The DNA of all organisms is continuously exposed to exogenous and endogenous genotoxic agents. Fortunately, through the concerted actions of several DNA repair and mutation avoidance pathways, DNA damage can be removed and an organism’s genomic stability maintained. DNA base-base mismatches are generated as a result of the inherent replication errors made by the DNA replication machinery, as well as during the meiotic pairing of homologous but non-identical chromosomes. Through the coordinated actions of the highly conserved DNA mismatch repair (MMR) system, these errors are detected, removed and corrected, thus restoring the integrity of the DNA. In the absence of DNA MMR, genetic instability is unavoidable, resulting in the accumulation of mutations, and in mammals, a susceptibility to cancer. To better understand the roles of the MMR system in mutation avoidance during DNA replication, meiosis, and in nuclear apoptosis, we have utilized the nuclear dimorphic, ciliate protozoan Tetrahymena thermophila. We have identified seven putative MMR homologues; two are similar to eukaryotic MLH1 and PMS2, respectively, and five are similar to eukaryotic MutS homologues, one with eukaryotic MSH2 and four with MSH6. Our studies demonstrate that during conjugation, the relative transcript abundance of each MMR homologue is increased compared to vegetatively growing or nutritionally deprived (starved) cells. Also, the expression profile throughout conjugation is bimodal, corresponding to micronuclear (MIC) meiosis and macronuclear (MAC) anlagen development, both periods in which DNA replication occurs. Cells containing macronuclear knockouts of the PMS2, MSH2 and MSH6_1 genes were unable to successfully pair and complete conjugation, but were viable throughout vegetative growth. Cells in which the macronuclear MSH6_2 gene was knocked out had a phenotype that was similar to wild-type cells, during conjugation and vegetative growth. Interestingly, we observed that the MIC of cells containing MAC knockouts of the PMS2 and TML1 genes appear to have decreased copy number of specific “target sequences”, as determined by qPCR using the Random Mutation Capture (RMC) assay. This decrease reflects neither a loss of micronuclei nor a reduction in total micronuclear DNA content. These studies demonstrate that the PMS2, TML1, MSH2, and MSH6_1 homologues are necessary for the maintenance of micronuclear function and stability during conjugal development and vegetative growth, whereas the remaining MSH6 homologues have less pronounced roles in DNA repair and development. Additionally, macronuclear development in Tetrahymena appears less reliant on the DNA mismatch repair system and perhaps uses alternate surveillance mechanisms to maintain genomic stability during asexual and sexual development. / Graduate / 0306 / 0379 / 0307