A colorful origin for the genetic code: Information theory, statistical mechanics and the emergence of molecular codes

Physics of Life Reviews

Volumn 7, Issue 3, 2010, Pages 362-376

  Tlusty, Tsvi ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

Biological information channels; Error load; Fitness; Molecular codes; Origin of life; Origin of the genetic code; Rate distortion theory

Indexed keywords

BIOLOGICAL INFORMATION; FITNESS; GENETIC CODE; MOLECULAR CODES; ORIGIN OF LIFE; RATE-DISTORTION THEORY;

ACIDS; ELECTRIC DISTORTION; INFORMATION THEORY; PHASE TRANSITIONS; SIGNAL DISTORTION; STATISTICAL MECHANICS;

HEALTH;

AMINO ACID;

BIOGENESIS; CHEMISTRY; GENETIC CODE; GENETICS; HUMAN; INFORMATION SCIENCE; METABOLISM; MOLECULAR EVOLUTION; REVIEW; STATISTICAL MODEL;

AMINO ACIDS; BIOGENESIS; EVOLUTION, MOLECULAR; GENETIC CODE; HUMANS; INFORMATION THEORY; MODELS, STATISTICAL;

EID: 77956061022     PISSN: 15710645     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.plrev.2010.06.002     Document Type: Review

References (105)

1. Tlusty T. Rate-distortion scenario for the emergence and evolution of noisy molecular codes. Phys Rev Lett 2008, 100:48101-48104.
2. Tlusty T. A model for the emergence of the genetic code as a transition in a noisy information channel. J Theor Biol 2007, 249:331-342.
3. Tlusty T. A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity and cost. Phys Biol 2008, 5:016001.
4. Tlusty T. Casting polymer nets to optimize noisy molecular codes. Proc Natl Acad Sci U S A 2008, 105:8238-8243.
5. Tlusty T. A relation between the multiplicity of the second eigenvalue of a graph Laplacian, Courant's nodal line theorem and the substantial dimension of tight polyhedral surfaces. Elec J Linear Algebra 2007, 16:315-324.
6. Crick F.H. The origin of the genetic code. J Mol Biol 1968, 38:367-379.
7. Crick F.H. Codon-anticodon pairing: the wobble hypothesis. J Mol Biol 1966, 19:548-555.
8. Osawa S., Jukes T.H., Watanabe K., Muto A. Recent-evidence for evolution of the genetic-code. Microbiol Rev 1992, 56:229-264.
9. Osawa S. Evolution of the genetic code 1995, Oxford University Press, Oxford, New York.
10. Woese C.R. Order in the genetic code. Proc Natl Acad Sci U S A 1965, 54:71-75.
11. Goldberg A.L., Wittes R.E. Genetic code: aspects of organization. Science 1966, 153:420-424.
12. Epstein C.J. Role of the amino-acid 'code' and of selection for conformation in the evolution of proteins. Nature 1966, 210:25-28.
13. Woese C.R. Evolution of the genetic code. Naturwissenschaften 1973, 60:447-459.
14. Butler T., Goldenfeld N., Mathew D., Luthey-Schulten Z. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys Rev E 2009, 79:60901-60904.
15. Grantham R. Amino acid difference formula to help explain protein evolution. Science 1974, 185:862-864.
16. Wolfenden R.V., Cullis P.M., Southgate C.C. Water, protein folding, and the genetic code. Science 1979, 206:575-577.
17. Sjöström M., Wold S. A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids. J Mol Evol 1985, 22:272-277.
18. Haig D., Hurst L.D. A quantitative measure of error minimization in the genetic-code. J Mol Evol 1991, 33:412-417.
19. Szathmáry E., Zintzaras E. A statistical test of hypotheses on the organization and origin of the genetic code. J Mol Evol 1992, 35:185-189.
20. Freeland S.J., Knight R.D., Landweber L.F., Hurst L.D. Early fixation of an optimal genetic code. Mol Biol Evol 2000, 17:511-518.
21. Sella G., Ardell D. The coevolution of genes and genetic codes: Crick's frozen accident revisited. J Mol Evol 2006, 63:297-313.
22. Pelc S.R., Welton M.G. Stereochemical relationship between coding triplets and amino-acids. Nature 1966, 209:868-870.
23. Weber A.L., Lacey J.C. Genetic code correlations - amino-acids and their anticodon nucleotides. J Mol Evol 1978, 11:199-210.
24. Jungck J.R. The genetic code as a periodic table. J Mol Evol 1978, 11:211-224.
25. Shimizu M. Molecular basis for the genetic code. J Mol Evol 1982, 18:297-303.
26. Lacey J.C., Wickramasinghe N., Cook G.W. Experimental studies on the origin of the genetic-code and the process of protein-synthesis - a review update. Orig Life Evol Biosph 1992, 22:243-275.
27. Yarus M. RNA-ligand chemistry: a testable source for the genetic code. RNA (New York, N. Y.) 2000, 6:475-484.
28. Lehmann J. Physico-chemical constraints connected with the coding properties of the genetic system. J Theor Biol 2000, 202:129-144.
29. Ikehara K., Omori Y., Arai R., Hirose A. A novel theory on the origin of the genetic code: a GNC-SNS hypothesis. J Mol Evol 2002, 54:530-538.
30. Rodin S.N., Rodin A.S. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 2008, 100:341-355.
31. Wong J.T. A co-evolution theory of the genetic code. Proc Natl Acad Sci U S A 1975, 72:1909-12.
32. Taylor F.J.R., Coates D. The code within the codons. Biosystems 1989, 22:177-187.
33. Davis B.K. Evolution of the genetic code. Prog Biophys Mol Biol 1999, 72:157-243.
34. Wong J.T. Coevolution theory of the genetic code at age thirty. Bioessays 2005, 27:416-425.
35. Figureau A. Optimization and the genetic code. Orig Life Evol Biosph 1989, 19:57-67.
36. Knight R.D., Freeland S.J., Landweber L.F. Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2001, 2:49-58.
37. Sella G., Ardell D.H. The impact of message mutation on the fitness of a genetic code. J Mol Evol 2002, 54:638-651.
38. Ardell D.H., Sella G. On the evolution of redundancy in genetic codes. J Mol Evol 2001, 53:269-281.
39. Ardell D.H., Sella G. No accident: genetic codes freeze in error-correcting patterns of the standard genetic code. Philos Trans R Soc Lond B Biol Sci 2002, 357:1625-1642.
40. Di Giulio M. The origin of the genetic code: theories and their relationships, a review. Biosystems 2005, 80:175-184.
41. Jungck J.R. Genetic codes as codes: Towards a theoretical basis for bioinformatics. BIOMAT 2008 2008, 300-337. World Scientific, Brazil. R.P. Mondaini (Ed.).
42. Chambers I., Frampton J., Goldfarb P., Affara N., McBain W., Harrison P.R. The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the 'termination' codon, TGA. EMBO J 1986, 5:1221-1227.
43. Srinivasan G., James C.M., Krzycki J.A. Pyrrolysine encoded by UAG in archaea: charging of a UAG-decoding specialized tRNA. Science 2002, 296:1459-1462.
44. Sonneborn T. Degeneracy of the genetic code: Extent, nature and genetic implication. Evolving genes and proteins 1965, 377-397. Academic, New York. V. Bryson, H. Vogel (Eds.).
45. Woese C.R. On the evolution of the genetic code. Proc Natl Acad Sci U S A 1965, 54:1546-1552.
46. Zuckerkandl E., Pauling L. Evolutionary divergence and convergence in proteins. Evolving genes and proteins 1965, 97-166. Academic, New York. V. Bryson, H. Vogel (Eds.).
47. Alff-Steinberger C. The genetic code and error transmission. Proc Natl Acad Sci U S A 1969, 64:584-591.
48. Lagerkvist U. Codon Misreading - a restriction operative in the evolution of the genetic-code. Am Sci 1980, 68:192-198.
49. Swanson R. A unifying concept for the amino acid code. Bull Math Biol 1984, 46:187-203.
50. Figureau A., Pouzet M. Genetic code and optimal resistance to the effects of mutations. Orig Life 1984, 14:579-588.
51. Trinquier G., Sanejouand Y.H. Which effective property of amino acids is best preserved by the genetic code? Protein Engineering Design and. Selection 1998, 11:153-169.
52. Goldman N. Further results on error minimization in the genetic code. J Mol Evol 1993, 37:662-664.
53. Freeland S.J., Hurst L.D. The genetic code is one in a million. J Mol Evol 1998, 47:238-248.
54. Ardell D.H. On error minimization in a sequential origin of the standard genetic code. J Mol Evol 1998, 47:1-13.
55. Gilis D., Massar S., Cerf N., Rooman M. Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biol 2001, 2. 0049.1-12.
56. Luo L., Li X. Coding rules for amino acids in the genetic code: The genetic code is a minimal code of mutational deterioration. Orig Life Evol Biosph 2002, 32:23-33.
57. Barreau G. The evolutionary consequences of redundancy in natural and artificial genetic codes 2002, University of Sussex.
58. Hoffmann G.W. On the origin of the genetic code and the stability of the translation apparatus. J Mol Biol 1974, 86:349-362.
59. Bedian V. The possible role of assignment catalysts in the origin of the genetic code. Orig Life Evol Biosph 1982, 12:181-204.
60. Vetsigian K., Woese C., Goldenfeld N. Collective evolution and the genetic code. Proc Natl Acad Sci U S A 2006, 103:10696-10701.
61. Shannon, CE. Coding theorems for a discrete source with a fidelity criterion. National Convention Record; 1959. p. 142-163.
62. Berger T. Rate distortion theory 1971, Prentice Hall, NJ.
63. Cover T.M., Thomas J.A. Elements of information theory 2006, Wiley-Interscience, Hoboken, NJ. 2nd ed.
64. Dyson F.J. A model for the origin of life. J Mol Evol 1982, 18:344-350.
65. Dyson F.J. Origins of life 1999, Cambridge Univ., Cambridge.
66. Szathmary E., Maynard Smith J. From replicators to reproducers: the first major transitions leading to life. J Theor Biol 1997, 187:555-571.
67. Szathmary E. The origin of the genetic code: amino acids as cofactors in an RNA world. Trends Genet 1999, 15:223-229.
68. Wachtershauser G. Groundworks for an evolutionary biochemistry: The iron-sulphur world. Prog Biophys Mol Biol 1992, 58:85-201.
69. Fitch W.M., Upper K. The phylogeny of transfer-RNA sequences provides evidence for ambiguity reduction in the origin of the genetic-code. Cold Spring Harb Symp Quant Biol 1987, 52:759-767.
70. Fox S.W. Self-ordered polymers and propagative cell-like systems. Naturwissenschaften 1969, 56:1-9.
71. Fox S.W. A theory of macromolecular and cellular origins. Nature 1965, 205:328-340.
72. Zeldovich K.B., Chen P., Shakhnovich B.E., Shakhnovich E.I. A first-principles model of early evolution: Emergence of gene families, species, and preferred protein folds. PLoS Comput Biol 2007, 3:e139.
73. Maynard Smith J., Szathmáry E. The major transitions in evolution 1995, W.H. Freeman Spektrum, Oxford, New York.
74. Edwards, A.W.F. Picturing the genetic code. Available from Nature Precedings 2007; doi:10.1038/npre.2007.682.1.
75. Pohlmeyer R. The genetic code revisited. J Theor Biol 2008, 253:623-624.
76. Davis B.K. On mapping the genetic code. J Theor Biol 2009, 259:860-862.
77. Hayes B. Ode to the code. Am Sci 2004, 92:494-498.
78. Gross J.L., Tucker T.W. Topological graph theory 1987, Wiley, New York.
79. Weber A.L., Miller S.L. Reasons for the occurrence of the twenty coded protein amino acids. J Mol Evol 1981, 17:273-284.
80. Trifonov E.N. Consensus temporal order of amino acids and evolution of the triplet code. Gene 2000, 261:139-151.
81. Tlusty T. The physical language of molecular codes: A rate-distortion approach to the evolution and emergence of biological codes. 43rd annual conference on information sciences and systems 2009, 841-846.
82. Kac M. Can one hear the shape of a drum?. Amer Math Monthly 1966, 73:1-23.
83. Courant R., Hilbert D. Methods of mathematical physics 1953, Interscience, New York.
84. Davies E.B., Gladwell G.M.L., Leydold J., Stadler P.F. Discrete nodal domain theorems. Linear Algebra Appl 2001, 336:51-60.
85. Eckmann J.-P. Trading codes for errors. Proc Natl Acad Sci U S A 2008, 105:8165-8166.
86. Ringel G., Youngs J.W.T. Solution of the Heawood map-coloring problem. Proc Natl Acad Sci U S A 1968, 60:438-445.
87. Banchoff T.F. Tightly embedded 2-dimensional polyhedral manifolds. Amer J Math 1965, 87:462-472.
88. Banchoff T.F., Kuhnel W. Tight submanifolds, smooth and polyhedral. Tight and taut submanifolds 1997, 51-118. Cambridge Univ., Cambridge.
89. Baranov P.V., Venin M., Provan G. Codon size reduction as the origin of the triplet genetic code. PLoS ONE 2009, 4:e5708.
90. Weberndorfer G., Hofacker I.L., Stadler P.F. On the evolution of primitive genetic codes. Orig Life Evol Biosph 2003, 33:491-514.
91. Wang L., Xie J., Schultz P.G. Expanding the genetic code. Annu Rev Biophys Biomol Struct 2006, 35:225-249.
92. Budisa N. Prolegomena to future experimental efforts on genetic code engineering by expanding its amino acid repertoire. Angew Chem Int Ed 2004, 43:6426-6463.
93. Osawa S., Jukes T.H. On codon reassignment. J Mol Evol 1995, 41:247-249.
94. Szathmáry E. Codon swapping as a possible evolutionary mechanism. J Mol Evol 1991, 32:178-182.
95. Lehman N., Jukes T.H. Genetic code development by stop codon takeover. J Theor Biol 1988, 135:203-214.
96. Shinar G., Dekel E., Tlusty T., Alon U. Rules for biological regulation based on error minimization. Proc Natl Acad Sci U S A 2006, 103:3999-4004.
97. Itzkovitz S., Tlusty T., Alon U. Coding limits on the number of transcription factors. BMC Genomics 2006, 7:239.
98. Dónaill D.A.M. Why nature chose A, C, G and U/T: An error-coding perspective of nucleotide alphabet composition. Orig Life Evol Biosph 2003, 33:433-455.
99. Wallace R. Metabolic constraints on the evolution of genetic codes: Did multiple 'preaerobic' ecosystem transitions entrain richer dialects via Serial Endosymbiosis? Available from Nature Precedings 2010. http://hdl.handle.net/10101/npre.2010.4120.3.
100. Savir Y., Tlusty T. Conformational proofreading: the impact of conformational changes on the specificity of molecular recognition. PLoS ONE 2007, 2:e468.
101. Savir Y., Tlusty T. Optimal design of a molecular recognizer: Molecular recognition as a Bayesian signal detection problem. IEEE J Selected Topics Signal Process 2008, 2:390-399.
102. Savir Y., Tlusty T. Molecular recognition as an information channel: The role of conformational changes. 43rd annual conference on information sciences and systems 2009, 835-840.
103. Tlusty T., Bar-Ziv R., Libchaber A. High-fidelity DNA sensing by protein binding fluctuations. Phys Rev Lett 2004, 93:258103.
104. Bar-Ziv R., Tlusty T., Libchaber A. Protein-DNA computation by stochastic assembly cascade. Proc Natl Acad Sci U S A 2002, 99:11589-11592.
105. Sagi D., Tlusty T., Stavans J. High fidelity of RecA-catalyzed recombination: a watchdog of genetic diversity. Nucleic Acids Res 2006, 34:5021-5031.