On the evolution of primitive genetic codes

Origins of Life and Evolution of the Biosphere

Volumn 33, Issue 4-5, 2003, Pages 491-514

  Weberndorfer, Günter ^a   Hofacker, Ivo L ^a   Stadler, Peter F ^a,b  

^a UNIVERSITY OF VIENNA   (Austria)

^b SANTA FE INSTITUTE   (United States)

Author keywords

Evolution; Genetic code; Minimal organism; Tank reactor

Indexed keywords

EVOLUTION; GENETICS;

AMINO ACID SEQUENCE; BASE SEQUENCE; EVOLUTION, MOLECULAR; GENETIC CODE; GENOME; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PROTEIN BIOSYNTHESIS; PROTEIN CONFORMATION; PROTEINS; RNA;

EID: 0142135396     PISSN: 01696149     EISSN: None     Source Type: Journal    
DOI: 10.1023/A:1025753712110     Document Type: Article

References (106)

1. Aita, T., Urata, S. and Yuzuru, H.: 2000, From Amino Acid Landscape to Protein Landscape: Analysis of Genetic Codes in Terms of Fitness Landscape, J. Mol. Evol. 52, 313-323.
2. Amirnovin, R.: 1997, An Analysis of the Metabolic Theory of the Origin of the Genetic Code, J. Mol. Evol. 44, 473-476.
3. Ancel, L. and Fontana, W.: 2000, Plasticity, Evolvability and Modularity in RNA, J. Exp. Zoology (Molecular and Developmental Evolution) 288, 242-283.
4. Andersson, S. G. and Kurland, C. G.: 1995, Genomic Evolution Drives the Evolution of the Translation System, Biochem. Cell Biol. 73, 775-787.
5. Ardell, D. H. and Sella, G.: 2001, On the Evolution of Redundancy in Genetic Codes, J. Mol. Evol. 53, 269-281.
6. Babajide, A., Farber, R., Hofacker, I. L., Inman, J., Lapedes, A. S. and Stadler, P. F.: 2001, Exploring Protein Sequence Space using Knowledge based Potentials, J. Theor. Biol. 212, 35-46.
7. Babajide, A., Hofacker, I. L., Sippl, M. J. and Stadler, P. F.: 1997, Neutral Networks in Protein Space: A Computational Study Based on Knowledge-Based Potentials of Mean Force, Folding and Design 2, 261-269.
8. Bartel, D. P. and Unrau, P. J.: 1999, Constructing an RNA World, Trends Biochem. Sci. 24, M9-M13.
9. Benner, S. A., Ellington, A. D. and Tauer, A.: 1989, Modern Metabolism as a Palimpsest of the RNA World, Proc. Natl. Acad. Sci. U.S.A. 86, 7054-7058.
10. Bowie, J. U., Luthy, R. and Eisenberg, D.: 1991, A Method to Identify Protein Sequences that Fold into a Known Three-Dimensional Structure, Science 253, 164-170.
11. Brooks, D. J. and Fresco, J. R.: 2002, Increased Frequency of Cysteine, Tyrosine, and Phenylalanine Residues Since the Last Universal Ancestor, Mol. Cell. Proteomics 1, 125-131.
12. Commans, S. and Böck, A.: 1999, Selenocysteine Inserting tRNAs: An Overview, FEMS Microbiol. Rev. 23, 335-351.
13. Crick, F. H. C.: 1968, The Origin of the Genetic Code, J. Mol. Biol. 38, 367-379.
14. Davidson, A. R. and Sauer, R. T.: 1994, Folded Proteins Occur Frequently in Libraries of Random Amino Acid Sequences, Proc. Natl. Acad. Sci. U.S.A. 91, 2146-2150.
15. De Duve, C.: 1988, Transfer RNAs: The Second Genetic Code, Nature 333, 117-118.
16. Eigen, M.: 1971, Selforganization of Matter and the Evolution of Macromolecules, Naturwiss. 58, 465-523.
17. Eigen, M., Lindemann, B. F., Tietze, M., Winkler-Oswatitsch, R., Dress, A. W. M. and Von Haeseler, A.: 1989a, How Old is the Genetic Code? Statistical Geometry of tRNA Provides an Answer, Science 244, 673-679.
18. Eigen, M., McCaskill, J. S. and Schuster, P.: 1989b, 'The Molecular Quasi-Species, Adv. Chem. Phys. 75, 149-263.
19. Eigen, M. and Schuster, P.: 1979, The Hypercycle, Springer-Verlag, New York, Berlin.
20. Ermolaeva, M. D.: 2001, Synonymous Codon Usage in Bacteria, Curr. Issues Mol. Biol. 3, 91-97.
21. Fitch, W. and Upper, K.: 1987, The Phylogeny of tRNA Sequences Provides Evidence for Ambiguity Reduction in the Origin of the Genetic Code, Cold Spring Harb. Symp. Quant. Biol. 52, 759-767.
22. Fontana, W. and Buss, L. W.: 1994, The Arrival of the Fittest: Towards a Theory of Biological Organisation, Bull. Math. Biol. 56, 1-64.
23. Fontana, W., Schnabl, W. and Schuster, P.: 1989, 'Physical Aspects of Evolutionary Optimization and Adaption, Phys. Rev. A 40, 3301-3321.
24. Fontana, W. and Schuster, P.: 1987, A Computer Model of Evolutionary Optimization, Biophys. Chem. 26, 123-147.
25. Fontana, W. and Schuster, P.: 1998, Continuity in Evolution: On the Nature of Transitions, Science 280, 1451-1455.
26. Freeland, S. J., Wu, T. and Keulmann, N.: 2003, The Case for an Error Minimizing Standard Genetic Code, Orig. Life. Evol. Biosph. 33, 479-489.
27. Freeland, S. J.: 2002b, The Darwinian Genetic Code: An Adaptation for Adapting?, J. Genet. Prog. Evolv. Matter 3, 113-127.
28. Freeland, S. J., Knight, R. D. and Landweber, L. F.: 1999, Do Proteins Predate DNA?, Science 286, 690-692.
29. Freeland, S. J., Knight, R. D., Landweber, L. F. and Hurst, L. D.: 2000, Early Fixation of an Optimal Genetic Code, Mol. Biol. Evol. 17, 511-518.
30. Gilbert, W.: 1986, The RNA World, Nature 319, 618.
31. Gillespie, D. T.: 1976, A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions, J. Comput. Phys. 22, 403.
32. Goldberg, D. E. and Deb, K.: 1991, 'A Comparative Analysis of Selection Schemes used in Genetic Algorithms', in G. J. E. Rawlins (ed.), Foundations of Genetic Algorithms, San Mateo, CA, pp. 69-93.
33. Hampl, H., Schulze, H. and Nierhaus, K. H.: 1981, Ribosomal Components from Escherichia coli 50S Subunits Involved in the Reconstitution of Peptidyltransferase Activity, J. Biol. Chem. 256, 2284-2288.
34. Happel, R. and Stadler, P. F.: 1999, Autocatalytic Replication in a CSTR and Constant Organization, J. Math. Biol. 38, 422-434.
35. Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G. and Sippl, M. J.: 1990, Identification of Native Protein Folds Amongst a Large Number of Incorrect Models - The Calculation of Low Energy Conformations from Potentials of Mean Force, J. Mol. Biol. 216, 167-180.
36. Hofacker, I. L., Fontana, W., Stadler, P. F., Bonhoeffer, L. S., Tacker, M. and Schuster, P.: 1994, Fast Folding and Comparison of RNA Secondary Structures, Monatsh. Chem. 125, 167-188.
37. Humphrey, W., Dalke, A. and Schulten, K.: 1996, VMD - Visual Molecular Dynamics, J. Molec. Graphics 14, 33-38. Software available on-line from http://www.ks.uiuc.edu/Research/vmd/.
38. Husimi, Y.: 1989, Selection and Evolution in Cellstat, Adv. Biophys. 25, 1-43.
39. Huynen, M. A., Stadler, P. F. and Fontana, W.: 1996, Smoothness within Ruggedness: The Role of Neutrality in Adaptation, Proc. Natl. Acad. Sci. U.S.A. 93, 397-401.
40. Ibba, M. and Söll, D.: 2001, The Renaissance of Aminoacyl-tRNA Synthesis, EMBO Reports 2, 382-387.
41. Ikehara, K.: 2002, Origins of Gene, Genetic Code, Protein and Life: Comprehensive View of Life Systems from a GNC-SNS Primitive Code Hypothesis, J. Biosci. 27, 165-186.
42. Illangasekare, M. and Yarus, M.: 2002, Phenylalanine-Binding RNAs and Genetic Code Evolution, J. Mol. Evol. 54, 298-311.
43. Jäschke, A.: 2001, RNA-catalyzed Carbon-Carbon Bond Formation, Biol. Chem. 382, 1321-1325.
44. Johnston, W. K., Unrau, P. J., Lawrence, M. J., Glasner, M. E. and Bartel, D. P.: 2001, RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension, Science 292, 1319-1325.
45. Kamtekar, S., Schiffer, J. M., Xiong, H., Babik, J. M. and Hecht, M. H.: 1993, Protein Design by Binary Patterning of Polar and Nonpolar Amino Acids, Science 262, 1680-1685.
46. Khaitovich, P., Mankin, A. S., Green, R., Lancaster, L. and Noller, H. F.: 1999, Characterization of Functionally Active Subribosomal Particles from Thermus aquaticus, Proc. Natl. Acad. Sci. U.S.A. 96, 85-90.
47. Knight, R. D., Freeland, S. J. and Landweber, L. F.: 2001a, Rewiring the Keyboard: Evolvability of the Genetic Code, Nat. Rev. Genet. 2, 49-58.
48. Knight, R. D., Freeland, S. J. and Landweber, L. F.: 2001b, A Simple Model based on Mutation and Selection Explains Trends in Codon and Amino-acid Usage and GC Composition within and across Genomes, Genome Biology 2, 1-13.
49. Knight, R. D. and Landweber, L. F.: 2000, 'The Early Evolution of the Genetic Code, Cell 101, 569-572.
50. Knight, R. D., Landweber, L. F. and Yarus, M.: 2001c, 'How Mitochondria Redefine the Code, J. Mol. Evol. 53, 299-313.
51. Konecny, J., Eckert, M., Schöniger, M. and Ludwig, H. G.: 1993, Neutral Adaptation of the Genetic Code to Double-strand Coding, J. Mol. Evol. 36, 407-416.
52. Lee, N., Bessho, Y., Wei, K., Szostak, J. W. and Suga, H.: 2000, 'Ribozyme-catalyzed tRNA Aminoacylation, Nat. Struct. Biol 7, 28-33.
53. Leinfelder, W., Zehelein, E., Mandrand-Berthelot, M. A. and Bock, A.: 1988, Gene for a Novel tRNA Species that Accepts L-serine and Cotranslationally Inserts Selenocysteine, Nature 331, 723-725.
54. Lenski, R. E. and Travisano, M.: 1994, Dynamics of Adaptation and Diversification: A 10,000-Generation Experiment with Bacterial Populations, Proc. Natl. Acad. Sci. U.S.A. 91, 6808-6814.
55. Lewontin, R. C.: 1974, The Genetic Basis of Evolutionary Change, Columbia University Press, New York, New York.
56. Liu, D. R. and Schultz, P. G.: 1999, Progress Toward the Evolution of an Organism with an Expanded Genetic Code, Proc. Natl. Acad. Sci. U.S.A. 96, 4780-4785.
57. Luo, L. and Li, X.: 2002, Construction of Genetic Code from Evolutionary Stability, Biosystems 65, 83-97.
58. Maeshiro, T. and Kimura, M.: 1998, The Role of Robustness and Changeability on the Orgin and Evolution of Genetic Codes, Proc. Natl. Acad. Sci. U.S.A. 95, 5088-5093.
59. Maizels, N. and Weiner, A. M.: 1994, Phylogeny from Function: Evidence from the Molecular Fossil Record that tRNA Originated in Replication, Not Translation, Proc. Natl. Acad. Sci. U.S.A. 91, 6729-6734.
60. McGinness, K. E. and Joyce, G. F.: 2002, RNA-Catalyzed RNA Ligation on an External RNA Template, Chem. Biol. 9, 297-307.
61. Miller, S. L. and Orgel, L. E.: 1974, The Origin of Life on the Earth, Prentice Hall.
62. Müller, G. B. and Wagner, G. P.: 1991, Novelty in Evolution: Restructuring the Concept, Annu. Rev. Ecol. Syst. 22, 229-256.
63. Munson, P. J. and Singh, R. K.: 1997, Statistical Significance of Hierarchical Multi-body Potentials based on Delauney Tessellation and their Application in Sequence-structure Alignment, Protein Sci. 6, 1467-1481.
64. Nelson, K. E., Levy, M. and Miller, S. L.: 2000, Peptide Nucleic Acids Rather than RNA May have been the First Genetic Molecule, Proc. Natl. Acad. Sci. U.S.A.. 97, 3868-3871.
65. Nitta, I., Kamada, Y., Noda, H., Ueda, T. and Watanabe, K.: 1998, Reconstitution of Peptide Bond Formation with Escherichia coli 23S Ribosomal RNA Domains, Science 281, 666-669.
66. Osawa, S.: 1995, Evolution of the Genetic Code, Oxford University Press, Oxford.
67. Osawa, S., Jukes, T. H., Watanabe, K. and Muto, A.: 1992, Recent Evidence for Evolution of the Genetic Code, Microbiol. Rev. 56, 229-264.
68. Penny, D. and Poole, A.: 1999, The Nature of the Last Common Ancestor, Curr. Opin. Genet. Devel. 9, 672-699.
69. Ramakrishnan, V. and Moore, P. B.: 2001, Atomic Structures at Last: The Ribosome in 2000, Curr. Opinions Struct. Biol. 11, 144-154.
70. Ribas de Pouplana, L., Turner, R. J., Steer, B. A. and Schimmel, P.: 1998, Genetic Code Origins: tRNAs Older than their Synthethases?, Proc. Natl. Acad. Sci. U.S.A. 95, 11295-11300.
71. Riddle, D. S., Santiago, J. V., Bray-Hall, S. T., Doshi, N., Grantcharova, V. P., Yi, Q. and Baker, D.: 1997, Functional Rapidly Folding Proteins from Simplified Amino Acid Sequences, Nat. Struct. Biol 10, 805-809.
72. Rodin, S. N. and Ohno, S.: 1997, Four Primordial Model of tRNA-Synthase Recognition, Determined by the (G,C) Operational Code, Proc. Natl. Acad. Sci. U.S.A. 94, 5183-5188.
73. Ronneberg, T. A., Landweber, L. F. and Freeland, S. J.: 2000, Testing a Biosynthetic Theory of the Genetic Code: Fact or Artifact?, Proc. Natl. Acad. Sci. U.S.A. 87, 13690-13695.
74. Roth, A. and Breaker, R.: 1998, An Amino Acid as a Cofactor for a Catalytic Polynucleotide, Proc. Natl. Acad. Sci. U.S.A. 95, 6027-6031.
75. Sauer, R. T.: 1996, Protein Folding from a Combinatorial Perspective, Folding and Design 1, R27-R29.
76. 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. U.S.A. 90, 8763-8768.
77. Schuster, P., Fontana, W., Stadler, P. F. and Hofacker, I. L.: 1994, 'From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures, Proc. Roy. Soc. Lond. B 255, 279-284.
78. Sella, G. and Ardell, D. H.: 2002, The Impact of Message Mutation on the Fitness of a Genetic Code, J. Mol. Evol. 54, 638-651.
79. Shibata, T., Nishinaka, T., Mikawa, T., Aihara, H., Kurumizaka, H., Yokoyama, S. and Ito, Y: 2001, Homologous Genetic Recombination as an Intrinsic Dynamic Property of a DNA Structure Induced by RecA/Rad51-family Proteins: A Possible Advantage of DNA over RNA as Genomic Material, Proc. Natl. Acad. Sci. U.S.A. 98, 8425-8432.
80. Shimizu, M.: 1982, Molecular Basis for the Genetic Code, J. Mol. Evol. 18, 297-303.
81. Singh, R. K., Tropsha, A. and Vaisman, I. I.: 1996, Delauney Tessellation of Proteins: Four Body Nearest Neighbor Propensity of Amino Acid Residues, J. Comp. Biol. 3, 213-221.
82. Sippl, M. J.: 1990, Calculation of Conformational Ensembles from Potentials of Mean Force - An Approach to the Knowledge-based Prediction of Local Structures in Globular Proteins, J. Mol. Biol. 213, 859-883.
83. Sippl, M. J.: 1993, Recognition of Errors in Three-Dimensional Structures of Proteins, Proteins 17, 355-362.
84. Soukup, G. A. and Breaker, R. R.: 2000, Allosteric Nucleic Acid Catalysis, Curr. Opin. Struct. Biol. 10, 318-325.
85. Sousa, R., Chung, Y. J., Rose, J. P. and Wang, B. C.: 1993, Crystal Structure of Bacteriophage T7 RNA Polymerase at 3.3 Å Resolution, Nature 364, 593-599.
86. Spiegelman, S.: 1971, An Approach to Experimental Analysis of Precellular Evolution, Quart. Rev. Biophys. 4, 213-253.
87. Srinivasan, G., James, C. M. and Kryzcki, J. A.: 2002, Pyrrolysine Encoded by UAG in Archea: Charging of a UAG-decoding Specialized tRNA, Science 296, 1459-1462.
88. Stadler, B. M. R., Stadler, P. F., Wagner, G. and Fontana, W.: 2001, 'The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change, J. Theor. Biol. 213, 241-274.
89. Syvanen, M.: 2002, Recent Emergence of the Modern Genetic Code: A Proposal, Trends Genetics 18, 245-248.
90. Szathmáry, E.: 1999, The Origin of the Genetic Code: Amino Acids as Cofactors in the RNA World, Trends Genet. 15, 223-229.
91. Szostak, J. W. and Ellington, A. D.: 1993, 'In Vitro Selection of Functional RNA Sequences', in R. F. Gesteland and J. F. Atkins (eds), The RNA World, Cold Spring Harbor Laboratory Press, Plainview, NY, pp. 511-533.
92. Wagner, A.: 1996, Does Evolutionary Plasticity Evolve?, Evolution 50, 1008-1023.
93. Wagner, A.: 1999, Redundant Gene Functions and Natural Selection, J. Evol. Biol. 12, 1-16.
94. Wagner, A.: 2002, Selection and Gene Duplication: A View from the Genome, Genome Biology 3, 1012.1-1012.3.
95. Wagner, A. and Stadler, P. F.: 1999, Viral RNA and Evolved Mutational Robustness, J. Exp. Zool./MDE 285, 119-127.
96. Wagner, G. P. and Altenberg, L.: 1996, Complex Adaptations and the Evolution of Evolvability, Evolution 50, 967-976.
97. Weberndorfer, G.: 2002, 'Computational Models of the Genetic Code Evolution Based on Empirical Potentials', Ph.D. Thesis, University of Vienna, Available from http://www.tbi.univie.ac.at/.
98. Weberndorfer, G., Hofacker, I. L. and Stadler, P. F.: 1999, 'An Efficient Potential for Protein Sequence Design', in Computer Science in Biology, Bielefeld, D., pp. 107-112. Proceedings of the GCB'99, Hannover, D.
99. Woese, C.: 1998, The Universal Ancestor, Proc. Natl. Acad. Sci. U.S.A. 95, 6854-6859.
100. Woese, C. R.: 1965, On the Evolution of the Genetic Code, Proc. Natl. Acad. Sci. U.S.A. 54, 1546-1552.
101. Wong, J. T.-F.: 1975, A Co-Evolution Theory of the Genetic Code, Proc. Natl. Acad. Sci. U.S.A. 72, 1909-1912.
102. Wong, J. T.-F.: 1980, Role of Minimization of Chemical Distances between Amino Acids in the Evolution of the Genetic Code, Proc. Natl. Acad. Sci. U.S.A. 77, 1083-1086.
103. Yarus, M.: 1999, Boundaries for an RNA World, Curr. Opinions Chem. Biol. 3, 260-267.
104. Yarus, M. and Schultz, D.: 1997, Toward a Theory of Malleability in Genetic Coding, J. Mol. Evol. 45, 3-6.
105. Zheng, W., Cho, S. J., Vaisman, I. I. and Tropsha, A.: 1996, 'Statistical Geometry Analysis of Proteins: Implications for inverted Structure Prediction', in L. Hunter and T. Klein (eds), Biocomputing: Proceedings of the 1996 Pacific Symposium, pp. 614-623.
106. Zuker, M.: 2000, Calculating Nucleic Acid Secondary Structure, Curr. Opin. Struct. Biol. 10, 303-310.