메뉴 건너뛰기




Volumn 30, Issue 10, 2013, Pages 2263-2267

Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates

Author keywords

Genetic drift; Mutational bias; Synonymous codon usage; Translational selection; Vertebrates

Indexed keywords

ARGININE; GLYCINE; LEUCINE; PROLINE; SERINE; TRANSFER RNA; VALINE;

EID: 84888623468     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst128     Document Type: Article
Times cited : (30)

References (44)
  • 1
    • 33846269602 scopus 로고    scopus 로고
    • TRNA's wobble decoding of the genome: 40 years of modification
    • Agris P, Vendeix F, Graham W. 2007. tRNA's wobble decoding of the genome: 40 years of modification. J Mol Biol. 366:1-13.
    • (2007) J Mol Biol , vol.366 , pp. 1-13
    • Agris, P.1    Vendeix, F.2    Graham, W.3
  • 2
    • 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
  • 4
    • 48249093081 scopus 로고    scopus 로고
    • Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host
    • Angov E, Hillier CJ, Kincaid RL, Lyon JA. 2008. Heterologous protein expression is enhanced by harmonizing the codon usage frequencies of the target gene with those of the expression host. PLoS One 3: e2189.
    • (2008) PLoS One , vol.3
    • Angov, E.1    Hillier, C.J.2    Kincaid, R.L.3    Lyon, J.A.4
  • 5
    • 0029587471 scopus 로고
    • The human genome: Organization and evolutionary history
    • Bernardi G. 1995. The human genome: organization and evolutionary history. Annu Rev Genet. 29:445-476.
    • (1995) Annu Rev Genet , vol.29 , pp. 445-476
    • Bernardi, G.1
  • 6
    • 0022914759 scopus 로고
    • Compositional constraints and genome evolution
    • Bernardi G, Bernardi G. 1986. Compositional constraints and genome evolution. J Mol Evol. 24:1-11.
    • (1986) J Mol Evol , vol.24 , pp. 1-11
    • Bernardi, G.1    Bernardi, G.2
  • 7
    • 84993842127 scopus 로고
    • Are codon usage patterns in unicellular organisms determined by selection-mutation balance?
    • Bulmer M. 1988. Are codon usage patterns in unicellular organisms determined by selection-mutation balance? J Evol Biol. 1:15-26.
    • (1988) J Evol Biol , vol.1 , pp. 15-26
    • Bulmer, M.1
  • 8
    • 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
  • 9
    • 58149189877 scopus 로고    scopus 로고
    • Gtrnadb: A database of transfer RNA genes detected in genomic sequence
    • Chan PP, Lowe TM. 2009. Gtrnadb: A database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res. 37: D93-D97.
    • (2009) Nucleic Acids Res , vol.37
    • Chan, P.P.1    Lowe, T.M.2
  • 10
    • 60349093708 scopus 로고    scopus 로고
    • Effective population size and patterns of molecular evolution and variation
    • Charlesworth B. 2009. Effective population size and patterns of molecular evolution and variation. Nat Rev Genet. 10:195-205.
    • (2009) Nat Rev Genet , vol.10 , pp. 195-205
    • Charlesworth, B.1
  • 11
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond DA, Wilke CO. 2008. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134:341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 12
    • 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
  • 13
    • 0033551151 scopus 로고    scopus 로고
    • Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis
    • Duret L, Mouchiroud D. 1999. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci U S A. 96:4482.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 4482
    • Duret, L.1    Mouchiroud, D.2
  • 15
    • 11144241326 scopus 로고    scopus 로고
    • Correlation of codon bias measures with mRNA levels: Analysis of transcriptome data from Escherichia coli
    • Goetz RM, Fuglsang A. 2005. Correlation of codon bias measures with mRNA levels: Analysis of transcriptome data from Escherichia coli. Biochem Biophys Res Commun. 327:4-7.
    • (2005) Biochem Biophys Res Commun , vol.327 , pp. 4-7
    • Goetz, R.M.1    Fuglsang, A.2
  • 16
    • 0020491327 scopus 로고
    • Codon usage in bacteria: Correlation with gene expressivity
    • Gouy M, Gautier C. 1982. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10:7055-7074.
    • (1982) Nucleic Acids Res , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 18
    • 42149137980 scopus 로고    scopus 로고
    • TRNA's modification brings order to gene expression
    • Gustilo E, Vendeix F, Agris P. 2008. tRNA's modification brings order to gene expression. Curr Opin Microbiol. 11:134-140.
    • (2008) Curr Opin Microbiol , vol.11 , pp. 134-140
    • Gustilo, E.1    Vendeix, F.2    Agris, P.3
  • 19
    • 80053121999 scopus 로고    scopus 로고
    • Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins
    • Hudson NJ, Gu Q, Nagaraj SH, Ding YS, Dalrymple BP, Reverter A. 2011. Eukaryotic evolutionary transitions are associated with extreme codon bias in functionally-related proteins. PLoS One 6: e25457.
    • (2011) PLoS One , vol.6
    • Hudson, N.J.1    Gu, Q.2    Nagaraj, S.H.3    Ding, Y.S.4    Dalrymple, B.P.5    Reverter, A.6
  • 20
    • 67349173173 scopus 로고    scopus 로고
    • More radical amino acid replacements in primates than in rodents: Support for the evolutionary role of effective population size
    • Hughes AL, Friedman R. 2009. More radical amino acid replacements in primates than in rodents: support for the evolutionary role of effective population size. Gene 440:50-56.
    • (2009) Gene, 440 , pp. 50-56
    • Hughes, A.L.1    Friedman, R.2
  • 21
    • 0019824131 scopus 로고
    • Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. Coli translational system
    • Ikemura T. 1981. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: A proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol. 151:389.
    • (1981) J Mol Biol , vol.151 , pp. 389
    • Ikemura, T.1
  • 22
    • 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
  • 23
    • 0032882170 scopus 로고    scopus 로고
    • Studies of codon usage and tRNA genes of 18 unicellular organisms and quantification of Bacillus subtilis tRNAS: Gene expression level and species-specific diversity of codon usage based on multivariate analysis
    • 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 expression level and species-specific diversity of codon usage based on multivariate analysis. Gene 238: 143-155.
    • (1999) Gene , vol.238 , pp. 143-155
    • Kanaya, S.1    Yamada, Y.2    Kudo, Y.3    Ikemura, T.4
  • 25
    • 0034086295 scopus 로고    scopus 로고
    • Absence of translationally selected synonymous codon usage bias in Helicobacter pylori
    • Lafay B, Atherton JC, Sharp PM. 2000. Absence of translationally selected synonymous codon usage bias in Helicobacter pylori. Microbiology 146:851-860.
    • (2000) Microbiology , vol.146 , pp. 851-860
    • Lafay, B.1    Atherton, J.C.2    Sharp, P.M.3
  • 26
    • 17444449846 scopus 로고    scopus 로고
    • Codon usage and the origin of P elements
    • Lerat E, Biémont C, Capy P. 2000. Codon usage and the origin of P elements. Mol Biol Evol. 17:467-468.
    • (2000) Mol Biol Evol , vol.17 , pp. 467-468
    • Lerat, E.1    Biémont, C.2    Capy, P.3
  • 27
    • 0030731696 scopus 로고    scopus 로고
    • Codon usage bias and tRNA abundance in Drosophila
    • Moriyama EN, Powell JR. 1997. Codon usage bias and tRNA abundance in Drosophila. J Mol Evol. 45:514-523.
    • (1997) J Mol Evol , vol.45 , pp. 514-523
    • Moriyama, E.N.1    Powell, J.R.2
  • 29
    • 34547709593 scopus 로고    scopus 로고
    • Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals
    • Parmley JL, Hurst LD. 2007. Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. Mol Biol Evol. 24:1600-1603.
    • (2007) Mol Biol Evol , vol.24 , pp. 1600-1603
    • Parmley, J.L.1    Hurst, L.D.2
  • 30
    • 84888611315 scopus 로고    scopus 로고
    • Dublin: Trinity College
    • Peden J. 1997. Codon W. Dublin: Trinity College.
    • (1997) Codon W
    • Peden, J.1
  • 31
    • 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
  • 32
    • 0037109119 scopus 로고    scopus 로고
    • Use and misuse of correspondence - Analysis in codon usage studies
    • Perrière G, Thioulouse J. 2002. Use and misuse of correspondence - Analysis in codon usage studies. Nucleic Acids Res. 30: 4548-4555.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4548-4555
    • Perrière, G.1    Thioulouse, J.2
  • 33
    • 82255194216 scopus 로고    scopus 로고
    • Mutation bias is the driving force of codon usage in the Gallus gallus genome
    • Rao Y, Wu G, Wang Z, Chai X, Nie Q, Zhang X. 2011. Mutation bias is the driving force of codon usage in the Gallus gallus genome. DNA Res. 18:499-512.
    • (2011) DNA Res , vol.18 , pp. 499-512
    • Rao, Y.1    Wu, G.2    Wang, Z.3    Chai, X.4    Nie, Q.5    Zhang, X.6
  • 34
    • 0242290126 scopus 로고    scopus 로고
    • The influence of translational selection on codon usage in fishes from the family cyprinidae
    • Romero H, Zavala A, Musto H, Bernardi G. 2003. The influence of translational selection on codon usage in fishes from the family cyprinidae. Gene 317:141-147.
    • (2003) Gene , vol.317 , pp. 141-147
    • Romero, H.1    Zavala, A.2    Musto, H.3    Bernardi, G.4
  • 35
    • 80052964856 scopus 로고    scopus 로고
    • Understanding the contribution of synonymous mutations to human disease
    • Sauna ZE, Kimchi-Sarfaty C. 2011. Understanding the contribution of synonymous mutations to human disease. Nat Rev Genet. 12: 683-691.
    • (2011) Nat Rev Genet , vol.12 , pp. 683-691
    • Sauna, Z.E.1    Kimchi-Sarfaty, C.2
  • 36
    • 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
  • 37
    • 0024116811 scopus 로고
    • Silent" sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons
    • Shields DC, Sharp PM, Higgins DG, Wright F. 1988. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol Biol Evol. 5:704-716.
    • (1988) Mol Biol Evol , vol.5 , pp. 704-716
    • Shields, D.C.1    Sharp, P.M.2    Higgins, D.G.3    Wright, F.4
  • 38
    • 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
  • 40
    • 0035671698 scopus 로고    scopus 로고
    • Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection
    • Urrutia AO, Hurst LD. 2001. Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics 159:1191-1199.
    • (2001) Genetics , vol.159 , pp. 1191-1199
    • Urrutia, A.O.1    Hurst, L.D.2
  • 41
    • 0142092546 scopus 로고    scopus 로고
    • The signature of selection mediated by expression on human genes
    • Urrutia AO, Hurst LD. 2003. The signature of selection mediated by expression on human genes. Genome Res. 13:2260-2264.
    • (2003) Genome Res , vol.13 , pp. 2260-2264
    • Urrutia, A.O.1    Hurst, L.D.2
  • 42
    • 39749161509 scopus 로고    scopus 로고
    • Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
    • Yang Z, Nielsen R. 2008. Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol. 25:568-579.
    • (2008) Mol Biol Evol , vol.25 , pp. 568-579
    • Yang, Z.1    Nielsen, R.2
  • 43
    • 84862827380 scopus 로고    scopus 로고
    • Codon Deviation Coefficient: A novel measure for estimating codon usage bias and its statistical significance
    • Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. 2012. Codon Deviation Coefficient: A novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 13:43.
    • (2012) BMC Bioinformatics , vol.13 , pp. 43
    • Zhang, Z.1    Li, J.2    Cui, P.3    Ding, F.4    Li, A.5    Townsend, J.P.6    Yu, J.7
  • 44
    • 67649356943 scopus 로고    scopus 로고
    • Translationally optimal codons associate with structurally sensitive sites in proteins
    • Zhou T, Weems M, Wilke CO. 2009. Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol. 26:1571-1580.
    • (2009) Mol Biol Evol , vol.26 , pp. 1571-1580
    • Zhou, T.1    Weems, M.2    Wilke, C.O.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.