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Volumn 127, Issue 3, 2008, Pages 249-270

A self-referential model for the formation of the genetic code

Author keywords

Early proteins; Gene definition; Genetic code; Palindromes; RNA protection; Self organization; Self reference; Stability

Indexed keywords

AMINO ACID; PALINDROMIC DNA; PURINE; PYRIMIDINE; TRANSFER RNA;

EID: 48549085638     PISSN: 14317613     EISSN: 16117530     Source Type: Journal    
DOI: 10.1007/s12064-008-0043-y     Document Type: Article
Times cited : (34)

References (68)
  • 3
    • 0032974859 scopus 로고    scopus 로고
    • Amino acid composition of protein termini are biased in different manners
    • IN Berezovsky G Kilosanidze VG Tumanyan 1999 Amino acid composition of protein termini are biased in different manners Protein Eng 12 23 30
    • (1999) Protein Eng , vol.12 , pp. 23-30
    • Berezovsky, I.N.1    Kilosanidze, G.2    Tumanyan, V.G.3
  • 4
    • 0034737704 scopus 로고    scopus 로고
    • A gene fusion event in the evolution of aminoacyl-tRNA synthetases
    • E Berthonneau M Mirande 2000 A gene fusion event in the evolution of aminoacyl-tRNA synthetases FEBS Lett 470 300 304
    • (2000) FEBS Lett , vol.470 , pp. 300-304
    • Berthonneau, E.1    Mirande, M.2
  • 5
    • 0003695480 scopus 로고    scopus 로고
    • Transfer RNA recognition by aminoacyl-tRNA synthetases
    • PJ Beuning K Musier-Forsyth 1999 Transfer RNA recognition by aminoacyl-tRNA synthetases Biopolymers 52 1 28
    • (1999) Biopolymers , vol.52 , pp. 1-28
    • Beuning, P.J.1    Musier-Forsyth, K.2
  • 6
    • 0021305496 scopus 로고
    • TRNA-rRNA sequence homologies: A model for the generation of a common ancestral molecule and prospects for its reconstruction
    • DP Bloch B McArthur R Widdowson 1984 tRNA-rRNA sequence homologies: a model for the generation of a common ancestral molecule and prospects for its reconstruction Orig Life Evol Biosph 14 571 578
    • (1984) Orig Life Evol Biosph , vol.14 , pp. 571-578
    • Bloch, D.P.1    McArthur, B.2    Widdowson, R.3
  • 7
    • 0024835378 scopus 로고
    • TRNA-rRNA sequence matches from inter- and intraspecies comparisons suggest common origins for the two RNAs
    • DP Bloch B McArthur RC Guimarães 1989 tRNA-rRNA sequence matches from inter- and intraspecies comparisons suggest common origins for the two RNAs Braz J Med Biol Res 22 931 944
    • (1989) Braz J Med Biol Res , vol.22 , pp. 931-944
    • Bloch, D.P.1    McArthur, B.2    Guimarães, R.C.3
  • 8
    • 15444380770 scopus 로고    scopus 로고
    • A mechanism for association of amino acids with their codons and the origin of the genetic code
    • SD Copley E Smith HJ Morowitz 2005 A mechanism for association of amino acids with their codons and the origin of the genetic code Proc Nat Acad Sci USA 102 4442 4447
    • (2005) Proc Nat Acad Sci USA , vol.102 , pp. 4442-4447
    • Copley, S.D.1    Smith, E.2    Morowitz, H.J.3
  • 10
    • 0032848426 scopus 로고    scopus 로고
    • Evolution of the genetic code
    • BK Davis 1999 Evolution of the genetic code Prog Biophys Mol Biol 72 157 243
    • (1999) Prog Biophys Mol Biol , vol.72 , pp. 157-243
    • Davis, B.K.1
  • 11
    • 0004149207 scopus 로고
    • Oxford University Press Oxford
    • Dawkins R (1976) The selfish gene. Oxford University Press, Oxford
    • (1976) The Selfish Gene
    • Dawkins, R.1
  • 12
    • 17044376643 scopus 로고    scopus 로고
    • The origin of the genetic code: Theories and their relationships, a review
    • M Di Giulio 2005 The origin of the genetic code: theories and their relationships, a review BioSystems 80 175 184
    • (2005) BioSystems , vol.80 , pp. 175-184
    • Di Giulio, M.1
  • 13
    • 37349009952 scopus 로고    scopus 로고
    • Aminoacyl-tRNA classes and groups in prokaryotes
    • ST Farias RC Guimarães 2007 Aminoacyl-tRNA classes and groups in prokaryotes J Theor Biol 250 221 229
    • (2007) J Theor Biol , vol.250 , pp. 221-229
    • Farias, S.T.1    Guimarães, R.C.2
  • 14
    • 33846850568 scopus 로고    scopus 로고
    • Structure of the genetic code suggested by the hydropathy correlation between anticodons and amino acid residues
    • ST Farias CHC Moreira RC Guimarães 2007 Structure of the genetic code suggested by the hydropathy correlation between anticodons and amino acid residues Orig Life Evol Biosph 37 83 103
    • (2007) Orig Life Evol Biosph , vol.37 , pp. 83-103
    • Farias, S.T.1    Moreira, C.H.C.2    Guimarães, R.C.3
  • 15
    • 0031201181 scopus 로고    scopus 로고
    • Vestiges of early molecular processes leading to the genetic code
    • R Ferreira ARO Cavalcanti 1997 Vestiges of early molecular processes leading to the genetic code Orig Life Evol Biosph 27 397 403
    • (1997) Orig Life Evol Biosph , vol.27 , pp. 397-403
    • Ferreira, R.1    Cavalcanti, A.R.O.2
  • 16
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • R Grantham 1974 Amino acid difference formula to help explain protein evolution Science 185 862 864
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 17
    • 85012743935 scopus 로고
    • Codon recognition: Evaluation of the effects of modified bases in the anticodon loop of tRNA using the temperature-jump relaxation method
    • Elsevier Amsterdam
    • Grosjean H, Houssier C (1990) Codon recognition: evaluation of the effects of modified bases in the anticodon loop of tRNA using the temperature-jump relaxation method. In: Gehrke CW, Kuo KCT (eds) Chromatography and modification of nucleotides. Elsevier, Amsterdam, pp A255-A295
    • (1990) Chromatography and Modification of Nucleotides
    • Grosjean, H.1    Houssier, C.2    Gehrke, C.W.3    Kuo, K.C.T.4
  • 18
  • 19
    • 24944527725 scopus 로고
    • Linguistics of biomolecules and the protein-first hypothesis for the origins of cells
    • RC Guimarães 1994 Linguistics of biomolecules and the protein-first hypothesis for the origins of cells J Biol Phys 20 193 199
    • (1994) J Biol Phys , vol.20 , pp. 193-199
    • Guimarães, R.C.1
  • 20
    • 33846802891 scopus 로고    scopus 로고
    • Anti-complementary order in the genetic coding system
    • RC Guimarães 1996 Anti-complementary order in the genetic coding system Int Conf Orig Life (ISSOL) 11 100
    • (1996) Int Conf Orig Life (ISSOL) , vol.11 , pp. 100
    • Guimarães, R.C.1
  • 23
    • 33751268484 scopus 로고    scopus 로고
    • An evolutionary definition of life-from metabolism to the genetic code
    • Elsevier Paris
    • Guimarães RC (2002) An evolutionary definition of life-from metabolism to the genetic code. In: Pályi G, Zucchi C, Caglioti L (eds) Fundamentals of life. Elsevier, Paris, pp 95-108
    • (2002) Fundamentals of Life , pp. 95-108
    • Guimarães, R.C.1    Pályi, G.2    Zucchi, C.3    Caglioti, L.4
  • 24
    • 9244239684 scopus 로고    scopus 로고
    • The genetic code as a self-referential and functional system
    • RC Guimarães 2004 The genetic code as a self-referential and functional system Int Conf Comput Commun Control Technol 7 160 165
    • (2004) Int Conf Comput Commun Control Technol , vol.7 , pp. 160-165
    • Guimarães, R.C.1
  • 25
    • 33846791965 scopus 로고    scopus 로고
    • Genetic code structure and evolution - Aminoacyl-tRNA synthetases and the principal dinucleotides
    • Elsevier Paris
    • Guimarães RC, Moreira CHC (2002) Genetic code structure and evolution - aminoacyl-tRNA synthetases and the principal dinucleotides. In: Pályi G, Zucchi C, Caglioti L (eds) Fundamentals of life. Elsevier, Paris, pp 249-276
    • (2002) Fundamentals of Life , pp. 249-276
    • Guimarães, R.C.1    Moreira, C.H.C.2    Pályi, G.3    Zucchi, C.4    Caglioti, L.5
  • 26
    • 17844402326 scopus 로고    scopus 로고
    • Genetic code: A self-referential and functional model
    • Pályi G, Zucchi C, Caglioti L (eds) Elsevier, Oxford
    • Guimarães RC, Moreira CHC (2004) Genetic code: a self-referential and functional model. In: Pályi G, Zucchi C, Caglioti L (eds) Progress in biological chirality. Elsevier, Oxford, pp 83-118. http://eprints.ictp.it/131
    • (2004) Progress in Biological Chirality , pp. 83-118
    • Guimarães, R.C.1    Moreira, C.H.C.2
  • 28
    • 0030707877 scopus 로고    scopus 로고
    • A euryarchaeal lysyl-tRNA synthetase: Resemblance to class I synthetases
    • M Ibba S Morgan AW Curnow 1997 A euryarchaeal lysyl-tRNA synthetase: resemblance to class I synthetases Science 278 1119 1122
    • (1997) Science , vol.278 , pp. 1119-1122
    • Ibba, M.1    Morgan, S.2    Curnow, A.W.3
  • 31
    • 0032706595 scopus 로고    scopus 로고
    • A tiny RNA that catalyzes both aminoacyl-tRNA and peptidyl-RNA synthesis
    • M Illangasekare M Yarus 1999 A tiny RNA that catalyzes both aminoacyl-tRNA and peptidyl-RNA synthesis RNA 5 1482 1489
    • (1999) RNA , vol.5 , pp. 1482-1489
    • Illangasekare, M.1    Yarus, M.2
  • 32
    • 33847752960 scopus 로고    scopus 로고
    • The expanded evolutionary synthesis-a response to Godfrey-Smith, Haig, and West-Eberhard
    • E Jablonka MJ Lamb 2007 The expanded evolutionary synthesis-a response to Godfrey-Smith, Haig, and West-Eberhard Biol Philos 22 453 472
    • (2007) Biol Philos , vol.22 , pp. 453-472
    • Jablonka, E.1    Lamb, M.J.2
  • 33
    • 0344146524 scopus 로고    scopus 로고
    • Protein evolution drives the evolution of the genetic code and vice-versa
    • MA Jiménez-Montaño 1999 Protein evolution drives the evolution of the genetic code and vice-versa BioSystems 54 47 64
    • (1999) BioSystems , vol.54 , pp. 47-64
    • Jiménez-Montaño, M.A.1
  • 34
    • 2342637052 scopus 로고    scopus 로고
    • Amino acids biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetases
    • L Klipcan M Safro 2004 Amino acids biogenesis, evolution of the genetic code and aminoacyl-tRNA synthetases J Theor Biol 228 389 396
    • (2004) J Theor Biol , vol.228 , pp. 389-396
    • Klipcan, L.1    Safro, M.2
  • 35
    • 0033152412 scopus 로고    scopus 로고
    • Selection, history and chemistry: The three faces of the genetic code
    • RD Knight SJ Freeland LF Landweber 1999 Selection, history and chemistry: the three faces of the genetic code Trends Biochem Sci 24 241 247
    • (1999) Trends Biochem Sci , vol.24 , pp. 241-247
    • Knight, R.D.1    Freeland, S.J.2    Landweber, L.F.3
  • 37
    • 0020730882 scopus 로고
    • Experimental studies related to the origin of the genetic code and the process of protein synthesis-a review
    • JC Lacey Jr DW Mullins Jr 1983 Experimental studies related to the origin of the genetic code and the process of protein synthesis-a review Orig Life Evol Biosph 13 3 42
    • (1983) Orig Life Evol Biosph , vol.13 , pp. 3-42
    • Lacey Jr., J.C.1    Mullins Jr., D.W.2
  • 38
    • 21244459165 scopus 로고    scopus 로고
    • A more complex isoleucine aptamer with a cognate triplet
    • M Legiewicz M Yarus 2005 A more complex isoleucine aptamer with a cognate triplet J Biol Chem 280 19815 19822
    • (2005) J Biol Chem , vol.280 , pp. 19815-19822
    • Legiewicz, M.1    Yarus, M.2
  • 39
    • 0036434298 scopus 로고    scopus 로고
    • Amplification of the sequences displaying the pattern RNY in the RNA world: The translation → translation/replication hypothesis
    • J Lehmann 2002 Amplification of the sequences displaying the pattern RNY in the RNA world: the translation → translation/replication hypothesis J Theor Biol 219 521 537
    • (2002) J Theor Biol , vol.219 , pp. 521-537
    • Lehmann, J.1
  • 41
    • 0036401273 scopus 로고    scopus 로고
    • On the dimerization of the primitive tRNAs: Implications in the origin of the genetic code
    • JA Martinez-Giménez R Tabarés-Seisdedos 2002 On the dimerization of the primitive tRNAs: implications in the origin of the genetic code J Theor Biol 217 493 498
    • (2002) J Theor Biol , vol.217 , pp. 493-498
    • Martinez-Giménez, J.A.1    Tabarés-Seisdedos, R.2
  • 42
    • 0019881806 scopus 로고
    • Effect of tRNA dimer formation on polyphenylalanine biosynthesis
    • DL Miller T Yamane JJ Hopfield 1981 Effect of tRNA dimer formation on polyphenylalanine biosynthesis Biochemistry 20 5457 5461
    • (1981) Biochemistry , vol.20 , pp. 5457-5461
    • Miller, D.L.1    Yamane, T.2    Hopfield, J.J.3
  • 43
    • 31144451338 scopus 로고    scopus 로고
    • Serine octamers: Cluster formation, reactions, and implications for biomolecule homochirality
    • SC Nanita RG Cooks 2006 Serine octamers: cluster formation, reactions, and implications for biomolecule homochirality Angew Chem Int Ed 45 554 569
    • (2006) Angew Chem Int Ed , vol.45 , pp. 554-569
    • Nanita, S.C.1    Cooks, R.G.2
  • 44
    • 26944459549 scopus 로고    scopus 로고
    • Catalytic activities of [GADV]-protein world for the emergence of life
    • T Oba J Fukushima M Maruyama 2005 Catalytic activities of [GADV]-protein world for the emergence of life Orig Life Evol Biosph 35 447 460
    • (2005) Orig Life Evol Biosph , vol.35 , pp. 447-460
    • Oba, T.1    Fukushima, J.2    Maruyama, M.3
  • 46
    • 0026705549 scopus 로고
    • A systemic concept of the gene
    • MIMC Pardini RC Guimarães 1992 A systemic concept of the gene Genet Mol Biol 15 713 721
    • (1992) Genet Mol Biol , vol.15 , pp. 713-721
    • Mimc, P.1    Guimarães, R.C.2
  • 47
    • 4344643959 scopus 로고    scopus 로고
    • An aminoacyl-tRNA synthetase that specifically activates pyrrolysine
    • C Polycarpo A Ambrogelly A Bérubé 2004 An aminoacyl-tRNA synthetase that specifically activates pyrrolysine Proc Nat Acad Sci USA 101 12450 12454
    • (2004) Proc Nat Acad Sci USA , vol.101 , pp. 12450-12454
    • Polycarpo, C.1    Ambrogelly, A.2    Bérubé, A.3
  • 49
    • 0035951403 scopus 로고    scopus 로고
    • Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem
    • LR Pouplana P Schimmel 2001 Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem Cell 104 191 193
    • (2001) Cell , vol.104 , pp. 191-193
    • Pouplana, L.R.1    Schimmel, P.2
  • 50
    • 0031464187 scopus 로고    scopus 로고
    • The p43 component of the mammalian multi-synthetase complex is likely to be the precursor of the endothelial monocyte-activating polypeptide II cytokine
    • S Quevillon F Agou JC Robinson 1997 The p43 component of the mammalian multi-synthetase complex is likely to be the precursor of the endothelial monocyte-activating polypeptide II cytokine J Biol Chem 272 32573 32579
    • (1997) J Biol Chem , vol.272 , pp. 32573-32579
    • Quevillon, S.1    Agou, F.2    Robinson, J.C.3
  • 51
    • 0027276319 scopus 로고
    • Transfer RNAs with complementary anticodons: Could they reflect early evolution of discriminative genetic code adaptors?
    • SN Rodin S Ohno A Rodin 1993 Transfer RNAs with complementary anticodons: could they reflect early evolution of discriminative genetic code adaptors? Proc Nat Acad Sci USA 90 4723 4727
    • (1993) Proc Nat Acad Sci USA , vol.90 , pp. 4723-4727
    • Rodin, S.N.1    Ohno, S.2    Rodin, A.3
  • 52
    • 0028921307 scopus 로고
    • An operational RNA code for amino acids and variations in critical nucleotide sequences in evolution
    • P Schimmel 1995 An operational RNA code for amino acids and variations in critical nucleotide sequences in evolution J Mol Evol 40 531 536
    • (1995) J Mol Evol , vol.40 , pp. 531-536
    • Schimmel, P.1
  • 53
    • 0036960547 scopus 로고    scopus 로고
    • Chemical interactions between amino acid and RNA: Multiplicity of the levels of specificity explains origin of the genetic code
    • H Seligmann GN Amzallag 2002 Chemical interactions between amino acid and RNA: multiplicity of the levels of specificity explains origin of the genetic code Naturwissenschaften 89 542 551
    • (2002) Naturwissenschaften , vol.89 , pp. 542-551
    • Seligmann, H.1    Amzallag, G.N.2
  • 54
    • 0031610693 scopus 로고    scopus 로고
    • A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases
    • G Simos A Sauer F Fasiolo 1998 A conserved domain within Arc1p delivers tRNA to aminoacyl-tRNA synthetases Mol Cell 1 235 242
    • (1998) Mol Cell , vol.1 , pp. 235-242
    • Simos, G.1    Sauer, A.2    Fasiolo, F.3
  • 55
    • 0141594580 scopus 로고    scopus 로고
    • A noncognate aminoacyl-tRNA synthetase that may resolve a missing link in protein evolution
    • S Skouloubris L de Ribas Pouplana H Reuse 2003 A noncognate aminoacyl-tRNA synthetase that may resolve a missing link in protein evolution Proc Nat Acad Sci USA 100 11296 11302
    • (2003) Proc Nat Acad Sci USA , vol.100 , pp. 11296-11302
    • Skouloubris, S.1    De Ribas Pouplana, L.2    Reuse, H.3
  • 56
    • 0040298763 scopus 로고
    • TRNA-tRNA interactions within cellular ribosomes
    • D Smith M Yarus 1989 tRNA-tRNA interactions within cellular ribosomes Proc Nat Acad Sci USA 86 4397 4401
    • (1989) Proc Nat Acad Sci USA , vol.86 , pp. 4397-4401
    • Smith, D.1    Yarus, M.2
  • 57
    • 27744581953 scopus 로고    scopus 로고
    • Conserved sequences of prokaryotic proteomes and their compositional age
    • Y Sobolevsky EN Trifonov 2005 Conserved sequences of prokaryotic proteomes and their compositional age J Mol Evol 61 1 7
    • (2005) J Mol Evol , vol.61 , pp. 1-7
    • Sobolevsky, Y.1    Trifonov, E.N.2
  • 58
    • 33751550510 scopus 로고    scopus 로고
    • Protein modules conserved since LUCA
    • Y Sobolevsky EN Trifonov 2006 Protein modules conserved since LUCA J Mol Evol 63 622 634
    • (2006) J Mol Evol , vol.63 , pp. 622-634
    • Sobolevsky, Y.1    Trifonov, E.N.2
  • 59
    • 0034695470 scopus 로고    scopus 로고
    • One polypeptide with two aminoacyl-tRNA synthetase activities
    • C Stathopoulos T Li R Longman 2000 One polypeptide with two aminoacyl-tRNA synthetase activities Science 287 479 482
    • (2000) Science , vol.287 , pp. 479-482
    • Stathopoulos, C.1    Li, T.2    Longman, R.3
  • 60
    • 0033152895 scopus 로고    scopus 로고
    • The origin of the genetic code: Amino acids as cofactors in an RNA world
    • E Szathmáry 1999 The origin of the genetic code: amino acids as cofactors in an RNA world Trends Genet 15 223 229
    • (1999) Trends Genet , vol.15 , pp. 223-229
    • Szathmáry, E.1
  • 61
    • 0042808612 scopus 로고    scopus 로고
    • Peptide synthesis with a template-like RNA guide and aminoacyl phosphate adaptor
    • K Tamura P Schimmel 2003 Peptide synthesis with a template-like RNA guide and aminoacyl phosphate adaptor Proc Nat Acad Sci USA 100 8666 8669
    • (2003) Proc Nat Acad Sci USA , vol.100 , pp. 8666-8669
    • Tamura, K.1    Schimmel, P.2
  • 62
    • 9244224677 scopus 로고    scopus 로고
    • Chance and necessity do not explain the origin of life
    • JT Trevors DL Abel 2004 Chance and necessity do not explain the origin of life Cell Biol Int 28 729 739
    • (2004) Cell Biol Int , vol.28 , pp. 729-739
    • Trevors, J.T.1    Abel, D.L.2
  • 63
    • 4143139971 scopus 로고    scopus 로고
    • The triplet code from first principles
    • EN Trifonov 2004 The triplet code from first principles J Biomol Struct Dyn 22 1 11
    • (2004) J Biomol Struct Dyn , vol.22 , pp. 1-11
    • Trifonov, E.N.1
  • 64
    • 0029861143 scopus 로고    scopus 로고
    • The N-end rule: Functions, mysteries, uses
    • A Varshavsky 1996 The N-end rule: functions, mysteries, uses Biochemistry 93 12142 12149
    • (1996) Biochemistry , vol.93 , pp. 12142-12149
    • Varshavsky, A.1
  • 65
    • 17844405021 scopus 로고    scopus 로고
    • Coevolution theory of the genetic code at age thirty
    • JTF Wong 2005 Coevolution theory of the genetic code at age thirty BioEssays 27 416 425
    • (2005) BioEssays , vol.27 , pp. 416-425
    • Wong, J.T.F.1
  • 66
    • 0019884736 scopus 로고
    • Interaction of elongation factor Tu with the aminoacyl-tRNA dimer Phe-tRNA:Glu-tRNA
    • T Yamane DL Miller JJ Hopfield 1981 Interaction of elongation factor Tu with the aminoacyl-tRNA dimer Phe-tRNA:Glu-tRNA Biochemistry 20 449 452
    • (1981) Biochemistry , vol.20 , pp. 449-452
    • Yamane, T.1    Miller, D.L.2    Hopfield, J.J.3
  • 67
    • 26844527683 scopus 로고    scopus 로고
    • On the structural regularity in nucleobases and amino acids and relationship to the origin and evolution of the genetic code
    • CM Yang 2005 On the structural regularity in nucleobases and amino acids and relationship to the origin and evolution of the genetic code Orig Life Evol Biosph 35 275 295
    • (2005) Orig Life Evol Biosph , vol.35 , pp. 275-295
    • Yang, C.M.1
  • 68
    • 0034695287 scopus 로고    scopus 로고
    • Perspectives: Protein synthesis-unraveling the riddle of ProCys tRNA synthetase
    • M Yarus 2000 Perspectives: protein synthesis-unraveling the riddle of ProCys tRNA synthetase Science 287 440 441
    • (2000) Science , vol.287 , pp. 440-441
    • Yarus, M.1


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