Affinage

MCM9

DNA helicase MCM9 · UniProt Q9NXL9

Length
1143 aa
Mass
127.3 kDa
Annotated
2026-04-28
29 papers in source corpus 15 papers cited in narrative 15 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

MCM9 is a vertebrate-specific MCM-family ATPase/helicase that functions in both homologous recombination (HR) and DNA mismatch repair (MMR) by forming obligate complexes with distinct partner sets. MCM9 heterodimerizes with MCM8 to form a helicase complex that is recruited by HROB to stalled replication forks and DNA interstrand crosslinks downstream of the Fanconi anemia pathway and FANCD2 monoubiquitination; a variant BRC motif in the MCM9 C-terminal extension directly engages RAD51, promoting its recruitment to damage sites and enabling recombination-associated DNA synthesis (PMID:22771120, PMID:22771115, PMID:31467087, PMID:33539926). Independently, MCM9 assembles with MMR initiation factors MSH2, MLH1, PMS1, and RFC, and its intrinsic helicase activity is required for mismatch repair, with MSH2-dependent chromatin loading of MCM9 stimulating MLH1 recruitment (PMID:26300262). Loss-of-function mutations in MCM9 cause gonadal failure and infertility in mice and humans—including Sertoli cell-only syndrome in males—reflecting an essential role in germ-cell proliferation and meiotic recombination (PMID:21987787, PMID:40593474).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2005 Low

    Identification of MCM9 as a vertebrate-specific MCM family member with predicted helicase motifs and a unique C-terminal domain established it as a candidate replicative or repair helicase distinct from MCM2-7.

    Evidence Bioinformatic and phylogenetic analysis of MCM family sequences

    PMID:16226853

    Open questions at the time
    • No experimental validation of helicase activity or cellular function
    • Computational prediction only
  2. 2008 Medium

    An early study proposed MCM9 as a licensing cofactor that binds Cdt1 and is required for MCM2-7 loading, suggesting a replication-initiation role; however, this model was not confirmed in subsequent studies.

    Evidence Xenopus egg extract depletion, chromatin fractionation, co-immunoprecipitation

    PMID:18657502

    Open questions at the time
    • Cdt1 interaction was not replicated in a later Xenopus system
    • Role in MCM2-7 loading contradicted by knockout mouse data
  3. 2012 High

    Three independent studies established that MCM9 is dispensable for replication licensing but essential for homologous recombination: MCM8-MCM9 form a complex that promotes RAD51/RPA recruitment to damage sites, acts downstream of the FA/BRCA2 pathways, and is required for germ-cell maintenance, resolving the functional identity of MCM9 as a repair helicase.

    Evidence Knockout mice (sterility, germ-cell depletion), chicken DT40 knockouts (ICL sensitivity, epistasis with FA/BRCA2), HR reporter assays, immunofluorescence for RAD51/RPA foci

    PMID:21987787 PMID:22771115 PMID:22771120 PMID:23518502

    Open questions at the time
    • Mechanism of MCM8-MCM9 recruitment to damage sites unknown
    • Whether the complex functions as a hexamer in vivo unresolved
    • Direct helicase activity not yet demonstrated biochemically
  4. 2013 High

    Confirmation in human cells that MCM8-MCM9 are rapidly recruited to DNA damage sites and promote RAD51 recruitment via ChIP, and that MCM8 stabilizes MCM9 protein, solidified the obligate heteromeric partnership.

    Evidence Co-immunoprecipitation, DR-GFP HR reporter, chromatin immunoprecipitation in human cells and Xenopus extract

    PMID:23401855

    Open questions at the time
    • Direct physical interaction with RAD51 not mapped
    • Helicase substrate specificity unknown
  5. 2014 Medium

    Human patient mutations in MCM9 were shown to produce truncated proteins unable to localize to DNA damage, directly linking MCM9 loss of function to impaired chromosome break repair in human somatic cells.

    Evidence Whole-exome sequencing of patients, splicing analysis, DNA damage recruitment and repair assays in patient lymphocytes

    PMID:25480036

    Open questions at the time
    • Small patient cohort
    • No rescue experiment with wild-type MCM9 in patient cells
  6. 2015 High

    Discovery that MCM9 assembles with MMR factors (MSH2, MLH1, PMS1, RFC) and that its helicase activity is required for mismatch repair revealed a second, independent genome-maintenance function for MCM9 beyond HR.

    Evidence Co-immunoprecipitation, MMR activity assay in cell extracts, helicase-dead mutagenesis and knockout rescue, microsatellite instability assay

    PMID:26300262

    Open questions at the time
    • Whether MMR and HR functions use the same MCM8-MCM9 complex or distinct assemblies unclear
    • Biochemical reconstitution of MCM9-dependent MMR not performed
    • MMR role not yet validated in vivo in mice
  7. 2015 Medium

    Genetic epistasis showed MCM9 promotes primordial germ-cell proliferation through a pathway distinct from FANCM, and independently of ATM-CHK2-p53-p21 signaling, refining the understanding of MCM9's gametogenesis role.

    Evidence Mouse genetics, Mcm9/Fancm double mutants, BrdU proliferation and apoptosis assays

    PMID:26388201

    Open questions at the time
    • Identity of the MCM9-dependent proliferation signal unknown
    • Whether germ-cell defect is solely due to HR or also MMR impairment not distinguished
  8. 2019 High

    HROB was identified as the factor that loads the MCM8-MCM9 helicase at damage sites, acting redundantly with HELQ, answering the long-standing question of how the complex is recruited to HR intermediates.

    Evidence Co-immunoprecipitation, HR reporter assay, mouse knockout phenocopying MCM8/9 infertility, epistasis with HELQ

    PMID:31467087

    Open questions at the time
    • Structural basis of HROB-MCM8/9 interaction unknown
    • Whether HROB is also required for MCM9's MMR function not tested
  9. 2020 Medium

    HORMAD1 was shown to sequester MCM8-MCM9 and impair its nuclear localization, linking cancer-associated HORMAD1 misexpression to MMR deficiency through MCM9, connecting germ-cell biology to tumor MMR phenotypes.

    Evidence Co-immunoprecipitation, immunofluorescence, chromatin fractionation for MLH1, MMR assay in HORMAD1-expressing cancer cells

    PMID:32647118

    Open questions at the time
    • Single-lab observation not independently replicated
    • HORMAD1-MCM8/9 interaction domain not mapped
  10. 2021 High

    Mapping of the MCM9 C-terminal extension identified a bipartite NLS required for nuclear import of both MCM8 and MCM9, and a BRC-variant motif that directly binds RAD51, explaining the molecular mechanism by which MCM9 promotes RAD51 recruitment.

    Evidence Domain mutagenesis of NLS and BRCv, immunofluorescence, co-immunoprecipitation, MCM9 knockout and patient cell assays

    PMID:33539926

    Open questions at the time
    • Crystal structure of BRCv-RAD51 interface not determined
    • Whether BRCv is sufficient for RAD51 filament remodeling unknown
  11. 2025 Medium

    MCM9 was shown to interact with MSH2 and MLH1 in human testis and to be enriched in spermatogonial stem cells; loss-of-function mutations cause Sertoli cell-only syndrome in human males, establishing a direct clinical link between MCM9 and male infertility.

    Evidence Co-immunoprecipitation from human testicular tissue, immunohistochemistry, HR repair assay in HEK293T knockout and mutant cells

    PMID:40593474

    Open questions at the time
    • Small patient cohort
    • Whether the infertility phenotype is driven by HR, MMR, or both is unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of MCM8-MCM9 hexamerization and its helicase mechanism on recombination intermediates, whether MMR and HR employ the same or distinct MCM9-containing complexes, and the molecular basis by which MCM9 loss selectively depletes germ cells while leaving somatic viability largely intact.
  • No high-resolution structure of the MCM8-MCM9 complex
  • In vivo reconstitution of MCM9-dependent MMR not performed
  • Tissue-specific regulation of MCM9 expression poorly characterized

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140657 ATP-dependent activity 3 GO:0140097 catalytic activity, acting on DNA 1
Localization
GO:0005634 nucleus 4 GO:0005694 chromosome 4
Pathway
R-HSA-73894 DNA Repair 6 R-HSA-1474165 Reproduction 3 R-HSA-1643685 Disease 3
Partners
FANCD2HORMAD1HROBMCM8MLH1MSH2PMS1RAD51
Complex memberships
MCM8-MCM9 helicase complexMCM9-MSH2-MLH1-PMS1-RFC MMR complex

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2008 MCM9 binds chromatin in an ORC-dependent manner and is required for recruitment of the MCM2-7 helicase onto chromatin; MCM9 forms a stable complex with the licensing factor Cdt1, preventing excess geminin on chromatin during the licensing reaction, acting as an essential activating linker between Cdt1 and the MCM2-7 complex. Xenopus egg extract depletion, chromatin fractionation, Co-immunoprecipitation, in vitro reconstitution Molecular cell Medium 18657502
2012 MCM8 and MCM9 form a complex; MCM9 knockout mice are sterile (females lack oocytes, males have reduced spermatozoa); MCM8/9-deficient embryonic fibroblasts show impaired chromatin recruitment of HR factors RAD51 and RPA, strongly reduced homologous recombination, and inability to overcome transient replication fork inhibition; MCM8 and MCM9 co-regulate each other's stability. Knockout mouse generation, co-immunoprecipitation, immunofluorescence, HR reporter assay, Western blot for protein stability Molecular cell High 22771120
2012 MCM8 and MCM9 form a complex required for homologous recombination repair induced by DNA interstrand crosslinks (ICLs); MCM8-9 forms nuclear foci that colocalize with RAD51; MCM8-9 acts downstream of the FA and BRCA2/RAD51 pathways and is required for HR-promoted sister chromatid exchanges, functioning probably as a hexameric ATPase/helicase. Chicken DT40 cell knockouts, ICL sensitivity assays, immunofluorescence for nuclear foci, epistasis analysis with FA/BRCA2 pathway mutants, sister chromatid exchange assay Molecular cell High 22771115
2011 MCM9 is dispensable for MCM2-7 loading and DNA replication in vivo; MCM9-deficient cells show elevated genomic instability and defective cell cycle re-entry following replication stress; MCM9 mutant mice show p53-independent embryonic germ-cell depletion in both sexes and males exhibit defective spermatogonial stem-cell renewal. Knockout mouse generation and phenotypic analysis, cell proliferation assays, replication stress experiments Proceedings of the National Academy of Sciences of the United States of America High 21987787
2013 MCM8 and MCM9 physically associate with each other; MCM8 is required for the stability of MCM9 protein; depletion of MCM8 or MCM9 reduces HR repair efficiency and sensitizes cells to ICL agents; MCM8 and MCM9 are rapidly recruited to DNA damage sites and promote RAD51 recruitment, as shown by ChIP in human DR-GFP cells and Xenopus egg extract. Co-immunoprecipitation, HR reporter (DR-GFP) assay, chromatin immunoprecipitation, Xenopus egg extract, Western blot, cisplatin sensitivity assay Molecular and cellular biology High 23401855
2013 In Xenopus laevis egg extract, MCM8 and MCM9 form a dimeric complex; they associate with chromatin at later stages of DNA replication and this association is stimulated by DNA damage; MCM9 is not essential for loading of MCM2-7 complex onto chromatin during origin licensing and does not detectably interact with Cdt1 in this system. Xenopus egg extract, co-immunoprecipitation, chromatin fractionation, DNA damage treatment Cell cycle Medium 23518502
2015 MCM9 forms a complex with MMR initiation proteins (MSH2, MSH3, MLH1, PMS1, and the clamp loader RFC) and is essential for DNA mismatch repair; the MCM9 complex has intrinsic helicase activity required for MMR (helicase-dead MCM9 fails to restore MMR in Mcm9-/- cells); MCM9 loading onto chromatin is MSH2-dependent; in turn, MCM9 stimulates recruitment of MLH1 to chromatin; Mcm9-/- cells display microsatellite instability. Co-immunoprecipitation, MMR activity assay in cell extracts, helicase-dead mutagenesis, chromatin fractionation, microsatellite instability assay, Mcm9 knockout cells Molecular cell High 26300262
2014 Human MCM9 splice-site variant (c.1732+2T>C) causes abnormal alternative splicing and truncated MCM9 forms that cannot be recruited to sites of DNA damage; a nonsense variant (p.Arg132*) causes loss of functional MCM9; both result in impaired chromosome break repair in patient lymphocytes, establishing MCM9 function in HR in human somatic cells. Whole-exome sequencing, splicing analysis, DNA damage recruitment assay (patient lymphocytes), chromosome break repair assay American journal of human genetics Medium 25480036
2019 HROB (C17orf53) is an OB-fold-containing factor that recruits the MCM8-MCM9 helicase to sites of DNA damage to promote recombination-associated DNA synthesis; the HROB-MCM8-MCM9 pathway acts redundantly with the HELQ helicase; combined loss of HROB and HELQ severely impairs HR, placing HROB upstream of MCM8-MCM9 in the HR pathway. Co-immunoprecipitation, HR reporter assay, immunofluorescence for foci, mouse knockout (infertility/meiotic arrest phenotype), epistasis analysis with HELQ double KO Genes & development High 31467087
2020 HORMAD1 interacts with the MCM8-MCM9 complex and prevents its efficient nuclear localization; HORMAD1-expressing cancer cells consequently have reduced MLH1 chromatin binding and DNA mismatch repair defects. Co-immunoprecipitation, immunofluorescence for nuclear localization, chromatin fractionation for MLH1, MMR assay in cancer cells with/without HORMAD1 expression Cell death & disease Medium 32647118
2021 The MCM9 C-terminal extension (CTE) contains a bipartite-like nuclear localization signal (NLS) required for nuclear import of both MCM8 and MCM9, and a variant BRC motif (BRCv) required for localization to MMC-induced DNA damage sites; the MCM9-BRCv directly interacts with and recruits RAD51 to MMC-induced damage. Mutagenesis of NLS and BRCv motifs, immunofluorescence for nuclear localization and RAD51 foci, co-immunoprecipitation, MCM9 knockout cells, patient lymphocyte RAD51 foci assay The Journal of biological chemistry High 33539926
2015 MCM9 deficiency causes reduced primordial germ cell proliferation (not apoptosis) that is independent of the ATM-CHK2-TRP53-P21 signaling pathway; germ cell depletion in Mcm9/Fancm double mutants is additive, indicating MCM9 and FANCM trigger distinct DDR pathways. Mouse genetics, PGC counting, BrdU proliferation assay, apoptosis assay, double-mutant epistasis analysis Genesis Medium 26388201
2005 MCM9 is a novel vertebrate-specific MCM family protein containing an MCM8-like ATP binding and hydrolysis motif (helicase activity motif) and a unique conserved carboxy-terminal domain absent in MCM2-8; it belongs to a distinct MCM subgroup with MCM8. Bioinformatics/sequence analysis, phylogenetic analysis, domain identification Gene Low 16226853
2025 MCM8/9 physically interacts with FANCD2 through its core domain independently of DNA; FANCD2 is essential for recruitment of MCM9 to ICL-induced nuclear foci, downstream of FANCD2 monoubiquitination; MCM8/9 ATPase activity and BRCv motif are required for foci formation but not for FANCD2 binding; combined loss of MCM9 and FANCD2 is epistatic, placing MCM8/9 as a downstream effector in the FA pathway. Co-immunoprecipitation, immunofluorescence for nuclear foci, MCM8/9 and FANCD2 knockout cells, γH2AX assay, cell survival assay, epistasis analysis bioRxivpreprint Medium bio_10.1101_2025.08.07.669127
2025 Human MCM9 interacts with MSH2 and MLH1 in testicular tissue; MCM9 is predominantly expressed in spermatogonial stem cells and spermatogonia; MCM9 loss-of-function mutations impair HR-mediated DNA repair capacity in HEK293T cells and cause Sertoli cell-only syndrome in human males. Co-immunoprecipitation (human testis), immunohistochemistry for MCM9 localization, HR repair assay in KO and mutant-overexpressing HEK293T cells Cell death discovery Medium 40593474

Source papers

Stage 0 corpus · 29 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2012 MCM8- and MCM9-deficient mice reveal gametogenesis defects and genome instability due to impaired homologous recombination. Molecular cell 174 22771120
2014 MCM9 mutations are associated with ovarian failure, short stature, and chromosomal instability. American journal of human genetics 158 25480036
2012 Mcm8 and Mcm9 form a complex that functions in homologous recombination repair induced by DNA interstrand crosslinks. Molecular cell 123 22771115
2013 The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination. Molecular and cellular biology 110 23401855
2017 MCM8 and MCM9 Nucleotide Variants in Women With Primary Ovarian Insufficiency. The Journal of clinical endocrinology and metabolism 87 27802094
2011 Minichromosome maintenance helicase paralog MCM9 is dispensible for DNA replication but functions in germ-line stem cells and tumor suppression. Proceedings of the National Academy of Sciences of the United States of America 72 21987787
2008 MCM9 binds Cdt1 and is required for the assembly of prereplication complexes. Molecular cell 65 18657502
2019 Control of homologous recombination by the HROB-MCM8-MCM9 pathway. Genes & development 62 31467087
2016 A non-sense MCM9 mutation in a familial case of primary ovarian insufficiency. Clinical genetics 60 26771056
2015 MCM9 Is Required for Mammalian DNA Mismatch Repair. Molecular cell 59 26300262
2015 Mutated MCM9 is associated with predisposition to hereditary mixed polyposis and colorectal cancer in addition to primary ovarian failure. Cancer genetics 49 26806154
2005 Identification of full genes and proteins of MCM9, a novel, vertebrate-specific member of the MCM2-8 protein family. Gene 46 16226853
2005 Identification of a novel cell-cycle-induced MCM family protein MCM9. Biochemical and biophysical research communications 45 15850810
2020 Aberrantly expressed HORMAD1 disrupts nuclear localization of MCM8-MCM9 complex and compromises DNA mismatch repair in cancer cells. Cell death & disease 35 32647118
2019 MCM8- and MCM9 Deficiencies Cause Lifelong Increased Hematopoietic DNA Damage Driving p53-Dependent Myeloid Tumors. Cell reports 30 31509747
2020 Novel pathogenic mutations in minichromosome maintenance complex component 9 (MCM9) responsible for premature ovarian insufficiency. Fertility and sterility 28 32145932
2013 Mcm8 and Mcm9 form a dimeric complex in Xenopus laevis egg extract that is not essential for DNA replication initiation. Cell cycle (Georgetown, Tex.) 26 23518502
2021 Motifs of the C-terminal domain of MCM9 direct localization to sites of mitomycin-C damage for RAD51 recruitment. The Journal of biological chemistry 21 33539926
2015 MCM9 deficiency delays primordial germ cell proliferation independent of the ATM pathway. Genesis (New York, N.Y. : 2000) 21 26388201
2023 Molecular functions of MCM8 and MCM9 and their associated pathologies. iScience 16 37378315
2021 MCM9 is associated with germline predisposition to early-onset cancer-clinical evidence. NPJ genomic medicine 12 34556653
2021 The etiology of Down syndrome: Maternal MCM9 polymorphisms increase risk of reduced recombination and nondisjunction of chromosome 21 during meiosis I within oocyte. PLoS genetics 9 33750944
2016 Pathogenic germline MCM9 variants are rare in Australian Lynch-like syndrome patients. Cancer genetics 8 27886675
2023 The Role of MCM9 in the Etiology of Sertoli Cell-Only Syndrome and Premature Ovarian Insufficiency. Journal of clinical medicine 7 36769638
2013 Identification, quantification, and evolutionary analysis of a novel isoform of MCM9. Gene 7 23403237
2015 Proteomic data on the nuclear interactome of human MCM9. Data in brief 5 26870752
2025 MCM9 deficiency impairs DNA damage repair during spermatogenesis, leading to Sertoli cell-only syndrome in humans. Cell death discovery 1 40593474
2025 Clinical syndromes linked to biallelic germline variants in MCM8 and MCM9. HGG advances 1 40684266
2024 MCM9 compound heterozygosity in an adolescent with premature ovarian insufficiency. Endocrinology, diabetes & metabolism case reports 1 39447595