Interference of mismatch and base excision repair during the processing of adjacent U/G mispairs may play a key role in somatic hypermutation

Abstract

In eukaryotic mismatch repair (MMR), degradation of the errorcontaining strand initiates at nicks or gaps that can be up to a kilobase away from the mispair. These discontinuities may be the ends of Okazaki fragments or the 3 -termini of the leading strands during replication, whereas the termini of invading strands may fulfill this role during recombination. Here we show that, in extracts of human cells, MMR can initiate also at sites of ongoing base excision repair. Although unlikely under normal circumstances, this situation may arise in vivo during somatic hypermutation (SHM) and class switch recombination of Ig genes, where activation-induced cytidine deaminase (AID) generates multiple U/G mismatches in the variable or switch regions. Uracil should normally be excised by base excision repair (BER), but we show here that MMR proteins activated by a nearby mismatch interfere with uracil processing to generate long single-stranded gaps. We postulate that, in a subset of the repair events, filling-in of the MMR-generated gaps might be catalyzed by the error-prone polymerase-, rather than by the high-fidelity polymerase-␦. Because polymerase-has a propensity to misinsertions opposite adenine residues, the above mechanism would help explain why SHM affects not only C/G, but also A/T base pairs.antibody diversity ͉ class switch recombination

Mammalian mismatch repair: error-free or error-prone?

“…Specifically, that MutSα/MutLα activated by binding to a U/G mismatch might "hijack" a cleaved abasic site generated by the sequential action of uracil DNA glycosylase (UDG) and AP-endonuclease APE1 during the processing of a nearby U/G mismatch that was being processed by BER (Figure 3Ac). This was indeed the case in vitro: when BER was inhibited, so was MMR [20]. This study clearly demonstrated that BER intermediates can be utilized as EXO1 entry points during MMR.…”

“…We could show that strand breaks or gaps generated during base excision repair (BER) could be utilized for MMR initiation [20]. Most recently, S. cerevisiae polymerase-ε, which catalyzes the synthesis of the leading strand [21], was shown to occasionally incorporate also ribonucleotides into DNA during replication [22].…”

“…If MMR indeed uses BER intermediates as initiation sites [20], how and why does the normally error-free repair of the exonuclease-generated gaps suddenly become error-prone, such that it might lead to extensive mutagenesis at the immunoglobulin loci? The answer to this question may be forthcoming: MMR protein concentration in cells has been reported to increase during S-phase [44] and they appear to be recruited to replicating DNA in a PCNA-dependent manner, at least in vitro [45].…”

Mechanism of somatic hypermutation at the WA motif by human DNA polymerase η

“…Although the mechanism of SHM and its target selection is incompletely understood, activation-induced cytidine deaminase (AID) (4,5), which converts cytosine into uracil, for example, in the RGYW motif, initiates SHM by converting a C:G base pair to a U:G mismatch. Removal of the U by uracil-DNA glycosylase (UNG) generates an abasic site in the DNA, which may lead to a variety of base substitutions (6)(7)(8). For the WA motif, it is suggested that after AID-dependent deamination of a cytosine, recognition of the U:G mismatch by mismatch repair protein MutSα (MSH2-MSH6 heterodimer, in which MSH stands for MutS Homolog) leads to the recruitment of DNA polymerase η (Pol η), and with an incision made by UNG the ensuing short-patch repair synthesis results in mutations of A:T pairs to G:C (Fig.…”

Differential expression of APE1 and APE2 in germinal centers promotes error-prone repair and A:T mutations during somatic hypermutation

“…10) is subsequently filled in by DNA Pols, including error-prone translesion Pols, which spreads mutations beyond the initiating AID-induced lesion. The combined, but noncompeting interaction of the UNG and MMR pathways in generating mutations at A:T base pairs (bp) has been described (10)(11)(12). This mismatch repair-dependent process has been termed phase II of SHM (3).…”