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Volumn 8, Issue 8, 2012, Pages

Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEX NETWORKS; NETWORK ARCHITECTURE; NOISE ABATEMENT; PROTEINS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

EID: 84866055481     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002672     Document Type: Article
Times cited : (18)

References (67)
  • 1
    • 54249116230 scopus 로고
    • Genetic regulatory mechanisms in the synthesis of proteins
    • Jacob F, Monod J, (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318-356.
    • (1961) J Mol Biol , vol.3 , pp. 318-356
    • Jacob, F.1    Monod, J.2
  • 3
    • 58449118337 scopus 로고    scopus 로고
    • The organization of the bacterial genome
    • Rocha EP, (2008) The organization of the bacterial genome. Annu Rev Genet 42: 211-233.
    • (2008) Annu Rev Genet , vol.42 , pp. 211-233
    • Rocha, E.P.1
  • 4
    • 22444441190 scopus 로고    scopus 로고
    • Operon formation is driven by co-regulation and not by horizontal gene transfer
    • Price MN, Huang KH, Arkin AP, Alm EJ, (2005) Operon formation is driven by co-regulation and not by horizontal gene transfer. Genome Res 15: 809-819.
    • (2005) Genome Res , vol.15 , pp. 809-819
    • Price, M.N.1    Huang, K.H.2    Arkin, A.P.3    Alm, E.J.4
  • 6
    • 33748878811 scopus 로고    scopus 로고
    • A quantitative study of the benefits of co-regulation using the spoIIA operon as an example
    • Iber D, (2006) A quantitative study of the benefits of co-regulation using the spoIIA operon as an example. Mol Syst Biol 2: 43.
    • (2006) Mol Syst Biol , vol.2 , pp. 43
    • Iber, D.1
  • 7
    • 77649220067 scopus 로고    scopus 로고
    • Adaptable functionality of transcriptional feedback in bacterial two-component systems
    • Ray JCJ, Igoshin OA, (2010) Adaptable functionality of transcriptional feedback in bacterial two-component systems. PLoS Comput Biol 6: e1000676.
    • (2010) PLoS Comput Biol , vol.6
    • Ray, J.C.J.1    Igoshin, O.A.2
  • 8
    • 79960614137 scopus 로고    scopus 로고
    • Fundamental relationship between operon organization and gene expression
    • Lim HN, Lee Y, Hussein R, (2011) Fundamental relationship between operon organization and gene expression. Proc Natl Acad Sci U S A 108: 10626-10631.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 10626-10631
    • Lim, H.N.1    Lee, Y.2    Hussein, R.3
  • 9
    • 33745616349 scopus 로고    scopus 로고
    • Analysis of gene expression in operons of Streptomyces coelicolor
    • Laing E, Mersinias V, Smith CP, Hubbard SJ, (2006) Analysis of gene expression in operons of Streptomyces coelicolor. Genome Biol 7: R46.
    • (2006) Genome Biol , vol.7
    • Laing, E.1    Mersinias, V.2    Smith, C.P.3    Hubbard, S.J.4
  • 10
    • 0029847554 scopus 로고    scopus 로고
    • Selfish operons: horizontal transfer may drive the evolution of gene clusters
    • Lawrence JG, Roth JR, (1996) Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143: 1843-1860.
    • (1996) Genetics , vol.143 , pp. 1843-1860
    • Lawrence, J.G.1    Roth, J.R.2
  • 11
    • 0030809629 scopus 로고    scopus 로고
    • Selfish operons and speciation by gene transfer
    • Lawrence JG, (1997) Selfish operons and speciation by gene transfer. Trends Microbiol 5: 355-359.
    • (1997) Trends Microbiol , vol.5 , pp. 355-359
    • Lawrence, J.G.1
  • 12
    • 17144459133 scopus 로고    scopus 로고
    • Evidence against the selfish operon theory
    • Pál C, Hurst LD, (2004) Evidence against the selfish operon theory. Trends Genet 20: 232-234.
    • (2004) Trends Genet , vol.20 , pp. 232-234
    • Pál, C.1    Hurst, L.D.2
  • 13
    • 0032169271 scopus 로고    scopus 로고
    • Conservation of gene order: a fingerprint of proteins that physically interact
    • Dandekar T, Snel B, Huynen M, Bork P, (1998) Conservation of gene order: a fingerprint of proteins that physically interact. Trends Biochem Sci 23: 324-328.
    • (1998) Trends Biochem Sci , vol.23 , pp. 324-328
    • Dandekar, T.1    Snel, B.2    Huynen, M.3    Bork, P.4
  • 14
    • 17444387728 scopus 로고    scopus 로고
    • The Bacillus subtilis SIN Operon: An Evolvable Network Motif
    • Voigt CA, Wolf DM, Arkin AP, (2005) The Bacillus subtilis SIN Operon: An Evolvable Network Motif. Genetics 169: 1187-1202.
    • (2005) Genetics , vol.169 , pp. 1187-1202
    • Voigt, C.A.1    Wolf, D.M.2    Arkin, A.P.3
  • 15
    • 8544264562 scopus 로고    scopus 로고
    • Efficient attenuation of stochasticity in gene expression through post-transcriptional control
    • Swain PS, (2004) Efficient attenuation of stochasticity in gene expression through post-transcriptional control. J Mol Biol 344: 965-976.
    • (2004) J Mol Biol , vol.344 , pp. 965-976
    • Swain, P.S.1
  • 16
    • 77955155615 scopus 로고    scopus 로고
    • Noise and robustness in prokaryotic regulatory networks
    • Silva-Rocha R, de Lorenzo V, (2010) Noise and robustness in prokaryotic regulatory networks. Annu Rev Microbiol 64: 257-275.
    • (2010) Annu Rev Microbiol , vol.64 , pp. 257-275
    • Silva-Rocha, R.1    de Lorenzo, V.2
  • 17
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanisms in gene expression
    • McAdams HH, Arkin A, (1997) Stochastic mechanisms in gene expression. Proc Natl Acad Sci USA 94: 814-819.
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 814-819
    • McAdams, H.H.1    Arkin, A.2
  • 18
    • 0842285841 scopus 로고    scopus 로고
    • Summing up the noise in gene networks
    • Paulsson J, (2004) Summing up the noise in gene networks. Nature 427: 415-418.
    • (2004) Nature , vol.427 , pp. 415-418
    • Paulsson, J.1
  • 19
    • 0017833657 scopus 로고
    • A model for the statistical fluctuations of protein numbers in a microbial population
    • Berg OG, (1978) A model for the statistical fluctuations of protein numbers in a microbial population. J Theor Biol 71: 587-603.
    • (1978) J Theor Biol , vol.71 , pp. 587-603
    • Berg, O.G.1
  • 20
    • 28944434119 scopus 로고    scopus 로고
    • Real-time kinetics of gene activity in individual bacteria
    • Golding I, Paulsson J, Zawilski SM, Cox EC, (2005) Real-time kinetics of gene activity in individual bacteria. Cell 123: 1025-1036.
    • (2005) Cell , vol.123 , pp. 1025-1036
    • Golding, I.1    Paulsson, J.2    Zawilski, S.M.3    Cox, E.C.4
  • 21
    • 48249138167 scopus 로고    scopus 로고
    • The generation of promoter-mediated transcriptional noise in bacteria
    • Mitarai N, Dodd IB, Crooks MT, Sneppen K, (2008) The generation of promoter-mediated transcriptional noise in bacteria. PLoS Comput Biol 4: e1000109.
    • (2008) PLoS Comput Biol , vol.4
    • Mitarai, N.1    Dodd, I.B.2    Crooks, M.T.3    Sneppen, K.4
  • 22
    • 0036790975 scopus 로고    scopus 로고
    • Intrinsic and extrinsic contributions to stochasticity in gene expression
    • Swain PS, Elowitz MB, Siggia ED, (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A 99: 12795-12800.
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 12795-12800
    • Swain, P.S.1    Elowitz, M.B.2    Siggia, E.D.3
  • 23
    • 66249146869 scopus 로고    scopus 로고
    • Stochasticity in protein levels drives colinearity of gene order in metabolic operons of Escherichia coli
    • Kovács K, Hurst LD, Papp B, (2009) Stochasticity in protein levels drives colinearity of gene order in metabolic operons of Escherichia coli. PLoS Biol 7: e1000115.
    • (2009) PLoS Biol , vol.7
    • Kovács, K.1    Hurst, L.D.2    Papp, B.3
  • 24
    • 69349099313 scopus 로고    scopus 로고
    • Role of translational coupling in robustness of bacterial chemotaxis pathway
    • Løvdok L, Bentele K, Vladimirov N, Müller A, Pop FS, et al. (2009) Role of translational coupling in robustness of bacterial chemotaxis pathway. PLoS Biol 7: e1000171.
    • (2009) PLoS Biol , vol.7
    • Løvdok, L.1    Bentele, K.2    Vladimirov, N.3    Müller, A.4    Pop, F.S.5
  • 25
    • 79952125361 scopus 로고    scopus 로고
    • Economy of operon formation: cotranscription minimizes shortfall in protein complexes
    • Sneppen K, Pedersen S, Krishna S, Dodd I, Semsey S, (2010) Economy of operon formation: cotranscription minimizes shortfall in protein complexes. MBio 1: e00177-00110.
    • (2010) MBio , vol.1
    • Sneppen, K.1    Pedersen, S.2    Krishna, S.3    Dodd, I.4    Semsey, S.5
  • 26
    • 0001424903 scopus 로고
    • An amplified sensitivity arising from covalent modification in biological systems
    • Goldbeter A, Koshland DE, (1981) An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A 78: 6840-6844.
    • (1981) Proc Natl Acad Sci U S A , vol.78 , pp. 6840-6844
    • Goldbeter, A.1    Koshland, D.E.2
  • 27
    • 0031855362 scopus 로고    scopus 로고
    • Development of competence in Streptococcus pneumoniae: pheromone autoinduction and control of quorum sensing by the oligopeptide permease
    • Alloing G, Martin B, Granadel C, Claverys J-P, (1998) Development of competence in Streptococcus pneumoniae: pheromone autoinduction and control of quorum sensing by the oligopeptide permease. Mol Microbiol 29: 75-83.
    • (1998) Mol Microbiol , vol.29 , pp. 75-83
    • Alloing, G.1    Martin, B.2    Granadel, C.3    Claverys, J.-P.4
  • 31
    • 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, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-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 Res 36: D120-D124.
    • (2008) Nucleic Acids Res , vol.36
    • Gama-Castro, S.1    Jiménez-Jacinto, V.2    Peralta-Gil, M.3    Santos-Zavaleta, A.4    Peñaloza-Spinola, M.I.5
  • 32
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT, (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340-2361.
    • (1977) J Phys Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 33
    • 22144443131 scopus 로고    scopus 로고
    • Nonlinear protein degradation and the function of genetic circuits
    • Buchler NE, Gerland U, Hwa T, (2005) Nonlinear protein degradation and the function of genetic circuits. Proc Natl Acad Sci U S A 102: 9559-9564.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 9559-9564
    • Buchler, N.E.1    Gerland, U.2    Hwa, T.3
  • 34
    • 56949098506 scopus 로고    scopus 로고
    • Molecular titration and ultrasensitivity in regulatory networks
    • Buchler NE, Louis M, (2008) Molecular titration and ultrasensitivity in regulatory networks. J Mol Biol 384: 1106-1119.
    • (2008) J Mol Biol , vol.384 , pp. 1106-1119
    • Buchler, N.E.1    Louis, M.2
  • 36
    • 0029843919 scopus 로고    scopus 로고
    • Inducer exclusion and the regulation of sugar transport
    • Saier MH, Crasnier M, (1996) Inducer exclusion and the regulation of sugar transport. Res Microbiol 147: 482-489.
    • (1996) Res Microbiol , vol.147 , pp. 482-489
    • Saier, M.H.1    Crasnier, M.2
  • 38
    • 84861204284 scopus 로고    scopus 로고
    • Cost-benefit tradeoffs in engineered lac operons
    • Eames M, Kortemme T, (2012) Cost-benefit tradeoffs in engineered lac operons. Science 336: 911-915.
    • (2012) Science , vol.336 , pp. 911-915
    • Eames, M.1    Kortemme, T.2
  • 40
    • 13444283630 scopus 로고    scopus 로고
    • Interaction network containing conserved and essential protein complexes in Escherichia coli
    • Butland G, Peregrín-Alvarez JM, Li J, Yang W, Yang X, et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-537.
    • (2005) Nature , vol.433 , pp. 531-537
    • Butland, G.1    Peregrín-Alvarez, J.M.2    Li, J.3    Yang, W.4    Yang, X.5
  • 43
    • 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
  • 44
    • 80054756690 scopus 로고    scopus 로고
    • Non-transcriptional regulatory processes shape transcriptional network dynamics
    • Ray JCJ, Tabor JJ, Igoshin OA, (2011) Non-transcriptional regulatory processes shape transcriptional network dynamics. Nat Rev Microbiol 9: 817-828.
    • (2011) Nat Rev Microbiol , vol.9 , pp. 817-828
    • Ray, J.C.J.1    Tabor, J.J.2    Igoshin, O.A.3
  • 45
    • 68049100110 scopus 로고    scopus 로고
    • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    • Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, et al. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat Chem Biol 5: 593-599.
    • (2009) Nat Chem Biol , vol.5 , pp. 593-599
    • Bennett, B.D.1    Kimball, E.H.2    Gao, M.3    Osterhout, R.4    van Dien, S.J.5
  • 47
    • 34547177356 scopus 로고    scopus 로고
    • Stochastic fluctuations in metabolic pathways
    • Levine E, Hwa T, (2007) Stochastic fluctuations in metabolic pathways. Proc Natl Acad Sci U S A 104: 9224-9229.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 9224-9229
    • Levine, E.1    Hwa, T.2
  • 49
    • 34347365309 scopus 로고    scopus 로고
    • The effect of stochasticity on the lac operon: an evolutionary perspective
    • van Hoek M, Hogeweg P, (2007) The effect of stochasticity on the lac operon: an evolutionary perspective. PLoS Comput Biol 3: e111.
    • (2007) PLoS Comput Biol , vol.3
    • van Hoek, M.1    Hogeweg, P.2
  • 50
    • 18844434690 scopus 로고    scopus 로고
    • The origin and evolution of operons: the piecewise building of the proteobacterial histidine operon
    • Fani R, Brilli M, Liò P, (2005) The origin and evolution of operons: the piecewise building of the proteobacterial histidine operon. J Mol Evol 60: 378-390.
    • (2005) J Mol Evol , vol.60 , pp. 378-390
    • Fani, R.1    Brilli, M.2    Liò, P.3
  • 52
    • 34248683237 scopus 로고    scopus 로고
    • Distinctive topologies of partner-switching signaling networks correlate with their physiological roles
    • Igoshin OA, Brody MS, Price CW, Savageau MA, (2007) Distinctive topologies of partner-switching signaling networks correlate with their physiological roles. J Mol Biol 369: 1333-1352.
    • (2007) J Mol Biol , vol.369 , pp. 1333-1352
    • Igoshin, O.A.1    Brody, M.S.2    Price, C.W.3    Savageau, M.A.4
  • 54
    • 80052643394 scopus 로고    scopus 로고
    • Chromosome organization by a nucleoid-associated protein in live bacteria
    • Wang W, Li G-W, Chen C, Xie XS, Zhuang X, (2011) Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333: 1445-1449.
    • (2011) Science , vol.333 , pp. 1445-1449
    • Wang, W.1    Li, G.-W.2    Chen, C.3    Xie, X.S.4    Zhuang, X.5
  • 55
    • 42649086146 scopus 로고    scopus 로고
    • Chance and necessity in chromosomal gene distributions
    • Hermsen R, Rein ten Wolde P, Teichmann S, (2008) Chance and necessity in chromosomal gene distributions. Trends Genet 24: 216-219.
    • (2008) Trends Genet , vol.24 , pp. 216-219
    • Hermsen, R.1    Rein ten Wolde, P.2    Teichmann, S.3
  • 56
    • 0000640710 scopus 로고    scopus 로고
    • Modulation of chemical composition and other parameters of the cell by growth rate
    • Neidhart FC, III RC, Ingraham JL, Lin ECC, Low KB et al., editors. 2nd edition. Washington: ASM Press
    • Bremer H, Dennis PP (1996) Modulation of chemical composition and other parameters of the cell by growth rate. In: Neidhart FC, III RC, Ingraham JL, Lin ECC, Low KB et al., editors. Escherichia coli and Salmonella: Cellular and Molecular Biology. 2nd edition. Washington: ASM Press.
    • (1996) Escherichia coli and Salmonella: Cellular and Molecular Biology
    • Bremer, H.1    Dennis, P.P.2
  • 57
    • 0020491327 scopus 로고
    • Codon usage in bacteria: correlation with gene expressivity
    • Gouy M, Gautier C, (1982) Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 10: 7055-7074.
    • (1982) Nucleic Acids Res , vol.10 , pp. 7055-7074
    • Gouy, M.1    Gautier, C.2
  • 58
    • 0035546157 scopus 로고    scopus 로고
    • Gene expression and molecular evolution
    • Akashi H, (2001) Gene expression and molecular evolution. Curr Opin Genet Dev 11: 660-666.
    • (2001) Curr Opin Genet Dev , vol.11 , pp. 660-666
    • Akashi, H.1
  • 59
    • 0346095291 scopus 로고    scopus 로고
    • Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae
    • Ihmels J, Levy R, Barkai N, (2004) Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae. Nat Biotechnol 22: 86-92.
    • (2004) Nat Biotechnol , vol.22 , pp. 86-92
    • Ihmels, J.1    Levy, R.2    Barkai, N.3
  • 60
    • 80054841161 scopus 로고    scopus 로고
    • Information transduction capacity of noisy biochemical signaling networks
    • Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A, (2011) Information transduction capacity of noisy biochemical signaling networks. Science 334: 354-358.
    • (2011) Science , vol.334 , pp. 354-358
    • Cheong, R.1    Rhee, A.2    Wang, C.J.3    Nemenman, I.4    Levchenko, A.5
  • 61
    • 25144450143 scopus 로고    scopus 로고
    • Contributions of low molecule number and chromosomal positioning to stochastic gene expression
    • Becskei A, Kaufmann BB, van Oudenaarden A, (2005) Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet 37: 937-944.
    • (2005) Nat Genet , vol.37 , pp. 937-944
    • Becskei, A.1    Kaufmann, B.B.2    van Oudenaarden, A.3
  • 63
    • 79960084618 scopus 로고    scopus 로고
    • Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise
    • Wang G-Z, Lercher MJ, Hurst LD, (2011) Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise. Genome Biol Evol 3: 320-331.
    • (2011) Genome Biol Evol , vol.3 , pp. 320-331
    • Wang, G.-Z.1    Lercher, M.J.2    Hurst, L.D.3
  • 64
    • 34249858233 scopus 로고    scopus 로고
    • Identifying clusters of functionally related genes in genomes
    • Yi G, Sze S-H, Thon MR, (2007) Identifying clusters of functionally related genes in genomes. Bioinformatics 23: 1053-1060.
    • (2007) Bioinformatics , vol.23 , pp. 1053-1060
    • Yi, G.1    Sze, S.-H.2    Thon, M.R.3
  • 65
    • 5444243359 scopus 로고    scopus 로고
    • Active genes dynamically colocalize to shared sites of ongoing transcription
    • Osborne CS, Chakalova L, Brown KE, Carter D, Horton A, et al. (2004) Active genes dynamically colocalize to shared sites of ongoing transcription. Nat Genet 36: 1065-1071.
    • (2004) Nat Genet , vol.36 , pp. 1065-1071
    • Osborne, C.S.1    Chakalova, L.2    Brown, K.E.3    Carter, D.4    Horton, A.5
  • 66
    • 73349090560 scopus 로고    scopus 로고
    • Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells
    • Schoenfelder S, Sexton T, Chakalova L, Cope NF, Horton A, et al. (2010) Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells. Nat Genet 42: 53-61.
    • (2010) Nat Genet , vol.42 , pp. 53-61
    • Schoenfelder, S.1    Sexton, T.2    Chakalova, L.3    Cope, N.F.4    Horton, A.5
  • 67
    • 78649983246 scopus 로고    scopus 로고
    • Human transcriptional interactome of chromatin contribute to gene co-expression
    • Dong X, Li C, Chen Y, Ding G, Li Y, (2010) Human transcriptional interactome of chromatin contribute to gene co-expression. BMC Genomics 11: 704.
    • (2010) BMC Genomics , vol.11 , pp. 704
    • Dong, X.1    Li, C.2    Chen, Y.3    Ding, G.4    Li, Y.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.