Loss of DNA mismatch repair due to mutation or diminished expression of the MLH1 gene is associated with genome instability and cancer. In this study, we used a yeast model system to examine three circumstances relevant to modulation of MLH1 function. First, overexpression of wild-type MLH1 was found to cause a strong elevation of mutation rates at three different loci, similar to the mutator effect of MLH1 gene inactivation. Second, haploid yeast strains with any of six mlh1 missense mutations that mimic germ line mutations found in human cancer patients displayed a strong mutator phenotype consistent with loss of mismatch repair function. Five of these mutations affect amino acids that are homologous to residues suggested by recent crystal structure and biochemical analysis of Escherichia coli MutL to participate in ATP binding and hydrolysis. Finally, using a highly sensitive reporter gene, we detected a mutator phenotype of diploid yeast strains that are heterozygous for mlh1 mutations. Evidence suggesting that this mutator effect results not from reduced mismatch repair in the MLH1/mlh1 cells but rather from loss of the wild-type MLH1 allele in a fraction of cells is presented. Exposure to bleomycin or to UV irradiation strongly enhanced mutagenesis in the heterozygous strain but had little effect on the mutation rate in the wild-type strain. This damage-induced hypermutability may be relevant to cancer in humans with germ line mutations in only one MLH1 allele.The stability of eukaryotic genomes depends heavily on several DNA repair processes, including correction of DNA replication errors by the DNA mismatch repair (MMR) system (reviewed in references 19, 26, and 46). Mutations in genes that inactivate mismatch repair strongly elevate spontaneous mutation rates and predispose humans to cancer. Current evidence suggests that germ line human MSH2 and MLH1 mutations account for a majority of hereditary nonpolyposis colorectal cancer (HNPCC) cases (31). Many of these result in loss of intact protein and are thus predicted to completely inactivate MMR. Others, such as the MLH1 missense mutations found in more than 30 HNPCC families (15,25,31), are often inferred to be pathogenic if they are nonconservative changes in evolutionary conserved amino acids, if they cosegregate with the disease, and/or if they are not observed in the normal population. However, unlike mutations that lead to protein truncation, single amino acid changes may not impair protein function or may only be partially inactivating.To assess the functional consequences of missense mutations in human MLH1, Shimodaira et al. (40) developed an assay in yeast, based on elimination of a dominant mutator phenotype conferred by expression of human MLH1 cDNA. They demonstrated that several human MLH1 missense mutations identified in HNPCC patients impair the function required for this dominant mutator effect. A more direct approach to address the effect of MLH1 missense mutations on MMR efficiency is based on the fact that the amino acid sequences of...