The integrity of the genetic code is continuously maintained by a complex network of cellular defense mechanisms. DNA must be copied with extraordinary precision every time a cell divides, but the DNA Polymerase occasionally incorporates an incorrect nucleotide during replication. DNA Mismatch Repair (MMR) proteins function as the cell’s immediate post-replication proofreading system. They scan the newly formed DNA strand for these subtle errors, correcting mistakes the polymerase missed and ensuring an extremely low overall mutation rate and preserving genomic stability.
Identifying DNA Errors
The Mismatch Repair system is highly specialized, primarily focusing on fixing errors that arise from the mechanical process of DNA replication. These replication mistakes fall into two main categories: base-base mismatches and small insertion or deletion loops (IDLs). A base-base mismatch occurs when the wrong base is incorporated, leading to an incorrect pairing, such as guanine (G) paired with thymine (T) instead of cytosine (C).
The second type of error, small IDLs, typically occurs in regions of the DNA known as microsatellites, which are short, repetitive sequences. When the DNA polymerase encounters these repetitive tracts, the two strands can slip against each other, causing the newly synthesized strand to gain or lose a few bases. The MMR system is specifically designed to recognize the resulting bulges or misalignments caused by these IDLs. The MMR pathway does not typically handle other forms of DNA damage, such as those caused by environmental factors, which are addressed by different repair systems like Nucleotide Excision Repair.
The Multi-Protein Repair Process
The correction of a replication error by the Mismatch Repair system occurs in distinct stages. The initial step is error recognition by protein complexes formed by MutS homologs. In human cells, this task is handled by two heterodimers: MSH2-MSH6, which identifies base-base mismatches and very small IDLs (1-base pair), and MSH2-MSH3, which preferentially recognizes the larger IDLs (two or more base pairs).
Once a mismatch is detected, the MSH complex recruits the MutL homolog, primarily the MLH1-PMS2 heterodimer. The assembly of these complexes around the error site marks the beginning of the targeting and excision phase. A challenge at this stage is distinguishing the faulty, newly synthesized strand from the correct, parental template strand.
In eukaryotes, the newly replicated strand is transiently marked by small breaks, or nicks. The MLH1-PMS2 complex acts as a coordinator, linking the MSH-bound mismatch to one of these nearby nicks on the new strand. This nick serves as a starting point for the excision machinery, which removes the segment of the new DNA strand containing the error. Exonuclease 1 (Exo1) is the primary enzyme responsible for this removal, degrading the DNA from the nick past the site of the mismatch.
The final stage is resynthesis, where the resulting gap is filled accurately. DNA Polymerase \(delta\) or \(epsilon\) uses the undamaged template strand as a guide to synthesize the correct sequence. The Polymerase can fill a gap that may span anywhere from a few to thousands of base pairs. Finally, DNA ligase seals the remaining break in the DNA backbone, completing the repair and restoring the original double helix.
Genetic Instability and Disease
A functional Mismatch Repair system maintains genomic stability, and defects in the genes encoding these proteins lead to instability. When MMR proteins are non-functional, the cell loses its ability to correct replication errors, and the spontaneous mutation rate increases dramatically, often by 100 to 1,000-fold. This failure is most evident in repetitive microsatellite sequences, where uncorrected IDLs lead to changes in repeat length, a phenomenon known as Microsatellite Instability (MSI).
The inheritance of a non-functional copy of an MMR gene, such as MLH1, MSH2, MSH6, or PMS2, is the genetic basis for Lynch Syndrome. This is the most common hereditary colorectal cancer syndrome, significantly increasing the lifetime risk for colorectal, endometrial, and other cancers. The presence of MSI-High (MSI-H) in a tumor is a direct molecular signature of a deficient MMR system and serves as an important clinical marker.
The high rate of mutation caused by deficient MMR drives the development of cancer by accelerating the accumulation of errors in genes that regulate cell growth and death. Errors accumulate in tumor suppressor genes and proto-oncogenes, disrupting their normal function and leading to uncontrolled cell proliferation. Understanding the molecular basis of MMR deficiency and MSI guides screening for Lynch Syndrome and informs treatment decisions, particularly concerning the use of immunotherapies.