Methods for studying IRES-mediated translation of positive-strand RNA viruses

Methods

Volumn 59, Issue 2, 2013, Pages 167-179

  Wang, Qing S ^a   Au, Hilda H T ^a   Jan, Eric ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

2A peptide; Bicistronic reporter; Ribosome; RNA; Toeprinting

Indexed keywords

ARTICLE; CONTROLLED STUDY; DICISTROVIRIDAE; FLAVIVIRUS; IN VITRO STUDY; IN VIVO STUDY; INTERNAL RIBOSOME ENTRY SITE; NONHUMAN; PICORNAVIRUS; PRIORITY JOURNAL; REPORTER GENE; RNA CLEAVAGE; RNA VIRUS; VIRUS TRANSCRIPTION;

ANIMALS; BASE SEQUENCE; GENETIC TECHNIQUES; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN BIOSYNTHESIS; RIBOSOMES; RNA VIRUSES;

RNA VIRUSES;

EID: 84875261548     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2012.09.004     Document Type: Article

References (74)

1. Walsh D., Mohr I. Nat. Rev. Microbiol. 2011, 9:860-875.
2. Doudna J.A., Sarnow P. Translation initiation by viral internal ribosome entry sites. Translation Control in Biology and Medicine 2007, 129. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. M.B. Mathews, N. Sonenberg, J. Hershey (Eds.).
3. Kieft J.S. Trends Biochem. Sci. 2008, 33:274-283.
4. Pestova T.V., Lorsch J.R., Hellen C.U. The mechanism of translation initiation in eukaryotes. Translational Control in Biology and Medicine 2007, 87. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. M.B. Mathews, N. Sonenberg, J. Hershey (Eds.).
5. Jackson R.J., Hellen C.U., Pestova T.V. Nat. Rev. Mol. Cell Biol. 2010, 11:113-127.
6. Filbin M.E., Kieft J.S. Curr. Opin. Struct. Biol. 2009, 19:267-276.
7. Pestova T.V., Hellen C.U. Methods 2005, 36:261-269.
8. Kolupaeva V.G., de Breyne S., Pestova T.V., Hellen C.U. Methods Enzymol. 2007, 430:409-439.
9. Weinlich S., Huttelmaier S., Schierhorn A., Behrens S.E., Ostareck-Lederer A., Ostareck D.H. RNA 2009, 15:1528-1542.
10. Pacheco A., Martinez-Salas E. J. Biomed. Biotechnol. 2010, 2010:458927.
11. King H.A., Cobbold L.C., Willis A.E. Biochem. Soc. Trans. 2010, 38:1581-1586.
12. Gradi A., Svitkin Y.V., Imataka H., Sonenberg N. Proc. Natl. Acad. Sci. USA 1998, 95:11089-11094.
13. Pestova T.V., Shatsky I.N., Fletcher S.P., Jackson R.J., Hellen C.U. Genes Dev. 1998, 12:67-83.
14. Skabkin M.A., Skabkina O.V., Dhote V., Komar A.A., Hellen C.U., Pestova T.V. Genes Dev. 2010, 24:1787-1801.
15. Dmitriev S.E., Terenin I.M., Andreev D.E., Ivanov P.A., Dunaevsky J.E., Merrick W.C., Shatsky I.N. J. Biol. Chem. 2010, 285:26779-26787.
16. Kim J.H., Park S.M., Park J.H., Keum S.J., Jang S.K. EMBO J. 2011, 30:2454-2464.
17. Pestova T.V., de Breyne S., Pisarev A.V., Abaeva I.S., Hellen C.U. EMBO J. 2008, 27:1060-1072.
18. Terenin I.M., Dmitriev S.E., Andreev D.E., Shatsky I.N. Nat. Struct. Mol. Biol. 2008, 15:836-841.
19. Jan E. Virus Res. 2006, 119:16-28.
20. Hertz M.I., Thompson S.R. Virology 2011, 411:355-361.
21. Nakashima N., Uchiumi T. Virus Res. 2008, 139:137-147.
22. Bonning B.C., Miller W.A. Annu. Rev. Entomol. 2010, 55:129-150.
23. Cox-Foster D.L., Conlan S., Holmes E.C., Palacios G., Evans J.D., Moran N.A., Quan P.L., Briese T., Hornig M., Geiser D.M., Martinson V., vanEngelsdorp D., Kalkstein A.L., Drysdale A., Hui J., Zhai J., Cui L., Hutchison S.K., Simons J.F., Egholm M., Pettis J.S., Lipkin W.I. Science 2007, 318:283.
24. Sasaki J., Nakashima N. J. Virol. 1999, 73:1219-1226.
25. Sasaki J., Nakashima N. Proc. Natl. Acad. Sci. USA 2000, 97:1512-1515.
26. Wilson J.E., Pestova T.V., Hellen C.U., Sarnow P. Cell 2000, 102:511-520.
27. Jan E., Sarnow P. J. Mol. Biol. 2002, 324:889-902.
28. Pestova T.V., Hellen C.U. Genes Dev. 2003, 17:181-186.
29. Jan E., Kinzy T.G., Sarnow P. Proc. Natl. Acad. Sci. USA 2003, 100:15410-15415.
30. Spahn C.M., Jan E., Mulder A., Grassucci R.A., Sarnow P., Frank J. Cell 2004, 118:465-475.
31. Schuler M., Connell S.R., Lescoute A., Giesebrecht J., Dabrowski M., Schroeer B., Mielke T., Penczek P.A., Westhof E., Spahn C.M. Nat. Struct. Mol. Biol. 2006, 13:1092.
32. Zhu J., Korostelev A., Costantino D.A., Donohue J.P., Noller H.F., Kieft J.S. Proc. Natl. Acad. Sci. USA 2011, 108:1839-1844.
33. Plank T.D., Kieft J.S. Wiley Interdiscip. Rev. RNA 2012, 3:195-212.
34. Firth A.E., Wang Q.S., Jan E., Atkins J.F. Virol. J. 2009, 6:193.
35. Ren Q., Wang Q.S., Firth A.E., Chan M.M., Gouw J.W., Guarna M.M., Foster L.J., Atkins J.F., Jan E. Proc. Natl. Acad. Sci. USA 2012, 109:E630-E639.
36. Nakashima N., Uchiumi T. Virus Res. 2009, 139:137-147.
37. Johannes G., Carter M.S., Eisen M.B., Brown P.O., Sarnow P. Proc. Natl. Acad. Sci. USA 1999, 96:13118-13123.
38. Vattem K.M., Wek R.C. Proc. Natl. Acad. Sci. USA 2004, 101:11269-11274.
39. Castagnetti S., Hentze M.W., Ephrussi A., Gebauer F. Development 2000, 127:1063-1068.
40. Iizuka N., Sarnow P. Methods 1997, 11:353-360.
41. Dorner A.J., Semler B.L., Jackson R.J., Hanecak R., Duprey E., Wimmer E. J. Virol. 1984, 50:507-514.
42. Hunt S.L., Kaminski A., Jackson R.J. Virology 1993, 197:801-807.
43. Wang T.H., Rijnbrand R.C., Lemon S.M. J. Virol. 2000, 74:11347-11358.
44. Shibuya N., Nishiyama T., Kanamori Y., Saito H., Nakashima N. J. Virol. 2010, 77(2003):12002-12010.
45. Shibuya N., Nishiyama T., Nakashima N. J. Biochem. 2004, 136:601-606.
46. Pestova T.V., Hellen C.U., Shatsky I.N. Mol. Cell. Biol. 1996, 16:6859-6869.
47. Jan E., Thompson S.R., Wilson J.E., Pestova T.V., Hellen C.U., Sarnow P. Cold Spring Harb. Symp. Quant. Biol. 2001, 66:285-292.
48. Cencic R., Robert F., Pelletier J. Methods Enzymol. 2007, 431:269-302.
49. Novac O., Guenier A.S., Pelletier J. Nucleic Acids Res. 2004, 32:902-915.
50. Cencic R., Hall D.R., Robert F., Du Y., Min J., Li L., Qui M., Lewis I., Kurtkaya S., Dingledine R., Fu H., Kozakov D., Vajda S., Pelletier J. Proc. Natl. Acad. Sci. USA 2010, 108:1046-1051.
51. Robert F., Kapp L.D., Khan S.N., Acker M.G., Kolitz S., Kazemi S., Kaufman R.J., Merrick W.C., Koromilas A.E., Lorsch J.R., Pelletier J. Mol. Biol. Cell 2006, 17:4632.
52. Dang Y., Kedersha N., Low W.K., Romo D., Gorospe M., Kaufman R., Anderson P., Liu J.O. J. Biol. Chem. 2006, 281:32870-32878.
53. Mazroui R., Sukarieh R., Bordeleau M.E., Kaufman R.J., Northcote P., Tanaka J., Gallouzi I., Pelletier J. Mol. Biol. Cell 2006, 17:4212-4219.
54. Carrasco L., Battaner E., Vazquez D. Methods Enzymol. 1974, 30:282-289.
55. Szer W., Kurylo-Borowska Z. Biochim. Biophys. Acta 1970, 224:477-486.
56. Brown J.D., Ryan M.D. Ribosome " Skipping" : " Stop-Carry On" or " StopGo" translation. Recoding: Expansion of Decoding Rules Enriches Gene Expression 2010, 101-121. Springer, NY. J.F. Atkins, R.F. Gesteland (Eds.).
57. Trichas G., Begbie J., Srinivas S. BMC Biol. 2008, 6:40.
58. Szymczak A.L., Workman C.J., Wang Y., Vignali K.M., Dilioglou S., Vanin E.F., Vignali D.A. Nat. Biotechnol. 2004, 22:589-594.
59. Donnelly M.L., Hughes L.E., Luke G., Mendoza H., ten Dam E., Gani D., Ryan M.D. J. Gen. Virol. 2001, 82:1027-1041.
60. Sharma P., Yan F., Doronina V.A., Escuin-Ordinas H., Ryan M.D., Brown J.D. Nucleic Acids Res. 2012, 40:3143-3151.
61. Pringle F.M., Gordon K.H., Hanzlik T.N., Kalmakoff J., Scotti P.D., Ward V.K. J. Gen. Virol. 1999, 80(Pt 7):1855-1863.
62. Gonzalez M., Martin-Ruiz I., Jimenez S., Pirone L., Barrio R., Sutherland J.D. Sci. Rep. 2011, 1:75.
63. Kim J.H., Lee S.R., Li L.H., Park H.J., Park J.H., Lee K.Y., Kim M.K., Shin B.A., Choi S.Y. PLoS One 2011, 6:e18556.
64. Rakotondrafara A.M., Miller W.A. Methods Mol. Biol. 2008, 451:113-124.
65. Staplin W.R., Miller W.A. Methods Mol. Biol. 2008, 451:99-112.
66. Kozak M. Gene 2003, 318:1-23.
67. Van Eden M.E., Byrd M.P., Sherrill K.W., Lloyd R.E. RNA 2004, 10:720-730.
68. Holcik M., Graber T., Lewis S.M., Lefebvre C.A., Lacasse E., Baird S. RNA 2005, 11:1605-1609.
69. Bert A.G., Grepin R., Vadas M.A., Goodall G.J. RNA 2006, 12:1074-1083.
70. Licursi M., Christian S.L., Pongnopparat T., Hirasawa K. Gene Ther. 2011, 18:631-636.
71. Ron D., Harding H.P. EIF2a phosphorylation in cellular stress responses and disease. Translational Control in Biology and Medicine 2007, 345. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. M.B. Mathews, N. Sonenberg, J. Hershey (Eds.).
72. Garrey J.L., Lee Y.Y., Au H.H., Bushell M., Jan E. J. Virol. 2010, 84:1124-1138.
73. Ingolia N.T., Ghaemmaghami S., Newman J.R., Weissman J.S. Science 2009, 324:218-223.
74. Ingolia N.T., Lareau L.F., Weissman J.S. Cell 2011, 147:789-802.