mcm-4

UniProt ID: A0A061AL94
Organism: Caenorhabditis elegans
Review Status: DRAFT
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Gene Description

A0A061AL94 is the 74-residue product predicted from transcript model Y39G10AR.14b of the C. elegans mcm-4 (lin-6) gene. Its sequence is identical to residues 750-823 of the canonical 823-residue MCM-4 protein (Q95XQ8, Y39G10AR.14a) and begins at an internal methionine within the last coding exon, so it consists only of the C-terminal winged-helix region of MCM-4 (Pfam WHD_MCM4). It lacks the N-terminal zinc-finger region and the entire AAA+ ATPase domain, including the Walker A and Walker B motifs, all ATP-binding residues and the arginine finger. The full-length MCM-4 protein is a subunit of the MCM2-7 replicative helicase and is required for DNA replication and the replication checkpoint in C. elegans embryos and postembryonic blast cells. Whether the short Y39G10AR.14b product is translated in vivo, and whether it has any activity of its own, is unknown; the cDNAs and northern analysis that defined the mcm-4 locus identified only the full-length transcript.

Core Functions

No independent molecular function is established for this 74-residue product. It is an N-terminally truncated mcm-4 gene product consisting only of the C-terminal winged-helix region (canonical MCM-4 residues 750-823). It contains neither half of an MCM ATPase site (no Walker A/B motifs, no arginine finger), so it cannot carry or contribute the ATP-dependent helicase activity that the full-length MCM-4 subunit contributes to the MCM2-7/CMG helicase. The replication functions of the mcm-4 gene are properties of the canonical 823-residue protein (Q95XQ8), and are not transferred to this fragment here.

Supporting Evidence:
  • file:CAEEL/A0A061AL94/A0A061AL94-bioinformatics/RESULTS.md
    The fragment is an exact substring of the canonical protein: canonical residues 750-823, 100% identity,
  • file:CAEEL/A0A061AL94/A0A061AL94-bioinformatics/RESULTS.md
    The fragment cannot form either half of an MCM ATPase site (it has neither the Walker A/B cis half nor
  • PMID:21146520
    All cDNAs contained sequences from 7 exons, a 3โ€ฒ poly(A) tract and are predicted to encode the MCM-4 protein of 823 amino acids.

References

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Suggested Questions for Experts

Q: Is the single-exon Y39G10AR.14b model (internal Met750 start in the last coding exon of mcm-4) supported by transcript evidence, and is its 74-residue product translated in vivo, or is it an annotation artefact of the gene model?

Q: If expressed, does the isolated MCM-4 C-terminal winged-helix region associate with the MCM2-7 ring or DNA, and could it act as a dominant-negative or regulatory fragment?

Suggested Experiments

Experiment: Use long-read RNA-seq or 5'-RACE from the mcm-4 3' exon to test for a transcript starting near the Met750 codon, and use targeted proteomics for an N-terminal peptide containing the fragment-specific initiator (acetylated Met-Ser-Ala-Ser-Gly...) to distinguish the fragment from full-length MCM-4.

Hypothesis: The Y39G10AR.14b transcript and its 74-residue product are not produced at detectable levels in vivo.

Type: transcript mapping and targeted mass spectrometry

Experiment: Express tagged full-length MCM-4 and the 74-residue fragment in C. elegans, and test co-immunoprecipitation with other MCM subunits and chromatin association.

Hypothesis: The isolated MCM-4 winged-helix region is not incorporated into MCM2-7 complexes.

Type: co-immunoprecipitation and fluorescence microscopy

External Prediction Reviews

These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.

ProtNLM2 External predictions

View prediction review YAML ยท A0A061AL94-protnlm-predictions-review.yaml ยท Review status: COMPLETE

A0A061AL94 is the 74-residue product of the C. elegans mcm-4 (lin-6) transcript model Y39G10AR.14b. It is identical to residues 750-823 of canonical MCM-4 (Q95XQ8), starts at an internal methionine in the last coding exon, and consists only of the C-terminal winged-helix region (Pfam WHD_MCM4), lacking the zinc finger and the whole AAA+ ATPase domain. The replication, chromatin and nuclear annotations of mcm-4 are carried by the canonical product, and whether this short product is translated in vivo is unknown. ProtNLM2 emitted two GO terms; neither can be confirmed for this fragment.

Source documents: genes/CAEEL/A0A061AL94/A0A061AL94-uniprot.txt ยท genes/CAEEL/A0A061AL94/A0A061AL94-goa.tsv ยท publications/PMID_21146520.md ยท genes/CAEEL/A0A061AL94/A0A061AL94-hypotheses/prediction-transcription-initiation/openscientist.md ยท genes/CAEEL/A0A061AL94/A0A061AL94-bioinformatics/RESULTS.md ยท publications/PMID_10454562.md ยท publications/PMID_12392551.md

Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.

GO:0006367 transcription initiation at RNA polymerase II promoter GO_BP
UNC โ€” Uncertain Review score: 1/2
Prediction method: ProtNLM2 ยท Version: UniProt 2024_06 pilot
Review rationale: No evidence places C. elegans mcm-4, or this 74-residue C-terminal winged-helix fragment of it (canonical MCM-4 residues 750-823), in Pol II transcription initiation. The characterized mcm-4 functions are DNA replication and the replication checkpoint (PMID:21146520), and neither the gene's existing annotations nor its re-reviewed gene record contain a transcription term, so the prediction is novel but unsupported. It is not refuted outright: vertebrate MCM subunits copurify with the Pol II holoenzyme (PMID:10454562), but that association was mapped to an N-terminal segment of MCM2 (residues 168-230; PMID:12392551), it is complex co-purification rather than evidence that MCM-4 performs a step of initiation, and nothing ties it to the MCM4 C-terminal winged-helix region that makes up this product. Whether the fragment is even translated is unknown. The OpenScientist analysis judged the prediction NPI from the replicative-helicase identity of MCM-4; its targeted moonlighting search found no primary evidence for an MCM role in Pol II transcription and did not retrieve the holoenzyme co-purification reports (PMID:10454562, PMID:12392551), which leave the term unsupported rather than refuted.
Supporting Evidence:
GO:0005634 nucleus GO_CC
UNC โ€” Uncertain Review score: 1/2
Prediction method: ProtNLM2 ยท Version: UniProt 2024_06 pilot
Review rationale: Nucleus is not novel at the gene level: the canonical mcm-4 product Q95XQ8 carries GO:0005634 by IDA from PMID:21146520, where MCM-4::mCherry was nuclear and associated with chromatin from late anaphase, and GOA keeps the gene's annotations on that representative product. Correctness for this accession is unresolved. A0A061AL94 is only the C-terminal winged-helix region (canonical residues 750-823) from an internal-start gene model, its translation in vivo has not been shown, and the gene review deliberately does not transfer full-length MCM-4 localization or replication functions to it. The prediction therefore agrees with the gene's annotation but lacks support for the deposited sequence itself.
Supporting Evidence:

Deep Research

Falcon

(A0A061AL94-deep-research-falcon.md)

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OpenScientist

(A0A061AL94-hypotheses/prediction-transcription-initiation/openscientist.md)

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๐Ÿ“š Additional Documentation

Notes

(A0A061AL94-notes.md)

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Bioinformatics Results

(RESULTS.md)

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๐Ÿ“„ View Raw YAML

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