Antibody diversification caused by disrupted mismatch repair and promiscuous DNA polymerases

Abstract

The enzyme activation-induced deaminase (AID) targets the immunoglobulin loci in activated B cells and creates DNA mutations in the antigen-binding variable region and DNA breaks in the switch region through processes known, respectively, as somatic hypermutation and class switch recombination. AID deaminates cytosine to uracil in DNA to create a U:G mismatch. During somatic hypermutation, the MutSα complex binds to the mismatch, and the error-prone DNA polymerase η generates mutations at A and T bases. During class switch recombination, both MutSα and MutLα complexes bind to the mismatch, resulting in double-strand break formation and end-joining. This review is centered on the mechanisms of how the MMR pathway is commandeered by B cells to generate antibody diversity.

Keywords: Activation-induced deaminase; Class switch recombination; DNA polymerase η; Mismatch repair; Somatic hypermutation.

Fig. 1. MMR proteins create mutations at A:T bp during SHM

AID deaminates cytosine to uracil in immunoglobulin variable region DNA and generates a U:G mismatch that is recognized by the MSH2-MSH6 heterodimer. A single-strand DNA gap is produced at the mismatch by EXO1 and an unknown nick instigator. Monoubiquitinated PCNA homotrimer recruits the error-prone DNA pol η to fill in the gap, copying the original T with a G instead of an A. DNA replication results in the G:T mismatch being permanently affixed in one of the two daughter cells as a mutation to G:C.

Fig. 2. MMR proteins assist in the conversion of BER-induced single-strand nicks to double-strand break substrates for CSR

AID-induced uracils in immunoglobulin switch region DNA can be bound by either BER or MMR proteins. In BER, UNG and APE remove the uracil and create a single-strand nick. MMR proteins MSH2-MSH6 and MLH1-PMS2 encounter a uracil on the opposite strand and attract EXO1 and PCNA to an adjacent nick. EXO1 excises the sequence between the nicks, leading to a 5’ overhang that is processed by PCNA and a translesion polymerase to create a blunt double-strand break. Alternatively, the overhang can be deleted by EXO1 or a 5’ flap endonuclease. An analogous process can occur with MMR proteins acting on a uracil located 3’ to the BER-induced nick (not shown). When double-strand breaks occur simultaneously in different switch regions, recombination produces a new switch junction mediated by NHEJ factors, as illustrated here between Sμ and Sγ1.