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Volumn 25, Issue 11, 2008, Pages 2279-2291

Coevolution of codon usage and tRNA genes leads to alternative stable states of biased codon usage

Author keywords

Codon usage; Translational efficiency; Translational kinetics; tRNA genes

Indexed keywords

AMINO ACID; TRANSFER RNA;

EID: 54149105223     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msn173     Document Type: Article
Times cited : (111)

References (39)
  • 1
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • Akashi H. 1994. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics. 136:927-935.
    • (1994) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1
  • 2
    • 0041817645 scopus 로고    scopus 로고
    • Translational selection and yeast proteome evolution
    • Akashi H. 2003. Translational selection and yeast proteome evolution. Genetics. 164:1291-1303.
    • (2003) Genetics , vol.164 , pp. 1291-1303
    • Akashi, H.1
  • 3
    • 33645052751 scopus 로고    scopus 로고
    • The genomic pattern of tDNA operon expression in E. coli
    • Ardell DH, Kirsebom LA. 2005. The genomic pattern of tDNA operon expression in E. coli. PLoS Comput Biol. 1(1):e12.
    • (2005) PLoS Comput Biol , vol.1 , Issue.1
    • Ardell, D.H.1    Kirsebom, L.A.2
  • 5
    • 0023126266 scopus 로고
    • Coevolution of codon usage and transfer RNA abundance
    • Bulmer M. 1987. Coevolution of codon usage and transfer RNA abundance. Nature. 325:728-730.
    • (1987) Nature , vol.325 , pp. 728-730
    • Bulmer, M.1
  • 6
    • 0025941139 scopus 로고
    • The selection-mutation-drift theory of synonymous codon usage
    • Bulmer M. 1991. The selection-mutation-drift theory of synonymous codon usage. Genetics. 129:897-907.
    • (1991) Genetics , vol.129 , pp. 897-907
    • Bulmer, M.1
  • 7
    • 0024962419 scopus 로고
    • Rates of aminoacyl-tRNA selection at 29 sense codons in vivo
    • Curran JF, Yarus M. 1989. Rates of aminoacyl-tRNA selection at 29 sense codons in vivo. J Mol Biol. 209:65-77.
    • (1989) J Mol Biol , vol.209 , pp. 65-77
    • Curran, J.F.1    Yarus, M.2
  • 8
    • 33747886005 scopus 로고    scopus 로고
    • The ribosome's response to codon-anticodon mismatches
    • Daviter T, Gromadski KB, Rodnina MV. 2006. The ribosome's response to codon-anticodon mismatches. Biochimie. 88:1001-1011.
    • (2006) Biochimie , vol.88 , pp. 1001-1011
    • Daviter, T.1    Gromadski, K.B.2    Rodnina, M.V.3
  • 9
    • 0030564828 scopus 로고    scopus 로고
    • Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates
    • Dong H, Nilsson L, Kurland CG. 1996. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 260:649-663.
    • (1996) J Mol Biol , vol.260 , pp. 649-663
    • Dong, H.1    Nilsson, L.2    Kurland, C.G.3
  • 10
    • 4644280499 scopus 로고    scopus 로고
    • Solving the riddle of codon usage preferences: A test for translational selection
    • Dos Reis M, Savva R, Wernisch L. 2004. Solving the riddle of codon usage preferences: a test for translational selection. Nucleic Acids Res. 32:5036-5044.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5036-5044
    • Dos Reis, M.1    Savva, R.2    Wernisch, L.3
  • 11
    • 0344237338 scopus 로고    scopus 로고
    • Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome
    • Dos Reis M, Wernisch L, Savva R. 2003. Unexpected correlations between gene expression and codon usage bias from microarray data for the whole Escherichia coli K-12 genome. Nucleic Acids Res. 31:6976-6985.
    • (2003) Nucleic Acids Res , vol.31 , pp. 6976-6985
    • Dos Reis, M.1    Wernisch, L.2    Savva, R.3
  • 13
    • 0034237669 scopus 로고    scopus 로고
    • tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes
    • Duret L. 2000. tRNA gene number and codon usage in the C. elegans genome are co-adapted for optimal translation of highly expressed genes. Trends Genet. 16:287-289.
    • (2000) Trends Genet , vol.16 , pp. 287-289
    • Duret, L.1
  • 14
    • 0344100118 scopus 로고    scopus 로고
    • A mathematical model for elongation of a peptide chain
    • Heyd A, Drew DA. 2003. A mathematical model for elongation of a peptide chain. Bull Math Biol. 65:1095-1109.
    • (2003) Bull Math Biol , vol.65 , pp. 1095-1109
    • Heyd, A.1    Drew, D.A.2
  • 15
    • 0142075820 scopus 로고    scopus 로고
    • The evolution of tRNA-Leucine genes in animal mitochondrial genomes
    • Higgs PG, Jameson D, Jow H, Rattray M. 2003. The evolution of tRNA-Leucine genes in animal mitochondrial genomes. J Mol Evol. 57:435-445.
    • (2003) J Mol Evol , vol.57 , pp. 435-445
    • Higgs, P.G.1    Jameson, D.2    Jow, H.3    Rattray, M.4
  • 16
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes
    • Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 151:389-409.
    • (1981) J Mol Biol , vol.151 , pp. 389-409
    • Ikemura, T.1
  • 17
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol Biol Evol. 2:13-34.
    • (1985) Mol Biol Evol , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 18
    • 38949118287 scopus 로고    scopus 로고
    • Codon usage in mitochondrial genomes: Distinguishing context-dependent mutation from translational selection
    • Jia W, Higgs PG. 2008. Codon usage in mitochondrial genomes: distinguishing context-dependent mutation from translational selection. Mol Biol Evol. 25:339-351.
    • (2008) Mol Biol Evol , vol.25 , pp. 339-351
    • Jia, W.1    Higgs, P.G.2
  • 19
    • 0032882170 scopus 로고    scopus 로고
    • Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs
    • Kanaya S, Yamada Y, Kudo Y, Ikemura T. 1999. Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAs. Gene. 238:143-155.
    • (1999) Gene , vol.238 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 20
    • 33845895536 scopus 로고    scopus 로고
    • The frequency of translational misreading errors in E. coli is largely determined by tRNA competition
    • Kramer EB, Farabaugh PJ. 2007. The frequency of translational misreading errors in E. coli is largely determined by tRNA competition. RNA. 13:87-96.
    • (2007) RNA , vol.13 , pp. 87-96
    • Kramer, E.B.1    Farabaugh, P.J.2
  • 21
    • 13944278871 scopus 로고    scopus 로고
    • Transfer RNA gene recruitment in mitochondrial DNA
    • Lavrov DV, Lang BF. 2005. Transfer RNA gene recruitment in mitochondrial DNA. Trends Genet. 21:129-133.
    • (2005) Trends Genet , vol.21 , pp. 129-133
    • Lavrov, D.V.1    Lang, B.F.2
  • 22
    • 0023064998 scopus 로고
    • Models of nearly neutral mutation with particular implications for nonrandom usage of synonymous codons
    • Li WH. 1987. Models of nearly neutral mutation with particular implications for nonrandom usage of synonymous codons. J Mol Evol. 24:337-345.
    • (1987) J Mol Evol , vol.24 , pp. 337-345
    • Li, W.H.1
  • 24
    • 33747889715 scopus 로고    scopus 로고
    • Multiple stages in codon-anticodon recognition: Double trigger mechanisms and geometric constraints
    • Ninio J. 2006. Multiple stages in codon-anticodon recognition: double trigger mechanisms and geometric constraints. Biochimie. 88:963-992.
    • (2006) Biochimie , vol.88 , pp. 963-992
    • Ninio, J.1
  • 25
    • 17444449538 scopus 로고    scopus 로고
    • Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae
    • Percudani R, Pavesi A, Ottonello S. 1997. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J Mol Biol. 268:322-330.
    • (1997) J Mol Biol , vol.268 , pp. 322-330
    • Percudani, R.1    Pavesi, A.2    Ottonello, S.3
  • 26
    • 8744310123 scopus 로고    scopus 로고
    • Codon usage bias from the tRNA's point of view: Redundancy, specialization, and efficient decoding for translational optimization
    • Rocha EPC. 2004. Codon usage bias from the tRNA's point of view: redundancy, specialization, and efficient decoding for translational optimization. Genome Res. 14:2279-2286.
    • (2004) Genome Res , vol.14 , pp. 2279-2286
    • Rocha, E.P.C.1
  • 27
    • 0034923932 scopus 로고    scopus 로고
    • Fidelity of aminoacyl-tRNA selection on the ribosome: Kinetic and structural mechanisms
    • Rodnina MV, Wintermeyer W. 2001. Fidelity of aminoacyl-tRNA selection on the ribosome: kinetic and structural mechanisms. Annu Rev Biochem. 70:415-435.
    • (2001) Annu Rev Biochem , vol.70 , pp. 415-435
    • Rodnina, M.V.1    Wintermeyer, W.2
  • 28
    • 0032513368 scopus 로고    scopus 로고
    • Evolution of a transfer RNA gene through a point mutation in the anticodon
    • Saks ME, Sampson JR, Abelson J. 1998. Evolution of a transfer RNA gene through a point mutation in the anticodon. Science. 279:1665-1667.
    • (1998) Science , vol.279 , pp. 1665-1667
    • Saks, M.E.1    Sampson, J.R.2    Abelson, J.3
  • 29
    • 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
  • 31
    • 0023762645 scopus 로고
    • Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within species diversity
    • Sharp PM, Cowe E, Higgins DG, Shields DC, Wolfe KH, Wright F. 1988. Codon usage patterns in Escherichia coli, Bacillus subtilis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Drosophila melanogaster and Homo sapiens; a review of the considerable within species diversity. Nucleic Acids Res. 16:8207-8211.
    • (1988) Nucleic Acids Res , vol.16 , pp. 8207-8211
    • Sharp, P.M.1    Cowe, E.2    Higgins, D.G.3    Shields, D.C.4    Wolfe, K.H.5    Wright, F.6
  • 32
    • 0023650543 scopus 로고
    • The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp PM, Li WH. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 33
    • 0025181355 scopus 로고
    • Switches in species-specific codon preferences: The influence of mutation biases
    • Shields DC. 1990. Switches in species-specific codon preferences: the influence of mutation biases. J Mol Evol. 31:71-80.
    • (1990) J Mol Evol , vol.31 , pp. 71-80
    • Shields, D.C.1
  • 34
    • 0031582214 scopus 로고    scopus 로고
    • Does Escherichia coli optimize the economics of the translation process?
    • Solomovici J, Lesnik T, Reiss C. 1997. Does Escherichia coli optimize the economics of the translation process? J Theor Biol. 185:511-521.
    • (1997) J Theor Biol , vol.185 , pp. 511-521
    • Solomovici, J.1    Lesnik, T.2    Reiss, C.3
  • 35
    • 0026409389 scopus 로고
    • Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate
    • Sorensen MA, Pedersen S. 1991. Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. J Mol Biol. 222:265-280.
    • (1991) J Mol Biol , vol.222 , pp. 265-280
    • Sorensen, M.A.1    Pedersen, S.2
  • 36
    • 33846786904 scopus 로고    scopus 로고
    • Synonymous codon usage in Escherichia coli: Selection for translational accuracy
    • Stoletzki N, Eyre-Walker A. 2007. Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol. 24:374-381.
    • (2007) Mol Biol Evol , vol.24 , pp. 374-381
    • Stoletzki, N.1    Eyre-Walker, A.2
  • 37
    • 33646886152 scopus 로고    scopus 로고
    • Archaeology and evolution of transfer RNA genes in the Escherichia coli genome
    • Withers M, Wernisch L, Dos Reis M. 2006. Archaeology and evolution of transfer RNA genes in the Escherichia coli genome. RNA. 12:933-942.
    • (2006) RNA , vol.12 , pp. 933-942
    • Withers, M.1    Wernisch, L.2    Dos Reis, M.3
  • 38
    • 0025318864 scopus 로고
    • The effective number of codons used in a gene
    • Wright F. 1990. The effective number of codons used in a gene. Gene. 87:23-29.
    • (1990) Gene , vol.87 , pp. 23-29
    • Wright, F.1
  • 39
    • 48349147235 scopus 로고    scopus 로고
    • The cost of wobble translation in fungal mitochondrial genomes: Integration of two traditional hypotheses
    • Xia X. 2008. The cost of wobble translation in fungal mitochondrial genomes: integration of two traditional hypotheses. BMC Evol Biol. 8:211.
    • (2008) BMC Evol Biol , vol.8 , pp. 211
    • Xia, X.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.