Genotypes with phenotypes: Adventures in an RNA toy world

Biophysical Chemistry

Volumn 66, Issue 2-3, 1997, Pages 75-110

  Schuster, Peter ^a,b  

^a UNIVERSITY OF VIENNA   (Austria)

^b SANTA FE INSTITUTE   (United States)

Author keywords

Dynamics of evolution; Evolutionary biotechnology; Fitness landscape; Molecular evolution; RNA structure; Selective neutrality

Indexed keywords

EVOLUTION; GENOTYPE; HUMAN; NONHUMAN; PHENOTYPE; POPULATION DYNAMICS; PRIORITY JOURNAL; REVIEW; RNA STRUCTURE;

EID: 0030798341     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(97)00058-6     Document Type: Article

References (95)

1. C. Amitrano, L. Peliti, and M. Saber. A spin-glass model of evolution. In A. S. Perelson and S. A. Kauffman, editors, Molecular Evolution on Rugged Landscapes, volume IX of Santa Fe Institute Studies in the Sciences of Complexity, pages 27-38. Addison-Wesley Publ. Co., Redwood City, CA, 1991.
2. D. P. Bartel and J. W. Szostak. Isolation of new ribozymes from a large pool of random sequences. Science, 261:1411-1418, 1993.
3. A. A. Beaudry and G. F. Joyce. Directed evolution of an RNA enzyme. Science, 257:635-641, 1992.
4. C. K. Biebricher. Replication and evolution of short-chained RNA species by Qβ replicase. Cold Spring Harbor Symp. Quant. Biol., 52:299-306, 1988.
5. C. K. Biebricher and M. Eigen. Kinetics of RNA replication by Qβ replicase. In E. Domingo, J. J. Holland, and P. Ahlquist, editors, RNA Genetics. Vol.I: RNA Directed Virus Replication, pages 1-21. CRC Press, Boca Raton, FL, 1988.
6. C. K. Biebricher, M. Eigen, W. C. Gardiner, Y. Husimi, H. C. Keweloh, and A. Obst. Modeling studies of RNA replication and viral infection. In J. Warnatz and W. Jäger, editors. Complex Chemical Reaction Systems: Mathematical Modeling and Simulation. Proceedings of the Second Workshop, pages 17-38, Berlin, 1987. Springer-Verlag.
7. T. R. Cech. RNA as an enzyme. Sci. Am., 255(5):76-84, 1986.
8. T. R. Cech. Self-splicing of group I introns. Ann. Rev. Biochem., 59:543-568, 1990.
9. K. B. Chapman and J. W. Szostak. In vitro selection of catalytic RNAs. Curr. Opinion in Struct. Biol., 4:618-622, 1994.
10. F. C. Christians and L. A. Loeb. Novel human DNA alkyltranferases obtained by random substitution and genetic selection in bacteria. Proc. Natl. Acad. Sci. USA, 93:6124-6128, 1996.
11. C. R. Darwin. The Origin of Species, page 81. Number 811 in Everyman's Library. J. M. Dent & Sons, Aldine House, Bedford Street, London, UK, 1928.
12. M. O. Dayhoff and W. C. Barker. Mechanisms in molecular evolution: Examples. In M. O. Dayhoff, editor, Atlas of Protein Sequence and Structure, Vol. 5, pages 41-45. Natl. Biomed. Res. Found., Silver Spring, MD, 1972.
13. L. Demetrius, P. Schuster, and K. Sigmund. Polynucleotide evolution and branching processes. Bull. Math. Biol., 47:239-262, 1985.
14. B. Derrida. Random-energy model: An exactly solvable model of disordered systems. Phys. Rev. B, 24:2613-2626, 1981.
15. B. Derrida and L. Peliti. Evolution in a flat fitness landscape. Bull. Math. Biol., 53:355-382, 1991.
16. T. Dobzhansky. Nothing in biolology makes sense except in the light of evolution. Am. Bio. Teacher, 35:125-129, 1973.
17. E. Domingo. Virus quasispecies: Impact for disease control. Futura, 3/90:6-8, 1990.
18. E. Domingo, M. Dávila, and J. Ortin. Nucleotide sequence heterogeneity of the RNA from a population of foot-and-mouth disease virus. Gene, 11:333-346, 1980.
19. E. Domingo, J. J. Holland, and P. Ahlquist, editors. RNA Genetics. CRC Press, Boca Raton, FL, 1988.
20. E. Domingo, D. Sabo, T. Taniguchi, and C. Weissmann. Nucleotide sequence heterogeneity of an RNA phage population. Cell, 13:735-744, 1978.
21. M. Eigen. Selforganization of matter and the evolution of biological macromolecules. Naturwissenschaften, 58:465-523, 1971.
22. M. Eigen. Macromolecular evolution: Dynamical ordering in sequence space. Ber. Bunsenges. Phys. Chem., 89:658-667, 1985.
23. M. Eigen and C. K. Biebricher. Sequence space and quasispecies distribution. In E. Domingo, J. J. Holland, and P. Ahlquist, editors, RNA Genetics. Vol.III: Variability of Virus Genomes, pages 211-245. CRC Press, Boca Raton, FL, 1988.
24. M. Eigen, C. K. Biebricher, M. Gebinoga, and W. C. Gardiner. The hypercycle. Coupling of RNA and protein biosynthesis in the infection cycle of art RNA bacteriophage. Biochemistry, 30:11005-11018, 1991.
25. M. Eigen and W. C. Gardiner. Evolutionary molecular engineering based on RNA replication. Pure Appl. Chem., 56:967-978, 1984.
26. M. Eigen, J. McCaskill, and P. Schuster. The molecular quasispecies. Adv. Chem. Phys., 75:149-263, 1989.
27. M. Eigen and P. Schuster. The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle. Naturwissenschaften, 64:541-565, 1977.
28. A. D. Ellington. Aptamers achieve the desired recognition. Current Biology, 4:427-429, 1994.
29. A. D. Ellington and J. W. Szostak. In vitro selection of RNA moleucles that bind specific ligands. Nature, 346:818-822, 1990.
30. C. Escarmís, M. Dávila, N. Charpentier, A. Bracho, A. Moya, and E. Domingo. Genetic lesions associated with muller's ratchet in an RNA virus. J. Mol. Biol., 264:255-267, 1996.
31. W. Fontana and L. Buss. "the arrival of the fittest": Toward a theory of biological organization. Bull. Math. Biol., 56:1-64, 1994.
32. W. Fontana and L. Buss. What would be conserved "if the tape were played twice". Proc. Natl. Acad. Sci. USA, 71:757-761, 1994.
33. W. Fontana, T. Griesmacher, W. Schnabl, P. F. Stadler, and P. Schuster. Statistics of landscapes based on free energies, replication and degradation rate constants of RNA secondary structures. Mh. Chem., 122:795-819, 1991.
34. W. Fontana, D. A. M. Konings, P. F. Stadler, and P. Schuster. Statistics of RNA secondary structures. Biopolymers, 33:1389-1404, 1993.
35. W. Fontana, W. Schnabl, and P. Schuster. Physical aspects of evolutionary optimization and adaptation. Phys. Rev. A, 40:3301-3321, 1989.
36. W. Fontana and P. Schuster. A computer model of evolutionary optimization. Biophys. Chem., 26:123-147, 1987.
37. Galileo Galilei. Opere, volume 6, page 232. Barbera, Firenze, Italy, A. Favaro edition, 1968. The original quotation reads: "... It (the great book of the universe) is written in the language of mathematics and its symbols are triangles, circles. ...".
38. L. M. Gierasch and J. King, editors. Protein Folding, Deciphering the Second Half of the Genetic Code. American Association for the Advancement of Science. Washington, DC, 1990.
39. W. Gilbert. The RNA world. Nature, 319:618, 1986.
40. W. Grüner, R. Giegerich, D. Strothmann, C. Reidys, J. Weber, I. L. Hofacker, P. F. Stadler, and P. Schuster. Analysis of RNA sequence structure maps by exhaustive enumeration. I. Neutral networks. Mh.Chem., 127:355-374, 1996.
41. W. Grüner, R. Giegerich, D. Strothmann, C. Reidys, J. Weber, I. L. Hofacker, P. F. Stadler, and P. Schuster. Analysis of RNA sequence structure maps by exhaustive enumeration. II. Structure of neutral networks and shape space covering. Mh. Chem., 127:375-389, 1996.
42. C. Guerrier-Takada, K. Gardiner, T. Marsh, N. Pace, and S. Altman. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell, 35:849-857, 1983.
43. R. W. Hamming. Error detecting and error correcting codes. Bell Syst. Tech. J., 29:147-160, 1950.
44. P. G. Higgs and B. Derrida. Stochastic models for species formation in evolving populations. J. Physics A, 24:L985-L991, 1991.
45. P. G. Higgs and B. Derrida. Genetic distance and species formation in evolving populations. J. Mol. Evol., 35:454-465, 1992.
46. I. L. Hofacker, W. Fontana, P. F. Stadler, S. Bonhoeffer, M. Tacker, and P. Schuster. Fast folding and comparison of RNA secondary structures. Mh. Chem., 125:167-188, 1994.
47. I. L. Hofacker, P. Schuster, and P. F. Stadler. Combinatorics of RNA secondary structures. Preprint, 1996.
48. P. Hogeweg and B. Hesper. Energy directed folding of RNA sequences. Nucleic Acids Research, 12:67-74, 1984.
49. M. A. Huynen, P. F.Stadler, and W. Fontana. Smoothness within ruggedness: The role of neutrality in adaptation. Proc. Natl. Acad. Sci. USA, 93:397-401, 1996.
50. R. D. Jenison, S. C. Gill, A. Pardi, and B. Polisky. High-resolution molecular discrimination by RNA. Science, 263:1425-1429, 1994.
51. G. F. Joyce. RNA evolution and the origins of life. Nature, 338:217-224, 1989.
52. G. F. Joyce. Directed molecular evolution. Sci. Am., 267(6):48-55, 1992.
53. H. F. Judson. The Eighth Day of Creation - The Makers of the Revolution in Biology. Jonathan Cape Ltd., London, 1979.
54. S. A. Kauffman. Autocatalytic sets of proteins. J. Theor. Biol., 119:1-24, 1986.
55. S. A. Kauffman. Applied molecular evolution. J. Theor. Biol., 157:1-7, 1992.
56. S. A. Kauffman and S. Levine. Towards a general theory of adaptive walks on rugged landscapes. J. Theor. Biol., 128:11-45, 1987.
57. S. A. Kauffman and E. D. Weinberger. The n-k model of rugged fitness landscapes and its application to maturation of the immune response. J. Theor. Biol., 141:211-245, 1989.
58. M. Kimura. The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK, 1983.
59. J. M. Köhler, R. Pechmann, A. Scharper, A. Schober, T. M. Jovin, M. Thürk, and A. Schwienhorst. Micromachanical elements for the detection of molecules and molecular design. Microsystems Technol., 1:202-208, 1995.
60. D. Konings and P. Hogeweg. Pattern analysis of RNA secondary structure. Similarity and consensus of minimal-energy folding. J. Mol. Biol., 207:597-614, 1989.
61. N. Lehman and G. F. Joyce. Evolution in vitro: Analysis of a lineage of ribozymes. Current Biology, 3:723-734, 1993.
62. R. E. Lenski and M. Travisano. Dynamics of adaptation and diversification: A 10,000-generation experiment with bacterial populations. Proc. Natl. Acad. Sci. USA, 91:6808-6814, 1994.
63. R. A. Lerner, S. J. Benkovic, and P. G. Schultz. At the crossroads of chemistry and immunology: Catalytic antibodies. Science, 252:659-667, 1991.
64. H. Li, R. Helling, C. Tang, and N. Wingreen. Emergence of preferred structures in a simple model of protein folding. Science, 273:666-669, 1996.
65. J. R. Lorsch and J. W. Szostak. In vitro evolution of new ribozymes with polynucleotide kinase activity. Nature, 371:31-36, 1994.
66. A. M. Martín-Hernández, E. Domingo, and L. Menédez-Arias. Human immunodeficiency virus reverse transcriptase: Role of tyr 115 in deoxynucleotide binding and misinsertion fidelity of DNA synthesis. EMBO J., 150:4434-4442, 1996.
67. D. R. Mills, R. L. Peterson, and S. Spiegelman. An extracellular Darwinian experiment with a self-duplicating nucleic acid molecule. Proc. Natl. Acad. Sci. USA, 58:217-224, 1967.
68. K. M. Munir, D. C. French, and L. A. Loeb. Thymidine kinase mutants obtained by random selection. Proc. Natl. Acad. Sci. USA, 90:4012-1016, 1993.
69. M. Nei and R. K. Koehn, editors. Evolution of Genes and Proteins. Sinauer Associates Inc., Sunderland, MA, 1983.
70. M. Nowak and P. Schuster. Error thresholds of replication in finite populations. Mutation frequencies and the onset of Muller's ratchet. J. Theor. Biol., 137:375-395, 1989.
71. D. Park. The How and the Why. An essay on the Origins and Development of Physical Theory. Princeton University Press, Princeton, NJ, 1988.
72. C. Reidys, C. V. Forst, and P. Schuster. Replication on neutral networks of RNA secondary structures. Preprint, 1996.
73. C. Reidys and P. F. Stadler. Bio-molecular shapes and algebraic structures. Computers Chem., 20:85-94, 1996.
74. C. Reidys, P. F. Stadler, and P. Schuster. Generic properties of combinatory maps - Neutral networks of RNA secondary structures. Bull. Math. Biol., 59:339-397, 1997.
75. A. Schober, A. Schwienhorst, J. M. Köhler, M. Fuchs, R. Günther, and M. Thürk. Microsystems for independent parallel chemical and biochemical processing. Microsystems Technol., 1:168-172, 1995.
76. A. Schober, N. G. Walter, U. Tangen, G. Strunk, T. Ederhof, J. Dapprich, and M. Eigen. Multichannel PCR and serial transfer machine as a future tool in evolutionary biotechnology. BioTechniques, 18:652-658, 1995.
77. P. G. Schultz. Catalytic antibodies. Angew.Chem., 28:1283-1295, 1989.
78. P. Schuster. Artificial life and molecular evolutionary biology. In F. Morán, A. Moreno, J. J. Morelo, and P. Chacón, editors, Advances in Artificial Life, volume 929 of Lecture Notes in Artificial Intelligence, pages 3-19. Springer-Verlag, Berlin, 1995.
79. P. Schuster. How to search for RNA structures. Theoretical concepts in evolutionary biotechnology. Journal of Biotechnology, 41:239-257, 1995.
80. P. Schuster. How does complexity arise in evolution? Complexity, 2:22-30, 1996.
81. P. Schuster, W. Fontana, P. F. Stadler, and I. L. Hofacker. From sequences to shapes and back: A case study in RNA secondary structures. Proc.Roy.Soc. (London) B, 255:279-284, 1994.
82. P. Schuster and P. F. Stadler. Landscapes: Complex optimization problems and biopolymer structures. Computers Chem., 18:295-314, 1994.
83. P. Schuster, P. F. Stadler, and A. Renner. RNA Structure and folding. From conventional to new issues in structure predictions. Curr. Opinion in Struct. Biol., 7(3), 1997. In press.
84. P. Schuster and J. Swetina. Stationary mutant distribution and evolutionary optimization. Bull. Math. Biol., 50:635-660, 1988.
85. S. Spiegelman. An approach to the experimental analysis of precellular evolution. Quart. Rev. Biophys., 4:213-253, 1971.
86. G. Strunk. Automatized evolution experiments in vitro and natural selection under controlled conditions by means of the serial transfer technique. PhD thesis, Universität Braunschweig, 1993.
87. J. Swetina and P. Schuster. Self-replication with errors - A model for polynucleotide replication. Biophys.Chem., 16:329-345, 1982.
88. M. Tacker, P. F. Stadler, E. G. Bornberg-Bauer, I. L. Hofacker, and P. Schuster. Algorithm independent properties of RNA secondary structure predictions. Eur.Biophys.J., 25:115-130. 1996.
89. M. Travisano and R. E. Lenski. Long-term experimental evolution in escherichia coli. IV. Targets of selection and the specificity of adaptation. Genetics, 143:15-26, 1996.
90. C. Tuerk and L. Gold. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science, 249:505-510, 1990.
91. M. S. Waterman. Secondary structure of single-stranded nucleic acids. Studies on foundations and combinatorics. Advances in Mathematics. Supplementary studies. Academic Press N. Y., 1:167-212, 1978.
92. J. Weber, C. Reidys, C. Forst, and P. Schuster. Evolutionary dynamics on neutral networks. Preprint, IMB Jena, Germany, 1996.
93. T. Wiehe, E. Baake, and P. Schuster. Error propagation in reproduction of diploid organisms. A case study in single peaked landscapes. J. Theor. Biol., 177:1-15, 1995.
94. S. Wright. The roles of mutation, inbreeding, crossbreeding and selection in evolution. In D. F. Jones, editor, Int. Proceedings of the Sixth International Congress on Genetics, volume 1, pages 356-366, 1932.
95. M. Zuker and D. Sankoff. RNA secondary structures and their prediction. Bull. Math. Biol., 46:591-621, 1984.