The Immunoglobulin Variable-Region Gene Repertoire and Its Analysis
Cliburn Chan, Michael G. Hudgens, Shein-Chung Chow in Quantitative Methods for HIV/AIDS Research, 2017
In addition to combinatorial diversity, IgVRG exhibits junctional diversity. The enzymatic complex consisting of the recombination activating genes RAG1 and RAG2 binds to a recombination signal (RS) adjacent to each of the V, D, and J genes, bringing the genes into close proximity. Proper ordering of the genes is enforced by the so-called 12/23 rule. There are two different types of RS, one with a 12-nucleotide spacer and one with a 23-base spacer. Synapsis occurs only between heterogeneous pairs. The recombinase nicks the DNA at the start of each RS, resulting in a DNA hairpin on each gene, which is then cleaved stochastically by the Artemis complex, resulting in variable recombination points. Because of the hairpin structure, this cleavage may occur beyond the end of the coding region into the noncoding strand, resulting in the appearance of p-nucleotides (p for palindromic). Terminal deoxynucleotidyl transferase may then add several n-nucleotides (n for nontemplated), which are yet another source of stochasticity. The strands then pair in complementary regions, and unpaired nucleotides are removed and filled in to form the final junction region [19,25,26]. The site of RAG-mediated cleavage and n-nucleotides together supply the junctional diversity of the antibody repertoire.
Intraepithelial T cells: Specialized T cells at epithelial surfaces
Phillip D. Smith, Richard S. Blumberg, Thomas T. MacDonald in Principles of Mucosal Immunology, 2020
Regardless of species, the γδ TCRs expressed by nIETs are largely distinct from their peripheral counterparts. Mouse TCRγδ IELs predominantly express Vγ5 and Vγ1.1, and a few use Vγ2. With respect to TCRγδ, depending on the strain, 15%–60% of the TCRγδ IETs express Vδ4 and some express Vδ5 or Vδ6. For humans, most (approximately 70%) colonic TCRγδ IETs utilize Vδ1. Furthermore, human IETs express a non-disulfide-linked form of the γδ TCR unlike peripheral γδ T cells. The complexity of the γδ TCR is largely contributed by the complementarity-determining region 3 (CDR3) of the δ chain and by random joining of the variable (V), diversity (D), and joining (J) segments, random N-region nontemplate deletions, and additions of nucleotide palindromes at the coding ends of the V, D, and J segments (P additions). The composition of the TCRγδ IETs changes with development with changes in V region usage and junctional diversity. The TCRδ of fetal intestinal T cells is polyclonal, with different CDR3 lengths and several template-encoded P-region, but no N-region, additions. This polyclonal nature is maintained until birth, but at that time the junctional regions become more complicated with numerous N-region insertions. With age the TCRδ repertoire becomes increasingly restricted, and in young adults the TCRδ usage is comparable with that in older adults. Despite the diversity of nIET γδ TCRs, the oligoclonal expansions are distinct between individuals but appear to be stable over time.
The Inducible Defense System: The Induction and Development of the Inducible Defence
Julius P. Kreier in Infection, Resistance, and Immunity, 2022
Although the antigen receptors for T cells and B cells are produced randomly by the combination of a limited number of DNA gene segments, they produce an extremely large number of possible antigen receptors. The combinational diversity produced through the random selection of V, D, and J segments, as well as junctional diversity caused by imprecise cutting of the DNA and the N and P nucleotide addition, dramatically increases the possible combinations. It is the combination of all of these random events that leads to the large number of diff eren t an tigen receptors needed by the immune system to recognize all the possible pathogens to which the body is exposed.
A perspective toward mass spectrometry-based de novo sequencing of endogenous antibodies
Published in mAbs, 2022
Sebastiaan C. de Graaf, Max Hoek, Sem Tamara, Albert J. R. Heck
Because there is an endless and constantly evolving pool of pathogens, the antibody repertoire needs to be incredibly diverse and versatile to counteract these challenges.24,25 In humans, this enormous diversity in the potential antibody repertoire is achieved through several mechanisms. Starting at the genomic level, the light and heavy chains are encoded in four genes each: Variable (V), Diversity (D), Joining (J), and Constant (C), with the light chain lacking the D-gene. These genes are encoded in multiple alleles, which can recombine to a staggering number of combinations (Figure 1b).26 The recombination process is also error-prone, leading to insertions and deletions at the junctions between the regions, referred to as junctional diversity. By recombination alone, the number of possible variable domain sequences already reaches tens of thousands. However, the eventual antibody diversity is expanded even further by natural polymorphisms, mutations, and class switching. As the major contributor to antibody hypervariability, somatic hypermutations can occur during B-cell affinity maturation and do so at a million-fold increased rate compared to the usual mutation rates.11 These mutations are largely concentrated in the complementarity-determining regions (CDR1-3), separated by framework regions (FR1-4), which form the conserved backbone of the Fab structure (Figure 1c). Located at the tips of the Y-shaped antibody structure, CDRs are primarily responsible for antigen binding, and, therefore, elucidation of their sequences is of the utmost importance for antibody discovery.
Restricted epitope specificity determined by variable region germline segment pairing in rodent antibody repertoires
Published in mAbs, 2020
Yi-Chun Hsiao, Ying-Jiun J. Chen, Leonard D. Goldstein, Jia Wu, Zhonghua Lin, Kellen Schneider, Subhra Chaudhuri, Aju Antony, Kanika Bajaj Pahuja, Zora Modrusan, Dhaya Seshasayee, Somasekar Seshagiri, Isidro Hötzel
Sequence and structural diversity in immunoglobulin variable regions enable antibodies to bind a virtually unlimited number of antigenic structures. Sequence diversity is generated somatically during the process of B cell maturation by recombination of germline-encoded heavy and light chain germline gene segments into full-length functional variable region exons.1 Light chain variable region sequence diversity is generated by recombination of VL and JL gene germline segments along with relatively limited junctional diversity generated by nucleotide nibbling and incorporation between these segments. By contrast, heavy chain variable region sequence diversity is generated by recombination of three germline segments, VH, DH and JH, which, along with significant nucleotide nibbling and incorporation, generates high sequence and length diversity in the third complementarity-determining region of the heavy chain (CDR H3).2,3 The CDR H3 region is located centrally in the interface between antibody and antigen and usually provides critical contacts with the antigen. The CDR H3 region is considered to be a major determinant of antibody specificity due to its high sequence diversity and central role in antigen binding.1,4
Expression and clinical significance of RAG1 in myelodysplastic syndromes
Published in Hematology, 2022
Xiaoke Huang, Xiaolin Liang, Shanhu Zhu, Qiongni Xie, Yibin Yao, Zeyan Shi, Zhenfang Liu
The plasticity of the acquired immune system in recognizing millions of possible antigens is largely due to the combinatorial joining of variable (V), diversity (D), and joining (J) gene segments that encode the antigen-binding regions of T cell receptors (TCRs) in T cells and B cell receptors (BCRs) in B cells, and the junctional diversity that can be introduced during the process of V(D)J recombination[5]. RAG1 and RAG2 proteins form a complex and initiate V(D)J recombination by introducing DNA double-strand breaks (DSBs) between the recombination signal sequences and the flanking V, D, or J gene segment. The human RAG1 protein consists of 1,043 amino acids, and the catalytic core (amino acids 387–1011) contains a nonamer-binding domain, a dimerization and DNA binding domain, a pre-RNase H and catalytic RNase H domain, 2 zinc-binding domains, and the carboxy-terminal domain, which are all crucial for V(D)J recombination[6, 7].
Related Knowledge Centers
- Antibody
- DNA
- Nucleotide
- Immune System
- Pathogen
- Gene
- V(D)J Recombination
- T-Cell Receptor
- Antigen
- Recombination-Activating Gene