메뉴 건너뛰기




Volumn 5, Issue 3, 2013, Pages 494-503

Why does a protein's evolutionary rate vary over time?

Author keywords

Evolutionary rate; Molecular clock; Overdispersion; Protein evolution

Indexed keywords

MAMMALIA;

EID: 84876565205     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt024     Document Type: Article
Times cited : (6)

References (31)
  • 1
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • Altschul SF, et al. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 3389-3402
    • Altschul, S.F.1
  • 2
    • 47649104264 scopus 로고    scopus 로고
    • Overdispersion of the molecular clock: Temporal variation of gene-specific substitution rates in Drosophila
    • Bedford T, Hartl DL. 2008. Overdispersion of the molecular clock: temporal variation of gene-specific substitution rates in Drosophila. Mol Biol Evol. 25:1631-1638.
    • (2008) Mol Biol Evol. , vol.25 , pp. 1631-1638
    • Bedford, T.1    Hartl, D.L.2
  • 3
    • 49849102382 scopus 로고    scopus 로고
    • Overdispersion of the molecular clock varies between yeast, Drosophila and mammals
    • Bedford T, Wapinski I, Hartl DL. 2008. Overdispersion of the molecular clock varies between yeast, Drosophila and mammals. Genetics 179: 977-984.
    • (2008) Genetics , vol.179 , pp. 977-984
    • Bedford, T.1    Wapinski, I.2    Hartl, D.L.3
  • 4
    • 33846515095 scopus 로고    scopus 로고
    • Thermodynamics of neutral protein evolution
    • Bloom JD, Raval A, Wilke CO. 2007. Thermodynamics of neutral protein evolution. Genetics 175:255-256.
    • (2007) Genetics , vol.175 , pp. 255-256
    • Bloom, J.D.1    Raval, A.2    Wilke, C.O.3
  • 5
    • 0031711923 scopus 로고    scopus 로고
    • Should we expect substitution rate to depend on population size?
    • Cherry JL. 1998. Should we expect substitution rate to depend on population size? Genetics 150:911-919.
    • (1998) Genetics , vol.150 , pp. 911-919
    • Cherry, J.L.1
  • 6
    • 34249804498 scopus 로고    scopus 로고
    • Using FlyAtlas to identify better Drosophila melanogaster models of human disease
    • Chintapalli VR, Wang J, Dow JAT. 2007. Using FlyAtlas to identify better Drosophila melanogaster models of human disease. Nat Genet. 39: 715-720.
    • (2007) Nat Genet. , vol.39 , pp. 715-720
    • Chintapalli, V.R.1    Wang, J.2    Dow, J.A.T.3
  • 7
    • 47149117454 scopus 로고    scopus 로고
    • Evolution of genes and genomes on the Drosophila phylogeny
    • Drosophila 12 Genomes Consortium, et al.
    • Drosophila 12 Genomes Consortium, et al. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450: 203-218.
    • (2007) Nature , vol.450 , pp. 203-218
  • 8
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond DA, Raval A, Wilke CO. 2006. A single determinant dominates the rate of yeast protein evolution. Mol Biol Evol. 23:327-337.
    • (2006) Mol Biol Evol. , vol.23 , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 9
    • 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
  • 10
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
    • (2004) Nucleic Acids Res. , vol.32 , pp. 1792-1797
    • Edgar, R.C.1
  • 11
    • 0024767023 scopus 로고
    • Lineage effects and the index of dispersion of molecular evolution
    • Gillespie JH. 1989. Lineage effects and the index of dispersion of molecular evolution. Mol Biol Evol. 6:636-647.
    • (1989) Mol Biol Evol. , vol.6 , pp. 636-647
    • Gillespie, J.H.1
  • 13
    • 46649115430 scopus 로고    scopus 로고
    • Splign: Algorithms for computing spliced alignments with identification of paralogs
    • Kapustin Y, Souvorov A, Tatusova T, Lipman D. 2008. Splign: algorithms for computing spliced alignments with identification of paralogs. Biol Direct. 3:20.
    • (2008) Biol Direct. , vol.3 , pp. 20
    • Kapustin, Y.1    Souvorov, A.2    Tatusova, T.3    Lipman, D.4
  • 15
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • Krylov DM, Wolf YI, Rogozin IB, Koonin EV. 2003. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13: 2229-2235.
    • (2003) Genome Res. , vol.13 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 16
    • 0016155942 scopus 로고
    • An estimation of the constancy of the rate of molecular evolution
    • Langley CH, Fitch CH. 1974. An estimation of the constancy of the rate of molecular evolution. J Mol Evol. 3:161-177.
    • (1974) J Mol Evol. , vol.3 , pp. 161-177
    • Langley, C.H.1    Fitch, C.H.2
  • 17
    • 78651285748 scopus 로고    scopus 로고
    • CDD: A conserved domain database for the functional annotation of proteins
    • Marchler-Bauer A, et al. 2011. CDD: a conserved domain database for the functional annotation of proteins. Nucleic Acids Res. 39:D225-D229.
    • (2011) Nucleic Acids Res. , vol.39
    • Marchler-Bauer, A.1
  • 18
    • 0030218056 scopus 로고    scopus 로고
    • The neutral theory is dead. The current significance and standing of neutral and nearly neutral theories
    • Ohta T. 1996. The neutral theory is dead. The current significance and standing of neutral and nearly neutral theories. Bioessays 18:673-677.
    • (1996) Bioessays , vol.18 , pp. 673-677
    • Ohta, T.1
  • 19
    • 0015162354 scopus 로고
    • On the constancy of the evolutionary rates of cistrons
    • Ohta T, Kimura M. 1971. On the constancy of the evolutionary rates of cistrons. J Mol Evol. 1:18-25.
    • (1971) J Mol Evol. , vol.1 , pp. 18-25
    • Ohta, T.1    Kimura, M.2
  • 20
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • Pál C, Papp B, Hurst LD. 2001. Highly expressed genes in yeast evolve slowly. Genetics 158:927-931.
    • (2001) Genetics , vol.158 , pp. 927-931
    • Pál, C.1    Papp, B.2    Hurst, L.D.3
  • 21
    • 33846057724 scopus 로고    scopus 로고
    • NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins
    • Pruitt KD, Tatusova T, Maglott DR. 2007. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35:D61-D65.
    • (2007) Nucleic Acids Res. , vol.35
    • Pruitt, K.D.1    Tatusova, T.2    Maglott, D.R.3
  • 22
    • 34247352040 scopus 로고    scopus 로고
    • Evolutionary and biomedical insights from the rhesus macaque genome
    • Rhesus Macaque Genome Sequencing and Analysis Consortium, et al.
    • Rhesus Macaque Genome Sequencing and Analysis Consortium, et al. 2007. Evolutionary and biomedical insights from the rhesus macaque genome. Science 316:222-234.
    • (2007) Science , vol.316 , pp. 222-234
  • 23
    • 1242284655 scopus 로고    scopus 로고
    • An analysis of determinants of amino acids substitution rates in bacterial proteins
    • Rocha EP, Danchin A. 2004. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol Biol Evol. 21:108-116.
    • (2004) Mol Biol Evol. , vol.21 , pp. 108-116
    • Rocha, E.P.1    Danchin, A.2
  • 24
    • 78651310799 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Sayers EW, et al. 2011. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 39:D38-D51.
    • (2011) Nucleic Acids Res. , vol.39
    • Sayers, E.W.1
  • 25
    • 84857745267 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • Sayers EW, et al. 2012. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 40:D13-D25.
    • (2012) Nucleic Acids Res. , vol.40
    • Sayers, E.W.1
  • 26
    • 65949096636 scopus 로고    scopus 로고
    • Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes
    • Schrimpf SP, et al. 2009. Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol. 7:e48.
    • (2009) PLoS Biol. , vol.7
    • Schrimpf, S.P.1
  • 27
    • 0023337434 scopus 로고
    • On the overdispersed molecular clock
    • Takahata N. 1987. On the overdispersed molecular clock. Genetics 116: 169-179.
    • (1987) Genetics , vol.116 , pp. 169-179
    • Takahata, N.1
  • 28
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Koonin EV, Lipman DJ. 1997. A genomic perspective on protein families. Science 278:631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 29
    • 66149123308 scopus 로고    scopus 로고
    • The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages
    • Wolf YI, Novichkov PS, Karev GP, Koonin EV, Lipman DJ. 2009. The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A. 106:7273-7280.
    • (2009) Proc Natl Acad Sci U S A. , vol.106 , pp. 7273-7280
    • Wolf, Y.I.1    Novichkov, P.S.2    Karev, G.P.3    Koonin, E.V.4    Lipman, D.J.5
  • 30
    • 80755189340 scopus 로고    scopus 로고
    • Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques
    • Yan G, et al. 2011. Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol. 29:1019-1023.
    • (2011) Nat Biotechnol. , vol.29 , pp. 1019-1023
    • Yan, G.1
  • 31
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 13:555-556.
    • (1997) Comput Appl Biosci. , vol.13 , pp. 555-556
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.