*5.2.2.3.2 AID, adaptive mutagenesis, and erroneous repair of uracil bases*

• *Cytosine deamination*. AID initiates the SHM process within target sequences by cytosine deamination in the rearranged variable regions and focuses on 3–4 bp SHM motifs that are greatly enriched in S regions and in portions of variable region exons that encode antigen-binding sites (CDR region). SHM of V(D)J exons in GC B-cells require transcription for AID targeting, as during CSR, and begins ∼150 bp downstream of the transcription start site (TSS) and extend

∼1–2 kb further downstream [50] (for review, see [51–54]). Hypermutable DNA sequences are found in the regions of IG genes, preferentially in sequences containing mutational "hotspots" corresponding predominantly to RGYW/WRCYmotifs (G: C is a mutable position, **R** = purine bases [A/G], **G** = guanine, **Y** = pyrimidine bases [C/T], **W** = A/T, **C** = cytosine) [55].


#### **Figure 8.**

*DNA deamination model of IG gene diversification by AID during SHM (adapted from [51]). AID creates mutations in DNA by deamination of cytosine base, which turns it into uracil, which is then targeted by BER or MMR mechanisms or simply replicated producing mutations. AID: activation-induced deaminase, APE: apyrimidinic/apurinic endonuclease, BER: base excision repair, bp: base pairs, CSR: class switch recombination, ExoI: mismatch repair exonuclease I, IG: immunoglobulin gene, IgV: immunoglobulin variable region, MMR: DNA mismatch repair, MSH2/6: mismatch recognition proteins, NHEJ: nonhomologous end joining, pol: polymerase, pol η: DNA polymerase eta, Rev1: Y-family DNA polymerase involved in DNA damage tolerance, SHM: somatic hypermutation, TLS: translesion DNA synthesis, UNG: uracil-DNA glycosylase, XRCC2/XRCC3: X-ray cross-complementing gene 2/3.*

**39**

clones.

activation.

*Immunogenetic Aspect of B-Cell Antigen Receptor Diversity Generation*

(pol η), a "wrong" TLS repair polymerase [56] (**Figure 8**).

mately ¾ basic changes modify the encoded amino acid [48]. *5.2.2.3.4 Impacts of mutations on affinity of BCR and secreted Ig*

b.If the U:G mismatch is recognized by the mismatch repair (MMR) protein pathway, the U:G lesion will be excised by Exonuclease I, resulting in degradation of the DNA strand surrounding the U, then the MSH2/MSH6 heterodimer induces the formation of a gap in the DNA. Unfaithful replication of a DNA strand will take place at the level of the gap by the TLS DNA polymerase eta

The frequency of IG region V gene mutations corresponds to approximately one bp change per 1000 bp per gene and per cell division/generation, while that affecting the rest of the cell DNA is much lower, and corresponds to about one bp change per 1010 bp per cell and per division. Of note, there is approximately a 50% chance during each division of B-cells that a mutation leads to a change in BCR, since it is known that each V region is encoded by approximately 360 bp and that approxi-

The low affinity of antibodies produced during the primary immune response tends to increase as the immune response progresses, thanks to the numerous point mutations in hypervariable regions of the IG V gene of the antigen-specific B-cell

Most mutations have no positive effect on the affinity of BCR or Ig produced,

Of the four types of possible mutations-silent, neutral, deleterious, and positiveonly deleterious mutations and positive mutations have an effect on the affinity of

i.The deleterious mutations are responsible for a decrease in the affinity of the antigen for its BCR, but also for the rapid division of B-cells (the expansion would overwhelm the lymphoid tissues), since they can induce modifications of the framework regions and thus disrupt the basic structure of Ig. The many B-cells that carry such mutations will be a target of apoptotic death by a negative selection process, either because they can no longer produce a functional BCR, or because they cannot efficiently internalize antigens through clonally distributed membrane BCRs. These apoptotic cells will invade GC and then be rapidly ingested by resident macrophages, giving rise to tingible body macrophages (TBM), containing dark nuclear debris in

ii.Positive mutations are less common than deleterious mutations and are responsible for increasing antigen affinity for its BCR and improving its binding. The small portion of daughter cells with many nucleotide substitutions in the Ig V region encoding gene that are derived from B-cell clones undergoing such mutations will be positively selected and will therefore have an increased survival rate relative to the cells expressing a low BCR affinity. Positive selection would be a consequence of the accumulation and concentration of many amino acid substitutions in CDRs of the Ig V region, as a result of nucleotide changes that alter amino acid sequences and so the

and frequently negatively affect their ability to bind antigen inducing B-cell

*DOI: http://dx.doi.org/10.5772/intechopen.90637*

*5.2.2.3.3 Frequencies of mutations*

the antigen for its appropriate BCR:

their cytoplasm [48].

protein structure.

b.If the U:G mismatch is recognized by the mismatch repair (MMR) protein pathway, the U:G lesion will be excised by Exonuclease I, resulting in degradation of the DNA strand surrounding the U, then the MSH2/MSH6 heterodimer induces the formation of a gap in the DNA. Unfaithful replication of a DNA strand will take place at the level of the gap by the TLS DNA polymerase eta (pol η), a "wrong" TLS repair polymerase [56] (**Figure 8**).
