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Volumn 8, Issue 1, 2012, Pages

A genome-wide analysis of promoter-mediated phenotypic noise in Escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA;

EID: 84857480997     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1002443     Document Type: Article
Times cited : (152)

References (71)
  • 4
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser JM, O'shea EK, (2004) Control of stochasticity in eukaryotic gene expression. Science 304: 1811-1814.
    • (2004) Science , vol.304 , pp. 1811-1814
    • Raser, J.M.1    O'shea, E.K.2
  • 5
    • 50049132233 scopus 로고    scopus 로고
    • Self-destructive cooperation mediated by phenotypic noise
    • Ackermann M, Stecher B, Freed NE, Songhet P, Hardt WD, et al. (2008) Self-destructive cooperation mediated by phenotypic noise. Nature 454: 987-990.
    • (2008) Nature , vol.454 , pp. 987-990
    • Ackermann, M.1    Stecher, B.2    Freed, N.E.3    Songhet, P.4    Hardt, W.D.5
  • 6
    • 58149147307 scopus 로고    scopus 로고
    • A Simple Screen to Identify Promoters Conferring High Levels of Phenotypic Noise
    • Freed NE, Silander OK, Stecher B, Bohm A, Hardt WD, et al. (2008) A Simple Screen to Identify Promoters Conferring High Levels of Phenotypic Noise. Plos Genetics 4: e1000307.
    • (2008) Plos Genetics , vol.4
    • Freed, N.E.1    Silander, O.K.2    Stecher, B.3    Bohm, A.4    Hardt, W.D.5
  • 8
    • 0037313182 scopus 로고    scopus 로고
    • Evolution of gene expression in the Drosophila melanogaster subgroup
    • Rifkin SA, Kim J, White KP, (2003) Evolution of gene expression in the Drosophila melanogaster subgroup. Nature Genetics 33: 138-144.
    • (2003) Nature Genetics , vol.33 , pp. 138-144
    • Rifkin, S.A.1    Kim, J.2    White, K.P.3
  • 9
    • 13244251285 scopus 로고    scopus 로고
    • Rates of divergence in gene expression profiles of primates, mice, and flies: Stabilizing selection and variability among functional categories
    • Lemos B, Meiklejohn CD, Caceres M, Hartl DL, (2005) Rates of divergence in gene expression profiles of primates, mice, and flies: Stabilizing selection and variability among functional categories. Evolution 59: 126-137.
    • (2005) Evolution , vol.59 , pp. 126-137
    • Lemos, B.1    Meiklejohn, C.D.2    Caceres, M.3    Hartl, D.L.4
  • 12
    • 18144405733 scopus 로고    scopus 로고
    • The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans
    • Denver DR, Morris K, Streelman JT, Kim SK, Lynch M, et al. (2005) The transcriptional consequences of mutation and natural selection in Caenorhabditis elegans. Nature Genetics 37: 544-548.
    • (2005) Nature Genetics , vol.37 , pp. 544-548
    • Denver, D.R.1    Morris, K.2    Streelman, J.T.3    Kim, S.K.4    Lynch, M.5
  • 13
    • 18844368812 scopus 로고    scopus 로고
    • Bacterial persistence: A model of survival in changing environments
    • Kussell E, Kishony R, Balaban NQ, Leibler S, (2005) Bacterial persistence: A model of survival in changing environments. Genetics 169: 1807-1814.
    • (2005) Genetics , vol.169 , pp. 1807-1814
    • Kussell, E.1    Kishony, R.2    Balaban, N.Q.3    Leibler, S.4
  • 14
    • 25444489027 scopus 로고    scopus 로고
    • Phenotypic diversity, population growth, and information in fluctuating environments
    • Kussell E, Leibler S, (2005) Phenotypic diversity, population growth, and information in fluctuating environments. Science 309: 2075-2078.
    • (2005) Science , vol.309 , pp. 2075-2078
    • Kussell, E.1    Leibler, S.2
  • 18
    • 33846076717 scopus 로고    scopus 로고
    • Phenotypic heterogeneity can enhance rare-cell survival in 'stress-sensitive' yeast populations
    • Bishop AL, Rab FA, Sumner ER, Avery SV, (2007) Phenotypic heterogeneity can enhance rare-cell survival in 'stress-sensitive' yeast populations. Molecular Microbiology 63: 507-520.
    • (2007) Molecular Microbiology , vol.63 , pp. 507-520
    • Bishop, A.L.1    Rab, F.A.2    Sumner, E.R.3    Avery, S.V.4
  • 19
    • 41349119880 scopus 로고    scopus 로고
    • Stochastic switching as a survival strategy in fluctuating environments
    • Acar M, Mettetal JT, van Oudenaarden A, (2008) Stochastic switching as a survival strategy in fluctuating environments. Nature Genetics 40: 471-475.
    • (2008) Nature Genetics , vol.40 , pp. 471-475
    • Acar, M.1    Mettetal, J.T.2    van Oudenaarden, A.3
  • 23
    • 77955102352 scopus 로고    scopus 로고
    • Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells
    • Taniguchi Y, Choi PJ, Li G-W, Chen H, Babu M, et al. (2010) Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells. Science 329: 533-538.
    • (2010) Science , vol.329 , pp. 533-538
    • Taniguchi, Y.1    Choi, P.J.2    Li, G.-W.3    Chen, H.4    Babu, M.5
  • 24
    • 33745220278 scopus 로고    scopus 로고
    • Single-cell proteomic analysis of S-cerevisiae reveals the architecture of biological noise
    • Newman JRS, Ghaemmaghami S, Ihmels J, Breslow DK, Noble M, et al. (2006) Single-cell proteomic analysis of S-cerevisiae reveals the architecture of biological noise. Nature 441: 840-846.
    • (2006) Nature , vol.441 , pp. 840-846
    • Newman, J.R.S.1    Ghaemmaghami, S.2    Ihmels, J.3    Breslow, D.K.4    Noble, M.5
  • 25
    • 42949131308 scopus 로고    scopus 로고
    • Selection to minimise noise in living systems and its implications for the evolution of gene expression
    • Lehner B, (2008) Selection to minimise noise in living systems and its implications for the evolution of gene expression. Molecular Systems Biology 4: 170.
    • (2008) Molecular Systems Biology , vol.4 , pp. 170
    • Lehner, B.1
  • 26
    • 78649708844 scopus 로고    scopus 로고
    • Conflict between Noise and Plasticity in Yeast
    • Lehner B, (2010) Conflict between Noise and Plasticity in Yeast. Plos Genetics 6: e1001185.
    • (2010) Plos Genetics , vol.6
    • Lehner, B.1
  • 27
    • 33746415885 scopus 로고    scopus 로고
    • A comprehensive library of fluorescent transcriptional reporters for Escherichia coli
    • Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nature Methods 3: 623-628.
    • (2006) Nature Methods , vol.3 , pp. 623-628
    • Zaslaver, A.1    Bren, A.2    Ronen, M.3    Itzkovitz, S.4    Kikoin, I.5
  • 28
    • 0033559974 scopus 로고    scopus 로고
    • Distribution of minichromosomes in individual Escherichia coli cells: implications for replication control
    • Lobner-Olesen A, (1999) Distribution of minichromosomes in individual Escherichia coli cells: implications for replication control. Embo Journal 18: 1712-1721.
    • (1999) Embo Journal , vol.18 , pp. 1712-1721
    • Lobner-Olesen, A.1
  • 29
    • 41549090370 scopus 로고    scopus 로고
    • New pSC101-derivative cloning vectors with elevated copy numbers
    • Peterson J, Phillips GJ, (2008) New pSC101-derivative cloning vectors with elevated copy numbers. Plasmid 59: 193-201.
    • (2008) Plasmid , vol.59 , pp. 193-201
    • Peterson, J.1    Phillips, G.J.2
  • 30
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • 946-U112
    • Salis HM, Mirsky EA, Voigt CA, (2009) Automated design of synthetic ribosome binding sites to control protein expression. Nature Biotechnology 27: 946-U112.
    • (2009) Nature Biotechnology , vol.27
    • Salis, H.M.1    Mirsky, E.A.2    Voigt, C.A.3
  • 31
    • 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
  • 33
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: Origins, consequences, and control
    • Raser JM, O'shea EK, (2005) Noise in gene expression: Origins, consequences, and control. Science 309: 2010-2013.
    • (2005) Science , vol.309 , pp. 2010-2013
    • Raser, J.M.1    O'shea, E.K.2
  • 36
    • 79955966186 scopus 로고    scopus 로고
    • Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics
    • Bollenbach T, Kishony R, (2011) Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics. Molecular Cell 42: 413-425.
    • (2011) Molecular Cell , vol.42 , pp. 413-425
    • Bollenbach, T.1    Kishony, R.2
  • 37
    • 34547913808 scopus 로고    scopus 로고
    • Construction of consecutive deletions of the Escherichia coli chromosome
    • Kato JI, Hashimoto M, (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Molecular Systems Biology 3: 132.
    • (2007) Molecular Systems Biology , vol.3 , pp. 132
    • Kato, J.I.1    Hashimoto, M.2
  • 38
    • 38549140094 scopus 로고    scopus 로고
    • RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation
    • Gama-Castro S, Jimenez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Penaloza-Spinola MI, et al. (2008) RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research 36: D120-D124.
    • (2008) Nucleic Acids Research , vol.36
    • Gama-Castro, S.1    Jimenez-Jacinto, V.2    Peralta-Gil, M.3    Santos-Zavaleta, A.4    Penaloza-Spinola, M.I.5
  • 39
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionarily conserved than are nonessential genes in bacteria
    • Jordan IK, Rogozin IB, Wolf YI, Koonin EV, (2002) Essential genes are more evolutionarily conserved than are nonessential genes in bacteria. Genome Research 12: 962-968.
    • (2002) Genome Research , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 40
    • 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 Research 13: 2229-2235.
    • (2003) Genome Research , vol.13 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 41
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells
    • Arkin A, Ross J, McAdams HH, (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149: 1633-1648.
    • (1998) Genetics , vol.149 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 42
    • 10644230266 scopus 로고    scopus 로고
    • A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land
    • Battistuzzi FU, Feijao A, Hedges SB, (2004) A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land. Bmc Evolutionary Biology 4: 44.
    • (2004) Bmc Evolutionary Biology , vol.4 , pp. 44
    • Battistuzzi, F.U.1    Feijao, A.2    Hedges, S.B.3
  • 43
    • 30344471824 scopus 로고    scopus 로고
    • Do different surrogate methods detect lateral genetic transfer events of different relative ages?
    • Ragan MA, Harlow TJ, Beiko RG, (2006) Do different surrogate methods detect lateral genetic transfer events of different relative ages? Trends in Microbiology 14: 4-8.
    • (2006) Trends in Microbiology , vol.14 , pp. 4-8
    • Ragan, M.A.1    Harlow, T.J.2    Beiko, R.G.3
  • 44
    • 59249089471 scopus 로고    scopus 로고
    • Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths
    • Touchon M, Hoede C, Tenaillon O, Barbe Vr, Baeriswyl S, et al. (2009) Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths. Plos Genetics 5: e1000344.
    • (2009) Plos Genetics , vol.5
    • Touchon, M.1    Hoede, C.2    Tenaillon, O.3    Barbe, V.R.4    Baeriswyl, S.5
  • 45
    • 3042569657 scopus 로고    scopus 로고
    • Bacterial Genomes as new gene homes: The genealogy of ORFans in E-coli
    • Daubin V, Ochman H, (2004) Bacterial Genomes as new gene homes: The genealogy of ORFans in E-coli. Genome Research 14: 1036-1042.
    • (2004) Genome Research , vol.14 , pp. 1036-1042
    • Daubin, V.1    Ochman, H.2
  • 46
    • 84857484983 scopus 로고    scopus 로고
    • Oklahoma University E. Coli Gene Expression Database
    • Conway T, (2009) Oklahoma University E. Coli Gene Expression Database. http://genexpdb.ou.edu/main/.
    • (2009)
    • Conway, T.1
  • 47
    • 0037057374 scopus 로고    scopus 로고
    • Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering
    • research0059-research0059.22
    • Gasch AP, Eisen MB, (2002) Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biology 3: research0059-research0059.22.
    • (2002) Genome Biology , vol.3
    • Gasch, A.P.1    Eisen, M.B.2
  • 48
    • 0034570532 scopus 로고    scopus 로고
    • MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products
    • Serres MH, Riley M, (2000) MultiFun, a multifunctional classification scheme for Escherichia coli K-12 gene products. Microb Comp Genomics 5: 205-222.
    • (2000) Microb Comp Genomics , vol.5 , pp. 205-222
    • Serres, M.H.1    Riley, M.2
  • 49
    • 66249146869 scopus 로고    scopus 로고
    • Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli
    • Kovacs K, Hurst LD, Papp B, (2009) Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli. Plos Biology 7: e1000115.
    • (2009) Plos Biology , vol.7
    • Kovacs, K.1    Hurst, L.D.2    Papp, B.3
  • 51
    • 2942555282 scopus 로고    scopus 로고
    • Stochastic gene expression in fluctuating environments
    • Thattai M, van Oudenaarden A, (2004) Stochastic gene expression in fluctuating environments. Genetics 167: 523-530.
    • (2004) Genetics , vol.167 , pp. 523-530
    • Thattai, M.1    van Oudenaarden, A.2
  • 52
    • 0037104993 scopus 로고    scopus 로고
    • Stress and the single cell: Intrapopulation diversity is a mechanism to ensure survival upon exposure to stress
    • Booth IR, (2002) Stress and the single cell: Intrapopulation diversity is a mechanism to ensure survival upon exposure to stress. International Journal of Food Microbiology 78: 19-30.
    • (2002) International Journal of Food Microbiology , vol.78 , pp. 19-30
    • Booth, I.R.1
  • 53
    • 0036178356 scopus 로고    scopus 로고
    • Phenotypic heterogeneity: differential stress resistance among individual cells of the yeast Saccharomyces cerevisiae
    • Sumner ER, Avery SV, (2002) Phenotypic heterogeneity: differential stress resistance among individual cells of the yeast Saccharomyces cerevisiae. Microbiology-Sgm 148: 345-351.
    • (2002) Microbiology-Sgm , vol.148 , pp. 345-351
    • Sumner, E.R.1    Avery, S.V.2
  • 54
    • 84857492903 scopus 로고    scopus 로고
    • Genome-wide predicitions: translation initiation rates
    • Salis HM, (2010) Genome-wide predicitions: translation initiation rates. https://salis.psu.edu/GenomeWidePredictions.shtml.
    • (2010)
    • Salis, H.M.1
  • 57
    • 0034981558 scopus 로고    scopus 로고
    • Noise in a minimal regulatory network: plasmid copy number control
    • Paulsson J, Ehrenberg M, (2001) Noise in a minimal regulatory network: plasmid copy number control. Quarterly Reviews of Biophysics 34: 1-59.
    • (2001) Quarterly Reviews of Biophysics , vol.34 , pp. 1-59
    • Paulsson, J.1    Ehrenberg, M.2
  • 59
    • 0037078982 scopus 로고    scopus 로고
    • Control, exploitation and tolerance of intracellular noise
    • Rao CV, Wolf DM, Arkin AP, (2002) Control, exploitation and tolerance of intracellular noise. Nature 420: 231-237.
    • (2002) Nature , vol.420 , pp. 231-237
    • Rao, C.V.1    Wolf, D.M.2    Arkin, A.P.3
  • 62
    • 34547519199 scopus 로고    scopus 로고
    • Evolution of chromosome organization driven by selection for reduced gene expression noise
    • Batada NN, Hurst LD, (2007) Evolution of chromosome organization driven by selection for reduced gene expression noise. Nature Genetics 39: 945-949.
    • (2007) Nature Genetics , vol.39 , pp. 945-949
    • Batada, N.N.1    Hurst, L.D.2
  • 63
    • 33745583768 scopus 로고    scopus 로고
    • A genetic signature of interspecies variations in gene expression
    • Tirosh I, Weinberger A, Carmi M, Barkai N, (2006) A genetic signature of interspecies variations in gene expression. Nature Genetics 38: 830-834.
    • (2006) Nature Genetics , vol.38 , pp. 830-834
    • Tirosh, I.1    Weinberger, A.2    Carmi, M.3    Barkai, N.4
  • 65
    • 33744988346 scopus 로고    scopus 로고
    • Fast, easy and efficient: site-specific insertion of transgenes into Enterobacterial chromosomes using Tn7 without need for selection of the insertion event
    • McKenzie GJ, Craig NL, (2006) Fast, easy and efficient: site-specific insertion of transgenes into Enterobacterial chromosomes using Tn7 without need for selection of the insertion event. Bmc Microbiology 6.
    • (2006) Bmc Microbiology , vol.6
    • McKenzie, G.J.1    Craig, N.L.2
  • 66
    • 35748932852 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Development Core Team
    • R Development Core Team (2007) R: A Language and Environment for Statistical Computing.
    • (2007)
  • 70
    • 77049084977 scopus 로고    scopus 로고
    • The constancy of gene conservation across divergent bacterial orders
    • Silander OK, Ackermann M, (2009) The constancy of gene conservation across divergent bacterial orders. BMC Research Notes 2: 2.
    • (2009) BMC Research Notes , vol.2 , pp. 2
    • Silander, O.K.1    Ackermann, M.2


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