DNA Mismatch Repair (MMR) in Eukaryotes
DNA mismatch repair (MMR), one of three excision mechanisms defending against DNA damage, recognizes nucleotide mismatches in newly replicated DNA. The area containing the nucleotide mismatch is excised, and the resulting gap is filled using DNA synthesis with the complementary strand as a template.
Pathway Summary
Major DNA repair mechanisms take advantage of the fact that DNA is double-stranded, with the same information on both strands. Consequently, in cases where damage is present in just one strand, the damage can be accurately repaired by excising and replacing it with new DNA, synthesized using the complementary strand as template. All organisms, prokaryotic and eukaryotic, employ at least three excision mechanisms: 1) mismatch repair, 2) base excision repair, and 3) nucleotide excision repair. Mismatch repair functions mainly in concert with replication and recognizes rare mismatches embedded in millions of correctly base-paired nucleotides in the newly replicated DNA. By virtue of the directionality of the replication machinery and the location of Okazaki fragments, repair is directed to the newly synthesized strand (26354434).Mismatch repair removes a section of nascent DNA, including the misincorporated nucleotide, terminating excision just beyond the mismatch. Finally, mismatch repair fills the excision gap by high fidelity DNA synthesis. Ligation subsequently restores strand continuity.DNA mismatch repair in eukaryotes is a complex, multistep process. First, the mismatch is bound by MutSα heterodimer MSH2/MSH6 (for base-base mismatches and one or two base loops), or MutSβ heterodimer MSH2/MSH3 for loops of 2-14 bp. The mismatch-bound Msh2/Msh6 undergoes an ATP-dependent conformational change which converts it to a sliding clamp capable of translocating along the DNA backbone. The MSH2/MSH6-ATP-DNA complex is bound by a second heterodimer composed of MLH1 and PMS2 (which compose MutLα) in a second ATP-dependent step. This complex can translocate in either direction in search of a strand discontinuity. MLH1 and PMS2 are endonucleases that create a series of nicks around the mispair to prime that strand for exonuclease digestion, and are stimulated by PCNA.Mismatch repair must be directed to the newly synthesized strand, which in eukaryotes can be distinguished from the template strand by the presence of gaps between Okazaki fragments on the lagging strand or by the free 3' terminus on the leading strand. The replication-derived strand break that directs correction can be located either 3' or 5' to the mispair, with mismatch provoked excision removing that portion of the incised strand spanning the two DNA sites. Communication appears to be through space, followed by translocation of the PCNA/RFC complex over the intervening DNA to the mismatch complex (17921148).In strand resynthesis the Msh2/Msh6 sliding clamp stimulates the activity of EXO1, a 5'-to-3' exonuclease that degrades a stretch of several hundred nucleotides starting from a nick situated 5' from the mispair and traveling towards the mispair. The resulting single stranded DNA is stabilized by RPA. This makes the gapped substrate refractory to further degradation by EXO1 until RPA is stimulated by further molecules of ATP-bound Msh2/Msh6 heterodimer arriving from the direction of the mispair. MSH2,3,6, MLH1, EXO1, PMS2, RPA, and DNA polymerase-δ support mismatch repair directed by a strand break located either 3' or 5' to the mispair, while RFC and PCNA are additionally required when the break is 3' to the mismatch. Polymerase-δ and its cofactors PCNA and RFC fill in the resulting single-stranded gap, and DNA ligase I seals the remaining nick. (Upgraded 04/2022)
DNA Mismatch Repair (MMR) in Eukaryotes Genes list
Explore Genes related to DNA Mismatch Repair (MMR) in Eukaryotes
- exonuclease 1EXO1
icon_0171_ls_qf_save_program-s - flap structure-specific endonuclease 1FEN1
icon_0171_ls_qf_save_program-s - DNA ligase 1LIG1
icon_0171_ls_qf_save_program-s - minichromosome maintenance 9 homologous recombination repair factorMCM9
icon_0171_ls_qf_save_program-s - mutL homolog 1MLH1
icon_0171_ls_qf_save_program-s - mutS homolog 2MSH2
icon_0171_ls_qf_save_program-s - mutS homolog 3MSH3
icon_0171_ls_qf_save_program-s - mutS homolog 6MSH6
icon_0171_ls_qf_save_program-s - proliferating cell nuclear antigenPCNA
icon_0171_ls_qf_save_program-s - PMS1 homolog 2, mismatch repair system componentPMS2
icon_0171_ls_qf_save_program-s - DNA polymerase delta 1, catalytic subunitPOLD1
icon_0171_ls_qf_save_program-s - replication factor C subunit 1RFC1
icon_0171_ls_qf_save_program-s - replication factor C subunit 2RFC2
icon_0171_ls_qf_save_program-s - replication factor C subunit 3RFC3
icon_0171_ls_qf_save_program-s - replication factor C subunit 4RFC4
icon_0171_ls_qf_save_program-s - replication factor C subunit 5RFC5
icon_0171_ls_qf_save_program-s - replication protein A1RPA1
icon_0171_ls_qf_save_program-s - solute carrier family 19 member 1SLC19A1
icon_0171_ls_qf_save_program-s
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What is DNA mismatch repair (MMR)?
Mismatch repair (MMR) is a highly conserved pathway present in both prokaryotes and eukaryotes, responsible for correcting base-pairing errors – a type of DNA damage that arises during DNA replication. These errors include mismatches and small insertion-deletion loops missed by the proofreading activity of DNA polymerases. In eukaryotes, MMR operates primarily during the S and G2 phases of the cell cycle, when replication-associated errors are most likely to occur, and shortly thereafter while strand discrimination signals remain intact. By maintaining the accuracy of DNA synthesis, MMR plays a key role in preventing microsatellite instability and significantly reduces the risk of cancer and other genetic diseases.
Steps in the DNA mismatch repair process
The DNA mismatch repair mechanism is generally broken down into five steps: recognition of the mismatch, recruitment of other repair proteins, strand discrimination, excision of the strand with the error and finally resynthesis and ligation.
Recognition of the DNA mismatch
The first and most critical step in mismatch repair of DNA is recognizing the mismatch. As new DNA is synthesized, specialized proteins including the MutSα and MutSβ complexes in eukaryotes scan the sequence looking for base-base mismatches and small insertion-deletion loops. Once detected, they bind the mismatch signaling that repair is needed.
Recruitment of other DNA mismatch repair proteins
As part of the signal that repair is needed, the MutS complexes recruit additional proteins, including the MutLα complex in eukaryotes, which coordinates the downstream steps. In some contexts, alternative MutL complexes (MutLβ or MutLγ) may be involved, particularly during meiosis or specialized repair processes.
Strand discrimination
As the DNA mismatch repair machinery assembles, its first task is to distinguish between the original template strand and the newly synthesized strand that contains the error. In eukaryotes, the repair machinery accomplishes strand discrimination through a combination of interaction with replication machinery components, specifically the replicative clamp PCNA (proliferating cell nuclear antigen), and detecting transient nicks present in the newly synthesized strand but not the template strand. This step is critical to ensuring that the erroneous sequence is removed.
Excision of the strand with the error
Repair of the DNA mismatch begins by nicking the newly synthesized strand near the site of the error. Exonucleases like EXO1 are then able to digest the region of the strand containing the mismatch, creating a segment with a single-stranded gap.
Resynthesis and ligation
In the final step of mismatch repair of DNA, DNA polymerase uses the template provided by the single strand to resynthesize the DNA, filling the gap with the correct sequence. Once the gap has been closed, DNA ligase seals the final nick in the DNA backbone, ensuring continuity of the strand.
Key proteins involved in the DNA mismatch repair pathway
Multiple proteins and complexes are involved in the DNA mismatch repair process. Key components include the MSH2-MSH6, MSH2-MSH3 and MLH1-PMS2 heterodimers, EXO1, PCNA, DNA polymerase δ and DNA ligase 1.
MSH2-MSH6 heterodimer
The MSH2–MSH6 heterodimer, also known as MutSα, is the primary sensor of mismatched DNA in eukaryotic cells. It specifically recognizes single base-base mismatches and small loops resulting from insertion or deletion of 1-2 nucleotides. After binding to the mismatch, MSH2-MSH6 undergoes a conformational change that enables it to slide along the DNA strand, recruiting additional components of the mismatch repair machinery.
MSH2-MSH3 heterodimer
The MSH2-MSH3 heterodimer, also known as MutSβ, plays a similar role as MSH2-MSH6, acting as a sensor of mismatched DNA in eukaryotic cells. It optimally recognizes larger loops resulting from insertion or deletion of >2 nucleotides – up to approximately 15 nucleotides. Larger loops are more likely to occur during replication of repetitive sequences, such as in microsatellite regions, resulting from DNA polymerase slippage. This makes MSH2-MSH3 especially important for maintaining microsatellite region stability.
MLH1-PMS2 heterodimer
The MLH1-PMS2 heterodimer, also known as MutLα, is recruited by MSH2-MSH6 and/or MSH2-MSH3. It acts as a coordinator and activator of downstream components that carry out repair of mismatched DNA. While MLH1 acts as a scaffold for complex assembly, PMS2 is an endonuclease that nicks the newly synthesized DNA strand resulting in recruitment of the EXO1 exonuclease.
EXO1
Exonuclease 1 (EXO1) is a 5’ to 3’ exonuclease. Once recruited to the site of the mismatch on the newly synthesized strand containing the error, EXO1 digests the DNA strand. Digestion starts at the nick introduced by MLH1-PMS2 and extends beyond the point of mismatch. EXO1 is capable of excising large stretches of the newly synthesized DNA strand, preventing mutations from becoming permanently fixed in the genome.
PCNA
Proliferating Cell Nuclear Antigen (PCNA) plays a key role in helping to recruit and stabilize mismatch repair machinery. It acts primarily as a molecular sliding clamp, encircling the DNA and sliding along it while coordinating both DNA synthesis and repair. PCNA acts as a scaffold, interacting with components like MSH6 and PMS2, tethering them to the site of the mismatch error. It coordinates first with EXO1 to excise the error-containing DNA strand, and then DNA polymerase δ to synthesize new DNA to fill the single-stranded gap.
DNA polymerase δ
Following excision of the DNA strand containing the mismatch error, DNA polymerase δ uses the error-free strand as a template, moving in a 5’ to 3’ direction to fill the gap with new DNA. When synthesizing DNA as part of normal replication processes, DNA polymerase δ simultaneously acts as a proofreader, identifying and removing incorrect nucleotides using its inherent 3’ to 5’ exonuclease activity. In the context of mismatch repair, this proofreading capability helps further ensure the fidelity of the repair.
DNA ligase I
Once the gap has been filled with new sequence, a nick remains in the DNA backbone. DNA ligase I catalyzes the formation of a phosphodiester bond between the exposed hydroxyl and phosphate groups, sealing the nick and completing the mismatch repair process.
MMR and chromatin remodeling
Eukaryotic DNA is packaged into nucleosomes, which can hinder repair factor access. DNA Mismatch Repair (MMR) machinery interacts with chromatin remodelers and histone chaperones (for example, CAF-1, FACT) to transiently displace or reposition nucleosomes near the mismatch, ensuring efficient repair before replication errors become permanent.
Health consequences of DNA mismatch repair dysfunction
Defects or dysfunction in the DNA mismatch repair system result in an increased rate of spontaneous mutation, leading to serious biological and clinical consequences.
Role in Lynch syndrome
Lynch syndrome, also known as hereditary nonpolyposis colorectal cancer, is a genetic disorder that increases an individual’s risk of developing certain types of cancers including colorectal and endometrial cancer. Loss-of-function mutations in DNA mismatch repair system components MSH2, MSH6, MLH1 and PMS2 result in hypermutation and are among the most common causes of Lynch syndrome.
Role in microsatellite instability (MSI) in cancer
Microsatellites are short, repetitive sequences of DNA that make slippage of DNA replication machinery more likely to occur, resulting in the introduction of errors. When the DNA mismatch repair system is compromised, these errors are less likely to be caught and fixed, making microsatellite instability a hallmark of some cancers.
Deficiency in MSH3 or MutSβ function frequently contributes to microsatellite instability, particularly in di- and tetranucleotide repeats which are less efficiently repaired by MutSα. MSH3 and MutSβ deficiency also contributes to Lynch syndrome, discussed above.
Other MMR-related disorders
Biallelic mutations in MMR genes cause constitutional mismatch repair deficiency (CMMRD), a rare pediatric condition characterized by early-onset brain tumors, hematologic malignancies and gastrointestinal cancers, along with café-au-lait skin spots resembling those in neurofibromatosis.
References
- Kunkel TA, Erie DA. Eukaryotic mismatch repair in relation to DNA replication. Annu Rev Genet. 2015;49:291–313.
- Peltomaki P, Nystrom M, Mecklin J, Seppala T. Lynch syndrome genetics and clinical implications. Gastroenterology. 2023;164(5):783–799.
- Gelsomino F, Barbolini M, Spallanzani A, Pugliese G, Cascinu S. The evolving role of microsatellite instability in colorectal cancer: A review. Cancer Treat Rev. 2016;51:19–26.