메뉴 건너뛰기




Volumn 489, Issue 7417, 2012, Pages 513-518

Genomic analysis of a key innovation in an experimental Escherichia coli population

Author keywords

[No Author keywords available]

Indexed keywords

CLADISTICS; COLIFORM BACTERIUM; EVOLUTIONARY BIOLOGY; GENE EXPRESSION; GENETIC ANALYSIS; GENOMICS; GENOTYPE; LIFE HISTORY TRAIT; MUTATION; PHYSIOLOGY;

EID: 84866944595     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature11514     Document Type: Article
Times cited : (441)

References (52)
  • 1
    • 0000476824 scopus 로고
    • ed. Tax, S. Univ. Chicago Press
    • Mayr, E. In Evolution after Darwin (ed. Tax, S.) Vol. 1, 349-380 (Univ. Chicago Press, 1960).
    • (1960) Evolution after Darwin , vol.1 , pp. 349-380
    • Mayr, E.1
  • 2
    • 62749090636 scopus 로고    scopus 로고
    • What, if anything, is an evolutionary novelty?
    • Pigliucci, M. What, if anything, is an evolutionary novelty? Philos. Sci. 75, 887-898 (2008).
    • (2008) Philos. Sci. , vol.75 , pp. 887-898
    • Pigliucci, M.1
  • 3
    • 0017771466 scopus 로고
    • Evolution and tinkering
    • Jacob, F. Evolution and tinkering. Science 196, 1161-1166 (1977).
    • (1977) Science , vol.196 , pp. 1161-1166
    • Jacob, F.1
  • 5
    • 0020402387 scopus 로고
    • Exaptation\a missing term in the science of form
    • Gould, S. J. & Vrba, E. S. Exaptation\a missing term in the science of form. Paleobiol. 8, 4-15 (1982).
    • (1982) Paleobiol. , vol.8 , pp. 4-15
    • Gould, S.J.1    Vrba, E.S.2
  • 6
    • 10944230777 scopus 로고    scopus 로고
    • Duplication and divergence: The evolution of new genes and old ideas
    • Taylor, J. S. & Raes, J. Duplication and divergence: the evolution of new genes and old ideas. Annu. Rev. Genet. 38, 615-643 (2004).
    • (2004) Annu. Rev. Genet. , vol.38 , pp. 615-643
    • Taylor, J.S.1    Raes, J.2
  • 7
    • 0032885169 scopus 로고    scopus 로고
    • Genome evolution and the evolution of exon-shuffling\a review
    • Patthy, L. Genome evolution and the evolution of exon-shuffling\a review. Gene 238, 103-114 (1999).
    • (1999) Gene , vol.238 , pp. 103-114
    • Patthy, L.1
  • 8
    • 0036439421 scopus 로고    scopus 로고
    • Gene co-option in physiological and morphological evolution
    • True, J. R. & Carroll, S. B. Gene co-option in physiological and morphological evolution. Annu. Rev. Cell Dev. Biol. 18, 53-80 (2002).
    • (2002) Annu. Rev. Cell Dev. Biol. , vol.18 , pp. 53-80
    • True, J.R.1    Carroll, S.B.2
  • 9
    • 0037500141 scopus 로고    scopus 로고
    • Evolution by gene duplication: An update
    • Zhang, J. Evolution by gene duplication: an update. Trends Ecol. Evol. 18, 292-298 (2003).
    • (2003) Trends Ecol. Evol. , vol.18 , pp. 292-298
    • Zhang, J.1
  • 10
    • 36749083463 scopus 로고    scopus 로고
    • Ohno's dilemma: Evolution of new genes under continuous selection
    • Bergthorsson, U., Andersson, D. I. & Roth, J. R. Ohno's dilemma: evolution of new genes under continuous selection. Proc. Natl Acad. Sci. USA 104, 17004-17009 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 17004-17009
    • Bergthorsson, U.1    Andersson, D.I.2    Roth, J.R.3
  • 11
    • 0038668776 scopus 로고    scopus 로고
    • The evolutionary originof complex features
    • Lenski, R. E., Ofria, C., Pennock, R. T. & Adami, C. The evolutionary originof complex features. Nature 423, 139-144 (2003).
    • (2003) Nature , vol.423 , pp. 139-144
    • Lenski, R.E.1    Ofria, C.2    Pennock, R.T.3    Adami, C.4
  • 12
    • 0038441327 scopus 로고    scopus 로고
    • Evolution experiments with microorganisms: The dynamics and genetic basesofadaptation
    • Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic basesofadaptation. Nature Rev. Genet. 4, 457-469 (2003).
    • (2003) Nature Rev. Genet. , vol.4 , pp. 457-469
    • Elena, S.F.1    Lenski, R.E.2
  • 13
    • 1842472689 scopus 로고    scopus 로고
    • Phenotypic and genomic evolution during a 20, 000-generation experiment with the bacterium Escherichia coli
    • Lenski, R. E. Phenotypic and genomic evolution during a 20, 000-generation experiment with the bacterium Escherichia coli. Plant Breed. Rev. 24, 225-265 (2004).
    • (2004) Plant Breed. Rev. , vol.24 , pp. 225-265
    • Lenski, R.E.1
  • 15
    • 84863393863 scopus 로고    scopus 로고
    • Repeatability and contingency in the evolution of a key innovation in phage lambda
    • Meyer, J. R., Dobias, D. T., Weitz, J. S., Barrick, J. E. & Lenski, R. E. Repeatability and contingency in the evolution of a key innovation in phage lambda. Science 335, 428-432 (2012).
    • (2012) Science , vol.335 , pp. 428-432
    • Meyer, J.R.1    Dobias, D.T.2    Weitz, J.S.3    Barrick, J.E.4    Lenski, R.E.5
  • 16
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome resequencing
    • Bentley, D. R. Whole-genome resequencing. Curr. Opin. Genet. Dev. 16, 545-552 (2006).
    • (2006) Curr. Opin. Genet. Dev. , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 17
    • 34147180389 scopus 로고    scopus 로고
    • Analysis of genetic systems using experimental evolution and whole-genome sequencing
    • Hegreness, M. & Kishony, R. Analysis of genetic systems using experimental evolution and whole-genome sequencing. Genome Biol. 8, 201 (2007).
    • (2007) Genome Biol. , vol.8 , pp. 201
    • Hegreness, M.1    Kishony, R.2
  • 18
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-term experiment with E. coli
    • Barrick, J. E. et al. Genome evolution and adaptation in a long-term experiment with E. coli. Nature 461, 1243-1247 (2009).
    • (2009) Nature , vol.461 , pp. 1243-1247
    • Barrick, J.E.1
  • 19
    • 77957746208 scopus 로고    scopus 로고
    • Genome-wide mutational diversity in an evolving population of Escherichia coli
    • Barrick, J. E. & Lenski, R. E. Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb. Symp. Quant. Biol. 74, 119-129 (2009).
    • (2009) Cold Spring Harb. Symp. Quant. Biol. , vol.74 , pp. 119-129
    • Barrick, J.E.1    Lenski, R.E.2
  • 20
    • 45849093668 scopus 로고    scopus 로고
    • Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
    • Blount, Z. D., Borland, C. Z. & Lenski, R. E. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl Acad. Sci. USA 105, 7899-7906 (2008).
    • (2008) Proc. Natl Acad. Sci. USA , vol.105 , pp. 7899-7906
    • Blount, Z.D.1    Borland, C.Z.2    Lenski, R.E.3
  • 21
    • 0002153005 scopus 로고
    • Correlation of citrate-utilization by members of the colon-aerogenes group with other differential characteristics and with habitat
    • Koser, S. A. Correlation of citrate-utilization by members of the colon-aerogenes group with other differential characteristics and with habitat. J. Bacteriol. 9, 59-77 (1924).
    • (1924) J. Bacteriol. , vol.9 , pp. 59-77
    • Koser, S.A.1
  • 22
    • 0019308686 scopus 로고
    • Why a co-substrate is required for anaerobic growth of Escherichia coli on citrate
    • Lütgens, M. & Gottschalk, G. Why a co-substrate is required for anaerobic growth of Escherichia coli on citrate. J. Gen. Microbiol. 119, 63-70 (1980).
    • (1980) J. Gen. Microbiol. , vol.119 , pp. 63-70
    • Lütgens, M.1    Gottschalk, G.2
  • 24
    • 0020319748 scopus 로고
    • Chromosomal mutation for citrate utilization by Escherichia coli K-12
    • Hall, B. G. Chromosomal mutation for citrate utilization by Escherichia coli K-12. J. Bacteriol. 151, 269-273 (1982).
    • (1982) J. Bacteriol. , vol.151 , pp. 269-273
    • Hall, B.G.1
  • 25
    • 70350686881 scopus 로고    scopus 로고
    • Genome sequences of Escherichia coli B strains REL606 and BL21(DE3)
    • Jeong, H. et al. Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J. Mol. Biol. 394, 644-652 (2009).
    • (2009) J. Mol. Biol. , vol.394 , pp. 644-652
    • Jeong, H.1
  • 26
    • 61849168524 scopus 로고    scopus 로고
    • Clonal interference, multiple mutations and adaptation in large asexual populations
    • Fogle, C. A., Nagle, J. L. & Desai, M. M. Clonal interference, multiple mutations and adaptation in large asexual populations. Genetics 180, 2163-2173 (2008).
    • (2008) Genetics , vol.180 , pp. 2163-2173
    • Fogle, C.A.1    Nagle, J.L.2    Desai, M.M.3
  • 27
    • 0031876504 scopus 로고    scopus 로고
    • Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli
    • Treves, D. S., Manning, S. & Adams, J. Repeated evolution of an acetate-crossfeeding polymorphism in long-term populations of Escherichia coli. Mol. Biol. Evol. 15, 789-797 (1998).
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 789-797
    • Treves, D.S.1    Manning, S.2    Adams, J.3
  • 28
    • 24744449974 scopus 로고    scopus 로고
    • Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism
    • Rozen, D. E., Schneider, D. & Lenski, R. E. Long-term experimental evolution in Escherichia coli. XIII. Phylogenetic history of a balanced polymorphism. J. Mol. Evol. 61, 171-180 (2005).
    • (2005) J. Mol. Evol. , vol.61 , pp. 171-180
    • Rozen, D.E.1    Schneider, D.2    Lenski, R.E.3
  • 29
    • 0005732728 scopus 로고
    • Escherichia coli mutator mutants deficient in methyl-instructed DNA mismatch correction
    • Glickman, B. W. & Radman, M. Escherichia coli mutator mutants deficient in methyl-instructed DNA mismatch correction. Proc. Natl Acad. Sci. USA 77, 1063-1067 (1980).
    • (1980) Proc. Natl Acad. Sci. USA , vol.77 , pp. 1063-1067
    • Glickman, B.W.1    Radman, M.2
  • 30
    • 0030620273 scopus 로고    scopus 로고
    • Evolution of high mutation rates in experimental populations of E. coli
    • Sniegowski, P. D., Gerrish, P. J. & Lenski, R. E. Evolution of high mutation rates in experimental populations of E. coli. Nature 387, 703-705 (1997).
    • (1997) Nature , vol.387 , pp. 703-705
    • Sniegowski, P.D.1    Gerrish, P.J.2    Lenski, R.E.3
  • 31
    • 0007974625 scopus 로고
    • Oxidation of citrate by Escherichia coli
    • Lara, F. J. S. & Stokes, J. L. Oxidation of citrate by Escherichia coli. J. Bacteriol. 63, 415-420 (1952).
    • (1952) J. Bacteriol. , vol.63 , pp. 415-420
    • Lara, F.J.S.1    Stokes, J.L.2
  • 32
    • 0031855687 scopus 로고    scopus 로고
    • The Escherichia coli citrate carrier CitT: A member of a novel eubacterial transporter family related to the 2-oxoglutarate/malate translocator from spinach chloroplasts
    • Pos, K. M., Dimroth, P. & Bott, M. The Escherichia coli citrate carrier CitT: a member of a novel eubacterial transporter family related to the 2-oxoglutarate/malate translocator from spinach chloroplasts. J. Bacteriol. 180, 4160-4165 (1998).
    • (1998) J. Bacteriol. , vol.180 , pp. 4160-4165
    • Pos, K.M.1    Dimroth, P.2    Bott, M.3
  • 33
    • 0026667856 scopus 로고
    • The escherichia coli rna gene encoding RNaseI:sequence and unusual promoter structure
    • Zhu, L. & Deutsher, M. P. The Escherichia coli rna gene encoding RNaseI:sequence and unusual promoter structure. Gene 119, 101-106 (1992).
    • (1992) Gene , vol.119 , pp. 101-106
    • Zhu, L.1    Deutsher, M.P.2
  • 34
    • 0028804968 scopus 로고
    • Regulation of nucleoside diphosphate kinase and an alternative kinase in Escherichia coli: Role of the sspA and rnk genes in nucleoside triphosphate formation
    • Shankar, S., Schlictman, D. & Chakrabarty, A. M. Regulation of nucleoside diphosphate kinase and an alternative kinase in Escherichia coli: role of the sspA and rnk genes in nucleoside triphosphate formation. Mol. Microbiol. 17, 935-943 (1995).
    • (1995) Mol. Microbiol. , vol.17 , pp. 935-943
    • Shankar, S.1    Schlictman, D.2    Chakrabarty, A.M.3
  • 35
    • 20444388986 scopus 로고    scopus 로고
    • An alien promoter capture as a primary step of the evolution of testes-expressed repeats in the Drosophila melanogaster genome
    • Usakin, L. A., Kogan, G. L., Kalmykova, A. I. & Gvozdev, V. A. An alien promoter capture as a primary step of the evolution of testes-expressed repeats in the Drosophila melanogaster genome. Mol. Biol. Evol. 22, 1555-1560 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1555-1560
    • Usakin, L.A.1    Kogan, G.L.2    Kalmykova, A.I.3    Gvozdev, V.A.4
  • 36
    • 0027464696 scopus 로고
    • Tumor suppression in Xiphophorus by an accidentally acquired promoter
    • Adam, D., Dimitrijevic, N. & Schartl, M. Tumor suppression in Xiphophorus by an accidentally acquired promoter. Science 259, 816-819 (1993).
    • (1993) Science , vol.259 , pp. 816-819
    • Adam, D.1    Dimitrijevic, N.2    Schartl, M.3
  • 37
    • 45549100129 scopus 로고    scopus 로고
    • Reconstructing evolution: Gene transfer from plastids to the nucleus
    • Bock, R. & Timmis, J. N. Reconstructing evolution: gene transfer from plastids to the nucleus. Bioessays 30, 556-566 (2008).
    • (2008) Bioessays , vol.30 , pp. 556-566
    • Bock, R.1    Timmis, J.N.2
  • 38
    • 0023334462 scopus 로고
    • Genetic rearrangements and gene amplificationin Escherichia coli: DNA sequencesat the junctures of amplified gene fusions
    • Whoriskey, S. K., Nghiem, V., Leong, P., Masson, J. & Miller, J. H. Genetic rearrangements and gene amplificationin Escherichia coli: DNA sequencesat the junctures of amplified gene fusions. Genes Dev. 1, 227-237 (1987).
    • (1987) Genes Dev. , vol.1 , pp. 227-237
    • Whoriskey, S.K.1    Nghiem, V.2    Leong, P.3    Masson, J.4    Miller, J.H.5
  • 40
    • 0032491390 scopus 로고    scopus 로고
    • Evidence that gene amplification underlies adaptivemutabilityofthe bacterial lacoperon
    • Andersson, D. I., Slechta, E. S. & Roth, J. R. Evidence that gene amplification underlies adaptivemutabilityofthe bacterial lacoperon. Science282, 1133-1135 (1998).
    • (1998) Science , vol.282 , pp. 1133-1135
    • Andersson, D.I.1    Slechta, E.S.2    Roth, J.R.3
  • 41
    • 77955876041 scopus 로고    scopus 로고
    • Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination
    • Reams, A. B., Kofoid, E., Savageau, M. & Roth, J. R. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics 184, 1077-1094 (2010).
    • (2010) Genetics , vol.184 , pp. 1077-1094
    • Reams, A.B.1    Kofoid, E.2    Savageau, M.3    Roth, J.R.4
  • 42
    • 0021943518 scopus 로고
    • Improved M13 phage cloning vectors andhost strains: Nucleotide sequencesoftheM13mpl8 and pUC19vectors
    • Yanisch-Perron, C., Vieira, J. & Messing, J. Improved M13 phage cloning vectors andhost strains: nucleotide sequencesoftheM13mpl8 and pUC19vectors. Gene 33, 103-119 (1985).
    • (1985) Gene , vol.33 , pp. 103-119
    • Yanisch-Perron, C.1    Vieira, J.2    Messing, J.3
  • 43
    • 0027989421 scopus 로고
    • Aerobic-anaerobic gene regulation in Escherichia coli: Control by the ArcAB and Fnr regulons
    • Gunsalus, R. P. & Park, S. J. Aerobic-anaerobic gene regulation in Escherichia coli: control by the ArcAB and Fnr regulons. Res. Microbiol. 145, 437-450 (1994).
    • (1994) Res. Microbiol. , vol.145 , pp. 437-450
    • Gunsalus, R.P.1    Park, S.J.2
  • 44
    • 61449092651 scopus 로고    scopus 로고
    • Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition
    • Nizam, S. A., Zhu, J., Ho, P. Y. & Shimizu, K. Effects of arcA and arcB genes knockout on the metabolism in Escherichia coli under aerobic condition. Biochem. Eng. J. 44, 240-250 (2009).
    • (2009) Biochem. Eng. J. , vol.44 , pp. 240-250
    • Nizam, S.A.1    Zhu, J.2    Ho, P.Y.3    Shimizu, K.4
  • 46
    • 0026279651 scopus 로고
    • Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2, 000 generations
    • Lenski, R. E., Rose, M. R., Simpson, S. C. & Tadler, S. C. Long-term experimental evolution in Escherichia coli. I. Adaptation and divergence during 2, 000 generations. Am. Nat. 138, 1315-1341 (1991).
    • (1991) Am. Nat. , vol.138 , pp. 1315-1341
    • Lenski, R.E.1    Rose, M.R.2    Simpson, S.C.3    Tadler, S.C.4
  • 48
    • 0000116740 scopus 로고
    • A method for deducing branching sequences in phylogeny
    • Camin, J. H. & Sokal, R. R. A method for deducing branching sequences in phylogeny. Evolution 19, 311-326 (1965).
    • (1965) Evolution , vol.19 , pp. 311-326
    • Camin, J.H.1    Sokal, R.R.2
  • 49
    • 0041530033 scopus 로고    scopus 로고
    • Genomic profiling of ironresponsive genes in Salmonella enterica serovar Typhimuriumby high-throughput screening of a random promoter library
    • Bjarnason, J., Southward, C. M. & Surette, M. G. Genomic profiling of ironresponsive genes in Salmonella enterica serovar Typhimuriumby high-throughput screening of a random promoter library. J. Bacteriol. 185, 4973-4982 (2003).
    • (2003) J. Bacteriol. , vol.185 , pp. 4973-4982
    • Bjarnason, J.1    Southward, C.M.2    Surette, M.G.3
  • 50
    • 33746415885 scopus 로고    scopus 로고
    • A comprehensive library of fluorescent transcriptional reporters for escherichia coli
    • Zaslaver, A. et al. A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nature Methods 3, 623-628 (2006).
    • (2006) Nature Methods , vol.3 , pp. 623-628
    • Zaslaver, A.1
  • 51
    • 0037633360 scopus 로고    scopus 로고
    • Gene replacement without selection: Regulated suppression of amber mutations in Escherichia coli
    • Herring, C. D., Glasner, J. D. & Blattner, F. R. Gene replacement without selection: regulated suppression of amber mutations in Escherichia coli. Gene 311, 153-163 (2003).
    • (2003) Gene , vol.311 , pp. 153-163
    • Herring, C.D.1    Glasner, J.D.2    Blattner, F.R.3
  • 52
    • 0003475715 scopus 로고
    • Hydrogen sulfide production and citrate utilization in the differentiating of enteric pathogens and coliform bacteria
    • Christensen, W. B. Hydrogen sulfide production and citrate utilization in the differentiating of enteric pathogens and coliform bacteria. Res. Bull. Weld County Health Dept. Greeley Colo. 1, 3-16 (1949).
    • (1949) Res. Bull. Weld County Health Dept. Greeley Colo. , vol.1 , pp. 3-16
    • Christensen, W.B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.