In budding yeast, the MLH1-PMS1 heterodimer is the major MutL homolog complex that acts to repair mismatches arising during DNA replication. Using a highly sensitive mutator assay, we observed that Saccharomyces cerevisiae strains bearing the S288c-strain-derived MLH1 gene and the SK1-strain-derived PMS1 gene displayed elevated mutation rates that conferred a long-term fitness cost. Dissection of this negative epistatic interaction using S288c-SK1 chimeras revealed that a single amino acid polymorphism in each gene accounts for this mismatch repair defect. Were these strains to cross in natural populations, segregation of alleles would generate a mutator phenotype that, although potentially transiently adaptive, would ultimately be selected against because of the accumulation of deleterious mutations. Such fitness ''incompatibilities'' could potentially contribute to reproductive isolation among geographically dispersed yeast. This same segregational mutator phenotype suggests a mechanism to explain some cases of a human cancer susceptibility syndrome known as hereditary nonpolyposis colorectal cancer, as well as some sporadic cancers.colorectal cancer ͉ incompatibility T he highly conserved mismatch repair (MMR) system contributes to genome stability by repairing errors that occur during DNA replication (1). In Escherichia coli, MMR is initiated by the binding of MutS protein to DNA mismatches. MutL interacts with the MutS-mismatch complex and activates downstream repair factors. Multiple MutS homologs (MSH) and MutL homologs (MLH) have evolved in eukaryotes that form heterodimers with specialized functions in DNA repair and recombination (2, 3). In Saccharomyces cerevisiae, MSH2-MSH3 and MSH2-MSH6 function in mismatch recognition, and MLH1-PMS1 is the primary MLH heterodimer in postreplicative MMR. Mutations in MSH and MLH genes that act in MMR elevate mutation rate, as measured in reversion and forward mutation assays, and reduce spore viability of diploid cells due to the accumulation of recessive lethal mutations (4-6). In addition, MMR proteins act to prevent recombination between divergent DNA sequences. This activity has been shown to prevent chromosomal rearrangements (7,8) and to enforce reproductive barriers between species (9, 10).Previously we created 60 alleles of the S. cerevisiae MLH1 gene from the S288c strain (cMLH1) in which clusters of charged residues were simultaneously changed to Ala (11). These alleles were tested for defects in MMR in the S288c (12) and SK1 (13) strains. More than one-third of the mutation set conferred a more severe MMR defect in SK1 strains than in S288c strains. Two mutations, cmlh1-29 and cmlh1-56, conferred wild-type-like phenotypes in S288c but null-like phenotypes in SK1. Introduction of the S288c PMS1 gene into the SK1 strain suppressed the mutator phenotype of these mutants, suggesting that the MMR phenotype was due to incompatibility, or negative epistasis, between MLH components (11).The influences of epistatic interactions on a wide variety of traits and proc...