Genetic Control of the Immune Response

Components of the Immune System

Three different types of white blood cells play central roles in the immune response in
vertebrates. These cells are :
1. B lymphocytes (called B cells because they are produced in bone marrow)
2. T lymphocytes (called T cells because they are produced in the thymus gland)
3. Macrophages
Antibodies are synthesized by B lymphocytes and are either secreted or remain membrane-
bound on the surface of B cell depending on the conditions. During the humoral immune
response, these antibodies bind to free antigens in the circulatory system and aglutinate them.
The resulting antibody-antigen complexes are then ingested are degraded by macrophages
(fig. 16.1, left). T lymphocytes mediate the cellular immune response. The T cells synthesize
antigen receptors that recognize antigens on cell surfaces and trigger the lysis of the antigen-
containning cells by activated T cells (fig. 16.1, right). Different T lymphocytes perform this
function in slightly different ways. However, in general, the attack of the T cell on the
antigen-carrying cell requires both the specific T cell receptor and one or more
histocompatibility antigen receptors. The mechanisms by which antibodies, T cell receptors,
and histocompatibility antigen receptors aare produced are discribed in the following sections
of this chapter.

Vast Repertore of Antibodies
The most remarkable aspect of the immune response, at least from a genetics
standpoint, is the seemingly infinite variety of antibodies that can be synthesized in response
to antigens that the animal has not previously encountered. How can an organism have
prepared to syhnthesize an antibody designed to bind very specifically to a particular antigen
without ever having made contact with the antigen ? Moreover, how can organism store
enough genetic information to code for the amino acid sequences of a virtually unlimited
variety of antibodies ? these and related questions about the immune response had puzzled
genetics for several decades. Within the last few years, however, the main features of the
answers to these questions have become clear.
We do not know how many diffeerent antibodies a mouse or a human can produce,
but we know that the number is very large, almost certainly in the millions. This presents a
paradox. The complete human genome contains about 3 x 10
9
nucleotide-pairs. If all of this
DNA were in the form of unintertide-pairs long, the genomewould contain a maximum of
about 3 million genes. Since we know that many of these genes code for various RNA
molecules, enzymes, and structural proteins, and we know that many of these genes contain
long noncoding introns, how can we account for the genetic information needed to code for
the plethora of different antibodies ?
Hypothese : Genetic Basis of Antibody Diversity
Past attempts to explain the genetic basis of antibody diversity can be roughly
grouped into three different hypotheses.
1. The grem line hypothesis stated that there is a separate germ line gene for each
antibody. (this agreed with our early knowledge about protein synthesis, but presented
the paradox of not enough DNA).
2. The somatic mutation hypothesis stated that there is only one or a few germ line
genes specifying each major class of antibodies amd that the diversity is generated by
a high frequency of somatic mutation mutation occuring lineages leading to
antibody-produc[ing cells. (there wasn no precedent for a high frequency of mutation
occuring in only certain genes and in only types of cells. By what mechanism could
occur, and how could it be regulated).
3. The minigene hypothesis stated that the diversity is generated by the shuffling of
many small segments of a few genes into a multitude of possible combinations. The
shuffling would occur by recombination processes in somatic cells. (this required
totally novel mechanisms for rearranging segments of DNA).
We know that the minigene hypothesis explains a great dela of the observed diversity.
However, we also know that somatic mutation contributes additional diversity. Finally, we
know that one segment (the constant region, see the following discussion) of each antibody
chain is specified by a gene or gene segment that is present in the genome in only a few
copies. Thus, all three hypotheses were correct in certain respects.

Structure of Antibodies
Antibodies belong to the class of proteins called immunoglobulins. Each antibody is a
tetramer composed of four polypeptides, two identical light chains and two identical heavy
chains, joined by disulfide bonds (fig. 16.2). the light chains are about 220 amino acids long,
and the heavy chains are about 440-450 amino acids long. Every chain, heavy and light, has
an amino-terminal variable region, within which the amino acid sequence varies among
antibodies specific for different antigens, and a carboxyl-terminal constant region, within
which the amino acid sequence is the same for all antibodies of a given immunoglobulin (Ig)
class, regardless of antigen-binding specificity. The variable regions of all antibody chains
are about 110amino acids long.
Regions of proteins that carry out particular functions are called domains. Each
antibody has two antigen-binding sites or domains, each of which is formed by the variable
regions of one light chain and heavy chain (fig. 16.3). in addition, the constant regions of the
two heavy chains interact to form a third domain, called the effector function domain, which
is responsible for the proper interaction of the antibody with other componentsof the immune
system.
There are five class of anttibodies : IgM, IgD, IgG, IgE, and IgA. The class to which
an antibody belongs, and thus the function that it carries out, is determined by the structure of
its heavy chain constant region (i.e., the structure of its effector function domain). For
example, IgD antibodies usually remain bound to the surfaces of the cells in which they are
synthesized, whereas IgG antibodies are usually secreted and circulate through the body in
bloodstream. The light chains of antibodies are two types, kappa and lambda, with type being
determined by the structure of the light chain constant rehion. As well shall see, antibodies
may have the same antigen-binding specifity, as determined by the variable regions of the
four chains, but different immunological functions, as determined by the constant regions of
the two heavy chains.
Thus, when we examine the structure of antibodies, we see that their diversity resides
almost entirely within the variable regions of the molecules. If these polypeptides were
synthesized from colinear nucleotide-pair sequences of genes, one gene per polypeptide
chain, the genome would have to contain a vas array of genes with highly variable sequences
at one end and essentially identical sequences at the other end. However, this is not the case.
Recombinant DNA techniques have made it possible to isolate and sequence many of the
segments of chromosomal DNA of mice and humans coding for antibody chains. The result
of these studies have provided an elegant explanation for the generation of proteins with great
diversity in certain regions and constancy in other regions.

Antibody Diversity : Genome Rearrangements During B Lymphocyte Differentiation
Very simply, the genetic information coding for antibody chains is stored in bits and
pieces, and these bits and pieces are put together in the appropriate sequences by genome
rearrangements occuring during the development of the antibody-producing cells (called B
lymphocytes) of the body. Each Blymphocyte produces only a single type of anjtibody, that
is, all the antibodies produced by a given B lymphocyte have the same antigen-binding
specificity.
Each antibody chain is synthesized using information stored in several different genes
of gene segments, and other prefer to call them gene segments. (some geneticsts call these
DNA sequences genes, and other prefer to call them gene segments. We call them gene
segments in the following discussion). Note that the classical concept of one gene-one
polypeptide is notadequate, at least in its simplest from, to explain gene-antibody
relationships.

Kappa Light Chains
Sypnthesis of the kappa light chain is controlled by three different gene segments :
1. A V
k
gene segment, coding for the N-terminal 95 amino acids of the variable region.
2. A J
k
gene segment (J for joining segment), coding for the last (constant region-
proximal) 13 amino acids of the variable region, and
3. A C
x
gene segment, coding for the C-terminal constant region.
A fourth gene segment, the L
k
segment, codes for an N-terminal hydrophobic leader sequence
17-20 amino acids long, which is essential for the transport of the antibody chain through the
cell membrane. The leader sequence is cleaved off the chainas it passes through the
membrane, and thus is not part of the final antibody.
The arrangement of the kapa chain gene segments in germ line cells (in fact, in all
cells not producing antibodies) is shown in fig. 16.4. in mice and humans, all the kappa chain
gene segments are located on the same chromosome (chromosome 2 in humans). The same is
true for the lambda gene segments (chromosome 22 in humans) and the heavy chain gene
segments (chromosome 14 in humans). There are a large number, probably about 300, of V
k

gene segments, each with a neaby L
k
gene segment (fig. 16.4a). on theother hand, there is
only one C
k
gene segment. Five J
k
gene segments (one of which is nonfunctional in the
mouse) are located between the V
k
gene segments and the C
k
gene segments.
In germ line cells, the five J
k
segments are separated from the V
k
segments by a long
(we dont yet know how long) noncoding sequence and from the C
k
segment by an
approximately 2000-nucleotide-pair-long noncoding sequence. During the development of a
B lymphocyte, the particular kappa light chain gene that will be expressed in that cell is
assembled from one L
k
-V
k
segment, one J
k
segment, and the single C
k
segment by a process
of somatic recombination (figs. 16.4a and b). This process joins any one of the approximately
300 L
k
-V
k
segments with any one of the five J
k
segments, with the deletion of all intervening
DNA (fig. 16.4b). It yields a fused V
k
J
k
gene segment coding for the entire variable region of
the kappa chain. The noncoding sequence between the J
k
gene-segment cluster and the C
k

gene segment, and the C
k
-proximal J
k
segments, if any, remain between the fused V
k
J
k

segment and the C
k
segment in the differentiated B lymphocytes (fig. 16.4b). This entire
DNA sequence (L
k
-V
k
J
k
-noncoding-C
k
) is transcribed (fig. 16.4c) and thenoncoding
sequences are removed during RNA processing (figs. 16.4c and d),just like the noncoding
sequences or introns of any other eukaryotic gene.

Lambda Light Chains
Lambda light chain genes are also assembled from separate segments during B
lymphocyte development. The major difference is that each J
lambda
gene segment comes with
its own C
lambda
gene segment, that is, the genome rearrangements required for lambda chain
synthesis join L
lambda
-V
lambda
segments to J
lambda
-C
lambda
segments. Mice have only four J
lambda
-
C
lambda
gene segments, whereas humans have six. This correlates with the fact that only 5
percent of the antibodies of mice are of the lambda type, whereas 40 percent of the antibodies
of humans have lambda light chains.

Heavy Chains
The genetic information coding for antibody heavy chains is organized into L
H
V
H
,
J
H
, and C
H
gene segments analogous to those for kappa light chains : but there is one
additional gene segment, called D for diversity, that codes for 2-13 amino acids of the
variable region. The variable region of the heavy chain is thus encoded in three separate gene
segments that must be joined during B lumphocyte development. In addition, there are from
one to four C
H
gene segments for each Ig class.
In the mouse, there are a total of eight C
H
gene segments, all functional, arrenged on
the chromosome in the sequence C
Hn
, C
Hteta
, C
Hgama3
, C
Hgama1
, C
Hgama2b
, C
Hgama2a
, C
He,
C
Halfa
(fig. 16.5a). C
Hn,
C
Hteta,
C
He,
and C
Halfa
code for IgA, respectively. Four gene segments,
C
Hgama3
, C
Hgama1
, C
Hgama2b
, and C
Hgama2a
code for IgG heavy chain constant regions.
In humans, there are 9 or 10 functional C
H
gene segments : C
Hn
, C
Hteta
, C
Hgama1
,
C
Hgama2,
C
Hgama3,
C
Hgama4,
C
He1,
probably C
He2,
C
Halfa1,
C
Halfa2.
The human C
H
gene cluster also
contains two nonfunctional genes, comonly called pseudogenes, with very similar structure.
Pseudogenes are partial duplicates of structural genes that have incorporated sufficient
changes that they are not biologically active and usually are not transcribed. Pseudogenes are
turning out to be quite common in eukaryotes.
In mouse germ line cells, there are about 300 L
H
- V
H
gene segments, something like
10-50 D gene segments, 4 J
H
gene segments, and 8 C
H
gene segments, arranged on yhe
chromosome in the preceding order (fig. 16.5a).during the development of a B lymphocyte
from a stem cell, somatic recombination joins one L
H
- V
H
gene segement with one D gene
segment, deleting the two intervening seequences of DNA, to form one continuous DNA
sequences (V
H
DJ
H
) that code for the entire heavy chain variable region (figs. 16.5a and b).

Class Switching
At the time that antibody synthesis begins in the developing B lymphocyte, all gene
the C
H
gene segments are still present, separated from the newly formed L
H
- V
H
DJ
H
gene
segment by a short noncoding sequence (fig. 16.5b). at this stage, all antibodies synthesized
have IgM heavy chains. If an antigen is recognized and bound to an antibody on the surface
of a developing B lymphocyte, however, that cell is stimulated to differentiate into a mature
B lymphocyte. During this differentiation, some Blymphocytes will switch from producing
antibodies of class IgM to producing antibodies of another class. This phenomenon, called
class switching, often involves further genome rearrangement during which the C
H
gene
segments closet to the previously joined L
H
- V
H
DJ
H
gene segments are deleted (figs. 16.5c-
e). The classof antibodies produced after class switching is determined by which gene is
brought into the closet proximity with the L
H
- V
H
DJ
H
gene segment, as illustrated in figs.
16.5c-6.

Antibody Diversity Alternate Pathways of Transcript Splicing
Another type of class sswitching during B lymphocyte differentiation occurs at the
level of RNA procesing. Certain mature B lymphocytes produce both IgM and IgD
antaibodies. It should be emphasized, however, that these antibodies differ only in their
effector function domains; they have identical antigen-bnding domains, specified by the same
V
k
J
k
or V
lambda
J
lambda
and V
H
DJ
H
fused gene segments. In these cells, a primary transcript that
extends through both the C
Hmikro
and C
Hgamma
gene segments is synthesized. During
processing, the V
H
DJ
H
transcript sequence may be spliced to either the CHmikro sequence or
the CHgamma sequence, such that both types of heavy chain are synthesized in the same cell
(Fig 16.6).
A further complexity observed in antibody synthesis is the sequential production of
membrane-bound and secreted forms of a given antibody. The first antibodies to appear in
developing B lymphocytes are membrane-bound IgM molecules. Subsequently, these cells
switch to the production of a secreted form of IgM. These two forms of IgM differ only in the
C-terminal portions of their heavy chains. The heavy chain of the membrane-bound form is
21 amino acids longer than that of the secreted form. The membrane-bound heavy chain has a
41-amino-acid-long hydrophobic sequence at the C terminus that is probably responsible for
anchoring it to the cell surface. This hydrophobic sequence is replaced by a 20-amino-acid-
longhydrophilic sequence in the secreted form.
The coding sequences (exons) of the C
H
gene segments are interrupted by noncoding
sequences (introns) just like those of many other eukaryotic genes (Chapter 13, pp 356-359).
The C
H
gene segments contain four to six exons and three to five introns (Fig 16.7). in
membrane-bound antibodies, the heavy chain constant regions are produced by splicing all
six exons together (Figs. 16.7a and b). the last two exons code for the hydrophobic tails of the
membrane-bound heavy chains. During synthesis of the membrane-bound form, the fifth C
H

exon is spliced to a site 20 codons from the end of the fourth exon (fig 16.7b), thus changing
the amino acid sequence of this portion of the heavy chain constant region. In secreted
antibodies, the heavy chain constant regions are therefore the product of the first four exons
(fig 16.7c).
The use of alternate pathways of transcription and RNA processing to synthesize
membrane-bound and secreted forms has been firmly established for the IgM class of
antibodies. Recent evidence suggests that similar alternate pathways of transcription and
splicing are responsible for the production of the membrane-bound and secreted forms of the
other classes of immunoglobulins as well.

Signal Sequences Govern Genome Rearrangements
How are the genome rearrangements that occur during B lymphocyte development
regulated? What controls the somatic recombination events such that a V gene segment is
joined to a J segment and not to another V segment or directly to a C segment? Several long
segments of chromosomal DNA carrying clusters of V gene segments, D gene segments, and
J gene segments of both mice and humans have now been sequenced, and the resulting
nucleotide-pair sequences suggest the presence of specific V-J, V-D, and D-J joining signals.
The same signal sequences are found adjacent to all V gene segments. Similarly, all J gene
segments have identical signal sequences located adjacent to their coding sequences;
however, their signal sequence is different from that adjacent to V gene segments. Likewise,
D and C gene segments have their own adjacent signal sequences.
The signal sequences controlling V-J, V-D, and D-J joining contain 7-base-pair
(heptamer) and 9-base-pair (nonamer)-long sequences separated by spacers of different, but
specific lengths. for V
K
-J
K
joining, the spacer in the V
K
signal sequence is 12 nucleotide-pairs
long, whereas that in the J
K
signal sequence is 22 nucleotide-pairs long. The heptamer and
nonamer sequences located after (to the right as drawn in Figs. 16.4 and 16.8) the V
K
gene
segments are complementary (with the exception of one base-pair) to those preceding (to
the left as drawn in figs. 16.4 and 16.8) the J
K
gene segments. These signal sequences have
the potential to form stem and loop structures as diagrammed in Fig. 16.8, thus bringing the
V
K
and J
K
gene segments into juxtaposition for joining. Apparently, joining will occur only
when one signal sequence contains a 12-base-pair spacer and the other contains a 22-base
pair spacer. This requirement would supposedly be enforced by the specific protein(s)
mediating the joining process. Very similar signal sequences appear to control V
H
-D and D-
J
H
joining, whereas somewhat different signal sequences mediate class switching (see P.
Leder, Sci Amer. 246(5): 102-115, 1982).

Antibody Diversity : Variable Joining Sites and Somatic Mutations
Acomparsion of the diversity of amino acid sequences present in antibody molecules
with that predicted fro the sequences of gene segments that encode these antibodies revealed
that thereis more variation in amino acid sequences at the V-J junctions than is predicted by
the nucleotide sequences. Subsequent studies showed that much of this additional diversity
could be explained by variation in the exact site of recombination during V-J joining events.
An example of the use of alternate sites of joining of V
k
and J
k
gene segments in the mouse is
illustrated in fig. 16.9. During the joining of gene segments V
k41
and J
5
, recombination has
been shown to occur between four adjacent nucleotide positions at the junction sites. As
shown in fig. 16.9d, these recombination events produce four different nucleotide sequences
that encode three distinct amino acids at position 96 in the mouse kappa light chain. Since
amino acid 96 occurs in a region ofthe antibody chain that is involved in antigen binding,
alternate V-J joining events of this type undoubtedly contribute significantly to the great
diversity of antibody specifity that is observed in vertebrates. Similar alternate joining events
have been documented for V
lambda
-J
lambda
and V
H
-D-J
H
joining reactions. Thus, the use of
alternate sites of recombination during the joining events that are involved in the assembly of
mature antibody genes provides an additional mechanism for generating antibody diversity.
Despite the vast array of antibody diversity produced by (1) the joining of large
jfamilies of V, D, and J gene segments and (2) the use of alternate positions of recombination
during the joining reactions, considerable data demonstrate that still another mechanism must
be involved in the generation of antibody diversity. This has been established by comparing
(1) the nucleotide-pair sequences of expressed genes with the sequences of germ line gene
segments and (2) the actual amino acid sequences of antibody chains with the amino acid
seuquences predicted from the nucleotide sequences of genes. For example, when the actual
amino acid sequences of different mouse lambda1 chains were compared with the preedicted
amino acid sequences of lambda1 light chains, differeces were found in the variable regions
away from the junction sites. Similar observation have been made in studies of heavy chain
variable hregions. In essentially all cases, lthe changes have resullted from single nucleotide-
pair substitutions. Such, substitutions may represent 1-2 percent of the nucleotide-pairs ofthe
gene segments encoding the variable regions of antibodies. These nucleotide-pair
substitutions are presumed to occur by some mechanism of somatic mutation that is restricted
to the DNA sequences encoding the variable regions of antibody chains. Because these
changes in the variable segments of antibody genes occur atsuch a high frequency, the
process by which they occur is often called somatic hypermutation. The mechanism by which
somatic hypermutation occurs is unknown.
Somatic hypermutation of regions of antibody genes that encode antigen-binding sites
may be of great value to theorganism. Without this mechanism for generating antibody
diversity, the range of available antibody specifitywould be fixed in terms of the sequencees
present in the genome brith and the levels of gene segment joining reactions. Viruses and
other patogens are constantly evolving and producing new variants with new antigenic
determinants. To provide an adequate defense against the changing antigenic composition of
these viruses and other components of the environmnet, the immune system must also be
capable of rapidly responding to these changes. What better way to provide this safeguard
than to endow antibody genes with their own mechanism for rapid adaptation to new antigens
that might evolve in the future somatic hypermutation ?

How Many Combinations ?
One can readly see that a large amount of diversity can be generated by the joining of
antibody gene segments as just described. For example, consider the number of different
kappa light chains possible in humans : 300 V
k
gene segments x 5 J
k
segments = 1500 fused
V
k
J
k
gene segments. The heavy chain variable region provides even greater diversity because
of the multiple D gene segments. If there are 300 V
H
gene segments, 25 D gene segments,
and 6 J
H
gene segments in human germ line cells, 45000 different jheavy chain variable
regions could be assembled. Using these estimates, 67500000 different antigen binding sites
couldbe produced using just kappa light chains. Lambda light chains produce another level of
diversity.
Clearly, these antibodiy gene segment fusions provide for a vast amount of antibody
diversity. We now know, however, that further diversity is generated in two additional ways
(1) somatic mutation and (2) variability in the sites at which V-J, V-D, and D-J joining events
occur. In total, the posible range of antibody diversity seems almost limitless.

Regulation of Transcription aTissue Specific Enhancer
It has been known for several years that germ line antibody genes are not transcribed
or are transcribed at very low levels. Yet, in antibody-producing B lymphocytes, 10 to 20
percent of the mRNA molecules are antibody gene transcripts. What, then, is responsible for
the activation of transcription of antibody genes that undergo rearrangements and become
active? In the case of the heavy chain genes, the answer appears to be that the rearrangement
proceess brings the promoters located upstream of L
H
-V
H
gene segments into the range of
influence of a strong enhancer element located in the intron between the J
H
gene segments
and the C
H
n gene segment (fig. 16.10). Each L
H
-V
H
gene segment contains an upstream
promoter. However, prior to the genomic rearrangement events that lead to heavy chain
synthesis, this enhancer is over 100000 nucleotide-pairs away from the closest L
H
-V
H

promoter (fig. 16.10 top). Presumably, this enhancer cannot activate transcription from
promoters that are locatedthat far away. However, rearrangemnet events occuring during B
cell differentiation (see fig. 16.5) move the promoter of the closet L
H
-V
H
gene segment to
within less than 2000 nucleotide-pairs from the enhancer (fig. 16.10, bottom). The enhancer
can now activate transcription from the promoter located upstream from the L
H
-V
H
gene
segment. The enhancer involved in the activation of heavy chain synthesis is tissue specific, it
activates transcription only in lymphocytes and has no effect in cells derived from other
tissues. Presumably, the activation process requires the presence ofa transcriptional activating
factor that is synthesized in lymphocytes, but not in other types of cells.
A similar enhancer elements has been found in the intron between the light chain J
k

gene segment cluster and the C
k
coding sequence. Thus, it seems likely that the movement of
antibody gene promoters into the range of influence of tissue specific enhancers may be a
general mechanism of activation of antibody genes during the differentiation.

Clonal Selection
Up to this point, we have avoided the question of how an organis initiates the
synthesis of antibodies specific to antigens that it has not previously encountered. This is
nicely explained by the clonal section theory. Recall thatall the antibodies produced by a
single B lymphocyte haave the same antigen-binding specifity. But different cells in
apopulation of B lymphocytes will have undergone different genome rearrangements leading
to the production of antibodies with different specifities. Thus, the population of B
lymphocytes in a human or amouse will be producing a very large variety of antibodies. The
clonal selection theory states that the binding of a particular foreign antigen to an antibody on
the surface of a B lymphocyte stimulates that cell to divide, producing large numbers of this
particular B lymphocyte and thus large amounts of the particular antibody that recognizes the
foreign antigen (fig. 16.11).

Allelic Exclusion
Consider one final point about the genetic control of antibody synthesis. Each B
lymphocyte makes only one type of antibody. Why ? Mammalian cells are diploid ; their
carry two sets of genetic information coding for each of the antibody chains. But only one
productive geome rearrangement of light chain coding sequences and one productive genome
rearrangement of heavy chain coding sequences occur in each B lymphocyte. This
phenomenon is called allelic exclusion because one of the alleles is excluded from being
expressed. How ? Why ? at present, we still dont know. Clearly, there must be some type of
a feedback mechanism that arrest recombination process involved in these antibody gene
rearrangements once a productive rearrangement has occured and the cell has started to
synthesize a functional body. The simplest mechanism would involve inhibition of this
process by the mature antibody itself. However, further work will be required to establish the
mechanism by which allelic exclusion occurs.

T CELL RECEPTOR VARIABILITY
T lymphocytes mediate the cellular immune response (see Fig. 16.1). The T cells
recognize antigens on the surface of cells and kill the cells carrying these antigens. Like the
antibodies produced by B lymphocytes, T cells can recognize and destroy cells carrying in
amazing variety of antigens. Thus, the T cell response also exhibits a phenomenal degree of
specificity. How is this specificity produced? The answer is that T cells produce membrane-
bound receptors that are very similar to the antibodies produced by B lymphocytes.
Moreover, the diversity of T cell receptor specifity is produced by genome rearrangements
analogous to those involved in antibody production (see the preceding sections of this
chapter). But how do T lymphocytes avoid interacting with free antigens to avoid duplicating
the function of B cells in the immune response? As it turns out, T cells must simultaneously
recognize both the offending antigen on the cell surface and another protein that occurs only
attached to cell surfaces. This second cell-surface protein that the T cell must recognize is the
product of one of many genes in the major histocompability complex (MHC). The MHC
locus (see the following section) encodes a complex group of proteins that are present on all
the cells in the body of human (or a mouse). Thus, T cells are able to recognize and destroy
any cell that is producing a given antigen (e.g., the coat protein of a virus) in any tissue of the
body. The interaction of the T cell receptor with the two types of cell-surface antigens (the
offending antigen and the histocompatibility antigen) is illustrated in Fig. 16.1
The T cell receptors are composed of two polypeptide chains, and , each encoded
by L-V, D, J, and C gene segments just like antibody chains. The - and -polypeptides, like
antibody chains, contain variable regions that form the antigen-binding sites and constant
regions that anchor the receptors on the cell surface (Fig. 16.12a). The variable regions of the
T cell receptors are encoded by multiple L-V, D, and J gene segments; the constant regions
are encoded by a small number of C gene segments. The T cell receptor genes are assembled
by genomic rearrangements that occur during the differentiation of T lymphocytes from stem
cells just as in the case antibody genes in developing B lymphocytes. Figyre 16.12b shows
the segments of the and T cell receptor polypeptides that are encoded by the L-V, D, J,
and C gene segments. The and receptor proteins are encoded by gene segments that are
lined up in clusters on chromosomes similar to those encoding antibody chains. In humans,
the and gene segment clusters are located on chromosomes 14 and 7, respectively.
(Another gene segment cluster encodes a third type of T cell receptor polypeptide designated
that is present on a specific type of T cell. There are several distinct types of T cells that
carry out different functions during the immune response.)
The structures of the T cell receptor gene clusters are very similar in humans and in
mice. The germ line organization of the gene segments that encode T cell receptor -
polypeptides is shown in Fig. 16.13a. The organization of a functional rearranged -
polypeptide gene is shown in Fig. 16.13.b. Heptamer and nonamer signal sequences that are
very similar to those that control antibody gene rearrangements are also present at essentially
the some locations in the T cell receptor gene clusters. Their presence in both types of gene
clusters suggests that the same mechanism of gene segment joining is employed during
rearrangements of both antibody genes and T cell receptor genes. The probably is somewhat
less total variability in T cell receptors than in antibodies. T cell receptor variable regions are
encoded by only about 30 V gene segments, whereas there are about 300 V gene segments for
both kappa light chains and heavy antibody chains. However, there are more J gene segments
in the T cell receptor gene clusters. For example, there are 12 functional J gene segments for
receptor polypeptides (Fig. 16.13). Moreover, we still do not know whether or not the
variable segments of the T cell receptor genes undergo somatic hypermutation. In any case, it
is clear that T cell receptors exhibit a great amount of diversity, and that this diversity is
generated by genome rearrangements during T lymphocyte differentiation in a manner
analogous to those involved in the production of antibody diversity in B lymphocytes.
As was mentioned earlier, there are several different types of T lymphocytes and they
play different roles in the cellular immune response. For an excellent discussion of the
different types of T cells and their functions, the reader is referred to Chapter 24,
Immunity, of Molecular Cell Biology by J. Darnell, H. Lodish, and D. Baltimore.
MAJOR HISTOCOMPABILITY COMPLEX
The immune response in mammals is a very complex process involvinf a large
number off different macromolecules and different cell types. Our discussion to this point has
been restricted to the genetic control of the synthesis of antibody chains and T cell receptor
proteins. Many of the other components of the immune response, such as the transplantation
antigens that are largely responsible for the rejection of foreign tissues in transplant
operations, are controlled by a multigene complex called the major histocompability complex
(MHC). In humans, the MHC proteins are encoded by the HLA (for Human Leukocyte
Antigen complex) locus on chromosome 6; in the mouse, the MHC locus is designated H-2
(Histocompatibility locus 2) and is on chromosome 17. In both mice and humans, the MHC
locus is very large (>2 x 10
6
nucleotide-pairs) and contains a large number of genes.
Moreover, there is a very large number of distinct alleles for many of these genes such that
the probability of any two individuals being identical for all the MHC genes is extremely
small. The MHC genes are said to be highly polymorphic because of the large number of
alleles of individual genes that are usually segregating in given population.
The MHC genes encode three different classes of proteins that are involved in
different aspects of the immune response. The structure of the human MHC (HLA) locus and
the relative locations of genes that encode the different classes of histocompatibility antigens
are shown in Fig. 16.14. The class I genes encode the transplantation antigens mentioned.
The class I proteins exist as glycoproteins anchored as integral membrane proteins with the
antigenic determinants exposed on the outside of cells. They are present on all cells of an
organism and permit T lymphocytes to distinguish self from foreign. The MHC class I
proteins are the antigens that usually are responsible for the rejection of foreign tissues in
tissue and organ transplants. As illustrated in Fig. 16.1, these antigens play a key role in the
recognition and destruction of cells carrying foreign antigens by cytotoxic T lymphocytes. A
single T cell receptor is believed to recognize both the foreign antigen and the class I
histocompatibility antigen during the cytotoxic T cell immune response.
The MHC class II genes encode polypeptides that are located primarily on the
surfaces of B lymphocytes and macrophages. MHC class II proteins provide a special type of
T lymphocyte called the T helper cell with the capacity for self-recognition and facilitate
communication between the different types of cells involved in the immune response. Finally,
the MHC class III genes encode complement proteins that interact with antibody-antigen
complexes and induce cell lysis.
The MHC class I and class II antigens are anchored in the cell membrane and have
structures very similar to the structures of T cell receptors (see Fig. 16.12). However, the
diversity of MHC antigens is much less than that of antibodies and T cell receptors, and, so
far as is known, no genomic rearrangement is involved in the genetic control of MHC antigen
diversity. Instead, the observed diversity results from the presence of a large number of
highly polymorphic MHC genes.