RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons

PLoS Biology

Volumn 3, Issue 6, 2005, Pages 0998-1011

  Kapitonov, Vladimir V ^a   Jurka, Jerzy ^a  

^a Genetic Information Research Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; RAG1 PROTEIN; RAG2 PROTEIN; HOMEODOMAIN PROTEIN; RAG 1 PROTEIN; RAG-1 PROTEIN; RECOMBINASE;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; CATALYSIS; COELENTERATE; DROSOPHILA; GENETIC CODE; GENOME; GENOMICS; HOOKWORM; HUMAN; MOSQUITO; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN DOMAIN; RUST (PLANT DISEASE); SEA URCHIN; SILKWORM; SOYBEAN; TRANSPOSON; VERTEBRATE; AEDES; ANEMONE; ANIMAL; GENE; GENETIC RECOMBINATION; GENETICS; METABOLISM;

AEDES AEGYPTI; ANCYLOSTOMA CANINUM; ANOPHELES GAMBIAE; BOMBYX MORI; DROSOPHILA MELANOGASTER; ECHINOIDEA; GLYCINE MAX; HYDRA; NEMATOSTELLA VECTENSIS; VERTEBRATA;

AEDES; ANEMONE; ANIMALS; DNA TRANSPOSABLE ELEMENTS; DROSOPHILA; GENES, RAG-1; GENOME; HOMEODOMAIN PROTEINS; HUMANS; HYDRA; RECOMBINATION, GENETIC; SEA URCHINS; VDJ RECOMBINASES;

EID: 22744445703     PISSN: 15449173     EISSN: 15457885     Source Type: Journal    
DOI: 10.1371/journal.pbio.0030181     Document Type: Article

References (51)

1. Tonegawa S (1983) Somatic generation of antibody diversity. Nature 302: 575-581.
2. Oettinger MA, Schatz DG, Gorka C, Baltimore D (1990) RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248: 1517-1523.
3. Gellert M (2002) V(D)J recombination: RAG proteins, repair factors, and regulation. Annu Rev Biochem 71: 101-132.
4. Sakano H, Huppi K, Heinrich G, Tonegawa S (1979) Sequences at the somatic recombination sites of immunoglobulin light-chain genes. Nature 280: 288-294.
5. Akira S, Okazaki K, Sakano H (1987) Two pairs of recombination signals are sufficient to cause immunoglobulin V-(D)-J joining. Science 238: 1134-1138.
6. Ramsden DA, Baetz K, Wu GE (1994) Conservation of sequence in recombination signal sequence spacers. Nucleic Acids Res 22: 1785-1796.
7. Lee AI, Fugmann SD, Cowell LG, Ptaszek LM, Kelsoe G, et al. (2003) A functional analysis of the spacer of V(D)J recombination signal sequences. PLoS Biol 1: E1.
8. Akamatsu Y, Oettinger MA (1998) Distinct roles of RAG1 and RAG2 in binding the V(D)J recombination signal sequences. Mol Cell Biol 18: 4670-4678.
9. Thompson CB (1995) New insights into V(D)J recombination and its role in the evolution of the immune system. Immunity 3: 531-539.
10. van Gent DC, Mizuuchi K, Gellert M (1996) Similarities between initiation of V(D)J recombination and retroviral integration. Science 271: 1592-1594.
11. Melek M, Gellert M, van Gent DC (1998) Rejoining of DNA by the RAG1 and RAG2 proteins. Science 280: 301-303.
12. 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.
13. 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.
14. Clatworthy AE, Valencia MA, Haber JE, Oettinger MA (2003) V(D)J recombination and RAG-mediated transposition in yeast. Mol Cell 12: 489-499.
15. Messier TL, O'Neill JP, Hou SM, Nicklas JA, Finette BA (2003) In vivo transposition mediated by V(D)J recombinase in human T lymphocytes. EMBO J 22: 1381-1388.
16. Lewis SM, Wu GE (2000) The old and the restless. J Exp Med 191: 1631-1636.
17. Kapitonov VV, Jurka J (2003) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A 100: 6569-6574.
18. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402.
19. Sadofsky MJ, Hesse JE, McBlane JF, Gellert M (1993) Expression and V(D)J recombination activity of mutated RAG-1 proteins. Nucleic Acids Res 21: 5644-5650.
20. Silver DP, Spanopoulou E, Mulligan RC, Baltimore D (1993) Dispensable sequence motifs in the RAG-1 and RAG-2 genes for plasmid V(D)J recombination. Proc Natl Acad Sci U S A 90: 6100-6104.
21. Kim DR, Dai Y, Mundy CL, Yang W, Oettinger MA (1999) Mutations of acidic residues in RAG1 define the active site of the V(D)J recombinase. Genes Dev 13: 3070-3080.
22. Landree MA, Wibbenmeyer JA, Roth DB (1999) Mutational analysis of RAG1 and RAG2 identifies three catalytic amino acids in RAG1 critical for both cleavage steps of V(D)J recombination. Genes Dev 13: 3059-3069.
23. Craig NL, Craigie R, Gellert M, Lambowitz AM, editors (2002) Mobile DNA II. Washington, D. C.: ASM Press. 1204 p.
24. Kapitonov VV, Jurka J (2004) Harbinger transposons and an ancient HARBI1 gene derived from a transposase. DNA Cell Biol 23: 311-324.
25. Zhou L, Mitra R, Atkinson PW, Hickman AB, Dyda F, et al. (2004) Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432: 995-1001.
26. Arbuckle JL, Fauss LA, Simpson R, Ptaszek LM, Rodgers KK (2001) Identification of two topologically independent domains in RAG1 and their role in macromolecular interactions relevant to V(D)J recombination. J Biol Chem 276: 37093-37101.
27. Mo X, Bailin T, Sadofsky MJ (2001) A C-terminal region of RAG1 contacts the coding DNA during V(D)J recombination. Mol Cell Biol 21: 2038-2047.
28. Difilippantonio MJ, McMahan CJ, Eastman QM, Spanopoulou E, Schatz DG (1996) RAG1 mediates signal sequence recognition and recruitment of RAG2 in V(D)J recombination. Cell 87: 253-262.
29. Spanopoulou E, Zaitseva F, Wang FH, Santagata S, Baltimore D, et al. (1996) The homeodomain region of Rag-1 reveals the parallel mechanisms of bacterial and V(D)J recombination. Cell 87: 263-276.
30. Rodgers KK, Bu Z, Fleming KG, Schatz DG, Engelman DM, et al. (1996) A zinc-binding domain involved in the dimerization of RAG1. J Mol Biol 260: 70-84.
31. Aidinis V, Dias DC, Gomez CA, Bhattacharyya D, Spanopoulou E, et al. (2000) Definition of minimal domains of interaction within the recombination-activating genes 1 and 2 recombinase complex. J Immunol 164: 5826-5832.
32. Tsai CL, Drejer AH, Schatz DG (2002) Evidence of a critical architectural function for the RAG proteins in end processing, protection, and joining in V(D)J recombination. Genes Dev 16: 1934-1949.
33. Solovyev VV (2002) Finding Genes by Computer: Probabilistic and Discriminative Approaches. In: Jiang T, Smith T, Xu Y, Zhang M, editors. Current Topics in Computational Biology: MIT Press. pp. 361-401.
34. Willett CE, Cherry JJ, Steiner LA (1997) Characterization and expression of the recombination activating genes (rag1 and rag2) of zebrafish. Immunogenetics 45: 394-404.
35. Bellon SF, Rodgers KK, Schatz DG, Coleman JE, Steitz TA (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.
36. Yurchenko V, Xue Z, Sadofsky M (2003) The RAG1 N-terminal domain is an E3 ubiquitin ligase. Genes Dev 17: 581-585.
37. Cannon JP, Haire RN, Rast JP, Litman GW (2004) The phylogenetic origins of the antigen-binding receptors and somatic diversification mechanisms. Immunol Rev 200: 12-22.
38. Venkatesh B, Erdmann MV, Brenner S (2001) Molecular synapomorphies resolve evolutionary relationships of extant jawed vertebrates. Proc Natl Acad Sci U S A 98: 11382-11387.
39. Jurka J (2000) Repbase update: A database and an electronic journal of repetitive elements. Trends Genet 16: 418-420.
40. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
41. Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci U S A 98: 8714-8719.
42. Kapitonov VV, Jurka J (2003) The esterase and PHD domains in CR1-like non-LTR retrotransposons. Mol Biol Evol 20: 38-46.
43. Nicholas KB, Nicholas HB Jr, Deerfield DW II (1997) GeneDoc: Analysis and Visualization of Genetic Variation. EMBNEW News 4: 14.
44. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Brief Bioinform 5: 150-163.
45. Schaffer AA, Aravind L, Madden TL, Shavirin S, Spouge JL, et al. (2001) Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res 29: 2994-3005.
46. Koonin EV, Galperin MY (2003) Sequence-evolution-function. Computational approaches in comparative genomics. Norwell (Massachusetts): Kluwer Academic Publishers.
47. Wootton JC, Federhen S (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266: 554-571.
48. Lupas A (1997) Predicting coiled-coil regions in proteins. Curr Opin Struct Biol 7: 388-393.
49. Douzery EJ, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution: Does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci U S A 101: 15386-15391.
50. Peterson KJ, Lyons JB, Nowak KS, Takacs CM, Wargo MJ, et al. (2004) Estimating metazoan divergence times with a molecular clock. Proc Natl Acad Sci U S A 101: 6536-6541.
51. Pires-daSilva A, Sommer RJ (2004) Conservation of the global sex determination gene tra-1 in distantly related nematodes. Genes Dev 18: 1198-1208.