Abstract
The enormous repertoire of the vertebrate specific immune system relies on the rearrangement of discrete gene segments into intact antigen receptor genes during the early stages of B-and T-cell development. This V(D)J recombination is initiated by a lymphoid-specific recombinase comprising the RAG1 and RAG2 proteins, which introduces double-strand breaks in the DNA adjacent to the coding segments. Much of the biochemical research into V(D)J recombination has focused on truncated or “core” fragments of RAG1 and RAG2, which lack approximately one third of the amino acids from each. However, genetic analyses of SCID and Omenn syndrome patients indicate that residues outside the cores are essential to normal immune development. This is in agreement with the striking degree of conservation across all vertebrate classes in certain non-core domains. Work from multiple laboratories has shed light on activities resident within these domains, including ubiquitin ligase activity and KPNA1 binding by the RING finger domain of RAG1 and the recognition of specific chromatin modifications as well as phosphoinositide binding by the PHD module of RAG2. In addition, elements outside of the cores are necessary for regulated protein expression and turnover. Here the current state of knowledge is reviewed regarding the non-core regions of RAG1 and RAG2 and how these findings contribute to our broader understanding of recombination.
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References
Agrawal A, Eastman QM, Schatz DG (1998) Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394: 744-751
Agrawal A, Schatz DG (1997) RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell 89: 43-53
Akamatsu Y, Monroe R, Dudley DD et al (2003) Deletion of the RAG2 C terminus leads to impaired lymphoid development in mice. Proc Natl Acad Sci USA 100: 1209-1214
Bellon SF, Rodgers KK, Schatz DG et al (1997) Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nat Struct Biol 4: 586-591
Chatterji M, Tsai CL, Schatz DG (2006) Mobilization of RAG-generated signal ends by transposition and insertion in vivo. Mol Cell Biol 26: 1558-1568
Chen HT, Bhandoola A, Difilippantonio MJ et al (2000) Response to RAG-mediated VDJ cleavage by NBS1 and gamma-H2AX. Science 290: 1962-1965
Clatworthy AE, Valencia MA, Haber JE et al (2003) V(D)J recombination and RAG-mediated transposition in yeast. Mol Cell 12: 489-499
Cortes P, Ye ZS, Baltimore D (1994) RAG-1 interacts with the repeated amino acid motif of the human homologue of the yeast protein SRP1. Proc Natl Acad Sci USA 91: 7633-7637
Cuomo CA, Kirch SA, Gyuris J et al (1994) Rch1, a protein that specifically interacts with the RAG-1 recombination-activating protein. Proc Natl Acad Sci USA 91: 6156-6160
Desiderio S, Lin WC, Li Z (1996) The cell cycle and V(D)J recombination. Curr Top Microbiol Immunol 217: 45-49
Dudley DD, Sekiguchi J, Zhu C et al (2003) Impaired V(D)J recombination and lymphocyte development in core RAG1-expressing mice. J Exp Med 198: 1439-1450
Eastman QM, Leu TM, Schatz DG (1996) Initiation of V(D)J recombination in vitro obeying the 12/23 rule. Nature 380: 85-88
Elkin SK, Ivanov D, Ewalt M et al (2005) A PHD finger motif in the C terminus of RAG2 modulates recombination activity. J Biol Chem 280: 28701-28710
Elkin SK, Matthews A, Oettinger M (2003) The C-terminal portion of RAG2 protects against transposition in vitro. EMBO J 22: 1931-1938
Fugmann SD, Messier C, Novack LA et al (2006) An ancient evolutionary origin of the Rag1/2 gene locus. Proc Natl Acad Sci USA 103: 3728-3733
Gellert M (2002) V(D)J recombination: RAG proteins, repair factors, and regulation. Annu Rev Biochem 71: 101-132
Hiom K, Melek M, Gellert M (1998) DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94: 463-470
Jackson PK, Eldridge AG, Freed E et al (2000) The lore of the RINGs: substrate recognition and catalysis by ubiquitin ligases. Trends Cell Biol 10: 429-439
Jiang H, Chang FC, Ross AE et al (2005) Ubiquitylation of RAG-2 by Skp2-SCF links destruction of the V(D)J recombinase to the cell cycle. Mol Cell 18: 699-709
Jiang H, Ross AE, Desiderio S (2004) Cell cycle-dependent accumulation in vivo of transposition-competent complexes between recombination signal ends and full-length RAG proteins. J Biol Chem 279: 8478-8486
Jones JM, Gellert M (2001) Intermediates in V(D)J recombination: A stable RAG1/2 complex sequesters cleaved RSS ends. Proc Nat Acad Sci USA 98: 12926-12931
Jones JM, Gellert M (2003) Auto-ubiquitylation of the V(D)J recombinase protein RAG1. Proc Natl Acad Sci USA 100: 15446-15451
Kapitonov VV, Jurka J (2003) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci USA 100: 6569-6574
Kapitonov VV, Jurka J (2005) RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3: e181
Kosak ST, Skok JA, Medina KL et al (2002) Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296: 158-162
Kwon J, Imbalzano AN, Matthews A et al (1998) Accessibility of nucleosomal DNA to V(D)J cleavage is modulated by RSS positioning and HMG1. Mol Cell 2: 829-839
Kwon J, Morshead KB, Guyon JR et al (2000) Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol Cell 6: 1037-1048
Lee J, Desiderio S (1999) Cyclin A/CDK2 regulates V(D)J recombination by coordinating RAG-2 accumulation and DNA repair. Immunity 11: 771-781
Leu TM, Schatz DG (1995) rag-1 and rag-2 are components of a high-molecular-weight complex, and association of rag-2 with this complex is rag-1 dependent. Mol Cell Biol 15: 5657-5670
Lewis SM, Hesse JE, Mizuuchi K et al (1988) Novel strand exchanges in V(D)J recombination. Cell 55: 1099-1107
Liang HE, Hsu LY, Cado D et al (2002) The "dispensable" portion of RAG2 is necessary for efficient V-to-DJ rearrangement during B and T cell development. Immunity 17: 639-651
Lin WC, Desiderio S (1994) Cell cycle regulation of V(D)J recombination-activating protein RAG-2. Proc Natl Acad Sci USA 91: 2733-2737
Lin WC, Desiderio S (1995) V(D)J recombination and the cell cycle. Immunol Today 16: 279-289
Liu Y, Subrahmanyam R, Chakraborty T, Sen R et al (2007) A plant homeodomain in RAG-2 that binds Hypermethylated lysine 4 of histone H3 is necessary for efficient antigen-receptor-gene rearrangement. Immunity 27: 561-671
Martelli AM, Manzoli L, Cocco L (2004) Nuclear inositides: facts and perspectives. Pharmacol Ther 101: 47-44
Matthews AG, Kuo AJ, Ramon-Maiques S et al (2007) RAG2 PHD finger couples histone H3 lysine 4 trimethylation with V(D)J recombination. Nature 450: 1106-1110
McMahan CJ, Difilippantonio MJ, Rao N et al (1997) A basic motif in the N-terminal region of RAG1 enhances V(D)J recombination activity. Mol Cell Biol 17: 4544-4552
Messier TL, O’Neill JP, Hou SM et al (2003) In vivo transposition mediated by V(D)J recombinase in human T lymphocytes. EMBO J 22: 1381-1388
Mizuta R, Mizuta M, Araki S et al (2002) RAG2 is down regulated by cytoplasmic sequestration and ubiquitin-dependent degradation. J Biol Chem 277: 41423-41427
Noordzij JG, de Bruin-Versteeg S, Verkaik NS et al (2002) The immunophenotypic and immunogenotypic B-cell differentiation arrest in bone marrow of RAG-deficient SCID patients corresponds to residual recombination activities of mutated RAG proteins. Blood 100: 2145-2152
Noordzij JG, Verkaik NS, Hartwig NG et al (2000) N-terminal truncated RAG1 proteins can direct T-cell but not immunoglobulin gene rearrangements. Blood 96: 203-209
Oettinger MA, Schatz DG, Gorka C et al (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248: 1517-1523
Patenge N, Elkin SK, Oettinger MA (2004) ATP-dependent remodeling by SWI/SNF and ISWI proteins stimulates V(D)J cleavage of 5 S arrays. J Biol Chem 279: 35360-35367
Pickart CM (2001) Mechanisms underlying ubiquitination. Annu Rev Biochem 70: 503-533
Pickart CM (2000) Ubiquitin in chains. Trends Biochem Sci 25: 544-548
Piirila H, Valiaho J, Vihinen M (2006) Immunodeficiency mutation databases (IDbases). Hum Mutat 27: 1200-1208
Ramon-Maiques S, Kuo AJ, Carney D et al (2007) The plant homeodomain finger of RAG2 recognizes histone H3 methylated at both lysine-4 and arginine-2. Proc Natl Acad Sci USA 104: 18993-18998
Ramsden CA, Gellert M (1995) Formation and resolution of double-strand break intermediates in V(D)J rearrangement. Genes Dev 9: 2409-2420
Raval P, Kriatchko AN, Kumar S et al (2008) Evidence for Ku70/Ku80 association with full-length RAG1. Nucleic Acids Res 36: 2060-2072
Rodgers KK, Bu Z, Fleming KG et al (1996) A zinc-binding domain involved in the dimerization of RAG1. J Mol Biol 260: 70-74
Roman CA, Cherry SR, Baltimore D (1997) Complementation of V(D)J recombination deficiency in RAG-1(-/-) B cells reveals a requirement for novel elements in the N-terminus of RAG-1. Immunity 7: 13-14
Roth DB, Menetski JP, Nakajima PB et al (1992) V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes. Cell 70: 983-991
Roth DB, Zhu C, Gellert M (1993) Characterization of broken DNA molecules associated with V(D)J recombination. Proc Nat Acad Sci U S A 90: 10788-10792
Sadofsky MJ, Hesse JE, Gellert M (1994) Definition of a core region of RAG-2 that is functional in V(D)J recombination. Nucleic Acids Res 22: 1805-1809
Sadofsky MJ, Hesse JE, McBlane JF et al (1993) Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res 21: 5644-5650
Sakano H, Huppi K, Heinrich G et al (1979) Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280: 288-294
Santagata S, Gomez CA, Sobacchi C et al (2000) N-terminal RAG1 frameshift mutations in Omenn’s syndrome: Internal methionine usage leads to partial V(D)J recombination activity and reveals a fundamental role in vivo for the N-terminal domains. Proc Natl Acad Sci USA 97: 14572-14577
Schatz DG, Oettinger MA, Baltimore D (1989) The V(D)J recombination activating gene, RAG-1. Cell 59: 1035-1048
Schatz DG, Spanopoulou E (2005) Biochemistry of V(D)J recombination. Curr Top Microbiol Immunol 290: 49-55
Schuetz C, Huck K, Gudowius S et al (2008) An immunodeficiency disease with RAG mutations and granulomas. N Engl J Med 358: 2030-2038
Sekiguchi JA, Whitlow S, Alt FW (2001) Increased accumulation of hybrid V(D)J joins in cells expressing truncated versus full-length RAGs. Mol Cell 8: 1383-1390
Silver DP, Spanopoulou E, Mulligan RC et al (1993) Dispensable sequence motifs in the RAG-1 and RAG-2 genes for plasmid V(D)J recombination. Proc Natl Acad Sci USA 90: 6100-6104
Simkus C, Anand P, Bhattacharyya A et al (2007) Biochemical and folding defects in a RAG1 variant associated with Omenn syndrome. J Immunol 179: 8332-8340
Simkus C, Mayika M, Jones JM (2008) Karyopherin alpha 1 is a putative substrate of the RAG1 ubiquitin ligase. Mol Immunol. Doi:10.1016/j.molimm.2008.11.009
Sobacchi C, Marrella V, Rucci F et al (2006) RAG-dependent primary immunodeficiencies. Hum Mutat 27: 1174-1184
Spanopoulou E, Cortes P, Shih C et al (1995) Localization, interaction, and RNA binding properties of the V(D)J recombination-activating proteins RAG1 and RAG2. Immunity 3: 715-726
Steen SB, Han JO, Mundy C et al (1999) Roles of the "dispensable" portions of RAG-1 and RAG-2 in V(D)J recombination. Mol Cell Biol 19: 3010-3017
Swanson PC, Volkmer D, Wang L (2004) Full-length RAG-2, and not full-length RAG-1, specifically suppresses RAG-mediated transposition, but not hybrid joint formation or disintegration. J Biol Chem 279: 4034-4044
Taccioli GE, Rathbun GA, Oltz EM et al (1993) Impairment of V(D)J recombination in double-strand break repair mutants. Science 260: 207-210
Talukder SR, Dudley DD, Alt FW et al (2004) Increased frequency of aberrant V(D)J recombination products in core RAG-expressing mice. Nucleic Acids Res 32: 4539-4549
Thompson CB (1995) New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 3: 531-539
Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302: 575-581
Tsai CL, Schatz DG (2003) Regulation of RAG1/RAG2-mediated transposition by GTP and the C-terminal region of RAG2. EMBO J 22: 1922-1930
van Gent DC, McBlane JF, Ramsden DA et al (1996) Initiation of V(D)J recombinations in a cell-free system by RAG1 and RAG2 proteins. Curr Top Microbiol Immunol 217: 1-20
van Gent DC, Ramsden DA, Gellert M (1996) The RAG1 and RAG2 proteins establish the 12/23 rule in V(D)J recombination. Cell 85: 107-113
Villa A, Sobacchi C, Notarangelo LD et al (2001) V(D)J recombination defects in lymphocytes due to RAG mutations: severe immunodeficiency with a spectrum of clinical presentations. Blood 97: 81-88
Weissman AM (2001) Themes and variations on ubiquitylation. Nat Rev Mol Cell Biol 2: 169-178
West KL, Singha NC, De Ioannes P et al (2005) A direct interaction between the RAG2 C terminus and the core histones is required for efficient V(D)J recombination. Immunity 23: 203-212
Willett CE, Cherry JJ, Steiner LA (1997) Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 45: 394-404
Wilson DR, Norton DD, Fugmann SD (2008) The PHD domain of the sea urchin RAG2 homolog, SpRAG2L, recognizes dimethylated lysine 4 in histone H3 tails. Dev Comp Immunol 32: 1221-1230
Yancopoulos GD, Alt FW (1986) Regulation of the assembly and expression of variable-region genes. Annu Rev Immunol 4: 339-368
Yurchenko V, Xue Z, Sadofsky M (2003) The RAG1 N-terminal domain is an E3 ubiquitin ligase. Genes Dev 17: 581-585
Zheng N, Wang P, Jeffrey PD et al (2000) Structure of a c-Cbl-UbcH7 complex: RING domain function in ubiquitin-protein ligases. Cell 102: 533-539
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Jones, J.M., Simkus, C. The roles of the RAG1 and RAG2 “non-core” regions in V(D)J recombination and lymphocyte development. Arch. Immunol. Ther. Exp. 57, 105–116 (2009). https://doi.org/10.1007/s00005-009-0011-3
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DOI: https://doi.org/10.1007/s00005-009-0011-3