VDJ rearrangement

The adaptive immune response is highly specific for each invader, and that’s because the cells of the adaptive immune response have receptors that differentiate friendly bacteria and potentially deadly pathogens from their unique parts - called antigens.

The key cells of the adaptive immune response are the lymphocytes- the B and T cells.

And the antigen receptors for T cells and B cells have a lot of things in common, one of which is that they share the same mechanism - called VDJ rearrangement - to generate a massively diverse set of receptors.

VDJ stands for variability, diversity, and joining, respectively, and VDJ rearrangement has 4 key characteristics that help ensure that each antigen receptor is unique.

First, each individual inherits multiple V, D, and J gene segments; second, the V, D, and J gene segments randomly recombine - meaning that any V can pair with any D and any J; third, there’s recombinational inaccuracy - meaning that this process is purposefully error prone - which leads to additional variation; and fourth, there’s random reassortment of two chains - meaning that this process involves two different chains that come together to make the receptor.

First, let’s look at our antigen receptors. The B cell receptor, or BCR, is essentially an antibody, except that it has a transmembrane part that goes through the membrane and attaches the receptor to the surface of a B cell.

Just like antibodies, the B cell receptor has a heavy chain and a light chain.

One region or fragment of the B cell receptor binds the antigen and it’s called the fragment - antigen binding or Fab region.

There are two Fab regions on every B cell receptor.

Then there’s the constant region or fragment called the fragment - constant or Fc region, which is the part that determines what class of B cell receptor it will be - for example, IgM or IgD, and whether or not it will remain a membrane bound B cell receptor or if it will get secreted as a free floating antibody.

The T cell receptor, or TCR, on the other hand looks quite different but still only has two chains.

In this case it has an alpha chain which is analogous to the B cell light chain, and a beta chain which is analogous to the B cell heavy chain.

Unlike the B cell receptor, the alpha and beta chains of the T cell receptor only form a transmembrane receptor - they don’t get secreted and there aren’t different classes. They also only have one antigen binding site.

So VDJ rearrangement, really only affects the portion of the protein that comes into contact with the antigen.

For both the BCR and TCR this is known as the variable region or V region.

This region is supported by a constant or C-region.

The variable regions of each of these receptors is highly diverse across the entire cell population -where no two T cells or B cells developed will recognize the same exact antigen.

This is accomplished by the significant variability in the genetic sequence that makes up the V region - but this variability is concentrated to certain segments of the V-region known as hypervariable regions or complementarity-determining regions.

These locations are brought together when the two chains of either the TCR or BCR are brought together to create one hypervariable site at the tip of each arm of the BCR or the tip of the TCR which is the antigen binding site.

So VDJ rearrangement is used to create the variability that is seen in these hypervariable regions which form the actual antigen binding site, and only that part of the protein.

The first step in VDJ rearrangement happens before we are born, in the sense that we inherit from each parent, multiple V, D, and J gene segments.

Each person has 44 V gene segments, 27 D segments, and 6 J segments and that is just for B cell heavy chains, there are more V, D, and J segments for the T cell receptor beta chain and of course there are more V and J segments for the B cell light chain and T cell alpha chain.

The various gene segments are all lined up on the DNA like box cars on a train.

The V gene segments are located furthest away from the genes that encode the constant gene segments, while the J segments are located fairly close to the constant gene segments.

And on the chromosomes that contain the genes for the heavy chain or beta chain the D gene segments sit between the V and J gene segments.

To generate diversity, these gene segments reassort randomly in both B cells and T cells.

A bit like how you might have several pairs of shoes, pants, and shirts and can mix and match them to create lots of different outfit combinations.

For B cell we’ll start with the heavy chain and for T cells we’ll start with the beta chain.

So let’s say for this heavy chain or beta chain rearranged to have V2-D2-J1, well this would be completely different and bind different antigens than a heavy chain or beta chain that rearranged to have V2-D3-J1.

So just by using a different D region, it completely changes what antigen these two cells might bind.

The rearrangement of these different exons is accomplished by having recombination signal sequences which are noncoding DNA sequences that flank the points where DNA needs to be cut and rearranged.

A recombination signal sequence has three parts to it.

First, there’s a 7 nucleotide sequence called a heptamer - 5’-CACAGTG-3’.