MEX-6 is a tandem CCCH zinc-finger RNA-binding protein that works partly redundantly with MEX-5 to establish cytoplasmic soma/germline asymmetry in early Caenorhabditis elegans embryos. Purified MEX-6 binds an AU-rich mRNA 3′-UTR element. The MEX-5/6 pair regulates maternal RNA expression in a target-dependent manner, including promotion of zif-1 expression and repression of mom-2 translation, and contributes to maternal RNA turnover. MEX-6 binds Polo-like kinases and helps establish asymmetric protein localization downstream of cortical PAR polarity. It is cytoplasmic, becomes anterior-enriched in early embryos, and tagged MEX-6 is also observed on granules in germline blastomeres.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0035925 mRNA 3'-UTR AU-rich region binding | IBA GO_REF:0000033 | ACCEPT | Summary: MEX-6 binds an AU-rich 3′-UTR substrate directly in purified-protein assays. Reason: The exact target inherits the positive PTN002648882 assertion and PMID:17264081 directly assays both paralogs against TNF-ARE. Preference for U-rich RNA with less discrimination than TTP is compatible with AU-rich region binding; the term does not require exclusive recognition of a canonical ARE. Supporting Evidence: file:worm/mex-5/mex-5-primary-evidence.md Both methods reveal that MEX-5 and MEX-6 bind to TNF-ARE RNA. file:worm/mex-6/mex-6-paint-lineage.md Both MEX-5 and MEX-6 descend from PTN002648882, which supplies the five source IBAs |
| GO:0000289 nuclear-transcribed mRNA poly(A) tail shortening | IBA GO_REF:0000033 | ACCEPT | Summary: MEX-6 retains the phylogenetically inferred contribution to mRNA poly(A) tail shortening. Reason: Actual descent from positive IBD PTN002648882 is verified. MEX-5/6-dependent maternal RNA turnover and recruitment of P-body decay machinery are biologically consistent with the transfer. Tail hydrolysis is performed by deadenylases; an RNA-binding adaptor may participate without being catalytic. These target observations do not by themselves measure tail shortening, but no target-specific loss contradicts the ancestral process assertion. Supporting Evidence: file:worm/mex-6/mex-6-paint-lineage.md Both MEX-5 and MEX-6 descend from PTN002648882, which supplies the five source IBAs file:worm/mex-6/mex-6-deep-research-falcon.md In embryos depleted of MEX-5/6, LSM-1 is not recruited to P bodies and maternal mRNAs remain stabilized, indicating that MEX-5/6 promote maternal mRNA turnover in somatic blastomeres |
| GO:0000900 mRNA regulatory element binding translation repressor activity | IBA GO_REF:0000033 | ACCEPT | Summary: MEX-6 participates in repression of maternal mom-2 translation. Reason: The positive repressor IBD at PTN002648882 agrees with maternal Wnt 3′-UTR experiments. MEX-5 is directly tested in RNA binding, while combined MEX-5/6 depletion establishes the pair-level repression phenotype. MEX-6 retains inherited activity with that experimental scope. Relief of POS-1 repression on zif-1 is target-dependent positive regulation and does not negate repression of mom-2. Supporting Evidence: file:worm/mex-5/mex-5-primary-evidence.md The contrary is true for mom-2, where POS-1 promotes translation in P2 and MEX-5/6 represses translation in EMS. file:worm/mex-6/mex-6-paint-lineage.md Both MEX-5 and MEX-6 descend from PTN002648882, which supplies the five source IBAs |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: MEX-6 is a cytoplasmic protein (UniProt SUBCELLULAR LOCATION Cytoplasm), imaged as a cytoplasmic GFP fusion in the early embryo (PMID:12588843) and consistent with the experimental IDA cytoplasm annotation. Cytosol is an appropriate active-location term for this non-membrane RNA-binding protein. Reason: MEX-6 acts in the cytoplasm/cytosol of the zygote, where it forms an anterior-enriched pool and regulates cytoplasmic determinant asymmetry. Consistent with both experimental imaging and the phylogenetic inference. Supporting Evidence: PMID:12588843 The kinase PAR-1 and the CCCH finger proteins MEX-5 and MEX-6 also function during the establishment phase in a feedback loop to regulate growth of the posterior domain. |
| GO:0160134 protein-RNA sequence-specific adaptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: MEX-6 retains inherited sequence-selective protein-RNA adaptor activity. Reason: The target descends from positive IBD PTN002648882. U-rich recognition is sequence preference even though many transcripts contain the motif and specificity is lower than TTP. The conserved RNA-binding module and protein interactions support adaptor function; lack of exclusive transcript recognition is not a biological refutation. Supporting Evidence: file:worm/mex-5/mex-5-primary-evidence.md Both methods reveal that MEX-5 and MEX-6 bind to TNF-ARE RNA. file:worm/mex-6/mex-6-paint-lineage.md Both MEX-5 and MEX-6 descend from PTN002648882, which supplies the five source IBAs PMID:18199581 We show that polo kinases, via their polo box domains, bind to and regulate the activity of two key polarity proteins, MEX-5 and MEX-6. |
| GO:0003729 mRNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: MEX-6 contains two tandem C3H1-type CCCH zinc fingers (UniProt ZN_FING 273-302, 317-347; InterPro IPR045877 ZFP36-like, IPR000571 CCCH), the RNA-binding module of the TTP/TZF family. mRNA binding is a core molecular function, independently supported by the experimental IDA for mRNA 3'-UTR binding (PMID:17264081, curated for mex-6). Reason: mRNA binding is well supported for this gene by domain architecture and by the curated experimental 3'-UTR-binding annotation. Core molecular function. Supporting Evidence: PMID:17264081 This sequence is remarkably abundant in the 3'-untranslated region of C. elegans transcripts |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Cytoplasmic localization inferred from the UniProt Swiss-Prot subcellular location. Consistent with the experimental IDA cytoplasm annotation (PMID:12588843) and UniProt SUBCELLULAR LOCATION Cytoplasm. Reason: MEX-6 is a cytoplasmic protein; this location is corroborated by direct imaging in the early embryo. Correct, if generic relative to the anterior-enriched cytoplasmic pool. Supporting Evidence: PMID:12588843 we have analyzed the localization dynamics of PAR-2, PAR-6, MEX-5, MEX-6 and PIE-1 in wild-type and mutant embryos |
| GO:0017148 negative regulation of translation | IEA GO_REF:0000108 | ACCEPT | Summary: MEX-6 contributes to negative regulation of maternal mom-2 translation. Reason: The electronic inference is consistent with the retained translation-repressor function and primary 3′-UTR regulatory experiments. Positive zif-1 regulation does not exclude a negative effect on another RNA; the MEX-6 functional evidence is paired depletion plus conserved ancestral inference. Supporting Evidence: file:worm/mex-5/mex-5-primary-evidence.md The contrary is true for mom-2, where POS-1 promotes translation in P2 and MEX-5/6 represses translation in EMS. |
| GO:0043186 P granule | IEA GO_REF:0000117 | ACCEPT | Summary: MEX-6 is observed on granules in germline blastomeres. Reason: PMID:12588843 explicitly reports the GFP-tagged target on granules. The early anterior cytoplasmic gradient, granule dissolution activity and later germline granule pool are compatible. Cellular-component membership does not require a permanent structural scaffold. Supporting Evidence: file:worm/mex-5/mex-5-primary-evidence.md PIE-1:GFP, GFP:MEX-5 and GFP:MEX-6 all accumulated on granules in germline blastomeres. |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: MEX-6 has two C3H1-type CCCH zinc fingers that each coordinate a zinc ion, the structural basis of its RNA-binding fold (UniProt ZN_FING; InterPro CCCH signatures). Metal ion binding is a correct, if generic, annotation. Reason: Zinc coordination is intrinsic to the CCCH zinc-finger fold of MEX-6. Correct though non-specific; zinc ion binding (GO:0008270) would be the more precise term. |
| GO:0005737 cytoplasm | ISS GO_REF:0000024 | ACCEPT | Summary: Cytoplasmic localization transferred by sequence similarity from the paralog MEX-5 (UniProtKB:Q9XUB2). This ortholog/paralog transfer is consistent with the independent experimental IDA (PMID:12588843) and with UniProt's Cytoplasm assignment. Reason: The cytoplasm location is correct for MEX-6 and is corroborated by direct experimental evidence, so the ISS transfer from MEX-5 is appropriate. Supporting Evidence: PMID:12588843 we have analyzed the localization dynamics of PAR-2, PAR-6, MEX-5, MEX-6 and PIE-1 in wild-type and mutant embryos |
| GO:0019901 protein kinase binding | IPI PMID:18199581 Polo kinases regulate C. elegans embryonic polarity via bind... | ACCEPT | Summary: PMID:18199581 demonstrates that the Polo-like kinases PLK-1 and PLK-2 bind directly to MEX-6 (named explicitly) via their polo-box domains, dependent on MBK-2/DYRK2-primed phosphorylation of the polo-docking threonine (Thr-190 in MEX-6; UniProt MOD_RES 190, MUTAGEN T190A/T190E abolish PLK binding). Curated by WormBase with plk-1 (WBGene00004042) and plk-2 (WBGene00004043) as interactors. Reason: Direct experimental protein-kinase-binding evidence naming MEX-6; functionally important for embryonic polarity. Core interaction. Supporting Evidence: PMID:18199581 We show that polo kinases, via their polo box domains, bind to and regulate the activity of two key polarity proteins, MEX-5 and MEX-6. |
| GO:0019904 protein domain specific binding | IPI PMID:18199581 Polo kinases regulate C. elegans embryonic polarity via bind... | ACCEPT | Summary: MEX-6 binds specifically to the polo-box domains of PLK-1 and PLK-2 (a phosphopeptide-docking domain), a bona fide domain-specific protein interaction (PMID:18199581), primed by MBK-2 phosphorylation at Thr-190. Reason: The interaction is with a defined protein domain (the polo-box domain), directly demonstrated for MEX-6. Supports protein domain specific binding. Supporting Evidence: PMID:18199581 We show that polo kinases, via their polo box domains, bind to and regulate the activity of two key polarity proteins, MEX-5 and MEX-6. |
| GO:0032880 regulation of protein localization | IGI PMID:18199581 Polo kinases regulate C. elegans embryonic polarity via bind... | ACCEPT | Summary: MEX-6, redundantly with MEX-5 (genetic interaction; WormBase with = mex-5 WBGene00003230), is required for the asymmetric localization of downstream determinants. Removing MEX-5 and MEX-6 disrupts asymmetric distribution of PLK-1 (and PIE-1, MEX-1, POS-1); UniProt DISRUPTION PHENOTYPE notes that mex-6 RNAi in a mex-5(zu199) background causes loss of plk-1 asymmetry (PMID:18199581). The polo kinases' asymmetric localization depends on MEX-5 and MEX-6. Reason: Regulation of the asymmetric localization of germline/polarity determinants is a core, experimentally supported biological process for the MEX-5/MEX-6 pair, with the genetic-interaction evidence specifically implicating mex-6 in a mex-5-sensitized background. Supporting Evidence: PMID:18199581 This asymmetric localization of polo kinases depends on MEX-5 and MEX-6, as well as genes regulating MEX-5 and MEX-6 asymmetry. |
| GO:0005737 cytoplasm | IDA PMID:12588843 Polarization of the C. elegans zygote proceeds via distinct ... | ACCEPT | Summary: Direct experimental (IDA, WormBase) cytoplasmic localization of MEX-6, imaged as a GFP fusion during zygote polarization (PMID:12588843). This is the primary-evidence cytoplasm annotation. Reason: Direct observation of cytoplasmic MEX-6 in the early embryo; the core cellular location of the protein. Supporting Evidence: PMID:12588843 we have analyzed the localization dynamics of PAR-2, PAR-6, MEX-5, MEX-6 and PIE-1 in wild-type and mutant embryos |
| GO:0043186 P granule | IDA PMID:12588843 Polarization of the C. elegans zygote proceeds via distinct ... | ACCEPT | Summary: MEX-6 is observed on granules in germline blastomeres. Reason: PMID:12588843 explicitly reports the GFP-tagged target on granules. The early anterior cytoplasmic gradient, granule dissolution activity and later germline granule pool are compatible. Cellular-component membership does not require a permanent structural scaffold. Supporting Evidence: file:worm/mex-5/mex-5-primary-evidence.md PIE-1:GFP, GFP:MEX-5 and GFP:MEX-6 all accumulated on granules in germline blastomeres. |
| GO:0003730 mRNA 3'-UTR binding | IDA PMID:17264081 Molecular basis of RNA recognition by the embryonic polarity... | ACCEPT | Summary: MEX-6 directly binds a TNF-alpha mRNA 3′-UTR AU-rich substrate. Reason: The full Results indexed for PMID:17264081 explicitly assay MEX-6 as well as MEX-5. The earlier abstract-based suggestion that MEX-6 activity was unverified is superseded by the target-specific EMSA and fluorescence-polarization evidence. Supporting Evidence: file:worm/mex-5/mex-5-primary-evidence.md Both methods reveal that MEX-5 and MEX-6 bind to TNF-ARE RNA. |
| GO:0008595 anterior/posterior axis specification, embryo | IMP PMID:10882103 MEX-5 and MEX-6 function to establish soma/germline asymmetr... | NEW | Summary: MEX-6, redundantly with MEX-5, links cortical PAR polarity to soma/germline asymmetry along the anterior-posterior axis of the early embryo (PMID:10882103, PMID:12588843). This biological process is not present in the current GOA for mex-6 but is a core role of the MEX-5/MEX-6 pair. Reason: Retain the existing proposal because the RNA-binding polarity regulators help execute spatial patterning of maternal determinants, not merely serve as a necessary substrate. PMID:10882103 establishes the link from PAR asymmetry to downstream protein asymmetry, and PMID:18199581 shows functional kinase recruitment. This axis-patterning process is distinct from the existing molecular binding and protein-localization terms. Supporting Evidence: PMID:10882103 We provide evidence that two nearly identical genes, mex-5 and mex-6, link PAR asymmetry to those subsequent protein asymmetries. PMID:12588843 Polarization of the C. elegans zygote along the anterior-posterior axis depends on cortically enriched (PAR) and cytoplasmic (MEX-5/6) proteins |
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Download this section (compressed HTML)Q: Which RNA targets or developmental contexts distinguish MEX-6 from MEX-5 despite their overlapping RNA binding and polarity functions?
Q: Which target RNAs and effector complexes mediate MEX-6 contributions to inherited poly(A)-tail shortening and translation repression?
Experiment: Perform iCLIP/CLIP-seq on endogenously tagged MEX-6 in early embryos to define its direct mRNA targets genome-wide and compare them to MEX-5 targets, testing whether MEX-6 has any private target repertoire.
Hypothesis: MEX-6 binds essentially the same poly-U-rich 3'-UTR set as MEX-5, consistent with full functional redundancy.
Experiment: Generate RNA-binding-deficient MEX-6 zinc-finger mutants at the endogenous locus in a mex-5 null background and assay embryonic viability and PLK-1/PIE-1 asymmetry, to test whether MEX-6 RNA binding is required for its polarity function.
Hypothesis: MEX-6 RNA binding is required for anterior enrichment and for establishing determinant asymmetry when MEX-5 is absent.
Experiment: Live-image endogenously tagged MEX-6 together with a P-granule marker (e.g. PGL-1) to determine whether the curated P-granule signal reflects stable residence or transient association, and whether MEX-6 promotes anterior P-granule dissolution as reported for MEX-5.
Hypothesis: MEX-6 is anterior-enriched and only transiently overlaps P granules, mirroring the P-granule-antagonizing behaviour of MEX-5.
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The non-redundant, MEX-6-specific contribution to embryonic polarity is undefined. It is unknown whether MEX-6 has any private target mRNA, tissue, developmental timing, or molecular activity distinct from its near-identical paralog MEX-5, or whether it is a functionally interchangeable backup copy.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: It is firmly established that mex-5 and mex-6 are nearly identical genes that act together to link PAR asymmetry to downstream determinant asymmetries, and that the mex-6 contribution is exposed genetically only in a mex-5-sensitized background (mex-6 RNAi in mex-5(zu199) causes loss of PLK-1 asymmetry). MEX-5 is consistently the dominant, better-characterized paralog.
Significance: Distinguishing genuine redundancy from division of labor is central to understanding the robustness of the soma/germline decision and whether MEX-6 is a dispensable paralog or a buffer with its own regulatory inputs.
What would resolve it: Endogenous single- and double-null comparisons with quantitative determinant readouts, plus paralog-specific CLIP-seq, to test for any MEX-6-only target or phenotype.
Provenance (the field's own admissions):
Gap: The direct mRNA targets of MEX-6 and its RNA-binding specificity have not been determined for MEX-6 itself. All biochemical RNA-recognition data (poly-U tract, high affinity, low specificity, discriminator residue) come from the paralog MEX-5.
OPEN BIOLOGY MF_DARK
What is known: MEX-6 has two tandem C3H1-type CCCH zinc fingers of the TTP/ZFP36 family and a curated experimental mRNA 3'-UTR-binding activity, so it is an mRNA-binding protein; but no MEX-6-specific binding constants, motif, or target set are published, and even for MEX-5 the field notes that its binding cannot by itself specify target selection.
Significance: Without direct MEX-6 targets it is impossible to assign a specific molecular mechanism (repression, competition, stabilization) to the polarity phenotype, leaving MEX-6 mechanistically dark despite a well-defined developmental role.
What would resolve it: MEX-6-specific in vitro binding measurements and in vivo CLIP-seq to define the motif preference and target set directly.
Provenance (the field's own admissions):
Gap: Whether MEX-6 RNA binding is required for its function in anterior-posterior polarity is untested for MEX-6. It is unknown whether zinc-finger/RNA-binding-dead MEX-6 can still form an anterior gradient, dock PLK-1/PLK-2, and support determinant asymmetry when MEX-5 is absent.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: The polo-docking arm of MEX-6 function is well mapped (MBK-2-primed Thr-190, polo-box binding, requirement for PLK-1/PLK-2 asymmetry), and the RNA-binding-to-polarity link has been argued for MEX-5; but no separation-of-function RNA-binding mutant of MEX-6 has been assayed in vivo.
Significance: This determines whether MEX-6's essential activity is RNA-binding, a protein-scaffold (polo-adaptor) role, or both, and therefore which molecular function should anchor its polarity annotation.
What would resolve it: Endogenous RNA-binding-deficient MEX-6 zinc-finger mutants assayed in a mex-5 null background for gradient formation, PLK-1 docking, and determinant asymmetry.
Provenance (the field's own admissions):
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Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)Actual PANTHER treeinfo POST response for PTHR12547 was traversed to the exact
accession-mapped target leaf. The extracted path, original positive IBD/IBA rows,
response size and SHA-256 are preserved in mex-6-paint-lineage.json.
Both MEX-5 and MEX-6 descend from PTN002648882, which supplies the five source IBAs
for AU-rich 3′-UTR binding, poly(A) tail shortening, translation repressor activity,
cytosol and protein-RNA sequence-specific adaptor activity. No target-lineage loss
was identified. Low specificity relative to TTP does not contradict preferential
recognition of U-rich RNA. Target inclusion among descendant evidence is legitimate,
not circular support. The paired paralogs have separate leaves and share this node.
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