-4 zygotes are reduced to **~11% of wild-type**. file:worm/meg-4/meg-4-deep-research-falcon.md MEG-3 and MEG-4 are reported as **~71% identical** and functionally redundant in embryonic P granule assembly. |
| GO:0036093 germ cell proliferation | IGI PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser... | KEEP AS NON CORE | 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. 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. Supporting Evidence: PMID:25535836 The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility file:worm/meg-4/meg-4-deep-research-falcon.md **meg-1 meg-3 meg-4** animals are reported as **100% sterile**, with larvae exhibiting **<10 germ cells** and failure of germ cell proliferation. |
| GO:0005515 protein binding | IPI PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser... | MODIFY | 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). 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 replacements: molecular condensate scaffold activity Supporting Evidence: PMID:25535836 we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules PMID:25535836 We demonstrate that MEG-1 and MEG-3 are substrates of the kinase MBK-2/DYRK and the phosphatase PP2A(PPTR-½) file:worm/meg-4/meg-4-deep-research-falcon.md MEG-4 is described as a large, serine/threonine-rich protein with extensive predicted disorder and low-complexity regions, consistent with roles as a condensate scaffold/regulator. |
| GO:0043186 P granule | IDA PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser... | ACCEPT | 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. 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. Supporting Evidence: PMID:25535836 GFP-tagged MEG-3 localizes to a dynamic domain that surrounds and penetrates each granule file:worm/meg-4/meg-4-deep-research-falcon.md A study reports experimental tagging of MEG-4 using **C-terminal 3×FLAG** via CRISPR for localization, supporting that MEG-4 itself is present in embryonic germ plasm granules. |
| GO:0140693 molecular condensate scaffold activity | IDA PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser... | NEW | 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. 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. Supporting Evidence: PMID:25535836 we present evidence that a group of intrinsically disordered, serine-rich proteins regulate the dynamics of P granules in C. elegans embryos PMID:25535836 Phosphorylation of the MEGs promotes granule disassembly and dephosphorylation promotes granule assembly file:worm/meg-4/meg-4-deep-research-falcon.md MEG-4 is predicted to be largely disordered (**~69% predicted disorder; 570/832 aa**) |
| GO:0060293 germ plasm | IDA PMID:25535836 Regulation of RNA granule dynamics by phosphorylation of ser... | NEW | Summary: MEG-4 is a germ plasm component that localizes to P granules in the posterior cytoplasm of early embryos. 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. Supporting Evidence: PMID:25535836 The MEG (maternal-effect germline defective) proteins are germ plasm components that are required redundantly for fertility file:worm/meg-4/meg-4-deep-research-falcon.md acts **redundantly with its close paralog MEG-3** to drive **cytoplasmic (embryonic) P granule assembly** |
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Download this section (compressed HTML)Q: Does MEG-4 bind RNA directly, or does it primarily function through protein-protein interactions?
Q: What is the precise molecular mechanism by which phosphorylation of MEG-4 promotes granule disassembly?
Q: Are there MEG-4-specific functions that are distinct from MEG-3, or are they fully redundant?
Experiment: 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
Type: biochemical reconstitution
Experiment: 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
Type: mutagenesis
Experiment: CLIP-seq to identify direct RNA targets of MEG-4
Hypothesis: MEG-4 directly binds specific mRNA populations that are recruited to P granules
Type: RNA-protein interaction
Experiment: 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
Type: structural biology
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