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Volumn 16, Issue 7, 2015, Pages 409-420

Determinants of the rate of protein sequence evolution

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; DNA; PROTEIN;

EID: 84931575424     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg3950     Document Type: Review
Times cited : (253)

References (116)
  • 3
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura, M. Evolutionary rate at the molecular level. Nature 217, 624-626 (1968).
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 4
    • 22944437097 scopus 로고    scopus 로고
    • Molecular clocks: Four decades of evolution
    • Kumar, S. Molecular clocks: four decades of evolution. Nat. Rev. Genet. 6, 654-662 (2005).
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 654-662
    • Kumar, S.1
  • 5
    • 34548575130 scopus 로고    scopus 로고
    • Molecular clock: An anti-neo-Darwinian legacy
    • Takahata, N. Molecular clock: an anti-neo-Darwinian legacy. Genetics 176, 1-6 (2007).
    • (2007) Genetics , vol.176 , pp. 1-6
    • Takahata, N.1
  • 8
    • 59249090568 scopus 로고    scopus 로고
    • Why is the correlation between gene importance and gene evolutionary rate so weak?
    • Wang, Z. & Zhang, J. Why is the correlation between gene importance and gene evolutionary rate so weak? PLoS Genet. 5, e1000329 (2009).
    • (2009) PLoS Genet. , vol.5
    • Wang, Z.1    Zhang, J.2
  • 9
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • This is the first report of the E-R anticorrelation.
    • Pal, C., Papp, B. & Hurst, L. D. Highly expressed genes in yeast evolve slowly. Genetics 158, 927-931 (2001). This is the first report of the E-R anticorrelation.
    • (2001) Genetics , vol.158 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 10
    • 26444621352 scopus 로고    scopus 로고
    • Why highly expressed proteins evolve slowly
    • This paper proposes the translational robustness hypothesis of the E-R anticorrelation.
    • Drummond, D. A., Bloom, J. D., Adami, C., Wilke, C. O. & Arnold, F. H. Why highly expressed proteins evolve slowly. Proc. Natl Acad. Sci. USA 102, 14338-14343 (2005). This paper proposes the translational robustness hypothesis of the E-R anticorrelation.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 14338-14343
    • Drummond, D.A.1    Bloom, J.D.2    Adami, C.3    Wilke, C.O.4    Arnold, F.H.5
  • 11
    • 84859473329 scopus 로고    scopus 로고
    • Protein misinteraction avoidance causes highly expressed proteins to evolve slowly
    • This paper proposes the protein misinteraction hypothesis of the E-R anticorrelation.
    • Yang, J. R., Liao, B. Y., Zhuang, S. M. & Zhang, J. Protein misinteraction avoidance causes highly expressed proteins to evolve slowly. Proc. Natl Acad. Sci. USA 109, E831-E840 (2012). This paper proposes the protein misinteraction hypothesis of the E-R anticorrelation.
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. E831-E840
    • Yang, J.R.1    Liao, B.Y.2    Zhuang, S.M.3    Zhang, J.4
  • 12
    • 84874250754 scopus 로고    scopus 로고
    • Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly
    • This paper proposes the mRNA folding requirement hypothesis of the E-R anticorrelation.
    • Park, C., Chen, X., Yang, J. R. & Zhang, J. Differential requirements for mRNA folding partially explain why highly expressed proteins evolve slowly. Proc. Natl Acad. Sci. USA 110, E678-E686 (2013). This paper proposes the mRNA folding requirement hypothesis of the E-R anticorrelation.
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. E678-E686
    • Park, C.1    Chen, X.2    Yang, J.R.3    Zhang, J.4
  • 13
    • 77958577844 scopus 로고    scopus 로고
    • Impact of translational error-induced and error-free misfolding on the rate of protein evolution
    • Yang, J. R., Zhuang, S. M. & Zhang, J. Impact of translational error-induced and error-free misfolding on the rate of protein evolution. Mol. Syst. Biol. 6, 421 (2010).
    • (2010) Mol. Syst. Biol. , vol.6 , pp. 421
    • Yang, J.R.1    Zhuang, S.M.2    Zhang, J.3
  • 14
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond, D. A. & Wilke, C. O. Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134, 341-352 (2008).
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 15
    • 84905375893 scopus 로고    scopus 로고
    • Codon-by-codon modulation of translational speed and accuracy via mRNA folding
    • This paper explains the underlying cause of the mRNA folding requirement that partially accounts for the E-R anticorrelation.
    • Yang, J. R., Chen, X. & Zhang, J. Codon-by-codon modulation of translational speed and accuracy via mRNA folding. PLoS Biol. 12, e1001910 (2014). This paper explains the underlying cause of the mRNA folding requirement that partially accounts for the E-R anticorrelation.
    • (2014) PLoS Biol. , vol.12
    • Yang, J.R.1    Chen, X.2    Zhang, J.3
  • 16
    • 77953212314 scopus 로고    scopus 로고
    • The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution
    • Gout, J. F., Kahn, D. & Duret, L. The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PLoS Genet. 6, e1000944 (2010).
    • (2010) PLoS Genet. , vol.6
    • Gout, J.F.1    Kahn, D.2    Duret, L.3
  • 17
    • 79952196607 scopus 로고    scopus 로고
    • Expression level, evolutionary rate, and the cost of expression
    • References 16 and 17 independently propose the expression cost hypothesis of the E-R anticorrelation
    • Cherry, J. L. Expression level, evolutionary rate, and the cost of expression. Genome Biol. Evol. 2, 757-769 (2010). References 16 and 17 independently propose the expression cost hypothesis of the E-R anticorrelation.
    • (2010) Genome Biol. Evol. , vol.2 , pp. 757-769
    • Cherry, J.L.1
  • 18
    • 0030451420 scopus 로고    scopus 로고
    • Among-site rate variation and its impact on phylogenetic analyses
    • Yang, Z. Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evol. 11, 367-372 (1996).
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 367-372
    • Yang, Z.1
  • 19
    • 33751381461 scopus 로고    scopus 로고
    • TimeTree: A public knowledge-base of divergence times among organisms
    • Hedges, S. B., Dudley, J. & Kumar, S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics 22, 2971-2972 (2006).
    • (2006) Bioinformatics , vol.22 , pp. 2971-2972
    • Hedges, S.B.1    Dudley, J.2    Kumar, S.3
  • 20
    • 0014680905 scopus 로고
    • Non-Darwinian evolution
    • King, J. L. & Jukes, T. H. Non-Darwinian evolution. Science 164, 788-798 (1969).
    • (1969) Science , vol.164 , pp. 788-798
    • King, J.L.1    Jukes, T.H.2
  • 23
    • 0016087667 scopus 로고
    • On some principles governing molecular evolution
    • This paper proposes the role of protein functional importance and functional constraint in determining the rate of protein sequence evolution.
    • Kimura, M. & Ohta, T. On some principles governing molecular evolution. Proc. Natl Acad. Sci. USA 71, 2848-2852 (1974). This paper proposes the role of protein functional importance and functional constraint in determining the rate of protein sequence evolution.
    • (1974) Proc. Natl Acad. Sci. USA , vol.71 , pp. 2848-2852
    • Kimura, M.1    Ohta, T.2
  • 25
    • 0033565762 scopus 로고    scopus 로고
    • Do essential genes evolve slowly?
    • This study was the first to test the relationship between protein functional importance and evolutionary rate based on a fairly large genomic data set.
    • Hurst, L. D. & Smith, N. G. Do essential genes evolve slowly? Curr. Biol. 9, 747-750 (1999). This study was the first to test the relationship between protein functional importance and evolutionary rate based on a fairly large genomic data set.
    • (1999) Curr. Biol. , vol.9 , pp. 747-750
    • Hurst, L.D.1    Smith, N.G.2
  • 26
    • 0033529707 scopus 로고    scopus 로고
    • Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis
    • Winzeler, E. A. et al. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285, 901-906 (1999).
    • (1999) Science , vol.285 , pp. 901-906
    • Winzeler, E.A.1
  • 27
    • 0035963414 scopus 로고    scopus 로고
    • Protein dispensability and rate of evolution
    • Hirsh, A. E. & Fraser, H. B. Protein dispensability and rate of evolution. Nature 411, 1046-1049 (2001).
    • (2001) Nature , vol.411 , pp. 1046-1049
    • Hirsh, A.E.1    Fraser, H.B.2
  • 28
    • 0032567081 scopus 로고    scopus 로고
    • Dissecting the regulatory circuitry of a eukaryotic genome
    • Holstege, F. C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728 (1998).
    • (1998) Cell , vol.95 , pp. 717-728
    • Holstege, F.C.1
  • 29
    • 0037472928 scopus 로고    scopus 로고
    • Genomic function: Rate of evolution and gene dispensability
    • Pal, C., Papp, B. & Hurst, L. D. Genomic function: rate of evolution and gene dispensability. Nature 421, 496-497 (2003).
    • (2003) Nature , vol.421 , pp. 496-497
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 30
    • 16344369543 scopus 로고    scopus 로고
    • Significant impact of protein dispensability on the instantaneous rate of protein evolution
    • Zhang, J. & He, X. Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol. Biol. Evol. 22, 1147-1155 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1147-1155
    • Zhang, J.1    He, X.2
  • 31
    • 17244367886 scopus 로고    scopus 로고
    • Functional genomic analysis of the rates of protein evolution
    • Wall, D. P. et al. Functional genomic analysis of the rates of protein evolution. Proc. Natl Acad. Sci. USA 102, 5483-5488 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 5483-5488
    • Wall, D.P.1
  • 32
    • 33749579409 scopus 로고    scopus 로고
    • Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins
    • Liao, B. Y., Scott, N. M. & Zhang, J. Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol. Biol. Evol. 23, 2072-2080 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 2072-2080
    • Liao, B.Y.1    Scott, N.M.2    Zhang, J.3
  • 33
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • Jordan, I. K., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Res. 12, 962-968 (2002).
    • (2002) Genome Res. , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 34
    • 1242284655 scopus 로고    scopus 로고
    • An analysis of determinants of amino acids substitution rates in bacterial proteins
    • Rocha, E. P. & Danchin, A. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol. Biol. Evol. 21, 108-116 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 108-116
    • Rocha, E.P.1    Danchin, A.2
  • 35
    • 80054973803 scopus 로고    scopus 로고
    • A high-resolution map of human evolutionary constraint using 29 mammals
    • Lindblad-Toh, K. et al. A high-resolution map of human evolutionary constraint using 29 mammals. Nature 478, 476-482 (2011).
    • (2011) Nature , vol.478 , pp. 476-482
    • Lindblad-Toh, K.1
  • 36
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • Pennacchio, L. A. et al. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502 (2006).
    • (2006) Nature , vol.444 , pp. 499-502
    • Pennacchio, L.A.1
  • 37
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • Krylov, D. M., Wolf, Y. I., Rogozin, I. B. & Koonin, E. V. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13, 2229-2235 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 38
    • 0141920354 scopus 로고    scopus 로고
    • Comparing protein abundance and mRNA expression levels on a genomic scale
    • Greenbaum, D., Colangelo, C., Williams, K. &Gerstein, M. Comparing protein abundance and mRNA expression levels on a genomic scale. Genome Biol. 4, 117 (2003).
    • (2003) Genome Biol. , vol.4 , pp. 117
    • Greenbaum, D.1    Colangelo, C.2    Williams, K.3    Gerstein, M.4
  • 39
    • 84858439862 scopus 로고    scopus 로고
    • Insights into the regulation of protein abundance from proteomic and transcriptomic analyses
    • Vogel, C. & Marcotte, E. M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 13, 227-232 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 227-232
    • Vogel, C.1    Marcotte, E.M.2
  • 40
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond, D. A., Raval, A. & Wilke, C. O. A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol. 23, 327-337 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 41
    • 80053163911 scopus 로고    scopus 로고
    • Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs
    • Shen, Y. et al. Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs. Proc. Natl Acad. Sci. USA 108, 15942-15947 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 15942-15947
    • Shen, Y.1
  • 42
    • 84858798657 scopus 로고    scopus 로고
    • Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs
    • Managadze, D., Rogozin, I. B., Chernikova, D., Shabalina, S. A. & Koonin, E. V. Negative correlation between expression level and evolutionary rate of long intergenic noncoding RNAs. Genome Biol. Evol. 3, 1390-1404 (2011).
    • (2011) Genome Biol. Evol. , vol.3 , pp. 1390-1404
    • Managadze, D.1    Rogozin, I.B.2    Chernikova, D.3    Shabalina, S.A.4    Koonin, E.V.5
  • 43
    • 79551674254 scopus 로고    scopus 로고
    • Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast
    • Geiler-Samerotte, K. A. et al. Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast. Proc. Natl Acad. Sci. USA 108, 680-685 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. 680-685
    • Geiler-Samerotte, K.A.1
  • 44
    • 70349333227 scopus 로고    scopus 로고
    • The evolutionary consequences of erroneous protein synthesis
    • Drummond, D. A. & Wilke, C. O. The evolutionary consequences of erroneous protein synthesis. Nat. Rev. Genet. 10, 715-724 (2009).
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 715-724
    • Drummond, D.A.1    Wilke, C.O.2
  • 45
    • 0028220048 scopus 로고
    • Synonymous codon usage in Drosophila melanogaster: Natural selection and translational accuracy
    • Akashi, H. Synonymous codon usage in Drosophila melanogaster: natural selection and translational accuracy. Genetics 136, 927-935 (1994).
    • (1994) Genetics , vol.136 , pp. 927-935
    • Akashi, H.1
  • 46
    • 77249122086 scopus 로고    scopus 로고
    • Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins
    • Cherry, J. L. Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins. Mol. Biol. Evol. 27, 735-741 (2010).
    • (2010) Mol. Biol. Evol. , vol.27 , pp. 735-741
    • Cherry, J.L.1
  • 47
    • 0033565815 scopus 로고    scopus 로고
    • Residue depth: A novel parameter for the analysis of protein structure and stability
    • Chakravarty, S. & Varadarajan, R. Residue depth: a novel parameter for the analysis of protein structure and stability. Structure 7, 723-732 (1999).
    • (1999) Structure , vol.7 , pp. 723-732
    • Chakravarty, S.1    Varadarajan, R.2
  • 48
    • 77649298024 scopus 로고    scopus 로고
    • Modulation of the vitamin D3 response by cancer-associated mutant p53
    • Stambolsky, P. et al. Modulation of the vitamin D3 response by cancer-associated mutant p53. Cancer Cell 17, 273-285 (2010).
    • (2010) Cancer Cell , vol.17 , pp. 273-285
    • Stambolsky, P.1
  • 49
    • 67649635978 scopus 로고    scopus 로고
    • Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity
    • Vavouri, T., Semple, J. I., Garcia-Verdugo, R. &Lehner, B. Intrinsic protein disorder and interaction promiscuity are widely associated with dosage sensitivity. Cell 138, 198-208 (2009).
    • (2009) Cell , vol.138 , pp. 198-208
    • Vavouri, T.1    Semple, J.I.2    Garcia-Verdugo, R.3    Lehner, B.4
  • 50
    • 49449110197 scopus 로고    scopus 로고
    • Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size
    • Zhang, J., Maslov, S. & Shakhnovich, E. I. Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size. Mol. Syst. Biol. 4, 210 (2008).
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 210
    • Zhang, J.1    Maslov, S.2    Shakhnovich, E.I.3
  • 51
    • 84870901239 scopus 로고    scopus 로고
    • Cellular crowding imposes global constraints on the chemistry and evolution of proteomes
    • Levy, E. D., De, S. & Teichmann, S. A. Cellular crowding imposes global constraints on the chemistry and evolution of proteomes. Proc. Natl Acad. Sci. USA 109, 20461-20466 (2012).
    • (2012) Proc. Natl Acad. Sci. USA , vol.109 , pp. 20461-20466
    • Levy, E.D.1    De, S.2    Teichmann, S.A.3
  • 52
    • 84857770146 scopus 로고    scopus 로고
    • Strong association between mRNA folding strength and protein abundance in S. cerevisiae
    • Zur, H. & Tuller, T. Strong association between mRNA folding strength and protein abundance in S. cerevisiae. EMBO Rep. 13, 272-277 (2012).
    • (2012) EMBO Rep. , vol.13 , pp. 272-277
    • Zur, H.1    Tuller, T.2
  • 53
    • 0037133671 scopus 로고    scopus 로고
    • Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
    • Akashi, H. & Gojobori, T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl Acad. Sci. USA 99, 3695-3700 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 54
    • 54949151498 scopus 로고    scopus 로고
    • Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution
    • Wolf, M. Y., Wolf, Y. I. & Koonin, E. V. Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution. Biol. Direct 3, 40 (2008).
    • (2008) Biol. Direct , vol.3 , pp. 40
    • Wolf, M.Y.1    Wolf, Y.I.2    Koonin, E.V.3
  • 55
    • 80052183299 scopus 로고    scopus 로고
    • The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate
    • Chen, S. C., Chuang, T. J. & Li, W. H. The relationships among microRNA regulation, intrinsically disordered regions, and other indicators of protein evolutionary rate. Mol. Biol. Evol. 28, 2513-2520 (2011).
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 2513-2520
    • Chen, S.C.1    Chuang, T.J.2    Li, W.H.3
  • 56
    • 70350469040 scopus 로고    scopus 로고
    • The relationship between the evolution of microRNA targets and the length of their UTRs
    • Cheng, C., Bhardwaj, N. & Gerstein, M. The relationship between the evolution of microRNA targets and the length of their UTRs. BMC Genomics 10, 431 (2009).
    • (2009) BMC Genomics , vol.10 , pp. 431
    • Cheng, C.1    Bhardwaj, N.2    Gerstein, M.3
  • 57
    • 33747817940 scopus 로고    scopus 로고
    • Toward a molecular understanding of pleiotropy
    • He, X. & Zhang, J. Toward a molecular understanding of pleiotropy. Genetics 173, 1885-1891 (2006).
    • (2006) Genetics , vol.173 , pp. 1885-1891
    • He, X.1    Zhang, J.2
  • 59
    • 2942624159 scopus 로고    scopus 로고
    • Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets
    • Bloom, J. D. & Adami, C. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol. Biol. 3, 21 (2003).
    • (2003) BMC Evol. Biol. , vol.3 , pp. 21
    • Bloom, J.D.1    Adami, C.2
  • 60
    • 0023764283 scopus 로고
    • Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
    • Hughes, A. L. & Nei, M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335, 167-170 (1988).
    • (1988) Nature , vol.335 , pp. 167-170
    • Hughes, A.L.1    Nei, M.2
  • 61
    • 0028900746 scopus 로고
    • Positive selection is a general phenomenon in the evolution of abalone sperm lysin
    • Lee, Y. H., Ota, T. & Vacquier, V. D. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Mol. Biol. Evol. 12, 231-238 (1995).
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 231-238
    • Lee, Y.H.1    Ota, T.2    Vacquier, V.D.3
  • 62
    • 84889593808 scopus 로고    scopus 로고
    • Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster
    • Dunn, J. G., Foo, C. K., Belletier, N. G., Gavis, E. R. &Weissman, J. S. Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. eLife 2, e01179 (2013).
    • (2013) eLife , vol.2
    • Dunn, J.G.1    Foo, C.K.2    Belletier, N.G.3    Gavis, E.R.4    Weissman, J.S.5
  • 63
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: Stochastic gene expression and its consequences
    • Raj, A. & van Oudenaarden, A. Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216-226 (2008).
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    Van Oudenaarden, A.2
  • 64
    • 84895562012 scopus 로고    scopus 로고
    • From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing
    • Marinov, G. K. et al. From single-cell to cell-pool transcriptomes: stochasticity in gene expression and RNA splicing. Genome Res. 24, 496-510 (2014).
    • (2014) Genome Res. , vol.24 , pp. 496-510
    • Marinov, G.K.1
  • 65
    • 69249106061 scopus 로고    scopus 로고
    • Positive selection for elevated gene expression noise in yeast
    • Zhang, Z., Qian, W. & Zhang, J. Positive selection for elevated gene expression noise in yeast. Mol. Syst. Biol. 5, 299 (2009).
    • (2009) Mol. Syst. Biol. , vol.5 , pp. 299
    • Zhang, Z.1    Qian, W.2    Zhang, J.3
  • 66
    • 79955613183 scopus 로고    scopus 로고
    • Impact of gene expression noise on organismal fitness and the efficacy of natural selection
    • Wang, Z. & Zhang, J. Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc. Natl Acad. Sci. USA 108, E67-E76 (2011).
    • (2011) Proc. Natl Acad. Sci. USA , vol.108 , pp. E67-E76
    • Wang, Z.1    Zhang, J.2
  • 67
    • 81355142140 scopus 로고    scopus 로고
    • Error prevention and mitigation as forces in the evolution of genes and genomes
    • Warnecke, T. & Hurst, L. D. Error prevention and mitigation as forces in the evolution of genes and genomes. Nat. Rev. Genet. 12, 875-881 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 875-881
    • Warnecke, T.1    Hurst, L.D.2
  • 68
    • 77956520011 scopus 로고    scopus 로고
    • Functional roles for noise in genetic circuits
    • Eldar, A. & Elowitz, M. B. Functional roles for noise in genetic circuits. Nature 467, 167-173 (2010).
    • (2010) Nature , vol.467 , pp. 167-173
    • Eldar, A.1    Elowitz, M.B.2
  • 69
    • 84896281082 scopus 로고    scopus 로고
    • Human coding RNA editing is generally nonadaptive
    • Xu, G. & Zhang, J. Human coding RNA editing is generally nonadaptive. Proc. Natl Acad. Sci. USA 111, 3769-3774 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111 , pp. 3769-3774
    • Xu, G.1    Zhang, J.2
  • 71
    • 0035065485 scopus 로고    scopus 로고
    • SNPs, protein structure, and disease
    • Wang, Z. & Moult, J. SNPs, protein structure, and disease. Hum. Mutat. 17, 263-270 (2001).
    • (2001) Hum. Mutat. , vol.17 , pp. 263-270
    • Wang, Z.1    Moult, J.2
  • 73
    • 84897463218 scopus 로고    scopus 로고
    • Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies
    • Wu, J., Li, Y. & Jiang, R. Integrating multiple genomic data to predict disease-causing nonsynonymous single nucleotide variants in exome sequencing studies. PLoS Genet. 10, e1004237 (2014).
    • (2014) PLoS Genet. , vol.10
    • Wu, J.1    Li, Y.2    Jiang, R.3
  • 74
    • 80051968181 scopus 로고    scopus 로고
    • Needles in stacks of needles: Finding disease-causal variants in a wealth of genomic data
    • Cooper, G. M. & Shendure, J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 12, 628-640 (2011).
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 628-640
    • Cooper, G.M.1    Shendure, J.2
  • 75
    • 73649150958 scopus 로고
    • The maintenance of the accuracy of protein synthesis and its relevance to ageing
    • Orgel, L. E. The maintenance of the accuracy of protein synthesis and its relevance to ageing. Proc. Natl Acad. Sci. USA 49, 517-521 (1963).
    • (1963) Proc. Natl Acad. Sci. USA , vol.49 , pp. 517-521
    • Orgel, L.E.1
  • 76
    • 65449173889 scopus 로고    scopus 로고
    • The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation
    • Silva, R. M. et al. The yeast PNC1 longevity gene is up-regulated by mRNA mistranslation. PLoS ONE 4, e5212 (2009).
    • (2009) PLoS ONE , vol.4
    • Silva, R.M.1
  • 77
    • 2342538485 scopus 로고    scopus 로고
    • Aberrant mRNA translation in cancer pathogenesis: An old concept revisited comes finally of age
    • Pandolfi, P. P. Aberrant mRNA translation in cancer pathogenesis: an old concept revisited comes finally of age. Oncogene 23, 3134-3137 (2004).
    • (2004) Oncogene , vol.23 , pp. 3134-3137
    • Pandolfi, P.P.1
  • 78
    • 84902592940 scopus 로고    scopus 로고
    • Somatic mosaicism and disease
    • Frank, S. A. Somatic mosaicism and disease. Curr. Biol. 24, R577-R581 (2014).
    • (2014) Curr. Biol. , vol.24 , pp. R577-R581
    • Frank, S.A.1
  • 79
    • 84923321398 scopus 로고    scopus 로고
    • Evolvability as a function of purifying selection in TEM-1 β-lactamase
    • Stiffler, M. A., Hekstra, D. R. & Ranganathan, R. Evolvability as a function of purifying selection in TEM-1 β-lactamase. Cell 160, 882-892 (2015).
    • (2015) Cell , vol.160 , pp. 882-892
    • Stiffler, M.A.1    Hekstra, D.R.2    Ranganathan, R.3
  • 80
    • 84922439802 scopus 로고    scopus 로고
    • Pervasive degeneracy and epistasis in a protein-protein interface
    • Podgornaia, A. I. & Laub, M. T. Pervasive degeneracy and epistasis in a protein-protein interface. Science 347, 673-677 (2015).
    • (2015) Science , vol.347 , pp. 673-677
    • Podgornaia, A.I.1    Laub, M.T.2
  • 82
    • 33646182934 scopus 로고    scopus 로고
    • An integrated view of protein evolution
    • Pal, C., Papp, B. & Lercher, M. J. An integrated view of protein evolution. Nat. Rev. Genet. 7, 337-348 (2006).
    • (2006) Nat. Rev. Genet. , vol.7 , pp. 337-348
    • Pal, C.1    Papp, B.2    Lercher, M.J.3
  • 83
    • 33746192317 scopus 로고    scopus 로고
    • Unifying measures of gene function and evolution
    • Wolf, Y. I., Carmel, L. & Koonin, E. V. Unifying measures of gene function and evolution. Proc. Biol. Sci. 273, 1507-1515 (2006).
    • (2006) Proc. Biol. Sci. , vol.273 , pp. 1507-1515
    • Wolf, Y.I.1    Carmel, L.2    Koonin, E.V.3
  • 84
    • 67650904949 scopus 로고    scopus 로고
    • Integrated assessment of genomic correlates of protein evolutionary rate
    • Xia, Y., Franzosa, E. A. & Gerstein, M. B. Integrated assessment of genomic correlates of protein evolutionary rate. PLoS Comput. Biol. 5, e1000413 (2009).
    • (2009) PLoS Comput. Biol. , vol.5
    • Xia, Y.1    Franzosa, E.A.2    Gerstein, M.B.3
  • 85
    • 84876565205 scopus 로고    scopus 로고
    • Why does a protein's evolutionary rate vary over time?
    • Du, X., Lipman, D. J. & Cherry, J. L. Why does a protein's evolutionary rate vary over time? Genome Biol. Evol. 5, 494-503 (2013).
    • (2013) Genome Biol. Evol. , vol.5 , pp. 494-503
    • Du, X.1    Lipman, D.J.2    Cherry, J.L.3
  • 86
    • 70349911882 scopus 로고    scopus 로고
    • Structural determinants of protein evolution are context-sensitive at the residue level
    • Franzosa, E. A. & Xia, Y. Structural determinants of protein evolution are context-sensitive at the residue level. Mol. Biol. Evol. 26, 2387-2395 (2009).
    • (2009) Mol. Biol. Evol. , vol.26 , pp. 2387-2395
    • Franzosa, E.A.1    Xia, Y.2
  • 87
    • 84891761205 scopus 로고    scopus 로고
    • Site-specific structural constraints on protein sequence evolutionary divergence: Local packing density versus solvent exposure
    • Yeh, S. W. et al. Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure. Mol. Biol. Evol. 31, 135-139 (2014).
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 135-139
    • Yeh, S.W.1
  • 88
    • 0031876602 scopus 로고    scopus 로고
    • Correlation between the substitution rate and rate variation among sites in protein evolution
    • Zhang, J. & Gu, X. Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149, 1615-1625 (1998).
    • (1998) Genetics , vol.149 , pp. 1615-1625
    • Zhang, J.1    Gu, X.2
  • 89
    • 84864229460 scopus 로고    scopus 로고
    • Assessing determinants of exonic evolutionary rates in mammals
    • Chen, F. C., Liao, B. Y., Pan, C. L., Lin, H. Y. &Chang, A. Y. Assessing determinants of exonic evolutionary rates in mammals. Mol. Biol. Evol. 29, 3121-3129 (2012).
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 3121-3129
    • Chen, F.C.1    Liao, B.Y.2    Pan, C.L.3    Lin, H.Y.4    Chang, A.Y.5
  • 91
    • 84857191660 scopus 로고    scopus 로고
    • Transcription as a source of genome instability
    • Kim, N. & Jinks-Robertson, S. Transcription as a source of genome instability. Nat. Rev. Genet. 13, 204-214 (2012).
    • (2012) Nat. Rev. Genet. , vol.13 , pp. 204-214
    • Kim, N.1    Jinks-Robertson, S.2
  • 92
    • 56749157389 scopus 로고    scopus 로고
    • Transcription-coupled DNA repair: Two decades of progress and surprises
    • Hanawalt, P. C. & Spivak, G. Transcription-coupled DNA repair: two decades of progress and surprises. Nat. Rev. Mol. Cell Biol. 9, 958-970 (2008).
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 958-970
    • Hanawalt, P.C.1    Spivak, G.2
  • 93
    • 84870627323 scopus 로고    scopus 로고
    • Genomic evidence for elevated mutation rates in highly expressed genes
    • Park, C., Qian, W. & Zhang, J. Genomic evidence for elevated mutation rates in highly expressed genes. EMBO Rep. 13, 1123-1129 (2012).
    • (2012) EMBO Rep. , vol.13 , pp. 1123-1129
    • Park, C.1    Qian, W.2    Zhang, J.3
  • 94
    • 84879365232 scopus 로고    scopus 로고
    • No gene-specific optimization of mutation rate in Escherichia coli
    • Chen, X. & Zhang, J. No gene-specific optimization of mutation rate in Escherichia coli. Mol. Biol. Evol. 30, 1559-1562 (2013).
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 1559-1562
    • Chen, X.1    Zhang, J.2
  • 95
    • 84907482328 scopus 로고    scopus 로고
    • Yeast mutation accumulation experiment supports elevated mutation rates at highly transcribed sites
    • Chen, X. & Zhang, J. Yeast mutation accumulation experiment supports elevated mutation rates at highly transcribed sites. Proc. Natl Acad. Sci. USA 111, E4062 (2014).
    • (2014) Proc. Natl Acad. Sci. USA , vol.111
    • Chen, X.1    Zhang, J.2
  • 96
    • 56649099178 scopus 로고    scopus 로고
    • Whole-genome mutational biases in bacteria
    • Lind, P. A. & Andersson, D. I. Whole-genome mutational biases in bacteria. Proc. Natl Acad. Sci. USA 105, 17878-17883 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 17878-17883
    • Lind, P.A.1    Andersson, D.I.2
  • 97
    • 66749175352 scopus 로고    scopus 로고
    • Transcription-associated recombination in eukaryotes: Link between transcription, replication and recombination
    • Gottipati, P. & Helleday, T. Transcription-associated recombination in eukaryotes: link between transcription, replication and recombination. Mutagenesis 24, 203-210 (2009).
    • (2009) Mutagenesis , vol.24 , pp. 203-210
    • Gottipati, P.1    Helleday, T.2
  • 98
    • 33646882591 scopus 로고    scopus 로고
    • Low rates of expression profile divergence in highly expressed genes and tissuespecific genes during mammalian evolution
    • Liao, B. Y. & Zhang, J. Low rates of expression profile divergence in highly expressed genes and tissuespecific genes during mammalian evolution. Mol. Biol. Evol. 23, 1119-1128 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1119-1128
    • Liao, B.Y.1    Zhang, J.2
  • 99
    • 84864112797 scopus 로고    scopus 로고
    • High expression hampers horizontal gene transfer
    • Park, C. & Zhang, J. High expression hampers horizontal gene transfer. Genome Biol. Evol. 4, 523-532 (2012).
    • (2012) Genome Biol. Evol. , vol.4 , pp. 523-532
    • Park, C.1    Zhang, J.2
  • 100
    • 1542286776 scopus 로고    scopus 로고
    • Mammalian housekeeping genes evolve more slowly than tissue-specific genes
    • Zhang, L. & Li, W. H. Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol. Biol. Evol. 21, 236-239 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 236-239
    • Zhang, L.1    Li, W.H.2
  • 101
    • 84876872011 scopus 로고    scopus 로고
    • The hourglass and the early conservation models - Co-existing patterns of developmental constraints in vertebrates
    • Piasecka, B., Lichocki, P., Moretti, S., Bergmann, S. &Robinson-Rechavi, M. The hourglass and the early conservation models - co-existing patterns of developmental constraints in vertebrates. PLoS Genet. 9, e1003476 (2013).
    • (2013) PLoS Genet. , vol.9
    • Piasecka, B.1    Lichocki, P.2    Moretti, S.3    Bergmann, S.4    Robinson-Rechavi, M.5
  • 102
    • 84907852635 scopus 로고    scopus 로고
    • Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate
    • Chuang, T. J. & Chiang, T. W. Impacts of pretranscriptional DNA methylation, transcriptional transcription factor, and posttranscriptional microRNA regulations on protein evolutionary rate. Genome Biol. Evol. 6, 1530-1541 (2014).
    • (2014) Genome Biol. Evol. , vol.6 , pp. 1530-1541
    • Chuang, T.J.1    Chiang, T.W.2
  • 103
    • 84865695733 scopus 로고    scopus 로고
    • Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition
    • Taipale, M. et al. Quantitative analysis of HSP90-client interactions reveals principles of substrate recognition. Cell 150, 987-1001 (2012).
    • (2012) Cell , vol.150 , pp. 987-1001
    • Taipale, M.1
  • 104
    • 77958507116 scopus 로고    scopus 로고
    • Chaperonin-dependent accelerated substitution rates in prokaryotes
    • Bogumil, D. & Dagan, T. Chaperonin-dependent accelerated substitution rates in prokaryotes. Genome Biol. Evol. 2, 602-608 (2010).
    • (2010) Genome Biol. Evol. , vol.2 , pp. 602-608
    • Bogumil, D.1    Dagan, T.2
  • 105
    • 77958489829 scopus 로고    scopus 로고
    • Impact of extracellularity on the evolutionary rate of mammalian proteins
    • Liao, B. Y., Weng, M. P. & Zhang, J. Impact of extracellularity on the evolutionary rate of mammalian proteins. Genome Biol. Evol. 2, 39-43 (2010).
    • (2010) Genome Biol. Evol. , vol.2 , pp. 39-43
    • Liao, B.Y.1    Weng, M.P.2    Zhang, J.3
  • 106
    • 84899738542 scopus 로고    scopus 로고
    • Couping between protein level selection and codon usage optimization in the evolution of bacteria and archaea
    • Ran, W., Kristensen, D. M. & Koonin, E. V. Couping between protein level selection and codon usage optimization in the evolution of bacteria and archaea. mBio 5, e00956-14 (2014).
    • (2014) mBio , vol.5 , pp. e00956-e100914
    • Ran, W.1    Kristensen, D.M.2    Koonin, E.V.3
  • 107
    • 0024966756 scopus 로고
    • Chromosomal location and evolutionary rate variation in enterobacterial genes
    • Sharp, P. M., Shields, D. C., Wolfe, K. H. & Li, W. H. Chromosomal location and evolutionary rate variation in enterobacterial genes. Science 246, 808-810 (1989).
    • (1989) Science , vol.246 , pp. 808-810
    • Sharp, P.M.1    Shields, D.C.2    Wolfe, K.H.3    Li, W.H.4
  • 108
    • 79952200926 scopus 로고    scopus 로고
    • Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus
    • Flynn, K. M., Vohr, S. H., Hatcher, P. J. & Cooper, V. S. Evolutionary rates and gene dispensability associate with replication timing in the archaeon Sulfolobus islandicus. Genome Biol. Evol. 2, 859-869 (2010).
    • (2010) Genome Biol. Evol. , vol.2 , pp. 859-869
    • Flynn, K.M.1    Vohr, S.H.2    Hatcher, P.J.3    Cooper, V.S.4
  • 109
    • 16344381521 scopus 로고    scopus 로고
    • Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks
    • Hahn, M. W. & Kern, A. D. Comparative genomics of centrality and essentiality in three eukaryotic protein-interaction networks. Mol. Biol. Evol. 22, 803-806 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 803-806
    • Hahn, M.W.1    Kern, A.D.2
  • 110
    • 33845875196 scopus 로고    scopus 로고
    • Relating three-dimensional structures to protein networks provides evolutionary insights
    • Kim, P. M., Lu, L. J., Xia, Y. & Gerstein, M. B. Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314, 1938-1941 (2006).
    • (2006) Science , vol.314 , pp. 1938-1941
    • Kim, P.M.1    Lu, L.J.2    Xia, Y.3    Gerstein, M.B.4
  • 111
    • 33745107471 scopus 로고    scopus 로고
    • Influence of metabolic network structure and function on enzyme evolution
    • Vitkup, D., Kharchenko, P. & Wagner, A. Influence of metabolic network structure and function on enzyme evolution. Genome Biol. 7, R39 (2006).
    • (2006) Genome Biol. , vol.7 , pp. R39
    • Vitkup, D.1    Kharchenko, P.2    Wagner, A.3
  • 112
    • 65449187535 scopus 로고    scopus 로고
    • Evolutionary rates and centrality in the yeast gene regulatory network
    • Jovelin, R. & Phillips, P. C. Evolutionary rates and centrality in the yeast gene regulatory network. Genome Biol. 10, R35 (2009).
    • (2009) Genome Biol. , vol.10 , pp. R35
    • Jovelin, R.1    Phillips, P.C.2
  • 113
    • 84962757509 scopus 로고    scopus 로고
    • Determinants of protein evolutionary rates in light of ENCODE functional genomics
    • Kryuchkova, N. & Robinson-Rechavi, M. Determinants of protein evolutionary rates in light of ENCODE functional genomics. BMC Bioinformatics 15 (Suppl. 3), A9 (2014).
    • (2014) BMC Bioinformatics , vol.15 , pp. A9
    • Kryuchkova, N.1    Robinson-Rechavi, M.2
  • 114
    • 33748143748 scopus 로고    scopus 로고
    • Structural determinants of the rate of protein evolution in yeast
    • Bloom, J. D., Drummond, D. A., Arnold, F. H. &Wilke, C. O. Structural determinants of the rate of protein evolution in yeast. Mol. Biol. Evol. 23, 1751-1761 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1751-1761
    • Bloom, J.D.1    Drummond, D.A.2    Arnold, F.H.3    Wilke, C.O.4
  • 115
    • 0036017388 scopus 로고    scopus 로고
    • Evolutionary rate heterogeneity in proteins with long disordered regions
    • Brown, C. J. et al. Evolutionary rate heterogeneity in proteins with long disordered regions. J. Mol. Evol. 55, 104-110 (2002).
    • (2002) J. Mol. Evol. , vol.55 , pp. 104-110
    • Brown, C.J.1


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