Processing and translation initiation of non-long terminal repeat retrotransposons by Hepatitis Delta Virus (HDV)-like self-cleaving ribozymes

Journal of Biological Chemistry

Volumn 286, Issue 48, 2011, Pages 41286-41295

  Ruminski, Dana J ^a   Webb, Chiu Ho T ^a   Riccitelli, Nathan J ^a   Lupta, Andrej ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HAMMERHEAD RIBOZYMES; HEPATITIS DELTA VIRUS; IN-VITRO; INSERTION SEQUENCES; INSERTION SITE; OPEN READING FRAME; RETROTRANSPOSITION; RIBOZYMES; STRUCTURE-BASED;

BIOINFORMATICS; GENES;

VIRUSES;

HEPATITIS DELTA VIRUS LIKE SELF CLEAVING RIBOZYME; RIBOSOME DNA; RIBOZYME; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTHROPOD; ARTICLE; BIOINFORMATICS; CHORDATA; CONTROLLED STUDY; DROSOPHILA MELANOGASTER; HEPATITIS DELTA VIRUS; IN VITRO STUDY; IN VIVO STUDY; INSECT CELL; MOLECULAR CLONING; NEMATODE; NON LONG TERMINAL REPEAT RETROTRANSPOSON; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; RETROPOSON; TRANSLATION INITIATION; WILD TYPE;

ANIMALS; CELL LINE; DROSOPHILA MELANOGASTER; HEPATITIS DELTA VIRUS; OPEN READING FRAMES; PEPTIDE CHAIN INITIATION, TRANSLATIONAL; RETROELEMENTS; RNA, CATALYTIC; RNA, VIRAL; TERMINAL REPEAT SEQUENCES;

EID: 82355171862     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M111.297283     Document Type: Article

References (74)

1. Han, J. S. (2010) Mob. DNA 1, 15
2. Bourque, G. (2009) Curr. Opin. Genet. Dev. 19, 607-612
3. Mourier, T., and Willerslev, E. (2009) Brief. Funct. Genomic Proteomic 8, 493-501
4. George, J. A., and Eickbush, T. H. (1999) Insect Mol. Biol. 8, 3-10
5. Webb, C. H., Riccitelli, N. J., Ruminski, D. J., and Lupták, A. (2009) Science 326, 953
6. Eickbush, D. G., and Eickbush, T. H. (2010) Mol. Cell. Biol. 30, 3142-3150
7. Sanchez-Luque, F. J., Lopez, M. C., Macias, F., Alonso, C., and Thomas, M. C. (2011) Nucleic Acids Res. 39, 8065-8077
8. Jakubczak, J. L., Burke, W. D., and Eickbush, T. H. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 3295-3299
9. Burke, W. D., Müller, F., and Eickbush, T. H. (1995) Nucleic Acids Res. 23, 4628-4634
10. Kubo, Y., Okazaki, S., Anzai, T., and Fujiwara, H. (2001) Mol. Biol. Evol. 18, 848-857
11. Kojima, K. K., and Fujiwara, H. (2003) Mol. Biol. Evol. 20, 351-361
12. Roiha, H., Miller, J. R., Woods, L. C., and Glover, D. M. (1981) Nature 290, 749-753
13. Jamrich, M., and Miller, O. L., Jr. (1984) EMBO J. 3, 1541-1545
14. Luan, D. D., Korman, M. H., Jakubczak, J. L., and Eickbush, T. H. (1993) Cell 72, 595-605
15. Kurzynska-Kokorniak, A., Jamburuthugoda, V. K., Bibillo, A., and Eickbush, T. H. (2007) J. Mol. Biol. 374, 322-333
16. Burke, W. D., Malik, H. S., Jones, J. P., and Eickbush, T. H. (1999) Mol. Biol. Evol. 16, 502-511
17. Yang, J., Malik, H. S., and Eickbush, T. H. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 7847-7852
18. Christensen, S. M., Ye, J., and Eickbush, T. H. (2006) Proc. Natl. Acad. Sci. U.S.A. 103, 17602-17607
19. Kierzek, E., Christensen, S. M., Eickbush, T. H., Kierzek, R., Turner, D. H., and Moss, W. N. (2009) J. Mol. Biol. 390, 428-442
20. Kojima, K. K., and Fujiwara, H. (2005) Mol. Biol. Evol. 22, 2157-2165
21. Salehi-Ashtiani, K., Lupták, A., Litovchick, A., and Szostak, J. W. (2006) Science 313, 1788-1792
22. Luptak, A., and Szostak, J. W. (2007) in Ribozymes and RNA Catalysis (Lilley, D. M. J., and Eckstein, F., eds) pp. 130-131, Royal Society of Chemistry, Cambridge, UK
23. Ferré-D'Amaré, A. R., Zhou, K., and Doudna, J. A. (1998) Nature 395, 567-574
24. Ke, A., Zhou, K., Ding, F., Cate, J. H., and Doudna, J. A. (2004) Nature 429, 201-205
25. Chen, J. H., Yajima, R., Chadalavada, D. M., Chase, E., Bevilacqua, P. C., and Golden, B. L. (2010) Biochemistry 49, 6508-6518
26. Riccitelli, N. J., and Lupták, A. (2010) Methods 52, 133-140
27. Webb, C. H., and Luptak, A. (2011) RNA Biol. 8, 719-727
28. Warren, A. M., Hughes, M. A., and Crampton, J. M. (1997) Mol. Gen. Genet. 254, 505-513
29. Ghesini, S., Luchetti, A., Marini, M., and Mantovani, B. (2011) J. Mol. Evol. 72, 296-305
30. Kojima, K. K., and Fujiwara, H. (2004) Mol. Biol. Evol. 21, 207-217
31. Burke, W. D., Malik, H. S., Lathe, W. C., 3rd, and Eickbush, T. H. (1998) Nature 392, 141-142
32. Rezende-Teixeira, P., Siviero, F., da Costa Rosa, M., and Machado-Santelli, G. M. (2009) Chromosome Res. 17, 455-467
33. Kawaoka, S., Hayashi, N., Katsuma, S., Kishino, H., Kohara, Y., Mita, K., and Shimada, T. (2008) Insect Biochem. Mol. Biol. 38, 1058-1065
34. De la Peña, M., Gago, S., and Flores, R. (2003) EMBO J. 22, 5561-5570
35. Khvorova, A., Lescoute, A., Westhof, E., and Jayasena, S. D. (2003) Nat. Struct. Biol. 10, 708-712
36. Jimenez, R. M., Delwart, E., and Lupták, A. (2011) J. Biol. Chem. 286, 7737-7743
37. Perreault, J., Weinberg, Z., Roth, A., Popescu, O., Chartrand, P., Ferbeyre, G., and Breaker, R. R. (2011) PLoS Comput. Biol. 7, e1002031
38. Been, M. D., Perrotta, A. T., and Rosenstein, S. P. (1992) Biochemistry 31, 11843-11852
39. Nishikawa, F., Roy, M., Fauzi, H., and Nishikawa, S. (1999) Nucleic Acids Res. 27, 403-410
40. Chadalavada, D. M., Knudsen, S. M., Nakano, S., and Bevilacqua, P. C. (2000) J. Mol. Biol. 301, 349-367
41. Jeong, S., Sefcikova, J., Tinsley, R. A., Rueda, D., and Walter, N. G. (2003) Biochemistry 42, 7727-7740
42. Hoskins, R. A., Carlson, J. W., Kennedy, C., Acevedo, D., Evans-Holm, M., Frise, E., Wan, K. H., Park, S., Mendez-Lago, M., Rossi, F., Villasante, A., Dimitri, P., Karpen, G. H., and Celniker, S. E. (2007) Science 316, 1625-1628
43. Tay, W. T., Behere, G. T., Batterham, P., and Heckel, D. G. (2010) BMC Evol. Biol. 10, 144
44. Ferbeyre, G., Smith, J. M., and Cedergren, R. (1998) Mol. Cell. Biol. 18, 3880-3888
45. de la Pena, M., and Garcia-Robles, I. (2010) EMBO Rep. 11, 711-716
46. de la Peña, M., and García-Robles, I. (2010) RNA 16, 1943-1950
47. McFarlane, C. T., and Docker, M. F. (2009) Conservation Genet. Resour. 1, 377-380
48. Bryan, M. B., Zalinski, D., Filcek, K. B., Libants, S., Li, W., and Scribner, K. T. (2005) Mol. Ecol. 14, 3757-3773
49. Kidd, S. J., and Glover, D. M. (1981) J. Mol. Biol. 151, 645-662
50. Long, E. O., Collins, M., Kiefer, B. I., and Dawid, I. B. (1981) Mol. Gen. Genet. 182, 377-384
51. Kamoshita, N., Nomoto, A., and RajBhandary, U. L. (2009) Mol. Cell 35, 181-190
52. Berry, K. E., Waghray, S., and Doudna, J. A. (2010) RNA 16, 1559-1569
53. Cech, T. R. (1993) in The RNA World (Atkins, J. F., ed) Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
54. Winkler, W. C., Nahvi, A., Roth, A., Collins, J. A., and Breaker, R. R. (2004) Nature 428, 281-286
55. Fedor, M. J., and Williamson, J. R. (2005) Nat. Rev. Mol. Cell Biol. 6, 399-412
56. Pfingsten, J. S., Costantino, D. A., and Kieft, J. S. (2006) Science 314, 1450-1454
57. Zhu, J., Korostelev, A., Costantino, D. A., Donohue, J. P., Noller, H. F., and Kieft, J. S. (2011) Proc. Natl. Acad. Sci. U.S.A. 108, 1839-1844
58. Bibiłło, A., and Eickbush, T. H. (2002) J. Mol. Biol. 316, 459-473
59. Bibillo, A., and Eickbush, T. H. (2004) J. Biol. Chem. 279, 14945-14953
60. Liu, F., and Gu, J. (2011) Protein Cell 2, 351-357
61. Duhamel, J., Liu, D. M., Evilia, C., Fleysh, N., Dinter-Gottlieb, G., and Lu, P. (1996) Nucleic Acids Res. 24, 3911-3917
62. Tang, J., and Breaker, R. R. (2000) Proc. Natl. Acad. Sci. U.S.A. 97, 5784-5789
63. Salehi-Ashtiani, K., and Szostak, J. W. (2001) Nature 414, 82-84
64. Legiewicz, M., Wichłacz, A., Brzezicha, B., and Ciesiołka, J. (2006) Nucleic Acids Res. 34, 1270-1280
65. Nehdi, A., and Perreault, J. P. (2006) Nucleic Acids Res. 34, 584-592
66. Malik, H. S., Burke, W. D., and Eickbush, T. H. (1999) Mol. Biol. Evol. 16, 793-805
67. Blesa, D., Gandía, M., and Martínez-Sebastián, M. J. (2001) Mol. Biol. Evol. 18, 585-592
68. Burke, W. D., Malik, H. S., Rich, S. M., and Eickbush, T. H. (2002) Mol. Biol. Evol. 19, 619-630
69. Epstein, L. M., and Gall, J. G. (1987) Cell 48, 535-543
70. Saville, B. J., and Collins, R. A. (1990) Cell 61, 685-696
71. Green, B., Pabón-Peña, L. M., Graham, T. A., Peach, S. E., Coats, S. R., and Epstein, L. M. (1993) Mol. Biol. Evol. 10, 732-750
72. Rojas, A. A., Vazquez-Tello, A., Ferbeyre, G., Venanzetti, F., Bachmann, L., Paquin, B., Sbordoni, V., and Cedergren, R. (2000) Nucleic Acids Res. 28, 4037-4043
73. Khan, H., Smit, A., and Boissinot, S. (2006) Genome Res. 16, 78-87
74. Belfort, M., Derbyshire, V., Parker, M. M., Cousineau, B., and Lambowitz, A. M. (2002) in Mobile DNA II (Craig, N. L., Craigie, R., Gellert, M., and Lambowitz, A. M., eds) pp. 761-783, American Society for Microbiology, Washington, D. C.