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The Early Phases of Genetic Code Origin: Conjectures on the Evolution of Coded Catalysis

  • Massimo Di GiulioEmail author
Article

Abstract

A review of the most significant contributions on the early phases of genetic code origin is presented. After stressing the importance of the key intermediary role played in protein synthesis, by peptidyl-tRNA, which is attributed with a primary function in ancestral catalysis, the general lines leading to the codification of the first amino acids in the genetic code are discussed. This is achieved by means of a model of protoribosome evolution which sees protoribosome as the central organiser of ancestral biosynthesis and the mediator of the encounter between compounds (metabolite-pre-tRNAs) and catalysts (peptidyl-pre-tRNAs). The encounter between peptidyl-pre-tRNA catalysts in protoribosome is favoured by metabolic pre-mRNAs and later resulted (given the high temperature at which this evolution is supposed to have taken place) in the evolution of mRNAs with codons of the type GNS. These mRNAs codified only for those amino acids that the coevolution theory of genetic code origin sees as the precursors of all other amino acids. Some aspects of the model here discussed might be rendered real by the transfer-messenger RNA molecule (tmRNA) which is here considered a molecular fossil of ancestral protein synthesis.

catalysis evolution peptidyl-pre-tRNA protein synthesis origin pre-tRNA protoribosome tmRNA 

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References

  1. Bar-Nun, A., Kochavi, E. and Bar-Nun, S.: 1994, Assemblies of Amino Acids as Possible Prebiotic Catalysts, J. Mol. Evol. 39, 116-122.Google Scholar
  2. Brack, A. and Orgel, L. E.: 1975, β-Structures of Alternating Polypeptides and their Possible Prebiotic Significance, Nature 256, 383-387.Google Scholar
  3. Campbell, J. H.: 1991, An RNA Replisome as Ancestor of Ribosome, J. Mol. Evol. 32, 3-5.Google Scholar
  4. Cedergren, R. and Grosjean, H.: 1987, On the Primacy of Primordial RNA, Biosystems 20, 175-180.Google Scholar
  5. Crothers, D. M.: 1982, Nucleic Acid Aggregation Geometry and the Possible Evolutionary Origin of Ribosomes and the Genetic Code, J. Mol. Biol. 162, 379-391.Google Scholar
  6. Danchin, A.: 1989, Homeotopic Transformation and the Origin of Translation, Prog. Biophys. Mol. Biol. 54, 81-86.Google Scholar
  7. De Duve, C.: 1987, Selection by Differential Molecular Survival: A Possible Mechanism of Early Chemical Evolution, Proc. Natl. Acad. Sci. U.S.A. 84, 8253-8256.Google Scholar
  8. De Duve, C.: 1988, Did God make RNA? Nature 336, 209-210.Google Scholar
  9. De Duve, C.: 1991, Blueprint for a Cell: The Nature and Origin of Life, Neil Patterson Publishers, Carolina Biological Supply Company, Burlington, NC.Google Scholar
  10. Di Giulio, M.: 1992, On the Origin of the Transfer RNA Molecule, J. Theor. Biol. 159, 199-214.Google Scholar
  11. Di Giulio, M.: 1994a, On the Origin of Protein Synthesis: A Speculative Model Based on Hairpin RNA Structures, J. Theor. Biol. 171, 303-308.Google Scholar
  12. Di Giulio, M.: 1994b, On the Origin of Protein Synthesis: A Speculative Model based on Hairpin RNA Structures, J. Theor. Biol. 171, 303-308.Google Scholar
  13. Di Giulio, M.: 1995, Was it an Ancient Gene Codifyng for a Hairpin RNA that, by Means of Direct Duplication, gave Rise to the Primitive tRNA Molecule? J. Theor. Biol. 177, 95-101.Google Scholar
  14. Di Giulio, M.: 1996a, The β-Sheets of Proteins, the Biosynthetic Relationships between Amino Acids, and the Origin of the Genetic Code, Orig. Life Evol. Biosph. 26, 589-609.Google Scholar
  15. Di Giulio, M.: 1996b, The Origin of Protein Synthesis: On some Molecular Fossils Identified through Comparison of Protein Sequences, Biosystems 39, 159-169.Google Scholar
  16. Di Giulio, M.: 1997a, On the Origin of the Genetic Code, J. Theor. Biol. 187, 573-581.Google Scholar
  17. Di Giulio, M.: 1997b, On the RNA World: Evidence in Favor of an Early Ribonucleopeptide World, J. Mol. Evol. 45, 571-578.Google Scholar
  18. Di Giulio, M.: 2001, The Non-universality of the Genetic Code: The Universal Ancestor was a Progenote, J. Theor. Biol. 209, 345-349.Google Scholar
  19. Di Giulio, M. and Medugno, M.: 1999, Physicochemical Optimization in the Genetic Code Origin as the Number of Codified Amino Acids Increases, J. Mol. Evol. 49, 1-10.Google Scholar
  20. Doolittle, W. F. and Brown, J. R.: 1994, Tempo, Mode, the Progenote, and the Universal Root, Proc. Natl. Acad. Sci. U.S.A. 91, 6721-6728.Google Scholar
  21. Dyson, F.: 1985, Origins of Life, Cambridge University Press, Cambridge.Google Scholar
  22. Edwards, M. R.: 1996, Metabolite Channeling in the Origin of Life, J. Theor. Biol. 179, 313-322.Google Scholar
  23. Edwards, M. R.: 1989, A Possible Origin of RNA Catalysis in Multienzyme Complexes, Orig. Life Evol. Biosph. 19, 69-72.Google Scholar
  24. Gibson, T. J. and Lamond, A. I.: 1990, Metabolic Complexity in the RNA World and Implications for the Origin of Proteins Synthesis, J. Mol. Evol. 30, 7-15.Google Scholar
  25. Gilbert, W.: 1986, The RNA World, Nature 319, 618.Google Scholar
  26. Gillet, R. and Felden, B.: 2001, Emerging Views on tmRNA-Mediated Protein Tagging and Ribosome Rescue, Mol. Microbiol. 42, 879-885.Google Scholar
  27. Ikehara, K., Omori, Y., Arai, R. and Hirose, A.: 2002, A Novel Theory on the Origin of the Genetic Code: A GNC-SNS Hypothesis, J. Mol. Evol. 54, 530-538.Google Scholar
  28. Hopfield, J. J.: 1978, Origin of the Genetic Code: A Testable Hypothesis Based on tRNA Structure, Sequence and Kinetic Proofreading, Proc. Natl. Acad. Sci. U.S.A. 75, 4334-4338.Google Scholar
  29. Joyce, G. F.: 1989, RNA Evolution and the Origins of Life, Nature 338, 217-224.Google Scholar
  30. Jurka, J. and Smith, T. F.: 1987a, β-Turn-driven Early Evolution: the Genetic Code and Biosynthetic Pathways, J. Mol. Evol. 25 15-19.Google Scholar
  31. Jurka, J. and Smith, T. F.: 1987b, ?-Turns in Early Evolution: Chirality, Genetic Code, and Biosynthetic Pathways, Cold Spring Harbor Symp. Quant. Biol. 52, 407-410.Google Scholar
  32. Kleinkauf, H. and Von Dohren, H.: 1990, Nonribosomal Biosynthesis of Peptide Antibiotics, Eur. J. Biochem. 192, 1-15.Google Scholar
  33. 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.Google Scholar
  34. Kyrpides, N. C. and Woese, C. R.: 1998b, Universally Conserved Translation Initiation Factors, Proc. Natl. Acad. Sci. U.S.A. 95, 224-228.Google Scholar
  35. Kyrpides, N. C. and Woese, C. R.: 1998b, Archaeal Translation Initiation Revisited: The Initiation Factor 2 and Eukaryotic Initiation Factor 2N ? ? ? ? ? Subunit Families. Proc. Natl. Acad. Sci. U.S.A. 95, 3726-3730.Google Scholar
  36. Lahav, N.: 1991, Prebiotic Co-Evolution of Self-Replication and Translation Or RNA World? J. Theor. Biol. 151, 531-539.Google Scholar
  37. Lamond, A. I. and Gibson, T. J.: 1990, Catalitic RNA and the Origin of Genetic Systems, Trends Genet 6, 145-149.Google Scholar
  38. Lipmann, F., 1965, In Origins of Prebiological Systems and of their Molecular Matrices, S. Fox (ed.), Academic, New York, pp. 259-280.Google Scholar
  39. Lipmann, F.: 1971, Attempts to Map a Process Evolution of Peptide Biosynthesis, Science 173, 875-884.Google Scholar
  40. Miller, S. L. and Schlesinger, G.: 1993, Prebiotic Syntheses of Vitamin Coenzymes: II. Pantoic Acid, Pantothenic Acid and the Composition of Coenzyme A. J. Mol. Evol. 36, 308-314.Google Scholar
  41. Muto, A., Ushida, C. and Himeno, H.: 1998, A Bacterial RNA that Functions as both a tRNA and an mRNA, Trends Biochem. Sci. 23, 25-29.Google Scholar
  42. Orgel, L. E.: 1968, Evolution of the Genetic Apparatus, J. Mol. Biol. 38, 381-393.Google Scholar
  43. Orgel, L. E.: 1975, Prebiotic Polynucleotides and Polypeptides, Isr. J. Chem. 14, 11-16Google Scholar
  44. Orgel, L. E.: 1977, '?-Turns and the Evolution of Protein Synthesis', in E. M. Bradbury and K. Javaherian (eds), The Organization and Expression of the Eukaryotic Genome: Proceedings of the International Symposium, 3-6 May 1976, Teheran. Academic Press, London, pp. 499-504.Google Scholar
  45. Orgel, L. E.: 1989, The Origin of Polynucleotide-Directed Protein Synthesis, J. Mol. Evol. 29, 465-474.Google Scholar
  46. Russell, J., Daia, D. E. and Hall, A. J.: 1998, 'The Emergence of Life From FeS Bubbles at Alkaline Hot Springs in an Acid Ocean', in J. Wiegel and W. W. Adams (eds), Thermophiles: The Keys to Molecular Evolution and the Origin of Life, Taylor and Francis, pp. 77-110.Google Scholar
  47. Reanney, D. C.: 1977, Aminoacyl Thiol Esters and the Origins of Genetic Specificity, J. Theor. Biol. 65, 555-569.Google Scholar
  48. Schimmel, P. and Henderson, B.: 1994, Possible Role of Aminoacyl-RNA Complex in Noncoded Peptide Synthesis and Origin of Coded Synthesis, Proc. Natl. Acad. Sci. U.S.A. 91, 11283-11286.Google Scholar
  49. Segré, D. and Lancet, D.: 1999, A Statistical Chemistry Approach to the Origin of Life, Chemtracts-Biochem. Mol. Biol. 12, 382-397.Google Scholar
  50. Szathmáry, E.: 1993, Coding Coenzyme Handles: A Hypothesis for the Origin of the Genetic Code, Proc. Natl. Acad. Sci. U.S.A. 90, 9916-9920.Google Scholar
  51. Szathmáry, E.: 1999, The Origin of the Genetic Code: Amino Acids as Cofactors in an RNA World, Trends Genet. 15, 223-229.Google Scholar
  52. Tyagi, S.: 1981, Origin of Translation: The Hypothesis of Permanently Attached Adaptors, Origins Life 11, 343-351.Google Scholar
  53. Trifonov, E. N.: 2000, Consensus Temporal Order of Amino Acids and Evolution of the Triplet Code, Gene 261, 139-151.Google Scholar
  54. Wachtershauser, G.: 1988, Before Enzymes and Templates: Theory of Surface Metabolism, Microbiol. Rev. 52, 452-484.Google Scholar
  55. Wachtershauser, G.: 1992, Groundworks for an Evolutionary Biochemistry: The Iron-SulphurWorld, Prog. Biophys. Mol. Biol. 58, 85-201.Google Scholar
  56. White III, H. B.: 1976, Coenzymes as Fossils of an EarlierMetabolic State, J. Mol. Evol. 7, 101-104.Google Scholar
  57. White, H. B.: 1982, 'Evolution of Coenzymes and the Origin of Pyridine Nucleotides', in J. Everse, B. Anderson and K. S. You (eds), The Pyridine Nucleotide Coenzymes, Academic Press, pp. 1-17.Google Scholar
  58. Woese, C. R.: 1998, The Universal Ancestor, Proc. Natl. Acad. Sci. U.S.A. 95, 6854-6859.Google Scholar
  59. Woese, C. R.: 2000, Interpreting the Universal Phylogenetic Tree, Proc. Natl. Acad. Sci. U.S.A. 97, 8392-8396.Google Scholar
  60. Wong, J. T.: 1975, A Co-evolution Theory of the Genetic Code, Proc. Natl. Acad. Sci. U.S.A. 72, 1909-1912.Google Scholar
  61. Wong, J.T.: 1991, Origin of Genetically Encoded Protein Synthesis: A Model Based On Selection for RNA Peptidation, Orig. Life Evol. Biosph. 21, 165-176.Google Scholar
  62. Wong, J. T. and Xue, H.: 2002, 'Self-perfecting Evolution of Heteropolymer Building Blocks and Sequences as the Basis of Life', in Fundamentals of Life, Editions Scientifiques et Medicales Elsevier SAS.Google Scholar

Copyright information

© Kluwer Academic Publishers 2003

Authors and Affiliations

  1. 1.Institute of Genetics and Biophysics Adriano Buzzati Traverso, CNRNaples, NapoliItaly

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