Genetic Code: A Self-Referential and Functional Model

Progress in Biological Chirality

Volumn , Issue , 2004, Pages 83-118

  Guimarães, Romeu Cardoso ^a   Moreira, Carlos Henrique Costa ^b  

^a Inst Ciências Biológicas   (Brazil)

^b FEDERAL UNIVERSITY OF MINAS GERAIS   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 17844402326     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1016/B978-008044396-6/50010-1     Document Type: Chapter

References (108)

1. Guimarães R.C. Life. Universes of Knowledge 2002, 149-200. (in Portuguese), Fac. Letras UFMG, Belo Horizonte. Brasil. R.P. Martins, H. Mari (Eds.).
2. Guimarães R.C. The gene as an RNA molecule. Ciência e Cultura Supl. 1986, 38:939-940. (in Portuguese).
3. th Internat. Conf. Origin Life 2002, 104. Abstract.
4. Guimarães R.C. Linguistics of biomolecules and the protein-first hypothesis for the origins of cells. J. Biol. Phys. 1994, 20:193-199.
5. Ferreira R., Coutinho K.R. Simulation studies of self-replicating oligoribotides, with a proposal for the transition to a peptide-assisted stage. J. Theor. Biol. 1993, 164:291-305.
6. Lehmann J. Physico-chemical constraints connected with the coding properties of the genetic system. J. Theor. Biol. 2000, 202:129-144.
7. Trifonov E.N. Consensus temporal order of amino acids and evolution of the triplet code. Gene 2000, 261:139-151.
8. Jiménez-Montaño M.A. Protein evolution drives the evolution of the genetic code and vice-versa. BioSystems 1999, 54:47-64.
9. 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.
10. Ninio J. Approches Moléculaires de l'Evolution 1979, (in French), Masson, Paris.
11. Poole A.M., Jeffares D.C., Penny D. The path from the RNA world. J. Mol. Evol. 1998, 46:1-17.
12. Trifonov E.N., Bettecken T. Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene 1997, 205:1-6.
13. Grosjean H., Houssier C. Codon recognition: evaluation of the effects of modified bases in the anticodon loop of tRNA using the temperature-jump relaxation method. Chromatography and Modification of Nucleosides 1990, A255-A295. Elsevier, Amsterdam. C.W. Gehrke, K.C.T. Kuo (Eds.).
14. Osawa S. Evolution of the Genetic Code 1995, Oxford Univ. Press, Oxford, UK.
15. Lagerkvist U. Two out of three: an alternative method of codon reading. Proc. Natl. Acad. Sci. USA 1978, 75:1759-1762.
16. Lacey J.C., Mullins D.W. Experimental studies related to the origin of the genetic code and the process of protein synthesis a review. Origin Life Evol. Biosphere 1983, 13:3-42.
17. Wong J.T.F. A co-evolution theory of the genetic code. Proc. Natl. Acad. Sci. USA 1975, 72:1909-1912.
18. Wong J.T.F. Evolution of the genetic code. Microbiol. Sci. 1988, 5:174-181.
19. Ribas de Pouplana L., Schimmel P. Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem. Cell 2001, 104:191-193.
20. Ribas de Pouplana L., Schimmel P. Aminoacyl-tRNA synthetases: potential markers of genetic code development. Trends Biochem. Sci. 2001, 26:591-596.
21. A.R.O. Cavalcanti, E.S. Leite, B. Barros Neto and R. Ferreira, On the classes of aminoacyl-tRNA synthetases, amino acids and the genetic code, in press.
22. Davis B.K. Evolution of the genetic code. Prog Biophys. Mol. Biol. 1999, 72:157-243.
23. Knight R.D., Freeland S.J., Landweber L.F. Selection, history and chemistry: the three faces of the genetic code. Trends Biochem. Sci. 1999, 24:241-247.
24. Ronneberg T.A., Landweber L.F., Freeland S.J. Testing a biosynthetic theory of the genetic code: fact or artifact?. Proc. Natl. Acad. Sci. USA 2000, 97:13690-13695.
25. Moras D. Structural and functional relationships between aminoacyl-tRNA synthetases. Trends Biochem. Sci. 1992, 17:159-164.
26. P. Schimmel and L. Ribas de Pouplana, Formation of two classes of tRNA synthetases in relation to editing functions and genetic code. Cold Spring Harbor Symposium on Quantitative Biology, in press.
27. Ibba M., Bono J.L., Rosa P.A., Söll D. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proc. Natl. Acad. Sci. USA 1997, 94:14383-14388.
28. Stathopoulos C., Li T., Longman R., Vothnecht U.C., Becker H.D., Ibba M., Söll D. One polypeptide with two aminoacyl-tRNA synthetase activities. Science 2000, 287:479-482.
29. Arnez J.G., Moras D. Structural and functional considerations of the aminoacylation reaction. Trends Biochem. Sci. 1997, 22:211-216.
30. Nagel G.M., Doolittle R.F. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J. Mol. Evol. 1995, 40:487-498.
31. Carter C.W. Cognition, mechanism, and evolutionary relationships in aminoacyl-tRNA synthetases. Ann. Rev. Biochem. 1993, 62:715-748.
32. Cavarelli J., Moras D. Recognition of tRNAs by aminoacyl-tRNA synthetases. FASEB J. 1993, 7:79-86.
33. Cusack S. Aminoacyl-tRNA synthetases. Curr. Opinion Struct. Biol. 1997, 7:881-889.
34. Brown J.R., Doolittle W.F. Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications. Proc. Natl. Acad. Sci. USA 1995, 92:2441-2445.
35. Nagel G.M., Doolittle R.F. Evolution and relatedness in two aminoacyl-tRNA synthetase families. Proc. Natl. Acad. Sci. USA 1991, 88:8121-8125.
36. Grantham R. Amino acid difference formula to help explain protein evolution. Science 1974, 185:862-864.
37. Guimarães R.C., Moreira C.H.C. Genetic code structure and evolution-aminoacyl-tRNA synthetases and principal dinucleotides. Fundamentals of Life 2002, 249-276. Elsevier and Accademia Nazionale di Scienze, Lettere ed Arti (Modena), Paris. G. Pályi, C. Zucchi, L. Caglioti (Eds.).
38. Di Giulio M. On the origin of the genetic code. J. Theor. Biol. 1997, 187:573-581.
39. Guimarães R.C. Non coding sequences original, genes derived: dinucleotide and hydropathic specificities of the aminoacyl-tRNA synthetase classes. Internat. Symp. Soc. Mol. Evol. 1997, 6.
40. Guimarães R.C. Genetic code: hydropathic, dinucleotide type and aminoacyl-tRNA synthetase class organization. Exobiology-Matter, Energy and Information in the Origin and Evolution of Life in the Universe 1998, 157-160. Kluwer, Dordrecht. J. Chela-Flores, F. Raulin (Eds.).
41. Knight R.D., Freeland S.J., Landweber L.F. Rewiring the keyboard: evolvability of the genetic code. Nature Rev. Genet. 2001, 2:49-58.
42. Curnow A.W., Ibba M., Söll D. Transfer RNA-dependent asparagine formation. Nature 1996, 382:589-590.
43. Rogers K.C., Söll D. Divergence of glutamate and glutamine aminoacylation pathways: providing the evolutionary rationale for mischarging. J. Mol. Evol. 1995, 40:476-481.
44. Yarus M. Amino acids as RNA ligands: a direct-RNA-template theory for the code's origin. J. Mol. Evol. 1998, 47:109-117.
45. Muth G.W., Donnelly L.O., Strobel S.A. A single adenosine with a neutral pKa in the ribosomal peptidyl-transferase center. Science 2000, 289:947-950.
46. Piccirilli J.A., McConnel T.S., Zaug A.J., Noller H.F., Cech T.R. Aminoacyl esterase activity of the tetrahymena ribozyme. Science 1992, 256:1420-1424.
47. Nissen P., Hansen J., Ban N., Moore P.B., Steitz T.A. The structural basis of ribosome activity in peptide bond synthesis. Science 2000, 289:920-930.
48. Carter A.P., Clemons W.M., Brodersen D.E., Morgan-Warren R.J., Hartsch T., Wimberly B.T., Ramakrishnan V. Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 2001, 291:498-501.
49. Ogle J.M., Brodersen D.E., Clemons W.M., Tarry M.J., Carter A.P., Ramakrishnan V. Recognition of cognate tRNA by the 30S ribosomal subunit. Science 2001, 292:897-902.
50. Rodin S.N., Ohno S., Rodin A. Transfer RNAs with complementary anticodons: could they reflect early evolution of discriminative genetic code adaptors?. Proc. Natl. Acad. Sci. USA 1993, 90:4723-4727.
51. Rodin S.N., Ohno S., Rodin A. A On concerted origin of transfer RNAs with complementary anticodons. Origin Life Evol. Biosphere 1993, 23:393-418.
52. Guimarães R.C., Erdmann V.A. Evolution of adenine clustering in 5S ribosomal RNA. Endocytobiol. Cell Res. 1992, 9:13-45.
53. Eigen M. The origin of genetic information: viruses as models. Gene 1993, 135:37-47.
54. Eigen M., Winkler-Oswatitsch R. Transfer-RNA, an early gene?. Naturwiss. 1981, 68:282-292.
55. th Internat. Conf. Origin Life 1999, 86. Abstract.
56. Staves M.P., Lacey J.C. On the probability of a common origin for tRNA and 5S ribosomal RNA. Z. Naturforsch. C 1989, 44:296-306.
57. Di Giulio M. Was it an ancient gene codifying for a hairpin RNA that, by means of direct duplication, gave rise to the primitive tRNA molecule?. J. Theor. Biol. 1995, 177:95-101.
58. Bloch D.P., McArthur B., Widdowson R., Spector D., Guimarães R.C., Smith J. tRNA-rRNA sequence homologies: evidence for a common evolutionary origin?. J Mol. Evol. 1983, 19:420-428.
59. Bloch D.P., McArthur B., Widdowson R., Spector D., Guimarãnes R.C., Smith J. tRNA-rRNA sequence homologies: a model for the generation of a common ancestral molecule and prospects for its reconstruction. Origin Life Evol. Biosphere 1984, 14:571-578.
60. Bloch D.P., McArthur B., Guimarães R.C., Smith J., Staves M.P. tRNA-rRNA sequence matches from inter- and intraspecies comparisons suggest common origins for the two RNAs. Braz. J. Med. Biol. Res. 1989, 22:931-944.
61. Nazarea A.D., Bloch D.P., Semrau A.C. Detection of a fundamental modular format common to transfer and ribosomal RNAs: second order spectral analysis. Proc. Natl. Acad. Sci. USA 1985, 82:5337-5341.
62. Editorial, Basic modular format in tRNA's and rRNA's. Science 1985, 229:1254.
63. Ohnishi K., Hokari S., Shutou H., Ohshima M., Furuichi N., Goda M. Origin of most primitive mRNAs and genetic codes codes via interactions between primitive tRNA ribozymes. Geonome Informatics 2002, 13:71-81.
64. Grosjean H., Houssier C., Cedergren R. Anticodon-anticodon interactions and tRNA sequence comparison approaches to codon recognition. Structure and Dynamics of RNA 1986, 161-174. Plenum, New York. P.H. Knippenberg, C.W. Hilbers (Eds.).
65. Yamane T., Miller D.L., Hopfield J.J. JJ 1981 Interaction of elongation factor Tu with the aminoacyl-tRNA dimer Phe-tRNA: Glu-tRNA. Biochemistry 1981, 20:449-452.
66. Miller D.L., Yamane T., Hopfield J.J. Effect of tRNA dimer formation on polyphenylalanine biosynthesis. Biochemistry 1981, 20:5457-5461.
67. Xia T., SantaLucia J., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox C., Turner D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 1998, 37:14719-14735.
68. Freier S.M., Kierzek R., Jaeger J.A., Sugimoto N., Caruthers M.H., Neilson T., Turner D.H. Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl. Acad. Sci. USA 1986, 83:9373-9377.
69. Woese C.R., Dugre D.H., Saxinger W.C., Dugre A.S. The molecular basis for the genetic code. Natl. Acad. Sci. USA 1966, 55:966-974.
70. Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982, 157:105-132.
71. Guimarães R.C., Moreira C.H.C. Average dinucleotide and amino acid residue hydropathy scales fit the genetic code correlation. Internat. Conf. Origin Life, ISSOL, San Diego 1999, 12:87.
72. th Internat. Conf. Origin Life 1996, 100. Abstract.
73. Saks M.E., Sampson J.R. Evolution of tRNA recognition systems and tRNA gene sequences. J. Mol. Evol. 1995, 40:509-518.
74. Schimmel P. An operational RNA code for amino acids and variations in critical nucleotide sequences in evolution. J. Mol. Evol. 1995, 40:531-536.
75. Rodin S.N., Rodin A., Ohno S. The presence of codon-anticodon pairs in the acceptor stems of tRNAs. Proc. Natl. Acad. Sci. USA 1996, 93:4537-4542.
76. Rodin S.N., Ohno S. Four primordial modes of tRNA-synthetase recognition, determined by the (G,C) operational code. Proc. Natl. Acad. Sci. USA 1997, 94:5183-5188.
77. Karzai A.W., Roche E.D., Sauer R.T. The SsrA-SmpB system for protein tagging, directed degradation and ribosome rescue. Nature Struct. Biol. 2000, 7:449-455.
78. Varshavsky A. The N-end rule: functions, mysteries, uses. Proc. Natl. Acad. Sci. USA 1996, 93:12142-12149.
79. Guimarães R.C. Two punctuation systems in the genetic code. First Steps in the Origin of Life in the Universe 2001, 91-94. Kluwer, Dordrecht. J. Chela-Flores, T. Owen, F. Raulin (Eds.).
80. Berezovsky I.N., Kilosanidze G.T., Tumanyan V.G., Kisselev L. COOH-terminal decamers in proteins are non-random. FEBS Lett. 1997, 404:140-142.
81. Berezovsky I.N., Kilosanidze G.T., Tumanyan V.G., Kisselev L. Amino acid composition of protein termini are biased in different manners. Protein Engin 1999, 12:23-30.
82. Nagai K., Mattaj I.W. RNA-Protein Interactions 1996, IRL/Oxford University Press, Oxford, UK.
83. Pabo C.O., Sauer R.T. Transcription factors: structural families and principles of DNA recognition. Ann. Rev. Biochem. 1992, 61:1053-1095.
84. Song H., Mugnier P., Das A.K., Webb H.M., Evans D.R., Tuite M.F., Hemmings B.A., Barford D. The crystal structure of human eukaryotic release factor eRF1-mechanism of stop codon recognition and peptidyl-tRNA hydrolysis. Cell 2000, 100:311-321.
85. Lewis H.A., Musurunu K., Jensen K.B., Edo C., Chen H., Darnell R.B., Burley S.K. Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome. Cell 2000, 100:323-332.
86. Ramos A., Grünert S., Adams J., Micklem D.R., Proctor M.R., Freund S., Byeroft M., StJohnston D., Varani G. RNA recognition by a Staufen double-stranded RNA binding domain. EMBO J. 2000, 19:997-1009.
87. Ryter J.M., Schultz S.C. Molecular basis of double-stranded RNA-protein interactions: structure of a double-stranded RNA binding doman complex with double-stranded RNA. EMBO J. 1998, 17:7505-7513.
88. Micklem D.R., Adams J., Grünert S., StJohnston D. Distinct roles of two conserved Staufen domains in 'oskar' mRNA localization and translation. EMBO J. 2000, 19:1366-1377.
89. Guimarães R.C., Moreira C.H.C., Melo R.C. The functional genetic code. Origin Life Evol. Biosphere 2002, 32:464-465.
90. Ferreira R., Cavalcanti A.R.O. Vestiges of early molecular processes leading to the genetic code. Origin Life Evol. Biosphere 1997, 27:397-403.
91. Rodin S.N., Ohno S. Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands of the same nucleic acid. Origin Life Evol. Biosphere 1995, 25:565-589.
92. Guimarães R.C. A systemic manifesto. Internat. Soc. Study Origin Life Newsletter 1995, 22:12.
93. Takagi H., Kaneko K., Yomo T. Evolution of genetic codes through isologous diversification of cellular states. Artificial Life 2000, 6:283-305.
94. Li W.H. Molecular Evolution 1997, Sinauer, Sunderland MA, USA.
95. Jurka J., Smith T.F. β-turn-driven early evolution: the genetic code and biosynthetic pathways. J. Mol. Evol. 1987, 25:15-19.
96. Di Giulio M. The β-sheets of proteins, the biosynthetic relationships between amino acids, and the origin of the genetic code. Origin Life Evol. Biosphere 1996, 26:589-609.
97. Chiusano M.L., Alvarez-Valin F., Di Giulio M., D'Onofrio G., Ammirato G., Colonna G., Bernardi G. Second codon positions of genes and the secondary structures of proteins. Relationships and implications for the origin of the genetic code. Gene 2000, 261:63-69.
98. Creighton T.E. Proteins: Structures and Molecular Properties 1993, Freeman, New York.
99. Pardini M.I.M.C., Guimarães R.C. A systemic concept of the gene. Gen. Mol. Biol. 1992, 15:713-721.
100. Pardini M.I.M.C. A Systemic-Functional Concept of the Gene. MSc Thesis 1989, (in Portuguese), Instituto de Biociências, UNESP, Botucatu, SP.
101. Guimarães R.C., Moreira C.H.C. The systemic concept of the gene-a decade after. Coleção CLE 30 2000, 249-280. (in Portuguese), Ed. UNICAMP, Campinas, São Paulo, Brazil. I.M.L. D'Ottaviano, M.E.Q. Gonzalez (Eds.).
102. Guimarães R.C. An evolutionary definition of life-from metabolism to the genetic code. Fundamentals of Life 2002, 95-108. Elsevier and Accademia Nazionale di Scienze, Lettere ed Arti (Modena), Paris. G. Pályi, C. Zucchi, L. Caglioti (Eds.).
103. Guimarães R.C. The concept of information in biology. Meeting the Cognitive Sciences 2 1998, 69-93. (in Portuguese), EdUNESP, Marília SP. M.E.Q. Gonzalez, M.C. Broens (Eds.).
104. Di Giulio M. The extension reached by the minimization of the polarity distances during the evolution of the genetic code. J. Mol. Evol. 1989, 29:288-293.
105. Di Giulio M., Rosaria-Capobianco M., Medugno M. On the optimization of the physicochemical distances between amino acids in the evolution of the genetic code. J. Theor. Biol. 1994, 168:43-51.
106. Cavalcanti A.R.O., Barros Neto B., Ferreira R. On the classes of aminoacyl-tRNA synthetases and the error minimization in the genetic code. J. Theor. Biol. 2000, 204:15-20.
107. Atkins J.F., Gesteland R. The 22nd amino acid. Science 2002, 296:1409-1410.
108. Hornos J.E.M., Hornos Y.M.M. Algebraic model for the evolution of the genetic code. Phys. Rev. Lett. 1993, 71:4401-4404.