Immunogenetics class 2: antibody diversity

How antibody diversity occurred.

How different gene segment for different antibody chains are arranged.

Image credit:


Antigen specific antibody is produced by each type of B lymphocyte cells. It is believed that human genome contains only around 15000 to 20000 genes, than how the diversity for different antibody gene segment is originated? Some of the proposed mechanism for antibody diversity are described here:

  • V-(D)-J joining
  • Junctional flexibility
  • P and N nucleotide addition
  • Somatic hyper mutation (SHM)
  • Clonal selection
  • Allelic exclusion

V-(D)-J joining

Different types of VH and VL chain regions are generated during the maturation of B cells. Here different combination of V-(D)-J and V-J polypeptide chains along with C region are arranged differently to form different gene segments. The process is called as site specific recombination.

From the latest discovery, it is conformed that rearrangement of V-J, V-D and D-J gene segments are clustered differently on different chromosomes but the joining sequences present between each of the segments gives signal for rearrangements, this sequences are termed as signal sequences. Each signal sequences are found near each segment (for example, V gene signal sequence near V gene segment).

The heptamers and nonamer sequences are controls the signal sequences of V-J, V-D and D-J gene segments. This heptamers and nonamers have capacity to form hairpin like structure which brings distal gene segments nearer and helps joining them.immunogenetics-class2.001.jpeg

Here V-(D)-J recombinase enzyme complex regulates the process of recombination in somatic cells. This enzyme is encoded by the  RAG1 and RAG2 gene family. In site specific recombination, junctional diversification plays essential role for providing diversity to different gene segments.

Random nucleotides are added or deleted from the gene segments which provides diversity to antibody and are called as junctional diversification.

After the completion of recombination, the joining of recombined segments are also influenced by some of the spacer sequences. Near the signal sequences of both the segments, one segment contain 12 nucleotide long spacer sequence and other segment contain 22 base pair long spacer sequences which helps in joining gene segments.

Remember, without the spacer sequences on both the segments, recombinated segments can never be joined.

After the completion of recombination, the newly created segment is joined with constant region, and under go transcription. The mature mRNA forms the specific type of antibody polypeptides for specific antigen.

Considering the environmental effects and other adverse conditions, pathogens are continuously alters their genetic composition to survive. For providing protection agains newly emerged pathogenic strains, SHM (somatic hypermutation) allows rapid changes in our genome with higher rate of mutation, and it creates new genetic combination for antibody coding genes which protect us against new strains of pathogen.

Junctional flexibility

The signal sequences are joined precisely but joining of coding sequences are imprecise. Which means one gene segments are joined with another gene segment, if the signal sequences and spacer sequences are matches exactly.

But in contrast, joining of gene segment is not regulated, if it is matches with any other gene signal sequence, it will recombined. This phenomenon which gives additional flexibility to each segment are called as junctional flexibility.

Nucleotide addition

P nucleotide addition is occurred during DNA repair mechanism. As we discussed earlier about the hairpin structure, when this hairpin structure is breaks down, some of the nucleotides are remain single stranded. To fill this gaps DNA polymerase adds palindromic P- nucleotides to fill this gap.

During the proofreading, sometime terminal deoxynucleotidyl transferase adds some additional nucleotide to repair the DNA segments are called as N- nucleotide addition. 

Somatic hypermutation

Mutations accumulated in antibody coding genes at the higher rate of 106 fold than normal mutation. The process is aimed to produce high affinity antibodies which is exactly matches the antigen.

Somatic hypermutation occurs in V region, J region or H region but SHM in CDR region (complementary determining region ) have higher affinity to antigen (antigen firstly presents at CDR region of antibody). Though SHM can produces antigen specific antibodies, some low affinity and non functional antibodies are also formed because the process of somatic hypermutation is random, it causes mutation or point mutation randomly on any of the gene sequences.

SHM is the key mechanism in antibody diversity generation. But still, it is not understood deeply. If SHM is not occurred, the genetic diversity for antibody coding gene sequences are fixed because diversity which are generated though rearrangement and recombination, are fixed within the genome. It means the available diversity is limited by birth.


Image explanation: somatic hyper mutation occures in antibody gene segments as shown into figure, the arrows are different types of somatichyper mutations. The gene segment which has higher binding affinity is selected.

This is the main reason why somatic hypermutation is very important for producing additional diversity. Another important mechanism which makes hypermutation most valuable is pathogen diversity.

Considering the environmental effects and other adverse conditions, pathogens are continuously alters their genetic composition to survive. For providing protection agains newly emerged pathogenic strains, SHM allows rapid changes in our genome with higher rate of mutation, and it creates new genetic combination for antibody coding genes which protect us against new strains of pathogen.

Clonal selection

When antigen binds to the antibody on the surface of B cell, it causes  B Lymphocyte cell to divide. Produce clones of that antigen-specific antibody producing B cells and select that cells to produce antibody. This mechanism is called as clonal selection.

The theory clearly states that, all the antibodies which are produces by a single type of B lymphocytes cells have same binding affinity to a single type of antigen. A population of different types of B cells produces antibody which have affinity to bind with different type of antigen.

immunogenetics class2.003

Image explanation: As shown into figure, the yellow coloured B lymphocyte which produces antibody, can not bind to antigen hence it is not selected for further dividion. while red coloured B lymphocyte- antibody which can binds to antigen and, are selected for differentiation. Clonal selection helps for mass production of that antigen specific antibody producing B lymphocyte cells.

Every time when a new antigen is comes in contact with membrane embedded antibodies (remember IgD and IgM), SHM helps in creation of new type of antibody gene segment ant that antibody is sythesized by a population of same type of B lymphocytes by clonal selection. 

Allelic exclusion

Somatic cell is diploid. It contains two copy for one particular gene. Firstly lets recall the diploid theory, for any type of somatic mutation one allele become dominant and other remain recessive.

If the progeny carries dominant allele it become affected otherwise it turn into carrier or normal due to the recessive allele. Is it possible for antibody gene segment to produce two different types of gene segments?

Well, in case of antibody coding gene segments, one productive genome rearrangement for light chain and one productive genome rearrangement for heavy chain coding sequences are occurred in single somatic B lymphocyte. One allele is excluded from each cell every time for being expressed.

immunogenetics class2.004

Image explanation: As shown in figure a one pair of chromosomal gene segment codes for two different type of chains (heavy chain and light chain) instead of providing additional diversity by allelic variation.

This is the reason why a single B lymphocyte cannot produce two different type of antibody gene segments.

Immunogenetics is still under expansion because we do not have enough data for each of the mechanism. Even we do not have much knowledge about gene segment rearrangement, recombination of gene segments and hypermutation. But antibody diversity has one of the pivotal role in our survival. 

Keep in mind, every time when you are attacked by unknown antigen, possibly second time your immune system can protect you from that particular antigen.

more related articles:

Immunogenetics class 1: different polypeptide chains of antibody

Story created by – Tushar Kachhadiya 

Article written and reviewed by- Tushar Chauhan

Leave a Reply