MCM-4 is the Caenorhabditis elegans ortholog of MCM4, a subunit of the heterohexameric MCM2-7 complex that functions as the core of the eukaryotic replicative DNA helicase. As part of the pre-replication complex (pre-RC), MCM2-7 is loaded onto replication origins during late mitosis and G1 to license them for replication; at the onset of S phase it is activated and, together with CDC45 and the GINS complex, forms the CMG helicase that unwinds template DNA at replication forks. The protein contains a conserved MCM AAA+ ATPase module, and the six ATPase active sites of the ring are built in trans from interfaces of neighboring subunits, so helicase and ATPase activities are properties of the assembled complex rather than any single subunit. In C. elegans, mcm-4 (also known as lin-6 and let-358) is required for postembryonic somatic DNA synthesis and for the replication checkpoint that couples mitotic entry to completion of S phase. The protein is expressed in all dividing cells during embryonic and postembryonic development and associates with chromatin in late anaphase. Loss of mcm-4 blocks DNA replication in postembryonic somatic lineages while mitosis still initiates, causing pleiotropic cell-lineage defects; expression of MCM-4 in the epidermis (hypodermis) is sufficient to rescue the associated growth retardation and lethality.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0042555 MCM complex | IBA GO_REF:0000033 | ACCEPT | Summary: MCM-4 is a subunit of the heterohexameric MCM2-7 (MCM) complex. This is the defining cellular component for the protein and is strongly supported phylogenetically (the IBA is propagated across MCM2-7 orthologs from yeast to mammals) and by direct C. elegans evidence. Reason: Core, well-established localization. MCM-4 is an integral subunit of the MCM2-7 pre-RC / replicative helicase complex, supported by orthology and by direct study in C. elegans. Supporting Evidence: PMID:21146520 lin-6 corresponds to mcm-4 and encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex. |
| GO:0003697 single-stranded DNA binding | IBA GO_REF:0000033 | ACCEPT | Summary: As a subunit of the MCM2-7 replicative helicase, MCM-4 contributes to binding and translocation along single-stranded DNA during origin unwinding and fork progression. ssDNA binding is a conserved property of the MCM ring. Reason: Conserved molecular function of MCM subunits within the helicase ring; consistent with the replicative helicase role established for C. elegans MCM-4. The activity is a property of the assembled complex, but the enables qualifier at the subunit level reflects standard MCM annotation practice. Supporting Evidence: PMID:21146520 encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex |
| GO:0017116 single-stranded DNA helicase activity | IBA GO_REF:0000033 | ACCEPT | Summary: MCM-4 contributes to the ssDNA-translocating helicase activity of the MCM2-7 / CMG complex that unwinds template DNA at replication forks. The contributes_to qualifier correctly reflects that helicase activity is a property of the assembled hexamer, not the isolated subunit. Reason: Conserved replicative helicase function, supported by orthology and by the C. elegans demonstration that MCM-4 is a component of the replicative helicase complex. The contributes_to qualifier is appropriate for a single MCM subunit. Supporting Evidence: PMID:31283754 is the DNA helicase complex responsible for unwinding the DNA at the origins of replication file:worm/mcm-4/mcm-4-deep-research-falcon.md MCM proteins carry ATP-binding motifs and are attributed ATPase and helicase activities, with ATP hydrolysis within the MCM ring driving DNA translocation and unwinding in CMG. |
| GO:0006271 DNA strand elongation involved in DNA replication | IBA GO_REF:0000033 | ACCEPT | Summary: The MCM2-7/CMG helicase unwinds DNA ahead of the replication fork during elongation, and MCM-4 is required for DNA synthesis in C. elegans somatic lineages. This process annotation is consistent with the replicative helicase role. Reason: Strand elongation requires continued fork unwinding by the MCM2-7 helicase; well supported by orthology and by the requirement of mcm-4 for postembryonic DNA synthesis. Supporting Evidence: PMID:21146520 C. elegans lin-6 mutants lack DNA synthesis in postembryonic somatic cell lineages, while entry into mitosis continues |
| GO:1902975 mitotic DNA replication initiation | IBA GO_REF:0000033 | ACCEPT | Summary: MCM2-7 licensing of origins is the central event in initiation of mitotic (S-phase) DNA replication, and MCM-4 is required for this process. The term captures the licensing/initiation role of the complex in the mitotic cell cycle. Reason: Replication licensing by MCM2-7 is required for initiation of mitotic DNA replication; supported by orthology and by the C. elegans replication defect on loss of mcm-4. Supporting Evidence: PMID:21146520 Our results support a conserved function of mcm-4 in replication licensing, DNA synthesis and the replication checkpoint |
| GO:0000727 double-strand break repair via break-induced replication | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: This IBA propagates a break-induced replication (BIR) role across the MCM family. BIR uses the replicative helicase to copy DNA from a broken end, so MCM involvement is mechanistically plausible, but there is no direct C. elegans evidence that MCM-4 functions specifically in BIR, and this is a narrow, specialized repair pathway relative to the core replication role. Reason: BIR is a specialized DNA double-strand break repair pathway; while the replicative helicase can be co-opted for BIR, this phylogenetically-propagated term over-specifies the role of MCM-4 in C. elegans, where the documented functions are bulk DNA replication and the replication checkpoint. No organism-specific evidence supports a dedicated BIR function. Retain as a recognized but non-core/over-annotated process rather than a core function. Supporting Evidence: PMID:21146520 Our results support a conserved function of mcm-4 in replication licensing, DNA synthesis and the replication checkpoint |
| GO:0003677 DNA binding | IEA GO_REF:0000002 | ACCEPT | Summary: MCM-4 binds DNA as part of the MCM2-7 helicase ring that encircles and translocates along DNA. This InterPro2GO electronic annotation is broad but correct. Reason: DNA binding is a general, correct parent term for the MCM helicase. The more specific single-stranded DNA binding annotation is also present; the broader IEA is acceptable. Supporting Evidence: PMID:31283754 MCM-4 is a component of the minichromosome maintenance complex which is responsible for licensing origins for DNA replication |
| GO:0003678 DNA helicase activity | IEA GO_REF:0000120 | ACCEPT | Summary: MCM-4 is part of the MCM2-7/CMG replicative DNA helicase. This is a core molecular function, correctly captured by this electronic annotation (and mirrored by ISS and IBA annotations to the more specific ssDNA helicase term). Reason: Correct core function for an MCM subunit; the activity is a property of the assembled complex but DNA helicase activity is the standard MF annotation for MCM proteins. Supporting Evidence: PMID:31283754 is the DNA helicase complex responsible for unwinding the DNA at the origins of replication file:worm/mcm-4/mcm-4-deep-research-falcon.md an MCM4/6/7 subcomplex exhibits intrinsic ssDNA-dependent ATP hydrolysis |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: MCM-4 contains a conserved MCM AAA+ ATPase module (Walker A/B motifs) that binds ATP; ATP binding and hydrolysis power the MCM2-7 helicase. The UniProt record annotates EC 3.6.4.12 ATP-dependent DNA helicase activity by similarity. This electronic annotation is correct. Reason: Direct consequence of the conserved AAA+ ATPase domain; ATP binding is a standard, well-supported molecular function for MCM subunits. Supporting Evidence: PMID:31283754 is the DNA helicase complex responsible for unwinding the DNA at the origins of replication |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: MCM-4 acts on nuclear chromatin during DNA replication and is detected in the nucleus / on chromatin in dividing cells. Nuclear localization is consistent with its function and is also directly supported (IDA). Reason: Correct subcellular localization, corroborated by direct C. elegans evidence (IDA, PMID:21146520) showing chromatin/nuclear association in dividing cells. Supporting Evidence: PMID:21146520 The MCM-4 protein is expressed in all dividing cells during embryonic and postembryonic development and associates with chromatin in late anaphase |
| GO:0005694 chromosome | IEA GO_REF:0000044 | ACCEPT | Summary: MCM-4 associates with chromatin/chromosomes as part of the pre-RC and replisome. This electronic annotation is corroborated by direct experimental evidence of chromatin association in late anaphase. Reason: Correct localization; MCM2-7 is loaded onto origins on chromosomes and MCM-4 is observed associating with chromatin (EXP/IDA, PMID:21146520). Supporting Evidence: PMID:21146520 associates with chromatin in late anaphase |
| GO:0006260 DNA replication | IEA GO_REF:0000002 | ACCEPT | Summary: A core biological process for MCM-4, which is required for DNA replication as a subunit of the replicative helicase. Directly supported by the C. elegans loss-of-function replication defect. Reason: Central, well-established function; mcm-4 mutants fail postembryonic DNA synthesis. Supporting Evidence: PMID:21146520 lin-6 mutants lack DNA synthesis in postembryonic somatic cell lineages |
| GO:0006270 DNA replication initiation | IEA GO_REF:0000002 | ACCEPT | Summary: MCM2-7 licensing/loading at origins is required for replication initiation, and MCM-4 is part of this process. Consistent with the conserved licensing role demonstrated for C. elegans mcm-4. Reason: Correct process annotation for an MCM subunit acting in origin licensing and initiation. Supporting Evidence: PMID:21146520 Our results support a conserved function of mcm-4 in replication licensing, DNA synthesis and the replication checkpoint |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000116 | ACCEPT | Summary: The MCM AAA+ module hydrolyzes ATP to drive DNA translocation/unwinding by the MCM2-7 ring. This Rhea-mapped electronic annotation is correct; ATP hydrolysis powers the replicative helicase. Reason: Direct consequence of the conserved ATPase domain; ATP hydrolysis powers the MCM2-7/CMG helicase that unwinds origin DNA. Supporting Evidence: PMID:31283754 is the DNA helicase complex responsible for unwinding the DNA at the origins of replication file:worm/mcm-4/mcm-4-deep-research-falcon.md MCM proteins carry ATP-binding motifs and are attributed ATPase and helicase activities, with ATP hydrolysis within the MCM ring driving DNA translocation and unwinding in CMG. |
| GO:0042555 MCM complex | IEA GO_REF:0000002 | ACCEPT | Summary: Electronic (InterPro2GO) annotation to the MCM complex, duplicating the well-supported IBA/NAS/ISS annotations to the same component. Correct. Reason: Correct core localization; redundant with the experimentally and phylogenetically supported MCM complex annotations. Supporting Evidence: PMID:21146520 encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex |
| GO:0005694 chromosome | EXP PMID:21146520 C. elegans MCM-4 is a general DNA replication and checkpoint... | ACCEPT | Summary: Direct experimental evidence that MCM-4 associates with chromatin (chromosomes) in dividing C. elegans cells, observed in late anaphase. This is the experimental basis for the chromosome localization. Reason: Strong direct evidence from the primary functional paper; MCM-4 is chromatin/chromosome-associated as expected for a pre-RC subunit. The cell-cycle dynamics (chromatin-associated only at specific cell-cycle windows) are consistent with regulated MCM loading. Supporting Evidence: PMID:21146520 The MCM-4 protein is expressed in all dividing cells during embryonic and postembryonic development and associates with chromatin in late anaphase file:worm/mcm-4/mcm-4-deep-research-falcon.md MCM-4 is nuclear during interphase, becomes diffuse upon nuclear envelope breakdown and is not associated with metaphase chromatin, and then reassociates with chromatin in late anaphase |
| GO:0016887 ATP hydrolysis activity | ISS GO_REF:0000024 | ACCEPT | Summary: ATP hydrolysis activity inferred from sequence/structural similarity to MCM4 orthologs bearing the conserved AAA+ ATPase module. Consistent with the Rhea-mapped IEA annotation to the same term. Reason: Correct; the conserved MCM ATPase domain supports ATP hydrolysis as part of the helicase mechanism. Supporting Evidence: PMID:31283754 is the DNA helicase complex responsible for unwinding the DNA at the origins of replication |
| GO:0006279 premeiotic DNA replication | NAS PMID:21146520 C. elegans MCM-4 is a general DNA replication and checkpoint... | KEEP AS NON CORE | Summary: Premeiotic (germline) DNA replication requires the MCM2-7 helicase. In mcm-4 mutants the germline retains substantial replication/division capacity from maternal/zygotic contribution, but MCM-4 is nonetheless a required replication component, including in germline lineages. This NAS annotation reflects a curator narrative statement. Reason: The core role of MCM-4 is general (mitotic) DNA replication; premeiotic replication is one specific replication context. The paper notes the germline continues replication relatively well in zygotic mcm-4 mutants, so this is a legitimate but specialized, non-core facet rather than the defining function. Supporting Evidence: PMID:21146520 In contrast to somatic cells in mcm-4 mutants, the gonad continues DNA replication and cell division until late larval development |
| GO:0042555 MCM complex | NAS PMID:21146520 C. elegans MCM-4 is a general DNA replication and checkpoint... | ACCEPT | Summary: Curator (NAS) statement that MCM-4 is a component of the MCM complex, drawn from the primary paper that identifies it as an MCM2-7 subunit. Duplicates the strongly supported IBA/IEA/ISS MCM complex annotations. Reason: Correct core localization, directly stated in the cited paper. Supporting Evidence: PMID:21146520 encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex |
| GO:0003678 DNA helicase activity | ISS GO_REF:0000024 | ACCEPT | Summary: DNA helicase activity inferred from sequence similarity to MCM4 orthologs, with the contributes_to qualifier correctly indicating that the activity belongs to the assembled MCM2-7 ring rather than the isolated subunit. Reason: Correct core molecular function; the contributes_to qualifier is the appropriate framing for a single MCM subunit within the helicase. Supporting Evidence: PMID:31283754 is the DNA helicase complex responsible for unwinding the DNA at the origins of replication |
| GO:0003697 single-stranded DNA binding | ISS GO_REF:0000024 | ACCEPT | Summary: ssDNA binding inferred from similarity to MCM4 orthologs; the MCM2-7 ring engages single-stranded DNA during unwinding. Duplicates the IBA annotation to the same term with a contributes_to qualifier. Reason: Conserved MCM function; contributes_to appropriately reflects activity at the complex level. Supporting Evidence: PMID:21146520 encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex |
| GO:0042555 MCM complex | ISS GO_REF:0000024 | ACCEPT | Summary: MCM complex membership inferred from sequence similarity to MCM4 orthologs. Duplicates the experimentally and phylogenetically supported MCM complex annotations. Reason: Correct core localization, redundant with stronger evidence lines. Supporting Evidence: PMID:21146520 encodes an evolutionarily conserved component of the MCM2-7 pre-RC and replicative helicase complex |
| GO:0005515 protein binding | IPI PMID:31283754 The demethylase NMAD-1 regulates DNA replication and repair ... | KEEP AS NON CORE | Summary: MCM-4 was identified in NMAD-1 immunoprecipitation/mass-spectrometry as a putative NMAD-1-binding protein and shown to bind NMAD-1 directly in vitro (recombinant His-tagged NMAD-1 pulldown of MCM-4). Notably, the authors were unable to confirm the NMAD-1/MCM-4 interaction in vivo (only the NMAD-1/TOP-2 interaction was confirmed in vivo). The direct in vitro binding supports the IPI annotation, but protein binding is an uninformative molecular function term per curation guidelines and does not, on its own, define a specific activity. Reason: The direct NMAD-1/MCM-4 interaction is supported by in vitro recombinant binding assays, but the in vivo interaction was not confirmed, and a bare protein binding term conveys no functional specificity. Retain as supporting evidence of a physical interaction but treat as non-core; the core MF terms are the helicase/ATPase activities. Supporting Evidence: PMID:31283754 NMAD-1 directly bound to MTSS-1, TOP-2, and MCM-4, components of the DNA replication machinery PMID:31283754 To test whether these candidate NMAD-1 binding proteins bound directly to NMAD-1, we performed in vitro binding assays using recombinant His-tagged NMAD-1 and GST-tagged or untagged candidate binders |
| GO:0007399 nervous system development | IMP PMID:7262539 Isolation and genetic characterization of cell-lineage mutan... | KEEP AS NON CORE | Summary: This annotation derives from the classic cell-lineage mutant screen in which lin-6(e1466) (= mcm-4) was isolated. The neuronal/lineage phenotypes are a pleiotropic downstream consequence of a general postembryonic DNA-replication defect in dividing cells, not evidence of a dedicated molecular role of MCM-4 in nervous system development. Reason: lin-6/mcm-4 mutants were recovered as postembryonic cell-lineage mutants; defective DNA replication in dividing neuroblasts secondarily disrupts nervous system development. This is non-core pleiotropy of the core replication defect. The supporting reference (PMID:7262539) is abstract-only in our cache, so the experimental IMP is retained (not removed) but reframed as non-core. Defer to the curator on the underlying assertion. Supporting Evidence: PMID:21146520 The lin-6(e1466) mutation was identified in the first systematic search for mutants with defects in the normally invariant postembryonic cell lineages of C. elegans |
| GO:0008406 gonad development | IMP PMID:7262539 Isolation and genetic characterization of cell-lineage mutan... | KEEP AS NON CORE | Summary: Like the nervous system annotation, this reflects pleiotropic cell-lineage defects of lin-6/mcm-4 mutants rather than a dedicated gonadal developmental function. The gonad/germline actually copes relatively well with loss of zygotic mcm-4, continuing replication and division into late larval stages. Reason: Gonad development defects are a secondary consequence of impaired postembryonic DNA replication in dividing somatic/germline precursors, not a core function of MCM-4. The IMP source (PMID:7262539) is abstract-only in our cache, so the experimental annotation is retained and reframed as non-core rather than removed. Supporting Evidence: PMID:21146520 the somatic gonad and germline show substantial ability to cope with lack of zygotic mcm-4 function |
| GO:0040011 locomotion | IMP PMID:7262539 Isolation and genetic characterization of cell-lineage mutan... | KEEP AS NON CORE | Summary: Locomotion defects in lin-6/mcm-4 mutants are again a pleiotropic, whole-organism consequence of impaired postembryonic cell divisions (slow growth, larval arrest/lethality, defective lineages), not evidence that MCM-4 has a specific molecular role in locomotion. Reason: Locomotion is a distal phenotype of the general replication/growth defect caused by loss of mcm-4; it does not represent a core molecular or cellular function. The IMP source (PMID:7262539) is abstract-only in our cache, so the annotation is retained and marked non-core rather than removed. Supporting Evidence: PMID:21146520 These mutants grow slowly and either die during larval development or develop into sterile adults |
| GO:0005634 nucleus | IDA PMID:21146520 C. elegans MCM-4 is a general DNA replication and checkpoint... | ACCEPT | Summary: Direct experimental evidence localizes MCM-4 to the nucleus / nuclear chromatin in dividing C. elegans cells. This is the experimental basis for the nuclear localization (consistent with the electronic GO:0005634 annotation). Reason: Strong direct evidence; nuclear/chromatin localization is expected and observed for a pre-RC subunit. MCM-4 is nuclear during interphase with a large soluble pool, consistent with regulated licensing. Supporting Evidence: PMID:21146520 The MCM-4 protein is expressed in all dividing cells during embryonic and postembryonic development and associates with chromatin in late anaphase file:worm/mcm-4/mcm-4-deep-research-falcon.md MCM-4 is nuclear during interphase, becomes diffuse upon nuclear envelope breakdown and is not associated with metaphase chromatin, and then reassociates with chromatin in late anaphase |
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Download this section (compressed HTML)Q: Does the apparent tolerance of the C. elegans germline and somatic gonad to loss of zygotic mcm-4 reflect maternal MCM-4 contribution, or a genuinely lower requirement for MCM-4 in those lineages?
Q: What is the functional significance of the physical interaction between MCM-4 and the DNA demethylase NMAD-1 (and TOP-2) for replication or repair in the germline?
Q: Why is epidermal (hypodermal) expression of MCM-4 specifically sufficient to rescue organismal growth and viability, given that MCM-4 is expressed in all dividing cells?
Q: Does MCM-4, as an obligate subunit of the CMG helicase, contribute to the proposed replication-independent / chromatin-handling role of CMG in asymmetric cell-fate divergence (reported for the GINS subunit PSF-2), or is that function genetically separable from MCM-4?
Experiment: Reconstitute or affinity-purify the C. elegans MCM2-7 / CMG complex and measure ATP-dependent single-stranded DNA helicase and ATPase activity to directly confirm MCM-4 incorporation and biochemical function.
Hypothesis: C. elegans MCM-4 assembles into a functional MCM2-7/CMG complex with ATP-dependent DNA helicase activity, as predicted from orthology.
Experiment: Use tissue-specific degron/auxin-inducible depletion of MCM-4 (germline vs. hypodermis vs. neurons) to dissect lineage-specific replication requirements and separate the primary replication defect from downstream developmental phenotypes.
Hypothesis: The developmental (nervous system, gonad, locomotion) phenotypes are secondary to loss of DNA replication in dividing precursors rather than a tissue-specific molecular function of MCM-4.
Experiment: Map the MCM-4/NMAD-1 interaction interface and test whether NMAD-1 demethylase activity modulates MCM-4 chromatin loading or replication/repair in the germline.
Hypothesis: NMAD-1 regulates MCM-4-dependent replication/repair in the germline through a direct physical interaction.
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