What can information-asymmetric games tell us about the context of Crick's 'frozen accident'?

Journal of the Royal Society Interface

Volumn 10, Issue 88, 2013, Pages

  Jee, Justin ^a,b   Sundstrom, Andrew ^a   Massey, Steven E ^c   Mishra, Bud ^a,b  

^a NEW YORK UNIVERSITY   (United States)

^b NEW YORK UNIVERSITY   (United States)

^c UNIVERSITY OF PUERTO RICO RIO PIEDRAS   (Puerto Rico)

Author keywords

Genetic code; Information asymmetric games; RNA world; Signalling

Indexed keywords

AMINO ACIDS; MOLECULAR BIOLOGY; OPTIMAL SYSTEMS; SIGNALING;

COMPUTATIONAL MODEL; FROZEN ACCIDENTS; GENETIC CODE; INFORMATION TRANSFERS; INFORMATION-ASYMMETRIC GAMES; MESSAGE COMPLEXITY; NOVEL APPLICATIONS; RNA WORLD;

RNA;

ARTICLE; GAME; INFORMATION PROCESSING; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; RNA ANALYSIS; RNA STRUCTURE;

EID: 84884839966     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2013.0614     Document Type: Article

References (37)

1. Woese CR. 1965 Order in the genetic code. Proc. Natl Acad. Sci. USA 54, 71-75. (doi:10.1073/pnas.54.1.71)
2. Alff-Sternberger C. 1969 The genetic code and error transmission. Proc. Natl Acad. Sci. USA 64, 584-591. (doi:10.1073/pnas.64.2.584)
3. Crick FHC. 1968 The origin of the genetic code. J. Mol. Biol. 38, 367-379. (doi:10.1016/0022-2836(68)90392-6)
4. Wong JT. 1975 A co-evolution theory of the genetic code. Proc. Natl Acad. Sci. USA 72, 1909-1912. (doi:10.1073/pnas.72.5.1909)
5. Vetsigian K, Woese C, Goldenfeld N. 2006 Collective evolution and the genetic code. Proc. Natl Acad. Sci. USA 103, 10696-10701. (doi:10.1073/pnas. 0603780103)
6. Osawa S, Jukes TH 1989 Codon reassignment (codon capture) in evolution. J. Mol. E Vol. 28, 271-278. (doi:10.1007/BF02103422)
7. Massey S. 2008 A neutral origin for error minimization in the genetic code. J. Mol. E Vol. 67, 510-516. (doi:10.1007/s00239-008-9167-4)
8. Sella G, Ardell DH 2006 The coevolution of genes and genetic codes: Crick's frozen accident revisited. J. Mol. E Vol. 63, 297-313. (doi:10.1007/s00239-004-0176-7)
9. Maynard Smith J., Parker GA 1976 The logic of asymmetric contests. Anim. Behav. 24, 159-175. (doi:10.1016/S0003-3472(76)80110-8)
10. Cho I-K, Kreps DM 1987 Signaling games and stable equlibria. Q. J. Econ. 102, 179-221. (doi:10.2307/1885060)
11. Skyrms B. 2010 Signals: evolution, learning and information. Oxford, UK: Oxford University Press. (doi:10.1093/acprof:oso/9780199580828.001.0001)
12. Jansen VAA, van Baalen M. 2006 Altruism through beard chromodynamics. Nature 440, 663-666. (doi:10.1038/nature04387)
13. Traulsen A, Nowak MA 2007 Chromodynamics of cooperation in finite populations. PLoS ONE 2, e270. (doi:10.1371/journal.pone.0000270)
14. Smith JM. 1999 The idea of information in biology. Q. Rev. Biol. 74, 395-400. (doi:10.1086/394109)
15. Tlusty T. 2008 A simple model for the evolution of molecular codes driven by the interplay of accuracy, diversity, and cost. Phys. Biol. 5, 016001. (doi:10.1088/1478-3975/5/1/016001)
16. Tlusty T. 2010 A colorful origin for the genetic code: information theory, statistical mechanics, and the emergence of molecular codes. Phys. Life Rev. 100, 048101.
17. Massey SE, Garey JR 2007 A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs. J. Mol. E Vol. 64, 399-410. (doi:10.1007/s00239-005-0260-7)
18. Turk RM, Chumachenko NV, Yarus M. 2010 Multiple translational products from a five-nucleotide ribozyme. Proc. Natl Acad. Sci. USA 107, 4585-4589. (doi:10.1073/pnas.0912895107)
19. Murakami H, Ohta A, Goto Y., Sako Y, Suga H. 2006 Flexizyme as a versatile tRNA acylation catalyst and the application for translation. Nucleic Acids Symp. Ser. 50, 35-36. (doi:10.1093/nass/nrl018)
20. Itzkovits S, Alon U. 2007 The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 17, 405-412. (doi:10.1101/gr.5987307)
21. Grosjean H, Fiers W. 1982 Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18, 199-209. (doi:10.1016/0378-1119(82)90157- 3)
22. Weber AL, Pizzarello S. 2006 The peptide-catalyzed stereospecitic synthesis of tetrose: a possible model for prebiotic molecular evolution. Proc. Natl Acad. Sci. USA 103, 12713-12717. (doi:10.1073/pnas.0602320103)
23. Mandecki W. 1990 A method for construction of long randomized open reading frames and polypeptides. Protein Eng. 3, 221-226. (doi:10.1093/protein/ 3.3.221)
24. Omo Y, Kino Y, Sasagawa N., Ishiura S. 2005 Comparative analysis of the cytotoxicity of homopolymeric amino acids. Biochim. Biophys. Acta 1748, 174-179. (doi:10.1016/j.bbapap.2004.12.017)
25. Keefe AD, Szostak JW 2001 Functional proteins from a random sequence library. Nature 410, 715-718. (doi:10.1038/35070613)
26. Hayashi Y, Sakata H, Maniko Y., Urabe I, Yomo T. 2003 Can an arbitrary sequence evolve towards acquiring a biological function? J. Mol. E Vol. 56, 162-168. (doi:10.1007/s00239-002-2389-y)
27. Ito Y, Kawama T, Urabe I., Yomo T. 2004 Evolution of an arbitrary sequence in solubility. J. Mol. E Vol. 58, 196-202. (doi:10.1007/s00239-003- 2542-2)
28. Gerhart J, Kirschner M. 2007 The theory of facilitated variation. Proc. Natl Acad. Sci. USA 104(Suppl. 1), 8582-8589. (doi:10.1073/pnas.0701035104)
29. Shoval O, Sheftel H, Shinar G., Hart Y, Ramote O, Mayo A., Dekel E, Kavanagh K, Alon U. 2012 Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space. Science 336, 1157-1160. (doi:10.1126/science. 1217405)
30. Wright S. 1931 Evolution in mendelian populations. Genetics 16, 97-153.
31. Eigen M. 1971 Self organization of matter and the evolution of biological macromolecules. Die Naturwissenchafen 58, 467-523. (doi:10.1007/BF00623322)
32. Grantham R. 1974 Amino acid difference formula to help explain protein evolution. Science 185, 862-864. (doi:10.1126/science.185.4154.862)
33. Kramer EB, Farabaugh PJ 2006 The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA 13, 87-96. (doi:10.1261/rna.294907)
34. Holland J, Spindler K, Horodyski F., Grabau E, Nichol S, VandePol S. 1982 Rapid evolution of RNA genomes. Science 215, 1577-1585. (doi:10.1126/science. 7041255)
35. Fisher RA. 1922 On the dominance ratio. Proc. Roy. Soc. Edinb. 42, 321-341.
36. Schultz DW, Yarus M. 1994 Transfer RNA mutation and the malleability of the genetic code. J. Mol. Biol. 235, 1377-1380. (doi:10.1006/jmbi.1994.1094)
37. Silva RM, Miranda I, Moura G., Santos MAS. 2004 Yeast as a model organism for studying the evolution of non-standard genetic codes. Brief. Funct. Genomics Proteomics 3, 35-46. (doi:10.1093/bfgp/3.1.35)