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Volumn 47, Issue 1, 1998, Pages 1-13

On error minimization in a sequential origin of the standard genetic code

Author keywords

Amino acid substitution matrices; Codon context; Error minimization; G C bias; RNA world; RNY hypothesis; Transition bias; Translational error

Indexed keywords

AMINO ACID; RNA;

EID: 0031777847     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006356     Document Type: Article
Times cited : (85)

References (62)
  • 1
    • 0014581827 scopus 로고
    • The genetic code and error transmission
    • Alff-Steinberger C (1969) The genetic code and error transmission. Proc Natl Acad Sci USA 64:584-591
    • (1969) Proc Natl Acad Sci USA , vol.64 , pp. 584-591
    • Alff-Steinberger, C.1
  • 2
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul S (1991) Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 219:555-565
    • (1991) J Mol Biol , vol.219 , pp. 555-565
    • Altschul, S.1
  • 3
    • 0028092214 scopus 로고
    • Amino acid substitution during functionally constrained divergent evolution of protein sequences
    • Benner S, Cohen M, Gonnet G (1994) Amino acid substitution during functionally constrained divergent evolution of protein sequences. Protein Eng 7(11):1323-1332
    • (1994) Protein Eng , vol.7 , Issue.11 , pp. 1323-1332
    • Benner, S.1    Cohen, M.2    Gonnet, G.3
  • 4
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick F (1968) The origin of the genetic code. J Mol Biol 38:367-379
    • (1968) J Mol Biol , vol.38 , pp. 367-379
    • Crick, F.1
  • 7
    • 0013914739 scopus 로고
    • A further study of misreading of codons induced by streptomycin and neomycin using ribopolynucleotides containing two nucleotides in alternating sequence as templates
    • Davies J, Jones D, Khorana H (1966) A further study of misreading of codons induced by streptomycin and neomycin using ribopolynucleotides containing two nucleotides in alternating sequence as templates. J Mol Biol 18:48-57
    • (1966) J Mol Biol , vol.18 , pp. 48-57
    • Davies, J.1    Jones, D.2    Khorana, H.3
  • 8
    • 0024745336 scopus 로고
    • The extension reached by the minimization of the polarity distances during the evolution of the genetic code
    • Di Giulio M (1989a) The extension reached by the minimization of the 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
    • 0024438078 scopus 로고
    • Some aspects of the organization and evolution of the genetic code
    • Di Giulio M (1989b) Some aspects of the organization and evolution of the genetic code. J Mol Evol 29:191-201
    • (1989) J Mol Evol , vol.29 , pp. 191-201
    • Di Giulio, M.1
  • 10
    • 0028275445 scopus 로고
    • On the optimization of the physicochemical distances between amino acids in the evolution of the genetic code
    • Di Giulio M (1994) On the optimization of the physicochemical distances between amino acids in the evolution of the genetic code. J Theor Biol 168:43-51
    • (1994) J Theor Biol , vol.168 , pp. 43-51
    • Di Giulio, M.1
  • 11
    • 0029449631 scopus 로고
    • The phylogeny of tRNAs seems to confirm the predictions of the coevolution theory of the origin of the genetic code
    • Di Giulio M (1995a) The phylogeny of tRNAs seems to confirm the predictions of the coevolution theory of the origin of the genetic code. Orig Life Evol Biosph 25:549-564
    • (1995) Orig Life Evol Biosph , vol.25 , pp. 549-564
    • Di Giulio, M.1
  • 12
    • 0028857719 scopus 로고
    • Was it an ancient gene codifying for a hairpin RNA that, by means of direct duplication, gave rise to the primitive tRNA molecule?
    • Di Giulio M (1995b) 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 177:95-101
    • (1995) J Theor Biol , vol.177 , pp. 95-101
    • Di Giulio, M.1
  • 15
    • 0029832218 scopus 로고    scopus 로고
    • RNA-catalyzed RNA polymerization using nucleoside triphosphates
    • Ekland E, Bartel DP (1996) RNA-catalyzed RNA polymerization using nucleoside triphosphates. Nature 382(6589):373-376
    • (1996) Nature , vol.382 , Issue.6589 , pp. 373-376
    • Ekland, E.1    Bartel, D.P.2
  • 16
    • 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(5031):25-28
    • (1966) Nature , vol.210 , Issue.5031 , pp. 25-28
    • Epstein, C.1
  • 17
    • 0024492327 scopus 로고
    • Optimization and the genetic code
    • Figureau A (1989) Optimization and the genetic code. Orig Life Evol Biosph 19:57-67
    • (1989) Orig Life Evol Biosph , vol.19 , pp. 57-67
    • Figureau, A.1
  • 18
    • 0013888042 scopus 로고
    • Evidence suggesting a partial, internal duplication in the ancestral gene for heme-containing globins
    • Fitch W (1966) Evidence suggesting a partial, internal duplication in the ancestral gene for heme-containing globins. J Mol Biol 16:1
    • (1966) J Mol Biol , vol.16 , pp. 1
    • Fitch, W.1
  • 19
    • 0023471213 scopus 로고
    • The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code
    • Fitch W, Upper K (1987) The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. Cold Spring Harbor Symp Quant Biol 52:759-767
    • (1987) Cold Spring Harbor Symp Quant Biol , vol.52 , pp. 759-767
    • Fitch, W.1    Upper, K.2
  • 20
    • 0020528412 scopus 로고
    • What is a conservative substitution?
    • French S, Robson B (1983) What is a conservative substitution? J Mol Evol 19:171-175
    • (1983) J Mol Evol , vol.19 , pp. 171-175
    • French, S.1    Robson, B.2
  • 22
    • 0014024955 scopus 로고
    • Genetic code: Aspects of organization
    • Goldberg AL, Wittes R (1966) Genetic code: aspects of organization. Science 153:420-424
    • (1966) Science , vol.153 , pp. 420-424
    • Goldberg, A.L.1    Wittes, R.2
  • 23
    • 0027484262 scopus 로고
    • Further results on error minimization in the genetic code
    • Goldman N (1993) Further results on error minimization in the genetic code. J Mol Evol 37:662-664
    • (1993) J Mol Evol , vol.37 , pp. 662-664
    • Goldman, N.1
  • 24
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862-864
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 25
    • 0000960472 scopus 로고
    • On the physical basis for ambiguity in genetic coding interactions
    • Grosjean H, de Henau S, Crothers D (1978) On the physical basis for ambiguity in genetic coding interactions. Proc Natl Acad Sci USA 75(2):610-614
    • (1978) Proc Natl Acad Sci USA , vol.75 , Issue.2 , pp. 610-614
    • Grosjean, H.1    De Henau, S.2    Crothers, D.3
  • 26
    • 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
  • 27
    • 0028335134 scopus 로고
    • Pattern generation in molecular evolution: Exploitation of the variation in RNA landscapes
    • Huynen M, Hogeweg P (1994) Pattern generation in molecular evolution: exploitation of the variation in RNA landscapes. J Mol Evol 39:71-79
    • (1994) J Mol Evol , vol.39 , pp. 71-79
    • Huynen, M.1    Hogeweg, P.2
  • 28
    • 0015881599 scopus 로고
    • Arginine as an evolutionary intruder into protein synthesis
    • Jukes T (1973) Arginine as an evolutionary intruder into protein synthesis. Biochem Biophys Res Commun 53(3):709-714
    • (1973) Biochem Biophys Res Commun , vol.53 , Issue.3 , pp. 709-714
    • Jukes, T.1
  • 29
    • 0018191721 scopus 로고
    • The genetic code as a periodic table
    • Juncgk J (1978) The genetic code as a periodic table. J Mol Evol 11:211-224
    • (1978) J Mol Evol , vol.11 , pp. 211-224
    • Juncgk, J.1
  • 30
    • 0026050396 scopus 로고
    • Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli dna photolyase
    • Kim S-T, Sancar A (1991) Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli dna photolyase. Biochemistry 30(35):8623-8630
    • (1991) Biochemistry , vol.30 , Issue.35 , pp. 8623-8630
    • Kim, S.-T.1    Sancar, A.2
  • 31
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111-120
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 32
    • 0014680905 scopus 로고
    • Non-darwinian evolution
    • King J, Jukes T (1969) Non-darwinian evolution. Science 164:788-798
    • (1969) Science , vol.164 , pp. 788-798
    • King, J.1    Jukes, T.2
  • 33
    • 0030931016 scopus 로고    scopus 로고
    • Mutation matrices and physical-chemical properties: Correlations and implications
    • Koshi J, Goldstein R (1997) Mutation matrices and physical-chemical properties: correlations and implications. Proteins 27:336-344
    • (1997) Proteins , vol.27 , pp. 336-344
    • Koshi, J.1    Goldstein, R.2
  • 34
    • 0024349094 scopus 로고
    • Strong inclination toward transitions in nucleotide substitutions by poliovirus replicase
    • Kuge S, Kawamura N, Nomoto A (1989) Strong inclination toward transitions in nucleotide substitutions by poliovirus replicase. J Mol Biol 207(1):175-182
    • (1989) J Mol Biol , vol.207 , Issue.1 , pp. 175-182
    • Kuge, S.1    Kawamura, N.2    Nomoto, A.3
  • 36
    • 0023488772 scopus 로고
    • What organic compounds could have occurred on the prebiotic earth?
    • Miller S (1987) What organic compounds could have occurred on the prebiotic earth? Cold Spring Harbor Symp Quant Biol 52:17-27
    • (1987) Cold Spring Harbor Symp Quant Biol , vol.52 , pp. 17-27
    • Miller, S.1
  • 37
    • 0024046665 scopus 로고
    • Cluster analysis of amino acid indices for prediction of protein structure and function
    • Nakai K, Kidera A, Kanehisa M (1988) Cluster analysis of amino acid indices for prediction of protein structure and function. Protein Eng 2:93-100
    • (1988) Protein Eng , vol.2 , pp. 93-100
    • Nakai, K.1    Kidera, A.2    Kanehisa, M.3
  • 38
    • 0024240385 scopus 로고
    • Differential pattern of misreading induced by streptomycin in vitro
    • Negre D, Cenatiempo Y, Cozzone A (1988) Differential pattern of misreading induced by streptomycin in vitro. J Mol Biol 204:213-216
    • (1988) J Mol Biol , vol.204 , pp. 213-216
    • Negre, D.1    Cenatiempo, Y.2    Cozzone, A.3
  • 40
    • 0014674269 scopus 로고
    • Nature of magnesium-induced miscoding: The in vitro synthesis of valine-tyrosine copolypeptide directed by poly-(U-G)
    • Nishimura S, Harada F, Hirabayashi M (1968) Nature of magnesium-induced miscoding: the in vitro synthesis of valine-tyrosine copolypeptide directed by poly-(U-G). J Mol Biol 40:173-186
    • (1968) J Mol Biol , vol.40 , pp. 173-186
    • Nishimura, S.1    Harada, F.2    Hirabayashi, M.3
  • 41
    • 0026574207 scopus 로고
    • Recent evidence for evolution of the genetic code
    • Osawa S, Jukes T, Watanabe K, Muto A (1992) Recent evidence for evolution of the genetic code. Microbiol Rev 56(1):229-264
    • (1992) Microbiol Rev , vol.56 , Issue.1 , pp. 229-264
    • Osawa, S.1    Jukes, T.2    Watanabe, K.3    Muto, A.4
  • 42
    • 0024722501 scopus 로고
    • Errors and alternatives in reading the universal genetic code
    • Parker J (1989) Errors and alternatives in reading the universal genetic code. Microbiol Rev 53(3):273-298
    • (1989) Microbiol Rev , vol.53 , Issue.3 , pp. 273-298
    • Parker, J.1
  • 43
    • 0029953930 scopus 로고    scopus 로고
    • The presence of codon-anticodon pairs in the acceptor stem of tRNAs
    • Rodin S, Rodin A, Ohno S (1996) The presence of codon-anticodon pairs in the acceptor stem of tRNAs. Proc Natl Acad Sci USA 93:4537-4542
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 4537-4542
    • Rodin, S.1    Rodin, A.2    Ohno, S.3
  • 44
    • 0024601947 scopus 로고
    • Genetic code preferentially conserves long-range interactions among the amino acids
    • Sitaramam V (1989) Genetic code preferentially conserves long-range interactions among the amino acids. FEBS Lett 247(1):46-50
    • (1989) FEBS Lett , vol.247 , Issue.1 , pp. 46-50
    • Sitaramam, V.1
  • 45
    • 0024601947 scopus 로고
    • Genetic code preferentially conserves long-range interactions among the amino acids
    • Sjöström M, Wold S (1985) Genetic code preferentially conserves long-range interactions among the amino acids. FEBS Lett 247(1): 46-50
    • (1985) FEBS Lett , vol.247 , Issue.1 , pp. 46-50
    • Sjöström, M.1    Wold, S.2
  • 46
    • 0002124567 scopus 로고
    • Degeneracy of the genetic code: Extent, nature, and genetic implications
    • Bryson V, Vogel H (eds.). Academic Press, New York
    • Sonneborn T (1965) Degeneracy of the genetic code: extent, nature, and genetic implications. In: Bryson V, Vogel H (eds.) Evolving genes and proteins. Academic Press, New York, pp 377-397
    • (1965) Evolving Genes and Proteins , pp. 377-397
    • Sonneborn, T.1
  • 47
    • 0015935451 scopus 로고
    • Analysis of specific misreading in Escherichia coli
    • Strigini P, Brickman E (1973) Analysis of specific misreading in Escherichia coli. J Mol Biol 75:659-672
    • (1973) J Mol Biol , vol.75 , pp. 659-672
    • Strigini, P.1    Brickman, E.2
  • 48
    • 0021317760 scopus 로고
    • A unifying concept for the amino acid code
    • Swanson R (1984) A unifying concept for the amino acid code. Bull Math Biol 46(2):187-203
    • (1984) Bull Math Biol , vol.46 , Issue.2 , pp. 187-203
    • Swanson, R.1
  • 49
    • 0025908021 scopus 로고
    • Codon swapping as a possible evolutionary mechanism
    • Szathmary E (1991) Codon swapping as a possible evolutionary mechanism. J Mol Evol 32:178-182
    • (1991) J Mol Evol , vol.32 , pp. 178-182
    • Szathmary, E.1
  • 50
    • 0026731915 scopus 로고
    • A statistical test of hypotheses on the organization and origin of the genetic code
    • Szathmary E, Zintzaras E (1992) A statistical test of hypotheses on the organization and origin of the genetic code. J Mol Evol 35:185-189
    • (1992) J Mol Evol , vol.35 , pp. 185-189
    • Szathmary, E.1    Zintzaras, E.2
  • 51
    • 0024488958 scopus 로고
    • The code within the codons
    • Taylor F, Coates D (1989) The code within the codons. BioSystems 22:177-187
    • (1989) BioSystems , vol.22 , pp. 177-187
    • Taylor, F.1    Coates, D.2
  • 52
    • 0028081516 scopus 로고
    • Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies
    • Tolstrup N, Toftgård J, Engelbrecht J, Brunak S (1994) Neural network model of the genetic code is strongly correlated to the GES scale of amino acid transfer free energies. J Mol Biol 243:816-820
    • (1994) J Mol Biol , vol.243 , pp. 816-820
    • Tolstrup, N.1    Toftgård, J.2    Engelbrecht, J.3    Brunak, S.4
  • 53
    • 0029922443 scopus 로고    scopus 로고
    • Analysis of amino-acid indexes and mutation matrices for sequence comparison and structure prediction of proteins
    • Tomii K, Kanehisa M (1996) Analysis of amino-acid indexes and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng 9(1):27-36
    • (1996) Protein Eng , vol.9 , Issue.1 , pp. 27-36
    • Tomii, K.1    Kanehisa, M.2
  • 54
    • 0029938421 scopus 로고    scopus 로고
    • Thermodynamics of base pairing
    • Turner DH (1996) Thermodynamics of base pairing. Curr Opp Struct Biol 6(3):299-304
    • (1996) Curr Opp Struct Biol , vol.6 , Issue.3 , pp. 299-304
    • Turner, D.H.1
  • 56
    • 0013824051 scopus 로고
    • On the evolution of the genetic code
    • Woese C (1965) On the evolution of the genetic code. Proc Natl Acad Sci USA 54:1546-1552
    • (1965) Proc Natl Acad Sci USA , vol.54 , pp. 1546-1552
    • Woese, C.1
  • 57
    • 0015910584 scopus 로고
    • Evolution of the genetic code
    • Woese C (1973) Evolution of the genetic code. Naturwissenschaften 60:447-459
    • (1973) Naturwissenschaften , vol.60 , pp. 447-459
    • Woese, C.1
  • 59
    • 0018582090 scopus 로고
    • Water, protein folding and the genetic code
    • Wolfenden R, Cullis P, Southgate C (1979) Water, protein folding and the genetic code. Science 206(2):575-577
    • (1979) Science , vol.206 , Issue.2 , pp. 575-577
    • Wolfenden, R.1    Cullis, P.2    Southgate, C.3
  • 60
    • 0001155613 scopus 로고
    • A co-evolution theory of the genetic code
    • Wong J (1975) A co-evolution theory of the genetic code. Proc Natl Acad Sci USA 72(5):1909-1912
    • (1975) Proc Natl Acad Sci USA , vol.72 , Issue.5 , pp. 1909-1912
    • Wong, J.1
  • 61
    • 0013592859 scopus 로고
    • Role of minimization of chemical distances between amino acids in the evolution of the genetic code
    • Wong J (1980) Role of minimization of chemical distances between amino acids in the evolution of the genetic code. Proc Natl Acad Sci USA 77(2):1083-1086
    • (1980) Proc Natl Acad Sci USA , vol.77 , Issue.2 , pp. 1083-1086
    • Wong, J.1
  • 62
    • 0028917227 scopus 로고
    • A periodic table of symmetric tandem mismatches in RNA
    • Wu M, McDowell J, Turner DH (1995) A periodic table of symmetric tandem mismatches in RNA. Biochemistry 34(10):3204-3211
    • (1995) Biochemistry , vol.34 , Issue.10 , pp. 3204-3211
    • Wu, M.1    McDowell, J.2    Turner, D.H.3


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