A view into the origin of life: Aminoacyl-tRNA synthetases

Cellular and Molecular Life Sciences

Volumn 57, Issue 6, 2000, Pages 865-870

  Ribas De Pouplana, L ^a   Schimmel, P ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

SYNTHETASE; TRANSFER RNA;

ENZYME STRUCTURE; LIFE; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NOTE; PRECURSOR;

EID: 0033912919     PISSN: 1420682X     EISSN: None     Source Type: Journal    
DOI: 10.1007/pl00000729     Document Type: Note

References (87)

1. 1 Joyce G. F. and Orgel L. E. (1993) Prospects for understanding the origin of the RNA world. In: The RNA World, pp. 1 26, Gesteland R. F. and Atkins J. F. (eds), Cold Spring Harbor Laboratory Press, New York
2. 2 Wachtershauser G. (1988) Before enzymes and templates: theory of surface metabolism. Microbiol. Rev. 52: 452-484
3. 3 Wachtershauser G. (1990) Evolution of the first metabolic cycles. Proc. Natl. Acad. Sci. USA 87: 200-204
4. 4 Wachtershauser G. (1992) Groundworks for an evolutionary biochemistry: the iron-sulphur world. Prog. Biophys. Mol. Biol. 58: 85-201
5. 5 Lazcano A. and Miller S. L. (1996) The origin and early evolution of life: prebiotic chemistry, the pre-RNA world, and time. Cell 85: 793-798
6. 6 Lazcano A. and Miller S. L. (1999) On the origin of metabolic pathways. J. Mol. Evol. 49: 424-431
7. 7 De Duve C. (1991) In: Blueprint for a Cell: The Nature and Origin of Life, Neil Patterson, Burlington, NC
8. 8 Szathmary E. and Smith J. M. (1995) The major evolutionary transitions. Nature 374: 227-232
9. 9 Crick F. H. (1968) The origin of the genetic code. J. Mol. Biol. 38: 367-379
10. 10 Kruger K., Grabowski P. J., Zaug A. J., Sands J., Gottschling D. E. and Cech T. R. (1982) Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell 31: 147-157
11. 11 Guerrier-Takada C., Gardiner K., Marsh T., Pace N. and Altman S. (1983) The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35: 849-857
12. 12 Ellington A. D. and Szostak J. W. (1990) In vitro selection of RNA molecules that bind specific ligands. Nature 346: 818-822
13. 13 Beaudry A. A. and Joyce G. F. (1992) Directed evolution of an RNA enzyme. Science 257: 635-641
14. 14 Bartel D. P. and Szostak J. W. (1993) Isolation of new ribozymes from a large pool of random sequences. Science 261: 1411-1418
15. 15 Schimmel P., Giegé R., Moras D. and Yokoyama S. (1993) An operational RNA code for amino acids and possible relationship to genetic code. Proc. Natl. Acad. Sci. USA 90: 8763-8768
16. 16 Wong J. T. (1975) A co-evolution theory of the genetic code. Proc. Natl. Acad. Sci. USA 72: 1909-1912
17. 17 Schimmel P. and Henderson B. (1994) Possible role of aminoacyl-RNA complexes in noncoded peptide synthesis and origin of coded synthesis. Proc. Natl. Acad. Sci. USA 91: 11283-11286
18. 18 Di Giulio M. (1998) Reflections on the origin of the genetic code: a hypothesis. J. Theor. Biol. 191: 191-196
19. 19 Knight R. D., Freeland S. J. and Landweber L. F. (1999) Selection, history and chemistry: the three faces of the genetic code. Trends Biochem. Sci. 24: 241-247
20. 20 Szathmary E. (1999) The origin of the genetic code: amino acids as cofactors in an RNA world. Trends Genet. 15: 223-229
21. 21 Schimmel P. and Kelley S. O. (2000) Exiting an RNA world. Nat. Struct. Biol. 7: 5-7
22. 22 Illangasekare M. and Yarus M. (1999) A tiny RNA that catalyzes both aminoacyl-RNA and peptidyl-RNA synthesis. RNA 5: 1482-1489
23. 23 Illangasekare M., Sanchez G., Nickles T. and Yarus M. (1995) Aminoacyl-RNA synthesis catalyzed by an RNA. Science 267: 643-647
24. 24 Lee N., Bessho Y., Wei K., Szostak J. W. and Suga H. (2000) Ribozyme-catalyzed tRNA aminoacylation. Nat. Struct. Biol. 7: 28-33
25. 25 Aberg A., Yaremchuk A., Tukalo M., Rasmussen B. and Cusack S. (1997) Crystal structure analysis of the activation of histidine by Thermus thermophilus histidyl-tRNA synthetase. Biochemistry 36: 3084-3094
26. 26 Berthet-Colominas C., Seignovert L., Hartlein M., Grotli M., Cusack S. and Leberman R. (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
27. 27 Biou V., Yaremchuk A., Tukalo M. and Cusack S. (1994) The 2.9 Å crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Science 263: 1404-1410
28. 28 Brakhage A. A., Wozny M. and Putzer H. (1990) Structure and nucleotide sequence of the Bacillus subtilis phenylalanyl-tRNA synthetase genes. Biochimie 72: 725-734
29. 29 Brick P., Bhat T. N. and Blow D. M. (1989) Structure of tyrosyl-tRNA synthetase refined at 2.3 Å resolution. Interaction of the enzyme with the tyrosyl adenylate intermediate. J. Mol. Biol. 208: 83-98
30. 30 Brunie S., Zelwer C. and Risler J. L. (1990) Crystallographic study at 2.5 Å resolution of the interaction of methionyl-tRNA synthetase from Escherichia coli with ATP. J. Mol. Biol. 216: 411-424
31. 31 Cavarelli J., Rees B., Ruff M., Thierry J. C. and Moras D. (1993) Yeast tRNA(Asp) recognition by its cognate class II aminoacyl-tRNA synthetase. Nature 362: 181-184
32. 32 Cura V., Kern D., Mitschler A. and Moras D. (1995) Crystallization of threonyl-tRNA synthetase from Thermus thermophilus and preliminary crystallographic data. FEBS Lett. 374: 110-112
33. 33 Cusack S., Yaremchuk A. and Tukalo M. (1996) The crystal structure of the ternary complex of T. thermophilus seryl-tRNA synthetase with tRNA(Ser) and seryl-adenylate analogue reveals a conformational switch in the active site. EMBO J. 15: 2834-2842
34. 34 Cusack S., Yaremchuk A. and Tukalo M. (1996) The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. EMBO J. 15: 6231-6334
35. 35 Cusack S. (1995) Eleven down and nine to go. Nat. Struct. Biol. 2: 824-831
36. 36 Dessen P., Ducruix A., May R. P. and Blanquet S. (1990) Low-resolution structure of the tetrameric phenylalanyl-tRNA synthetase from Escherichia coli. A neutron small-angle scattering study of hybrids composed of protonated and deuterated protomers. Biochemistry 29: 3039-3046
37. 37 Doublie S., Bricogne G., Gilmore C. and Carter C. W. Jr (1995) Tryptophanyl-tRNA synthetase crystal structure reveals an unexpected homology to tyrosyl-tRNA synthetase. Structure 3: 17-31
38. 38 Fujinaga M, Berthet-Colominas C., Yaremchuk A. D., Tukalo M. A. and Cusack S. (1993) Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5Å resolution. J. Mol. Biol. 234: 222-233
39. 39 Delarue M., Poterszman A., Nikonov S., Garber M., Moras D. and Thierry J. C. (1994) Crystal structure of a prokaryotic aspartyl tRNA-synthetase. EMBO J. 14: 3219-3229
40. 40 Logan D. T., Mazauric M. H., Kern D. and Moras D. (1995) Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus. EMBO J. 14: 4156-4167
41. 41 Onesti S., Miller A. D. and Brick P. (1995) The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli. Structure 3: 163-176
42. 42 Nureki O., Vassylyev D. G., Katayanagi K., Shimizu T., Sekine S., Kigawa T. et al. (1995) Architectures of class-defining and specific domains of glutamyl-tRNA synthetase. Science 267: 1958-1965
43. 43 Nureki O., Vassylyev D. G., Tateno M., Shimada A., Nakama T., Fukai S. et al. (1998) Enzyme structure with two catalytic sites for double-sieve selection of substrate. Science 280: 578-582
44. 44 Reshetnikova L., Chernaya M., Ankilova V., Lavrik O., Delarue M., Thierry J. C. et al. (1992) Three-dimensional structure of phenylalanyl-transfer RNA synthetase from Thermus thermophilus HB8 at 0.6-nm resolution. E. J. Biochem. 208: 411-417
45. 45 Rould M. A., Perona J. J., Söll D. and Steitz T. A. (1989) Structure of E. coli glutaminyl-tRNA synthetase complexed with tRNA(Gln) and ATP at 2.8 Å resolution. Science 246: 1135-1142
46. 46 Ruff M., Krishnaswamy S., Boeglin M., Poterzman A., Mitschler A., Podjarny A. et al. (1991) Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNA(Asp). Science 252: 1682-1689
47. 47 Sankaranarayanan R., Dock-Bregeon A. C., Romby P., Caillet J., Springer M., Rees B. et al. (1999) The structure of threonyl-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site. Cell 97: 371-381
48. 48 Jasin M., Regan L. and Schimmel P. (1983) Modular arrangement of functional domains along the sequence of an aminoacyl tRNA synthetase. Nature 306: 441-447
49. 49 Cusack S. (1997) Aminoacyl-tRNA synthetases. Curr. Opin. Struct. Biol. 7: 881-889
50. 50 Moras D. (1992) Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem. Sci. 17: 159-164
51. 51 Schimmel P. and Ribas de Pouplana L. (1995) Transfer RNA: from minihelix to genetic code. Cell 81: 983-986
52. 52 Hountondji C., Dessen P. and Blanquet S. (1986) Sequence similarities among the family of aminoacyl-tRNA synthetases. Biochimie 68: 1071-1078
53. 53 Eriani G., Delarue M., Poch O., Gangloff J. and Moras D. (1990) Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347: 203-206
54. 54 Webster T., Tsai H., Kula M., Mackie G. A. and Schimmel P. (1984) Specific sequence homology and three-dimensional structure of an aminoacyl transfer RNA synthetase. Science 226: 1315-1317
55. 55 Ludmerer S. W. and Schimmel P. (1987) Gene for yeast glutamine tRNA synthetase encodes a large amino-terminal extension and provides a strong confirmation of the signature sequence for a group of the aminoacyl-tRNA synthetases. J. Biol. Chem. 262: 10801-10806
56. 56 Cavarelli J., Rees B., Thierry J. C. and Moras D. (1993) Yeast aspartyl-tRNA synthetase: a structural view of the aminoacylation reaction. Biochimie 75: 1117-1123
57. 57 Schimmel P. and Ribas de Pouplana L. (1999) Genetic code origins: experiments confirm phylogenetic predictions and may explain a puzzle. Proc. Natl. Acad. Sci. USA 96: 327-328
58. 58 Lamour V., Quevillon S., Diriong S., N'Guyen V. C., Lipinski M. and Mirande M. (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
59. 59 Kong L., Fromant M., Blanquet S. and Plateau P. (1991) Evidence for a new Escherichia coli protein resembling a lysyl-tRNA synthetase. Gene 108: 163-164
60. 60 Sissler M., Delorme C., Bond J., Ehrlich S. D., Renault P. and Francklyn C. (1999) An aminoacyl-tRNA synthetase paralog with a catalytic role in histidine biosynthesis. Proc. Natl. Acad. Sci. USA 96: 8985-8990
61. 61 Schimmel P. and Ribas de Pouplana L. (2000) Footprints of Aminoacyl-tRNA synthetases are everywhere. Trends Biochem. Sci. 25: 207-209
62. 62 Nagel G. M. and Doolittle R. F. (1991) Evolution and relatedness in two aminoacyl-tRNA synthetase families. Proc. Natl. Acad. Sci. USA 88: 8121-8125
63. 63 Nagel G. M. and Doolittle R. F. (1995) Phylogenetic analysis of the aminoacyl-tRNA synthetases. J. Mol. Evol. 40: 487-498
64. 64 Brown J. R. and Doolittle W. F. (1995) Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA 92: 2441-2445
65. 65 Bull C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G. et al. (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273: 1058-1073
66. 66 Ibba M., Morgan S., Curnow A. W., Pridmore D. R., Vothknecht U. C., Gardner W. et al. (1997) A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278: 1119-1122
67. 67 Ibba M., Losey H. C., Kawarabayasi Y., Kikuchi H., Bunjun S. and Söll D. (1999) Substrate recognition by class I lysyl-tRNA synthetases: a molecular basis for gene displacement. Proc. Natl. Acad. Sci. USA 96: 418-423
68. 68 Ribas de Pouplana L., Turner R. J., Steer B. A. and Schimmel P. (1998) Genetic code origins: tRNAs older than their synthetases? Proc. Natl. Acad. Sci. USA 95: 11295-11300
69. 69 Lapointe J., Duplain L. and Proulx M. (1986) A single glutamyl-tRNA synthetase aminoacylates tRNAGlu and tRNAGln in Bacillus subtilis and efficiently misacylates Escherichia coli tRNAGln1 in vitro. J. Bacteriol. 165: 88-93
70. 70 Strauch M. A., Zalkin H. and Aronson A. I. (1988) Characterization of the glutamyl-tRNA(Gln)-to-glutaminyl-tRNA(Gln) amidotransferase reaction of Bacillus subtilis. J. Bacteriol. 170: 916-920
71. 71 Brown J. R. and Doolittle W. F. (1999) Gene descent, duplication, and horizontal transfer in the evolution of glutamly-and glutaminyl-tRNA synthetases. J. Mol. Evol. 49: 485-495
72. 72 Handy J. and Doolittle R. F. (1999) An attempt to pinpoint the phylogenetic introduction of glutaminyl-tRNA synthetase among bacteria. J. Mol. Evol. 49: 709-715
73. 73 Hong K. W., Ibba M. and Söll D. (1998) Retracing the evolution of amino acid specificity in glutaminyl-tRNA synthetase. FEBS Lett. 434: 149-154
74. 74 Rogers K. C. and Söll D. (1995) Divergence of glutamate and glutamine aminoacylation pathways: providing the evolutionary rationale for mischarging. J. Mol. Evol. 40: 476-481
75. 75 Cavalier-Smith T. (1987) The simultaneous symbiotic origin of mitochondria, chloroplasts, and microbodies. Ann. N.Y. Acad. Sci. 503: 55-71
76. 76 Margulis L. (1996) Archaeal-eubacterial mergers in the origin of Eukarya: phylogenetic classification of life. Proc. Natl. Acad. Sci. USA 93: 1071-1076
77. 77 Hasegawa M., Hashimoto T., Adachi J., Iwabe N. and Miyata T. (1993) Early branchings in the evolution of eukaryotes: ancient divergence of entamoeba that lacks mitochondria revealed by protein sequence data. J. Mol. Evol. 36: 380-388
78. 78 Keeling P. J. and Doolittle W. F. (1996) A non-canonical genetic code in an early diverging eukaryotic lineage. EMBO J. 15: 2285-2290
79. 79 Moreira D. and Lopez-Garcia P. (1998) Symbiosis between methanogenic archaea and delta-proteobacteria as the origin of eukaryotes: the syntrophic hypothesis. J. Mol. Evol. 47: 517-530
80. 80 Martin W. and Muller M. (1998) The hydrogen hypothesis for the first eukaryote. Nature 392: 37-41
81. 81 Gogarten J. P., Kibak H., Dittrich P., Taiz L., Bowman E. J., Bowman B. J. et al. (1989) Evolution of the vacuolar H +-ATPase: implications for the origin of eukaryotes. Proc. Natl. Acad. Sci. USA 86: 6661-6665
82. 82 Gupta R. S., Aitken K., Falah M. and Singh B. (1994) Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum. Proc. Natl. Acad. Sci. USA 91: 2895-2899
83. 83 Embley T. M. and Hirt R. P. (1998) Early branching eukaryotes? Curr. Opin. Genet. Dev. 8: 624-629
84. 84 Brown J. R. and Doolittle W. F. (1997) Archaea and the prokaryote-to-eukaryote transition. Microbiol. Mol. Biol. Rev. 61: 456-502
85. 85 Vellai T., Takacs K. and Vida G. (1998) A new aspect to the origin and evolution of eukaryotes. J. Mol. Evol. 46: 499-507
86. 86 Lang B. F., Burger G., O'Kelly C. J., Cedergren R., Golding G. B., Lemieux C. et al. (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 29: 454-455
87. 87 Hashimoto T., Sanchez L. B., Shirakura T., Muller M. and Hasegawa M. (1998) Secondary absence of mitochondria in Giardia lamblia and Trichomonas vaginalis revealed by valyl-tRNA synthetase phytogeny. Proc. Natl. Acad. Sci. USA 95: 6860-6865