Adaptive immunity is so complex it's difficult to know where to begin. Do I start with the cells or the molecules? Actually, I've decided to do neither. Since my main interest is in genetics, I'm going to lead with genes. In particular, the genes for antibodies.
Recall that antibodies are proteins expressed by B lymphocytes (small white blood cells) that consist of four chains of two types: heavy and light. There's one kind of heavy chain and two light ones (called lambda and kappa). Since DNA sequences encode proteins, that must mean that there are must be three genes that are responsible for specifying antibody molecules. And there are. All big ones. The heavy chain gene is found on the 14th chromosome in humans. It's very long, about 1.24 million bases. One of the light chain genes, kappa, located on chromosome two, is even longer, at 1.8 million bases. The other light chain gene, lambda, is found on the 22nd chromosome and stretches over one million bases. (I'm omitting the fact that humans have two of each chromosome, and therefore twice as many antibody genes as I've described. The immune system deals with these two sets of genes in an interesting way. Stay tuned).
But there's a problem. I've already noted that there are at least millions of different antibodies. Put another way, there are millions of antibody proteins each with a distinct amino acid sequence. You'll recall from elementary molecular biology that the sequence of a protein is specified by a gene. That must mean that there must be millions of antibody genes. Which is it? Just three or millions of genes? The fact is that if there were millions of antibody genes and each one was more than a million bases long, the genome would need to be a thousand times bigger than it is. On the other hand, how can three genes dictate the sequence of millions of proteins?
The answer to this conundrum is that antibody genes have some unique properties that allow a single DNA sequence to specify more than one protein. In simplest terms, it accomplishes this task by randomly mixing and matching gene segments, taking a piece from one region and pasting it onto a piece from another and deleting the region between the two. (There is another mechanism for generating multiple proteins from a single gene: alternative splicing. That process is entirely different than the one described here. Alternative splicing occurs in the RNA transcript. Antibody diversity in the variable regions of light and heavy chains is generated by changes in the DNA).
At the right is a diagram of the human heavy chain gene. It's composed of a series of different segments. There are 40 or so "V" or variable segments, each about 300 bases long. Adjoining them are about two dozen relatively short "D" or diversity segments. Next come six "J" or joining stretches, each some 3 to 6 dozen bases long. Finally, some nine or so "C" or constant regions make up a region near the end of the gene. Both the kappa and lambda light chains are similarly structured although light chains lack D sequences and have different numbers of V, J, and C regions.
In a complicated series of enzymatic reactions, these gene pieces are randomly assembled together into a different functional gene in each antibody producing cell (see three of the possible arrangements in the figure above). Notice that substantial portions of the gene are discarded in this process. It's also important to emphasize that these rearrangements only occurs in B lymphocytes. In all other cells in the body the heavy chain and two light chain genes remain unmodified.
The events leading to antibody diversity begin with the joining of one of the D segments to one of the J's. Intervening DNA is thrown away. Subsequently, a V segment joins the group, again with the removal of the bases in between. The J's remain attached to the C regions. The result is an edited gene consisting of one V, D, and J region, the three of which code for the variable portion of the heavy chain, followed by the constant region segments.
How many different antibody producing cells could result from these operations? Simple probability tells us that all the possible combinations in the variable region can be calculated by simply multiplying the number of potential V, D, and J segments. This comes to 45 X 23 X 6, or about 6,000. There's a lesser number of combinations possible from the V-J joining in light chains, say 200. Multiplying 6,000 by 200 yields about a little more than a million. While this is an impressive number, it doesn't take into account the fact (see below) that many combinations of heavy and light chains don't yield functional antibodies. This leaves us short of the millions of different antibodies that is claimed for the immune system. Quite a bit of added diversity comes from the results of joining the D to J and V to DJ segments together. Because this process is imprecise, bases are added, lost, and changed at random at the junctions. While inefficient, often leading to antibodies that can't possibly bind to anything, it results in a tremendous increase in the number of DNA sequences. As we'll see, the immune system employs an evolutionary process that rids the body of defective antibodies and selects for the ones that work well.
As I've noted, all these gene rearrangements occur only in B lymphocytes, the cells responsible for antibody production. However, somewhat similar changes to DNA sequence occur in T cells, the other major player in the adaptive immune system, the one responsible for cellular immunity. In T cells, the proteins analogous to antibodies are the T cell receptors. There are two genes responsible for the synthesis of 95% of these proteins (I've omitted the two other genes that code for the minor forms of the T cell receptor for simplicity's sake). The T cell receptor beta chain gene, about 600,000 bases long, lies on chromosome 7. The T cell receptor alpha chain gene, about a million bases long, is located on chromosome 14. Like the antibody genes, the T cell receptor genes carry repeated V, D, and J segments (D is absent from the alpha chain sequence) and these are rearranged in a similar manner to produce many millions of T cell receptors. A cartoon portrait of the T cell receptor is shown at the right. As in antibodies, these receptors bind to their targets via the variable regions shown near the top of the figure.
Back to B lymphocytes... Their development occurs in the bone marrow in humans and in a specialized structure called the bursa of Fabricus in birds, hence the "B". One of the first events in a B cell's life is the rearrangement of the heavy chain's gene on one chromosome as described above. Remarkably, if this process is successful, the heavy gene on the other chromosome doesn't undergo rearrangement. If not, it does. In either case, only one of the two chromosome 14's bearing the heavy chain gene participate in antibody formation. In those cases where both chromosomes can't specify functional proteins, the cell commits suicide, programmed cell death.
If a pre-B cell survives this checkpoint, it somehow tells the kappa light chain to begin rearranging the segments on its gene. Again, this process is restricted to only one of the two chromosomes. If both chromosomes fail to make a complete kappa light chain protein, only then will the lambda light gene come into play. This mechanism ensures that the B cell will only bear one of the two light chains. If both kappa and lambda chains aren't functional, the cell will die. In summary, a B lymphocyte gets six shots at survival. Two come when each of the sister chromosomes bearing the heavy chain chains rearrange, and four after rearrangement of the kappa and lambda light chain genes.
A surviving B cell will now transcribe its rearranged gene to form an RNA. The protein specified by this processed transcript is capable of binding an antigen. But before it can do so, it must survive an additional test. I'll put that off for the next post.