J. G. Arnez and D. Moras, Structural and functional considerations of the aminoacylation reaction, Trends Biochem. Sci, vol.22, pp.211-216, 1997.

J. Balakrishnan, Symmetry scheme for amino acids codons, Phys. Rev. E, vol.65, pp.21912-21916, 2002.

J. D. Bashford, I. Tsohantjis, J. , and P. D. , A supersymmetric model for the evolution of the genetic code, Proc. Natl. Acad. Sci, vol.95, pp.987-992, 1998.

H. Bedouelle, Recognition of tRNA-Tyr by tyrosyl-tRNA synthetase, Biochimie, vol.72, pp.589-598, 1990.

B. Berger and T. Leighton, Protein folding in the hydrophobichydrophilic HP model is NP-complete, J. Comput. Biol, vol.5, pp.27-40, 1998.

D. J. Brooks and J. R. Fresco, Increased frequency of Cysteine, Tyrosine and Phenylalanine residues since the last universal ancestor, Mol. Cell. Proteomics, vol.12, pp.125-131, 2002.

J. A. Carrodeguas, R. Kobayashi, S. E. Lim, W. C. Copeland, and D. F. Bogenhagen, The accessory subunit of Xenopus laevis mitochondrial DNA polymerase g increases processivity of the catalytic subunit of human DNA polymerase g and is related to Class II aminoacyl-tRNA synthetases, Mol. Cell. Biol, vol.19, pp.4039-4046, 1999.

C. W. Carter and W. L. Duax, Did tRNA synthetase classes arise on opposite strands of the same gene?, Mol. Cell, vol.10, pp.705-708, 2002.

H. S. Chan, Folding alphabets, Nat. Struct. Biol, vol.6, pp.994-996, 1999.

H. S. Chan and K. A. Dill, Comparing folding codes for proteins and polymers, Proteins, vol.24, pp.335-344, 1996.

F. H. Crick, The origin of the genetic code, J. Mol. Biol, vol.38, pp.367-379, 1968.

S. Cusack, M. Hartlein, and R. Leberman, Sequence, structure and evolutionary relationships between Class 2 aminoacyl-tRNA synthetases, Nucleic Acid Res, vol.19, pp.3489-3498, 1991.

C. De-duve, tRNA: The second genetic code, Nature, vol.333, pp.117-118, 1988.

M. Delarue and D. Moras, Aminoacyl-tRNA synthetases: Partition into two classes, Nucleic acids and molecular biology, 1992.

F. Eckstein and D. M. Lilley, , vol.6, pp.203-224

M. Delarue and D. Moras, The aminoacyl-tRNA synthetase family: Modules at work, Bioessays, vol.15, pp.675-687, 1993.

M. Di-giulio, The origin of the genetic code: Theories and their relationships, a review, Biosystems, vol.80, pp.175-184, 2005.

M. Eigen, B. Lindemann, M. Tietze, R. Winkler-oswatitsch, A. Dress et al., How old is the genetic code? Statistical geometry provides an answer, Science, vol.244, pp.673-678, 1989.

G. Eriani, M. Delarue, O. Poch, J. Gangloff, and D. Moras, Partition of aminoacyl-tRNA synthetases into two classes based on mutually exclusive sets of conserved motifs, Nature, vol.347, pp.203-206, 1990.

A. V. Finkelstein, A. M. Gutin, A. Badretdinov, and . Ya, Why are the same protein folds used to perform different functions?, FEBS Lett, vol.325, pp.23-28, 1993.

W. M. Fitch and K. Upper, The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code, Cold Spring Harb. Symp. Quant. Biol, vol.52, pp.759-767, 1987.

T. H. Fraser and A. Rich, Amino acids are not all initially attached to the same position on transfer RNA molecules, Proc. Natl. Acad. Sci, vol.72, pp.3044-3048, 1975.

S. J. Freeland and L. D. Hurst, The genetic code is one in a million, J. Mol. Evol, vol.47, pp.238-248, 1998.

Y. Goldgur, L. Mosyak, L. Reshetnikova, V. Ankilova, O. Lavrik et al., Crystal structure of phenylalanyl-tRNA synthetase from Th. thermophilus complexed with cognate tRNAPhe, Structure, vol.5, pp.59-68, 1996.

S. Hauenstein, C. M. Zhang, Y. M. Hou, and J. J. Perona, Shape-selective RNA recognition by cysteinyl-tRNA synthetase, Nat. Struct. Mol. Biol, vol.11, pp.1134-1141, 2004.

S. M. Hecht and A. C. Chinault, Position of aminoacylation of individual Escherichia coli and yeast tRNAs, Proc. Natl. Acad. Sci, vol.73, pp.405-409, 1976.

J. E. Hornos and Y. M. Hornos, Algebraic model for the evolution of the genetic code, Phys. Rev. Lett, vol.71, pp.4401-4404, 1993.

M. Ibba, S. Morgan, A. W. Curnow, D. R. Pridmore, U. C. Vothknecht et al., An euryarchaeal lysyl-tRNA synthetase: Resemblance to Class I synthetase, Science, vol.278, pp.1119-1122, 1997.

G. F. Joyce, The antiquity of RNA-based evolution, Nature, vol.418, pp.214-221, 2002.

A. Klar, Differentiated parental DNA strands confer developmental asymmetry on daughter cells in fission yeast, Nature, vol.326, pp.466-470, 1987.

R. D. Knight, S. J. Freeland, and L. F. Landweber, Selection, history and chemistry: The three faces of the genetic code, Trends Biochem. Sci, vol.24, pp.241-247, 1999.

A. Lescoute and E. Westhof, The A-minor motifs in the decoding recognition process, Biochimie, vol.88, pp.993-999, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00093007

H. Liang and L. F. Landweber, Molecular mimicry: Quantitative methods to study similarity between tRNA and proteins, RNA, vol.11, pp.1167-1172, 2005.

D. A. Macdonaill, G. , and T. /. , U: An errorcoding perspective of nucleotide alphabet composition, Orig. Life Evol. Biosph, vol.33, pp.433-455, 2003.

M. Mezard, G. Parisi, and R. Zecchina, Analytic and algorithmic solution of random satisfiability problems, Science, vol.297, pp.812-815, 2002.

S. L. Miller, Which organic compounds could have occurred on the prebiotic earth?, Cold Spring Harb. Symp. Quant. Biol, vol.52, pp.17-27, 1987.

J. Miller, C. Zeng, N. S. Wingreen, and C. Tang, Emergence of highly designable protein-backbone conformations in an offlattice model, Proteins, vol.47, pp.506-512, 2002.

G. M. Nagel and R. F. Doolittle, Phylogenetic analysis of aminoacyl-tRNA synthetases, J. Mol. Evol, vol.40, pp.487-498, 1995.

H. B. Nicholas and W. H. Mcclain, Searching tRNA sequences for relatedness to aminoacyl-tRNA synthetase families, J. Mol. Evol, vol.40, pp.482-486, 1995.

V. Pezo, D. Metzgar, T. L. Hendrickson, W. F. Waas, S. Hazebrouck et al., Artificially ambiguous genetic code confers growth yield advantage, Proc. Natl. Acad. Sci, vol.101, pp.7593-7597, 2004.

C. Polycarpo, A. Ambrogelly, B. Ruan, D. Tumbula-hansen, S. F. Ataide et al., Activation of Pyrrolysine suppressor tRNA requires formation of a ternary complex with Class I and Class II Lysyl-tRNA synthetases, Mol. Cell, vol.12, pp.287-294, 2003.

C. Polycarpo, A. Ambrogelly, A. Berube, S. M. Winbush, J. A. Mccloskey et al., An aminoacyl-tRNA synthetase that specifically activates pyrrolysine, Proc. Natl. Acad. Sci, vol.101, pp.12450-12454, 2004.

L. Ribas-de-pouplana and P. Schimmel, Aminoacyl-tRNA synthetases: Potential markers of genetic code development, Trends Biochem. Sci, vol.26, pp.591-596, 2001.

L. Ribas-de-pouplana and P. Schimmel, Two classes of tRNA synthetases suggested by sterically compatible docking on tRNA acceptor stem, Cell, vol.104, pp.191-193, 2001.

S. Rodin and S. Ohno, Two types of aminoacyl-tRNA synthetases could be originally encoded by complementary strands on the same nucleic acid, Orig. Life Evol. Biosph, vol.25, pp.565-589, 1995.

S. Rodin and S. Ohno, Four primordial modes of tRNAsynthetase recognition, determined by the (G, C) operational code, Proc. Natl. Acad. Sci, vol.94, pp.5183-5188, 1997.

S. Rodin, A. Rodin, and S. Ohno, The presence of codonanticodon pairs in the acceptor stem of tRNAs, Proc. Natl. Acad. Sci, vol.93, pp.4537-4542, 1996.

M. A. Santos, C. Cheesman, V. Costa, P. Morades-feirrara, and M. F. Tuite, Selective advantage created by codon ambiguity allowed for the evolution of an alternative code in Candida spp, Mol. Microbiol, vol.31, pp.937-947, 1999.

P. Schimmel, R. Giégé, D. Moras, Y. , and S. , An operational RNA code for amino acids and possible relationship to genetic code, Proc. Natl. Acad. Sci, vol.90, pp.8763-8768, 1993.

S. Sengupta and P. G. Higgs, A unified model of codon reassignment in alternative genetic codes, Genetics, vol.170, pp.831-840, 2005.

S. Shitivelband and Y. M. Hou, Breaking the stereo barrier of amino acid attachment to tRNA by a single nucleotide, J. Mol. Biol, vol.348, pp.513-521, 2005.

T. Sonneborn, Degeneracy of the genetic code: Extent, nature and genetic implications, Evolving genes and proteins, pp.377-397, 1965.

M. Sprinzl and F. Cramer, Site of aminoacylation of tRNAs from Escherichia coli with respect to the 29-or 39-hydroxyl group of the terminal adenosine, Proc. Natl. Acad. Sci, vol.72, pp.3049-3053, 1975.

G. Srinivasan, C. M. James, and J. A. Krzycki, Pyrrolysine encoded by UAG in Archea: Charging of a UAG-decoding specialized tRNA, Science, vol.296, pp.1459-1462, 2002.

E. Szathmary, Codon swapping as a possible evolutionary mechanism, J. Mol. Evol, vol.32, pp.178-182, 1991.

G. Trinquier and Y. H. Sanejouand, Which effective property of amino acids is best preserved by the genetic code?, Protein Eng, vol.11, pp.153-169, 1998.

K. Vetsigian, C. R. Woese, and N. Goldenfeld, Collective evolution and the genetic code, Proc. Natl. Acad. Sci, vol.103, pp.10696-10701, 2006.

M. V. Volkenstein, The genetic coding of protein structures, Biochim. Biophys. Acta, vol.119, pp.421-424, 1966.

J. Wang and W. Wang, A computational approach to simplifying the protein folding alphabet, Nat. Struct. Biol, vol.6, pp.1033-1038, 1999.

C. R. Woese, On the evolution of the genetic code, Proc. Natl. Acad. Sci, vol.54, pp.1546-1552, 1965.

C. R. Woese, Order in the genetic code, Proc. Natl. Acad. Sci, vol.54, pp.71-75, 1965.

C. R. Woese, Translation: In retrospect and prospect, RNA, vol.7, pp.1055-1067, 2001.

C. R. Woese, G. J. Olsen, M. Ibba, and D. Söll, AminoacyltRNA synthetases, the genetic code and the evolutionary process. Microbiol, Mol. Biol. Rev, vol.64, pp.202-236, 2000.

Y. I. Wolf, L. Aravind, N. V. Grishin, and E. V. Koonin, Evolution of aminoacyl-tRNA synthetases: Analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfers, Genet. Res, vol.9, pp.689-710, 1999.

J. T. Wong, A co-evolution theory of the genetic code, Proc. Natl. Acad. Sci, vol.72, pp.1909-1912, 1975.

H. Xue, K. L. Tong, C. Marck, H. Grosjean, and J. T. Wong, Transfer RNA paralogs: Evidence for genetic code-amino acid biosynthesis coevolution and an archeal tree of life, Gene, vol.310, pp.59-66, 2003.

A. Yaremchuk, I. Kriklivyi, M. Tukhalo, and S. Cusack, Class I tyrosyl-tRNA synthetase has a Class II mode of tRNA recognition, EMBO J, vol.21, pp.3829-3840, 2002.

M. Yarus, J. G. Caporaso, and R. Knight, Origins of the genetic code: The escaped-triplet theory, Annu. Rev. Biochem, vol.74, pp.179-198, 2005.

C. M. Zhang, J. J. Perona, K. Ryu, C. Francklyn, and Y. M. Hou, Distinct kinetic mechanisms of the two classes of aminoacyl-tRNA synthetases, J. Mol. Biol, vol.361, pp.300-311, 2006.