AID mutates E. coli suggesting a DNA deamination mechanism for antibody diversification

Abstract

After gene rearrangement, immunoglobulin variable genes are diversified by somatic hypermutation or gene conversion, whereas the constant region is altered by class-switch recombination. All three processes depend on activation-induced cytidine deaminase (AID), a B-cell-specific protein that has been proposed (because of sequence homology) to function by RNA editing. But indications that the three gene diversification processes might be initiated by a common type of DNA lesion, together with the proposal that there is a first phase of hypermutation that targets dC/dG, suggested to us that AID may function directly at dC/dG pairs. Here we show that expression of AID in Escherichia coli gives a mutator phenotype that yields nucleotide transitions at dC/dG in a context-dependent manner. Mutation triggered by AID is enhanced by a deficiency of uracil-DNA glycosylase, which indicates that AID functions by deaminating dC residues in DNA. We propose that diversification of functional immunoglobulin genes is triggered by AID-mediated deamination of dC residues in the immunoglobulin locus with the outcome--that is, hypermutation phases 1 and 2, gene conversion or switch recombination--dependent on the way in which the initiating dU/dG lesion is resolved.

Immunoglobulin gene conversion in chicken DT40 cells largely proceeds through an abasic site intermediate generated by excision of the uracil produced by AID‐mediated deoxycytidine deamination

“…Inhibition of UDG correlates with diminished IgV Q gene conversion in a frameshift reversion assay. (A) Components of two main DNA repair pathways are envisaged to compete for processing the AID-generated initiating dU/dG lesion in the DNA deamination model of antibody gene diversification [5]. APE, apurinic/apyrimidinic site endonuclease; ExoI, exonuclease 1; Ts, transition mutation; Tv, transversion mutations.…”

“…Mechanistically, both processes appear to be triggered by activation-induced deaminase (AID)-catalyzed deamination of deoxycytidine (dC) to deoxyuridine (dU) within the IgV gene [1][2][3][4][5][6]. Although gene conversion is presumably achieved by recombination-mediated repair of the resultant DNA lesion using proximal IgV pseudogenes [7], the precise mechanism remains obscure.…”

Down-regulation of DNA polymerase β accompanies somatic hypermutation in human BL2 cell lines

“…It is thought that this process is initiated with conversion of cytosine to uracil by the enzymatic activity of the activation-induced cytidine deaminase (AID) [3][4][5]. It has been proposed that uracil-DNA formed by AID is removed by uracil-DNA glycosylase (UDG) leaving the toxic apurinic/apyrimidinic (AP) site.…”

Biased dA/dT somatic hypermutation as regulated by the heavy chain intronic iEμ enhancer and 3′Eα enhancers in human lymphoblastoid B cells

“…As such, AID was thought to edit an unknown mRNA precursor to yield novel mRNAs, which would in turn encode endonucleases to cleave targeted DNA at hypermutating V(D)J regions or switch (S) regions (RNA editing hypothesis) (Honjo et al, 2002Doi et al, 2003;Begum et al, 2004;Nagaoka et al, 2005). However, mounting evidence indicates that AID directly deaminates DNA dC residues (Petersen-Mahrt et al, 2002;Pham et al, 2003), yielding dU:dG mispairs, which are replicated over or dealt with either the base excision repair (BER) or the mismatch repair (MMR) pathways to introduce mutations through the intervention of translesion DNA polymerases, such as pol ζ, pol η and pol θ (Rada et al, 2004). In addition, accumulating evidence suggests that mutations can be introduced by the same translesion DNA polymerases (Zan et al, 2001;Diaz and Casali, 2002;Diaz and Lawrence, 2005) while repairing DNA breaks, including double stranded DNA breaks (DSBs) involving resected ends generated through AID-dependent DNA deamination (Bross et al, 2000;Papavasiliou and Schatz, 2000;Wu et al, 2003;Zan et al, 2003;Nagaoka et al, 2005;Xu et al, 2005).…”