Abstract
During protein synthesis, codons in mRNA are translated sequentially in frame on the ribosome following strict decoding rules. This process is usually very accurate. However, in some cases, recoding events occur at selected codons, leading to a high frequency of frameshifting or stop codon readthrough. The factors influencing these noncanonical decoding events are very diverse; among them are the codon usage and context, the presence of a stable mRNA secondary structure downstream of the decoding sites and the type and relative abundance of normally modified tRNA. Here, we discuss the role of certain modified nucleotides of tRNAs in a few cases of frameshifting and readthrough that occur in Bacteria and Eukarya. While in some cases the effect of a given modified nucleotide in a tRNA is to increase accuracy of the recoding process, in a few other cases the reverse has been observed. This review illustrates the power of using well characterized recoding systems, coupled with specific defects of RNA modification enzymes to assay for translational fidelity under in vivo conditions.
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References
1. Adamski FM, Donly BC, Tate WP (1993) Competition between frameshifting, termination and suppression at the frameshift site in the Escherichia coli release factor-2 mRNA. Nucleic Acids Res 21:5074-5078
2. Agris PF (1996) The importance of being modified: roles of modified nucleosides and Mg2+ in RNA structure and function. Prog Nucleic Acid Res Mol Biol 53:79-129
3. Agris PF (2004) Decoding the genome: a modified view. Nucleic Acids Res 32:223-238
4. Atkins JF, Herr AJ, Massire C, O’Connor M, Ivanov I, Gesteland R (2000) Poking a hole in the sanctity of the triplet code: Inferences for framing. In: R. A. Garrett SRD, A. Liljas, A. T. Matheson, P. B. Moore, H. F. Noller (ed) The ribosome: Structure, function, antibiotics and cellular interactions. ASM Press, Washington, D.C. pp369-384
5. Baranov PV, Gurvich OL, Hammer AW, Gesteland RF, Atkins AF (2003) RECODE 2003. Nucleic Acids Res 31:87-89
6. Baranov PV, Gesteland RF, Atkins JF (2002) Recoding: translational bifurcations in gene expression. Gene 286:187-201
7. Baum M, Beier H (1998) Wheat cytoplasmic arginine tRNA isoacceptor with a U*CG anticodon is an efficient UGA suppressor in vitro. Nucleic Acids Res 26:1390-1395
8. Beier H, Barciszewska M, Krupp G, Mitnacht R, Gross HJ (1984) UAG readthrough during TMV RNA translation: Isolation and sequence of two tRNAsTyr with suppressor activity from tobacco plants. EMBO J 3:351-356
9. Beier H, Grimm M (2001) Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs. Nucleic Acids Res 29:4767-4782
10. Bekaert M, Rousset JP (2005) An extended signal involved in eukaryotic -1 frameshifting operates through modification of the E site tRNA. Mol Cell 17 : 61-68
11. Bertram G, Innes S, Minella O, Richardson J, Stansfield I (2001) Endless possibilities: translation termination and stop codon recognition. Microbiology 147:255-269
12. Bertrand C, Prere MF, Gesteland RF, Atkins JF, Fayet O (2002) Influence of the stacking potential of the base 3’ of tandem shift codons on -1 ribosomal frameshifting used for gene expression. RNA 8:16-28
13. Beuning PJ, Musier-Forsyth K (1999) Transfer RNA recognition by aminoacyl-tRNA synthetases. Biopolymers 52:1-28
14. Bidou L, Hatin I, Perez N, Allamand V, Panthier JJ, Rousset JP (2004) Premature stop codons involved in muscular dystrophies show a broad spectrum of readthrough efficiencies in response to gentamicin treatment. Gene Ther 11:619-627
15. Björk GR (1995) Genetic dissection of synthesis and function of modified nucleosides in bacterial transfer RNA. Prog Nucleic Acid Res Mol Biol 50:263-338
16. Björk GR, Durand JM, Hagervall TG, Leipuviene R, Lundgren HK, Nilsson K, Chen P, Qian Q, Urbonavicius J (1999) Transfer RNA modification: influence on translational frameshifting and metabolism. FEBS Lett 452:47-51
17. Björk GR, Rasmuson T (1998) Links between tRNA modification and metabolism and modified nucleosides as tumor markers. In: Grosjean H, Benne R (eds) Modification and editing of RNA, ASM press. Washington D.C. pp 471-491
18. Blight SK, Larue RC, Mahapatra A, Longstaff DG, Chang E, Zhao G, Kang PT, Green-Church KB, Chan MK, Krzycki JA (2004) Direct charging of tRNA(CUA) with pyrrolysine in vitro and in vivo. Nature 431:333-335
19. Blum H, Gross HJ, Beier H (1989) The expression of the TMV-specific 30-kDa protein in tobacco protoplasts is strongly and selectively enhanced by actinomycin. Virology 169:51-61
20. Bonetti B, Fu LW, Moon J, Bedwell DM (1995) The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J Mol Biol 251:334-345
21. Brégeon D, Colot V, Radman M, Taddei F (2001) Translational misreading: a tRNA modification counteracts a +2 ribosomal frameshift. Genes Dev 15:2295-2306
22. Brierley I, Meredith MR, Bloys AJ, Hagervall TG (1997) Expression of a coronavirus ribosomal frameshift signal in Escherichia coli: influence of tRNA anticodon modification on frameshifting. J Mol Biol 270:360-373
23. Bubienko E, Cruz P, Thomason JF, Borer PN (1983) Nearest-neighbor effects in the structure and function of nucleic acids. Prog Nucleic Acid Res Mol Biol 30:41-90
24. Buck M, Ames BN (1984) A modified nucleotide in tRNA as a possible regulator of aerobiosis: synthesis of cis-2-methyl-thioribosylzeatin in the tRNA of Salmonella. Cell 36:523-531
25. Buckingham RH, Grosjean H (1986) The accuracy of mRNA-tRNA recognition. In: Kirkwood TB, Rosenberger RF, Galas DJ (eds) Accuracy in Molecular Processes. Chapman and Hall Ltd, London, pp 83-115
26. Bujnicki JM, Droogmans L, Grosjean H, K. PS, Lapeyre B (2004) Bioinformatics-guided identification and experimental characterization of novel RNA methyltransferases. In: Bujnicki JM (ed) Practical Bioinformatics. Springer-Verlag, Berlin, Heidelberg pp 139-168
27. Burkhardt N, Junemann R, Spahn CM, Nierhaus KH (1998) Ribosomal tRNA binding sites: three-site models of translation. Crit Rev Biochem Mol Biol 33:95-149
28. Carlson BA, Mushinski JF, Henderson DW, Kwon SY, Crain PF, Lee BJ, Hatfield DL (2001) 1-Methylguanosine in place of Y base at position 37 in phenylalanine tRNA is responsible for its shiftiness in retroviral ribosomal frameshifting. Virology 279:130-135
29. Carlson BA, Kwon SY, Lee BJ, Hatfield D (2000) Yeast asparagine (Asn) tRNA without Q base promotes eukaryotic frameshifting more efficiently than mammalian Asn tRNAs with or without Q base. Mol Cells 10:113-118
30. Cassan M, Delaunay N, Vaquero C, Rousset JP (1994) Translational frameshifting at the gag-pol junction of human immunodeficiency virus type 1 is not increased in infected T-lymphoid cells. J Virol 68:1501-1508
31. Cassan M, Rousset JP (2001) UAG readthrough in mammalian cells: Effect of upstream and downstream stop codon contexts reveal different signals. BMC Mol Biol 2:3
32. Chittum HS, Lane WS, Carlson BA, Roller PP, Lung FD, Lee BJ, Hatfield DL (1998) Rabbit beta-globin is extended beyond its UGA stop codon by multiple suppressions and translational reading gaps. Biochemistry 37:10866-10870
33. Cobucci-Ponzano B, Trincone A, Giordano A, Rossi M, Moracci M (2003) Identification of an archaeal alpha-L-fucosidase encoded by an interrupted gene. Production of a functional enzyme by mutations mimicking programmed -1 frameshifting. J Biol Chem 278:14622-14631
34. Craigen WJ, Caskey CT (1986) Expression of peptide chain release factor 2 requires high-efficiency frameshift. Nature 322:273-275
35. Crick FH (1966) Codon–anticodon pairing: the wobble hypothesis. J Mol Biol 19(2):548-55
36. Curran JF (1998) Modified nucleosides in translation. In: Grosjean H, Benne R (eds) Modification and editing of RNA, ASM Press, Washington, D.C., pp493-516
37. Dao V, Guenther R, Malkiewicz A, Nawrot B, Sochacka E, Kraszewski A, Jankowska J, Everett K, Agris PF (1994) Ribosome binding of DNA analogs of tRNA requires base modifications and supports the ”extended anticodon”. Proc Natl Acad Sci USA 91:2125-2129
38. Davis DR (1998) Biophysical and conformational properties of modified nucleosides in RNA (nuclear magnetic resonance studies). In: Grosjean H, Benne R (eds) Modification and editing of RNA, ASM Press, Washington, DC pp 85-102
39. Davis DR, Veltri CA, Nielsen L (1998) An RNA model system for investigation of pseudouridine stabilization of the codon-anticodon interaction in tRNALys, tRNAHis and tRNATyr. J Biomol Struct Dyn 15:1121-1132
40. De Crécy-Lagard V (2004) Finding missing tRNA modification genes: a comparative goldmine. In: Bujnicki JM (ed) Practical Bioinformatics. Springer-Verlag, Berlin, Heidelberg pp 169-190
41. Decatur WA, Fournier MJ (2002) rRNA modifications and ribosome function. Trends Biochem Sci 27:344-351
42. Driscoll DM, Copeland PR (2003) Mechanism and regulation of selenoprotein synthesis. Annu Rev Nutr 23:17-40
43. Edmonds CG, Crain PF, Gupta R, Hashizume T, Hocart CH, Kowalak JA, Pomerantz SC, Stetter KO, McCloskey JA (1991) Posttranscriptional modification of tRNA in thermophilic archaea (Archaebacteria). J Bacteriol 173:3138-3148
44. Farabaugh PJ (1996) Programmed translational frameshifting. Annu Rev Genet 30:507-528
45. Fearon K, McClendon V, Bonetti B, Bedwell DM (1994) Premature translation termination mutations are efficiently suppressed in a highly conserved region of yeast Ste6p, a member of the ATP-binding cassette (ABC) transporter family. J Biol Chem 269:17802-17808
46. Feng YX, Hatfield DL, Rein A, Levin JG (1989) Translational readthrough of the murine leukemia virus gag gene amber codon does not require virus-induced alteration of tRNA. J Virol 63:2405-2410
47. Feng YX, Yuan H, Rein A, Levin JG (1992) Bipartite signal for read-through suppression in murine leukemia virus mRNA: an eight-nucleotide purine-rich sequence immediately downstream of the gag termination codon followed by an RNA pseudoknot. J Virol 66:5127-5132
48. Forster C, Chakraburtty K, Sprinzl M (1993) Discrimination between initiation and elongation of protein biosynthesis in yeast: identity assured by a nucleotide modification in the initiator tRNA. Nucleic Acids Res 21:5679-5683
49. Gallant JA, Lindsley D (1992) Leftward ribosome frameshifting at a hungry codon. J Mol Biol 223:31-40
50. Gesteland RF, Atkins JF (1996) Recoding: dynamic reprogramming of translation. Annu Rev Biochem 65:741-768
51. Gesteland RF, Weiss RB, Atkins JF (1992) Recoding: Reprogrammed genetic decoding. Science 257:1640-1643
52. Giegé R, Sissler M, Florentz C (1998) Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 26:5017-5035
53. Grentzmann G, Ingram JA, Kelly PJ, Gesteland RF, Atkins JF (1998) A dual-luciferase reporter system for studying recoding signals. RNA 4:479-486
54. Grosjean H, Benne R (eds) (1998) Modification and editing of RNA, ASM press edn. ASM Press, Washington, D.C.
55. Grosjean H, Houssier C, Romby P, Marquet R (1998) Modulatory role of modified nucleotides in RNA loop-loop interactions. In: Grosjean H, Benne R (eds) Modification and editing of RNA, ASM press, Washington D.C., pp 113-133
56. Grosshans H, Lecointe F, Grosjean H, Hurt E, Simos G (2001) Pus1p-dependent tRNA pseudouridinylation becomes essential when tRNA biogenesis is compromised in yeast. J Biol Chem 276:46333-46339
57. Hansen TM, Baranov PV, Ivanov IP, Gesteland RF, Atkins JF (2003) Maintenance of the correct open reading frame by the ribosome. EMBO Rep 4:499-504
58. Harger JW, Dinman JD (2003) An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae. RNA 9:1019-1024
59. Harrell L, Melcher U, Atkins JF (2002) Predominance of six different hexanucleotide recoding signals 3’ of read-through stop codons. Nucleic Acids Res 30:2011-2017
60. Hatfield D, Feng YX, Lee BJ, Rein A, Levin JG, Oroszlan S (1989) Chromatographic analysis of the aminoacyl-tRNAs which are required for translation of codons at and around the ribosomal frameshift sites of HIV, HTLV-1, and BLV. Virology 173:736-742
61. Hatfield DL, Gladyshev VN (2002) How selenium has altered our understanding of the genetic
62. Hoja U, Wellein C, Greiner E, Schweizer E (1998) Pleiotropic phenotype of acetyl-CoA-carboxylase-defective yeast cells-viability of a BPL1-amber mutation depending on its readthrough by normal tRNA(Gln)(CAG). Eur J Biochem 254:520-526
63. Hopper AK, Phizicky EM (2003) tRNA transfers to the limelight. Genes Dev 17:162-180
64. Horsfield JA, Wilson DN, Mannering SA, Adamski FM, Tate WP (1995) Prokaryotic ribosomes recode the HIV-1 gag-pol-1 frameshift sequence by an E/P site post-translocation simultaneous slippage mechanism. Nucleic Acids Res 23:1487-1494
65. Houssier C, Grosjean H (1985) Temperature jump relaxation studies on the interactions between transfer RNAs with complementary anticodons. The effect of modified bases adjacent to the anticodon triplet. J Biomol Struct Dyn 3:387-408
66. Huang B, Johansson JO, Byström AS (2005) An early step in wobble uridine tRNA modification requires the elongator complex. RNA (in press)
67. Jacks T, Madhani HD, Masiarz HD, Varmus HE (1988) Signals for ribosomal frameshifting in the Rous sarcoma virus gag-pol region. Cell 55:447-458
68. Jameson RR, Diamond AM (2004) A regulatory role for Sec tRNA[Ser]Sec in selenoprotein synthesis. RNA 10:1142-1152
69. Kadaba S, Krueger A, Trice T, Krecic AM, Hinnebusch AG, Anderson J (2004) Nuclear surveillance and degradation of hypomodified initiator tRNAMet in S. cerevisiae. Genes Dev 18:1227-1240
70. Kuchino Y, Beier H, Akita N, Nishimura S (1987) Natural UAG suppressor glutamine tRNA is elevated in mouse cells infected with Moloney murine leukemia virus. Proc Natl Acad Sci USA 84:2668-2672
71. Kuchino Y, Muramatsu T (1996) Nonsense suppression in mammalian cells. Biochimie 78:1007-1015
72. Kurland C, Gallant J (1996) Errors of heterologous protein expression. Curr Opin Biotechnol 7:489-493
73. Kurland CG (1992) Translational accuracy and the fitness of bacteria. Annu Rev Genet 26:29-50
74. Lafontaine DL, Preiss T, Tollervey D (1998) Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis? Mol Cell Biol 18:2360-2370
75. Landick R, Turnbough CL, Yanofsky C (1996) Transcription attenuation. In: F.C. Neidhardt RC, E.C.C. Lin, K.B. Low, B. Magasanik, J.L. Ingraham, W.S. Reznikoff, M. Riley, M. Schaeffer, H.E. Umbarger (ed) Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edition. ASM Press, Washington, D.C. pp1263-1286
76. Larsen B, Peden J, Matsufuji S, Matsufuji T, Brady K, Maldonado R, Wills NM, Fayet O, Atkins JF, Gesteland RF (1995) Upstream stimulators for recoding. Biochem Cell Biol 73:1123-1129
77. Lecointe F, Namy O, Hatin I, Simos G, Rousset JP, Grosjean H (2002) Lack of pseudouridine 38/39 in the anticodon arm of yeast cytoplasmic tRNA decreases in vivo recoding efficiency. J Biol Chem 277:30445-30453
78. Leger M, Sidani S, Brakier-Gingras L (2004) A reassessment of the response of the bacterial ribosome to the frameshift stimulatory signal of the human immunodeficiency virus type 1. RNA 10:1225-1235
79. Li G, Rice CM (1993) The signal for translational readthrough of a UGA codon in Sindbis virus RNA involves a single cytidine residue immediately downstream of the termination codon. J Virol 67:5062-5067
80. Li GP, Rice CM (1989) Mutagenesis of the in-frame opal termination codon preceding nsP4 of Sindbis virus: studies of translational readthrough and its effect on virus replication. J Virol 63:1326-1337
81. Lovett PS, Ambulos NP Jr, Mulbry W, Noguchi N, Rogers EJ (1991) UGA can be decoded as tryptophan at low efficiency in Bacillus subtilis. J Bacteriol 173:1810-1812
82. Manuvakhova M, Keeling K, Bedwell DM (2000) Aminoglycoside antibiotics mediate context-dependent suppression of termination codons in a mammalian translation system. RNA 6:1044-1055
83. Marck C, Grosjean H (2002) tRNomics: analysis of tRNA genes from 50 genomes of Eukarya, Archaea, and Bacteria reveals anticodon-sparing strategies and domain-specific features. RNA 8:1189-1232
84. Marczinke B, Hagervall T, Brierley I (2000) The Q-base of asparaginyl-tRNA is dispensable for efficient -1 ribosomal frameshifting in eukaryotes. J Mol Biol 295:179-191
85. Marquez V, Wilson DN, Tate WP, Triana-Alonso F, Nierhaus KH (2004) Maintaining the ribosomal reading frame: the influence of the E site during translational regulation of release factor 2. Cell 118:45-55
86. McCloskey JA, Rozenski J (2005) The small subunit rRNA modification database. Nucleic Acids Res (in press)
87. McCloskey JA, Graham DE, Zhou S, Crain PF, Ibba M, Konisky J, Soll D, Olsen GJ (2001) Post-transcriptional modification in archaeal tRNAs: identities and phylogenetic relations of nucleotides from mesophilic and hyperthermophilic Methanococcales. Nucleic Acids Res 29:4699-4706
88. Motorin Y, Grosjean H (1999) Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA 5:1105-1118
89. Murgola EJ (1985) tRNA, suppression, and the code. In: Inc AR (ed) Annual Review of Genetics, pp 57-80
90. Murgola EJ (1995) Translational suppression: when two wrongs do make a right. In: D. Söll and UL RajBhandary (eds) tRNA: structure, biosynthesis and function. ASM Press, Washington, D.C. pp 491-509
91. Murgola EJ, Arkov AL, Chernyaeva NS, Hedenstierna KOF, Pagel FT (2000) rRNA functional sites and structures for peptide chain termination. In: R. A. Garrett SRD, A. Liljas, A. T. Matheson, P. B. Moore, H. F. Noller (eds) The ribosome: Structure, function, antibiotics and cellular interactions. ASM Press, Washington, D.C. pp509-518
92. Namy O, Hatin I, Stahl G, Liu H, Barnay S, Bidou L, Rousset JP (2002) Gene overexpression as a tool for identifying new trans-acting factors involved in translation termination in Saccharomyces cerevisiae. Genetics 161:585-594
93. Namy O, Hatin I, Rousset JP (2001) Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep 2:787-793
94. Namy O, Rousset JP, Napthine S, Brierley I (2004) Reprogrammed genetic decoding in cellular gene expression. Mol Cell 13:157-168
95. Napthine S, Vidakovic M, Girnary R, Namy O, Brierley I (2003) Prokaryotic-style frameshifting in a plant translation system: conservation of an unusual single-tRNA slippage event. EMBO J 22:3941-3950
96. Nierhaus KH, Spahn CM, Burkhardt N, Dabrowski M, Diedrich G, Einfeldt E, Kamp D, Marquez V, Patzke S, Schafer MA, Stelzl U, Blaha G, Willumeit R, B. SH (2000) Ribosomal elongation cycle. In: R. A. Garrett SRD, A. Liljas, A. T. Matheson, P. B. Moore and H. F. Noller (ed) The ribosome: Structure, function, antibiotics and cellular interactions. ASM Press, Washington, D.C.
97. Noller HF, Yusupov MM, Yusupova GZ, Baucom A, Cate JH (2002) Translocation of tRNA during protein synthesis. FEBS Lett 514:11-16
98. Ofengand J (2002) Ribosomal RNA pseudouridines and pseudouridine synthases. FEBS Lett 514:17-25
99. Ofengand J, Del Campo M (2005) Modified nucleotides of Escherichia coli ribosomal RNA. In: F.C. Neidhardt RC, E.C.C. Lin, K.B. Low, B. Magasanik, J.L. Ingraham, W.S. Reznikoff, M. Riley, M. Schaeffer, H.E. Umbarger eds Escherichia coli and Salmonella: Cellular and Molecular Biology, 3rd edition. ASM Press, Washington, D.C., (in press)
100. Ogle JM, Carter AP, Ramakrishnan V (2003) Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 28:259-266
101. Paul CP, Barry JK, Dinesh-Kumar SP, Brault V, Miller WA (2001) A sequence required for -1 ribosomal frameshifting located four kilobases downstream of the frameshift site. J Mol Biol 310:987-999
102. Persson BC (1993) Modification of tRNA as a regulatory device. Mol Microbiol 8:1011-1016
103. Pure GA, Robinson GW, Naumovski L, Friedberg EC (1985) Partial suppression of an ochre mutation in Saccharomyces cerevisiae by multicopy plasmids containing a normal yeast tRNAGln gene. J Mol Biol 183:31-42
104. Reil H, Hoxter M, Moosmayer D, Pauli G, Hauser H (1994) CD4 expressing human 293 cells as a tool for studies in HIV-1 replication: the efficiency of translational frameshifting is not altered by HIV-1 infection. Virology 205:371-375
105. Rodnina MV, Daviter T, Gromadski K, Wintermeyer W (2002) Structural dynamics of ribosomal RNA during decoding on the ribosome. Biochimie 84:745-754
106. Rodnina MV, Pape T, Savelsbergh A, Mohr D, Matassova NB, Wintermeyer W (2000) Mechanisms of partial reactions of the elongation cycle catalyzed by elongation factors Tu and G. In: R. A. Garrett SRD, A. Liljas, A. T. Matheson, P. B. Moore, H. F. Noller (eds) The ribosome: Structure, function, antibiotics and cellular interactions. ASM Press, Washington, D.C. pp301-317
107. Rodnina MV, Wintermeyer W (2001) Ribosome fidelity: tRNA discrimination, proofreading and induced fit. Trends Biochem Sci 26:124-130
108. Rozenski J, Crain PF, McCloskey JA (1999) The RNA modification database: 1999 update. Nucleic Acids Res 27:196-197
109. Satoh A, Takai K, Ouchi R, Yokoyama S, Takaku H (2000) Effects of anticodon 2’-O-methylations on tRNA codon recognition in an Escherichia coli cell-free translation. RNA 6:680-686
110. Schmeing TM, Moore PB, Steitz TA (2003) Structures of deacylated tRNA mimics bound to the E site of the large ribosomal subunit. RNA 9:1345-1352
111. Skuzeski JM, Nichols LM, Gesteland RF, Atkins JF (1991) The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. J Mol Biol 218:365-373
112. Sprinzl M, Horn C, Brown M, Ioudovitch A, Steinberg S (1998) Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 26:148-153
113. Stahl G, Ben Salem S, Li Z, McCarty G, Raman A, Shah M, Farabaugh PJ (2001) Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction. Cold Spring Harb Symp Quant Biol 66:249-258
114. Stahl G, Bidou L, Rousset JP, Cassan M (1995) Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells. Nucleic Acids Res 23:1557-1560
115. Steitz TA, Moore PB (2003) RNA, the first macromolecular catalyst: the ribosome is a ribozyme. Trends Biochem Sci 28:411-418
116. Takai K, Yokoyama S (2003) Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons. Nucleic Acids Res 31:6383-6391
117. Takkinen K (1986) Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus. Nucleic Acids Res 14:5667-5682
118. Tork S, Hatin I, Rousset JP, Fabret C (2004) The major 5’ determinant in stop codon read-through involves two adjacent adenines. Nucleic Acids Res 32:415-421
119. Tujebajeva RM, Copeland PR, Xu XM, Carlson BA, Harney JW, Driscoll DM, Hatfield DL, Berry MJ (2000) Decoding apparatus for eukaryotic selenocysteine insertion. EMBO Rep 1:158-163
120. Tzeng TH, Tu CL, Bruenn JA (1992) Ribosomal frameshifting requires a pseudoknot in the Saccharomyces cerevisiae double-stranded RNA virus. J Virol 66:999-1006
121. Urbonavicius J, Stahl G, Durand JM, Ben Salem SN, Qian Q, Farabaugh PJ, Bjork GR (2003) Transfer RNA modifications that alter +1 frameshifting in general fail to affect -1 frameshifting. RNA 9:760-768
122. Urbonavicius J, Qian Q, Durand JM, Hagervall TG, Björk GR (2001) Improvement of reading frame maintenance is a common function for several tRNA modifications. EMBO J 20:4863-4873
123. Walczak R, Westhof E, Carbon P, Krol A (1996) A novel RNA structural motif in the selenocysteine insertion element of eukaryotic selenoprotein mRNAs. RNA 2:367-379
124. Warner GJ, Berry MJ, Moustafa ME, Carlson BA, Hatfield DL, Faust JR (2000) Inhibition of selenoprotein synthesis by selenocysteine tRNASec lacking isopentenyladenosine. J Biol Chem 275:28110-28119
125. Weissenbach J, Dirheimer G, Falcoff R, Sanceau J, Falcoff E (1977) Yeast tRNALeu (anticodon UAG) translates all six leucine codons in extracts from interferon treated cells. FEBS Lett 82:71-76
126. Weissenbach J, Grosjean H (1981) Effect of threonylcarbamoyl modification (t6A) in yeast tRNA Arg III on codon-anticodon and anticodon-anticodon interactions. A thermodynamic and kinetic evaluation. Eur J Biochem 116:207-213
127. Widerak M, Kern R, Malki A, Richarme G (2005) U2552 methylation at the ribosomal A-site is a negative modulator of translational accuracy. Gene (in press)
128. Wilson DN, Dalphin ME, Pel HJ, Major LL, Mansell JB, Tate W (2000) Factor-mediated termination of protein synthesis: a welcome return to the mainstream of translation. In: R. A. Garrett SRD, A. Liljas, A. T. Matheson, P. B. Moore, H. F. Noller (eds) The ribosome: Structure, function, antibiotics and cellular interactions. ASM Press, Washington, D.C. pp 495-508
129. Winkler ME (1998) Genetics and regulation of base modification in the tRNA and rRNA of prokaryotes and eukaryotes. In: Grosjean H, Benne R (eds) Modification and editing of RNA, ASM Press, Washington, D.C. pp 441-469
130. Yarian CS, Basti MM, Cain RJ, Ansari G, Guenther RH, Sochacka E, Czerwinska G, Malkiewicz A, Agris PF (1999) Structural and functional roles of the N1- and N3-protons of psi at tRNA’s position 39. Nucleic Acids Res 27:3543-3549
131. Yarus M (1982) Translational efficiency of transfer RNA’s: uses of an extended anticodon. Science 218:646-652
132. Yokoyama S, Nishimura S (1995) Modified nucleosides and codon recognition. In: D. Söll and UL RajBhandary (eds) tRNA: structure, biosynthesis and function. ASM Press, Washington, D.C. pp 207-223
133. Yu YT, Shu MD, Steitz JA (1997) A new method for detecting sites of 2’-O-methylation in RNA molecules. RNA 3:324-331
134. Yusupova GZ, Yusupov MM, Cate JH, Noller HF (2001) The path of messenger RNA through the ribosome. Cell 106:233-241
135. Zerfass K, Beier H (1992a) The leaky UGA termination codon of tobacco rattle virus RNA is suppressed by tobacco chloroplast and cytoplasmic tRNAs(Trp) with CmCA anticodon. EMBO J 11:4167-4173
136. Zerfass K, Beier H (1992b) Pseudouridine in the anticodon G-psi-A of plant cytoplasmic tRNA(Tyr) is required for UAG and UAA suppression in the TMV-specific context. Nucleic Acids Res 20:5911-5918
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Namy, O., Lecointe, F., Grosjean, H., Rousset, JP. Translational Recoding and RNA Modifications. In: Grosjean, H. (eds) Fine-Tuning of RNA Functions by Modification and Editing. Topics in Current Genetics, vol 12. Springer, Berlin, Heidelberg. https://doi.org/10.1007/b106847
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