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Volumn 43, Issue 6, 2013, Pages 465-489

Revisiting the Physico-Chemical Hypothesis of Code Origin: An Analysis Based on Code-Sequence Coevolution in a Finite Population

Author keywords

Finite population; Genetic code; Natural selection; Optimization; Origin

Indexed keywords

AMINO ACID; COEVOLUTION; DNA; EMERGENCE; FIXATION; NATURAL SELECTION; OPTIMIZATION; ORIGIN OF LIFE; PROBABILITY; RNA;

EID: 84896733379     PISSN: 01696149     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11084-014-9353-x     Document Type: Article
Times cited : (13)

References (57)
  • 1
    • 0031777847 scopus 로고    scopus 로고
    • On error minimization in a sequential origin of the standard genetic code
    • Ardell DH (1998) On error minimization in a sequential origin of the standard genetic code. J Mol Evol 47: 1-13.
    • (1998) J Mol Evol , vol.47 , pp. 1-13
    • Ardell, D.H.1
  • 2
    • 0034837877 scopus 로고    scopus 로고
    • On the evolution of redundancy in genetic codes
    • Ardell DH, Sella G (2001) On the evolution of redundancy in genetic codes. J Mol Evol 53: 269-281.
    • (2001) J Mol Evol , vol.53 , pp. 269-281
    • Ardell, D.H.1    Sella, G.2
  • 3
    • 0037448622 scopus 로고    scopus 로고
    • Greater GNN pattern bias in sequence elements encoding conserved residues of ancient proteins may be an indicator of amino acid composition of early proteins
    • Brooks DJ, Fresco JR (2003) Greater GNN pattern bias in sequence elements encoding conserved residues of ancient proteins may be an indicator of amino acid composition of early proteins. Gene 303: 177-185.
    • (2003) Gene , vol.303 , pp. 177-185
    • Brooks, D.J.1    Fresco, J.R.2
  • 4
    • 33748505624 scopus 로고    scopus 로고
    • Genetic code from tRNA point of view
    • Chechetkin VR (2006) Genetic code from tRNA point of view. J Theor Biol 242: 922-934.
    • (2006) J Theor Biol , vol.242 , pp. 922-934
    • Chechetkin, V.R.1
  • 5
    • 70350575251 scopus 로고    scopus 로고
    • Local stability and evolution of the genetic code
    • Chechetkin VR, Lobzin VV (2009) Local stability and evolution of the genetic code. J Theor Biol 261: 643-653.
    • (2009) J Theor Biol , vol.261 , pp. 643-653
    • Chechetkin, V.R.1    Lobzin, V.V.2
  • 6
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick FHC (1968) The origin of the genetic code. J Mol Biol 38: 367-379.
    • (1968) J Mol Biol , vol.38 , pp. 367-379
    • Crick, F.H.C.1
  • 7
    • 33846427338 scopus 로고    scopus 로고
    • An asymmetric underlying rule in the assignment of codons: possible clue to a quick early evolution of the genetic code via successive binary choices
    • Delarue M (2007) 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: 161-169.
    • (2007) Rna , vol.13 , pp. 161-169
    • Delarue, M.1
  • 8
    • 0024745336 scopus 로고
    • The extension reached by the minimization of polarity distances during the evolution of the genetic code
    • Di Giulio M (1989) The extension reached by the minimization of polarity distances during the evolution of the genetic code. J Mol Evol 29: 288-293.
    • (1989) J Mol Evol , vol.29 , pp. 288-293
    • Di Giulio, M.1
  • 9
    • 0030334119 scopus 로고    scopus 로고
    • The β-sheets of proteins, the biosynthetic relationships between amino acids and the origin of the genetic code
    • Di Giulio M (1996) The β-sheets of proteins, the biosynthetic relationships between amino acids and the origin of the genetic code. Orig Life Evol Biosph 26: 589-609.
    • (1996) Orig Life Evol Biosph , vol.26 , pp. 589-609
    • Di Giulio, M.1
  • 10
    • 0036841366 scopus 로고    scopus 로고
    • Genetic code origin: are the pathways of type Glu-tRNA(Gln) - > Gln-tRNA(Gln) molecular fossils or not?
    • Di Giulio M (2002) Genetic code origin: are the pathways of type Glu-tRNA(Gln) - > Gln-tRNA(Gln) molecular fossils or not? J Mol Evol 55: 616-622.
    • (2002) J Mol Evol , vol.55 , pp. 616-622
    • Di Giulio, M.1
  • 11
    • 17044376643 scopus 로고    scopus 로고
    • The origin of the genetic code: theories and their relationships, a review
    • Di Giulio M (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
  • 12
    • 52449089127 scopus 로고    scopus 로고
    • An extension of the coevolution theory of the origin of the genetic code
    • Di Giulio M (2008) An extension of the coevolution theory of the origin of the genetic code. Biol Direct 3: 37.
    • (2008) Biol Direct , vol.3 , pp. 37
    • Di Giulio, M.1
  • 13
    • 0031810657 scopus 로고    scopus 로고
    • The historical factor: The biosynthetic relationships between amino acids and their physicochemical properties in the origin of the genetic code
    • Di Giulio M, Medugno M (1998) The historical factor: The biosynthetic relationships between amino acids and their physicochemical properties in the origin of the genetic code. J Mol Evol 46: 615-621.
    • (1998) J Mol Evol , vol.46 , pp. 615-621
    • Di Giulio, M.1    Medugno, M.2
  • 14
    • 0032976509 scopus 로고    scopus 로고
    • Physicochemical optimization in the genetic code origin as the number of codified amino acids increases
    • Di Giulio M, Medugno M (1999) Physicochemical optimization in the genetic code origin as the number of codified amino acids increases. J Mol Evol 49: 1-10.
    • (1999) J Mol Evol , vol.49 , pp. 1-10
    • Di Giulio, M.1    Medugno, M.2
  • 15
    • 0035052003 scopus 로고    scopus 로고
    • The level and landscape of optimization in the origin of the genetic code
    • Di Giulio M, Medugno M (2001) The level and landscape of optimization in the origin of the genetic code. J Mol Evol 52: 372-382.
    • (2001) J Mol Evol , vol.52 , pp. 372-382
    • Di Giulio, M.1    Medugno, M.2
  • 16
    • 0014021204 scopus 로고
    • Triplet nucleotide-amino-acid pairing; a stereochemical basis for the division between protein and non-protein amino-acids
    • Dunnill P (1966) Triplet nucleotide-amino-acid pairing; a stereochemical basis for the division between protein and non-protein amino-acids. Nature 210: 1265-1267.
    • (1966) Nature , vol.210 , pp. 1265-1267
    • Dunnill, P.1
  • 17
    • 0014003909 scopus 로고
    • Role of the amino-acid "code" and of selection for conformation in the evolution of proteins
    • Epstein C (1966) Role of the amino-acid "code" and of selection for conformation in the evolution of proteins. Nature 210: 25-28.
    • (1966) Nature , vol.210 , pp. 25-28
    • Epstein, C.1
  • 18
    • 0031662136 scopus 로고    scopus 로고
    • The genetic code is one in a million
    • Freeland SJ, Hurst LD (1998) The genetic code is one in a million. J Mol Evol 47: 238-248.
    • (1998) J Mol Evol , vol.47 , pp. 238-248
    • Freeland, S.J.1    Hurst, L.D.2
  • 19
    • 84863865655 scopus 로고    scopus 로고
    • Origin and evolution of genes and genomes. Crucial role of triplet expansions
    • Frenkel ZM, Trifonov EN (2012) Origin and evolution of genes and genomes. Crucial role of triplet expansions. J Biomol Struct Dyn 30(2): 201-210.
    • (2012) J Biomol Struct Dyn , vol.30 , Issue.2 , pp. 201-210
    • Frenkel, Z.M.1    Trifonov, E.N.2
  • 20
    • 0035233646 scopus 로고    scopus 로고
    • Optimality of the genetic code with respect to protein stability and amino-acid frequencies
    • Gilis D, Massar S, Cerf NJ, Rooman M (2001) Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biol 2: 49. 1-49. 12.
    • (2001) Genome Biol , vol.2 , pp. 1-12
    • Gilis, D.1    Massar, S.2    Cerf, N.J.3    Rooman, M.4
  • 21
    • 0014024955 scopus 로고
    • Genetic code: aspects of organization
    • Goldberg AL, Wittes RE (1966) Genetic code: aspects of organization. Science 153: 420-424.
    • (1966) Science , vol.153 , pp. 420-424
    • Goldberg, A.L.1    Wittes, R.E.2
  • 22
    • 7544235210 scopus 로고    scopus 로고
    • On the optimality of the genetic code, with the consideration of termination codons
    • Goodarzi H, Nejad HA, Torabi N (2004) On the optimality of the genetic code, with the consideration of termination codons. Biosystems 77: 163-173.
    • (2004) Biosystems , vol.77 , pp. 163-173
    • Goodarzi, H.1    Nejad, H.A.2    Torabi, N.3
  • 23
    • 18844462433 scopus 로고    scopus 로고
    • On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices
    • Goodarzi H, Najafabadi HS, Hassani K et al (2005) On the optimality of the genetic code, with the consideration of coevolution theory by comparison of prominent cost measure matrices. J Theor Biol 235: 318-325.
    • (2005) J Theor Biol , vol.235 , pp. 318-325
    • Goodarzi, H.1    Najafabadi, H.S.2    Hassani, K.3
  • 24
    • 0026327996 scopus 로고
    • A quantitative measure of error minimization in the genetic code
    • Haig D, Hurst LD (1991) A quantitative measure of error minimization in the genetic code. J Mol Evol 33: 412-417.
    • (1991) J Mol Evol , vol.33 , pp. 412-417
    • Haig, D.1    Hurst, L.D.2
  • 25
    • 67449137928 scopus 로고    scopus 로고
    • A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code
    • Higgs PG (2009) A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biol Direct 4: 16.
    • (2009) Biol Direct , vol.4 , pp. 16
    • Higgs, P.G.1
  • 27
    • 67449120846 scopus 로고    scopus 로고
    • A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code
    • Higgs PG, Pudritz RE (2009) A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology 9: 483-490.
    • (2009) Astrobiology , vol.9 , pp. 483-490
    • Higgs, P.G.1    Pudritz, R.E.2
  • 28
    • 0015881599 scopus 로고
    • Arginine as an evolutionary intruder into protein synthesis
    • Jukes TH (1973) Arginine as an evolutionary intruder into protein synthesis. Biochem Biophys Res Commun 53: 709-714.
    • (1973) Biochem Biophys Res Commun , vol.53 , pp. 709-714
    • Jukes, T.H.1
  • 29
    • 0033993457 scopus 로고    scopus 로고
    • Guilt by association: the arginine case revisited
    • Knight RD, Landweber LF (2000) Guilt by association: the arginine case revisited. RNA 6: 499-510.
    • (2000) Rna , vol.6 , pp. 499-510
    • Knight, R.D.1    Landweber, L.F.2
  • 30
    • 0035234558 scopus 로고    scopus 로고
    • Rewiring the keyboard: evolvability of the genetic code
    • Knight RD, Freeland SJ, Landweber LF (2001) Rewiring the keyboard: evolvability of the genetic code. Nat Rev Genet 2: 49-58.
    • (2001) Nat Rev Genet , vol.2 , pp. 49-58
    • Knight, R.D.1    Freeland, S.J.2    Landweber, L.F.3
  • 31
    • 63449132404 scopus 로고    scopus 로고
    • Origin and evolution of the genetic code: the universal enigma
    • Koonin EV, Novozhilov AS (2009) Origin and evolution of the genetic code: the universal enigma. IUBMB Life 61: 99-111.
    • (2009) IUBMB Life , vol.61 , pp. 99-111
    • Koonin, E.V.1    Novozhilov, A.S.2
  • 32
    • 71549166642 scopus 로고    scopus 로고
    • Exceptional error minimization in putative primordial genetic codes
    • Novozhilov AS, Koonin EV (2009) Exceptional error minimization in putative primordial genetic codes. Biol Direct 4: 44.
    • (2009) Biol Direct , vol.4 , pp. 44
    • Novozhilov, A.S.1    Koonin, E.V.2
  • 33
    • 38549109625 scopus 로고    scopus 로고
    • Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape
    • Novozhilov AS, Wolf YI, Koonin EV (2007) Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape. Biol Direct 2: 24.
    • (2007) Biol Direct , vol.2 , pp. 24
    • Novozhilov, A.S.1    Wolf, Y.I.2    Koonin, E.V.3
  • 34
    • 0031714655 scopus 로고    scopus 로고
    • The population genetics of adaptation: the distribution of factors fixed during adaptive evolution
    • Orr HA (1998) The population genetics of adaptation: the distribution of factors fixed during adaptive evolution. Evolution (N Y) 52: 935.
    • (1998) Evolution (N Y) , vol.52 , pp. 935
    • Orr, H.A.1
  • 35
    • 0036340979 scopus 로고    scopus 로고
    • The population genetics of adaptation: the adaptation of DNA sequences
    • Orr HA (2002) The population genetics of adaptation: the adaptation of DNA sequences. Evolution (N Y) 56: 1317-1330.
    • (2002) Evolution (N Y) , vol.56 , pp. 1317-1330
    • Orr, H.A.1
  • 36
    • 0013844009 scopus 로고
    • Correlation between coding-triplets and amino-acids
    • Pelc S (1965) Correlation between coding-triplets and amino-acids. Nature 207: 597-599.
    • (1965) Nature , vol.207 , pp. 597-599
    • Pelc, S.1
  • 37
    • 0014028423 scopus 로고
    • Stereochemical relationship between coding triplets and amino-acids
    • Pelc S, Welton M (1966) Stereochemical relationship between coding triplets and amino-acids. Nature 209: 868-870.
    • (1966) Nature , vol.209 , pp. 868-870
    • Pelc, S.1    Welton, M.2
  • 38
    • 0036214921 scopus 로고    scopus 로고
    • The impact of message mutation on the fitness of a genetic code
    • Sella G, Ardell DH (2002) The impact of message mutation on the fitness of a genetic code. J Mol Evol 54: 638-651.
    • (2002) J Mol Evol , vol.54 , pp. 638-651
    • Sella, G.1    Ardell, D.H.2
  • 39
    • 33748959526 scopus 로고    scopus 로고
    • The coevolution of genes and genetic codes: Crick's frozen accident revisited
    • Sella G, Ardell DH (2006) The coevolution of genes and genetic codes: Crick's frozen accident revisited. J Mol Evol 63: 297-313.
    • (2006) J Mol Evol , vol.63 , pp. 297-313
    • Sella, G.1    Ardell, D.H.2
  • 40
    • 22144437754 scopus 로고    scopus 로고
    • A unified model of codon reassignment in alternative genetic codes
    • Sengupta S, Higgs PG (2005) A unified model of codon reassignment in alternative genetic codes. Genetics 170: 831-840.
    • (2005) Genetics , vol.170 , pp. 831-840
    • Sengupta, S.1    Higgs, P.G.2
  • 41
    • 34250704167 scopus 로고    scopus 로고
    • The mechanisms of codon reassignments in mitochondrial genetic codes
    • Sengupta S, Yang X, Higgs PG (2007) The mechanisms of codon reassignments in mitochondrial genetic codes. J Mol Evol 64: 662-688.
    • (2007) J Mol Evol , vol.64 , pp. 662-688
    • Sengupta, S.1    Yang, X.2    Higgs, P.G.3
  • 42
    • 0002124567 scopus 로고
    • Degeneracy of the genetic code: extent, nature, and genetic implications
    • Press New York
    • Sonneborn T (1965) Degeneracy of the genetic code: extent, nature, and genetic implications. Evol genes proteins Acad Press New York 377-397.
    • (1965) Evol genes proteins Acad , pp. 377-397
    • Sonneborn, T.1
  • 43
    • 14644437032 scopus 로고    scopus 로고
    • Mitochondrial genetic codes evolve to match amino acid requirements of proteins
    • Swire J, Judson OP, Burt A (2005) Mitochondrial genetic codes evolve to match amino acid requirements of proteins. J Mol Evol 60: 128-139.
    • (2005) J Mol Evol , vol.60 , pp. 128-139
    • Swire, J.1    Judson, O.P.2    Burt, A.3
  • 44
    • 0024488958 scopus 로고
    • The code within the codons
    • Taylor FJR, Coates D (1989) The code within the codons. BioSystems 22: 177-187.
    • (1989) BioSystems , vol.22 , pp. 177-187
    • Taylor, F.J.R.1    Coates, D.2
  • 45
    • 0034736513 scopus 로고    scopus 로고
    • Consensus temporal order of amino acids and the evolution of the triplet code
    • Trifonov EN (2000) Consensus temporal order of amino acids and the evolution of the triplet code. Gene 261: 139-151.
    • (2000) Gene , vol.261 , pp. 139-151
    • Trifonov, E.N.1
  • 46
    • 4143139971 scopus 로고    scopus 로고
    • The triplet code from first principles
    • Trifonov EN (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
  • 47
    • 0031593213 scopus 로고    scopus 로고
    • Sequence fossils, triplet expansion, and reconstruction of earliest codons
    • Trifonov EN, Bettecken T (1997) Sequence fossils, triplet expansion, and reconstruction of earliest codons. Gene 205: 1-6.
    • (1997) Gene , vol.205 , pp. 1-6
    • Trifonov, E.N.1    Bettecken, T.2
  • 49
  • 51
    • 34347347191 scopus 로고    scopus 로고
    • On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization
    • Wolf YI, Koonin EV (2007) On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biol Direct 2: 14.
    • (2007) Biol Direct , vol.2 , pp. 14
    • Wolf, Y.I.1    Koonin, E.V.2
  • 52
    • 0001155613 scopus 로고
    • A co-evolution theory of the genetic code
    • Wong JT (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci U S A 72: 1909-1912.
    • (1975) Proc Natl Acad Sci U S A , vol.72 , pp. 1909-1912
    • Wong, J.T.1
  • 53
    • 0001155614 scopus 로고
    • The evolution of a universal genetic code
    • Wong JT (1976) The evolution of a universal genetic code. Proc Natl Acad Sci U S A 73: 2336-2340.
    • (1976) Proc Natl Acad Sci U S A , vol.73 , pp. 2336-2340
    • Wong, J.T.1
  • 54
    • 0013592859 scopus 로고
    • Role of minimization of chemical distances between amino acids in the evolution of the genetic code
    • Wong JT (1980) Role of minimization of chemical distances between amino acids in the evolution of the genetic code. Proc Natl Acad Sci U S A 77: 1083-1086.
    • (1980) Proc Natl Acad Sci U S A , vol.77 , pp. 1083-1086
    • Wong, J.T.1
  • 55
    • 17844405021 scopus 로고    scopus 로고
    • Coevolution theory of the genetic code at age thirty
    • Wong JT (2005) Coevolution theory of the genetic code at age thirty. Bioessays 27: 416-425.
    • (2005) Bioessays , vol.27 , pp. 416-425
    • Wong, J.T.1
  • 56
    • 0034002683 scopus 로고    scopus 로고
    • RNA-ligand chemistry: a testable source for the genetic code
    • Yarus M (2000) RNA-ligand chemistry: a testable source for the genetic code. RNA 6: 475-484.
    • (2000) Rna , vol.6 , pp. 475-484
    • Yarus, M.1
  • 57
    • 32144446421 scopus 로고    scopus 로고
    • The standard genetic code enhances adaptive evolution of proteins
    • Zhu W, Freeland S (2006) The standard genetic code enhances adaptive evolution of proteins. J Theor Biol 239: 63-70.
    • (2006) J Theor Biol , vol.239 , pp. 63-70
    • Zhu, W.1    Freeland, S.2


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