Evolution of a transfer RNA gene through a point mutation in the anticodon

Science

Volumn 279, Issue 5357, 1998, Pages 1665-1670

  Saks, Margaret E ^a,b   Sampson, Jeffrey R ^a,c   Abelson, John ^a  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b UNIVERSITY OF OREGON   (United States)

^c HEWLETT PACKARD LABORATORIES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ARGININE; DNA; MESSENGER RNA; NUCLEOTIDE; SYNTHETASE; THREONINE; TRANSFER RNA;

AMINOACYLATION; ANTICODON; ARTICLE; CODON; ESCHERICHIA COLI; EVOLUTION; GENE; HAEMOPHILUS INFLUENZAE; NONHUMAN; NORTHERN BLOTTING; PHYLOGENY; POINT MUTATION; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE HOMOLOGY;

ANTICODON; ARGININE; BASE COMPOSITION; BASE SEQUENCE; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENES, BACTERIAL; HAEMOPHILUS INFLUENZAE; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; NUCLEIC ACID CONFORMATION; POINT MUTATION; POLYMERASE CHAIN REACTION; RECOMBINATION, GENETIC; RNA, BACTERIAL; RNA, TRANSFER, ARG; RNA, TRANSFER, THR; TEMPERATURE; THREONINE; TRANSFORMATION, BACTERIAL;

ESCHERICHIA COLI; HAEMOPHILUS INFLUENZAE; NEGIBACTERIA;

EID: 0032513368     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.279.5357.1665     Document Type: Article

References (76)

1. R. Giegé, J. D. Puglisi, C. Florentz, Prog. Nucleic Acid Res. Mol. Biol. 45, 129 (1993).
2. W. H. McClain, J. Mol. Biol. 234, 257 (1993).
3. M. E. Saks, J. R. Sampson, J. N. Abelson, Science 263, 191 (1994).
4. S. A. Martinis and P. Schimmel, in tRNA: Structure, Biosynthesis, and Function, D. Söll and U. L. Raj-Bhandary, Eds. (ASM Press, Washington, DC, 1995), pp. 349-370.
5. L. Pallanck, M. Pak, L. H. Schulman, ibid., pp. 371-394.
6. M. Eigen et al., Science 244, 673 (1989).
7. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
8. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
9. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
10. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
11. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
12. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
13. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
14. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
15. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
16. A. M. Weiner and N. Maizels, Proc. Natl. Acad. Sci. U.S.A. 84, 7383 (1987); N. Maizels and A. Weiner, ibid. 91, 6729 (1994); P. Schimmel and B. Henderson, ibid., p. 11283; P. Schimmel, R. Giegé, D. Moras, S. Yokoyama, ibid. 90, 8763 (1993); S. Rodin, S. Ohno, A. Rodin, ibid., p. 4723; S. N. Rodin and S. Ohno, ibid. 94, 5183 (1997); P. Schimmel and L. Ribas de Pouplana, Cell 81, 983 (1995); M. Di Giulio, J. Theor. Biol. 171, 303 (1994); W. Möller and G. M. G. Janssen, Biochimie 72, 361 (1990); J. C. Lacey and M. P. Staves, Origins Life Evol. Biosphere 20, 303 (1990).
17. D. P. Bloch, B. McArthur, S. Mirrop, Biosystems 17, 209 (1985); M. Di Giulio, ibid. 177, 95 (1995).
18. D. P. Bloch, B. McArthur, S. Mirrop, Biosystems 17, 209 (1985); M. Di Giulio, ibid. 177, 95 (1995).
19. H. F. Noller, in The RNA World, R. F. Gesteland and J. F. Atkins, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993), pp. 137-156; S. Rodin, A. Rodin, S. Ohno, Proc. Natl. Acad. Sci. U.S.A. 93, 4537 (1996); W. Möller and G. M. C. Janssen, J. Mol. Evol. 34, 471 (1992); T. P. Dick and W. W. A. Schamel, ibid. 41, 1 (1995).
20. H. F. Noller, in The RNA World, R. F. Gesteland and J. F. Atkins, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993), pp. 137-156; S. Rodin, A. Rodin, S. Ohno, Proc. Natl. Acad. Sci. U.S.A. 93, 4537 (1996); W. Möller and G. M. C. Janssen, J. Mol. Evol. 34, 471 (1992); T. P. Dick and W. W. A. Schamel, ibid. 41, 1 (1995).
21. H. F. Noller, in The RNA World, R. F. Gesteland and J. F. Atkins, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993), pp. 137-156; S. Rodin, A. Rodin, S. Ohno, Proc. Natl. Acad. Sci. U.S.A. 93, 4537 (1996); W. Möller and G. M. C. Janssen, J. Mol. Evol. 34, 471 (1992); T. P. Dick and W. W. A. Schamel, ibid. 41, 1 (1995).
22. H. F. Noller, in The RNA World, R. F. Gesteland and J. F. Atkins, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993), pp. 137-156; S. Rodin, A. Rodin, S. Ohno, Proc. Natl. Acad. Sci. U.S.A. 93, 4537 (1996); W. Möller and G. M. C. Janssen, J. Mol. Evol. 34, 471 (1992); T. P. Dick and W. W. A. Schamel, ibid. 41, 1 (1995).
23. W. M. Fitch and K. Upper, Cold Spring Harbor Symp. Quant. Biol. 52, 759 (1987).
24. R. J. Cedergren, B. LaRue, D. Sankoff, G. Lapalme, H. Grosjean, Proc. Natl. Acad. Sci. U.S.A. 77, 2791 (1980); C. Squires and J. Carbon, Nature New Biol. 233, 274 (1971); M. P. Staves, D. P. Bloch, J. J. C. Lacey, Z. Naturforsch. Teil C Biochem. Biophys. Biol. Virol. 42, 129 (1987); M. P. Staves, D. P. Bloch, J. C. Lacey, Origins Life Evol. Biosphere 18, 97 (1988).
25. R. J. Cedergren, B. LaRue, D. Sankoff, G. Lapalme, H. Grosjean, Proc. Natl. Acad. Sci. U.S.A. 77, 2791 (1980); C. Squires and J. Carbon, Nature New Biol. 233, 274 (1971); M. P. Staves, D. P. Bloch, J. J. C. Lacey, Z. Naturforsch. Teil C Biochem. Biophys. Biol. Virol. 42, 129 (1987); M. P. Staves, D. P. Bloch, J. C. Lacey, Origins Life Evol. Biosphere 18, 97 (1988).
26. R. J. Cedergren, B. LaRue, D. Sankoff, G. Lapalme, H. Grosjean, Proc. Natl. Acad. Sci. U.S.A. 77, 2791 (1980); C. Squires and J. Carbon, Nature New Biol. 233, 274 (1971); M. P. Staves, D. P. Bloch, J. J. C. Lacey, Z. Naturforsch. Teil C Biochem. Biophys. Biol. Virol. 42, 129 (1987); M. P. Staves, D. P. Bloch, J. C. Lacey, Origins Life Evol. Biosphere 18, 97 (1988).
27. R. J. Cedergren, B. LaRue, D. Sankoff, G. Lapalme, H. Grosjean, Proc. Natl. Acad. Sci. U.S.A. 77, 2791 (1980); C. Squires and J. Carbon, Nature New Biol. 233, 274 (1971); M. P. Staves, D. P. Bloch, J. J. C. Lacey, Z. Naturforsch. Teil C Biochem. Biophys. Biol. Virol. 42, 129 (1987); M. P. Staves, D. P. Bloch, J. C. Lacey, Origins Life Evol. Biosphere 18, 97 (1988).
28. S. A. Benner, M. A. Cohen, G. H. Gonnet, D. B. Berkowitz, K. P. Johnsson, in The RNA World, R. F. Gesteland and J. F. Atkins, Eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 1993), pp. 27-70.
29. M. Sprinzl, C. Steegborn, F. Hubel, S. Steinberg, Nucleic Acids Res. 24, 68 (1996).
30. Y. Komine, T. Adahi, H. Inokuchi, H. Ozeki, J. Mol. Biol. 212, 579 (1990).
31. F. R. Blattner, V. D. Burland, G. Plunkett III, H. J. Sofia, D. L. Daniels, Nucleic Acids Res. 21, 5408 (1993); F. R. Blattner et al., Science 277, 1453 (1997).
32. F. R. Blattner, V. D. Burland, G. Plunkett III, H. J. Sofia, D. L. Daniels, Nucleic Acids Res. 21, 5408 (1993); F. R. Blattner et al., Science 277, 1453 (1997).
33. R. D. Fleischmann et al., Science 269, 496 (1995).
34. Homologous regions of type I tRNAs were aligned according to the standard tRNA secondary structure [D. H. Gauss, F. Grüter, M. Sprinzl, in Transfer RNA: Structure, Properties, and Recognition, P. R. Schimmel, D. Söll, J. N. Abelson, Eds. (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1979), pp. 518-519]. Type II tRNAs (serine, leucine, and tyrosine) were excluded because their extra stem-loop structures simply relegate them to a cluster apart from the more common type I tRNAs.
35. G. J. Olsen, C. R. Woese, R. Overbeek, J. Bacteriol. 176, 1 (1994); H. Ochman and A. C. Wilson, J. Mol. Evol. 26, 74 (1987).
36. G. J. Olsen, C. R. Woese, R. Overbeek, J. Bacteriol. 176, 1 (1994); H. Ochman and A. C. Wilson, J. Mol. Evol. 26, 74 (1987).
37. In a gene tree constructed with the Fitch-Margoliash method [W. M. Fitch and E. Margoliash, Science 155, 279 (1967)] from maximum-likelihood distances [J. Felsenstein, Phytogeny Inference Package (PHYLIP)], the degree of certainty for the distal nodes averaged 85.5% but the proximal nodes were typically poorly resolved.
38. In a gene tree constructed with the Fitch-Margoliash method [W. M. Fitch and E. Margoliash, Science 155, 279 (1967)] from maximum-likelihood distances [J. Felsenstein, Phytogeny Inference Package (PHYLIP)], the degree of certainty for the distal nodes averaged 85.5% but the proximal nodes were typically poorly resolved.
39. M. E. Saks and J. R. Sampson, J. Mol. Evol. 40, 509 (1995).
40. M. A. Rould, J. J. Perona, T. A. Steitz, Nature 352, 213 (1991); M. Ruff et al., Science 252, 1682 (1991); S. Cusack, A. Yaremchuk, M. Tukalo, EMBO J. 15, 6321 (1996).
41. M. A. Rould, J. J. Perona, T. A. Steitz, Nature 352, 213 (1991); M. Ruff et al., Science 252, 1682 (1991); S. Cusack, A. Yaremchuk, M. Tukalo, EMBO J. 15, 6321 (1996).
42. M. A. Rould, J. J. Perona, T. A. Steitz, Nature 352, 213 (1991); M. Ruff et al., Science 252, 1682 (1991); S. Cusack, A. Yaremchuk, M. Tukalo, EMBO J. 15, 6321 (1996).
43. L. H. Schulman and H. Pelka, Science 242, 765 (1988).
44. _, ibid. 246, 1595 (1989).
45. _, Nucleic Acids Res. 18, 285 (1990).
46. J. Normanly, L. G. Kleina, J.-M. Masson, J. Abelson, J. H. Miller, J. Mol. Biol. 213, 719 (1990); L. Pallanck, S. Li, L. H. Schulman, J. Biol. Chem. 267, 7221 (1992); S. Li, H. Pelka, L. H. Schulman, ibid. 268, 18335 (1993); M. Pak, L. Pallanck, L. H. Schulman, Biochemistry 31, 3303 (1992).
47. J. Normanly, L. G. Kleina, J.-M. Masson, J. Abelson, J. H. Miller, J. Mol. Biol. 213, 719 (1990); L. Pallanck, S. Li, L. H. Schulman, J. Biol. Chem. 267, 7221 (1992); S. Li, H. Pelka, L. H. Schulman, ibid. 268, 18335 (1993); M. Pak, L. Pallanck, L. H. Schulman, Biochemistry 31, 3303 (1992).
48. J. Normanly, L. G. Kleina, J.-M. Masson, J. Abelson, J. H. Miller, J. Mol. Biol. 213, 719 (1990); L. Pallanck, S. Li, L. H. Schulman, J. Biol. Chem. 267, 7221 (1992); S. Li, H. Pelka, L. H. Schulman, ibid. 268, 18335 (1993); M. Pak, L. Pallanck, L. H. Schulman, Biochemistry 31, 3303 (1992).
49. J. Normanly, L. G. Kleina, J.-M. Masson, J. Abelson, J. H. Miller, J. Mol. Biol. 213, 719 (1990); L. Pallanck, S. Li, L. H. Schulman, J. Biol. Chem. 267, 7221 (1992); S. Li, H. Pelka, L. H. Schulman, ibid. 268, 18335 (1993); M. Pak, L. Pallanck, L. H. Schulman, Biochemistry 31, 3303 (1992).
50. W. H. McClain, K. Foss, R. A. Jenkins, J. Schneider, Proc. Natl. Acad. Sci. U.S.A. 87, 9260 (1990).
51. R. Chattapadhyay, H. Pelka, L. H. Schulman, Biochemistry 29, 4263 (1990); L. Pallanck and L. H. Schulman, Proc. Natl. Acad. Sci. U.S.A. 88, 3872 (1991).
52. R. Chattapadhyay, H. Pelka, L. H. Schulman, Biochemistry 29, 4263 (1990); L. Pallanck and L. H. Schulman, Proc. Natl. Acad. Sci. U.S.A. 88, 3872 (1991).
53. J. Normanly, J. M. Masson, L. G. Kleina, J. Abelson, J. H. Miller, Proc. Natl. Acad. Sci. U.S.A. 83, 6548 (1986); J. Normanly, R. C. Ogden, S. J. Horvath, J. Abelson, Nature 321, 213 (1986).
54. J. Normanly, J. M. Masson, L. G. Kleina, J. Abelson, J. H. Miller, Proc. Natl. Acad. Sci. U.S.A. 83, 6548 (1986); J. Normanly, R. C. Ogden, S. J. Horvath, J. Abelson, Nature 321, 213 (1986).
55. C. M. Hamilton, M. Aldea, B. K. Washburn, P. Babitzke, S. R. Kushner, J. Bacteriol. 171, 4617 (1989).
56. K. Gabriel, J. Schneider, W. H. McClain, Science 271, 195 (1996).
57. Transfer RNA genes are named by the three-letter abbreviation for the amino acid that they accept and their three anticodon nucleotides.
58. Thr-Drd I gene.
59. UGU gene was obtained by PCR amplification of a portion of the tuf B operon (nucleotides 40,152 to 41,148 of GenBank accession number U00006) followed by digestion with the restriction endonucleases BstU I and Aci I (New England BioLabs). The other tRNA genes were constructed from six overlapping DNA oligonucleotides that included a T7 promoter at the 5′ end and a BstN I restriction endonuclease site at the 3′ end.
60. UGU gene was obtained by PCR amplification of a portion of the tuf B operon (nucleotides 40,152 to 41,148 of GenBank accession number U00006) followed by digestion with the restriction endonucleases BstU I and Aci I (New England BioLabs). The other tRNA genes were constructed from six overlapping DNA oligonucleotides that included a T7 promoter at the 5′ end and a BstN I restriction endonuclease site at the 3′ end.
61. K. Tamura, H. Himeno, H. Asahara, T. Hasegawa, M. Shimizu, Nucleic Acids Res. 20, 2335 (1992).
62. Aminoacyl-tRNA synthetases for each amino acid are abbreviated with the standard three-letter amino acid abbreviation followed by RS (for example, arginyl-tRNA synthetase, ArgRS).
63. T. Hasegawa et al., Biochem. Biophys. Res. Commun. 184, 478 (1992).
64. Y. Nakamura, T. Gojobori, T. Ikemura, Nucleic Acids Res. 25, 244 (1997).
65. T. Ikemura, J. Mol. Biol. 146, 1 (1981).
66. R. B. Loftfield, Biochem. J. 89, 82 (1963).
67. W. H. McClain and H. B. Nicholas, J. Mol. Biol. 194, 635 (1987).
68. T. H. Jukes, S. Osawa, A. Muto, Nature 325, 668 (1987); _, N. Lehman, Cold Spring Harbor Symp. Quant. Biol. 52, 769 [1987); S. Osawa, T. H. Jukes, K. Watanabe, A. Muto, Microbiol. Rev. 56, 229 (1992).
69. T. H. Jukes, S. Osawa, A. Muto, Nature 325, 668 (1987); _, N. Lehman, Cold Spring Harbor Symp. Quant. Biol. 52, 769 [1987); S. Osawa, T. H. Jukes, K. Watanabe, A. Muto, Microbiol. Rev. 56, 229 (1992).
70. T. H. Jukes, S. Osawa, A. Muto, Nature 325, 668 (1987); _, N. Lehman, Cold Spring Harbor Symp. Quant. Biol. 52, 769 [1987); S. Osawa, T. H. Jukes, K. Watanabe, A. Muto, Microbiol. Rev. 56, 229 (1992).
71. DNA templates were obtained from cloned genes by PCR amplification with Vent polymerase (New England BioLabs) and transcribed with T7-RNA polymerase. The products were gel-purified [J. R. Sampson and M. E. Saks, Nucleic Acids Res. 21, 4467 (1993)].
72. Partially purified E. coli ThrRS and ArgRS were obtained from an S100 extract prepared through the DEAE-cellulose chromatographic step [K. H. Muench and P. Berg, in Procedures in Nucleic Acid Research, G. L. Cantoni and D. R. Davies, Eds. (Harper & Row, New York, 1966), pp. 375-383]. The specific activities per milligram of protein for ThrRS and ArgRS were 3.4 and 5.7, respectively. One unit is defined as the amount of synthetase required to aminoacylate 1.0 nmol of the cognate tRNA per minute at 5 μM tRNA under the reaction conditions described in Table 1.
73. Genetics Computer Group, Program Manual for the Wisconsin Package, version 8, September 1994.
74. The knockout strain was transformed with the relevant p177 constructs and grown on LB/Kan plates at 30°C. Dilute cell suspensions were made from the resulting colonies. A 1-μl sample of each cell suspension (6700 to 19,200 cells) was pipetted onto the test plates and incubated at the appropriate temperature for 24 hours.
75. R→T(U20), positions 38 to 62. Band intensities were quantified with a Molecular Dynamics Phosphorlmager and associated software.
76. We thank S. R. Kushner, V. Maples, and H. Shizuya for providing E. coli strains and for guidance in constructing the knockout strain, and A. Zera, F. Gould, and M. Lynch for thoughtful comments. Supported by NIH grant GM 48560.