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The accuracy of mRNA—tRNA recognition

  • Chapter
Accuracy in Molecular Processes

Abstract

In order to synthesize functional proteins, mRNA must be translated by the ribosome with a certain level of accuracy. As we will discuss below, our knowledge concerning the levels of precision ultimately attained by the translational machinery, especially at the level of the nascent polypeptide chain, is still incomplete. Furthermore, it will be interesting to compare the sparse data that exist with the results of a naïve calculation of the following type: in order to synthesize correctly at least 50% of the polypeptide chains of an enzyme as large as β-galactosidase which contains 1169 amino acid residues, an average error no larger than 1 in 1700 per amino acid residue can be tolerated (Fig. 5.1). Why should attaining this level of accuracy pose a problem?

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References

  • Abraham, A. K. (1983) The fidelity of translation. Prog. Nucl. Ac. Res. Mol. Biol., 28, 81–100.

    Article  Google Scholar 

  • Ames, B. N. and Hartman, P. E. (1963) The histidine operon. Cold Spring Harbor Symp. Quant. Biol., 28, 349–356.

    Google Scholar 

  • Anderson, S., Bankier, A. T., Barrell, B. G. etal. (1981) Sequence and organization of the human mitochondrial genome. Nature, 290, 457–464.

    Article  Google Scholar 

  • Andersson, D. I. and Kurland, C. G. (1983) Ram ribosomes are defective proofreaders. Mol. Gen. Genet., 191, 378–381.

    Article  Google Scholar 

  • Andersson, S. G. E., Buckingham, R. H. and Kurland, C. G. (1984) Does codon-anticodon composition influence ribosome functions? EMBO J., 3, 91–94.

    Google Scholar 

  • Atkins, J. F., Elseviers, D. and Gorini, L. (1972) Low activity of 0-galactosidase in frameshift mutants of Escherichia coli. Proc. Natl Acad. Sci. USA, 69, 1192–1195.

    Article  Google Scholar 

  • Atkins, J. F., Gesteland, R. F., Reid, B. R. and Anderson, C. W. (1979) Normal tRNAs promote ribosomal frame shifting. Cell, 18, 1119–1131.

    Article  Google Scholar 

  • Atkins, J. F., Nichols, B. P. and Thompson, S. (1983) The nucleotide sequence of the first externally suppressible —1 frameshift mutant, and of some nearly leaky frameshift mutants. EMBO J., 2, 1345–1350.

    Google Scholar 

  • Bare, L., Bruce, A. G., Gesteland, R. and Uhlenbeck, O. C. (1983) Uridine-33 in yeast tRNA not essential for amber suppression. Nature, 305, 554–556.

    Article  Google Scholar 

  • Barrell, B. G., Anderson, S., Bankier, A. T. etal. (1980) Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proc. Natl Acad. Sci. USA, 77, 3164–3166.

    Google Scholar 

  • Beier, H., Barciszewska, M., Sickinger, H. D. (1984) The molecular basis for the differential translation of TMV RNA in tobacco protoplasts and wheat germ extract. EMBO J., 3, 1091–1096.

    Google Scholar 

  • Bennetzen, J. L. and Hall, B. D. (1982) Codon selection in yeast. J. Biol. Chem., 257, 3026–3031.

    Google Scholar 

  • Berman, H. M., Marcu, D., Narayana, P., Fissekis, J. D. and Lipnick, R. L. (1978) Modified bases in transfer-RNA. Structures of 5-carbamoylmethyl uridine and 5-carboxymethyl uridine. Nucl. Acid Res., 5, 593–903.

    Article  Google Scholar 

  • Bienz, M. and Kubli, E. (1981) Wild-type tRNA TyrG reads the TMV-RNA stop codon, but Q base-modified tRNA TyrQ does not. Nature, 294, 188–190.

    Article  Google Scholar 

  • Björk, G. R. (1984) Modified nucleosides in RNA: their formation and function. In Processing of RNA (ed. D. Apirion) CRC Press Inc., Boca, Raton, Florida, pp. 291–330.

    Google Scholar 

  • Björk, G. R. and Neidhardt, F. C. (1975) Physiological and biochemical studies on the function of 5-methyluridine in the tRNA of E. coli. J. Bacteriol., 124, 99–111.

    Google Scholar 

  • Bohman, K., Ruusala, T., Jelenc, P. C. and Kurland, C. G. (1984) Kinetic impairment of restrictive streptomycin resistant ribosomes. Mol. Gen. Genet., 198, 90–99.

    Article  Google Scholar 

  • Bonitz, S. G., Berlani, R., Coruzzi, G. etal. (1980) Codon recognition rules in yeast mitochondria. Proc. Natl Acad. Sci. USA, 77, 3167–3170.

    Google Scholar 

  • Bossi, L. (1983) Context effects: translation of UAG codon by suppressor tRNA is affected by the sequence following UAG in the message. J. Mol. Biol., 164, 73–87.

    Article  Google Scholar 

  • Bossi, L. and Roth, J. R. (1980) The influence of codon context on genetic code translation. Nature, 286, 123–127.

    Article  Google Scholar 

  • Bouadloun, F., Donner, D. and Kurland, C. G. (1983) Codon-specific missense errors in vivo. EMBO J., 2, 1351–1356.

    Google Scholar 

  • Bruce, A. G., Atkins, J. F., Wills, N., Uhlenbeck. O., Gesteland, R. F. (1982) Replacement of anticodon loop nucleotides to produce functional tRNA: amber suppressors derived from yeast tRNA-Phe. Proc. Natl Acad. Sci. USA, 79, 7129–7131.

    Google Scholar 

  • Bubienko, E., Cruz, P., Thomason, J. F. and Borer, P. N. (1983) Nearest-neighbor effects in the structure and function of nucleic acids. Progr. Nucl. Ac. Res. Mol. Biol., 30, 41–90.

    Article  Google Scholar 

  • Buchanan, J. H. and Stevens, A. S. (1978) Fidelity of histone synthesis in cultured human fibroblasts. Mech. Ageing Dev., 1, 321–334.

    Article  Google Scholar 

  • Buck, M. and Ames, B. N. (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.

    Article  Google Scholar 

  • Bückel, P., Piepersberg, W. and Böck, A. (1976) Suppression of temperature- sensitive aminoacyl-tRNA synthetase mutations by ribosomal mutations: a possible mechanism. Mol. Gen. Genet., 149, 51–61.

    Article  Google Scholar 

  • Buckingham, R. H. (1976) Anticodon conformation and accessibility in wild-type and suppressor tryptophan tRNA from E. coli. Nucl. Acids Res., 3, 965–975.

    Google Scholar 

  • Buckingham, R. H. and Kurland, C. G. (1977) Codon specificity of UGA suppressor tRNATrp from E. coli. Proc. Natl Acad. Sci. USA, 74, 5496–5498.

    Article  Google Scholar 

  • Buckingham, R. H. and Kurland, C. G. (1980) Interactions between UGA suppressor tRNATrp and the ribosome: mechanisms of tRNA selection. In Transfer RNA, Biological Aspects (eds D. Soli, J. N. Abelson and P. R. Schimmel ), Cold Spring Harbor Laboratory, New York, monograph 9B, pp. 421–26.

    Google Scholar 

  • Cabanas, M. J. and Modolell, J. (1980) Non-enzymatic translocation and spontaneous release of non-cognate peptidyl-tRNA from E. coli ribosomes. Biochemistry, 19, 5411–5416.

    Google Scholar 

  • Caplan, A. B. and Menninger, J. R. (1979) Tests of the ribosomal editing hypothesis: amino acid starvation differentially enhances the dissociation of peptidyl-tRNA from the ribosome. J. Mol. Biol., 134, 621–637.

    Article  Google Scholar 

  • Carrier, M. J. and Buckingham, R. H. (1984) An effect of codon context in the mistranslation of UGU codons in vitro. J. Mol. Biol., 175, 29–38.

    Article  Google Scholar 

  • Cedergren, R. J., La Rue, B., Sankoff, D. and Grosjean, H. (1981) The evolving tRNA molecule. In CRC Critical Reviews in Biochemistry, Vol. 11, CRC Press, Florida, pp. 35–104.

    Google Scholar 

  • Chavancy, G. and Garel, J. P. (1981) Does quantitative tRNA adaptation to codon content in mRNA optimise the ribosomal translation efficiency? Proposal for a translation system model. Biochimie, 63, 187–195.

    Article  Google Scholar 

  • Chavancy, G., Daillie, J. and Garel, J. P. (1971) Adaptation fonctionnelle des tRNA à la biosynthèse protéique dans un système cellulaire hautement différencié. IV - Evolution des tRNA dans la glande séricigène de Bombyx mori L. au cours du dernier âge larvaire. Biochimie, 53, 1187–1197.

    Article  Google Scholar 

  • Chavancy, G., Chevallier, A., Fournier, A. and Garel, J. P. (1979) Adaptation of iso-tRNA concentration to mRNA codon frequency in the eukaryotic cell. Biochimie, 61, 71–78.

    Article  Google Scholar 

  • Cody, J. D. M. and Conway, T. W. (1981) Defective lysis of streptomycin-resistant E. coli cells infected with bacteriophage f2. J. Virology, 37, 813–820.

    Google Scholar 

  • Colby, D. S., Schedel, P. and Guthrie, C. (1976) A functional requirement for modification of the wobble nucleotide in the anticodon of a T4 suppressor tRNA. Cell, 9, 449–463.

    Article  Google Scholar 

  • Coons, S. F., Smith, L. F. and Loftfield, R. B. (1979) The nature of amino acids errors in in vivo biosynthesis of rabbit hemoglobin. Fed. Proc., 38, 328.

    Google Scholar 

  • Crick, F. H. C. (1966) Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol., 19, 548–555.

    Article  Google Scholar 

  • De Wilde, M., Cabezon, T., Herzog, A., Bollen, A. (1977) Apport de la génétique à la connaissance du ribosome bactérien. Biochimie, 59, 125–140.

    Article  Google Scholar 

  • Diamond, A., Dudock, B. and Hatfield, D. (1981) Structure and properties of a bovine liver UGA suppressor serine tRNA with a tryptophan anticodon. Cell, 25, 497–506.

    Article  Google Scholar 

  • Dirheimer, G. (1983) Chemical nature, properties, location and physiological variations of modified nucleosides in tRNAs. In Recent Results in Cancer Research, Vol. 84, Springer Verlag, Berlin and Heidelberg, pp. 15–46.

    Google Scholar 

  • Dunn, J. J. and Studier, F. W. (1983) Complete nucleotide sequence of bacteriophage T7 DNA and the location of T7 genetic elements. J. Mol. Biol., 166, 477–535.

    Article  Google Scholar 

  • Dunn, R., McCoy, J., Simsek, M., Majumdar, A., Chang, S. H., RajBhandar, U. L. and Khorana, H. G. (1981) The bacteriorhodopsin gene. Proc. Natl Acad. Sci. USA, 78, 6744–6748.

    Article  Google Scholar 

  • Edelmann, P. and Gallant, J. (1977) Mistranslation in E. coli. Cell, 10, 131–137.

    Google Scholar 

  • Eigen, M. and Winkler-Oswatitsch, R. (1981) Transfer-RNA, an early gene? Naturwissenschaften, 68, 282–292.

    Article  Google Scholar 

  • Eisenberg, S. P., Yarns, M. and Söll, L. (1979) The effect of an E. coli regulatory mutation on tRNA structure. J. Mol. Biol., 135, 111–126.

    Google Scholar 

  • Engelberg-Kulka, H. (1981) UGA suppression by normal tRNATrp in E. coli: codon context effects. Nucl. Acids Res., 9, 983–991.

    Google Scholar 

  • Etcheverry, T., Colby, D. and Guthrie, C. (1979) A precursor to a minor species of yeast tRNASer contains an intervening sequence. Cell, 18, 11–26.

    Article  Google Scholar 

  • Feinstein, S. I. and Altman, S. (1978) Context effects on nonsense codon suppression in E. coli Genetics, 88, 201–219.

    Google Scholar 

  • Fiers, S. (1979) Structure and function of RNA bacteriophages. In Comprehensive Virology (eds H. Fraenkel-Conrat and R. R. Wagner), Vol. 13, Plenum Publishing Corp., New York, pp. 69–203.

    Google Scholar 

  • Follon, A. M., Jinks, C. S., Strycharz, G. D. and Nomura, M. (1979) Regulation of ribosomal protein synthesis in E. coli by selective mRNA inactivation. Proc. Natl Acad. ScL USA, 76, 3411–3415.

    Article  Google Scholar 

  • Fox, T. D. and Weiss-Brummer, B. (1980) Leaky +1 and —1 frameshift mutations at the same site in yeast mitochondrial gene. Nature, 288, 60–64.

    Article  Google Scholar 

  • Fuller, W. and Hodgson, A. (1967) Conformation of the anticodon loop in tRNA. Nature, 215, 817–821.

    Article  Google Scholar 

  • Gallant, J. and Foley, D. (1979) On the causes and prevention of mistranslation. In Ribosomes, Structure, Function and Genetics (eds G. Chambliss, G. R. Craven, J. Davies, K. Davis, L. Kahan and M. Nomura ), University Park Press, Baltimore, pp. 615–638.

    Google Scholar 

  • Gallant, J., Ehrlich, H., Weiss, R., Palmer, L. and Nyari, L. (1982) Nonsense suppression in aminoacyl-tRNA limited cells. Mol. Gen. Genet., 186, 221–227.

    Article  Google Scholar 

  • Ganoza, M. C., Fraser, A. R. and Neilson, T. (1978) Nucleotides contiguous to AUG affect translational initiation. Biochemistry, 17, 2769–2776.

    Article  Google Scholar 

  • Garel, J. P. (1974) Functional adaptation of tRNA population. J. Theor. Biol., 43, 211–225.

    Article  Google Scholar 

  • Garel, J. P. (1976) Quantitative adaptation of isoacceptor tRNAs to mRNA codons of alanine, glycine and serine. Nature, 260, 805–806.

    Article  Google Scholar 

  • Gauss, D. H. and Sprinzl, M. (1981) Compilation of tRNA sequences. Nucl. Acids Res., 9, r1–r42.

    Article  Google Scholar 

  • Gauss, D. A. and Sprinzl, M. (1984) Compilation of tRNA sequences and of tRNA genes. Nucl. Acids Res., 12, r1–rl31.

    Article  Google Scholar 

  • Geerdes, H. A., Van Boom, J. H. and Hilbers, C. W. (1980) Codon-anticodon interaction in tRNA: NMR study of the binding of the codon UUC. J. Mol. Biol., 142, 219–230.

    Article  Google Scholar 

  • Gefter, M. L. and Russel, R. L. (1969) Role of modifications in tyrosine tRNA: a modified base affecting ribosome binding. J. Mol. Biol., 39, 145–157.

    Article  Google Scholar 

  • Gheysen, D., Iserentant, D., Derom, C. and Fiers, W. (1982) Systematic alteration of the nucleotide sequence preceding the translation initiation codon and the effects on bacterial expression of the cloned SV 40 small-T antigen gene. Gene, 17, 55–63.

    Article  Google Scholar 

  • Goldberg, A. L. and St John, A. C. (1976) Intracellular protein degradation in mammalian and bacterial cells: Part 2. Ann. Rev. Biochem., 45, 747–803.

    Article  Google Scholar 

  • Goldman, E. (1982) Effect of rate-limiting elongation on bacteriophage MS2 RNA- directed protein synthesis in extracts of E. coli. J. Mol. Biol., 158, 619–636.

    Google Scholar 

  • Goldman, E., Holmes, W. M. and Hatfield, G. W. (1979) Specificity of codon recognition by Escherichia coli isoaccepting species determined by protein synthesis in vitro directed by phage RNA. J. Mol. Biol., 129, 567–585.

    Article  Google Scholar 

  • Gorenstein, D. G. and Goldfield, E. M. (1982) High-resolution phosphorus nuclear magnetic resonance spectroscopy of tRNAs: multiple conformations in the anticodon loop. Biochemistry, 21, 5839–5849.

    Article  Google Scholar 

  • Gorini, L. (1974) Streptomycin and misreading of the genetic code. In Ribosomes (eds M. Nomura, A. Tissières and P. Lengyel ), Cold Spring Harbor Laboratory, New York, pp. 791–803.

    Google Scholar 

  • Gouy, M. arid Gautier, R. (1982) Codon usage in bacteria: a correlation with gene expressivity. Nucl. Acids Res., 10, 7055–7074.

    Google Scholar 

  • Grantham, R., Gautier, C., Gouy, M., Jacobzone, M. and Merrier, R. (1981) Codon catalogue is a genome strategy for gene expressivity. Nucl. Acids Res., 9, r43–r74.

    Article  Google Scholar 

  • Grosjean, H. (1979) Codon usage in several organisms. In Transfer RNA: Biological Aspects (eds D. Söll, J. N. Abelson and P. Schimmel ), Cold Spring Harbor Laboratory, ftew York, monograph 9B, pp. 565–569.

    Google Scholar 

  • Grosjean, H. and Fiers, W. (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anticodon energy hypothesis. Gene, 18, 199–209.

    Article  Google Scholar 

  • Grosjean, H., Cedergren, R. J. and McKay, W. (1982) Structure in tRNA data. Biochimie, 64, 387–397.

    Article  Google Scholar 

  • Grosjean, H., de Henau, S. and Crothers, D. M. (1978) On the physical basis for ambiguity in genetic coding interactions. Proc. Nad Acad. Sci. USA, 75, 610–614.

    Google Scholar 

  • Grosjean, H., Soli, D. and Crothers, D. M. (1976) Studies of the complex between tRNA with complementary anticodons. J. Mol. Biol., 103, 499–518.

    Article  Google Scholar 

  • Grosjean, H., Sankoff, D., Jou, M. J., Fiers, W. and Cedergren, R. J. (1978) Bacteriophage MS2 RNA: a correlation between the stability of the codon:anti- codon interaction and the choice of code words. J. Mol. Evol., 12, 113–119.

    Article  Google Scholar 

  • Grosjean, H., de Henau, S., Houssier, C. and Buckingham, R. H. (1980) Wild-type E. coli tRNA efficiency suppresses UGA opal codon in an eukaryotic cell-free protein synthesis: evolutionary implications. Arch. Internat. Physiol. Biochim., 88, 168–169.

    Google Scholar 

  • Gu, X., Nicoghosian, K., Cedergren, R. J. and Wong, J. T. (1983) Sequence of halobacterial tRNAs and the paucity of U in the first position of their anticodons. Nucl. Acids Res., 11, 5443–5450.

    Article  Google Scholar 

  • Gupta, R. (1984) Halobacterium volcanii tRNAs: identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J. Biol. Chem., 259, 9461 - 9471.

    Google Scholar 

  • Harley, C. B., Pollard, J. W. and Stanners, C. P. (1981) Model for messenger RNA translation during amino acid starvation applied to the calculation of protein synthetic error rates. J. Biol. Chem., 256, 10786–10794.

    Google Scholar 

  • Hatfield, D., Diamond, A. and Dudock, B. (1982) Opal suppressor serine tRNAs from bovine liver form phosphoseryl-tRNA. Proc. Nad Acad. Sci. USA, 79, 6215–6219.

    Article  Google Scholar 

  • Hatfield, D., Varrichio, F., Rich, M. and Forget, B. G. (1982) The aminoacyl-tRNA population of human reticulocytes. J. Biol. Chem., 257, 3183–3188.

    Google Scholar 

  • Heckman, J. E., Sarnoff, J., Alzner-Deweerd, B., Yin, S. and Rajbhandary, U. L. (1980) Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc. Natl Acad. Sci. USA, 77, 3159–3163.

    Article  Google Scholar 

  • Hensgens, L. A., Brakenhoff, J., de Vries, B. F., Sloof, P., Tromp, M. C., Van Boom, J. H. and Benne, R. (1984) The sequence of the gene for cytochrome oxydase sub-unit I, a frameshift containing gene for cytochrome oxydase II and seven unassigned reading frames in Trypanosoma brucei mitochondrial maxi circle DNA. Nucl. Acids Res., 12, 7327–7344.

    Article  Google Scholar 

  • Heyer, W. D., Thuriaux, P., Kohli, J., Ebert, P., Kersten, H., Gehrke, C., Kuo, K. and Agris, P. F. (1984) An antisuppressor mutation of S. pombe affects the post- transcriptional modification of the ‘wobble’ base in the anticodon of tRNAs. J. Biol. Chem., 259, 2856–2862.

    Google Scholar 

  • Hillen, W., Egert, E., Lindner, H. J. and Gassen, H. G. (1978) Restriction or amplification of wobble recognition: the structure of 2-thio-5-methylaminomethyl- uridine and the interaction of odd uridines with the anticodon loop backbone. FEBS Lett., 94, 361–364.

    Article  Google Scholar 

  • Hirsh, D. (1971) Tryptophan transfer RNA as the UGA suppressor. J. Mol Biol., 58, 439–458.

    Article  Google Scholar 

  • Högenauer, G. (1974) Binding of UGA to wild type and suppressor tryptophan tRNA from E. coli FEBS Lett., 39, 310–316.

    Article  Google Scholar 

  • Holmes, W. M., Goldman, E., Miner, T. A. and Hatfield, G. W. (1977) Differential utilization of leucyl-tRNAs by Escherichia coli. Proc. Natl Acad. Sci. USA, 74, 1393–1397.

    Article  Google Scholar 

  • Hornig, H., Woolley, P. and Lührmann, R. (1984) Decoding at the ribosomal A-site: the effect of a defined codon-anticodon mismatch upon the behaviour of bound aminoacyl-tRNA. J. Biol. Chem., 259, 5632–5636.

    Google Scholar 

  • Igarashi, K., Hashimoto, S., Miyake, A., Kashiwagi, K. and Hirose, S. (1982) Increase of fidelity of polypeptide synthesis by spermidine in eukaryotic cell-free system. Eur. J. Biochem., 128, 597–604.

    Article  Google Scholar 

  • Ikemura, T. (1981a) Correlation between the abundance of E. coli tRNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol., 146, 1–21.

    Article  Google Scholar 

  • Ikemura, T. (1981b) Correlation between the abundance of E. coli tRNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J. Mol. Biol., 151, 389–409.

    Article  Google Scholar 

  • Ikemura, T. (1982) Correlation between the abundance of yeast tRNAs and the occurrence of the respective codons in protein genes. J. Mol. Biol., 158, 573–597.

    Article  Google Scholar 

  • Inokuchi, H., Yamao, F., Sakano, H. and Ozeki, H. (1979) Identification of tRNA suppressors in E. coli 1. Amber suppressor su+2, an anticodon mutant of tRNA Glu2 . J. Mol. Biol., 132, 649–662.

    Article  Google Scholar 

  • Jank, P., Shindo-Okado, N., Nishimura, S. and Gross, H. J. (1977) Rabbit liver tRNA Val1 . I. Primary structure and unusual codon recognition. Nucl Acid Res., 4, 1999–2008.

    Article  Google Scholar 

  • Jelenc, P. C. and Kurland, C. G. (1979) Nucleotide triphosphate regeneration decreases the frequency of translation errors. Proc. Natl Acad. Sci. USA, 76, 3174–3178.

    Article  Google Scholar 

  • Johnston, P. D. and Redfield, A. G. (1979) Proton FT-NMR studies of tRNA structure and dynamics. In Structure, Properties and Recognition (eds P. Schimmel, D. Söll and J. N. Abelson ), Cold Spring Harbor, monograph 9A, pp. 191–206.

    Google Scholar 

  • Kagawa, Y., Nojima, H., Nukiwa, N., Ishizuka, M., Nakajima, T., Yasuhara, T., Tanaka, T. and Oshima, T. (1984) High guanine plus cytosine content in the third letter of codons of an extreme thermophile. J. Biol Chem., 259, 2956–2960.

    Google Scholar 

  • Kastelein, R. and Van Duin, J. (1982) Ribosomal frameshift errors control the expression of an overlapping gene in RNA phage. In Interaction of Translational and Transcriptional Controls in the Regulation of Gene Expression (eds M. Grunberg- Manago and B. Safer ), Elsevier Biomedical, New York, pp. 221–240.

    Google Scholar 

  • Kastelein, R. A., Berkhout, B. and Van Duin, J. (1983) Opening the closed ribosome- binding site of the lysis cistron of bacteriophage MS2. Nature, 305, 741–744.

    Article  Google Scholar 

  • Kawasaki, M., Tsonis, P. A., Nishio, K. and Takemura, S. (1980) Abnormal codon recognition of glycyl-tRNA from the posterior silk glands of Bombix mori. J. Biochem. (Tokyo), 88, 1151–1157.

    Google Scholar 

  • Khazaie, K., Buchanan, J. H. and Rosenberger, R. F. (1984a) The accuracy of Qß RNA translation. I. Errors during the synthesis of Qβ protein by intact Escherichia coli cells. Eur. J. Biochem., 144, 485–489.

    Article  Google Scholar 

  • Khazaie, K., Buchanan, J. H. and Rosenberger, R. F. (1984b) The accuracy of Qß RNA translation. II. Errors during the synthesis of Qβ proteins by cell-free Escherichia coli extracts. Eur. J. Biochem., 144, 491–495.

    Article  Google Scholar 

  • Kim, C. H. and Warner, J. R. (1983) Messenger RNA for ribosomal protein in yeast. J. Mol Biol, 165, 79–89.

    Article  Google Scholar 

  • Kohli, J. (1983) The genetics concerning modified nucleotides in relation to their influence on tRNA function. In The Modified Nucleosides of tRNA, Vol. II (eds P. F. Agris and R. A. Kopper ), Alan R. Liss, New York.

    Google Scholar 

  • Kohli, J. and Grosjean, H. (1981) Usage of the three termination codons: compilation and analysis of the known eukaryotic and prokaryotic translation termination sequences. Mol Gen. Genet., 182, 430–439.

    Article  Google Scholar 

  • Konigsberg, W. and Godson, G.N. (1983) Evidence for use of rare codons in the DNA C-gene and other regulatory genes of E. coli. Proc. Natl Acad. Sci. USA, 80, 687–691.

    Article  Google Scholar 

  • Kopelowitz, J., Schoulaker-Schwarz, R., Lebanon, A. and Engelberg-Kulka, H. (1984) Modulation of E. coli tryptophan attenuation by the UGA readthrough process. Mol. Gen. Genet., 196, 541–545.

    Google Scholar 

  • Kruse, T. A., Clark, B. F. C., Appel, B. and Erdmann, V. A. (1980) The structure of the CCA end of tRNA, aminoacyl-tRNA and aminoacyl-tRNA in the ternary complex. FEBS Lett., 117, 315–318.

    Article  Google Scholar 

  • Kubli, E. (1980) Transfer RNA modification in eukaryotes: an evolutionary interpretation. Trends in Biochem. Sci., 5, 190–191.

    Article  Google Scholar 

  • Kurland, C. G. (1979) Reading frame errors on ribosomes. In Nonsense Mutations and tRNA Suppressors (eds J. E. Celis and J. D. Smith ), Academic Press, New York, pp. 98–108.

    Google Scholar 

  • Labuda, D. and Pörschke, D. (1980) Multistep mechanism of codon recognition by tRNA. Biochemistry, 19, 3799–3805.

    Article  Google Scholar 

  • Labuda, D., Striker, G. and Pörschke, D. (1984) Mechanism of codon recognition by tRNA and codon-induced tRNA association. J. Mol. Biol., 174, 587–604.

    Article  Google Scholar 

  • Lagerkvist, U. (1978) ‘Two out of three’: an alternative method of codon reading. Proc. Natl Acad. Sei. USA, 75, 1759–1762.

    Google Scholar 

  • Lagerkvist, U. (1981) Unorthodox codon reading and the evolution of the genetic code. Cell, 23, 305–306.

    Article  Google Scholar 

  • Larue, B., Cedergren, R. J., Sankoff, D. and Grosjean, H. (1979) Evolution of methionine initiator and phenylalanine tRNA. J. Mol Evol., 14, 287–300.

    Article  Google Scholar 

  • Laten, H. M. (1984) Antisuppression of class I suppressors in an isopentenylated- tRNA deficient mutant of S. cerevisiae. Current Genetics, 8, 29–32.

    Article  Google Scholar 

  • Loftfield, R. B. (1963) The frequency of errors in protein biosynthesis. Biochem. J., 89, 89–92.

    Google Scholar 

  • Loftfield, R. B. and Vanderjagt, D. (1972) The frequency of errors in protein biosynthesis. Biochem. J., 128, 1353–1356.

    Google Scholar 

  • Lomant, A. J. and Fresco, J. R. (1975) Structural and energetic consequences of non-complementary base oppositions in nucleic acid helix. Progr. Nucl. Acids Res. Mol. Biol., 15, 185–218.

    Article  Google Scholar 

  • Lührmann, R., Eckhardt, H. and Stöffler, G. (1979) Codon-anticodon interaction at the ribosomal peptidyl-site. Nature, 280, 423–425.

    Article  Google Scholar 

  • Lustig, F., Elias, P., Axberg, T., Samuelson, T., Tittawella, I. and Lagerkvist, U. (1981) Codon reading and translation error: reading of the glutamine and lysine codons during protein synthesis in vitro. J. Biol. Chem., 256, 2635–2643.

    Google Scholar 

  • Macreadie, I. G., Novitski, C. E., Maxwell, R. J., John, U., Ooi, B. G., McMullen, G. L., Lukins, H. B., Linnane, A. W. and Nagley, P. (1983) Biogenesis of mitochondria; the mitochondrial gene aap 1 coding for mitochondrial ATPase subunit 8 in S. cerevisiae. Nucl. Acids Res., 11, 4435–4451.

    Article  Google Scholar 

  • Manley, J. L. (1978a) Synthesis and degradation of termination and premature- termination fragments of β-galactosidase in vitro and in vivo. J. Mol. Biol., 125, 407–432.

    Article  Google Scholar 

  • Manley, J. L. (1978b) Synthesis of internal re-initiation fragments of β-galactosidase in vitro and in vivo. J. Mol. Biol., 125, 449–466.

    Article  Google Scholar 

  • Medvedev, Z. A. and Medvedeva, M. N. (1978) Use of HI histone to test the fidelity of protein biosynthesis in mouse tissues. Biochem. Soc. Trans, 6, 610–612.

    Google Scholar 

  • Meier, F., Suter, B., Grosjean, H., Keith, G. and Kubli, E. (1985) Modification of the wobble base in tRNAHis influences in vivo decoding properties. EMBO J., 4, 823–827.

    Google Scholar 

  • Menninger, J. R. (1983) Computer simulation of ribosome editing. J. Mol. Biol., 171, 383–399.

    Article  Google Scholar 

  • Miller, J. H. and Albertini, A. M. (1983) Effects of surrounding sequence on the suppression of nonsense codon. J. Mol. Biol., 164, 59–71.

    Article  Google Scholar 

  • Mitra, S. K., Lustig, F., Akesson, B. and Lagerkvist, U. (1977) Codon:anticodon recognition in the valine codon family. J. Biol. Chem., 255, 471–478.

    Google Scholar 

  • Mitra, S. K., Lustig, F., Akesson, B., Axberg, T., Elias, P. and Lagerkvist, U. (1979) Relative efficiency of anticodons in reading the valine codons during protein synthesis in vitro. J. Biol. Chem., 254, 6397–6401.

    Google Scholar 

  • Moras, D., Comarmond, M. B., Fischer, J., Weiss, R., Thierry, J. C., Ebel, J. P. and Giégé, R. (1980) Crystal structure of yeast tRNA. Nature, 288, 669–674.

    Article  Google Scholar 

  • Mount, D. W. (1980) The genetics of protein degradation in bacteria. Ann. Rev. Genet., 14, 279–319.

    Article  Google Scholar 

  • Munz, P., Leupold, U., Agris, P. and Kohli, J. (1981) In vivo decoding rules in Schizosaccharomycespombe are at variance with in vitro data. Nature, 294, 187–188.

    Google Scholar 

  • Murgola, E. and Pagel, F. T. (1980) Codon recognition by glycine transfer RNAs of Escherichia coli in vivo. J. Mol. Biol., 138, 833–844.

    Article  Google Scholar 

  • Murgola, E. J., Pagel, F. T. and Hijazi, K. A. (1984) Codon context effects in missense suppression. J. Mol. Biol., 175, 19–27.

    Article  Google Scholar 

  • Murgola, J., Prather, N. E., Mims, P. H. and Ishigazi, K. A. (1983) Missense and nonsense suppressors derived from a glycine tRNA by nucleotides insertion and deletion in vivo. Mol. Gen. Genet., 193, 76–81.

    Article  Google Scholar 

  • Ninio, J. (1971) Codon-anticodon recognition: the missing triplet hypothesis. J. Mol. Biol., 6, 63–82.

    Article  Google Scholar 

  • Ninio, J. (1973) Recognition in nucleic acids and the anticodon families. Progr. Nucl. Acids Res. Mol. Biol., 13, 301–337.

    Article  Google Scholar 

  • Nishimura, S. (1979) Modified nucleosides in tRNA. In Transfer RNA: Structure, Properties and Recognition (eds P. R. Schimmel, D. Söll and J. B. Abelson ). Cold Spring Harbor Laboratory, New York, monograph 9A, pp. 59–79.

    Google Scholar 

  • O’Farrell, P. H. (1978) The suppression of defective translation by ppGpp and its role in the stringent response. Cell, 15, 545–547.

    Article  Google Scholar 

  • Parker, J. (1981) Mistranslated protein in E. coli. J. Biol. Chem., 256, 9770–9773.

    Google Scholar 

  • Parker, J., Pollard, J., Friesen, J. D. and Stanners, C. P. (1978) Stuttering: high level mistranslation in animal and bacterial cells. Proc. Natl Acad. Sci. USA, 75, 1091–1095.

    Article  Google Scholar 

  • Parker, J., Johnston, T. C., Borgia, P. T., Holtz, G., Remaut, E. and Fiers, W. (1983) Codon usage and mistranslation. J. Biol. Chem., 258, 10 007–10 012.

    Google Scholar 

  • Pedersen, S. (1984) Escherichia coli ribosomes translate in vivo with variable rate. EMBO J., 3, 2895–2898.

    Google Scholar 

  • Peters, M. and Yarns, M. (1979) Transfer RNA selection at the ribosomal A and P sites. J. Mol. Biol., 134, 471–491.

    Article  Google Scholar 

  • Petrullo, L. A., Gallagher, P. J. and Elseviers, D. (1983) The role of 2-methylthio-N6- isopentenyladenosine in readthrough and suppression of nonsense codons in E. coli. Mol. Gen. Genet., 190, 289–294.

    Article  Google Scholar 

  • Picard-Bennoun, M. (1982) Does translational ambiguity increase during cell differentiation? FEBS Lett., 149, 167–170.

    Article  Google Scholar 

  • Picard-Bennoun, M. and Becqueret, J. (1981) Genetic analysis of cytoplasmic ribosomes in fungi. Trends in Biochem. Sci., 6, 272–274.

    Article  Google Scholar 

  • Pope, W. T., Brown, A. and Reeves, R. H. (1978) The identification of the tRNA substrates for the supK tRNA methylase. Nucl. Acids Res., 5, 1041–1057.

    Article  Google Scholar 

  • Pörschke, D. and Labuda, D. (1982) Codon induced tRNA association: quantitative analysis by sedimentation equilibrium. Biochemistry, 21, 53–56.

    Article  Google Scholar 

  • Post, L. E. and Nomura, M. (1980) DNA sequences from the str operon of E. coli. J. Biol. Chem., 255, 4660–4666.

    Google Scholar 

  • Quigley, G. H. and Rich, A. (1976) Structural domains of transfer RNA molecules. Science, 194, 796–806.

    Article  Google Scholar 

  • Ramstein, J. and Buckingham, R. (1981) Tritium exchange on tRNA: slowly exchanging protons sensitive to a change in the dihydrouridine stem. Proc. Natl Acad. Sci. USA, 78, 1567–1571.

    Article  Google Scholar 

  • Rice, J. B., Libby, R. J. and Reeve, J. N. (1984) Mistranslation of the mRNA encoding bacteriophage T7-0.3 protein. J. Biol. Chem., 259, 6505–6510.

    Google Scholar 

  • Robertson, J. M. and Wintermeyer, W. (1981) Effect of translocation on topology and conformation of anticodon and D-loops of tRNA. J. Mol. Biol., 151, 57–69.

    Article  Google Scholar 

  • Robinson, M., Lilley, R., Little, S., Emtage, J. S., Yarranton, G., Millican, A., Eaton, M. and Humphreys, G. (1984) Codon usage can affect efficiency of translation of genes in E. coli. Nucl. Acids Res., 12, 6663–6672.

    Article  Google Scholar 

  • Rosenberger, R. F. and Foskett, G. (1981) The estimate of the frequency of in vivo transcriptional errors at a nonsense codon in E. coli. Mol. Gen. Genet., 183, 561–563.

    Article  Google Scholar 

  • Roth, J. R. (1981) Frameshift suppression. Cell, 24, 601–602.

    Article  Google Scholar 

  • Ruusala, T., Ehrenberg, M. and Kurland, C. G. (1982a) Catalytic effects of elongation factors Ts on polypeptide synthesis. EMBO J., 1, 75–78.

    Google Scholar 

  • Ruusala, T., Ehrenberg, M. and Kurland, C. G. (1982b) Is there proofreading during polypeptide synthesis? EMBO J., 1, 741–745.

    Google Scholar 

  • Ryoji, M., Hsia, K. and Kaji, A. (1983) Read-through translation. Trends in Biochem. Sci., 8, 88–90.

    Article  Google Scholar 

  • Samuelsson, T., Elias, P., Lustig, F. et al. (1980) Aberrations of the classic reading scheme during protein synthesis in vitro. J. Biol. Chem., 255, 4583–4588.

    Google Scholar 

  • Samuelsson, T., Axberg, T., Boren, T. and Lagerkvist, U. (1983) Unconventional reading of the glycine codons. J. Biol. Chem., 258, 13 178–13 184.

    Google Scholar 

  • Schmitt, M., Kyriatsoulis, A. and Gassen, H. G. (1982) The context theory as applied to the decoding of the initiator tRNA by E. coli ribosomes. Eur. J. Biochem., 125, 389–394.

    Google Scholar 

  • Sedlacek, J., Fabry, M. and Rychlik, I. (1979) The arrangement of nucleotides in the coding regions of natural templates. Mol. Gen. Genet., 172, 31–36.

    Article  Google Scholar 

  • Sharma, O. K. and Kuchino, Y. (1977) Infidelity of translation of encephalomyo- carditis viral RNA with tRNA from human malignant trophoblastic cells. Biochem. Biophys. Res. Commun., 78, 591–595.

    Article  Google Scholar 

  • Sharma, O. K., Beezley, D. N. and Roberts, W. K. (1975) Limitation of reticulocyte tRNA in the translation of heterologous mRNAs. Biochemistry, 15, 4313–4318.

    Article  Google Scholar 

  • Smiley, B. L., Lupski, J. R., Svec, P. S., McMacken, R. and Godson, G. N. (1982) Sequences of the E. coli dnaG primase gene and regulation of its expression. Proc. Natl Acad. Sci. USA, 79, 4550–4554.

    Article  Google Scholar 

  • Smith, D. W. E. (1975) Reticulocyte tRNA and hemoglobin synthesis: tRNA availability may regulate hemoglobin synthesis in developing red blood cells. Science, 190, 529–534.

    Article  Google Scholar 

  • Smith, D. W. E., McNamara, L., Rice, M. and Hatfield, D. L. (1981) The effects of posttranscriptional modification on the function of tRNALys isoaccepting species in translation. J. Biol. Chem., 256, 10033–10036.

    Google Scholar 

  • Smith, D. W. E., McNamara, A. L., Mushinski, J. F. and Hatfield, D. L. (1984) Tumor-specific hypomodified Phe-tRNA is utilised in translation in preference to the fully-modified isoacceptor of normal cells. J. Biol. Chem., 260, 147–151.

    Google Scholar 

  • Sommer, S. S. and Cohen, J. E. (1980) The size distribution of protein, mRNA and nuclear RNA. J. Mol. Evol, 15, 37–57.

    Article  Google Scholar 

  • Springer, M., Trudel, M., Graffe, M., Plumbridge, J. A., Fayat, G., Mayaux, J. F., Sacerdot, C., Blanquet, S., Grunberg-Manago, M. (1983) E. coli Phe-tRNA synthetase operon is controlled by attenuation in vivo. J. Mol. Biol., 171, 263–279.

    Google Scholar 

  • Sprinzl, M., Helk, B. and Baumann, U. (1983) Structural and functional studies on the anticodon and T-loop of tRNA. In Gene Expression, the Translation Step and its Control (eds B. Clark andH. U. Petersen ), Munksgaard, Copenhagen, pp. 235–254.

    Google Scholar 

  • Stent, G. S. (1964) The operon: on its third anniversary. Science, 144, 816.

    Article  Google Scholar 

  • Stöffler, G., Hasenbank, R. and Dabbs, E. R. (1981) Expression of the L1-L11 operon in mutants of E. coli lacking the ribosomal protein L1 or L11. Mol. Gen. Genet., 181, 164–168.

    Google Scholar 

  • Sussman, J. F., Holbrook, S. R., Warrant, R. W., Church, G. M. and Kim, S. H. (1978) Crystal structure of yeast phenylalanine tRNA. J. Mol. Biol., 123, 607–630.

    Article  Google Scholar 

  • Takemoto, T., Takeishi, S., Nishimura, S. and Ukita, T. (1973) Transfer of valine into rabbit haenioglobin from various isoaccepting species of valyl-tRNA differing in codon recognition. Eur. J. Biochem., 38, 489–496.

    Article  Google Scholar 

  • Tamura, F., Nishimura, S. and Ohki, M. (1984) The E. coli div-E mutation which differentially inhibits synthesis of certain proteins, is in tRNA. EMBO J., 3, 1103–1107.

    Google Scholar 

  • Taniguchi, T. and Weissmann, C. (1978) Site-directed mutagens in the initiator region of the bacteriophage Qβ coat cistron and their effect on ribosome binding. J. Mol. Biol., 118,533–565.

    Article  Google Scholar 

  • Thompson, R. C., Cline, S. W. and Yarns, M. (1982) Site-directed mutagenesis of the anticodon region: the universal U is not essential to tRNA synthesis and function. In Interaction of Translational and Transcriptional Controls in the Regulation of Gene Expression (eds M. Grunberg-Manago and B. Safer ), Elsevier Biomedical, New York, pp. 189–220.

    Google Scholar 

  • Thompson, R. C., Dix, D. B., Gerson, R. B. and Karim, A. M. (1981) A GTPase reaction accompanying the rejection of Leu-tRNA2 by UUU-programiped ribosomes. J. Biol. Chem., 256, 81–86.

    Google Scholar 

  • Tsang, T. H., Buck, M. and Ames, B. N. (1983) Sequence specificity of tRNA- modifying enzymes: an analysis of 258 tRNA sequences. Biochim. Biophys. Acta, 741, 180–196.

    Google Scholar 

  • Vacher, J., Grosjean, H., de Henau, S., Finelli, J. and Buckingham, R. H. (1984a) Eur. J. Biochem., 138, 77–81.

    Article  Google Scholar 

  • Vacher, J., Grosjean, H., Houssier, C. and Buckingham, R. H. (1984b) The effect of point mutations affecting E. coli tryptophan-tRNA on anticodon:anticodon inter-actions and on UGA suppression. J. Mol. Biol., 177, 329–342.

    Article  Google Scholar 

  • Varenne, S., Buc, J., Lloubes, R. and Lazdunski, C. (1984) Translation is a non-uniform process: effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol., 180, 549–576.

    Article  Google Scholar 

  • Wagner, E. G. H. and Kurland, C. G. (1980) Translation accuracy enhanced in vitro by (p)ppGpp. Mol. Gen. Genet., 180, 139–145.

    Article  Google Scholar 

  • Wagner, E. G. H., Jelenc, P. C., Ehrenberg, M. and Kurland, C. G. (1982) Rate of elongation of polyphenylalanine in vitro. Eur. J. Biochem., 122, 193–197.

    Article  Google Scholar 

  • Weiss, G. B. (1973) Translational control of protein synthesis by tRNA unrelated to changes in tRNA concentration. J. Mol. Evol., 2, 199–204.

    Article  Google Scholar 

  • Weiss, R. and Gallant, J. (1983) Mechanism of ribosome frameshifting during translation of the genetic code. Nature, 302, 389–393.

    Article  Google Scholar 

  • Weissenbach, J. and Grosjean, H. (1981) Effect of threonylcarbomoyl modification (t6 A) in yeast tRNA on codon: anticodon and anticodon: anticodon interactions: a thermodynamic and kinetic evaluation. Eur. J. Biochem., 116, 207–213.

    Article  Google Scholar 

  • Weissenbach, J., Dirheimer, G., Faleoff, R., Sanceau, J. and Falcoff, E. (1977) Yeast tRNA (anticodon UAG) translates all six leucine codons in extracts from interferon treated cells. FEBS Lett., 82, 71–76.

    Article  Google Scholar 

  • Westhof, E., Dumas, P. and Moras, D. (1983) Loop stereochemistry and dynamics in tRNA. J. Biomol. Struct. And Dyn., 1, 337–355.

    Google Scholar 

  • Woese, C. (1967) The Genetic Code: the Molecular Basis for Genetic Expression. Harper and Row, New York.

    Google Scholar 

  • Wurmbach, P. and Nierhaus, K. H. (1979) Codon-anticodon interaction at the ribosomal P (peptidyl-tRNA) site. Proc. Natl Acad. Sci. USA, 76, 2143–2147.

    Article  Google Scholar 

  • Yanofsky, C. (1981) Attenuation in the control of expression of bacterial operon. Nature, 289, 751–758.

    Article  Google Scholar 

  • Yarus, M. (1979) The accuracy of translation. Progr. Nucl. Acids Res. Mol. Biol., 23, 195–225.

    Article  Google Scholar 

  • Yarus, M. (1982) Translational efficiency of tRNAs: uses of an extended anticodon. Science, 218, 646–652.

    Article  Google Scholar 

  • Yarus, M. and Thompson, R. C. (1984) Precision of protein biosynthesis. In Gene Function in Prokaryotes, Cold Spring Harbor Laboratory, New York, pp. 23–63.

    Google Scholar 

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  1. R. H. Buckingham
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  1. National Institute for Medical Research, London, UK

    T. B. L. Kirkwood  & R. F. Rosenberger  & 

  2. University of Southern California, Los Angeles, USA

    D. J. Galas

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Buckingham, R.H., Grosjean, H. (1986). The accuracy of mRNA—tRNA recognition. In: Kirkwood, T.B.L., Rosenberger, R.F., Galas, D.J. (eds) Accuracy in Molecular Processes. Springer, Dordrecht. https://doi.org/10.1007/978-94-009-4097-0_5

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