메뉴 건너뛰기




Volumn 30, Issue 3, 2013, Pages 549-560

Good codons, bad transcript: Large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme

Author keywords

codon usage bias; codon usage evolution; fitness; Methylobacterium extorquens; ribosome sequestration

Indexed keywords

ENZYME;

EID: 84873601673     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss273     Document Type: Article
Times cited : (109)

References (40)
  • 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
    • 0028797897 scopus 로고
    • Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA
    • Akashi H. 1995. Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics 139: 1067-1076.
    • (1995) Genetics , vol.139 , pp. 1067-1076
    • Akashi, H.1
  • 3
    • 77955931732 scopus 로고    scopus 로고
    • Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage
    • Amoros-Moya D, Bedhomme S, Hermann M, Bravo IG. 2010. Evolution in regulatory regions rapidly compensates the cost of nonoptimal codon usage. Mol Biol Evol. 27:2141-2151.
    • (2010) Mol Biol Evol , vol.27 , pp. 2141-2151
    • Amoros-Moya, D.1    Bedhomme, S.2    Hermann, M.3    Bravo, I.G.4
  • 4
    • 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
  • 6
    • 3042742751 scopus 로고    scopus 로고
    • Experimental reduction of codon bias in the Drosophila alcohol dehydrogenase gene results in decreased ethanol tolerance of adult flies
    • Carlini DB. 2004. Experimental reduction of codon bias in the Drosophila alcohol dehydrogenase gene results in decreased ethanol tolerance of adult flies. J Evolution Biol. 17:779-785.
    • (2004) J Evolution Biol , vol.17 , pp. 779-785
    • Carlini, D.B.1
  • 7
    • 0037274714 scopus 로고    scopus 로고
    • In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein
    • Carlini DB, Stephan W. 2003. In vivo introduction of unpreferred synonymous codons into the Drosophila Adh gene results in reduced levels of ADH protein. Genetics 163:239-243.
    • (2003) Genetics , vol.163 , pp. 239-243
    • Carlini, D.B.1    Stephan, W.2
  • 8
    • 0037967152 scopus 로고    scopus 로고
    • Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view
    • Chistoserdova L, Chen S-W, Lapidus A, Lidstrom ME. 2003. Methylotrophy in Methylobacterium extorquens AM1 from a genomic point of view. J Bacteriol. 185:2980-2987.
    • (2003) J Bacteriol , vol.185 , pp. 2980-2987
    • Chistoserdova, L.1    Chen, S.-W.2    Lapidus, A.3    Lidstrom, M.E.4
  • 9
    • 84861135633 scopus 로고    scopus 로고
    • Optimization of gene expression through divergent mutational paths
    • Chou H-H, Marx CJ. 2012. Optimization of gene expression through divergent mutational paths. Cell Rep. 1:133-140.
    • (2012) Cell Rep , vol.1 , pp. 133-140
    • Chou, H.-H.1    Marx, C.J.2
  • 12
    • 0024962419 scopus 로고
    • Rates of aminoacyl-tRNA selection at 29 sense codons in vivo
    • Curran JF, Yarrus 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    Yarrus, M.2
  • 13
    • 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
  • 14
    • 0023886015 scopus 로고
    • Posttranscriptional regulatory mechanisms in Escherichia coli
    • Gold L. 1988. Posttranscriptional regulatory mechanisms in Escherichia coli. Annu Rev Biochem. 57:199-233.
    • (1988) Annu Rev Biochem , vol.57 , pp. 199-233
    • Gold, L.1
  • 16
    • 77749268307 scopus 로고    scopus 로고
    • Experimentally increased codon bias in the Drosophila adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity
    • Hense W, Anderson N, Hutter S, Stephan W, Parsch J, Carlini DB. 2010. Experimentally increased codon bias in the Drosophila adh gene leads to an increase in larval, but not adult, alcohol dehydrogenase activity. Genetics 184:547-555.
    • (2010) Genetics , vol.184 , pp. 547-555
    • Hense, W.1    Anderson, N.2    Hutter, S.3    Stephan, W.4    Parsch, J.5    Carlini, D.B.6
  • 18
    • 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
  • 19
    • 0242371471 scopus 로고    scopus 로고
    • Horizontal gene transfer accelerates genome innovation and evolution
    • Jain R, Rivera MC, Moore JE, Lake JA. 2003. Horizontal gene transfer accelerates genome innovation and evolution. Mol Biol Evol. 20: 1598-1602.
    • (2003) Mol Biol Evol , vol.20 , pp. 1598-1602
    • Jain, R.1    Rivera, M.C.2    Moore, J.E.3    Lake, J.A.4
  • 21
    • 58149199728 scopus 로고    scopus 로고
    • A pause for thought along the co-translational folding pathway
    • Komar AA. 2009. A pause for thought along the co-translational folding pathway. Trends Biochem Sci. 34:16-24.
    • (2009) Trends Biochem Sci , vol.34 , pp. 16-24
    • Komar, A.A.1
  • 22
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla G, Murray AW, Tollervey D, Plotkin JB. 2009. Coding-sequence determinants of gene expression in Escherichia coli. Science 324: 255-258.
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 23
    • 84860231100 scopus 로고    scopus 로고
    • The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria
    • Li G-W, Oh E, Weissman JS. 2012. The anti-Shine-Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484:538-541.
    • (2012) Nature , vol.484 , pp. 538-541
    • Li, G.-W.1    Oh, E.2    Weissman, J.S.3
  • 24
    • 78149293610 scopus 로고    scopus 로고
    • Mutational robustness of ribosomal protein genes
    • Lind PA, Berg OG, Andersson DI. 2010. Mutational robustness of ribosomal protein genes. Science 330:825-827.
    • (2010) Science , vol.330 , pp. 825-827
    • Lind, P.A.1    Berg, O.G.2    Andersson, D.I.3
  • 25
    • 77349104670 scopus 로고    scopus 로고
    • Compensatory gene amplification restores fitness after inter-species gene replacements
    • Lind PA, Tobin C, Berg OG, Kurland CG, Andersson DI. 2010. Compensatory gene amplification restores fitness after inter-species gene replacements. Mol Microbiol. 75:1078-1089.
    • (2010) Mol Microbiol , vol.75 , pp. 1078-1089
    • Lind, P.A.1    Tobin, C.2    Berg, O.G.3    Kurland, C.G.4    Andersson, D.I.5
  • 26
    • 77954002740 scopus 로고    scopus 로고
    • Gene optimization mechanisms: A multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli
    • (11 co-authors)
    • Maertens B, Spriestersbach A, Groll von U, et al. (11 co-authors). 2010. Gene optimization mechanisms: a multi-gene study reveals a high success rate of full-length human proteins expressed in Escherichia coli. Protein Sci. 19:1312-1326.
    • (2010) Protein Sci , vol.19 , pp. 1312-1326
    • Maertens, B.1    Spriestersbach, A.2    Von U, G.3
  • 27
    • 0345097575 scopus 로고    scopus 로고
    • Formaldehydedetoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1
    • Marx CJ, Chistoserdova L, Lidstrom ME. 2003. Formaldehydedetoxifying role of the tetrahydromethanopterin-linked pathway in Methylobacterium extorquens AM1. J Bacteriol. 185: 7160-7168.
    • (2003) J Bacteriol , vol.185 , pp. 7160-7168
    • Marx, C.J.1    Chistoserdova, L.2    Lidstrom, M.E.3
  • 28
    • 37349095608 scopus 로고    scopus 로고
    • Implementation of microarrays for Methylobacterium extorquens AM1
    • Okubo Y, Skovran E, Guo X, Sivam D, Lidstrom ME. 2007. Implementation of microarrays for Methylobacterium extorquens AM1. OMICS 11:325-340.
    • (2007) OMICS , vol.11 , pp. 325-340
    • Okubo, Y.1    Skovran, E.2    Guo, X.3    Sivam, D.4    Lidstrom, M.E.5
  • 29
    • 34250212837 scopus 로고    scopus 로고
    • How do synonymous mutations affect fitness?
    • Parmley JL, Hurst LD. 2007. How do synonymous mutations affect fitness? Bioessays 29:515-519.
    • (2007) Bioessays , vol.29 , pp. 515-519
    • Parmley, J.L.1    Hurst, L.D.2
  • 30
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: The causes and consequences of codon bias
    • Plotkin JB, Kudla G. 2010. Synonymous but not the same: the causes and consequences of codon bias. Nat Rev Genet. 12:32-42.
    • (2010) Nat Rev Genet , vol.12 , pp. 32-42
    • Plotkin, J.B.1    Kudla, G.2
  • 31
  • 32
    • 14544277543 scopus 로고    scopus 로고
    • Variation in the strength of selected codon usage bias among bacteria
    • Sharp PM. 2005. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res. 33:1141-1153.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1141-1153
    • Sharp, P.M.1
  • 33
    • 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
  • 34
    • 0024405193 scopus 로고
    • Codon usage determines translation rate in Escherichia coli
    • Sørensen MA, Kurland CG, Pedersen S. 1989. Codon usage determines translation rate in Escherichia coli. J Mol Biol. 207: 365-377.
    • (1989) J Mol Biol , vol.207 , pp. 365-377
    • Sørensen, M.A.1    Kurland, C.G.2    Pedersen, S.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
    • Sørensen 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
    • Sørensen, M.A.1    Pedersen, S.2
  • 38
    • 0034460957 scopus 로고    scopus 로고
    • Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol
    • Vorholt JA, Marx CJ, Lidstrom ME, Thauer RK. 2000. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J Bacteriol. 182: 6645-6650.
    • (2000) J Bacteriol , vol.182 , pp. 6645-6650
    • Vorholt, J.A.1    Marx, C.J.2    Lidstrom, M.E.3    Thauer, R.K.4
  • 40
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.