AIDing antibody diversity by error-prone mismatch repair

Abstract

The creation of a highly diverse antibody repertoire requires the synergistic activity of a DNA mutator, known as activation-induced deaminase (AID), coupled with an error-prone repair process that recognizes the DNA mismatch catalyzed by AID. Instead of facilitating the canonical error-free response, which generally occurs throughout the genome, DNA mismatch repair (MMR) participates in an error-prone repair mode that promotes A:T mutagenesis and double-strand breaks at the immunoglobulin (Ig) genes. As such, MMR is capable of compounding the mutation frequency of AID activity as well as broadening the spectrum of base mutations; thereby increasing the efficiency of antibody maturation. We here review the current understanding of this MMR-mediated process and describe how the MMR signaling cascade downstream of AID diverges in a locus dependent manner and even within the Ig locus itself to differentially promote somatic hypermutation (SHM) and class switch recombination (CSR) in B cells.

Figure 1. MMR cascade during A:T mutagenesis at ssDNA patches in Ig genes

MMR pathway plays the major role introducing A:T mutations during SHM in B-cells. The MutSα heterodimer composed of MSH2 and MSH6 recognizes the AID-generated U:G mismatch. This initiates a series of processes to create a ssDNA gap around the original AID-induced lesion, by recruiting scaffolding proteins (e.g. PCNA), nucleases (e.g. EXO1), and yet unknown factors and activities such as the instigation of nick-directed mismatch repair. Finally, the ssDNA patch is resynthesized through a complex cycle of DNA polymerization, which involves the recruitment of low-fidelity error-prone polymerases, like Polη and Polκ, as opposed to the use of canonical high-fidelity polymerases like Polδ and Polε. Post-translational modifications of PCNA, mainly through ubiquitylation, have been shown to play a role in regulating the usage of these polymerases and in orchestrating the decision between error-free and error-prone repair.

Figure 2. MMR cascade orchestrates DSB-repair at Ig genes

DSBs are required to initiate CSR at S regions, and the MMR pathway plays a significant role promoting DSB formation. Similar to SHM, the MutSα heterodimer senses the AID-generated U:G mismatch, but here, the coordination of EXO1 nuclease activities and the MutLα heterodimer composed of MLH1 and PMS2, relays the MMR signaling cascade to favor the formation of DSBs. While Polη does not play a major role during CSR, PCNA ubiquitylation has been shown to be important for efficient CSR, therefore suggesting additional role(s). Once the break is produced, canonical DSB sensors like 53BP1, the ubiquitin ligases RNF8/RNF168 and the phosphorylated form of H2AX (γH2AX) ensure the initiation of recombination and ligation of the S junctions through non-homologous end joining (NHEJ) mechanisms. At this stage, MMR scaffolding functions and yet unknown regulating signals fine tune processing of the S-S junctions, balancing the use of two seemingly distinct versions of NHEJ: the canonical pathway and the alternative pathway.