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Volumn 6, Issue 10, 2010, Pages 1-10

Transition from positive to neutral in mutation fixation along with continuing rising fitness in thermal adaptive evolution

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; CELL GROWTH; ESCHERICHIA COLI; GENE MUTATION; LABORATORY; MOLECULAR EVOLUTION; NEUTRAL GENE THEORY; NONHUMAN; SEQUENCE ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM; TEMPERATURE ACCLIMATIZATION; TEMPERATURE STRESS; TRANSITION TEMPERATURE; ADAPTATION; CHEMISTRY; DIRECTED MOLECULAR EVOLUTION; DNA SEQUENCE; GENETIC SELECTION; GENETICS; GROWTH, DEVELOPMENT AND AGING; INDEL MUTATION; METHODOLOGY; MUTATION; TEMPERATURE; TIME;

EID: 78449239214     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1001164     Document Type: Article
Times cited : (66)

References (44)
  • 1
    • 25844495901 scopus 로고    scopus 로고
    • Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states
    • Fong SS, Joyce AR, Palsson BO (2005) Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states. Genome Res 15: 1365-1372.
    • (2005) Genome Res , vol.15 , pp. 1365-1372
    • Fong, S.S.1    Joyce, A.R.2    Palsson, B.O.3
  • 2
    • 33751544539 scopus 로고    scopus 로고
    • Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale
    • Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, et al. (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38: 1406-1412.
    • (2006) Nat Genet , vol.38 , pp. 1406-1412
    • Herring, C.D.1    Raghunathan, A.2    Honisch, C.3    Patel, T.4    Applebee, M.K.5
  • 3
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with Escherichia coli
    • Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, et al. (2009) Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461: 1243-1247.
    • (2009) Nature , vol.461 , pp. 1243-1247
    • Barrick, J.E.1    Yu, D.S.2    Yoon, S.H.3    Jeong, H.4    Oh, T.K.5
  • 5
    • 0027385183 scopus 로고
    • Regulation of the heat-shock response in bacteria
    • Yura T, Nagai H, Mori H (1993) Regulation of the heat-shock response in bacteria. Annu Rev Microbiol 47: 321-350.
    • (1993) Annu Rev Microbiol , vol.47 , pp. 321-350
    • Yura, T.1    Nagai, H.2    Mori, H.3
  • 6
    • 33646127577 scopus 로고    scopus 로고
    • Molecular chaperones and protein quality control
    • Bukau B, Weissman J, Horwich A (2006) Molecular chaperones and protein quality control. Cell 125: 443-451.
    • (2006) Cell , vol.125 , pp. 443-451
    • Bukau, B.1    Weissman, J.2    Horwich, A.3
  • 7
    • 0037040541 scopus 로고    scopus 로고
    • Molecular chaperones in the cytosol: From nascent chain to folded protein
    • Hartl FU, Hayer-Hartl M (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295: 1852-1858.
    • (2002) Science , vol.295 , pp. 1852-1858
    • Hartl, F.U.1    Hayer-Hartl, M.2
  • 8
    • 55649090339 scopus 로고    scopus 로고
    • Thermal adaptation of soil microbial respiration to elevated temperature
    • Bradford MA, Davies CA, Frey SD, Maddox TR, Melillo JM, et al. (2008) Thermal adaptation of soil microbial respiration to elevated temperature. Ecol Lett 11: 1316-1327.
    • (2008) Ecol Lett , vol.11 , pp. 1316-1327
    • Bradford, M.A.1    Davies, C.A.2    Frey, S.D.3    Maddox, T.R.4    Melillo, J.M.5
  • 9
    • 0033042865 scopus 로고    scopus 로고
    • Evolutionary adaptation to temperature. VII. Extension of the upper thermal limit of Escherichia coli
    • Mongold JA, Bennett AF, Lenski RE (1999) Evolutionary adaptation to temperature. VII. Extension of the upper thermal limit of Escherichia coli. Evolution 53: 386-394.
    • (1999) Evolution , vol.53 , pp. 386-394
    • Mongold, J.A.1    Bennett, A.F.2    Lenski, R.E.3
  • 10
    • 34547418221 scopus 로고    scopus 로고
    • An experimental test of evolutionary trade-offs during temperature adaptation
    • Bennett AF, Lenski RE (2007) An experimental test of evolutionary trade-offs during temperature adaptation. Proc Natl Acad Sci U S A 104 Suppl 1: 8649-8654.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , Issue.SUPPL. 1 , pp. 8649-8654
    • Bennett, A.F.1    Lenski, R.E.2
  • 11
    • 0033058808 scopus 로고    scopus 로고
    • Chromosomal changes during experimental evolution in laboratory populations of Escherichia coli
    • Bergthorsson U, Ochman H (1999) Chromosomal changes during experimental evolution in laboratory populations of Escherichia coli. J Bacteriol 181: 1360-1363.
    • (1999) J Bacteriol , vol.181 , pp. 1360-1363
    • Bergthorsson, U.1    Ochman, H.2
  • 12
    • 0035895278 scopus 로고    scopus 로고
    • Genetic architecture of thermal adaptation in Escherichia coli
    • Riehle MM, Bennett AF, Long AD (2001) Genetic architecture of thermal adaptation in Escherichia coli. Proc Natl Acad Sci U S A 98: 525-530.
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 525-530
    • Riehle, M.M.1    Bennett, A.F.2    Long, A.D.3
  • 13
    • 0041625721 scopus 로고    scopus 로고
    • Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature
    • Riehle MM, Bennett AF, Lenski RE, Long AD (2003) Evolutionary changes in heat-inducible gene expression in lines of Escherichia coli adapted to high temperature. Physiol Genomics 14: 47-58.
    • (2003) Physiol Genomics , vol.14 , pp. 47-58
    • Riehle, M.M.1    Bennett, A.F.2    Lenski, R.E.3    Long, A.D.4
  • 14
    • 0028365256 scopus 로고
    • Dynamics of adaptation and diversification: A 10,000-generation experiment with bacterial populations
    • Lenski RE, Travisano M (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci U S A 91: 6808-6814.
    • (1994) Proc Natl Acad Sci U S A , vol.91 , pp. 6808-6814
    • Lenski, R.E.1    Travisano, M.2
  • 15
    • 73049105558 scopus 로고    scopus 로고
    • Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus
    • Azuma Y, Hosoyama A, Matsutani M, Furuya N, Horikawa H, et al. (2009) Whole-genome analyses reveal genetic instability of Acetobacter pasteurianus. Nucleic Acids Res 37: 5768-5783.
    • (2009) Nucleic Acids Res , vol.37 , pp. 5768-5783
    • Azuma, Y.1    Hosoyama, A.2    Matsutani, M.3    Furuya, N.4    Horikawa, H.5
  • 17
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3: 418-426.
    • (1986) Mol Biol Evol , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 18
    • 27944474033 scopus 로고    scopus 로고
    • Selectionism and neutralism in molecular evolution
    • Nei M (2005) Selectionism and neutralism in molecular evolution. Mol Biol Evol 22: 2318-2342.
    • (2005) Mol Biol Evol , vol.22 , pp. 2318-2342
    • Nei, M.1
  • 19
    • 0029563023 scopus 로고
    • A method for estimating the numbers of synonymous and nonsynonymous substitutions per site
    • Comeron JM (1995) A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J Mol Evol 41: 1152-1159.
    • (1995) J Mol Evol , vol.41 , pp. 1152-1159
    • Comeron, J.M.1
  • 20
    • 0026454741 scopus 로고
    • Evolutionary adaptation to temperature. I. Fitness responses of Escherichia coli to changes in its thermal environment
    • Bennett AF, Lenski RE, Mittlter JE (1992) Evolutionary adaptation to temperature. I. Fitness responses of Escherichia coli to changes in its thermal environment. Evolution 46: 16-30.
    • (1992) Evolution , vol.46 , pp. 16-30
    • Bennett, A.F.1    Lenski, R.E.2    Mittlter, J.E.3
  • 21
    • 0030620273 scopus 로고    scopus 로고
    • Evolution of high mutation rates in experimental populations of E. coli
    • Sniegowski PD, Gerrish PJ, Lenski RE (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387: 703-705.
    • (1997) Nature , vol.387 , pp. 703-705
    • Sniegowski, P.D.1    Gerrish, P.J.2    Lenski, R.E.3
  • 24
    • 0037381428 scopus 로고    scopus 로고
    • Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations
    • Lenski RE, Winkworth CL, Riley MA (2003) Rates of DNA sequence evolution in experimental populations of Escherichia coli during 20,000 generations. J Mol Evol 56: 498-508.
    • (2003) J Mol Evol , vol.56 , pp. 498-508
    • Lenski, R.E.1    Winkworth, C.L.2    Riley, M.A.3
  • 25
    • 33646397599 scopus 로고    scopus 로고
    • Evolution of mutation rates in bacteria
    • Denamur E, Matic I (2006) Evolution of mutation rates in bacteria. Mol Microbiol 60: 820-827.
    • (2006) Mol Microbiol , vol.60 , pp. 820-827
    • Denamur, E.1    Matic, I.2
  • 26
    • 0036889468 scopus 로고    scopus 로고
    • Evolution of synonymous codon usage in metazoans
    • Duret L (2002) Evolution of synonymous codon usage in metazoans. Curr Opin Genet Dev 12: 640-649.
    • (2002) Curr Opin Genet Dev , vol.12 , pp. 640-649
    • Duret, L.1
  • 27
    • 0019297501 scopus 로고
    • Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent
    • Maruyama T, Kimura M (1980) Genetic variability and effective population size when local extinction and recolonization of subpopulations are frequent. Proc Natl Acad Sci U S A 77: 6710-6714.
    • (1980) Proc Natl Acad Sci U S A , vol.77 , pp. 6710-6714
    • Maruyama, T.1    Kimura, M.2
  • 28
    • 0029867157 scopus 로고    scopus 로고
    • Selection intensity for codon bias and the effective population size of Escherichia coli
    • Berg OG (1996) Selection intensity for codon bias and the effective population size of Escherichia coli. Genetics 142: 1379-1382.
    • (1996) Genetics , vol.142 , pp. 1379-1382
    • Berg, O.G.1
  • 29
    • 23944490117 scopus 로고    scopus 로고
    • Missense meanderings in sequence space: A biophysical view of protein evolution
    • DePristo MA, Weinreich DM, Hartl DL (2005) Missense meanderings in sequence space: a biophysical view of protein evolution. Nat Rev Genet 6: 678-687.
    • (2005) Nat Rev Genet , vol.6 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 30
    • 28444484984 scopus 로고    scopus 로고
    • Genomic buffering mitigates the effects of deleterious mutations in bacteria
    • Maisnier-Patin S, Roth JR, Fredriksson A, Nystrom T, Berg OG, et al. (2005) Genomic buffering mitigates the effects of deleterious mutations in bacteria. Nat Genet 37: 1376-1379.
    • (2005) Nat Genet , vol.37 , pp. 1376-1379
    • Maisnier-Patin, S.1    Roth, J.R.2    Fredriksson, A.3    Nystrom, T.4    Berg, O.G.5
  • 31
    • 66649132872 scopus 로고    scopus 로고
    • Chaperonin overexpression promotes genetic variation and enzyme evolution
    • Tokuriki N, Tawfik DS (2009) Chaperonin overexpression promotes genetic variation and enzyme evolution. Nature 459: 668-673.
    • (2009) Nature , vol.459 , pp. 668-673
    • Tokuriki, N.1    Tawfik, D.S.2
  • 32
    • 76149095944 scopus 로고    scopus 로고
    • GroEL dependency affects codon usage-support for a critical role of misfolding in gene evolution
    • Warnecke T, Hurst LD (2010) GroEL dependency affects codon usage-support for a critical role of misfolding in gene evolution. Mol Syst Biol 6: 340.
    • (2010) Mol Syst Biol , vol.6 , pp. 340
    • Warnecke, T.1    Hurst, L.D.2
  • 33
    • 0032577365 scopus 로고    scopus 로고
    • Continuity in evolution: On the nature of transitions
    • Fontana W, Schuster P (1998) Continuity in evolution: on the nature of transitions. Science 280: 1451-1455.
    • (1998) Science , vol.280 , pp. 1451-1455
    • Fontana, W.1    Schuster, P.2
  • 34
    • 0034698298 scopus 로고    scopus 로고
    • One sequence, two ribozymes: Implications for the emergence of new ribozyme folds
    • Schultes EA, Bartel DP (2000) One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289: 448-452.
    • (2000) Science , vol.289 , pp. 448-452
    • Schultes, E.A.1    Bartel, D.P.2
  • 35
    • 34547769282 scopus 로고    scopus 로고
    • Mutational reversions during adaptive protein evolution
    • DePristo MA, Hartl DL, Weinreich DM (2007) Mutational reversions during adaptive protein evolution. Mol Biol Evol 24: 1608-1610.
    • (2007) Mol Biol Evol , vol.24 , pp. 1608-1610
    • DePristo, M.A.1    Hartl, D.L.2    Weinreich, D.M.3
  • 36
    • 35648966472 scopus 로고    scopus 로고
    • Inherent characteristics of gene expression for buffering environmental changes without the corresponding transcriptional regulations
    • Suzuki T, Kashiwagi A, Urabe I, Yomo T (2006) Inherent characteristics of gene expression for buffering environmental changes without the corresponding transcriptional regulations. Biophysics 2: 63-77.
    • (2006) Biophysics , vol.2 , pp. 63-77
    • Suzuki, T.1    Kashiwagi, A.2    Urabe, I.3    Yomo, T.4
  • 37
    • 0034612342 scopus 로고    scopus 로고
    • One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
    • Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97: 6640-6645.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 6640-6645
    • Datsenko, K.A.1    Wanner, B.L.2
  • 38
    • 55549133238 scopus 로고    scopus 로고
    • Construction of Escherichia coli gene expression level perturbation collection
    • Kashiwagi A, Sakurai T, Tsuru S, Ying BW, Mori K, et al. (2009) Construction of Escherichia coli gene expression level perturbation collection. Metab Eng 11: 56-63.
    • (2009) Metab Eng , vol.11 , pp. 56-63
    • Kashiwagi, A.1    Sakurai, T.2    Tsuru, S.3    Ying, B.W.4    Mori, K.5
  • 40
    • 0022744245 scopus 로고
    • Timing of initiation of chromosome replication in individual Escherichia coli cells
    • Skarstad K, Boye E, Steen HB (1986) Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5: 1711-1717.
    • (1986) EMBO J , vol.5 , pp. 1711-1717
    • Skarstad, K.1    Boye, E.2    Steen, H.B.3
  • 41
    • 43349089844 scopus 로고    scopus 로고
    • An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays
    • Ono N, Suzuki S, Furusawa C, Agata T, Kashiwagi A, et al. (2008) An improved physico-chemical model of hybridization on high-density oligonucleotide microarrays. Bioinformatics 24: 1278-1285.
    • (2008) Bioinformatics , vol.24 , pp. 1278-1285
    • Ono, N.1    Suzuki, S.2    Furusawa, C.3    Agata, T.4    Kashiwagi, A.5
  • 42
    • 38049134171 scopus 로고    scopus 로고
    • Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays
    • Suzuki S, Ono N, Furusawa C, Kashiwagi A, Yomo T (2007) Experimental optimization of probe length to increase the sequence specificity of high-density oligonucleotide microarrays. BMC Genomics 8: 373.
    • (2007) BMC Genomics , vol.8 , pp. 373
    • Suzuki, S.1    Ono, N.2    Furusawa, C.3    Kashiwagi, A.4    Yomo, T.5
  • 43
    • 58049209790 scopus 로고    scopus 로고
    • Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays
    • Furusawa C, Ono N, Suzuki S, Agata T, Shimizu H, et al. (2009) Model-based analysis of non-specific binding for background correction of high-density oligonucleotide microarrays. Bioinformatics 25: 36-41.
    • (2009) Bioinformatics , vol.25 , pp. 36-41
    • Furusawa, C.1    Ono, N.2    Suzuki, S.3    Agata, T.4    Shimizu, H.5
  • 44
    • 0038729666 scopus 로고    scopus 로고
    • A model of molecular interactions on short oligonucleotide microarrays
    • Zhang L, Miles MF, Aldape KD (2003) A model of molecular interactions on short oligonucleotide microarrays. Nat Biotechnol 21: 818-821.
    • (2003) Nat Biotechnol , vol.21 , pp. 818-821
    • Zhang, L.1    Miles, M.F.2    Aldape, K.D.3


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