Affinage

MCM9

DNA helicase MCM9 · UniProt Q9NXL9

Length
1143 aa
Mass
127.3 kDa
Annotated
2026-06-10
29 papers in source corpus 16 papers cited in narrative 16 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

MCM9 is a vertebrate-specific MCM-family ATPase/helicase that operates principally in DNA repair and the maintenance of genome stability rather than in bulk DNA replication (PMID:21987787, PMID:22771120, PMID:22771115). It forms an obligate heteromeric complex with MCM8 in which the two subunits reciprocally stabilize each other, and this MCM8-MCM9 complex is rapidly recruited to DNA damage sites where it promotes loading of RPA and RAD51 to drive homologous recombination (PMID:22771120, PMID:22771115, PMID:23401855). The complex acts downstream of the Fanconi anemia pathway and BRCA2/RAD51 to repair DNA interstrand crosslinks and to support recombination-associated DNA synthesis, with recruitment mediated by the OB-fold loader HROB and acting redundantly with the HELQ helicase (PMID:22771115, PMID:31467087). MCM9 contributes its own recruitment and effector functions: a C-terminal extension carries an NLS required for nuclear import of both MCM8 and MCM9 and a variant BRC (BRCv) motif that directly binds RAD51 and recruits it to crosslink-induced damage (PMID:33539926). Independently of recombination, MCM9 assembles with mismatch repair initiation factors MSH2, MSH3, MLH1, PMS1 and the clamp loader RFC, and its intrinsic helicase activity is required for efficient mismatch repair; MCM9 chromatin loading is MSH2-dependent and in turn stimulates MLH1 recruitment, with loss causing microsatellite instability (PMID:26300262). These activities make MCM9 dispensable for cell viability but essential for germ cell development, genome stability, and tumor suppression, and loss-of-function variants in patients impair recruitment to damage sites and chromosomal break repair (PMID:21987787, PMID:25480036).

Mechanistic history

Synthesis pass · year-by-year structured walk · 11 steps
  1. 2008 Medium

    The first functional study tested whether MCM9 participates in replication licensing, proposing it as an activating linker coupling Cdt1 to MCM2-7 loading.

    Evidence Xenopus egg extract depletion/add-back with chromatin fractionation and Co-IP

    PMID:18657502

    Open questions at the time
    • Single-system biochemical claim later contradicted in the same extract system
    • No in vivo test of the proposed pre-RC role
  2. 2011 High

    Genetic knockout in mice directly tested the replication-licensing hypothesis and instead established MCM9 as nonessential for bulk replication but required for genome stability, germ-line maintenance, and tumor suppression.

    Evidence Constitutive/conditional knockout mice with proliferation, replication-stress, and genomic instability assays

    PMID:21987787

    Open questions at the time
    • Molecular mechanism of the genome-instability and germ-cell phenotype not resolved here
    • Did not identify direct repair partners
  3. 2012 High

    Independent knockout studies defined the MCM8-MCM9 heterocomplex as a homologous recombination factor that reciprocally stabilizes its subunits and is needed for RAD51/RPA loading and ICL repair.

    Evidence Knockout MEFs and DT40 cells with reciprocal Co-IP, chromatin recruitment, HR reporter, and FA/BRCA2 epistasis analysis

    PMID:22771115 PMID:22771120

    Open questions at the time
    • How the complex is recruited to damage sites unknown
    • Helicase/ATPase activity inferred rather than directly reconstituted
  4. 2013 High

    Mammalian and Xenopus studies confirmed the physical interaction, MCM8-dependent MCM9 stability, and damage-site recruitment, while a parallel egg-extract study refuted the earlier pre-RC loading role.

    Evidence Co-IP, ChIP at damage sites, HR reporter and cisplatin assays; gel filtration and chromatin fractionation in Xenopus extract

    PMID:23401855 PMID:23518502

    Open questions at the time
    • Reconciliation of the two conflicting egg-extract reports incomplete
    • Recruitment factor still unidentified
  5. 2015 High

    A second, recombination-independent function was established: MCM9 helicase activity is required for mismatch repair within a complex containing MSH2/MSH3/MLH1/PMS1/RFC.

    Evidence Mcm9 knockout cells with helicase-dead rescue, Co-IP, chromatin loading and microsatellite instability assays

    PMID:26300262

    Open questions at the time
    • DNA substrate unwound during MMR not defined
    • How MCM9 partitions between MMR and HR roles unclear
  6. 2014 Medium

    Patient loss-of-function variants demonstrated that recruitment of MCM9 to damage sites is required for chromosomal break repair in humans.

    Evidence Patient lymphocyte DNA repair assay, splicing analysis, and immunofluorescence for MCM9 recruitment

    PMID:25480036

    Open questions at the time
    • Single study
    • Did not define the molecular determinant of recruitment
  7. 2019 High

    The recruitment problem was solved by identifying HROB as an OB-fold loader that brings MCM8-MCM9 to damage, acting downstream of RAD51 redundantly with HELQ.

    Evidence Mouse knockout genetic epistasis with double mutants, foci colocalization, HR assays, and infertility phenotyping

    PMID:31467087

    Open questions at the time
    • Structural basis of HROB-MCM8/9 engagement unknown
    • Division of labor between HELQ and MCM8/9 branches not fully mapped
  8. 2021 High

    Domain mapping resolved how MCM9 itself contributes to nuclear import and RAD51 recruitment, identifying an NLS and a RAD51-binding BRCv motif in its C-terminal extension.

    Evidence Domain deletion/point mutants, damage-foci immunofluorescence, Co-IP of MCM9-BRCv with RAD51 in multiple cell systems

    PMID:33539926

    Open questions at the time
    • Structure of the BRCv-RAD51 interface not determined
    • Relationship between BRCv-mediated and HROB-mediated recruitment unresolved
  9. 2020 Medium

    Regulation of the complex was probed by showing HORMAD1 sequesters MCM8-MCM9 in the cytoplasm, linking aberrant expression to MMR defects in cancer.

    Evidence Co-IP, nuclear/cytoplasmic fractionation, immunofluorescence, and MLH1 chromatin binding assay

    PMID:32647118

    Open questions at the time
    • Single lab
    • Generality across tumor types not tested
  10. 2025 Medium

    The MMR-associated role of MCM9 was extended to human spermatogonial stem cells, tying its interactions with MSH2 and MLH1 to germ-line genome integrity.

    Evidence Co-IP in human testicular tissue, cell-type-specific immunostaining, and HR assay in knockout HEK293T cells

    PMID:40593474

    Open questions at the time
    • Single study
    • Causal link between MMR defect and human fertility outcomes not established
  11. 2025 Medium

    A direct FANCD2-MCM8/9 interaction was reported, placing the complex as a downstream effector of FANCD2 monoubiquitination in ICL repair.

    Evidence Co-IP, damage-foci immunofluorescence, and double-knockout epistasis (preprint)

    PMID:bio_10.1101_2025.08.07.669127

    Open questions at the time
    • Preprint, not yet peer-reviewed
    • Direct binding interface and dependence on DNA require validation

Open questions

Synthesis pass · forward-looking unresolved questions
  • How MCM9 mechanistically partitions between its HR/ICL-repair and mismatch-repair functions, and the precise DNA substrates its helicase activity acts upon in each pathway, remains unresolved.
  • No reconstituted helicase reaction defining physiological substrate
  • No structure of the MCM8-MCM9 complex bound to DNA or partners
  • Mechanism choosing between MMR and HR engagement unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0003677 DNA binding 2 GO:0060090 molecular adaptor activity 2 GO:0140657 ATP-dependent activity 2 GO:0140097 catalytic activity, acting on DNA 1
Localization
GO:0000228 nuclear chromosome 3 GO:0005634 nucleus 2
Pathway
R-HSA-73894 DNA Repair 5 R-HSA-1474165 Reproduction 4
Partners
FANCD2HORMAD1HROBMCM8MLH1MSH2RAD51RFC
Complex memberships
MCM8-MCM9 helicase complex

Evidence

Reading pass · 16 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2008 MCM9 binds to chromatin in an ORC-dependent manner and forms a stable complex with the licensing factor Cdt1, preventing excess geminin on chromatin during the licensing reaction; MCM9 is required for recruitment of the MCM2-7 helicase onto chromatin and pre-RC assembly, acting as an essential activating linker between Cdt1 and the MCM2-7 complex. Xenopus egg extract system; chromatin fractionation; depletion/add-back experiments; co-immunoprecipitation Molecular cell Medium 18657502
2012 MCM8 and MCM9 form a complex and co-regulate each other's stability; loss of either gene impairs chromatin recruitment of HR factors RAD51 and RPA, strongly reduces homologous recombination, and prevents cells from overcoming transient inhibition of replication fork progression. Knockout mouse embryonic fibroblasts; co-immunoprecipitation; chromatin recruitment assays; HR reporter assays Molecular cell High 22771115 22771120
2012 MCM8 and MCM9 form a complex required for HR repair induced by DNA interstrand crosslinks (ICLs); in DT40 cells lacking MCM8 or MCM9, RAD51 foci partially colocalize with MCM8-MCM9 foci; MCM8-9 works downstream of the FA pathway and BRCA2/RAD51, likely as a hexameric ATPase/helicase, to promote sister chromatid exchanges. Chicken DT40 knockout cells; immunofluorescence; epistasis analysis with FA/BRCA2 pathway mutants; ICL sensitivity assays Molecular cell High 22771115
2013 MCM8 and MCM9 physically associate, MCM8 is required for stability of MCM9 protein; both proteins are rapidly recruited to DNA damage sites and promote RAD51 recruitment there; depletion of MCM8 or MCM9 significantly reduces HR repair efficiency and sensitizes cells to ICL agents. Co-immunoprecipitation in mammalian cells; chromatin immunoprecipitation (ChIP) in human DR-GFP cells and Xenopus egg extract; HR reporter assay; cisplatin sensitivity assays Molecular and cellular biology High 23401855
2013 In Xenopus egg extract, MCM8 and MCM9 form a dimeric complex (not a role in Cdt1-dependent MCM2-7 loading); they associate with chromatin at later stages of DNA replication, and this association is stimulated by DNA damage, suggesting their primary function is in DNA repair analogous to that in somatic cells. Xenopus egg extract; gel filtration; chromatin fractionation; DNA damage stimulation assay; no interaction with Cdt1 detected (negative result for pre-RC role) Cell cycle Medium 23518502
2015 MCM9 forms a complex with MMR initiation proteins MSH2, MSH3, MLH1, PMS1, and the clamp loader RFC; MCM9 helicase activity is required for efficient mismatch repair (MMR), as wild-type but not helicase-dead MCM9 restores MMR in Mcm9−/− cells; MCM9 loading onto chromatin is MSH2-dependent, and MCM9 in turn stimulates recruitment of MLH1 to chromatin; Mcm9−/− cells display microsatellite instability. Mcm9 knockout cells; co-immunoprecipitation; helicase-dead point mutant rescue experiments; microsatellite instability assay; chromatin recruitment assay Molecular cell High 26300262
2005 MCM9 is a vertebrate-specific MCM family member containing an MCM8-like ATP-binding and hydrolysis motif implicated in helicase activity, plus a unique carboxy-terminal domain conserved only in MCM9 homologs; it is most closely related to MCM8 and does not group with MCM2-7. Bioinformatics/sequence analysis; phylogenetic analysis; domain identification Gene Low 16226853
2011 Ablation of Mcm9 in mice is compatible with cell proliferation and viability, showing MCM9 is nonessential for MCM2-7 loading or bulk DNA replication; however, MCM9-deficient cells show elevated genomic instability and defective cell cycle re-entry following replication stress, and MCM9 is required for germ-line stem cell maintenance and tumor suppression. Conditional/constitutive knockout mice; cell proliferation assays; replication stress (HU) challenge; genomic instability assays PNAS High 21987787
2014 A human MCM9 splice-site variant (c.1732+2T>C) produces truncated MCM9 forms that are unable to be recruited to sites of DNA damage, resulting in impaired chromosomal break repair in patient lymphocytes; a second nonsense variant (p.Arg132*) causes loss of functional MCM9 and the same DNA repair defect, establishing that MCM9 recruitment to damage sites is required for HR-mediated repair. Patient lymphocyte DNA repair assay; splicing analysis; immunofluorescence for MCM9 recruitment to damage sites 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 downstream of RAD51, and combined loss of HROB and HELQ severely impairs HR. Genetic epistasis in mouse knockout models; foci co-localization; HR assays; infertility phenotype analysis Genes & development High 31467087
2020 HORMAD1 interacts with the MCM8-MCM9 complex and prevents its efficient nuclear localization; as a consequence, HORMAD1-expressing cancer cells have reduced MLH1 chromatin binding and MMR defects. Co-immunoprecipitation; nuclear/cytoplasmic fractionation; immunofluorescence; MLH1 chromatin binding assay Cell death & disease Medium 32647118
2021 The MCM9 C-terminal extension (CTE) contains a bipartite-like NLS required for nuclear import of both MCM8 and MCM9, and a variant BRC motif (BRCv) necessary for localization to MMC-induced damage sites; the MCM9-BRCv directly interacts with RAD51 and recruits it downstream to MMC-induced damage; cells lacking functional MCM9 have significantly impaired RAD51 foci formation after MMC treatment. Domain deletion and point mutant analysis; immunofluorescence of damage foci; co-immunoprecipitation of MCM9-BRCv with RAD51; patient lymphocyte and MCM9 KO cell assays Journal of biological chemistry High 33539926
2013 MCM9 exists as two isoforms (MCM9L and MCM9M) generated by alternative splicing; both are cell cycle regulated (induced in S-phase, decreased in G2/M); MCM9L expression is specifically induced by mitomycin C (ICL damage) but not by hydroxyurea (replication fork stalling), consistent with a specific role in ICL/HR repair rather than general replication. qRT-PCR of isoforms across cell lines; cell cycle synchronization; drug treatment (MMC vs. HU) Gene Low 23403237
2015 MCM9 deficiency causes reduced primordial germ cell (PGC) proliferation (not apoptosis) through a mechanism independent of the ATM-CHK2-TRP53-P21 signaling pathway; germ cell depletion in Mcm9 and Fancm double-mutant mice is additive, indicating that MCM9 and FANCM deficiency trigger different DDR pathways. Mouse knockout genetics; PGC counting; apoptosis assays; genetic epistasis with ATM/p53 pathway mutants and Fancm mutants Genesis Medium 26388201
2025 In human testicular cells, MCM9 interacts with both MSH2 and MLH1, confirming involvement of the MCM9-mediated MMR pathway in maintaining genomic integrity in spermatogonial stem cells; MCM9 is predominantly expressed in spermatogonial stem cells and spermatogonia in human testes. Co-immunoprecipitation in human testicular tissue; immunohistochemistry/immunofluorescence for cell-type-specific expression; HEK293T knockout and mutant overexpression HR assay Cell death discovery Medium 40593474
2025 MCM8/9 physically interacts with FANCD2 through the MCM8/9 core domain, independently of DNA; FANCD2 is essential for recruitment of MCM9 to ICL-induced nuclear foci, acting downstream of FANCD2 monoubiquitination; combined loss of MCM9 and FANCD2 is epistatic (no additive DNA damage), placing MCM8/9 as a downstream effector within the FA pathway for ICL repair. Co-immunoprecipitation; immunofluorescence of damage foci; MCM8/9 knockout cells; epistasis analysis by γH2AX and cell survival assays bioRxivpreprint Medium bio_10.1101_2025.08.07.669127

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 178 22771120
2014 MCM9 mutations are associated with ovarian failure, short stature, and chromosomal instability. American journal of human genetics 161 25480036
2012 Mcm8 and Mcm9 form a complex that functions in homologous recombination repair induced by DNA interstrand crosslinks. Molecular cell 126 22771115
2013 The MCM8-MCM9 complex promotes RAD51 recruitment at DNA damage sites to facilitate homologous recombination. Molecular and cellular biology 114 23401855
2017 MCM8 and MCM9 Nucleotide Variants in Women With Primary Ovarian Insufficiency. The Journal of clinical endocrinology and metabolism 90 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 74 21987787
2019 Control of homologous recombination by the HROB-MCM8-MCM9 pathway. Genes & development 66 31467087
2008 MCM9 binds Cdt1 and is required for the assembly of prereplication complexes. Molecular cell 65 18657502
2015 MCM9 Is Required for Mammalian DNA Mismatch Repair. Molecular cell 62 26300262
2016 A non-sense MCM9 mutation in a familial case of primary ovarian insufficiency. Clinical genetics 61 26771056
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 40 32647118
2019 MCM8- and MCM9 Deficiencies Cause Lifelong Increased Hematopoietic DNA Damage Driving p53-Dependent Myeloid Tumors. Cell reports 31 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 24 33539926
2015 MCM9 deficiency delays primordial germ cell proliferation independent of the ATM pathway. Genesis (New York, N.Y. : 2000) 22 26388201
2023 Molecular functions of MCM8 and MCM9 and their associated pathologies. iScience 19 37378315
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 13 33750944
2021 MCM9 is associated with germline predisposition to early-onset cancer-clinical evidence. NPJ genomic medicine 12 34556653
2013 Identification, quantification, and evolutionary analysis of a novel isoform of MCM9. Gene 9 23403237
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
2015 Proteomic data on the nuclear interactome of human MCM9. Data in brief 5 26870752
2024 MCM9 compound heterozygosity in an adolescent with premature ovarian insufficiency. Endocrinology, diabetes & metabolism case reports 2 39447595
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

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