Non-canonical actions of mismatch repair

Abstract

At the heart of the mismatch repair (MMR) system are proteins that recognize mismatches in DNA. Such mismatches can be mispairs involving normal or damaged bases or insertion/deletion loops due to strand misalignment. When such mispairs are generated during replication or recombination, MMR will direct removal of an incorrectly paired base or block recombination between nonidentical sequences. However, when mispairs are recognized outside the context of replication, proper strand discrimination between old and new DNA is lost, and MMR can act randomly and mutagenically on mispaired DNA. Such non-canonical actions of MMR are important in somatic hypermutation and class switch recombination, expansion of triplet repeats, and potentially in mutations arising in nondividing cells. MMR involvement in damage recognition and signaling is complex, with the end result likely dependent on the amount of DNA damage in a cell.

Keywords: DNA damage; DNA replication fidelity; Mispaired base; Mutagenesis; Replication; Strand discrimination.

Fig. 1

Variable effects of MMR recognition of a lesion-containing mismatch. A blue line indicates the template strand of replication, and red indicates the newly synthesized strand. (A) MMR recognition of a mismatch containing a lesion on the primer strand will result in degradation of the primer strand followed by resynthesis and elimination of the lesion. (B) MMR recognition of a mismatch containing a lesion on the template strand can result in degradation of the primer strand, but resynthesis will not remove the lesion. (C) MMR recognition of a mismatch containing a lesion outside of replication is problematical. In the absence of a nick in the DNA, there will likely be no DNA excision. However, the appearance of a nick, either spontaneously or by activation of MutLα (see text), could give rise to DNA excision, independent of which strand was newly replicated or contained a lesion.

Fig. 2

Action of MMR on base-base mispair outside of replication. An oligonucleotide (purple segment) is used to introduce a wild-type sequence into a mutant TRP5 gene. If the oligonucleotide is not removed by MMR during replication and persists into G2, tryptophan can be made if the oligonucleotide sequence is on the transcribed strand (TS), but not if the oligonucleotide is directed to the nontranscribed strand (NTS). In the presence of MMR, but not in the absence, there are many more Trp+ revertant cells when the oligonucleotide is directed to the NTS, and fewer when the oligonucleotide is directed to the TS [71].

Fig. 3

MMR activity on an 8-oxoG-A mispair. 8-oxoGTP is introduced into yeast cells and can be incorporated into the genome; indicated here is 8-oxoGTP incorporated into the NTS of a mutant TRP5 gene. If the 8-oxoGTP persists in the genome into G2 phase, in the absence of MMR no tryptophan can be produced and no revertant cells appear on selective plates. However, in the presence of MMR, recognition of the 8-oxoG-A mispair can result in excision of the template strand opposite the 8-oxoG followed by insertion of a C, which allows tryptophan production [71].

Fig. 4

MMR and 8-oxoG replication. (A) In wild-type cells, reversion of the trp5-A149C allele is very low. In ogg1 cells, which do not repair 8-oxoG opposite a C, reversion rates are increased more than 10-fold, indicating that many insertions of A opposite 8-oxoG are tolerated. In the further absence of MMR (msh6), reversion rates are increased another order of magnitude, indicating that many A-8-oxoG mispairs were eliminated by MMR [13]. (B) An 8-oxoG was placed into a single location in the yeast genome and its replication monitored [88]. In wild-type cells, replication was 98% accurate. Accuracy was only slightly decreased in the absence of MMR, to 95%. Pol η is the only DNA polymerase that is able to replicate 8-oxoG accurately, and in its absence, but in the presence of MMR, overall accuracy of 8-oxoG replication was 93%. The absence of both MMR and Pol η led to very inaccurate replication, an average of 40%. These experiments suggest that when low levels of 8-oxoG are present in cells, the presence of either Pol η or MMR is sufficient to prevent most mutations, but when higher levels of 8-oxoG are present in the cell (as in ogg1 cells), both Pol η and MMR are necessary. Even higher levels of oxidative damage in the cell can outstrip the capacity of Ogg1, Pol η, and MMR to prevent mutation [13].