Recombination-activating gene

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recombination-activating gene 1
Symbol RAG1
Entrez 5896
HUGO 9831
OMIM 179615
RefSeq NM_000448
UniProt P15918
Other data
Locus Chr. 11 p13
recombination-activating gene 2
Symbol RAG2
Entrez 5897
HUGO 9832
OMIM 179616
RefSeq NM_000536
UniProt P55895
Other data
Locus Chr. 11 p13
Recombination-activating protein 2
Symbol RAG
Pfam PF03089
InterPro IPR004321
Recombination-activating protein 1
Symbol RAG
Pfam PF12940
InterPro IPR004321

The recombination-activating genes (RAGs) encode enzymes that play an important role in the rearrangement and recombination of the genes of immunoglobulin and T cell receptor molecules during the process of VDJ recombination. There are two recombination-activating gene products known as RAG-1 and RAG-2, whose cellular expression is restricted to lymphocytes during their developmental stages. RAG-1 and RAG-2 are essential to the generation of mature B and T lymphocytes, two cell types that are crucial components of the adaptive immune system.[1]


In the vertebrate immune system, each antibody is customized to attack one particular antigen (foreign proteins and carbohydrates) without attacking the body itself. The human genome has at most 30,000 genes, and yet it generates millions of different antibodies, which allows it to be able to respond to invasion from millions of different antigens. The immune system generates this diversity of antibodies by shuffling, cutting and recombining a few hundred genes (the VDJ genes) to create millions of permutations, in a process called VDJ recombination.[1] RAG-1 and RAG-2 are proteins at the ends of VDJ genes that separate, shuffle, and rejoin the VDJ genes. This shuffling takes place inside B cells and T cells during their maturation.

RAG enzymes work as a multi-subunit complex to induce cleavage of a single double stranded DNA (dsDNA) molecule between the antigen receptor coding segment and a flanking recombination signal sequence (RSS). They do this in two steps. They initially introduce a ‘nick’ in the 5' (upstream) end of the RSS heptamer (a conserved region of 7 nucleotides) that is adjacent to the coding sequence, leaving behind a specific biochemical structure on this region of DNA: a 3'-hydroxyl (OH) group at the coding end and a 5'-phosphate (PO4) group at the RSS end. The next step couples these chemical groups, binding the OH-group (on the coding end) to the PO4-group (that is sitting between the RSS and the gene segment on the opposite strand). This produces a 5'-phosphorylated double-stranded break at the RSS and a covalently closed hairpin at the coding end. The RAG proteins remain at these junctions until other enzymes (notably, TDT) repair the DNA breaks.

The RAG proteins initiate V(D)J recombination, which is essential for the maturation of pre-B and pre-T cells. Activated mature B cells also possess two other remarkable, RAG-independent phenomena of manipulating their own DNA: so-called class-switch recombination (AKA isotype switching) and somatic hypermutation (AKA affinity maturation).


As with many enzymes, RAG proteins are fairly large. For example, mouse RAG-1 contains 1040 amino acids and mouse RAG-2 contains 527 amino acids. The enzymatic activity of the RAG proteins is concentrated largely in a core region; Residues 384–1008 of RAG-1 and residues 1–387 of RAG-2 retain most of the DNA cleavage activity. The RAG-1 core contains three acidic residues (D600, D708, and E962) in what is called the DDE motif, the major active site for DNA cleavage. These residues are critical for nicking the DNA strand and for forming the DNA hairpin. Residues 384–454 of RAG-1 comprise a nonamer-binding region (NBR) that specifically binds the conserved nonomer (9 nucleotides) of the RSS and the central domain (amino acids 528–760) of RAG-1 binds specifically to the RSS heptamer. The core region of RAG-2 is predicted to form a six-bladed beta-propeller structure that appears less specific than RAG-1 for its target.


Based on core sequence homology, it is believed that the RAG-1 protein evolved from a transposon of the Transib superfamily.[2] Although the transposon origins of these genes are well-established, there is still no consensus on when the ancestral RAG1/2 became present in the vertebrate genome. Because agnathans (a class of jawless fish) lack a core RAG1 element, it was traditionally assumed that RAG1 invaded after the agnathan/gnathostome split 1001 to 590 million years ago (MYA).[3] However, the core sequence of RAG1 has been identified in the echinoderm Strongylocentrotus purpuratus (purple star fish),[4] the amphioxi Branchiostoma floridae (Florida lancelet).[5] Sequences with homology to RAG1 have also been identified in Lytechinus veriegatus (green sea urchin), Patiria minata (sea star),[6] and the mollusk Aplysia californica[7].

These findings indicate that the Transib family transposon invaded multiple times in non-vertebrate species, and invaded the ancestral jawed vertebrate genome about 500 MYA.[6] It should also be noted that RAG1/2 is only found in gnathostomes, and not in agnathans. It is currently hypothesized that the invasion of RAG1/2 is the most important evolutionary event in terms of shaping the gnathostome adaptive immune system vs. the agnathan variable lymphocyte receptor system.

Selective Pressures[edit]

It is still unclear what forces led to the development of a RAG1/2-mediated immune system exclusively in jawed vertebrates and not in any invertebrate species that also acquired the RAG1/2-containing transposon. Current hypotheses include two whole-genome duplication events in vertebrates,[8] which would provide the genetic raw material for the development of the adaptive immune system, and the development of endothelial tissue, greater metabolic activity, and a decreased blood volume-to-body weight ratio, all of which are more specialized in vertebrates than invertebrates and facilitate adaptive immune responses.[9]

See also[edit]


  1. ^ a b Jones JM, Gellert M (Aug 2004). "The taming of a transposon: V(D)J recombination and the immune system". Immunological Reviews 200: 233–48. doi:10.1111/j.0105-2896.2004.00168.x. PMID 15242409. 
  2. ^ Kapitonov VV, Jurka J (Jun 2005). "RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons". PLoS Biology 3 (6): e181. doi:10.1371/journal.pbio.0030181. PMC 1131882. PMID 15898832. 
  3. ^ Kasahara M, Suzuki T, Pasquier LD (Feb 2004). "On the origins of the adaptive immune system: novel insights from invertebrates and cold-blooded vertebrates" (PDF). Trends in Immunology 25 (2): 105–11. doi:10.1016/ PMID 15102370. 
  4. ^ Fugmann SD, Messier C, Novack LA, Cameron RA, Rast JP (Mar 2006). "An ancient evolutionary origin of the Rag1/2 gene locus". Proceedings of the National Academy of Sciences of the United States of America 103 (10): 3728–33. doi:10.1073/Pnas.0509720103. PMC 1450146. PMID 16505374. 
  5. ^ Holland LZ, Albalat R, Azumi K, Benito-Gutiérrez E, Blow MJ, Bronner-Fraser M, Brunet F, Butts T, Candiani S, Dishaw LJ, Ferrier DE, Garcia-Fernàndez J, Gibson-Brown JJ, Gissi C, Godzik A, Hallböök F, Hirose D, Hosomichi K, Ikuta T, Inoko H, Kasahara M, Kasamatsu J, Kawashima T, Kimura A, Kobayashi M, Kozmik Z, Kubokawa K, Laudet V, Litman GW, McHardy AC, Meulemans D, Nonaka M, Olinski RP, Pancer Z, Pennacchio LA, Pestarino M, Rast JP, Rigoutsos I, Robinson-Rechavi M, Roch G, Saiga H, Sasakura Y, Satake M, Satou Y, Schubert M, Sherwood N, Shiina T, Takatori N, Tello J, Vopalensky P, Wada S, Xu A, Ye Y, Yoshida K, Yoshizaki F, Yu JK, Zhang Q, Zmasek CM, de Jong PJ, Osoegawa K, Putnam NH, Rokhsar DS, Satoh N, Holland PW (Jul 2008). "The amphioxus genome illuminates vertebrate origins and cephalochordate biology" (PDF). Genome Research 18 (7): 1100–11. doi:10.1101/gr.073676.107. PMC 2493399. PMID 18562680. 
  6. ^ a b Kapitonov VV, Koonin EV (2015-04-28). "Evolution of the RAG1-RAG2 locus: both proteins came from the same transposon". Biology Direct 10 (1): 20. doi:10.1186/s13062-015-0055-8. PMC 4411706. PMID 25928409. 
  7. ^ Panchin Y, Moroz LL (May 2008). "Molluscan mobile elements similar to the vertebrate Recombination-Activating Genes". Biochemical and Biophysical Research Communications 369 (3): 818–23. doi:10.1016/j.bbrc.2008.02.097. PMC 2719772. PMID 18313399. 
  8. ^ Kasahara M (Oct 2007). "The 2R hypothesis: an update". Current Opinion in Immunology. Hematopoietic cell death/Immunogenetics/Transplantation 19 (5): 547–52. doi:10.1016/j.coi.2007.07.009. PMID 17707623. 
  9. ^ van Niekerk G, Davis T, Engelbrecht AM (2015-09-04). "Was the evolutionary road towards adaptive immunity paved with endothelium?". Biology Direct 10 (1): 47. doi:10.1186/s13062-015-0079-0. PMC 4560925. PMID 26341882. 

Further reading[edit]

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