Each light-chain V region, for example, is encoded by a DNA sequence assembled from two gene segments—a long V gene segment and a short joining or J gene segment (Figure 24–28). Each heavy-chain V region is similarly constructed by combining gene segments, but here an additional diversity segment, or D gene segment, is also required (Figure 24–29). In addition to bringing together the separate gene segments of the Ig gene, these rearrangements also activate transcription from the gene promoter through changes in the relative positions of the cis-regulatory DNA sequences acting on the gene. Thus, a complete Ig chain can be synthesized only after the DNA has been rearranged.
The large number of inherited V, J, and D gene segments available for encoding Ig chains contributes substantially to Ig diversity, and the combinatorial joining of these segments (called combinatorial diversification) greatly increases this contribution. Any of the 35 or so functional V segments in our κ light-chain locus, for example, can be joined to any of the 5 J segments (see Figure 24–28), so that this locus can encode at least 175 (35 × 5) different κ-chain V regions. Similarly, any of the 40 V segments in the human heavy-chain locus can be joined to any of the 23 or so D segments and to any of the 6 J segments to encode at least 5520 (40 × 23 × 6) different heavy-chain V regions. By this mechanism alone, called V(D)J recombination, a human can produce 295 different VL regions (175 κand 120 λ) and 5520 different VH regions. In principle, these could then be combined to make over 1.5 × 106 (295 × 5520) different antigen-binding sites.
V(D)J recombination is mediated by an enzyme complex called V(D)J recombinase, which recognizes recombination signal sequences in the DNA that flanks each gene segment to be joined. Although the process ensures that only appropriate gene segments recombine, a variable number of nucleotides are often lost from the ends of the recombining gene segments, and one or more randomly regions of DNA to be joined chosen nucleotides are also inserted. This random loss and gain of nucleotides at joining sites is called junctional diversification, and it enormously increases the diversity of V-region coding sequences created by V(D)J recombination (up to about 108-fold), specifically in the third hypervariable region. This increased diversification comes at a price, however. In many cases, it shifts the reading frame to produce a nonfunctional gene, in which case the developing B cell fails to make a functional Ig molecule and consequently dies in the bone marrow. Once a B cell makes a functional heavy chain and light chain that form an antigen-binding site, it turns off the V(D)J recombination process, thereby ensuring that the cell makes Ig of only one antigen-binding specificity.
B cells making BCRs that bind strongly to self antigens in the bone marrow would be dangerous. Such B cells maintain expression of an active V(D)J recombinase and are activated by such self-binding to undergo a second round of V(D)J recombination in a light-chain locus, thereby changing the specificity of its BCR—the process of receptor editing discussed earlier; self-reactive B cells that fail to change their specificity die by apoptosis, in the process of clonal deletion (see Figure 24–21).
As mentioned earlier, with the passage of time following an infection or vaccination, there is usually a progressive increase in the affinity of the antibodies produced against the pathogen. This phenomenon of affinity maturation is due to