Genetic code origin: Are the pathways of type Glu-tRNAGln→Gln-tRNAGln molecular fossils or not?

Journal of Molecular Evolution

Volumn 55, Issue 5, 2002, Pages 616-622

  Giulio, Massimo ^a  

^a INSTITUTE OF GENETICS AND BIOPHYSICS ADRIANO BUZZATI TRAVERSO   (Italy)

Author keywords

Coevolution theory; Genetic code origin; Molecular fossils; Precursor product amino acids; RNA world; Unusual biosynthetic pathways

Indexed keywords

GLUTAMIC ACID; GLUTAMINE; TRANSFER RNA;

ARTICLE; BIOSYNTHESIS; COEVOLUTION; FOSSIL; GENETIC CODE; MOLECULAR EVOLUTION; THEORY;

EVOLUTION, MOLECULAR; GENETIC CODE; MODELS, GENETIC; PHYLOGENY; RNA, TRANSFER, AMINO ACYL; RNA, TRANSFER, GLN; RNA, TRANSFER, GLU;

EID: 0036841366     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-002-2357-6     Document Type: Article

References (63)

1. Ardell DH, Sella G (2001) On the evolution of redundacy in the genetic codes. J Mol Evol 53:269-281
2. Balasubramanian R, Seetharamulu P, Raghunathan G (1980) A conformational rationale for the origin of the mechanism of nucleicacid-directed protein synthesis of 'living' organisms. Origins Life 10:15-30
3. Baron C, Bock A (1995) The selenocysteine-inserting tRNA species: Structure and function. In: Soll D, RajBhandary UL (ed) tRNA structure, biosynthesis, and function. ASM Press, Washington, DC, pp 529-544
4. Benner SA, Ellington AD, Tauer A (1989) Modern metabolism as a palimpsest of the RNA world. Proc Natl Acad Sci USA 86:7054-7058
5. Bermudez CI, Daza EE, Andrade E (1999) Characterization and comparison of Escherichia coli transfer RNAs by graph theory based on secondary structure. J Theor Biol 197:193-205
6. Bock A, Forchhammer K, Heider J, Baron C (1991a) Selenoprotein synthesis: an expansion of the genetic code. Trends Biochem Sci 16:463-467
7. Bock A, Forchhammer K, Heider J, Leinfelder W, Sawers G, Veprek B, Zinoni (1991b) Selenocysteine: The 21st amino acid. Mol Microbiol 5:515-520
8. Cavalier-Smith T (2001) Obcells as proto-organisms: Membrane heredity, lithophosphorilation, and the origins of the genetic code, the first cell, and photosynthesis. J Mol Evol 53:555-595
9. Chaley MB, Korotkov EV, Phoenix DA (1999) Relationships among isoacceptor tRNA seems to support the coevolution theory of the origin of the genetic code. J Mol Evol 48:168-177
10. Danchin A (1989) Homeotopic transformation and the origin of translation. Prog Biophys Mol Biol 54:81-86
11. de Duve C (1991) Blueprint for a cell: The nature and origin of life. Neil Patterson, Carolina Biological Supply Company, Burlington, NC, pp 175-181
12. Di Giulio M (1989) Some aspects of the organization and evolution of the genetic code. J Mol Evol 29:191-201
13. Di Giulio M (1992a) On the origin of the genetic code. Trends Ecol Evol 7:176-178
14. Di Giulio M (1992b) The evolution of aminoacyl-tRNA synthetases, the biosynthetic pathways of amino acids and the genetic code. Origins Life Evol Biosph 22:309-319
15. Di Giulio M (1993) Origin of glutaminyl-tRNA synthetase: An example of palimpsest? J Mol Evol 37:5-10
16. Di Giulio M (1996) The β-sheets of proteins, the biosynthetic relationships between amino acids, and the origin of the genetic code. Origins Life Evol Biosph 26:589-609
17. Di Giulio M (1997a) On the origin of the genetic code. J Theor Biol 187:573-581
18. Di Giulio M (1997b) The origin of the genetic code. Trends Biochem Sci 22:49
19. Di Giulio M (1997c) On the RNA world: Evidence in favor of an early ribonucleopeptide world. J Mol Evol 45:571-578
20. Di Giulio M (1999) The coevolution theory of the origin of the genetic code. J Mol Evol 48:253-254
21. Di Giulio M (2000) The RNA world, the genetic code and the tRNA molecule. Trends Genet 16:17-18
22. Di Giulio M (2001a) A blind empiricism against the coevolution theory of the origin of the genetic code. J Mol Evol 53:724-732
23. Di Giulio M (2001b) The non-universality of the genetic code: The universal ancestor was a progenote. J Theor Biol 209:345-349
24. Di Giulio M, Medugno M (1998) The historical factor: the biosynthetic relationships between amino acids and their physicochemical properties in the origin of the genetic code. J Mol Evol 46:615-621
25. Di Giulio M, Medugno M (1999) Physicochemical optimization in the genetic code origin as the number of codified amino acids increases. J Mol Evol 49:1-10
26. Di Giulio M, Medugno M (2000) The robust statistical bases of the coevolution theory of the genetic code. J Mol Evol 50:258-263
27. Di Giulio M, Medugno M (2001) The level and landscape of optimization in the origin of the genetic code. J Mol Evol 52:372-382
28. Di Giulio M, Capobianco MR, Medugno M (1994) On the optimization of the physicochemical distances between amino acids in the evolution of the genetic code. J Theor Biol 186:43-51
29. Dillon LS (1973) The origins of the genetic code. Bot Rev 39:301-345
30. Edwards MR (1996) Metabolite channeling in the origin of life. J Theor Biol 179:313-322
31. Fitch W, Upper K (1987) The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harbor Symp Quant Biol 52:759-767
32. Gibson TJ, Lamond AI (1990) Metabolic complexity in the RNA world and implications for the origin of proteins synthesis. J Mol Evol 30:7-15
33. Gilbert W (1986) The RNA world. Nature 319:618
34. Greenstein JP, Winitz M (1961) Glutamic acid and glutamine. In: Chemistry of amino acids, Vol 3. John Wiley, New York, pp 1929-1954
35. Guarlerzi CO, Pon CL (1990) Initiation of mRNA translation in prokaryotes. Biochemistry 29:5881-5889
36. Handy J, Doolittle RF (1999) An attempt to pinpoint the phylogenetic introduction of glutaminyl-tRNA synthetase among bacteria. J Mol Evol 49:709-715
37. Ibba M, Curnow AW, Soll D (1997) Aminoacyl-tRNA synthesis: Divergent routes to a common goal. Trends Biochem Sci 22:39-42
38. Ibba M, Becker HD, Stathopoulos C, Tumbula DL, Soll D (2000) The adaptor hypothesis revisited. Trends Biochem Sci 25:311-316
39. Kozak M (1999) Initiation of translation in prokaryotes and eukaryotes. Gene 234:187-208
40. Lamour V, Quevillon S, Diriong S, Guyen VC, Lipinski M, 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
41. McClendon JH (1986) The relationship between the origins of the biosynthetic paths to the amino acids and their coding. Origins Life 16:260-270
42. Miseta A (1989) The role of protein associated amino acid precursor molecules in the organization of genetic codons. Physiol Chem Phys Med NMR 21:237-242
43. Morowitz HJ (1992) Beginnings of cellular life: Metabolism recapitulates biogenesis. Yale University, Vail-Ballou Press, Binghamton, NY, pp 160-171
44. Nelsestuen GL (1978) Amino acid-directed nucleic acid synthesis. A possible mechanism in the origin of life. J Mol Evol 11:109-120
45. Osawa S, Jukes TH (1988) Evolution of the genetic code as affected by anticodon content. Trends Genet 4:191-198
46. Pain VM (1996) Initiation of protein synthesis in eukaryotic cells. Eur J Biochem 236:747-771
47. Poole AM, Jeffares DC, Penny D (1998) The path from the RNA world. J Mol Evol 46:1-17
48. Ronneberg TA, Landweber LF, Freeland SL (2000) Testing a biosynthetic theory of the genetic code: Fact or artifact? Proc Natl Acad Sci USA 97:13690-13695
49. Shimizu M (1982) Molecular basis for the genetic code. J Mol Evol 18:297-303
50. Sjostrom M, Wold S (1985) A multivariate study of the relationship between the genetic code and the physico-chemical properties of amino acids. J Mol Evol 22:272-277
51. Taylor FJR, Coates D (1989) The code within the codons. BioSystems 22:177-187
52. Tumbula DL, Becker HD, Chang WZ, Soll D (2000) Domain-specific recruitment of amide amino acids for protein synthesis. Nature 407:106-110
53. Wachtershauser G (1988) Before enzymes and templates: theory of surfage metabolism. Microbiol Rev 52:452-484
54. White III HB (1976) Coenzymes as fossils of an earlier metabolic state. J Mol Evol 7:101-104
55. Wong JT (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci USA 72:1909-1912
56. Wong JT (1976) The evolution of a universal genetic code. Proc Natl Acad Sci USA 73:2336-2340
57. Wong JT (1980) Role of minimization of chemical distances between amino acids in the evolution of the genetic code. Proc Natl Acad Sci USA 77:1083-1086
58. Wong JT (1988) Evolution of the genetic code. Microbiol Sci 5:174-182
59. Woese CR (1965) On the origin of the genetic code. Proc Natl Acad Sci USA 54:1546-1552
60. Woese CR (1967) The genetic code. Harper & Row, New York
61. Woese CR, Dugre DH, Dugre SA, Kondo M, Saxinger WC (1966) On the fundamental nature and evolution of the genetic code. Cold Spring Harbor Symp Quant Biol 31:723-736
62. Wolfenden RV, Cullis PM, Southgate CCF (1979) Water, protein folding, and the genetic code. Science 206:575-577
63. Yarus M (1998) Amino acids as RNA ligands: A direct-RNA-template theory for the code's origin. J Mol Evol 47:109-117