메뉴 건너뛰기




Volumn 54, Issue 1-2, 1999, Pages 47-64

Protein evolution drives the evolution of the genetic code and vice versa

Author keywords

Aminoacyl tRNA synthetases; Codon reassignments; Codon anticodon interaction; Developmental pathway; Primeval code; Protein evolution

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE;

EID: 0344146524     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(99)00058-1     Document Type: Article
Times cited : (30)

References (76)
  • 2
    • 0031011715 scopus 로고    scopus 로고
    • An analysis of the metabolic theory of the origin of the genetic code
    • Amirnovin R. An analysis of the metabolic theory of the origin of the genetic code. J. Mol. Evol. 44:1997;473-476.
    • (1997) J. Mol. Evol. , vol.44 , pp. 473-476
    • Amirnovin, R.1
  • 3
    • 0029402902 scopus 로고
    • Genomic evolution drives the evolution of the translation system
    • Andersson S.G.E., Kurland C.G. Genomic evolution drives the evolution of the translation system. Biochem. Cell. Biol. 73:1995;775-787.
    • (1995) Biochem. Cell. Biol. , vol.73 , pp. 775-787
    • Andersson, S.G.E.1    Kurland, C.G.2
  • 4
    • 0018618823 scopus 로고
    • Group graph of the genetic code
    • Bertman M.O., Jungck J.R. Group graph of the genetic code. J. Heredity. 70:1979;379-384.
    • (1979) J. Heredity , vol.70 , pp. 379-384
    • Bertman, M.O.1    Jungck, J.R.2
  • 5
    • 0345218474 scopus 로고
    • Learning from positive-only examples: The subset principle and three cases studies
    • R. Michalski, J. Carbonell, Mitchel T. California: Morgan Kaufmann
    • Berwick R. Learning from positive-only examples: The subset principle and three cases studies. Michalski R., Carbonell J., Mitchel T. Machine learning, an artificial intelligence approach. II:1986;Morgan Kaufmann, California.
    • (1986) Machine Learning, An Artificial Intelligence Approach , vol.2
    • Berwick, R.1
  • 6
    • 0025969881 scopus 로고
    • Suggestions for 'safe' residue substitutions in site-directed mutagenesis
    • Bordo D., Argos P. Suggestions for 'safe' residue substitutions in site-directed mutagenesis. J. Mol. Biol. 217:1991;721-729.
    • (1991) J. Mol. Biol. , vol.217 , pp. 721-729
    • Bordo, D.1    Argos, P.2
  • 8
    • 0003166498 scopus 로고    scopus 로고
    • Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics
    • Chan H.S., Dill K.A. Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics. Proteins Struct. Funct. Genet. 30:1998;2-33.
    • (1998) Proteins Struct. Funct. Genet. , vol.30 , pp. 2-33
    • Chan, H.S.1    Dill, K.A.2
  • 9
    • 0019544314 scopus 로고
    • Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model
    • Chavancy G., Garel J.P. Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model. Biochemie. 63:1981;187-195.
    • (1981) Biochemie , vol.63 , pp. 187-195
    • Chavancy, G.1    Garel, J.P.2
  • 10
    • 0013936167 scopus 로고
    • Codon anticodon pairing: The wobble hypothesis
    • Crick F.H.C. Codon anticodon pairing: The wobble hypothesis. J. Mol. Biol. 19:1966;548-555.
    • (1966) J. Mol. Biol. , vol.19 , pp. 548-555
    • Crick, F.H.C.1
  • 11
    • 0016796651 scopus 로고
    • Symmetries of genetic code-doublets
    • Danckwerts H.J., Neubert D. Symmetries of genetic code-doublets. J. Mol. Evol. 5:1975;327-332.
    • (1975) J. Mol. Evol. , vol.5 , pp. 327-332
    • Danckwerts, H.J.1    Neubert, D.2
  • 13
    • 0032555408 scopus 로고    scopus 로고
    • Amino acid contribution to the genetic code structure: End-atom chemical rules of doublet composition
    • Davydov O.V. Amino acid contribution to the genetic code structure: end-atom chemical rules of doublet composition. J. Theor. Biol. 193:1998;679-690.
    • (1998) J. Theor. Biol. , vol.193 , pp. 679-690
    • Davydov, O.V.1
  • 15
    • 0031582635 scopus 로고    scopus 로고
    • Genetic code synonym quotas and amino acid complexity: Cutting the cost of proteins?
    • Dufton M.J. Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins? J. Theor. Biol. 187:1997;165-173.
    • (1997) J. Theor. Biol. , vol.187 , pp. 165-173
    • Dufton, M.J.1
  • 16
    • 0015133749 scopus 로고
    • Self-organization of matter and the evolution of biological macromolecules
    • Eigen M. Self-organization of matter and the evolution of biological macromolecules. Naturwiss. 58:1971;465-532.
    • (1971) Naturwiss. , vol.58 , pp. 465-532
    • Eigen, M.1
  • 19
    • 0014003909 scopus 로고
    • Role of the amino-acid 'code' and of selection for conformation in the evolution of proteins
    • Epstein C. Role of the amino-acid 'code' and of selection for conformation in the evolution of proteins. Nature. 210:1966;25-28.
    • (1966) Nature , vol.210 , pp. 25-28
    • Epstein, C.1
  • 20
    • 0025158208 scopus 로고
    • Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs
    • Eriani G., Delarue M., Poch O., Gangloff J., Moras D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature. 347:1990;203-206.
    • (1990) Nature , vol.347 , pp. 203-206
    • Eriani, G.1    Delarue, M.2    Poch, O.3    Gangloff, J.4    Moras, D.5
  • 21
    • 0031662136 scopus 로고    scopus 로고
    • The genetic code is one in a million
    • Freeland S.J, Hurst D.H. The genetic code is one in a million. J. Mol. Evol. 47:1998;238-248.
    • (1998) J. Mol. Evol. , vol.47 , pp. 238-248
    • Freeland, S.J.1    Hurst, D.H.2
  • 22
    • 0003604405 scopus 로고
    • Cold Spring Harbor Lab. Press, Plainview, NY
    • Gesteland, Atkins, 1993. The RNA World. Cold Spring Harbor Lab. Press, Plainview, NY.
    • (1993) The RNA World
    • Gesteland1    Atkins2
  • 23
    • 0014024955 scopus 로고
    • Genetic code: Aspects of organization
    • Goldberg A.L., Wittes R.E. Genetic code: aspects of organization. Science. 153:1966;420-424.
    • (1966) Science , vol.153 , pp. 420-424
    • Goldberg, A.L.1    Wittes, R.E.2
  • 24
    • 0027484262 scopus 로고
    • Further results on error minimization in the genetic code
    • Goldman N. Further results on error minimization in the genetic code. J. Mol. Evol. 37:1993;662-664.
    • (1993) J. Mol. Evol. , vol.37 , pp. 662-664
    • Goldman, N.1
  • 25
    • 0026327996 scopus 로고
    • A quantitative measure of error minimization in the genetic code
    • Haig D., Hurst L.D. A quantitative measure of error minimization in the genetic code. J. Mol. Evol. 33:1991;412-417.
    • (1991) J. Mol. Evol. , vol.33 , pp. 412-417
    • Haig, D.1    Hurst, L.D.2
  • 26
    • 0019055919 scopus 로고
    • On the antisymmetry of the amino acid code table
    • Hasegawa M., Miyata T. On the antisymmetry of the amino acid code table. Orig. Life. 10:1980;265-270.
    • (1980) Orig. Life , vol.10 , pp. 265-270
    • Hasegawa, M.1    Miyata, T.2
  • 27
    • 0028906228 scopus 로고
    • Speculations on the origin of the genetic code
    • Hartman H. Speculations on the origin of the genetic code. J. Mol. Evol. 40:1995;541-544.
    • (1995) J. Mol. Evol. , vol.40 , pp. 541-544
    • Hartman, H.1
  • 28
    • 0040456003 scopus 로고
    • Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs
    • Heckman J.E., Sarnoff J., Alzner-de Weerd B., Yin S., Raj Bhandary U.L. Novel features in the genetic code and codon reading patterns in Neurospora crassa mitochondria based on sequences of six mitochondrial tRNAs. Proc. Natl. Acad. Sci. U.S.A. 77:1980;3159-3163.
    • (1980) Proc. Natl. Acad. Sci. U.S.A. , vol.77 , pp. 3159-3163
    • Heckman, J.E.1    Sarnoff, J.2    Alzner-De Weerd, B.3    Yin, S.4    Raj Bhandary, U.L.5
  • 29
    • 0026410103 scopus 로고
    • Automated assembly of protein blocks for data base searching
    • Henikoff S., Henikoff J.G. Automated assembly of protein blocks for data base searching. Nucleic Acids Res. 19:1991;6565-6572.
    • (1991) Nucleic Acids Res. , vol.19 , pp. 6565-6572
    • Henikoff, S.1    Henikoff, J.G.2
  • 30
    • 0001523629 scopus 로고
    • Algebraic model for the evolution of the genetic code
    • Hornos J.E.M., Hornos Y.M.M. Algebraic model for the evolution of the genetic code. Phys. Rev. Lett. 71:1993;4401-4404.
    • (1993) Phys. Rev. Lett. , vol.71 , pp. 4401-4404
    • Hornos, J.E.M.1    Hornos, Y.M.M.2
  • 31
    • 0031716525 scopus 로고    scopus 로고
    • Directionally evolving genetic code: The UGA codon from stop to tryptophan in mitochondria
    • Inagaki Y., Ehara M., Watanabe K.I., Hayashi-Ishimaru Y., Ohama T. Directionally evolving genetic code: The UGA codon from stop to tryptophan in mitochondria. J. Mol. Evol. 47:1998;378-384.
    • (1998) J. Mol. Evol. , vol.47 , pp. 378-384
    • Inagaki, Y.1    Ehara, M.2    Watanabe, K.I.3    Hayashi-Ishimaru, Y.4    Ohama, T.5
  • 32
    • 0000827027 scopus 로고
    • On the syntactic structure of protein sequences, and concept of grammar complexity
    • Jiménez-Montaño M.A. On the syntactic structure of protein sequences, and concept of grammar complexity. Bull. Math. Biol. 46:1984;641-660.
    • (1984) Bull. Math. Biol. , vol.46 , pp. 641-660
    • Jiménez-Montaño, M.A.1
  • 33
    • 0028349715 scopus 로고
    • On the syntactic structure and redundancy distribution of the genetic code
    • Jiménez-Montaño M.A. On the syntactic structure and redundancy distribution of the genetic code. BioSystems. 32:1994;11-23.
    • (1994) BioSystems , vol.32 , pp. 11-23
    • Jiménez-Montaño, M.A.1
  • 35
    • 0029784751 scopus 로고    scopus 로고
    • The hypercube structure of the genetic code explains conservative and non-conservative aminoacid substitutions in vivo and in vitro
    • Jiménez-Montaño M.A., de la Mora-Basañez R., Pöschel T. The hypercube structure of the genetic code explains conservative and non-conservative aminoacid substitutions in vivo and in vitro. BioSystems. 39:1996;117-125.
    • (1996) BioSystems , vol.39 , pp. 117-125
    • Jiménez-Montaño, M.A.1    De La Mora-Basañez, R.2    Pöschel, T.3
  • 37
    • 0029589301 scopus 로고
    • On the origin and evolution of the genetic code
    • Jiménez-Sánchez A. On the origin and evolution of the genetic code. J. Mol. Biol. 41:1995;712-716.
    • (1995) J. Mol. Biol. , vol.41 , pp. 712-716
    • Jiménez-Sánchez, A.1
  • 38
    • 0345650266 scopus 로고
    • Coding triplets and their possible evolutionary implications
    • Jukes T.H. Coding triplets and their possible evolutionary implications. Biochem. Biophys. Res. Commun. 19:1965;391-396.
    • (1965) Biochem. Biophys. Res. Commun. , vol.19 , pp. 391-396
    • Jukes, T.H.1
  • 39
    • 0015881599 scopus 로고
    • Arginine as an evolutionary intruder into protein synthesis
    • Jukes T.H. Arginine as an evolutionary intruder into protein synthesis. Biochem. Biophys. Res. Comm. 53:1973;709-714.
    • (1973) Biochem. Biophys. Res. Comm. , vol.53 , pp. 709-714
    • Jukes, T.H.1
  • 40
    • 0025610787 scopus 로고
    • Genetic code 1990 Outlook
    • Jukes T.H. Genetic code 1990 Outlook. Experientia. 46:1990;1149-1157.
    • (1990) Experientia , vol.46 , pp. 1149-1157
    • Jukes, T.H.1
  • 41
    • 23444436172 scopus 로고
    • Protein design by binary patterning of polar and nonpolar amino acid sequences
    • Kamtekar S., Schiffer J.M., Xiong H., Babik J.M., Hecht M.H. Protein design by binary patterning of polar and nonpolar amino acid sequences. Science. 262:1993;1680-1685.
    • (1993) Science , vol.262 , pp. 1680-1685
    • Kamtekar, S.1    Schiffer, J.M.2    Xiong, H.3    Babik, J.M.4    Hecht, M.H.5
  • 42
    • 0004778276 scopus 로고    scopus 로고
    • Topological structure of the genetic code
    • Karasev V.A., Sorokin S.G. Topological structure of the genetic code. Russ. J. Genet. 33:1997;622-628.
    • (1997) Russ. J. Genet. , vol.33 , pp. 622-628
    • Karasev, V.A.1    Sorokin, S.G.2
  • 43
    • 0003694798 scopus 로고
    • New York: Oxford University Press
    • Kauffman S.A. The origins of order. 1993;367 Oxford University Press, New York.
    • (1993) The Origins of Order , pp. 367
    • Kauffman, S.A.1
  • 44
    • 0027194317 scopus 로고
    • The physical bases of the genetic code: The choice between speed and precision
    • Klump H.H. The physical bases of the genetic code: the choice between speed and precision. Archv. Biochem. Biophys. 301:1993;207-209.
    • (1993) Archv. Biochem. Biophys. , vol.301 , pp. 207-209
    • Klump, H.H.1
  • 45
    • 0000565157 scopus 로고
    • The thermodynamic basis of the genetic code
    • Klump H.H., Maeder D.L. The thermodynamic basis of the genetic code. Pure Appl. Chem. 63:1991;1357-1366.
    • (1991) Pure Appl. Chem. , vol.63 , pp. 1357-1366
    • Klump, H.H.1    Maeder, D.L.2
  • 47
    • 0345345078 scopus 로고
    • Two out of three: An alternative method for codon reading
    • Langerkvist U. Two out of three: an alternative method for codon reading. Proc. Natl. Acad. Sci. U.S.A. 75:1978;1759-1762.
    • (1978) Proc. Natl. Acad. Sci. U.S.A. , vol.75 , pp. 1759-1762
    • Langerkvist, U.1
  • 48
    • 0031558228 scopus 로고    scopus 로고
    • The emergence of genetic coding in physical systems
    • Nieselt-Struwe K., Wills P.R. The emergence of genetic coding in physical systems. J. Theor. Biol. 187:1997;1-14.
    • (1997) J. Theor. Biol. , vol.187 , pp. 1-14
    • Nieselt-Struwe, K.1    Wills, P.R.2
  • 49
    • 0020072660 scopus 로고
    • On order and complexity. II. Application to chemical and biochemical structures
    • Papentin F. On order and complexity. II. Application to chemical and biochemical structures. J. Theor. Biol. 95:1982;225-245.
    • (1982) J. Theor. Biol. , vol.95 , pp. 225-245
    • Papentin, F.1
  • 51
    • 0029953930 scopus 로고    scopus 로고
    • The presence of codon-anticodon pairs in the acceptor stem of tRNAs
    • Rodin S., Rodin A., Ohno S. The presence of codon-anticodon pairs in the acceptor stem of tRNAs. Proc. Natl. Acad. Sci. U.S.A. 93:1996;4537-4542.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 4537-4542
    • Rodin, S.1    Rodin, A.2    Ohno, S.3
  • 52
    • 0014355152 scopus 로고
    • Systematization of codons in the genetic code
    • Rumer, Yu. B., 1968. Systematization of codons in the genetic code. Dokl. Akad. Nauk. SSSR 183, 225-226.
    • (1968) Dokl. Akad. Nauk. SSSR , vol.183 , pp. 225-226
    • Rumer, Yu.B.1
  • 53
    • 0032513368 scopus 로고    scopus 로고
    • Evolution of a transfer RNA gene through a point mutation in the anticodon
    • Saks M.E., Sampson J.R., Abelson J. Evolution of a transfer RNA gene through a point mutation in the anticodon. Science. 279:1997;1665-1670.
    • (1997) Science , vol.279 , pp. 1665-1670
    • Saks, M.E.1    Sampson, J.R.2    Abelson, J.3
  • 55
    • 0027436686 scopus 로고
    • An operational RNA code for amino acids and possible relationship to genetic code
    • Schimmel P., Giegé R., Moras D., Yokoyama S. An operational RNA code for amino acids and possible relationship to genetic code. Proc. Natl. Acad. Sci. U.S.A. 90:1993;8763-9768.
    • (1993) Proc. Natl. Acad. Sci. U.S.A. , vol.90 , pp. 8763-9768
    • Schimmel, P.1    Giegé, R.2    Moras, D.3    Yokoyama, S.4
  • 56
    • 0030138792 scopus 로고    scopus 로고
    • On malleability in the genetic code
    • Schultz D.W, Yarus M. On malleability in the genetic code. J. Mol. Evol. 42:1996;597-601.
    • (1996) J. Mol. Evol. , vol.42 , pp. 597-601
    • Schultz, D.W.1    Yarus, M.2
  • 59
    • 0002124567 scopus 로고
    • Degeneracy of the genetic code, extent, nature, and genetic implications
    • V. Bryson, & H.J. Vogel. New York: Academic Press
    • Sonneborn T.M. Degeneracy of the genetic code, extent, nature, and genetic implications. Bryson V., Vogel H.J. Evolving genes and proteins. 1965;377-397 Academic Press, New York.
    • (1965) Evolving Genes and Proteins , pp. 377-397
    • Sonneborn, T.M.1
  • 60
    • 0021317760 scopus 로고
    • A unifying concept for the amino acid code
    • Swannson R. A unifying concept for the amino acid code. Bull. Math. Biol. 46:1984;187-203.
    • (1984) Bull. Math. Biol. , vol.46 , pp. 187-203
    • Swannson, R.1
  • 61
    • 0022591495 scopus 로고
    • The classification of amino acid conservation
    • Taylor W.R. The classification of amino acid conservation. J. Theor. Biol. 119:1986;205-218.
    • (1986) J. Theor. Biol. , vol.119 , pp. 205-218
    • Taylor, W.R.1
  • 62
    • 0024488958 scopus 로고
    • The code within the codons
    • Taylor F.J.R., Coates D. The code within the codons. BioSystems. 22:1989;177-187.
    • (1989) BioSystems , vol.22 , pp. 177-187
    • Taylor, F.J.R.1    Coates, D.2
  • 64
    • 0028905116 scopus 로고
    • Evolution of the aminoacyl-tRNA synthetases and the origin of the genetic code
    • Wentzel R. Evolution of the aminoacyl-tRNA synthetases and the origin of the genetic code. J. Mol. Evol. 40:1995;545-550.
    • (1995) J. Mol. Evol. , vol.40 , pp. 545-550
    • Wentzel, R.1
  • 65
    • 0013824051 scopus 로고
    • On the evolution of the genetic code
    • Woese C.R. On the evolution of the genetic code. Proc. Natl. Acad. Sci. U.S.A. 54:1965;1546-1552.
    • (1965) Proc. Natl. Acad. Sci. U.S.A. , vol.54 , pp. 1546-1552
    • Woese, C.R.1
  • 67
    • 0015910584 scopus 로고
    • Evolution of the genetic code
    • Woese C.R. Evolution of the genetic code. Naturwiss. 60:1973;447-459.
    • (1973) Naturwiss. , vol.60 , pp. 447-459
    • Woese, C.R.1
  • 69
    • 0027083319 scopus 로고
    • Animal mitochondria DNA: Structure and evolution
    • Wolstenholme D.R. Animal mitochondria DNA: structure and evolution. Int. Rev. Cytol. 141:1992;173-216.
    • (1992) Int. Rev. Cytol. , vol.141 , pp. 173-216
    • Wolstenholme, D.R.1
  • 70
    • 0001155613 scopus 로고
    • A co-evolution theory of the genetic code
    • Wong J.T.F. A co-evolution theory of the genetic code. Proc. Natl. Acad. Sci. U.S.A. 72:1975;1909-1912.
    • (1975) Proc. Natl. Acad. Sci. U.S.A. , vol.72 , pp. 1909-1912
    • Wong, J.T.F.1
  • 71
    • 0001155614 scopus 로고
    • The evolution of a universal genetic code
    • Wong J.T.F. The evolution of a universal genetic code. Proc. Natl. Acad. Sci. U.S.A. 73:1976;2336-2340.
    • (1976) Proc. Natl. Acad. Sci. U.S.A. , vol.73 , pp. 2336-2340
    • Wong, J.T.F.1
  • 72
    • 0003068637 scopus 로고
    • Coevolution of the genetic code and amino acid biosynthesis
    • Wong J.T.F. Coevolution of the genetic code and amino acid biosynthesis. Trends Biochem. Sci. 6:1981;33-35.
    • (1981) Trends Biochem. Sci. , vol.6 , pp. 33-35
    • Wong, J.T.F.1
  • 73
    • 0030332666 scopus 로고    scopus 로고
    • Discovering empirically conserved amino acid substitution groups in databases of protein families
    • In: States, D.J., Awarwal, P., Gaasterland, T., Hunter, L., Smith, R. (Eds.) AAAI Press, California
    • Wu, T.D., Brutlag, D.L., 1996. Discovering empirically conserved amino acid substitution groups in databases of protein families. In: States, D.J., Awarwal, P., Gaasterland, T., Hunter, L., Smith, R. (Eds.) Proceedings of the IV International conference on intelligent systems for molecular biology, AAAI Press, California, pp. 230-240.
    • (1996) Proceedings of the IV International Conference on Intelligent Systems for Molecular Biology , pp. 230-240
    • Wu, T.D.1    Brutlag, D.L.2
  • 74
    • 0031766244 scopus 로고    scopus 로고
    • What amino acid properties affect protein evolution?
    • Xia X., Li W.H What amino acid properties affect protein evolution? J. Mol. Evol. 47:1998;557-564.
    • (1998) J. Mol. Evol. , vol.47 , pp. 557-564
    • Xia, X.1    Li, W.H.2
  • 75
    • 0029064713 scopus 로고
    • Peridocity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides
    • Xiong H., Buckwalter B.L., Shieh H.M., Hecht M.H. Peridocity of polar and nonpolar amino acids is the major determinant of secondary structure in self-assembling oligomeric peptides. Proc. Natl. Acad. Sci. U.S.A. 92:1995;6349-6353.
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 6349-6353
    • Xiong, H.1    Buckwalter, B.L.2    Shieh, H.M.3    Hecht, M.H.4
  • 76
    • 0031558402 scopus 로고    scopus 로고
    • A symmetrical theory of DNA sequences and its applications
    • Zhang C.T. A symmetrical theory of DNA sequences and its applications. J. Theor. Biol. 187:1997;297-306.
    • (1997) J. Theor. Biol. , vol.187 , pp. 297-306
    • Zhang, C.T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.