Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process

Microbiology and Molecular Biology Reviews

Volumn 64, Issue 1, 2000, Pages 202-236

  Woese, Carl R ^a   Olsen, Gary J ^a   Ibba, Michael ^b   Söll, Dieter ^c  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; MONOMER; TETRAMER;

ARCHAEBACTERIUM; ENZYME ANALYSIS; FLEXIBACTERACEAE; GENE ORDER; GENE STRUCTURE; GENE TRANSFER; GENETIC ANALYSIS; GENETIC CODE; GRAM POSITIVE BACTERIUM; MOLECULAR EVOLUTION; MYCOPLASMA; NONHUMAN; PHYLOGENY; REVIEW; RICKETTSIA; SPIROCHETE;

ARCHAEA; BACTERIA (MICROORGANISMS); FLEXIBACTERACEAE; MYCOPLASMA; POSIBACTERIA; PROKARYOTA; RICKETTSIA; RICKETTSIALES; SPIROCHAETALES;

EID: 0034053846     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/MMBR.64.1.202-236.2000     Document Type: Review

References (77)

1. Adduce, J., and M. Hoosegow. 1992. MOLPHY: programs for maximum likelihood inference of protein phylogeny. Computer science monographs, no. 27. Institute of Statistical Mathematics, Tokyo, Japan.
2. Andersson, S. G., A. Zomorodipour, J. O. Andersson, T. Sicheritz-Ponten, U. C. Alsmark, R. M. Podowski, A. K. Naslund, A. S. Eriksson, H. H. Winkler, and C. G. Kurland. 1998. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature 396:133-140.
3. Arnez, J. G., and D. Moras. 1997. Structural and functional considerations of the aminoacylation reaction. Trends Biochem. Sci. 22:211-216.
4. Berthet-Colominas, C., L. Seignovert, M. Härtlein, M. Grotli, S. Cusack, and R. Leberman. 1998. The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid. EMBO J. 17:2947-2960.
5. Brown, J. R. 1998. Aminoacyl-tRNA synthetases: evolution of a troubled family, p. 217-230. In J. Wiegel and M. H. W. Adams (ed.), Thermophiles: the keys to molecular evolution and the origin of life? Taylor & Francis, London, United Kingdom.
6. Brown, J. R., F. T. Robb, R. Weiss, and W. F. Doolittle. 1997. Evidence for the early divergence of tryplophanyl- and tyrosyl-tRNA synthetases. J. Mol. Evol. 45:9-16.
7. Brown, J. R., and W. F. Doolittle. 1995. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA 92:2441-2445.
8. Brown, J. R., and W. F. Doolittle. 1999. Gene descent, duplication, and horizontal transfer in the evolution of glutamyl- and glutaminyl-tRNA synthetases. J. Mol. Evol. 49:485-495.
9. Brown, J. R., J. Zhang, and J. E. Hodgson. 1998. A bacterial antibiotic resistance gene with eukaryotic origins. Curr. Biol. 8:R365-R367.
10. Burbaum, J. J., and P. Schimmel. 1991. Structural relationships and the classification of aminoacyl-tRNA synthetases. J. Biol. Chem. 266:16965-16968.
11. Commans, S., and A. Böck. 1999. Selenocysteine inserting tRNAs: an overview. FEMS Microbiol. Rev. 23:335-351.
12. Gln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proc. Natl. Acad. Sci. USA 94:11819-11826.
13. Gln amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. Proc. Natl. Acad. Sci. USA 95:12838-12843.
14. Cusack, S. 1997. Aminoacyl-tRNA synthetases. Curr. Opin. Struct. Biol. 7:881-889.
15. Dennis, P. P. 1997. Ancient ciphers: translation in Archaea. Cell 89:1007-1010.
16. Diaz-Lazcoz, Y., J. C. Aude, P. Nitschke, H. Chiapello, and C. Landes-Devauchelle. 1998. Evolution of genes, evolution of species: the case of aminoacyl-tRNA synthetascs. Mol. Biol. Evol. 15:1548-1561.
17. Doolittle, R. F., and J. Handy. 1998. Evolutionary anomalies among the aminoacyl-tRNA synthetases. Curr. Opin. Genet. Dev. 8:630-636.
18. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
19. Doublié, S., G. Bricogne, C. Gilmore, and C. W. Carter, Jr. 1995. Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure 3:17-31.
20. Eriani, G., M. Delarue, O. Poch, J. Gangloff, and D. Moras. 1990. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347:203-206.
21. Felsenstein, J. 1978. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27:401-410.
22. First, E. A. 1998. Catalysis of aminoacylation by class I and class II aminoacyl-tRNA synthetases, p. 573-607. In M. L. Sinnott (ed.), Comprehensive biological catalysis. Academic Press, Ltd., London, United Kingdom.
23. Freeland, S. J., and L. D. Hurst. 1998. The genetic code is one in a million. J. Mol. Evol. 47:238-248.
24. Gln transamidation pathway among bacteria. A member of the α purple bacteria lacks glutaminyl-tRNA synthetase. J. Biol. Chem. 271:14856-14863.
25. Gamow, G. A. 1954. Possible relation between deoxyribonucleic acid and protein structures. Nature 173:318.
26. Goldman, N. 1993. Further results on error minimization in the genetic code. J. Mol. Evol. 37:662-664.
27. Gray, M. W., B. F. Lang, R. Cedergren, G. B. Golding, C. Lemieux, D. Sankoff, M. Turmel, N. Brossard, E. Delage, T. G. Littlejohn, I. Plante, P. Rioux, D. Saint-Louis, Y. Zhu, and G. Burger. 1998. Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res. 26:865-878.
28. Haig, D., and L. D. Hurst. 1991. A quantitative measure of error minimization in the genetic code. J. Mol. Evol. 33:412-417.
29. Hashimoto, T., L. B. Sanchez, T. Shirakura, M. Muller, and M. Hasegawa. 1998. Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phylogeny. Proc. Natl. Acad. Sci. USA 95:6860-6865.
30. Hamann, C. S., K. R. Sowers, R. S. Lipman, and Y. M. Hou. 1999. An archaeal aminoacyl-tRNA synthetase missing from genomic analysis. J. Bacteriol. 181:5880-5884.
31. Henikoff, S., and J. G. Henikoff. 1992. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89:10915-10919.
32. Ibba, M., J. L. Bono, P. A. Rosa, and D. Söll. 1997. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete, Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA 94:14383-14388.
33. Ibba, M., A. W. Curnow, and D. Söll. 1997. Aminoacyl-tRNA synthesis: divergent routes to a common goal. Trends Biochem. Sci. 22:39-42.
34. Ibba, M., C. H. Losey, Y. Kawarabayasi, H. Kikuchi, S. Bunjun, and D. Söll. 1999. Substrate recognition hy class I lysyl-tRNA synthetases: a molecular basis for gene displacement. Proc. Natl. Acad. Sci. USA 96:418-423.
35. Ibba, M., S. Morgan, A. W. Curnow, D. R. Pridmore, U. C. Vothknecht, W. Gardner, W. Lin, C. R. Woese, and D. Söll. 1997. A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278:1119-1122.
36. Kandler, O. 1994. Cell wall biochemistry in Archaea and its phylogenetic implications. J. Biol. Phys. 20:165-169.
37. Kim, H. S., U. C. Vothknecht, R. Hedderich, I. Celic, and D. Söll. 1998. Sequence divergence of seryl-tRNA synthetases in Archaea. J. Bacteriol. 180:6446-6449.
38. Lamour, V., S. Quevillon, S. Diriong, V. C. N'Guyen, M. Lipinski, and M. Mirande. 1994. Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer. Proc. Natl. Acad. Sci. USA 91:8670-8674.
39. Lenhard, B., O. Orellana, M. Ibba, and I. Weygand-Durasevic. 1999. tRNA recognition and evolution of determinants in seryl-tRNA synthesis. Nucleic Acids Res. 27:721-729.
40. Li, T., D. Graham, C. Stathopoulos, P. Haney, H.-S. Kim, U. Vothknecht, M. Kitabatake, K.-W. Hong, G. Eggertsson, A. W. Curnow, W. Lin, I. Celic, W. Whitman, and D. Söll. 1999. Cysteinyl-tRNA formation: the last puzzle of aminoacyl-tRNA synthesis. FEBS Lett. 462:302-306.
41. Marsh, T. L., C. I. Reich, R. B. Whitelock, and G. J. Olsen. 1994. Transcription tactor IID in the Archaea: Sequences in the Thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes. Proc. Natl. Acad. Sci. USA 81:4180-4184.
42. Martinis, S. A., P. Plateau, J. Cavarelli, and C. Florentz. 1999. Aminoacyl-tRNA synthetases: a family of expanding functions. Mittelwihr, France, October 10-15. EMBO J. 18:4591-4596.
43. Martinis, S. A., P. Plateau, J. Cavarelli, and C. Florentz. 1999. Aminoacyl-tRNA synthetases: a new image for a classical family. Biochimie 81:683-700.
44. Mazauric, M. H., G. Keith, D. Logan, R. Kreutzer, R. Giegé, and D. Kern. 1998. Glycyl-tRNA synthetase from Thermus thermophilus-wide structural divergence with other prokaryotic glycyl-tRNA synthetases and functional inter-relation with prokaryotic and eukaryotic glycylation systems. Eur. J. Biochem. 251:744-757.
45. Nagel, G. M., and R. F. Doolittle. 1995. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J. Mol. Evol. 40:487-498.
46. Nureki, O., D. G. Vassylyev, K. Katayanagi, T. Shimizu, S. Sekine, T. Kigawa, T. Miyazawa, S. Yokoyama, and K. Morikawa. 1995. Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science 267:1958-1965.
47. Olsen, G. J., C. R. Woese, and R. Overbeck. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
48. RajBhandary, U. L. 1997. Once there were twenty. Proc. Natl. Acad. Sci. USA 94:11761-11763.
49. Ribas de Pouplana, L., D. Buechter, N. Y. Sardesai, and P. Schimmel. 1998. Functional analysis of peptide motif for RNA microhelix binding suggests new family of RNA-binding domains. EMBO J. 17:5449-5457.
50. Saks, M. E., J. R. Sampson, and J. Abelson. 1998. Evolution of a transfer RNA gene through a point mutation in the anticodon. Science 279:1665-1670.
51. Schimmel, P., and T. Ripmaster. 1995. Modular design of components of the operational RNA code for alanine in evolution. Trends Biochem. Sci. 20: 333-334.
52. Shiba, K., H. Motegi, M. Yoshida, and T. Noda. 1998. Human asparaginyl-tRNA synthetase: molecular cloning and the inference of the evolutionary history of Asx-tRNA synthetase family. Nucleic Acids Res. 26:5045-5051.
53. Siatecka, M., M. Rozek, J. Barciszewski, and M. Mirande. 1998. Modular evolution of the Glx-tRNA synthetase family - rooting of the evolutionary tree between the bacteria and archaea/eukarya branches. Eur. J. Biochem. 256:80-87.
54. Simos, G., A. Sauer, F. Fasiolo, and E. C. Hurt. 1998. A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases. Mol. Cell 1:235-242.
55. Simpson, G. G. 1944. Tempo and mode in evolution. Columbia University Press, New York, N.Y.
56. Sissler, M., C. Delorme, J. Bond, S. D. Elrlich, P. Renault, and C. Francklyn. 1999. An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc. Natl. Acad. Sci. USA 96:8985-8990.
57. Söll, D., and M. Ibba. Aminoacyl-tRNA synthesis. Annu. Rev. Biochem., in press.
58. Söll, D., and U. L. RajBhandary. 1995. tRNA: structure, biosynthesis and function. ASM Press, Washington, D.C.
59. Sonneborn, T. M. 1965. Degeneracy of the genetic code: extent, nature and genetic implications, p. 377-397. In V. Bryson and J. H. Vogel (ed.), Evolving genes and proteins. Academic Press, Inc., New York, N.Y.
60. Stathopoulos, C., T. Li, R. Longman, U. C. Vothkneeht, H. Becker, M. Ibba, and D. Söll. 2000. One polypeptide with two aminoacyl-tRNA synthetase activities. Science 287:479-482.
61. Swofford, D. L. 1999. PAUP 4.0: phylogenetic analysis using parsimony (and other methods). Sinauer Associates, Sunderland, Mass.
62. Taupin, C. M., and R. Leberman. 1999. Archaebacterial seryl-tRNA synthetases: adaptation to extreme environments and evolutionary analysis. J. Mol. Evol. 48:408-420.
63. Tumbula, D., U. C. Vothknecht, H. S. Kim, M. Ibba, B. Min, T. Li, J. T. Pelaschier, C. Stathopoulos, H. Becker, and D. Söll. 1999. Archaeal aminoacyl-tRNA synthesis: diversity replaces dogma. Genetics 152:1269-1276.
64. Wakasugi, K., and P. Schimmel. 1999. Two distinct cytokines released from a human aminoacyl-tRNA synthetase. Science 284:147-151.
65. Watanabe, K., and S. Osawa. 1995. In D. Söll and U. RajBhandary (ed.), tRNA: structure, biosynthesis, and function. ASM Press, Washington, D.C.
66. Woese, C. R. 1965. On the evolution of the genetic code. Proc. Natl. Acad. Sci. USA 54:1546-1552.
67. Woese, C. R. 1982. Archaebacteria and cellular origins: an overview. Zertbl. Bakteriol. Mikrobiol. Hyg. I Abt. Orig. C 3:1-17.
68. Woese, C. R. 1987. Bacterial evolution. Microbiol. Rev. 51:221-271.
69. Woese, C. R. 1998. The universal ancestor. Proc. Natl. Acad. Sci. USA 95:6854-6859.
70. Woese, C. R., D. H. Dugre, S. A. Dugre, M. Kondo, and W. C. Saxinger. 1966. On the fundamental nature and evolution of the genetic code. Cold Spring Harbor Symp. Quant. Biol. 31:723-736.
71. Woese, C. R., D. H. Dugre, W. C. Saxinger, and S. A. Dugre. 1966. The molecular basis for the genetic code. Proc. Natl. Acad. Sci. USA 55:966-974.
72. Woese, C. R., and G. E. Fox. 1977. The concept of cellular evolution. J. Mol. Evol. 10:1-6.
73. Woese, C. R., O. Kandler, and M. L. Wheelis. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc. Natl. Acad. Sci. USA 87:4576-4579.
74. Woese, C. R., L. Mandelco, D. Yang, R. Gherna, and M. T. Madigan. 1990. The case for relationship of the flavobacteria and their relatives to the green sulfur bacteria. Syst. Appl. Microbiol. 13:258-262.
75. Wolf, Y. I., L. Aravind, N. V. Grishin, and E. V. Koonin. 1999. Evolution of aminoacyl-tRNA synthetases-analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9:689-710.
76. Yarus, M. 1998. Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J. Mol. Evol. 47:109-117.
77. Yarus, M., and M. Illangasekare. 1999. Aminoacyl-tRNA synthetases and self acylating ribozymes, p. 183-196. In R. F. Gesteland, T. R. Cech, and J. F. Atkins (ed.), The RNA world. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.