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DNA bending in the synaptic complex in V(D)J recombination: turning an ancestral transpososome upside down

DISCOVERIES (ISSN 2359-7232), 2014, January-March


Ciubotaru M, Surleac M, Mihaela G. Musat MG, Rusu AM, Ionita E, Albu PCC. DNA bending in the synaptic complex in V(D)J recombination; turning an ancestral transpososome upside down. Discoveries 2014, Jan-Mar; 2(1): e13. DOI: 10.15190/d.2014.5;

Submitted: March 17, 2014; Published online:March 29, 2014

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DNA bending in the synaptic complex in V(D)J recombination: turning an ancestral transpososome upside down

(1,2,*), (3), (2) (2), (2) and (2)

(1) Department of Immunobiology, Yale University School of Medicine, 300 Cedar St., TAC S620, New Haven, CT 06511, USA. (2) National Institute for Physics and Nuclear Engineering Horia Hulubei, Department of Life and Environmental Physics, Atomistilor Str., 077125, Bucharest-Magurele, Romania. (3) Department of Bioinformatics and Structural Biochemistry, Institute of Biochemistry of the Romanian Academy, Splaiul Independentei 296, 060031, Bucharest, Romania

*Correspondence should be addressed to: Mihai Ciubotaru, PhD, Department of Immunobiology, Yale University School of Medicine, 300 Cedar St., TAC S620, New Haven, CT 06511, USA, Phone: 011-1-203-785-3247; Fax: 011-1-203-785-3855; Email: mihai.ciubotaru@yale.edu


In all jawed vertebrates RAG (recombination activating gene) recombinase orchestrates V(D)J recombination in B and T lymphocyte precursors, assembling the V, D and J germline gene segments into continuous functional entities which encode the variable regions of their immune receptors. V(D)J recombination is the process by which most of the diversity of our specific immune receptors is acquired and is thought to have originated by domestication of a transposon in the genome of a vertebrate. Although RAG reaction mechanism resembles that of some insect mobile element transposases and RAG itself can inefficiently perform intra and intermolecular integration into target DNA, for it, inside the nuclei of the developing lymphocytes transposition is extremely rare and is kept under proper surveillance. Our review may help understanding how RAG synaptic complex organization prevents deleterious transposition. The phosphoryl transfer reaction mechanism of RNAseH-like fold DDE motif enzymes, including RAG, is discussed accentuating the peculiarities described for various transposases from the light of their available high resolution structures (Tn5, Mu, Mos1 and Hermes). Contrasting the structural 3D organization of DNA in these transpososomes with that of the RSSs (recombination signal sequences)-DNA in RAG paired complex (PC) allows us to propose several clues for how evolutionarily RAG may have become “specialized” in recombination versus transposition.

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1. Venter, J. C. et al. The sequence of the human genome. Science 291, 1304-1351, (2001).
2. Bordenstein, S. R. & Reznikoff, W. S. Mobile DNA in obligate intracellular bacteria. Nat Rev Microbiol 3, 688-699, (2005).
3. Brouha, B. et al. Hot L1s account for the bulk of retrotransposition in the human population. Proc Natl Acad Sci U S A 100, 5280-5285, (2003).
4. Agrawal, A., Eastman, Q. M. & Schatz, D. G. Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system. Nature 394, 744-751, (1998).
5. Chatterji, M., Tsai, C. L. & Schatz, D. G. New concepts in the regulation of an ancient reaction: transposition by RAG1/RAG2. Immunol Rev 200, 261-271, (2004).
6. Chatterji, M., Tsai, C. L. & Schatz, D. G. Mobilization of RAG-generated signal ends by transposition and insertion in vivo. Mol Cell Biol 26, 1558-1568, (2006).
7. Hiom, K., Melek, M. & Gellert, M. DNA transposition by the RAG1 and RAG2 proteins: a possible source of oncogenic translocations. Cell 94, 463-470, (1998).
8. Reddy, Y. V., Perkins, E. J. & Ramsden, D. A. Genomic instability due to V(D)J recombination-associated transposition. Genes Dev 20, 1575-1582, (2006).
9. Kapitonov, V. V. & Jurka, J. RAG1 core and V(D)J recombination signal sequences were derived from Transib transposons. PLoS Biol 3, e181, (2005).
10. Gellert, M. V(D)J recombination: RAG proteins, repair factors, and regulation. Annu Rev Biochem 71, 101-132 (2002).
11. Schatz, D. G. & Swanson, P. C. V(D)J recombination: mechanisms of initiation. Annu Rev Genet 45, 167-202, (2011).
12. Hickman, A. B. et al. Molecular architecture of a eukaryotic DNA transposase. Nat Struct Mol Biol 12, 715-721, (2005).
13. Zhou, L. et al. Transposition of hAT elements links transposable elements and V(D)J recombination. Nature 432, 995-1001, (2004).
14. Davies, D. R., Goryshin, I. Y., Reznikoff, W. S. & Rayment, I. Three-dimensional structure of the Tn5 synaptic complex transposition intermediate. Science 289, 77-85, (2000).
15. Maertens, G. N., Hare, S. & Cherepanov, P. The mechanism of retroviral integration from X-ray structures of its key intermediates. Nature 468, 326-329, (2010).
16. Montano, S. P., Pigli, Y. Z. & Rice, P. A. The mu transpososome structure sheds light on DDE recombinase evolution. Nature 491, 413-417, (2012).
17. Rice, P. & Mizuuchi, K. Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell 82, 209-220, (1995).
18. Richardson, J. M., Colloms, S. D., Finnegan, D. J. & Walkinshaw, M. D. Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote. Cell 138, 1096-1108, (2009).
19. Tonegawa, S. Somatic generation of antibody diversity. Nature 302, 575-581 (1983).
20. Eastman, Q. M., Leu, T. M. & Schatz, D. G. Initiation of V(D)J recombination in vitro obeying the 12/23 rule. Nature 380, 85-88 (1996).
21. Grundy, G. J., Hesse, J. E. & Gellert, M. Requirements for DNA hairpin formation by RAG1/2. Proc Natl Acad Sci U S A 104, 3078-3083 (2007).
22. Agrawal, A. & Schatz, D. G. RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell 89, 43-53, (1997).
23. Oettinger, M. A., Schatz, D. G., Gorka, C. & Baltimore, D. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248, 1517-1523 (1990).
24. Schatz, D. G., Oettinger, M. A. & Baltimore, D. The V(D)J recombination activating gene, RAG-1. Cell 59, 1035-1048, (1989).
25. Gellert, M. et al. V(D)J recombination: links to transposition and double-strand break repair. Cold Spring Harbor Symposia on Quantitative Biology 64, 161-167 (1999).
26. Hickman, A. B., Chandler, M. & Dyda, F. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit Rev Biochem Mol Biol 45, 50-69, (2010).
27. Nesmelova, I. V. & Hackett, P. B. DDE transposases: Structural similarity and diversity. Adv Drug Deliv Rev 62, 1187-1195, (2010).
28. Ciubotaru, M. et al. RAG1-DNA binding in V(D)J recombination. Specificity and DNA-induced conformational changes revealed by fluorescence and CD spectroscopy. J Biol Chem 278, 5584-5596, (2003).
29. Shlyakhtenko, L. S. et al. Molecular mechanism underlying RAG1/RAG2 synaptic complex formation. J Biol Chem 284, 20956-20965, (2009).
30. Ji, Y. et al. The in vivo pattern of binding of RAG1 and RAG2 to antigen receptor loci. Cell 141, 419-431, (2010).
31. Little, A. J., Corbett, E., Ortega, F. & Schatz, D. G. Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA. Nucleic Acids Res 41, 3289-3301, (2013).
32. Mundy, C. L., Patenge, N., Matthews, A. G. & Oettinger, M. A. Assembly of the RAG1/RAG2 synaptic complex. Mol Cell Biol 22, 69-77 (2002).
33. Montano, S. P. & Rice, P. A. Moving DNA around: DNA transposition and retroviral integration. Curr Opin Struct Biol 21, 370-378, (2011).
34. Rice, P., Craigie, R. & Davies, D. R. Retroviral integrases and their cousins. Curr Opin Struct Biol 6, 76-83, (1996).
35. Yin, F. F. et al. Structure of the RAG1 nonamer binding domain with DNA reveals a dimer that mediates DNA synapsis. Nat Struct Mol Biol 16, 499-508, (2009).
36. Clubb, R. T. et al. A novel class of winged helix-turn-helix protein: the DNA-binding domain of Mu transposase. Structure 2, 1041-1048 (1994).
37. Clubb, R. T., Schumacher, S., Mizuuchi, K., Gronenborn, A. M. & Clore, G. M. Solution structure of the I gamma subdomain of the Mu end DNA-binding domain of phage Mu transposase. J Mol Biol 273, 19-25, (1997).
38. Yang, W., Hendrickson, W. A., Crouch, R. J. & Satow, Y. Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Science 249, 1398-1405 (1990).
39. Dyda, F. et al. Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266, 1981-1986 (1994).
40. Maignan, S., Guilloteau, J. P., Zhou-Liu, Q., Clement-Mella, C. & Mikol, V. Crystal structures of the catalytic domain of HIV-1 integrase free and complexed with its metal cofactor: high level of similarity of the active site with other viral integrases. J Mol Biol 282, 359-368, (1998).
41. Hencken, C. G., Li, X. & Craig, N. L. Functional characterization of an active Rag-like transposase. Nat Struct Mol Biol 19, 834-836, (2012).
42. Huye, L. E. & Roth, D. B. Differential requirements for cis and trans V(D)J cleavage: effects of substrate length. Nucleic Acids Res 28, 4903-4911 (2000).
43. Ciubotaru, M. & Schatz, D. G. Synapsis of recombination signal sequences located in cis and DNA underwinding in V(D)J recombination. Mol Cell Biol 24, 8727-8744, (2004).
44. Dodson, K. W. & Berg, D. E. Factors affecting transposition activity of IS50 and Tn5 ends. Gene 76, 207-213 (1989).
45. Kumar, S. & Swanson, P. C. Full-length RAG1 promotes contact with coding and intersignal sequences in RAG protein complexes bound to recombination signals paired in cis. Nucleic Acids Res 37, 2211-2226, (2009).
46. Engelman, A., Hickman, A. B. & Craigie, R. The core and carboxyl-terminal domains of the integrase protein of human immunodeficiency virus type 1 each contribute to nonspecific DNA binding. J Virol 68, 5911-5917 (1994).
47. Swanson, P. C. Fine structure and activity of discrete RAG-HMG complexes on V(D)J recombination signals. Mol Cell Biol 22, 1340-1351 (2002).
48. Mizuuchi, K., Baker, T. A. in Mobile DNA II (ed N. L. Craig, Craigie R., Gellert M., Lambowitz AM.) 12-23 (ASM Press, Washington DC, 2002).
49. Bailin, T., Mo, X. & Sadofsky, M. J. A RAG1 and RAG2 tetramer complex is active in cleavage in V(D)J recombination. Mol Cell Biol 19, 4664-4671 (1999).
50. Grundy, G. J. et al. Initial stages of V(D)J recombination: the organization of RAG1/2 and RSS DNA in the postcleavage complex. Mol Cell 35, 217-227, (2009).
51. Swanson, P. C. The DDE motif in RAG-1 is contributed in trans to a single active site that catalyzes the nicking and transesterification steps of V(D)J recombination. Mol Cell Biol 21, 449-458, (2001).
52. Swanson, P. C. A RAG-1/RAG-2 tetramer supports 12/23-regulated synapsis, cleavage, and transposition of V(D)J recombination signals. Mol Cell Biol 22, 7790-7801 (2002).
53. Pavlicek, J. W., Lyubchenko, Y. L. & Chang, Y. Quantitative analyses of RAG-RSS interactions and conformations revealed by atomic force microscopy. Biochemistry 47, 11204-11211, (2008).
54. Ciubotaru, M., Kriatchko, A. N., Swanson, P. C., Bright, F. V. & Schatz, D. G. Fluorescence resonance energy transfer analysis of recombination signal sequence configuration in the RAG1/2 synaptic complex. Mol Cell Biol 27, 4745-4758, (2007).
55. Ciubotaru, M. et al. RAG and HMGB1 create a large bend in the 23RSS in the V(D)J recombination synaptic complexes. Nucleic Acids Res 41, 2437-2454, (2013).
56. Gupta, K. et al. Solution conformations of prototype foamy virus integrase and its stable synaptic complex with U5 viral DNA. Structure 20, 1918-1928, (2012).
57. Allet, B. Mu insertion duplicates a 5 base pair sequence at the host inserted site. Cell 16, 123-129, (1979).
58. Eastman, Q. M., Villey, I. J. & Schatz, D. G. Detection of RAG protein-V(D)J recombination signal interactions near the site of DNA cleavage by UV cross-linking. Mol Cell Biol 19, 3788-3797 (1999).

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