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Chapter 30 : Poking a Hole in the Sanctity of the Triplet Code: Inferences for Framing

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Abstract:

A restrictive EF-G mutant acts as an anti-suppressor of the frameshift causing properties of the tRNA position 74 substitutions but not of the sufS or tRNA hopping mutants described in this chapter. Furthermore, extensive important work on frameshift mutant suppression in Bjork’s laboratory has also focused attention on frameshifting mediated by WT near-cognate tRNAs in the presence of mutant cognate tRNAs. Farabaugh and Bjork extended the model to include the possibility that instead of a normal near-cognate tRNA an undermodified tRNA or a cognate tRNA altered in some other way may also be prone to frameshifting (due to slippage in the P site). This model also proposed that in the absence of mutant tRNAs, nearcognate tRNAs cause frameshifting. Currently two rather different philosophical views about ribosomal frameshifting are being taken. One is to consider programmed frameshifting as amplified errors whose main interest is the insight they provide into translational errors. The other is to value the richness of nature’s exploitation of opportunities to generate high-efficiency frameshifting at particular sites for gene expression purposes.

Citation: Atkins J, Herr A, Ivanov I, Gesteland R, Massire C, O'Connor M. 2000. Poking a Hole in the Sanctity of the Triplet Code: Inferences for Framing, p 396-383. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch30

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Figures

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Figure 1

Frameshifting near the end of the coat protein gene of the single-stranded RNA phage MS2 results in products larger than the coat protein. The first part of the lysis gene overlaps the end of the coat protein gene, and +1 frameshifting at an unknown site near the end of the coat protein gene yields a coat-lysis hybrid termed protein 5. Reading of the fourthto- last GCA alanine codon in the coat protein gene by math type causes a shift to the -1 frame, resulting in the synthesis of protein 6. Similar -1 frameshifting at any of the last three GCA codons yields protein 7, which, though it contains the same number of amino acids as protein 6, due to its different composition migrates faster on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Increasing the ratio of math type (which normally reads AGC) to math type (which normally reads GCA) (the numbers under the right-hand part of the autoradiogram give the amounts in micrograms per standard 12.5-μl reaction mixture) gives increasing levels of -1 frameshifting at GCA codons. The highest concentrations shown result in termination, to yield protein 9, at the last stop codon before the zero-frame terminator is reached. With elevated levels of math type (2 μg), increasing the relative amount of math type (the amounts in micrograms are given under the left-hand part of the autoradiogram) decreases the amount of frameshifting to the point where the only obvious product is the regular coat protein. The model for how stacking of 2 bases on the 5' side and 5 bases on the 3' side of the anticodon loop of math type could mediate the shift to the -1 frame is indicated at the top left of the figure. With the normal balance of tRNAs in an extract (i.e., without tRNA addition), a -1 frameshift product, 66K, that is longer than the synthetase (the virus-encoded component of replicase) is detectable. This is due to an analogous type of noncognate decoding of a proline codon by math type.

Citation: Atkins J, Herr A, Ivanov I, Gesteland R, Massire C, O'Connor M. 2000. Poking a Hole in the Sanctity of the Triplet Code: Inferences for Framing, p 396-383. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch30
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Image of Figure 2
Figure 2

(Top) Stereographic representation of the three-dimensional modeling of the canonical interaction between a GCA codon (white) and the anticodon loop of tRNA. The anticodon loop displays the classical 2:5 stack. U33 (red) adopts a U-turn conformation. (Bottom) Stereographic representation of the three-dimensional modeling of the putative interaction between a GCA codon (white) and the anticodon loop of tRNA, involving a -1 frameshift. The anticodon loop displays an alternative 1:6 stack, with U33 flipped over to base-pair with codon base A. The trace of the GCA codon in the case of the canonical interaction is shown in gray. (These models were constructed with the MANIP modeling tool [Massire and Westhof, 1998]. The ribbon drawings were produced with DRAWNA software [ ].)

Citation: Atkins J, Herr A, Ivanov I, Gesteland R, Massire C, O'Connor M. 2000. Poking a Hole in the Sanctity of the Triplet Code: Inferences for Framing, p 396-383. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch30
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Image of Figure 3
Figure 3

(A) Ribosomes bypass 50 nucleotides to decode phage T4 gene . The signals important for bypass are matched “take-off” and “landing” sites (GGA), a stop codon immediately 3' of the take-off site, a stem-loop at the beginning of the coding gap, and a critical region of the nascent peptide that acts within the ribosome. (B) An autoregulatory +1 frameshift at codon 26 is required to synthesize release factor (RF) 2, which mediates polypeptide chain release at UGA. tRNA Leu dissociates from pairing with its codon CUU to re-pair to the mRNA via the overlapping +1 frame codon UUU, which includes the first base of a zero-frame UGA stop codon. An SD sequence 3 bases 5' of the shift site is important for the efficiency of the frameshifting. (C) Two-thirds of the way through the coding sequence of , 50% of the ribosomes shift to the -1 frame to synthesize the gamma product. Gamma and the product of standard decoding are present in a 1:1 ratio as subunits of DNA polymerase III. A “slippery” heptanucleotide shift site, a 5' SD sequence sense by translating ribosomes, and a 3' stem-loop are important for frameshifting.

Citation: Atkins J, Herr A, Ivanov I, Gesteland R, Massire C, O'Connor M. 2000. Poking a Hole in the Sanctity of the Triplet Code: Inferences for Framing, p 396-383. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch30
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References

/content/book/10.1128/9781555818142.chap30
1. Adamski, F. M.,, B. Moore,, R. F. Gesteland,, and J. F. Atkins. Unpublished data.
2. Adamski, F. M.,, J. F. Atkins,, and R. F. Gesteland. 1996. Ribosomal protein L9 interactions with 23S rRNA: the use of a translational bypass assay to study the effect of amino acid substitutions. J. Mol. Biol. 261: 357 371.
3. Agris, P. F.,, R. Guenther,, P. C. Ingram,, M. M. Basti,, J. W. Stuart,, E. Sochacka,, and A. Malkiewicz. 1997. Unconventional structure of tRNA Lys SUU anticodon explains tRNA’s role in bacterial and mammalian ribosomal frameshifting and primer selection by HIV-1. RNA 3: 420 428.
4. Ashraf, S. S.,, G. Ansari,, R. Guenther,, E. Sochacka,, A. J. Malkiewicz,, and P. F. Agris. 1999a. The uridine in “U-turn”: contributions to tRNA-ribosomal binding. RNA 5: 503 511.
5. Ashraf, S. S.,, E. Sochacka,, R. Cain,, R. Guenther,, A. Malkiewicz,, and P. F. Agris. 1999b. Single atom modification (O→S) of tRNA confers ribosome binding. RNA 5: 188 194.
6. Atkins J. F., , and R. F. Gesteland,. 1995. Discontinuous triplet decoding with or without re-pairing by peptidyl tRNA, p. 471 490. In D. Söll, and U. RajBhandary (ed.), tRNA: Structure, Biosynthesis, and Function. ASM Press, Washington, D.C.
7. Atkins, J. F.,, and S. Ryce. 1974. UGA and non-triplet suppressor reading of the genetic code. Nature 249: 527 530.
8. Atkins, J. F.,, D. Elseviers,, and L. Gorini. 1972. Low activity of β- galactosidase in frameshift mutants of Escherichia coli. Proc. Natl. Acad. Sci. USA 69: 1192 1195.
9. Atkins, J. F.,, R. F. Gesteland,, B. R. Reid,, and C. W. Anderson. 1979. Normal tRNAs promote ribosomal frameshifting. Cell 18: 1119 1131.
10. Atkins, J. F.,, B. P. Nichols,, and S. Thompson. 1983. The nucleotide sequence of the first externally suppressible -1 frameshift mutant, and of some nearby leaky frameshift mutants. EMBO J. 2: 1345 1350.
11. Aufinger, P.,, and E. Westhof. 1999. Singly and bifurcated hydrogen- bonded base-pairs in tRNA anticodon hairpins and ribozymes. J. Mol. Biol. 292: 467 483.
12. Ayer, D.,, and M. Yarus. 1986. The context effect does not require a fourth base pair. Science 231: 393 395.
13. Bare, L.,, A. G. Bruce,, R. F. Gesteland,, and O. C. Uhlenbeck. 1983. Uridine-33 in yeast tRNA is not essential for amber suppression. Nature 305: 554 556.
14. Belitsina, N. V.,, G. Z. Tnalina,, and A. S. Spirin. 1981. Template-free ribosomal synthesis of polylysine from lysyl-tRNA. FEBS Lett. 131: 289 292.
15. Björk, G. R.,, P. M. Wikstrom,, and A. S. Bystrom. 1989. Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science 244: 986 989.
16. Björnsson, A.,, S. Mottagui-Tabar,, and L. A. Isaksson. 1996. Structure of the C-terminal end of the nascent peptide influences translation termination. EMBO J. 15: 1696 1704.
17. Bossi, L.,, and D. M. Smith. 1984. Suppressor sufJ: a novel type of tRNA mutant that induces translational frameshifting. Proc. Natl. Acad. Sci. USA 81: 6105 6109.
18. Brierley, I.,, A. J. Jenner,, and S. C. Inglis. 1992. Mutational analysis of the “slippery sequence” component of a coronavirus ribosomal frameshifting signal. J. Mol. Biol. 227: 463 479.
19. Bruce, A. G.,, J. F. Atkins,, and R. F. Gesteland. 1986. tRNA anticodon replacement experiments show that ribosomal frameshifting can be caused by doublet decoding. Proc. Natl. Acad. Sci. USA 83: 5062 5066.
20. Choi, K. M.,, J. F. Atkins,, R. F. Gesteland,, and R. Brimacombe. 1998. Flexibility of the nascent polypeptide chain within the ribosome: contacts from the peptide N terminus to a specific region of the 30S subunit. Eur. J. Biochem. 255: 409 413.
21. Condron, B. G.,, J. F. Atkins,, and R. F. Gesteland. 1991a. Frameshifting in gene 10 of bacteriophage T7. J. Bacteriol. 173: 6998 7003.
22. Condron, B. G.,, R. F. Gesteland,, and J. F. Atkins. 1991b. An analysis of sequences stimulating frameshifting in the decoding of gene 10 of bacteriophage T7. Nucleic Acids Res. 19: 5607 5612.
23. Curran, J. F. 1995. Decoding with an A:I wobble pair is inefficient. Nucleic Acids Res. 23: 683 688.
24. Curran, J. F. 1998. Modified nucleosides in translation, p. 493 516. In H. Grosjean and R. Benne (ed.), Modification and Editing of RNA. ASM Press, Washington, D.C.
25. Curran, J. F.,, and B. L. Gross. 1994. Evidence that GHN phase bias does not constitute a framing code. J. Mol. Biol. 235: 389 395.
26. Curran, J. F., , and M. Yarus. 1987. Reading frame selection and transfer RNA anticodon loop stacking. Science 238: 1545 1550.
27. Curran, J. F.,, and M. Yarus. 1988. Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2. J. Mol. Biol. 203: 75 83.
28. Dahlfors, A. A. R.,, and C. G. Kurland. 1990. Novel mutants of elongation factor G. J. Mol. Biol. 215: 549 557.
29. Dayhuff, T. J.,, J. F. Atkins,, and R. F. Gesteland. 1986. Characterization of ribosomal frameshift events by protein sequence analysis. J. Biol. Chem. 261: 7491 7500.
30. Dinman, J. D.,, and T. G. Kinzy. 1997. Translational misreading: mutations in translation elongation factor 1 α differentially affect programmed ribosomal frameshifting and drug sensitivity. RNA 3: 870 881.
31. Dinman, J. D.,, and R. B. Wickner. 1995. 5S rRNA is involved in fidelity of translational reading frame. Genetics 141: 95 105.
32. Dong, H.,, L. Nilsson,, and C. G. Kurland. 1996. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J. Mol. Biol. 260: 649 663.
33. Doyon, L.,, C. Payant,, L. Brakier-Gingras,, and D. Lamarre. 1998. Novel Gag-Pol frameshift site in human immunodeficiency virus type 1 variants resistant to protease inhibitors. J. Virol. 72: 6146 6150.
34. Farabaugh, P. J. 1997. Programmed Alternative Reading of the Genetic Code, p. 1 208. R. G. Lanes Co., Austin, Tex.
35. Farabaugh, P. J.,, and G. R. Björk. 1999. How translational accuracy influences reading frame maintenance. EMBO J. 18: 1427 1434.
36. Farabaugh, P. J.,, and A. Vimaladithan. 1998. Effect of frameshift-inducing mutants of elongation factor 1 α on programmed +1 frameshifting in yeast. RNA 4: 38 46.
37. Farabaugh, P. J.,, H. Zhao,, and A. Vimaladithan. 1993. A novel programmed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frameshifting without tRNA slippage. Cell 74: 93 103.
38. Fox, T. D.,, and B. Weiss-Brummer. 1980. Leaky +1 and -1 frameshift mutations at the same site in a yeast mitochondrial gene. Nature 288: 60 63.
39. Fu, C.,, and J. Parker. 1994. A ribosomal frameshifting error during translation of the argI mRNA of Escherichia coli. Mol. Gen. Genet. 243: 434 441.
40. Gaber, R. F.,, and M. R. Culbertson. 1984. Codon recognition during frameshift suppression in Saccharomyces cerevisiae. Mol. Cell. Biol. 4: 2052 2061.
41. Gallant, J. A.,, and D. Lindsley. 1998. Ribosomes can slide over and beyond “hungry” codons, resuming protein chain elongation many nucleotides downstream. Proc. Natl. Acad. Sci. USA 95: 13771 13776.
42. Gavrilova, L. P.,, and A. S. Spirin. 1971. Stimulation of “non-enzymatic” translocation in ribosomes by p-chloromercuribenzoate. FEBS Lett. 17: 324 326.
43. Gollnick, P.,, C. C. Hardin,, and J. Horowitz. 1987. 19F nuclear magnetic resonance as a probe of anticodon structure in 5-fluorouracil- substituted Escherichia coli transfer RNA. J. Mol. Biol. 197: 571 584.
44. Green, R.,, C. Switzer,, and H. F. Noller. 1998. Ribosome-catalyzed peptide-bond formation with an A-site substrate covalently linked to 23S ribosomal RNA. Science 280: 286 289
45. Gregory, S. T.,, K. R. Lieberman,, and A. E. Dahlberg. 1994. Mutations in the peptidyl transferase region of E. coli 23S rRNA affecting translational accuracy. Nucleic Acids Res. 22: 279 284.
46. Hagervall, T. G.,, T. M. F. Tuohy,, J. F. Atkins,, and G. R. Björk. 1993. Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocation. J. Mol. Biol. 232: 756 765.
47. Herbst, K. L.,, L. M. Nichols,, R. F. Gesteland,, and R. B. Weiss. 1994. A mutation in ribosomal protein L9 affects ribosomal hopping during translation of gene 60 from bacteriophage T4. Proc. Natl. Acad. Sci. USA 91: 12525 12529.
48. Herr, A. J. Unpublished data.
49. Herr, A. J.,, J. F. Atkins,, and R. F. Gesteland. 1999. Mutations which alter the elbow region of tRNA2Gly reduce T4 gene 60 translational bypassing efficiency. EMBO J. 18: 2886 2896.
50. Herr, A. J.,, R. F. Gesteland,, and J. F. Atkins. Unpublished data.
51. Heurgué-Hamard, V.,, L. Mora,, G. Guarneros,, and R. H. Buckingham. 1996. The growth defect in Escherichia coli deficient in peptidyl-tRNA hydrolase is due to starvation for Lys-tRNA Lys. EMBO J. 15: 2826 2833.
52. Himeno, H.,, M. Sato,, T. Tadaki,, M. Fukushima,, C. Ushida,, and A. Muto. 1997. In vitro trans-translation mediated by alanine-charged 10Sa RNA. J. Mol. Biol. 268: 803 808.
53. Horsfield, J. A.,, D. N. Wilson,, S. A. Mannering,, F. M. Adamski,, and W. P. Tate. 1995. Prokaryotic ribosomes recode the HIV- gag-pol-1 frameshift sequence by an E/P site post-translocation simultaneous slippage mechanism. Nucleic Acids Res. 23: 1487 1494.
54. Hou, Y.,, E. S. Yaskowiak,, and P. E. March. 1994. Carboxyl-terminal amino acid residues in elongation factor G essential for ribosome association and translocation. J. Bacteriol. 176: 7038 7044.
55. Hughes, D.,, J. F. Atkins,, and S. Thompson. 1987. Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense readthrough. EMBO J. 6: 4235 4239.
56. Hüttenhofer, A.,, B. Weiss-Brummer,, G. Dirheimer,, and R. P. Martin. 1990. A novel type of +1 frameshift suppressor: a base substitution in the anticodon stem of a yeast mitochondrial serine-tRNA causes frameshift suppression. EMBO J. 9: 551 558.
57. Ivanov, I. P.,, R. F. Gesteland,, and J. F. Atkins. 1998. A second mammalian antizyme: conservation of programmed ribosomal frameshifting. Genomics 52: 119 129.
58. Ivanov, I. P.,, S. Matsufuji,, R. F. Gesteland,, and J. F. Atkins. Unpublished data.
59. Johnston, C. Unpublished data.
60. Kawakami, K.,, and Y. Nakamura. 1990. Autogenous suppression of an opal mutation in the gene encoding peptide chain release factor 2. Proc. Natl. Acad. Sci. USA 87: 8432 8436.
61. Keiler, K. C.,, P. R. H. Waller,, and R. T. Sauer. 1996. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271: 990 993.
62. Kromayer, M.,, R. Wilting,, P. Tormay,, and A. Böck. 1996. Domain structure of the prokaryotic selenocysteine-specific elongation factor SELB. J. Mol. Biol. 262: 413 420.
63. Kumar, R. K.,, and D. R. Davis. 1997. Synthesis and studies on the effect of 2-thiouridine and 4-thiouridine on sugar conformation and RNA duplex stability. Nucleic Acids Res. 25: 1272 1280.
64. Labuda, D.,, G. Stricker,, H. Grosjean,, and D. Pörschke. 1985. Mechanism of codon recognition by transfer RNA studies with oligonucleotides larger than triplets. Nucleic Acids Res. 13: 3667 3683.
65. Lagunez-Otero, J.,, and E. N. Trifonov. 1992. mRNA periodical infrastructure complementary to the proof-reading site in the ribosome. J. Biomol. Struct. Dyn. 10: 455 464.
66. Larsen, B.,, N. M. Wills,, and R. F. Gesteland. 1994. rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift. J. Bacteriol. 176: 6842 6851.
67. Levin, M. E.,, R. W. Hendrix,, and S. R. Casjens. 1993. A programmed translational frameshift is required for the synthesis of a bacteriophage λ tail assembly protein. J. Mol. Biol. 234: 124 139.
68. Lim, V. I. 1995. Analysis of action of the wobble adenine on codon reading within the ribosome. J. Mol. Biol. 252: 277 282.
69. Lim, V. I. 1997. Analysis of interactions between the codon-anticodon duplexes within the ribosome: their role in translocation. J. Mol. Biol. 266: 877 890.
70. MacVanin, M.,, M. E. Johanson,, and D. Hughes. Submitted for publication.
71. Massire, C.,, and E. Westhof. 1998. MANIP: an interactive tool for modeling RNA. J. Mol. Graph. Model. 16: 197 205.
72. Massire, C.,, C. Gaspin,, and E. Westhof. 1994. DRAWNA: a program for drawing schematic views of nucleic acids. J. Mol. Graph. 12: 201 206.
73. Matsufuji, S.,, T. Matsufuji,, Y. Miyazaki,, Y. Murakami,, J. F. Atkins,, R. F. Gesteland,, and S. Hayashi. 1995. Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell 80: 51 60.
74. Matsufuji, S. Unpublished data.
75. Mayrand, S.-M.,, and W. R. Green. 1998. Non-traditionally derived CTL epitopes: exceptions that prove the rules? Immunol. Today 19: 551 556.
76. Mejlhede, N.,, J. F. Atkins,, and J. Neuhard. 1999. Ribosomal -1 frameshifting during decoding of Bacillus subtilis cdd occurs at the sequence CGA AAG. J. Bacteriol. 181: 2930 2937.
77. Mims, B. H.,, N. E. Prather,, and E. J. Murgola. 1985. Isolation and nucleotide sequence analysis of RNA Ala GGC from Escherichia coli K-12. J. Bacteriol. 162: 837 839.
78. Moore, B.,, B. Persson,, C. C. Nelson,, R. F. Gesteland,, and J. F. Atkins. Quadruplet codons: implications for code expansion and the specification of translation step size. Submitted for publication.
79. Moriya, H.,, H. Kasai,, and K. Isono. 1995. Cloning and characterization of the hrpA gene in the terC region of Escherichia coli that is highly similar to the DEAH family RNA helicase genes of Saccharomyces cerevisiae. Nucleic Acids Res. 23: 595 598.
80. O’Connor, M. 1998. tRNA imbalance promotes -1 frameshifting via near-cognate decoding. J. Mol. Biol. 279: 727 736.
81. O’Connor, M. Unpublished data.
82. O’Connor, M.,, and J. F. Atkins. Unpublished results.>
83. O’Connor, M.,, and A. E. Dahlberg. 1993. Mutations at U2555, a tRNA-protected base in 23S rRNA, affect translational fidelity. Proc. Natl. Acad. Sci. USA 90: 9214 9218.
84. O’Connor, M.,, and A. E. Dahlberg. 1995. The involvement of two distinct regions of 23S ribosomal RNA in tRNA selection. J. Mol. Biol. 254: 838 847.
85. O’Connor, M.,, and A. E. Dahlberg. 1996. The influence of base identity and base pairing on the function of the α-sarcin loop of 23S rRNA. Nucleic Acids Res. 24: 2701 2705.
86. O’Connor, M.,, R. F. Gesteland,, and J. F. Atkins. 1989. tRNA hopping: enhancement by an expanded anticodon. EMBO J. 8: 4315 4323.
87. O’Connor, M.,, H. U. Goringer,, and A. E. Dahlberg. 1992. A ribosomal ambiguity mutation in the 530 loop of E. coli. Nucleic Acids Res. 20: 4221 4227.
88. O’Connor, M.,, N. M. Wills,, L. Bossi,, R. F. Gesteland,, and J. F. Atkins. 1993. Functional tRNAs with altered 3' ends. EMBO J. 12: 2559 2566.
89. O’Connor, M.,, C. L. Thomas,, R. A. Zimmermann,, and A. E. Dahlberg. 1997. Decoding fidelity at the ribosomal A and P sites: influence of mutations in three different regions of the decoding domain in 16S rRNA. Nucleic Acids Res. 25: 1185 1193.
90. O’Mahony, D. J.,, D. Hughes,, S. Thompson,, and J. F. Atkins. 1989a. Suppression of a -1 frameshift mutation by a recessive tRNA suppressor which causes doublet decoding. J. Bacteriol. 171: 3824 3830.
91. O’Mahony, D. J.,, B. H. Mims,, S. Thompson,, E. J. Murgola,, and J. F. Atkins. 1989b. Glycine tRNA mutants with normal anticodon loop size cause -1 frameshifting. Proc. Natl. Acad. Sci. USA 86: 7979 7983.
92. Pagel, F. T.,, and E. J. Murgola. 1996. A base substitution in the amino acid acceptor stem of tRNA Lys causes both misacylation and altered decoding. Gene Expr. 6: 101 112.
93. Pagel, F. T.,, T. M. F. Tuohy,, J. F. Atkins,, and E. J. Murgola. 1992. Doublet translocation at GGA is mediated directly by mutant math type. J. Bacteriol. 174: 4179 4182.
94. Peska, S. 1969. Studies on the formation of transfer ribonucleic acid-ribosome complexes. J. Biol. Chem. 244: 1533 1539.
95. Peter, K.,, D. Lindsley,, L. Peng,, and J. A. Gallant. 1992. Context rules of rightward overlapping reading. New Biol. 4: 520 526.
96. Prère, M. F.,, C. Bertrand,, R. F. Gesteland,, J. F. Atkins,, and O. Fayet. Unpublished data.
97. Qian, Q. 1997. Transfer RNA modification and translational frameshifting. Ph.D. thesis. Umea University, Umeå, Sweden.
98. Qian, Q.,, and G. R. Björk. 1997. Structural alterations far from the anticodon of the tRNA Pro GGG of Salmonella typhimurium induce +1 frameshifting at the peptidyl-site. J. Mol. Biol. 273: 978 992.
99. Qian, Q.,, J.-N. Li,, H. Zhao,, T. G. Hagervall,, P. J. Farabaugh,, and G. R. Björk. 1998. A new model for phenotypic suppression of frameshift mutations by mutant tRNAs. Mol. Cell 1: 471 482.
100. Quigley, G. J.,, and A. Rich. 1976. Structural domains of transfer RNA molecules. Science 194: 796 806.
101. Rettberg, C. C.,, M. F. Pre`re,, R. F. Gesteland,, J. F. Atkins,, and O. Fayet. 1999. A three-way junction and constituent stem-loops as the stimulator for programmed -1 frameshifting in bacterial insertion sequence IS911. J. Mol. Biol. 286: 1365 1378.
102. Riddle, D. L.,, and J. Carbon. 1973. Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA. Nat. New Biol. 242: 230 234.
103. Riyasaty, S.,, and J. F. Atkins. 1968. External suppression of a frameshift mutant in Salmonella. J. Mol. Biol. 34: 541 557.
104. Samaha, R. R.,, R. Green,, and H. F. Noller. 1995. A base pair between tRNA and 23S rRNA in the peptidyl transferase centre of the ribosome. Nature 377: 309 314.
105. Sandbaken, M. G.,, and M. R. Culbertson. 1988. Mutations in elongation factor EF-1 α affect the frequency of frameshifting and amino acid misincorporation in the yeast Saccharomyces cerevisiae. Genetics 120: 923 934.
106. Santos, M. A. S.,, T. Ueda,, K. Watanabe,, and M. F. Tuite. 1997. The non-standard genetic code of Candida spp.: an evolving genetic code or a novel mechanism for adaptation? Mol. Microbiol. 26: 423 431.
107. Schwartz, R.,, and J. F. Curran. 1997. Analysis of frameshifting at UUU-pyrimidine runs. Nucleic Acids Res. 25: 2005 2011.
108. Smith, D.,, and M. Yarus. 1989. tRNA-tRNA interactions within cellular ribosomes. Proc. Natl. Acad. Sci. USA 86: 4397 4401.
109. Trifonov, E. N. 1987. Translation framing code and frame-monitoring mechanism as suggested by the analysis of mRNA and 16S rRNA nucleotide sequences. J. Mol. Biol. 194: 643 652.
110. Trifonov, E. N. 1992. Recognition of correct reading frame by the ribosome. Biochimie 74: 357 362.
111. Tsuchihashi, Z.,, and P. O. Brown. 1992. Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA Lys and an AAG lysine codon. Genes Dev. 6: 511 519.
112. Tucker, S. D.,, E. J. Murgola,, and F. T. Pagel. 1989. Missense and nonsense suppressors can correct frameshift mutants. Biochimie 71: 729 739.
113. Tuohy, T. M. F.,, S. Thompson,, R. F. Gesteland,, D. Hughes,, and J. F. Atkins. 1990. The role of EF-Tu and other translation components in determining translocation step size. Biochim. Biophys. Acta 1050: 274 278. ( Erratum, 1087:347.)
114. Tuohy, T. M. F.,, S. Thompson,, R. F. Gesteland,, and J. F. Atkins. 1992. Seven, eight and nine-membered anticodon loop mutants of math type which cause +1 frameshifting. Tolerance of DHU arm and other secondary mutations. J. Mol. Biol. 228: 1042 1054.
115. Vijgenboom, E.,, and L. Bosch. 1989. Translational frameshifts induced by mutant species of the polypeptide chain elongation factor Tu of Escherichia coli. J. Biol. Chem. 264: 13012 13017.
116. Vimaladithan, A.,, and P. J. Farabaugh. 1994. Special peptidyltRNA molecules promote translational frameshifting without slippage. Mol. Cell. Biol. 14: 8107 8116.
117. von Ahsen, U.,, R. Green,, R. Schroeder,, and H. F. Noller. 1997. Identification of 2'-hydroxyl groups required for interaction of a tRNA anticodon stem-loop region with the ribosome. RNA 3: 49 56.
118. Watanabe, K.,, N. Hayashi,, A. Oyama,, K. Nishikawa,, T. Ueda,, and K. Miura. 1994. Unusual anticodon loop structure found in E. coli lysine tRNA. Nucleic Acids Res. 22: 79 87.
119. Weiss, R. B.,, D. M. Dunn,, J. F. Atkins,, and R. F. Gesteland. 1987. Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5 and +6 ribosomal frameshifting. Cold Spring Harbor Symp. Quant. Biol. 52: 687 693.
120. Weiss, R. B.,, D. M. Dunn,, A. E. Dahlberg,, J. F. Atkins,, and R. F. Gesteland. 1988. Reading frame switch caused by base-pair formation between the 3' end of 16S rRNA and the mRNA during elongation of protein synthesis in Escherichia coli. EMBO J. 7: 159 169.
121. Weiss, R. B.,, D. M. Dunn,, M. Shuh,, J. F. Atkins,, and R. F. Gesteland. 1989. E. coli ribosomes re-phase on retroviral frameshift signals at rates ranging from 2 to 50 percent. New Biol. 1: 159 169.
122. Weiss, R. B.,, D. M. Dunn,, J. F. Atkins,, and R. F. Gesteland. 1990a. Ribosomal frameshifting from -2 to +50 nucleotides. Prog. Nucleic Acids Res. Mol. Biol. 39: 159 183.
123. Weiss, R. B.,, W. M. Huang,, and D. M. Dunn. 1990b A nascent peptide is required for ribosomal bypass of the coding gap in bacteriophage T4 gene 60. Cell 62: 117 126.
124. Williams, K. P.,, K. A. Martindale,, and D. P. Bartel. 1999. Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J. 18: 5423 5433.
125. Wilson, K. S.,, and H. F. Noller. 1998. Molecular movement inside the translational engine. Cell 92: 337 349.
126. Yourno, J. 1972. Externally suppressible +1 “glycine” frameshift: possible quadruplet isomers for glycine and proline. Nat. New Biol. 239: 219 221.

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