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Chapter 18 : tRNA Discrimination in Aminoacylation

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tRNA Discrimination in Aminoacylation, Page 1 of 2

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Abstract:

The recognition of a tRNA by its aminoacyl-tRNA synthetase is a classic example of the specificity often encountered in biology. Each of the 20 aminoacyl-tRNA synthetases in a cell must distinguish its own set of isoacceptor tRNAs from the many noncognate tRNAs and efficiently catalyze the covalent attachment of the correct amino acid to the 3' end of only these species. Ultimately, the fate of the cell rests on this interaction, as there are no subsequent proof-reading steps in protein synthesis whereby the amino acid is matched against the anticodon to ensure that the proper amino acid is inserted in response to a given codon. How an aminoacyl-tRNA synthetase is able to select its tRNA substrates from a pool of noncognate species sharing similar tertiary structure has been the focus of over 20 years of research. Recent technical refinements in the types of assays used to study this interaction have contributed a wealth of new information to this field, allowing the identification of nucleotides conferring a particular amino acid acceptor identity for a number of tRNAs. The goal of this chapter is to summarize these more recent developments in tRNA recognition.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

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Figures

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Figure 1

(A) Cloverleaf structure of a typical class I tRNA, numbered according to Sprinzl et al. ( ). Bases conserved in all tRNAs are included. (B) Three-dimensional structure of yeast tRNA ( ).

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18
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Image of Figure 2
Figure 2

Major recognition elements of tRNA (A), tRNA (B), yeast tRNA (C), and tRNA (D).

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18
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Image of Figure 3
Figure 3

Kinetic effect of nucleotide substitutions of yeast, and human tRNAPhe on aminoacylation by the cognate synthetase ( ). The numbers shown refer to the fold reduction in on substitution at that site. Where variable effects of aminoacylation were observed, kinetic data for the nucleotide substitution causing the largest defect are shown.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18
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References

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1. Altman, S.,, C. Guerrier-Takada,, H. M. Frankfort,, and H. D. Robertson,. 1982. RNA processing nucleases, p. 243274. In S. Linn, and R. Roberts (ed.), Nucleases. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
2. Atilgan, X.,, H. B., Nicholas, Jr.,, and W. H. McClain. 1986. A statistical method for correlating tRNA sequence with amino acid specificity. Nucleic Acids Res. 14:375380.
3. Bare, L. A.,, and O. C. Uhlenbeck. 1985. Aminoacylation of anticodon loop substituted yeast tyrosine transfer RNA. Biochemistry 24:23542360.
4. Bare, L. A.,, and O. C. Uhlenbeck. 1986. Specific substitutions into the anticodon loop of yeast tyrosine transfer RNA. Biochemistry 25:58255830.
5. Böck, A. 1991. Personal communication.
6. Bruce, A. G.,, and O. C. Uhlenbeck. 1982. Enzymatic replacement of the anticodon of yeast phenylalanine transfer ribonucleic acid. Biochemistry 21:855861.
7. Bruce, A. G.,, and O. C. Uhlenbeck. 1982. Specific interaction of anticodon loop residues with yeast phenylalanyl-tRNA synthetase. Biochemistry 21:39213926.
8. Celis, J. E.,, M. L. Hooper,, and J. D. Smith. 1973. Amino acid acceptor stem of E. coli suppressor tRNATyr is a site of synthetase recognition. Nature New Biol. 244:261264.
9. Chakraburtty, K. 1975. Effect of sodium bisulfite modification on the arginine acceptance of E. coli tRNAArg. Nucleic Acids Res. 2:17931804.
10. Chambers, R. W.,, S. Aoyasi,, Y. Furukawa,, H. Zawadzka,, and O. Bhanot. 1973. Inactivation of valine acceptor activity by a C -U missense change in the anticodon of yeast valine transfer ribonucleic acid. J. Biol. Chem. 248:55495551.
11. Chambers, R. W.,, O. S. Bhanot,, S. Aoyasi,, Y. Furukawa,, and H. Zawadzka. 1974. Effects of C → U transitions on the adaptor function of tRNA and tRNAAlalab. Fed. Proc. 33:1422.
12. Chattapadhyay, R.,, H. Pelka,, and L. H. Schulman. 1990. Initiation of in vivo protein synthesis with non-methionine amino acids. Biochemistry 29:42634268.
13. Cigan, A. M.,, L. Feng,, and T. F. Donahue. 1988. tRNAMet1-functions in directing the scanning ribosome to the start site of translation. Science 242:9397.
14. Crothers, D. M.,, T. Seno,, and D. G. Soil. 1972. Is there a discriminator site in transfer RNA? Proc. Natl. Acad. Sci. USA 69:30633067.
15. deDuve, C. 1988. The second genetic code. Nature (London) 333:117118.
16. Dreher, T. W.,, C. Florentz,, and R. Giege. 1988. Valylation of tRNA-like transcripts from cloned cDNA of turnip yellow mosaic virus RNA demonstrate that the L-shaped region at the 3' end of the viral RNA is not sufficient for optimal aminoacylation. Biochimie 70:17191727.
17. Edwards, H.,, V. Trezeguet, and R Schimmel. 1991. An Escherichia coli tyrosine transfer RNA is a leucine-specific transfer RNA in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 88:11531156.
18. Fasiolo, F.,, L. Despons,, M. Laforet,, J. R Ebel,, and P. Walter. 1991. Anticodon mediated tRNA recognition of yeast methionyl-tRNA synthetase requires at least two distinct helices in the C-terminal domain, p. 136. Abstr. 14th International tRNA Workshop.
19. Fasiolo, F.,, T. Glade,, G. Keith,, V. Büttcher,, F. Cramer,, and U. English. 1993. The codon and amino acid specificity of the yeast isoleucine transfer RNAs are dependent on two distinct modified wobble bases, p. 76. Abstr. 15th International tRNA Workshop.
20. Fersht, A., 1985. The basic equations of enzyme kinetics, p. 98120. In A. Fersht (ed.), Enzyme Structure and Mechanism. W. H. Freeman, New York.
21. Florentz, C.,, T. W. Dreher,, J. Rudinger,, and R. Giege. 1991. Specific valylation identity of turnip yellow mosaic virus RNA by yeast valyl-tRNA synthetase is directed by the anticodon in a kinetic rather than affinity-based discrimination. Eur. J. Biochem. 195:229234.
22. Fralova, L.,, and L. L. Kisselev. 1964. Biokhimiya 29:1177.
23. Francis, M. A.,, and B. S. Dudock. 1982. Nucleotide sequence of a spinach chloroplast isoleucine tRNA. J. Biol. Chem. 257:1119511198.
24. Francklyn, C.,, and R. Schimmel. 1989. Aminoacylation of RNA minihelices with alanine. Nature (London) 337:478482.
25. Francklyn, C.,, and R. Schimmel. 1990. Enzymatic aminoacylation of an eight-base-pair microhelix with histidine. Proc. Natl. Acad. Sci USA 87:86558659.
26. Francklyn, C.,, and R. Schimmel. 1991. Overlapping nucleotide determinants for specific aminoacylation of RNA micro-helices. Science 255:11211125.
27. Garcia, A.,, R. Giege,, and J.-P. Behr. 1990. New photoactivatable structural and affinity probes of RNAs: specific features and applications for mapping of spermine binding sites in yeast tRNAAsp and interactions of this tRNA with yeast aspartyl-tRNA synthetase. Nucleic Acids Res. 18:8995.
28. Garrett, M.,, B. LaBouesse,, S. Litvak,, P. Romby,, J.-P. Ebel,, and R. Giege. 1984. Tertiary structure of animal tRNATrp in solution and interaction of tRNATrp with tryptophanyl-tRNA synthetase. Eur. J. Biochem. 138:6775.
29. Ghosh, G.,, H. Pelka,, and L. H. Schulman. 1990. Identification of the tRNA anticodon recognition site of E. coli. Biochemistry 29:22202225.
30. Ghysen, A.,, and J. E. Celis. 1974. Mischarging single and double mutants of Escherichia coli sup3 tyrosine transfer RNA.J. Mol. Biol. 83:333351.
31. Giege, R.,, J. P. Briand,, R. Mengual,, J.-P. Ebel,, and L. Hirth. 1978. Valylation of the two RNA components of turnip yellow mosaic virus and specificity of the tRNA aminoacylation reaction. Eur. J. Biol. 84:251256.
32. Guillemaut, P.,, and J. H. Weil. 1975. Aminoacylation of Phaseolus vulgaris cytoplasmic chloroplastic and mitochondrial tRNAsMet and of Escherichia coli tRNAsMet by homologous and heterologous enzymes. Biochim. Biophys. Acta 407:240248.
33. Guthrie, C.,, and W. H. McClain. 1979. Rare transfer ribonucleic acid essential for phage growth. Nucleotide sequence comparison of normal and mutant T4 isoleucine-accepting transfer ribonucleic acid. Biochemistry 18:37863795.
34. Hall, K. B.,, J. R. Sampson,, O. C. Uhlenbeck,, and A. G. Redfield. 1989. Structure of an unmodified tRNA molecule. Biochemistry 28:57945801.
35. Harada, F.,, and S. Nishimura. 1974. Purification and characterization of AUA specific isoleucine transfer ribonucleic acid from Escherichia coli B. Biochemistry 13:300307.
36. Hasegawa, T.,, H. Himeno,, H. Ishikura,, and M. Shimizu. 1989. Discriminator base of tRNAAsp is involved in amino acid acceptor activity. Biochem. Biophys. Res. Commun. 163:15341538.
37. Hayase, Y.,, M. Jahn,, M. J. Rogers,, L. A. Sylvers,, M. Koizumi,, H. Inoue,, E. Ohtsuka,, and D. Soil. 1992. Recognition of bases in Escherichia coli tRNAGln by glutaminyl-tRNA synthetase: a complete identity set. EMBO J. 11:41594165.
38. Hill, C. W.,, G. Combriato,, and W. Dolph. 1973. Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA. Nature New Biol. 242:230234.
39. Himeno, H.,, T. Hasegawa,, H. Asahara,, K. Tamura,, and M. Shimizu. 1991. Identity determinants of E. coli tryptophan tRNA. Nucleic Acids Res. 19:63796382.
40. Himeno, H.,, T. Hasegawa,, T. Ueda,, K. Watanabe,, K. Miura,, and M. Shimizu. 1989. Role of the extra G-C pair at the end of the acceptor stem of tRNAHis in aminoacylation. Nucleic Acids Res. 17:78557863.
41. Himeno, H.,, T. Hasegawa,, T. Ueda,, K. Watanabe,, and M. Shimizu. 1990. Conversion of aminoacylation specificity from tRNATyr to tRNASer in vitro. Nucleic Acids Res. 18:68156819.
42. Hoben, P.,, N. Royal,, A. Cheung,, F. Yamao,, K. Biemann,, and D. Soil. 1982. Escherichia coli glutaminyl-tRNA synthetase. J. Biol. Chem. 257:1164411650.
43. Hooper, M. L.,, R. Russell,, and J. D. Smith. 1972. Mischarging in mutant tyrosine transfer RNAs. FEBS Lett. 22:149155.
44. Horowitz, J.,, W.-C. Chu,, V. Feiz,, and W. B. Derrick. 1991. Recognition of E. coli valine tRNA by its cognate synthetase, p. 158. Abstr. 14th International tRNA Workshop.
45. Hou, Y.-M.,, and P. Schimmel. 1988. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature (London) 333:140145.
46. Hou, Y.-M.,, and P. Schimmel. 1989. Modeling with in vitro kinetic parameters for the elaboration of transfer RNA identity in vivo. Biochemistry 28:49424947.
47. Hou, Y.-M.,, and P. Schimmel. Evidence that a major determinant for the identity of a transfer RNA is conserved in evolution. Biochemistry 28:68006804.
48. Hou, Y.-M.,, and P. Schimmel. 1992. Functional compensation of a recognition-defective transfer RNA by a distal base pair substitution. Biochemistry 31:1031010314.
49. Imura, N.,, G. B. Weiss,, and R. W. Chambers. 1969. Recon-stitution of alanine acceptor activity from fragments of yeast tRNAAla2. Nature (London) 222:11471148.
50. Inokuchi, H.,, J. E. Celis,, and J. D. Smith. 1974. Mutant tyrosine transfer ribonucleic acids of Escherichia coli: construction by recombination of a double mutant A1G82 chargeable with glutamine.J. Mol. Biol. 85:187191.
51. Jahn, M.,, M. J. Rogers,, and D. Söll. 1991. Anticodon and acceptor stem nucleotides in tRNAGln are major recognition elements for E. coli glutaminyl-tRNA synthetase. Nature (London) 352:258260.
52. Jin, Y. X.,, M. S. Qiu,, W. Q. Li,, K. Q. Zeng,, D. Wang,, J. Bao,, P. Gong,, R. Wu,, and D. Wang. 1987. Effect of the anticodon loop size of yeast alanyl-tRNA on its biological activity. Anal. Biochem. 161:453459.
53. Kern, D.,, and J. Lapointe. 1979. Glutamyl transfer ribonucleic acid synthetase of Escherichia coli. Effect of alteration of the 5-(methylaminomethyl)-2-thiouridine in the anticodon of glutamic acid transfer ribonucleic acid on the catalytic mechanism. Biochemistry 18:58195826.
54. Kim, S.-H.,, F. L. Suddath,, G. J. Quigley,, A. McPherson,, J. L. Sussman,, A. H. J. Wang,, N. C. Seeman,, and A. Rich. 1974. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185:435440.
55. Kisselev, L. L. 1985. The role of the anticodon in recognition of tRNA by aminoacyl-tRNA synthetases. Prog. Nucleic Acid Res. Mol. Biol. 32:237266.
56. Kleina, L. G.,, J.-M. Masson,, J. Normanly,, J. Abelson,, and J. H. Miller. 1990. Construction of Escherichia coli amber suppressor tRNA genes. II. Synthesis of additional tRNA genes and improvement of suppressor efficiency. J. Mol. Biol. 213:705717.
57. Knowlton, R. G.,, L. Soil,, and M. Yarus. 1980. Dual specificity of su + 7 tRNA. Evidence for translational discrimination.J. Mol. Biol. 139:705720.
58. Komatsoulis, G.,, and J. Abelson. 1993. Recognition of transfer RNA (CYS) by Escherichia coli cysteinyl-transfer RNA synthetase. Biochemistry 32:74357444.
59. Labouze, E.,, and H. Bedouelle. 1989. Structural and kinetic bases for the recognition of tRNATyr by tyrosyl-tRNA synthetase.J. Mol. Biol. 205:729735.
60. Ladner, J. E.,, A. Jack,, J. D. Robertus,, R. S. Brown,, D. Rhodes,, B. F. C. Clark,, and A. Klug. 1975. Structure of yeast phenylalanine transfer RNA at 2.5 A resolution. Proc. Natl. Acad. Sci. USA 72:44144418.
61. Lee, C. P.,, M. R. Dyson,, N. Mandal,, U. Varshney,, B. Bahramian,, and U. L. RajBhandary. 1992. Striking effects of coupling mutations in the acceptor stem on recognition of tRNAs by Escherichia coli Met-tRNA synthetase and Met-tRNA transformylase. Proc. Natl. Aacad. Sci. USA 89:92629266.
62. Lee, C. P.,, B. L. Seong,, and U. L. RajBhandary. 1991. Structural and sequence elements important for recognition of E. coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem. J. Biol. Chem. 266:1801218017.
63. Leinfelder, W.,, K. Forchhammer,, B. Veprek,, E. Zehelein,, and A. Böck. 1990. In vitro synthesis of selenocysteinyl-tRNA(UCA) from seryl-tRNA(UCA): involvement and characterization of the selD gene product. Proc. Natl. Acad. Sci. USA 87:543547.
64. Leinfelder, W.,, E. Zehelein,, M. Mandrand-Berthelot,, and A. Bock. 1988. Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine. Nature (London) 331:723725.
65. Li, S.,, H. Pelka,, and L. H. Schulman. 1993. The anticodon and discriminator base are important for aminoacylation of Escherichia coli tRNAAsn. J. Biol. Chem. 268:1833518339.
66. Marinus, M. G.,, R. N. Morris,, D. Soil,, and J. C. Kwong. 1975. Isolation and partial characterization of three Escherichia coli mutants with altered transfer ribonucleic acid methylases. J. Bacteriol. 122:257265.
67. Martinis, S. A.,, and P. Schimmel. 1992. Enzymatic aminoacylation of sequence-specific RNA minihelices and hybrid duplexes with methionine. Proc. Natl. Acad. Sci. USA 89:6569.
68. Masson, J.-M.,, and J. H. Miller. 1986. Expression of synthetic suppressor tRNA genes under the control of a synthetic promoter. Gene 47:179183.
69. McClain, W. H.,, Y.-M. Chen,, K. Foss,, and J. Schneider. 1988. Association of transfer RNA acceptor identity with a helical irregularity. Science 242:16811684.
70. McClain, W. H.,, and K. Foss. 1988. Changing the identity of a tRNA by introducing a G-U wobble pair near the 3' acceptor end. Science 240:793796.
71. McClain, W. H.,, and K. Foss. 1988. Changing the acceptor identity of a transfer RNA by altering nucleotides in a variable pocket. Science 241:18041807.
72. McClain, W. H.,, and K. Foss. 1988. Nucleotides that contribute to the identity of Escherichia coli tRNAPhe. J. Mol. Biol. 202:697709.
73. McClain, W. H.,, K. Foss,, R. A. Jenkins,, and J. Schneider. 1990. Nucleotides that determine Escherichia coli tRNA Arg and tRNALys identities revealed by analyses of mutant opal and amber suppressor tRNAs. Proc. Natl. Acad. Sci. USA 87:92609264.
74. McClain, W. H.,, K. Foss,, R. A. Jenkins,, and J. Schneider. 1991. Rapid determination of nucleotides that define tRNA G1y acceptor identity. Proc. Natl. Acad. Sci. USA 88:61476151.
75. McClain, W. H.,, K. Foss,, R. A. Jenkins,, and J. Schneider. 1991. Four sites in the acceptor helix and one site in the variable pocket of tRNAAla determine the molecule's acceptor identity. Proc. Natl. Acad. Sci. USA 88:92729276.
76. McClain, W. H.,, and H. B. Nicholas, Jr. 1987. Differences between transfer RNA molecules. J. Mol. Biol. 194:635642.
77. Meinnel, T.,, Y. Mechulam,, G. Fayat,, and S. Blanquet. 1992. Involvement of the size and sequence of the anticodon loop in tRNA recognition by mammalian and E. coli methionyl-tRNA synthetases. Nucleic Acids Res. 20:47414746.
78. Meinnel, T.,, Y. Mechulam,, G. Fayat,, and S. Blanquet. 1993. Critical role of the acceptor stem of tRNAsMet in their aminoacylation by Escherichia coli methionyl-tRNA synthetase. J. Mol. Biol. 229:2636.
79. Meinnel, T.,, Y. Mechulam,, D. LeCorre,, M. Panvert,, S. Blanquet,, and G. Fayat. 1991. Selection of suppressor methionyl-tRNA synthetases: mapping the tRNA anticodon binding site. Proc. Natl. Acad. Sci. USA 88:291295.
80. Moine, H.,, P. Romby,, M. Springer,, M. Grunberg-Manago,, J.-P. Ebel,, C. Ehresmann,, and B. Ehresmann. 1988. Messenger RNA structure and gene regulation at the translational level in Escherichia coli: the case of threonine:tRNAThr lig-ase. Proc. Natl. Acad. Sci. USA 85:78927896.
81. Muramatsu, T.,, K. Nishikawa,, F. Nemoto,, Y. Kuchino,, S. Nishimura,, T. Miyazawa,, and S. Yokoyama. 1988. Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature (London) 336:179181.
82. Muramatsu, T.,, S. Yokoyama,, N. Horie,, A. Matsuda,, T. Ueda,, Z. Yamaizumi,, Y. Kuchino,, S. Nishimura,, and T. Miyazawa. 1988. A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli. J. Biol. Chem. 263:92619267.
83. Musier-Forsyth, K.,, N. Usman,, S. Scaringe,, J. Doudna,, R. Green,, and P. Schimmel. 1991. Specificity for aminoacylation of an RNA helix: an unpaired exocyclic amino group in the minor groove. Science 253:784786.
84. Nameki, N.,, K. Tamura,, H. Himeno,, H. Asahara,, T. Hasa-gawa,, and M. Shimizu. 1992. Escherichia coli tRNA Asp recognition mechanism differing from that of the yeast system. Biochem. Biophys. Res. Commun. 189:856862.
85. Nazarenko, I.,, E. Tinkle-Peterson,, O. D. Zakharova,, O. I. Lavrik,, and O. C. Uhlenbeck. 1992. Recognition nucleotides for human phenylalanyl-tRNA synthetase. Nucleic Acids Res. 20:475478.
86. Nicholas, H. B.,, and W. H. McClain. 1987. An algorithm for discriminating sequences and its application to yeast transfer RNA. Cabios 3:53.
87. Niimi, T.,, O. Nureki,, N. Hayashi,, K. Nishikawa,, K. Watanabe,, and S. Yokoyama. 1993. Recognition of a modified nucleoside residue at position 37 of tRNAIle1 by isoleucyl-tRNA synthetase from E. coli, p. 301. Abstr. 15th International tRNA Workshop.
88. Normanly, J.,, and J. Abelson. 1989. tRNA identity. Annu. Rev. Biochem. 58:10291049.
89. Normanly, J.,, L. G. Kleina,, J.-M. Masson,, J. Abelson,, and J. H. Miller. 1990. Construction of Escherichia coli amber suppressor tRNA genes. III. Determination of tRNA specificity.J. Mol. Biol. 213:719726.
90. Normanly, J.,, J.-M. Masson,, L. G. Kleina,, J. Abelson,, and J. H. Miller. 1986. Construction of two Escherichia coli amber suppressor genes: tRNAPhe (CUA) and tRNACys (CUA). Proc. Natl. Acad. Sci USA 85:65486552.
91. Normanly, J.,, R. C. Ogden,, S. J. Horvath,, and J. Abelson. 1986. Changing the identity of a transfer RNA. Nature (London) 321:213219.
92. Ozeki, H.,, H. Inokuchi,, F. Yamao,, M. Kodaira,, T. Sakano,, T. Ikemura,, and P. R. Schimmel,. 1980. Genetics of nonsense suppressor tRNAs in Escherichia coli, p. 341362. In D. Soil,, J. Abelson,, and P. R. Schimmel (ed.), Transfer RNA: Biological Aspects. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y..
93. Pak, M.,, L. Pallanck,, and L. H. Schulman. 1992. Conversion of a methionine initiator tRNA into a tryptophan-insert-ing elongator tRNA in vivo. Biochemistry 31:33033309.
94. Pak, M.,, and L. H. Schulman. 1993. Unpublished data.
95. Pallanck, L. 1992. Ph.D. thesis, Albert Einstein College of Medicine, Bronx, N.Y..
96. Pallanck, L.,, S. Li,, and L. H. Schulman. 1992. The anticodon and discriminator base are major determinants of cysteine tRNA identity in vivo.J. Biol. Chem. 267:72217223.
97. Pallanck, L.,, and L. H. Schulman. 1991. Anticodon-dependent aminoacylation of a noncognate tRNA with isoleucine, valine, and phenylalanine in vivo. Proc. Natl. Acad. Sci. USA 88:38723876.
98. Park, S. J.,, Y.-M. Hou,, and P. Schimmel. 1989. A single base pair affects binding and catalytic parameters in the molecular recognition of a transfer RNA. Biochemistry 28:27402746.
99.. Park, S. J.,, and P. Schimmel. 1988. Evidence for interaction of an aminoacyl transfer RNA synthetase with a region important for the identity of its cognate transfer RNA. J. Biol. Chem. 263:1652716530.
100. Pelka, H.,, and L. H. Schulman. 1986. Study of the interaction of Escherichia coli methionyl-tRNA synthetase with tRNAfMet using chemical and enzymatic probes. Biochemistry 25:44504456.
101. Perona, J. J.,, R. Swanson,, T. A. Steitz,, and D. Soil. 1988. Overproduction and purification of Escherichia coli tRNAGln and its use in crystallization of the glutaminyl-tRNA synthetase-tRNAGln complex. J. Mol. Biol. 202:121126.
102. Perret, V.,, A. Garcia,, H. Grosjean,, J.-P. Ebel,, C. Florentz,, and R. Giege. 1990. Relaxation of a transfer RNA specificity by removal of modified nucleotides. Nature (London) 344:787789.
103. Petrissant, G.,, M. Boisnard,, and C. Puissant. 1970. Purification d'un tRNA accepteur de la methionine dans le foie de lapin. Biochim. Biophys. Acta 213:223225.
104. Pinck, M.,, P. Yot,, F. Chapeville,, and H. M. Duranton. 1970. A new principle of RNA folding based on pseudoknotting. Nucleic Acids Res. 13:17171731.
105. Piitz, J.,, J. D. Puglisi,, C. Florentz,, and R. Giege. 1991. Identity elements for specific aminoacylation of yeast tRNA Asp by cognate aspartyl-tRNA synthetase. Science 252:16961699.
106. Qiu, M. S.,, Y. X. Jin,, W. Q. Li,, J. R. Bao,, and D. Wang. 1988. Biological function of modified nucleotides in tRNA molecules—synthesis and biological activity of the analogues of yeast alanyl-tRNA with I34 replaced by A34 or G34. Sci. Sin.[B] 31:695701.
107. RajBhandary, U. L. 1988. Genetic code. Modified bases and aminoacylation. Nature (London) 336:112113.
108. RajBhandary, U. L.,, and H. P. Ghosh. 1969. Studies on polynucleotides. XCI. Yeast methionine transfer ribonucleic acid: purification, properties and terminal nucleotide sequences. J. Biol. Chem. 244:11041113.
109. Riddle, D. L.,, and J. Carbon. 1973. Frameshift suppression: a nucleotide addition in the anticodon of a glycine transfer RNA. Nature New Biol. 242:230234.
110. Robertes, J. D.,, J. E. Ladner,, J. T. Finch,, D. Rhodes,, R. S. Brown,, B. F. C. Clark,, and A. Klug. 1974. Structure of yeast phenylalanine tRNA at 3 Å resolution. Nature (London) 250:546551.
111. Roberts, J. W.,, and J. Carbon. 1974. Molecular mechanism for missense suppression in E. coli. Nature (London) 250:412414.
112. Rogers, M. J.,, and D. Söll. 1988. Discrimination between glutaminyl-tRNA synthetase and seryl-tRNA synthetase involves nucleotides in the acceptor helix of tRNA. Proc. Natl. Acad. Sci. USA 85:66276631.
113. Romby, P.,, D. Moras,, M. Bergdoll,, P. Dumas,, V. V. Vlassov,, E. Westhof,, J.-P. Ebel,, and R. Giege. 1985. Yeast tRNA Asp tertiary structure in solution and areas of interaction of the tRNA with aspartyl-tRNA synthetase. A comparative study of the yeast phenylalanine system by phosphate alkylation experiments with ethylnitrosourea. J. Mol. Biol. 184:455471.
114. Rould, M. A.,, J. J. Perona,, D. Söll,, and T. A. Steitz. 1989. Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNAGln and ATP at 2.8 Å resolution. Science 246:11351142.
115. Rould, M. A.,, J. J. Perona,, and T. A. Steitz. 1991. Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase. Nature (London) 352:213218.
116. Ruff, M.,, S. Krishnaswamy,, M. Boeglin,, A. Poterszman,, A. Mitschler,, A. Podjarny,, B. Rees,, J. C. Thierry,, and D. Moras. 1991. Class II aminoacyl-transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNAAsp. Science 252:16821689.
117. Sabban, E. L.,, and O. Bhanot. 1982. The effect of bisulfite-induced C → U transitions on aminoacylation of Escherichia coli glycine tRNA. J. Biol. Chem. 257:47964805.
118. Saks, P.,, J. R. Sampson,, and J. Abelson. 1993. Unpublished data.
119. Sampson, J. R.,, A. B. DiRenzo,, L. S. Behlen,, and O. C. Uhlenbeck. 1989. Nucleotides in yeast tRNAPhe required for the specific recognition by its cognate synthetase. Science 243:13631366.
120. Sampson, J. R.,, A. B. DiRenzo,, L. S. Behlen,, and O. C. Uhlenbeck. 1990. Role of the tertiary nucleotides in the interaction of yeast phenylalanine tRNA with its cognate synthetase. Biochemistry 29:25232537.
121. Sampson, J. R.,, and O. C. Uhlenbeck. 1988. Biochemical and physical characterization of an unmodified yeast phenylalanine transfer RNA in vitro. Proc. Natl. Acad. Sci. USA 85:10331037.
122. Samualsson, T.,, T. Boren,, T.-I. Johanson,, and F. Lustig. 1988. Properties of a transfer RNA lacking modified nucleosides. J. Biol. Chem. 263:1369213699.
123. Saneyoshi, M.,, and S. Nishimura. 1971. Selective inactiva-tion of amino acid acceptor and ribosome binding activities of Escherichia coli tRNA by modification with cyanogen bromide. Biochim. Biophys. Acta 246:123131.
124. Schatz, D.,, R. Leberman,, and F. Eckstein. 1991. Interaction of Escherichia coli tRNASer with its cognate aminoacyl-tRNA synthetase as determined by footprinting with phos-phorothioate containing tRNA transcripts. Proc. Natl. Acad. Sci. USA 88:61326136.
125. Scheinker, V.,, S. F. Beresten,, T. D. Mashkova,, A. M. Mazo,, and L. L. Kisselev. 1981. Role of exposed cytosine residues in aminoacylation activity of tRNATrp. FEBS Lett. 132:349352.
126. Schimmel, P. 1987. Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs. Annu. Rev. Biochem. 56:125158.
127. Schimmel, P. 1989. Parameters for the molecular recognition of transfer RNAs. Biochemistry 28:27472759.
128. Schulman, L. H. 1991. Recognition of tRNAs by aminoacyl-tRNA synthetases. Prog. Nucleic Acid Res. Mol. Biol. 41:2387.
129. Schulman, L. H.,, and J. Abelson. 1988>. Recent excitement in understanding transfer RNA identity. Science 240:15911592.
130. Schulman, L. H.,, and J. P. Goddard. 1973. Loss of methionine acceptor activity resulting from a base change in the anticodon of Escherichia coli formylmethionine transfer ribonucleic acid. J. Biol. Chem. 248:13411345.
131. Schulman L. H.,, and H. Pelka. 1977. Structural requirements for aminoacylation of E. coli formylmethionine tRNA. Biochemistry 16:42564265.
132. Schulman, L. H.,, and H. Pelka. 1983. Anticodon loop size and sequence requirements for recognition of formylmethionine tRNA by methionyl-tRNA synthetase. Proc. Natl. Acad. Sci. USA 80:67556759.
133. Schulman, L. H.,, and H. Pelka. 1985. In vitro conversion of a methionine to a glutamine-acceptor tRNA. Biochemistry 24:73097314.
134. Schulman, L. H.,, and H. Pelka. 1988. Anticodon switching changes the identity of methionine and valine transfer RNAs. Science 242:765768.
135. Schulman, L. H.,, and H. Pelka. 1989. The anticodon contains a major element of the identity of arginine transfer RNAs. Science 246:15951597.
136. Schulman, L. H.,, and H. Pelka. 1990. An anticodon change switches the identity of E. coli tRNAMetm from methionine to threonine. Nucleic Acids Res. 18:285289.
137. Schulman, L. H.,, and H. Pelka. 1991. Unpublished data.
138. Senger, B.,, L. Despons,, P. Walter,, and F. Fasiolo. 1992. The anticodon triplet is not sufficient to confer methionine acceptance to a transfer RNA. Proc. Natl. Acad. Sci. USA 89:1076810771.
139. Seong, B. L.,, C.-P. Lee,, and U. L. RajBhandary. 1989. Suppression of amber codons in vivo as evidence that mutants derived from Escherichia coli initiator tRNA can act at the step of elongation in protein synthesis. J. Biol. Chem. 264:65046508.
140. Seong, B. L.,, and U. L. RajBhandary. 1987. Mutants of Escherichia coli formylmethionine tRNA: a single base change enables initiator tRNA to act as an elongator in vitro. Proc. Natl. Acad. Sci. USA 84:88598863.
141. Shi, J.-P.,, C. Francklyn,, K. Hill,, and P. Schimmel. 1990. A nucleotide that enhances the charging of RNA minihelix sequence variants with alanine. Biochemistry 29:36213626.
142. Shi, J.-P.,, and P. Schimmel. 1991. Aminoacylation of alanine minihelices. J. Biol. Chem. 266:27052708.
143. Shimizu, M. 1991. Personal communication.
144. Shimizu, M.,, H. Asahara,, K. Tamura,, T. Hasegawa,, and H. Himeno. 1992. The role of anticodon bases and the discriminator nucleotide in the recognition of some E. coli tRNAs by their aminoacyl-tRNA synthetases. J. Mol. Evol. 35:436443.
145. Shimura, Y.,, A. Aono,, H. Ozeki,, A. Sabrabhai,, H. Lamfrom,, and J. Abelson. 1972. Mutant tyrosine tRNA of altered amino acid specificity. FEBS Lett. 22:144148.
146. Singer, C. E.,, and G. R. Smith. 1972. Histidine regulation in Salmonella typhimurium.J. Biol. Chem. 247:29893000.
147. Smith, J. D., 1979. Suppressor tRNAs in prokaryotes, p. 109125. In J. E. Celis, and J. D. Smith (ed.), Nonsense Mutations and tRNA Suppressors. Academic Press, Inc., New York.
148. Smith, J. D.,, and J. E. Celis. 1973. Mutant tyrosine transfer RNA that can be charged with glutamine. Nature New Biol. 243:6671.
149. Springer, M.,, M. Graffe,, J. S. Butler,, and M. Grunberg-Manago. 1986. Genetic definition of the translational operator of the threonine-tRNA ligase gene in Escherichia coli. Proc. Natl. Acad. Sci. USA 83:43844388.
150. Springer, M.,, M. Graffe,, J. Dondon,, and M. Grunberg-Manago. 1989. tRNA-like structures and gene regulation at the translational level: a case of molecular mimicry in Escherichia coli. EMBO J. 8:24172424.
151. Springer, M.,, M. Graffe,, J. Dondon,, M. Grunberg-Manago,, P. Romby,, B. Ehresmann,, and C. Ehresmann,, and J.-P. Ebel. 1988. Translational control in E. coli: the case of threonyl-tRNA synthetase. Biosci. Rep. 8:619632.
152. Sprinzl, M.,, T. Hartmann,, J. Weber,, J. Blank,, and R. Zeidler. 1989. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 17:rlrl72.
153. Squires, C.,, and J. Carbon. 1971. Normal and mutant glycine transfer RNAs. Nature New Biol. 233:274277.
154. Stern, L.,, and L. H. Schulman. 1977. Role of anticodon bases in aminoacylation of E. coli methionine tRNAs. J. Biol. Chem. 252:64036408.
155. Swanson, R.,, P. Hoben,, M. Sumner-Smith,, H. Uemura,, L. Watson,, and D. Soil. 1988. Accuracy of in vivo aminoacylation requires proper balance of tRNA and aminoacyl-tRNA synthetase. Science 242:15481551.
156. Sylvers, L. A.,, K. C. Rogers,, M. Shimizu,, E. Ohtsuka,, and D. Soli. 1993. A 2-thiouridine derivative in tRNAGlu is a positive determinant for aminoacylation by Escherichia coli glutamyl-tRNA synthetase. Biochemistry 32:38363841.
157. Tamura, K.,, H. Himeno,, H. Asahara,, T. Hasegawa,, and M. Shimizu. 1992. In vitro study of E. coli tRNAArg and tRNA Lys identity elements. Nucleic Acids Res. 20:23352339.
158. Theobald, A.,, M. Springer,, M. Grunberg-Manago,, J.-P. Ebel,, and R. Giege. 1974. Tertiary structure of Escherichia coli tRNATHR3 in solution and interaction of this tRNA with the cognate threonyl-tRNA synthetase. Eur. J. Biochem. 175:511524.
159. Tinkle-Peterson, E.,, and O. C. Uhlenbeck. 1992. Determination of recognition nucleotides for Escherichia coli phe-nylalanyl-tRNA synthetase. Biochemistry 31:1038010389.
160. Tsai, C.-H.,, and T. W. Dreher. 1991. Turnip yellow mosaic virus RNAs with anticodon loop substitutions that result in decreased valylation fail to replicate efficiently. J. Virol. 65:30603067.
161. Uhlenbeck, O. C. 1986. Structure and function of RNA. Chemica Scripta 26B:97.
162. Varshney, U.,, C.-P. Lee,, and U. L. RajBhandary. 1991. Direct analysis of aminoacylation levels of tRNAs in vivo. Application to studying recognition of Escherichia coli initiator tRNA mutants by glutaminyl-tRNA synthetase. J. Biol. Chem. 266:2471224718.
163. Varshney, U.,, C. P. Lee,, B. L. Seong,, and U. L. RajBhandary. 1991. Mutants of initiator tRNA that function both as initiators and elongators. J. Biol. Chem. 266:1801818024.
164. Varshney, U.,, and U. L. RajBhandary. 1990. Initiation of protein synthesis from a termination codon. Proc. Natl. Acad. Sci. USA 87:15861590.
165. Westhof, E.,, P. Dumas,, and D. Moras. 1985. Crystallographic refinement of yeast aspartic acid transfer RNA. J. Mol. Biol. 184:119145.
166. Yamao, F.,, H. Inokuchi,, A. Cheung,, H. Ozeki,, and D. Söll. 1982. Escherichia coli glutaminyl-tRNA synthetase. J. Biol. Chem. 257:1163911643.
167. Yaniv, M.,, W. R. Folk,, P. Berg,, and L. Soli. 1974. A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J. Mol. Biol. 86:245260.
168. Yams, M. 1972. Intrinsic precision of aminoacyl-tRNA synthesis enhanced through parallel systems of ligands. Nature New Biol. 239:106108.
169. Yarus, M. 1988. tRNA identity: a hair of the dogma that bit us. Cell 55:739741.
170. Yarus, M.,, S. W. Cline,, P. Wier,, L. Breeden,, and R. C. Thompson. 1986. Actions of the anticodon arm in translation on the phenotypes of RNA mutants. J. Mol. Biol. 192:235255.
171. Yarus, M.,, R. G. Knowlton,, and L. Soli,. 1977. Aminoacylation of the ambivalent Su+7 amber suppressor tRNA, p. 391408. In H. Vogel (ed.), Nucleic Acid-Protein Recognition. Academic Press, Inc., New York.
172. Yokoyama, S. 1991. Personal communication.

Tables

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Table 1

Role of the anticodon in recognition of tRNAs

Ec, Sc, L, lysidine; H, Human; Bov, bovine; Q, queuosine; and W, wheat germ.

The tRNA amber and opal suppressors are inactive in vivo.

Anticodon is required for in vivo identity ( ).

, and refer to positions of the three anticodon nucleotides.

See text for additional references.

Based on the fact that serine isoacceptor tRNAs contain base changes at all three positions of the anticodon.

Additional anticodon recognition sites may exist.

Data using the tRNA-like structure from TYMV RNA.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18
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Table 2

amber-suppressor tRNAs classified according to their amino acid acceptor identities

Data from reference and additional references therein.

Also known as (SuUAG).

Also known as (SuUAG), (SuUAG), and (SuUAG), respectively.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18
Generic image for table
Table 3

Role of discriminator base in identity of tRNAs

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18
Generic image for table
Table 4

Summary of known recognition elements for some tRNAs

Additional as yet unidentified recognition elements may also be present. See Table 1 for abbreviations.

See text for additional references.

See Table 3 for additional references.

See Table 1 for additional references.

Citation: Pallanck L, Pak M, Schulman L. 1995. tRNA Discrimination in Aminoacylation, p 371-394. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch18

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