Local stability and evolution of the genetic code

Journal of Theoretical Biology

Volumn 261, Issue 4, 2009, Pages 643-653

  Chechetkin, V R ^a   Lobzin, V V ^b  

^a TROITSK INSTITUTE FOR INNOVATION AND FUSION RESEARCH   (Russian Federation)

^b UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Error minimization theory; Evolution; Genetic code; Mutational and translational stability; Natural selection; Stability function

Indexed keywords

AMINO ACID; GAUSSIAN METHOD; GENETICS; MUTATION; NATURAL SELECTION;

AMINO ACID SEQUENCE; ARTICLE; DNA MODIFICATION; GENETIC CODE; GENETIC STABILITY; GENETIC VARIABILITY; MOLECULAR EVOLUTION; NORMAL DISTRIBUTION; PRIORITY JOURNAL; STATISTICAL ANALYSIS; STOP CODON;

AMINO ACIDS; EVOLUTION, MOLECULAR; GENETIC CODE; GENETIC VARIATION; GENOMIC INSTABILITY; HUMANS; MODELS, GENETIC; MUTATION; PROTEIN BIOSYNTHESIS;

EID: 70350575251     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.08.031     Document Type: Article

References (63)

1. Abel D.L., and Trevors J.T. Self-organization vs. self-ordering events in life-origin models. Phys. Life Rev. 3 (2006) 211-228
2. Alff-Steinberger C. The genetic code and error transmission. Proc. Natl. Acad. Sci. USA 64 (1969) 584-591
3. Ardell D.H. On error minimization in a sequential origin of the standard genetic code. J. Mol. Evol. 47 (1998) 1-13
4. Amirnovin R. An analysis of the metabolic theory of the origin of the genetic code. J. Mol. Evol. 44 (1997) 473-476
5. Archetti M. Codon usage bias and mutation constraints reduce the level of error minimization of the genetic code. J. Mol. Evol. 59 (2004) 258-266
6. In: Barbieri M. (Ed). Biosemiotics. vol. 1. The Codes of Life. The Rules of Macroevolution (2008), Springer, Amsterdam
7. Benner S.A., Cohen M.A., and Gonnet G.H. Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng. 7 (1994) 1323-1332
8. Black S.D., and Mould D.R. Development of hydrophobicity parameters to analyze proteins which bear post or cotranslational modifications. Anal. Biochem. 193 (1991) 72-82
9. Blalock J.E., and Smith E.M. Hydropathic anti-complementarity of amino acids based on the genetic code. Biochem. Biophys. Res. Commun. 121 (1984) 203-207
10. Cavalcanti A.R.O., De Barros Neto B., and Ferreira R. On the classes of aminoacyl-tRNA synthetases and the error minimization in the genetic code. J. Theor. Biol. 204 (2000) 15-20
11. Chechetkin V.R. Block structure and stability of the genetic code. J. Theor. Biol. 222 (2003) 177-188
12. Chechetkin V.R. Genetic code from tRNA point of view. J. Theor. Biol. 242 (2006) 922-934
13. Copley S.D., Smith E., and Morowitz H.J. A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc. Natl. Acad. Sci. USA 102 (2005) 4442-4447
14. Crick F.H. The origin of genetic code. J. Mol. Biol. 38 (1968) 367-379
15. Delarue M. An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices. RNA 13 (2007) 161-169
16. Di Giulio M. Some aspects of the organization and evolution of the genetic code. J. Mol. Evol. 29 (1989) 191-201
17. Di Giulio M. The origin of the genetic code: theories and their relationships, a review. BioSystems 80 (2005) 175-184
18. Di Giulio M., and Medugno M. The historical factor: the biosynthetic relationships between amino acids and their physicochemical properties in the origin of genetic code. J. Mol. Evol. 46 (1998) 615-621
19. Freeland S.J., and Hurst L.D. The genetic code is one in a million. J. Mol. Evol. 47 (1998) 238-248
20. Freeland S.J., Knight R.D., Landweber L.F., and Hurst L.D. Early fixation of an optimal genetic code. Mol. Biol. Evol. 17 (2000) 511-518
21. Gamow G. Possible relation between deoxyribonucleic acid and protein structures. Nature (London) 173 (1954) 318
22. Gilis D., Massar S., Cerf N.J., and Rooman M. Optimality of the genetic code with respect to protein stability and amino acid frequencies. Genome Biol. 2 11 (2001) 49.1-49.12
23. Goldman N. Further results on error minimization in the genetic code. J. Mol. Evol. 37 (1993) 662-664
24. Goodarzi H., Nejad H.A., and Torabi N. On the optimality of the genetic code, with the consideration of termination codons. BioSystems 77 (2004) 163-173
25. Goodarzi H., Najafabadi H.S., Hassani K., Nejad H.A., and Torabi N. On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. J. Theor. Biol. 235 (2005) 318-325
26. Haig D., and Hurst L.D. A quantitative measure of error minimization on the genetic code. J. Mol. Evol. 33 (1991) 412-417
27. Henikoff S., and Henikoff G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 89 (1992) 10915-10919
28. Hurst L.D., Feil E.J., and Rocha E.P.C. Causes of trends in amino-acid gain and loss. Nature (London) 442 (2006) E11-E12
29. Ivanov V., Beniaminov A., Mikheyev A., and Minyat E. A mechanism for stop codon recognition by the ribosome: a bioinformatic approach. RNA 7 (2001) 1683-1692
30. Johnson N.L., and Leone F.C. Statistics and Experimental Design in Engineering and the Physical Sciences (1977), Wiley, New York
31. Jordan I.K., Kondrashov F.A., Adzhubei I.A., Wolf Y.I., Koonin E.V., Kondrashov A.S., and Sunyaev S. A universal trend of amino acid gain and loss in protein evolution. Nature (London) 433 (2005) 633-638
32. Jungck J.R. The genetic code as a periodic table. J. Mol. Evol. 11 (1978) 211-224
33. Knight R.D., Freeland S.J., and Landweber L.F. Rewiring the keyboard: evolvability of the genetic code. Nat. Rev. Genet. 2 (2001) 49-58
34. Koonin E.V., and Novozhilov A.S. Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61 (2009) 99-111
35. Luo L., and Li X. Coding rules for amino acids in the genetic code: the genetic code is a minimal code of mutational deterioration. Orig. Life Evol. Biosphere 32 (2002) 23-33
36. Miyata T., Miyzawa S., and Yasunaga T. Two types of amino acid substitution in protein evolution. J. Mol. Evol. 12 (1979) 219-236
37. Novozhilov A.S., Wolf Y.I., and Koonin E.V. Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape. Biol. Dir. 2 (2007) 24
38. Ogle J.M., and Ramakrishnan V. Structural insights into translational fidelity. Annu. Rev. Biochem. 74 (2005) 129-177
39. Parker J. Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53 (1989) 273-298
40. Pelc S.R. Correlation between coding triplets and amino acids. Nature (London) 207 (1965) 597-599
41. Pelc S.R., and Welton M.G.E. Specificity of the stereochemical relationship between ribonucleic acid-triplets and amino acids. Nature (London) 209 (1966) 868-872
42. Ribas de Pouplana L., and Schimmel P. Operational RNA code for amino acids in relation to genetic code in evolution. J. Biol. Chem. 276 (2001) 6881-6884
43. Rodin S.N., and Rodin A.S. Partitioning of aminoacyl-tRNA synthetases in two classes could have been encoded in a strand-symmetric RNA world. DNA and Cell Biol. 25 (2006) 617-626
44. Rodin S.N., and Rodin A.S. On the origin of the genetic code: signatures of its primordial complementarity in tRNAs and aminoacyl-tRNA synthetases. Heredity 100 (2008) 341-355
45. Root-Bernstein R.S. On the origin of the genetic code. J. Theor. Biol. 94 (1982) 895-904
46. Rumer Yu.B. Systematization of codons in the genetic code. Dokl. Acad. Nauk SSSR 183 (1968) 225-226 (in Russian)
47. Santos M.A.S., Moura1 G., Massey S.E., and Tuite M.F. Driving change: the evolution of alternative genetic codes. Trends Genet. 20 (2004) 95-102
48. Sella G., and Ardell D.H. The coevolution of genes and genetic codes: Crick's frozen accident revisited. J. Mol. Evol. 63 (2006) 297-313
49. Szathmary E. Coding coenzyme handles: a hypothesis for the origin of genetic code. Proc. Natl. Acad. Sci. USA 90 (1993) 9916-9920
50. Taylor F.J., and Coates D. The code within the codons. BioSystems 22 (1989) 177-187
51. Weir B.S. Genetic Data Analysis: Methods for Discrete Population Genetic Data (1990), Sinauer, Sunderland, Massachusetts
52. Wilhelm T., and Nikolaeva S. A new classification scheme of the genetic code. J. Mol. Evol. 59 (2004) 598-605
53. Woese C.R. On the evolution of the genetic code. Proc. Natl. Acad. Sci. USA 54 (1965) 1546-1552
54. Woese C.R., Dugre D.H., Saxinger W.C., and Dugre S.A. The molecular basis for the genetic code. Proc. Natl. Acad. Sci. USA 55 (1966) 966-974
55. Woese C.R., Olsen G.J., Ibba M., and Söll D. Aminoacyl-tRNA synthetases, the genetic code, and the evolutionary process. Microbiol. Mol. Biol. Rev. 64 (2000) 202-236
56. Wolfenden R.V., Cullis P.M., and Southgate C.C.F. Water, protein folding, and the genetic code. Science 206 (1979) 575-577
57. Wong J.T.-F. A co-evolution theory of the genetic code. Proc. Natl. Acad. Sci. USA 72 (1975) 1909-1912
58. Wong J.T.-F. Coevolution theory of the genetic code at age thirty. BioEssays 27 (2005) 416-425
59. Xia X., and Li W.-H. What amino acid properties affect protein evolution?. J. Mol. Evol. 47 (1998) 557-564
60. Yarus M. Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J. Mol. Evol. 47 (1998) 109-117
61. Yarus M., Caporaso J.G., and Knight R. Origins of the genetic code: the escaped triplet theory. Annu. Rev. Biochem. 74 (2005) 179-198
62. Zamjatnin A.A. Protein volume in solution. Prog. Biophys. Mol. Biol. 24 (1972) 109-123
63. Zhu C.-T., Zeng X.-B., and Huang W.-D. Codon usage decreases the error minimization within the genetic code. J. Mol. Evol. 57 (2003) 533-537