On the origin of the genetic code: Signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases

Heredity

Volumn 100, Issue 4, 2008, Pages 341-355

  Rodin, S N ^a   Rodin, A S ^b  

^a CITY OF HOPE NATIONAL MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

Complementary symmetry; Genetic code; RNA world; tRNA aminoacylation

Indexed keywords

AMINO ACID; AMINO ACID TRANSFER RNA LIGASE; TRANSFER RNA;

COMPLEMENTARITY; ENZYME; GENETICS; RNA; SYMMETRY;

AMINOACYLATION; ANTICODON; CHEMISTRY; CODON; ESCHERICHIA COLI; GENETIC CODE; GENETICS; METABOLISM; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REVIEW;

AMINO ACIDS; AMINO ACYL-TRNA SYNTHETASES; ANTICODON; BASE SEQUENCE; CODON; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; GENETIC CODE; MOLECULAR SEQUENCE DATA; RNA, TRANSFER; TRANSFER RNA AMINOACYLATION;

EID: 41149161126     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6801086     Document Type: Review

References (62)

1. Bloch D, McArthur B, Mirrop S (1985). tRNA-rRNA sequence homologies: evidence for an ancient modular format shared by tRNAs and rRNAs. BioSystems 17: 209-225.
2. Caporaso JG, Yarus M, Knight R (2005). Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code. J Mol Evol 61: 597-607.
3. Carter Jr CW (1993). Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Annu Rev Biochem 62: 715-748.
4. Carter Jr CW, Duax WL (2002). Did tRNA synthetase classes arise on opposite strands of the same gene? Mol Cell 10: 705-708.
5. Crick FHC (1958). On protein synthesis. Symp Soc Exp Biol 12: 138-163.
6. Crick FHC (1968). The origin of the genetic code. J Mol Biol 38: 367-380.
7. Crick FHC, Brenner S, Klug A, Pieczenik G (1976). A speculation on the origin of protein synthesis. Orig Life 7: 389-397.
8. Cusack S (1997). Aminoacyl-tRNA synthetases. Curr Opin Struct Biol 7: 881-889.
9. Cusack S, Berthet-Colominas C, Härtlein M, Nassar N, Leberman R (1990). A second class of synthetase structure revealed by X-ray analysis of Escherichia coli seryl-tRNA synthetase at 2.5Å. Nature 347: 249-255.
10. De Duve C (1988). The second genetic code. Nature 333: 117-118.
11. Delarue M (2007). An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13: 1-9.
12. Di Giulio M (1992). On the origin of the transfer RNA molecule. J Theor Biol 159: 199-214.
13. Di Giulio M (2002). Genetic code origin: are the pathways of type Glu-tRNA(Gln) → Gln-tRNA(Gln) molecular fossils or not? J Mol Evol 55: 616-622.
14. Eigen M, Schuster P (1979). Hypercycle: a Principle of Natural Self-organization. Heidelberg: Springer-Verlag.
15. Eriani G, Delarue M, Poch O, Gangloff J, Moras D (1990). Partition of aminoacyl-tRNA synthetases into two classes based on mutually exclusive sets of conserved motifs. Nature 347: 203-206.
16. Frugier M, Florentz C, Schimmel P, Giege R (1993). Triple aminoacylation of a chimerized transfer RNA. Biochemistry 32: 14053-14061.
17. Fukuchi S, Otsuka J (1992). Evolution of metabolic pathway by chance assembly of enzyme proteins generated from sense and antisense strands of pre-existing genes. J Theor Biol 158: 271-291.
18. Phe. Structure 5: 59-68.
19. Hou Y-M, Schimmel P (1988). A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 333: 140-145.
20. Ibba M, Becker HD, Stathopoulos C, Tumbula DL, Söll D (2000). The adaptor hypothesis revisited. Trends Biochem Sci 25: 311-316.
21. Ibba M, Morgan S, Curnow AW, Pridmore DR, Vothknecht UC, Gardner W et al. (1997). Euryarchael lysyl-tRNA synthetase: resemblance to class I synthetases. Science 278: 1119-1122.
22. Klipcan L, Safro M (2004). Amino acid biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetases. J Theor Biol 228: 389-396.
23. Knight RD, Freeland SJ, Landweber LF (2001). Rewriting the keyboard: evolvability of the genetic code. Nature Rev Genet 2: 49-58.
24. Kuhns ST, Joyce GF (2003). Perfectly complementary nucleic acid enzymes. J Mol Evol 56: 711-717.
25. Liang H, Landweber LF (2005). Molecular mimicry: quantitative methods to study structural similarity between protein and RNA. RNA 11: 1167-1172.
26. Maizels N, Weiner AM (1994). Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation. Proc Natl Acad Sci USA 91: 6729-6734.
27. Majerfeld I, Yarus M (1994). An RNA pocket for an aliphatic hydrophobe. Nature Struct Biol 1: 287-292.
28. Miller SL (1987). Which organic compounds could have occurred on the prebiotic earth. Cold Spring Harbor Symp Quant Biol 52: 17-27.
29. Nakamura Y (2001). Molecular mimicry between protein and tRNA. J Mol Evol 53: 282-289.
30. Cys formation. Proc Natl Acad Sci 102: 19003-19008.
31. Patel A (2005). The triplet genetic code had a doublet predecessor. J Theor Biol 233: 527-532.
32. Patel A (2007). Towards understanding the origin of genetic languages. In: Abbott D, Davies PCW, Pati AK (eds). Quantum Aspects of Life. Imperial College Press: London.
33. Pham Y, Li L, Kim A, Erdogan O, Weinreb V, Butterfoss GL et al. (2007). A minimal Trp RS catalytic domain supports sense/antisense ancestry of class I and II aminoacyl-tRNA synthetases. Mol Cell 25: 851-862.
34. Ribas de Pouplana L, Schimmel P (2001a). Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem. Cell 104: 191-193.
35. Ribas de Pouplana L, Schimmel P (2001b). Aminoacyl-tRNA synthetases: potential markers of genetic code development. Trends Biochem Sci 26: 591-596.
36. Rodin S, Ohno S (1995). Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands of the same nucleic acid. Origins Life Evol Biosphere 25: 565-589.
37. Rodin S, Rodin A, Ohno S (1996). The presence of codon-anticodon pairs in the acceptor stem of tRNAs. Proc Natl Acad Sci USA 93: 4537-4542.
38. Rodin SN, Ohno S (1997). Four primordial modes of tRNA-synthetase recognition, determined by the (G,C) operational code. Proc Natl Acad Sci USA 94: 5183-5188.
39. Rodin SN, Rodin AS (2006a). Origin of the genetic code: first aminoacyl-tRNA synthetases could replace isofunctional ribozymes when only the second base of codons was established. DNA Cell Biol 25: 365-375.
40. Rodin SN, Rodin AS (2006b). Partitioning of aminoacyl-tRNA synthetases in two classes could have been encoded in a strand-symmetric RNA world. DNA Cell Biol 25: 617-626.
41. Rodin SN, Rodin AS (2007). Evolution by gene duplications: From the origin of the genetic code to the human genome. In: Dobretzov N, Kolchanov N (eds). Biosphere Origin and Evolution. Springer: Berlin, pp 253-272.
42. Gln and ATP at 2.8Å resolution. Science 246: 1135-1142.
43. Ruff M, Krishnaswamy S, Boeglin M, Postersman A, Mitschler A, Rodjarny A et al. (1991). Class II aminoacyl transfer RNA synthetases: crystal structure of yeast aspartyl-trNA synthetase complexed with tRNA. Science 252: 1682-1689.
44. Schimmel P, Beebe K (2006). Aminoacyl tRNA synthetases: from the RNA world to the theater of proteins. In: Gesteland RF, Cech TR, Atkins JF (eds). The RNA World. Cold Spring Harbor Lab. Press, Plainview, NY, pp 227-255.
45. Schimmel P, Giege R, Moras D, Yokoyama S (1993). An operational RNA code for amino acids and possible relation to genetic code. Proc Natl, Acad Sci USA 90: 8763-8768.
46. Shimizu M (1982). Molecular basis for the genetic code. J Mol Evol 18: 297-303.
47. Sissler M, Eriani G, Martin F, Giege R, Florentz C (1997). Mirror image alternative interaction patterns of the same tRNA with either class I arginyl-tRNA synthetase or class II aspartyl-tRNA synthetase. Nucleic Acid Res 25: 4899-4906.
48. Sprinzl M, Vassilenko KS (2005). Compilation of tRNA sequences and sequences of tRNA genes. Nucl Acids Res 1:33: D139-D140.
49. Szathmary E (1991). Codon swapping as a possible evolutionary mechanism. J Mol Evol 32: 178-182.
50. Szathmary E (1993). Coding coenzyme handles: a hypothesis for the origin of the genetic code. Proc Natl Acad Sci USA 90: 9916-9920.
51. Szathmary E (1999). The origin of the genetic code: amino acids as cofactors in an RNA world. Trends Genet 15: 223-229.
52. Trifonov EN (2005). Theory of early molecular evolution: predictions and confirmations. in: Eisenhaber F (ed). Discovering Biomolecular Mechanisms with Computational Biology. Landes Bioscience, Georgetown, pp 107-116.
53. Weiner AM, Maizels N (1987). TRNA-like structures tag the 3′ ends of genomic RNA molecules for replication: Implications for the origin of protein synthesis. Proc Natl Acad Sci USA 84: 7383-7387.
54. Weiner AM, Maizels N (1999). The genomic tag hypothesis: modern viruses as molecular fossils of ancient strategies for genomic replication, and clues regarding the origin of protein synthesis. Biol Bull 196: 327-330.
55. Woese CR (1965). On the evolution of the genetic code. Proc Natl Acad Sci USA 54: 1546-1552.
56. Yang X, Otero FJ, Ewalt KL, Liu J, Swairjo MA, Köhrer C et al. (2006). Two conformations of a crystalline human tRNA synthetase-tRNA complex: implications for protein synthesis. EMBO J 25: 2919-2929.
57. Yanofsky C (2007). Establishing the triplet nature of the genetic code. Cell 128: 815-818.
58. Yaremchuk A, Kriklivyi I, Tukalo M, Cusack S (2002). Class I tyrosyltRNA synthetase has a class II mode of cognate tRNA recognition. EMBO J 21: 3829-3840.
59. Yarus M (1991). An RNA-amino acid complex and the origin of the genetic code. New Biol 3: 183-189.
60. Yarus M (1993). An RNA-amino acid affinity. In: Gesteland RF, Atkins JF (eds). The RNA World. Cold Spring Harbor Lab. Press, Plainview, NY, pp 205-217.
61. Yarus M (1998). Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J Mol Evol 47: 109-117.
62. Yarus M, Caporaso JG, Knight R (2005). Origins of the genetic code: the escaped triplet theory. Annu Rev Biochem 74: 125-151.