DNA Mismatch Repair (MMR) is a quality control system that significantly increases the accuracy of genetic information transmitted during cell division. Although the primary replication machinery, DNA polymerase, is highly effective, it still makes occasional errors, such as misincorporations or the creation of small loops of extra or missing bases, called insertion or deletion loops. The MMR system acts as a post-replicative correction mechanism, sweeping the newly synthesized DNA strand to find and fix these remaining errors. This pathway corrects the vast majority of replication mistakes that escape initial proofreading, thereby maintaining the fidelity of the genome and dramatically reducing the mutation rate.
Essential Components of the MMR System
The molecular machinery responsible for mismatch repair is highly conserved across all life forms, though the specific proteins involved differ between simple bacteria and complex eukaryotes. The components are broadly categorized into two functional groups: recognition factors, which identify the error, and linking/execution factors, which coordinate the subsequent steps of the repair process. In bacteria like E. coli, the core components are MutS, MutL, and MutH. In eukaryotes, the system involves multiple homologous proteins. Eukaryotic recognition factors are heterodimers of MutS homologs (MSH). MutS\(\alpha\) (MSH2/MSH6) primarily detects single base mismatches and small insertion/deletion loops. MutS\(\beta\) (MSH2/MSH3) specializes in recognizing larger insertion/deletion loops, which can contain up to 16 excess nucleotides.
Linking and Execution Factors
The linking and execution functions are carried out by MutL homologs (MLH) in eukaryotes, forming heterodimers like MutL\(\alpha\) (MLH1/PMS2). These complexes act as molecular matchmakers, bridging the initial mismatch recognition complex to the downstream machinery necessary for excision. Accessory proteins, including DNA helicases and specialized exonucleases, are then recruited to carry out the physical removal of the damaged DNA segment.
The Repair Pathway: Mismatch Recognition and Strand Discrimination
The repair pathway begins when recognition factors, such as MutS\(\alpha\), bind to the mispaired bases or insertion/deletion loops that distort the DNA helix. Upon binding, the MutS complex undergoes a conformational change and recruits the MutL complex, forming a molecular signaling hub. This complex then scans the adjacent DNA segments, searching for a signal to identify the newly synthesized, error-containing strand. This process, known as strand discrimination, is essential because repairing the parental strand would permanently encode the error into the genome.
Strand Discrimination in Bacteria and Eukaryotes
In bacteria, strand discrimination uses transient DNA methylation. The parent strand is marked by methyl groups, while the new strand remains unmethylated, allowing the MutH enzyme to cleave the unmethylated strand near the mismatch. Eukaryotic cells lack MutH and rely on physical breaks (nicks) in the new strand, which naturally occur during replication. The MSH/MLH complex tracks along the DNA from the mismatch until it encounters the nearest nick, which serves as the entry point for the repair machinery. Proliferating Cell Nuclear Antigen (PCNA), loaded at the nick site, acts as a guiding factor to help the MutL\(\alpha\) complex correctly mark the error-containing strand for excision.
The Repair Pathway: Excision and Gap Filling
Once the newly synthesized strand is identified, the excision phase begins, requiring the coordinated action of several enzymes. The MutL\(\alpha\) complex, often stimulated by PCNA, introduces a nick on the error-containing strand near the mismatch, providing a clear start site for removal. A DNA helicase then separates the two strands, moving from the nick toward the mismatch. Following the helicase, a specialized exonuclease, such as Exonuclease 1 (Exo1) in eukaryotes, digests the single-stranded DNA segment containing the error. This “long-patch” excision removes a substantial segment of DNA, often spanning a thousand bases or more.
The resulting single-strand gap is filled by DNA polymerase \(\delta\), which uses the intact parental strand as a template. This polymerase works with the PCNA sliding clamp to ensure processivity and accuracy during the resynthesis. Finally, DNA ligase seals the remaining nick in the sugar-phosphate backbone, completing the repair.
Consequences of Defective Mismatch Repair
When the genes encoding the mismatch repair components are mutated or silenced, the system’s ability to correct replication errors is impaired. Failure in MMR leads to a significant increase in the spontaneous mutation rate, often by several hundredfold, a condition known as a mutator phenotype. This increased mutation rate is most noticeable in short, repetitive DNA sequences called microsatellites, resulting in a characteristic genomic instability known as microsatellite instability (MSI). This genomic instability accelerates the accumulation of mutations in genes controlling cell growth and survival, fueling cancer development.
MMR Deficiency and Cancer
Inherited defects in MMR genes, particularly MLH1 and MSH2, are the underlying cause of Lynch Syndrome (Hereditary Non-Polyposis Colorectal Cancer). This autosomal-dominant disorder significantly increases the lifetime risk of developing colorectal, endometrial, ovarian, and other cancers, often at an earlier age. MMR deficiency also occurs in sporadic cancers, commonly through the epigenetic silencing of the MLH1 gene. The inability to correct mispairs leads to a high tumor mutational burden, which is a distinguishing feature of MMR-deficient tumors. Recognizing this defect confirms diagnoses like Lynch Syndrome and influences treatment decisions, as these tumors often respond differently to certain therapies.