Antigen Receptor Diversity

The human genome is presently estimated to contain from 70 thousand to as many as 100 thousand (10⁵) genes (in a few years we should know the number exactly). The number of T-cell receptors for antigen (TCRs) that we make is estimated at 2.5 x 10⁷; the number of different kinds of antibody molecules (BCRs) is probably about the same.

Link to discussion of the structure of BCRs and TCRs.

How could 10⁵genes encode 2.5 x 10⁷ different TCRs and the same number of different BCRs?

The answer: each receptor chain (heavy, kappa, and lambda chains for BCRs; alpha and beta chains for TCRs) is encoded by several different gene segments.

The genome contains a pool of gene segments for each type of chain. Random assortment of these segments makes the largest contribution to receptor diversity.

B cells

Gene segment usage for BCRs

For the heavy (H) chains of BCR's (antibodies), the gene segments are:

About 50 V_H segments. Each of these encodes most of the N-terminal of the antibody, including the first two (but not the third) hypervariable region.
About 29 D_H (="diversity") gene segments. These encode part of the third hypervariable region.
6 J_H (="joining") gene segments. These encode the remainder of the V region of the BCR (including the remainder of the third hypervariable region).
9 C_H gene segments. These encode the C region of the BCR (and the antibody derived from it). The C gene segments are
- 1 mu; encodes the C region of IgM
- 1 delta for IgD
- 4 gamma gene segments for the four types of IgG
- 1 epsilon for IgE
- 2 alpha gene segments for the two types of IgA

All of these gene segments are clustered in a complex locus on chromosome 14.

During the differentiation of the B cell (and long before any possible encounter with an antigen), the DNA in this locus is cut and recombined to make an intact gene for the heavy chain. This gene can then be transcribed into mRNA, which is, in turn, translated into the heavy (H) polypeptide chain.

The random assembly of 50 V_H, 29 D_H, and 6 J_H gene segments provides a minimum of 8.7 x 10³ different possible combinations.

But the possibilities of antibody V region diversity turn out to be greater than that. The recombination process is not precise.

the exact points of splicing
- between V_H and D_H and
- between D_H and J_H
can vary over several nucleotides
extra nucleotides, called N regions, can also be inserted at these joints
once the H chain gene is assembled, transcribed, and translated, the resulting H chain can pair with an L chain that is itself the product of a similar recombination process occurring
- on chromosome 22 for lambda gene segments
- on chromosome 2 for kappa gene segments.
In the case of kappa light chains, a B cell can generate one of as many as 1.6 x 10⁴ possible V-kappa regions.

As the table shows, this lays the foundation for a potential B-cell repertoire of 14 x 10⁹ different antibody V regions.

Antibodies (BCRs)	Gene Segments	Combinations
V-kappa	32
J-kappa	5
N regions	100	1.6 x 10⁴ kappa chains
V_H	50
D_H	29
J_H	6
N regions	100	8.7 x 10⁵ H chains
Any H chain with any kappa L chain		14 x 10⁹

Diversity comes at a price

The combining of V, D, and J gene segments coupled with the random incorporation of extra nucleotides (N regions) at the joints, creates enormous coding variability. It also creates a high risk (two times out of three) of introducing a frameshift so that the codons for the rest of the V region encode nonsense. Although many B cells are wasted, the odds are not quite as bad as they seem:

If the B cell fails to make a functional product from the cluster of gene segments on one of its chromosomes, it can turn to the gene segments on its homolog and try again.
If it fails both times to make a functional kappa L chains, it still has two tries at making a functional lambda L chain.

Somatic Mutation and Antibody Diversity

The diversifying mechanisms described above take place before the B cell encounters antigen. After a B cell encounters antigen, it may begin mitosis, growing into a clone of cells synthesizing the same BCR (and, eventually, secreting antibodies with the same binding site). As in any dividing cell, point mutations occur. While most are deleterious, those occurring in the DNA encoding the hypervariable regions MAY generate a binding site with increased affinity for its epitope. These are favorable mutations, and the "sub-clone" in which they occur tends to be favored and may replace the ancestral clone. The result is affinity maturation, the production of antibodies of ever-increasing affinity for the antigen.

Switching C_H regions

As B cells grow into a clone in response to antigen, they may rearrange their DNA once again. For example, a B cell that has assembled a complete gene for the H chain of IgM (mu), may cut the gene on the 3´ side of the assembled V-region segments and move the assembly to the 5´ side of another of its C-region gene segments. Now the cell begins to make a different kind of antibody, such as IgG or IgA. But the antigen-specificity of the antibody remains the same because the N-terminal of the H chain remains unchanged (as does the L chain).

This switching mechanism enables the body to produce antibodies with different effector functions; that is, different means of dealing with the same antigen.

The ability of a B cell to switch C_H gene segments depends on its receiving help from helper T cells.

T Cells

Alpha/beta T cells

The most abundant T cells in the blood express a receptor for antigen (TCR) that is a heterodimer of two chains designated alpha and beta. Each of these is encoded by a gene assembled from V, D, J, and C gene segments. Like BCRs, there are multiple variants of these gene segments arranged in clusters:

alpha chain gene segments on chromosome 14 and
beta chain gene segments on chromosome 7

As the table shows, the potential repertoire of receptors for alpha/beta T cells appears to be somewhat greater than we found for B cells. However, T cells do not seem to use somatic mutation to increase receptor diversity. And, actual measurements of the repertoire in humans reveals a figure closer to 2.5 x 10⁷.

T cell receptors (TCRs)	Gene segments	Combinations
V-alpha	50
J-alpha	50
N regions	100	2.5 x 10⁵ alpha chains
V-beta	20
J-beta	13
D-beta	2
N regions	100	5.2 x 10⁴ beta chains
Any alpha with any beta chain		1.3 x 10¹⁰

Gamma/delta T cells

The TCR repertoire of gamma/delta T cells seems much less than that for their alpha/beta cousins. The

gamma chain gene segments are clustered on chromosome 7
the delta chain gene segments are clustered on chromosome 14 (within the alpha chain cluster)

Welcome&Next Search

4 November 1999