Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

1320 Chapter 24: The Innate and Adaptive Immune Systems
antigenic determinant, albeit with low affinity—K a ≈ 10 5 –10 7 liters/mole. After
stimulation by antigen and helper T cells, B cells can switch from making IgM and
IgD to making other classes of Ig—a process called class switching. In addition, the
binding affinity of these Igs for their antigen progressively increases over time—a
process called affinity maturation. Thus, antigen stimulation generates a secondary
Ig repertoire, with a greatly increased affinity (K a up to 10 11 liters/mole) and
diversity of both Ig classes and antigen-binding sites.
How can each of us make so many different Igs? The problem is not quite as
formidable as it might first appear. Recall that the variable regions of the Ig light
and heavy chains usually combine to form the antigen-binding site. Thus, if we
had 1000 genes encoding light chains and 1000 genes encoding heavy chains, we
could, in principle, combine their products in 1000 × 1000 different ways to make
10 6 different antigen-binding sites. Nonetheless, we have evolved special genetic
mechanisms to enable our B cells to generate an almost unlimited number of different
light and heavy chains in a remarkably economical way. We do so in two
steps. First, before antigen stimulation, developing B cells join together separate
gene segments in DNA to create the genes that encode the primary repertoire of
low-affinity IgM and IgD proteins. Second, after antigen stimulation, the assembled
Ig genes can undergo two further changes—mutations that can increase the
affinity of their antigen-binding site and DNA rearrangements that switch the
class of Ig made. Together, these changes produce the secondary repertoire of
high-affinity IgG, IgE, and IgA proteins.
We produce our primary Ig repertoire by joining separate Ig gene segments
together during B cell development. Each type of Ig chain—κ light chains, λ light
chains, and heavy chains—is encoded by a separate locus on a separate chromosome.
Each locus contains a large number of gene segments encoding the V region
of an Ig chain, and one or more gene segments encoding the C region. During the
development of a B cell in the bone marrow, a complete coding sequence for each
of the two Ig chains to be synthesized is assembled by site-specific genetic recombination
(discussed in Chapter 5). Once a V‐region coding sequence is assembled
next to a C‐region sequence, it can then be co-transcribed and the resulting RNA
transcript processed to produce an mRNA molecule that codes for the complete
Ig polypeptide chain.
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 V L regions (175 κ and 120 λ)
and 5520 different V H regions. In principle, these could then be combined to make
over 1.5 × 10 6 (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