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

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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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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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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. 261:357371.
3. Agris, P. F.,, R. Guenther,, P. C. Ingram,, M. M. Basti,, J. W. Stuart,, E. Sochacka,, and A. Malkiewicz. 1997. Unconventional structure of tRNALys SUU anticodon explains tRNA’s role in bacterial and mammalian ribosomal frameshifting and primer selection by HIV-1. RNA 3:420428.
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 5:503511.
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 5:188194.
6. Atkins J. F., , and R. F. Gesteland,. 1995. Discontinuous triplet decoding with or without re-pairing by peptidyl tRNA, p. 471490. 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 249:527530.
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 69:11921195.
9. Atkins, J. F.,, R. F. Gesteland,, B. R. Reid,, and C. W. Anderson. 1979. Normal tRNAs promote ribosomal frameshifting. Cell 18: 11191131.
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. 2:13451350.
11. Aufinger, P.,, and E. Westhof. 1999. Singly and bifurcated hydrogen- bonded base-pairs in tRNA anticodon hairpins and ribozymes. J. Mol. Biol. 292:467483.
12. Ayer, D.,, and M. Yarus. 1986. The context effect does not require a fourth base pair. Science 231:393395.
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 305:554556.
14. Belitsina, N. V.,, G. Z. Tnalina,, and A. S. Spirin. 1981. Template-free ribosomal synthesis of polylysine from lysyl-tRNA. FEBS Lett. 131:289292.
15. Björk, G. R.,, P. M. Wikstrom,, and A. S. Bystrom. 1989. Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science 244:986989.
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. 15:16961704.
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 81:61056109.
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. 227:463479.
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 83:50625066.
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. 255:409413.
21. Condron, B. G.,, J. F. Atkins,, and R. F. Gesteland. 1991a. Frameshifting in gene 10 of bacteriophage T7. J. Bacteriol. 173: 69987003.
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. 19:56075612.
23. Curran, J. F. 1995. Decoding with an A:I wobble pair is inefficient. Nucleic Acids Res. 23:683688.
24. Curran, J. F. 1998. Modified nucleosides in translation, p. 493516. 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. 235:389395.
26. Curran, J. F., , and M. Yarus. 1987. Reading frame selection and transfer RNA anticodon loop stacking. Science 238:15451550.
27. Curran, J. F.,, and M. Yarus. 1988. Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2. J. Mol. Biol. 203:7583.
28. Dahlfors, A. A. R.,, and C. G. Kurland. 1990. Novel mutants of elongation factor G. J. Mol. Biol. 215:549557.
29. Dayhuff, T. J.,, J. F. Atkins,, and R. F. Gesteland. 1986. Characterization of ribosomal frameshift events by protein sequence analysis. J. Biol. Chem. 261:74917500.
30. Dinman, J. D.,, and T. G. Kinzy. 1997. Translational misreading: mutations in translation elongation factor 1α differentially affect programmed ribosomal frameshifting and drug sensitivity. RNA 3:870881.
31. Dinman, J. D.,, and R. B. Wickner. 1995. 5S rRNA is involved in fidelity of translational reading frame. Genetics 141:95105.
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. 260:649663.
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. 72:61466150.
34. Farabaugh, P. J. 1997. Programmed Alternative Reading of the Genetic Code, p. 1208. R. G. Lanes Co., Austin, Tex.
35. Farabaugh, P. J.,, and G. R. Björk. 1999. How translational accuracy influences reading frame maintenance. EMBO J. 18:14271434.
36. Farabaugh, P. J.,, and A. Vimaladithan. 1998. Effect of frameshift-inducing mutants of elongation factor 1α on programmed +1 frameshifting in yeast. RNA 4:3846.
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 74:93103.
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 288:6063.
39. Fu, C.,, and J. Parker. 1994. A ribosomal frameshifting error during translation of the argI mRNA of Escherichia coli. Mol. Gen. Genet. 243:434441.
40. Gaber, R. F.,, and M. R. Culbertson. 1984. Codon recognition during frameshift suppression in Saccharomyces cerevisiae. Mol. Cell. Biol. 4:20522061.
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 95:1377113776.
42. Gavrilova, L. P.,, and A. S. Spirin. 1971. Stimulation of “non-enzymatic” translocation in ribosomes by p-chloromercuribenzoate. FEBS Lett. 17:324326.
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. 197:571584.
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 280:286289
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. 22:279284.
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. 232:756765.
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 91:1252512529.
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. 18:28862896.
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-tRNALys. EMBO J. 15:28262833.
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. 268:803808.
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. 23:14871494.
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. 176:70387044.
55. Hughes, D.,, J. F. Atkins,, and S. Thompson. 1987. Mutants of elongation factor Tu promote ribosomal frameshifting and nonsense readthrough. EMBO J. 6:42354239.
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. 9:551558.
57. Ivanov, I. P.,, R. F. Gesteland,, and J. F. Atkins. 1998. A second mammalian antizyme: conservation of programmed ribosomal frameshifting. Genomics 52:119129.
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 87:84328436.
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 271:990993.
62. Kromayer, M.,, R. Wilting,, P. Tormay,, and A. Böck. 1996. Domain structure of the prokaryotic selenocysteine-specific elongation factor SELB. J. Mol. Biol. 262:413420.
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. 25:12721280.
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: 36673683.
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. 10:455464.
66. Larsen, B.,, N. M. Wills,, and R. F. Gesteland. 1994. rRNA-mRNA base pairing stimulates a programmed -1 ribosomal frameshift. J. Bacteriol. 176:68426851.
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. 234:124139.
68. Lim, V. I. 1995. Analysis of action of the wobble adenine on codon reading within the ribosome. J. Mol. Biol. 252:277282.
69. Lim, V. I. 1997. Analysis of interactions between the codon-anticodon duplexes within the ribosome: their role in translocation. J. Mol. Biol. 266:877890.
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. 16:197205.
72. Massire, C.,, C. Gaspin,, and E. Westhof. 1994. DRAWNA: a program for drawing schematic views of nucleic acids. J. Mol. Graph. 12:201206.
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 80:5160.
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 19:551556.
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. 181:29302937.
77. Mims, B. H.,, N. E. Prather,, and E. J. Murgola. 1985. Isolation and nucleotide sequence analysis of RNAAla GGC from Escherichia coli K-12. J. Bacteriol. 162:837839.
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. 23:595598.
80. O’Connor, M. 1998. tRNA imbalance promotes -1 frameshifting via near-cognate decoding. J. Mol. Biol. 279:727736.
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 90:92149218.
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. 254:838847.
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. 24:27012705.
86. O’Connor, M.,, R. F. Gesteland,, and J. F. Atkins. 1989. tRNA hopping: enhancement by an expanded anticodon. EMBO J. 8: 43154323.
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. 20:42214227.
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. 12:25592566.
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. 25:11851193.
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. 171:38243830.
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 86:79797983.
92. Pagel, F. T.,, and E. J. Murgola. 1996. A base substitution in the amino acid acceptor stem of tRNALys causes both misacylation and altered decoding. Gene Expr. 6:101112.
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. 174:41794182.
94. Peska, S. 1969. Studies on the formation of transfer ribonucleic acid-ribosome complexes. J. Biol. Chem. 244:15331539.
95. Peter, K.,, D. Lindsley,, L. Peng,, and J. A. Gallant. 1992. Context rules of rightward overlapping reading. New Biol. 4:520526.
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. 273:978992.
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 1:471482.
100. Quigley, G. J.,, and A. Rich. 1976. Structural domains of transfer RNA molecules. Science 194:796806.
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. 286:13651378.
102. Riddle, D. L.,, and J. Carbon. 1973. Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA. Nat. New Biol. 242:230234.
103. Riyasaty, S.,, and J. F. Atkins. 1968. External suppression of a frameshift mutant in Salmonella. J. Mol. Biol. 34:541557.
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 377:309314.
105. Sandbaken, M. G.,, and M. R. Culbertson. 1988. Mutations in elongation factor EF-1α affect the frequency of frameshifting and amino acid misincorporation in the yeast Saccharomyces cerevisiae. Genetics 120:923934.
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. 26:423431.
107. Schwartz, R.,, and J. F. Curran. 1997. Analysis of frameshifting at UUU-pyrimidine runs. Nucleic Acids Res. 25:20052011.
108. Smith, D.,, and M. Yarus. 1989. tRNA-tRNA interactions within cellular ribosomes. Proc. Natl. Acad. Sci. USA 86:43974401.
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. 194:643652.
110. Trifonov, E. N. 1992. Recognition of correct reading frame by the ribosome. Biochimie 74:357362.
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 tRNALys and an AAG lysine codon. Genes Dev. 6:511519.
112. Tucker, S. D.,, E. J. Murgola,, and F. T. Pagel. 1989. Missense and nonsense suppressors can correct frameshift mutants. Biochimie 71:729739.
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 1050:274278. (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. 228:10421054.
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. 264:1301213017.
116. Vimaladithan, A.,, and P. J. Farabaugh. 1994. Special peptidyltRNA molecules promote translational frameshifting without slippage. Mol. Cell. Biol. 14:81078116.
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 3:4956.
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. 22:7987.
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. 52:687693.
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. 7:159169.
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. 1:159169.
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. 39:159183.
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 62:117126.
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. 18:54235433.
125. Wilson, K. S.,, and H. F. Noller. 1998. Molecular movement inside the translational engine. Cell 92:337349.
126. Yourno, J. 1972. Externally suppressible +1 “glycine” frameshift: possible quadruplet isomers for glycine and proline. Nat. New Biol. 239:219221.

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