메뉴 건너뛰기




Volumn 195, Issue 6, 2013, Pages 1109-1119

DNA Looping in Prokaryotes: Experimental and theoretical approaches

Author keywords

[No Author keywords available]

Indexed keywords

LAC REPRESSOR;

EID: 84874702922     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.02038-12     Document Type: Article
Times cited : (71)

References (136)
  • 1
    • 9144264275 scopus 로고    scopus 로고
    • Macrodomain organization of the Escherichia coli chromosome
    • Valens M, Penaud S, Rossignol M, Cornet F, Boccard F. 2004. Macrodomain organization of the Escherichia coli chromosome. EMBO J. 23:4330-4341.
    • (2004) EMBO J , vol.23 , pp. 4330-4341
    • Valens, M.1    Penaud, S.2    Rossignol, M.3    Cornet, F.4    Boccard, F.5
  • 2
    • 79959843457 scopus 로고    scopus 로고
    • Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in Gram negative bacteria
    • doi: 10.1371/journal.pgen.1002123
    • Dame RT, Kalmykowa OJ, Grainger DC. 2011. Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in Gram negative bacteria. PLoS Genet. 7:e1002123. doi: 10.1371/journal.pgen.1002123.
    • (2011) PLoS Genet , vol.7
    • Dame, R.T.1    Kalmykowa, O.J.2    Grainger, D.C.3
  • 3
    • 0001436751 scopus 로고    scopus 로고
    • Neidhardt F. C., Curtiss R., III, Ingraham J. L., Lin E. C. C., Low K. B., Magasanik B., Reznikoff W. S., Riley M., Schaechter M, Umbarger H. E. (ed), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, DC
    • Pettijohn D. 1996. The nucleoid, p 158-166. In Neidhardt F. C., Curtiss R., III, Ingraham J. L., Lin E. C. C., Low K. B., Magasanik B., Reznikoff W. S., Riley M., Schaechter M, Umbarger H. E. (ed), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, DC.
    • (1996) The nucleoid , pp. 158-166
    • Pettijohn, D.1
  • 4
    • 0017045430 scopus 로고
    • Electron microscopy of membrane-free folded chromosomes from Escherichia coli
    • Kavenoff R, Bowen BC. 1976. Electron microscopy of membrane-free folded chromosomes from Escherichia coli. Chromosoma 59:89-101.
    • (1976) Chromosoma , vol.59 , pp. 89-101
    • Kavenoff, R.1    Bowen, B.C.2
  • 5
    • 25144495578 scopus 로고    scopus 로고
    • Organization of supercoil domains and their reorganization by transcription
    • Deng S, Stein RA, Higgins NP. 2005. Organization of supercoil domains and their reorganization by transcription. Mol. Microbiol. 57: 1511-1521.
    • (2005) Mol. Microbiol. , vol.57 , pp. 1511-1521
    • Deng, S.1    Stein, R.A.2    Higgins, N.P.3
  • 6
    • 0018962604 scopus 로고
    • Torsional tension in the DNA double helix measured with trimethylpsoralen in living Escherichia coli cells: analogous measurements in insect and human cells
    • Sinden RR, Carlson JO, Pettijohn DE. 1980. Torsional tension in the DNA double helix measured with trimethylpsoralen in living Escherichia coli cells: analogous measurements in insect and human cells. Cell 21: 773-783.
    • (1980) Cell , vol.21 , pp. 773-783
    • Sinden, R.R.1    Carlson, J.O.2    Pettijohn, D.E.3
  • 7
    • 3142774839 scopus 로고    scopus 로고
    • Topological domain structure of the Escherichia coli chromosome
    • Postow L, Hardy CD, Arsuaga J, Cozzarelli NR. 2004. Topological domain structure of the Escherichia coli chromosome. Genes Dev. 18: 1766-1779.
    • (2004) Genes Dev , vol.18 , pp. 1766-1779
    • Postow, L.1    Hardy, C.D.2    Arsuaga, J.3    Cozzarelli, N.R.4
  • 8
    • 76949089832 scopus 로고    scopus 로고
    • Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
    • Dillon SC, Dorman CJ. 2010. Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nat. Rev. Microbiol. 8:185-195.
    • (2010) Nat. Rev. Microbiol. , vol.8 , pp. 185-195
    • Dillon, S.C.1    Dorman, C.J.2
  • 9
    • 0017745436 scopus 로고
    • Construction, isolation and implications of repressor-galactosidase-beta-galactosidase hybrid molecules
    • Kania J, Müller-Hill B. 1977. Construction, isolation and implications of repressor-galactosidase-beta-galactosidase hybrid molecules. Eur. J. Biochem. 79:381-386.
    • (1977) Eur. J. Biochem. , vol.79 , pp. 381-386
    • Kania, J.1    Müller-Hill, B.2
  • 10
    • 0021188333 scopus 로고
    • An operator at-280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression
    • Dunn TM, Hahn S, Ogden S, Schleif RF. 1984. An operator at _280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression. Proc. Natl. Acad. Sci. U. S. A. 81:5017-5020.
    • (1984) Proc. Natl. Acad. Sci. U. S. A. , vol.81 , pp. 5017-5020
    • Dunn, T.M.1    Hahn, S.2    Ogden, S.3    Schleif, R.F.4
  • 11
    • 0024811753 scopus 로고
    • Multipartite genetic control elements: communication by DNA loop
    • Adhya S. 1989. Multipartite genetic control elements: communication by DNA loop. Annu. Rev. Genet. 23:227-250.
    • (1989) Annu. Rev. Genet. , vol.23 , pp. 227-250
    • Adhya, S.1
  • 15
    • 39449115716 scopus 로고    scopus 로고
    • Ab initio thermodynamic modeling of distal multisite transcription regulation
    • Saiz L, Vilar JMG. 2008. Ab initio thermodynamic modeling of distal multisite transcription regulation. Nucleic Acids Res. 36:726-731.
    • (2008) Nucleic Acids Res , vol.36 , pp. 726-731
    • Saiz, L.1    Vilar, J.M.G.2
  • 16
    • 65549143001 scopus 로고    scopus 로고
    • A thermodynamic model for the agglomeration of DNA-looping proteins
    • 005. doi:10. 1088/1742-5468/2008/11/
    • Sumedha, Weigt M. 2008. A thermodynamic model for the agglomeration of DNA-looping proteins. J. Stat. Mech. 11:005. doi:10.1088/1742-5468/2008/11/P11005.
    • (2008) J. Stat. Mech. , vol.11
    • Sumedha1    Weigt, M.2
  • 17
    • 0042622638 scopus 로고    scopus 로고
    • DNA looping and physical constraints on transcription regulation
    • Vilar JMG, Leibler S. 2003. DNA looping and physical constraints on transcription regulation. J. Mol. Biol. 331:981-989.
    • (2003) J. Mol. Biol. , vol.331 , pp. 981-989
    • Vilar, J.M.G.1    Leibler, S.2
  • 18
    • 0028365289 scopus 로고
    • Quality and position of the three lac operators of Escherichia coli define efficiency of repression
    • Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B, Müller-Hill B. 1994. Quality and position of the three lac operators of Escherichia coli define efficiency of repression. EMBO J. 13:3348-3355.
    • (1994) EMBO J , vol.13 , pp. 3348-3355
    • Oehler, S.1    Amouyal, M.2    Kolkhof, P.3    von Wilcken-Bergmann, B.4    Müller-Hill, B.5
  • 19
    • 0025343547 scopus 로고
    • The three operators of the lac operon cooperate in repression
    • Oehler S, Eismann ER, Krämer H, Müller-Hill B. 1990. The three operators of the lac operon cooperate in repression. EMBO J. 9:973-979.
    • (1990) EMBO J , vol.9 , pp. 973-979
    • Oehler, S.1    Eismann, E.R.2    Krämer, H.3    Müller-Hill, B.4
  • 20
    • 0013556017 scopus 로고
    • Interaction of spatially separated protein-DNA complexes for control of gene expression: operator conversions
    • Haber R, Adhya S. 1988. Interaction of spatially separated protein-DNA complexes for control of gene expression: operator conversions. Proc. Natl. Acad. Sci. U. S. A. 85:9683-9687.
    • (1988) Proc. Natl. Acad. Sci. U. S. A. , vol.85 , pp. 9683-9687
    • Haber, R.1    Adhya, S.2
  • 21
    • 0025216961 scopus 로고
    • DNA looping in cellular repression of transcription of the galactose operon
    • Mandal N, Su W, Haber R, Adhya S, Echols H. 1990. DNA looping in cellular repression of transcription of the galactose operon. Genes Dev. 4:410-418.
    • (1990) Genes Dev , vol.4 , pp. 410-418
    • Mandal, N.1    Su, W.2    Haber, R.3    Adhya, S.4    Echols, H.5
  • 22
    • 0024413926 scopus 로고
    • Single and double loop formation when DeoR repressor binds to its natural operator sites
    • Amouyal M, Mortensen L, Buc H, Hammer K. 1989. Single and double loop formation when DeoR repressor binds to its natural operator sites. Cell 58:545-551.
    • (1989) Cell , vol.58 , pp. 545-551
    • Amouyal, M.1    Mortensen, L.2    Buc, H.3    Hammer, K.4
  • 23
    • 0022759236 scopus 로고
    • DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor
    • Valentin-Hansen P, Albrechtsen B, Larsen JEL. 1986. DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor. EMBO J. 5:2015-2021.
    • (1986) EMBO J , vol.5 , pp. 2015-2021
    • Valentin-Hansen, P.1    Albrechtsen, B.2    Larsen, J.E.L.3
  • 24
    • 0025971343 scopus 로고
    • CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli
    • Plumbridge J, Kolb A. 1991. CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli. J. Mol. Biol. 217:661-679.
    • (1991) J. Mol. Biol. , vol.217 , pp. 661-679
    • Plumbridge, J.1    Kolb, A.2
  • 25
    • 0027742098 scopus 로고
    • DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo
    • Plumbridge J, Kolb A. 1993. DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo. Mol. Microbiol. 10:973-981.
    • (1993) Mol. Microbiol. , vol.10 , pp. 973-981
    • Plumbridge, J.1    Kolb, A.2
  • 26
    • 0025938894 scopus 로고
    • Prokaryotic transcriptional enhancers and enhancer-binding proteins
    • Kustu S, North AK, Weiss DS. 1991. Prokaryotic transcriptional enhancers and enhancer-binding proteins. Trends Biochem. Sci. 16:397-402.
    • (1991) Trends Biochem. Sci. , vol.16 , pp. 397-402
    • Kustu, S.1    North, A.K.2    Weiss, D.S.3
  • 27
    • 0022446209 scopus 로고
    • Transcription of glnA in Escherichia coli is stimulated by activator bound to sites far from the promoter
    • Reitzer LJ, Magasanik B. 1986. Transcription of glnA in Escherichia coli is stimulated by activator bound to sites far from the promoter. Cell 45:785-792.
    • (1986) Cell , vol.45 , pp. 785-792
    • Reitzer, L.J.1    Magasanik, B.2
  • 28
    • 77955128598 scopus 로고    scopus 로고
    • Mechanisms for activating bacterial RNA polymerase
    • Ghosh T, Bose D, Zhang X. 2010. Mechanisms for activating bacterial RNA polymerase. FEMS Microbiol. Rev. 34:611-627.
    • (2010) FEMS Microbiol. Rev. , vol.34 , pp. 611-627
    • Ghosh, T.1    Bose, D.2    Zhang, X.3
  • 30
    • 0027340543 scopus 로고
    • 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains
    • 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 175:6067-6074.
    • (1993) J. Bacteriol. , vol.175 , pp. 6067-6074
    • Morett, E.1    Segovia, L.2
  • 31
    • 0037332383 scopus 로고    scopus 로고
    • 54-dependent transcriptional activators
    • 54-dependent transcriptional activators. J. Bacteriol. 185:1757-1767.
    • (2003) J. Bacteriol. , vol.185 , pp. 1757-1767
    • Studholme, D.J.1    Dixon, R.2
  • 32
    • 80052450772 scopus 로고    scopus 로고
    • DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays
    • Hirsh AD, Lillian TD, Lionberger TA, Perkins NC. 2011. DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays. Biophys. J. 101:718-726.
    • (2011) Biophys. J. , vol.101 , pp. 718-726
    • Hirsh, A.D.1    Lillian, T.D.2    Lionberger, T.A.3    Perkins, N.C.4
  • 34
    • 33744807717 scopus 로고    scopus 로고
    • DNA looping: the consequences and its control
    • Saiz L, Vilar JMG. 2006. DNA looping: the consequences and its control. Curr. Opin. Struct. Biol. 16:344-350.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 344-350
    • Saiz, L.1    Vilar, J.M.G.2
  • 37
    • 0037126028 scopus 로고    scopus 로고
    • Physical constraints and functional characteristics of transcription factor-DNA interaction
    • Gerland U, Moroz JD, Hwa T. 2002. Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc. Natl. Acad. Sci. U. S. A. 99:12015-12020.
    • (2002) Proc. Natl. Acad. Sci. U. S. A. , vol.99 , pp. 12015-12020
    • Gerland, U.1    Moroz, J.D.2    Hwa, T.3
  • 38
    • 0021739440 scopus 로고
    • Demonstration of two operator elements in gal: in vitro repressor binding studies
    • Majumdar A, Adhya S. 1984. Demonstration of two operator elements in gal: in vitro repressor binding studies. Proc. Natl. Acad. Sci. U. S. A. 81:6100-6104.
    • (1984) Proc. Natl. Acad. Sci. U. S. A. , vol.81 , pp. 6100-6104
    • Majumdar, A.1    Adhya, S.2
  • 40
    • 0022521842 scopus 로고
    • Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix
    • Hochschild A, Ptashne M. 1986. Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix. Cell 44:681-687.
    • (1986) Cell , vol.44 , pp. 681-687
    • Hochschild, A.1    Ptashne, M.2
  • 41
    • 0022476864 scopus 로고
    • Structure of DNase I at 2 0-ngstrom resolution suggests a mechanism for binding to and cutting DNA
    • Suck D, Oefner C. 1986. Structure of DNase I at 2.0 _ngstrom resolution suggests a mechanism for binding to and cutting DNA. Nature 321: 620-625.
    • (1986) Nature , vol.321 , pp. 620-625
    • Suck, D.1    Oefner, C.2
  • 42
    • 78649709362 scopus 로고    scopus 로고
    • Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments
    • Lipfert J, Kerssemakers JWJ, Jager T, Dekker NH. 2010. Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments. Nat. Methods 7:977-980.
    • (2010) Nat. Methods , vol.7 , pp. 977-980
    • Lipfert, J.1    Kerssemakers, J.W.J.2    Jager, T.3    Dekker, N.H.4
  • 43
    • 0021320555 scopus 로고
    • Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling
    • Horowitz DS, Wang JC. 1984. Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. J. Mol. Biol. 173:75-91.
    • (1984) J. Mol. Biol. , vol.173 , pp. 75-91
    • Horowitz, D.S.1    Wang, J.C.2
  • 44
    • 0031576995 scopus 로고    scopus 로고
    • Thermodynamics of the interactions of Lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site
    • Frank DE, Saecker RM, Bond JP, Capp MW, Tsodikov OV, Melcher SE, Levandoski MM, Record MT. 1997. Thermodynamics of the interactions of Lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site. J. Mol. Biol. 267:1186-1206.
    • (1997) J. Mol. Biol. , vol.267 , pp. 1186-1206
    • Frank, D.E.1    Saecker, R.M.2    Bond, J.P.3    Capp, M.W.4    Tsodikov, O.V.5    Melcher, S.E.6    Levandoski, M.M.7    Record, M.T.8
  • 45
    • 27244460904 scopus 로고    scopus 로고
    • Protein-DNA binding specificity predictions with structural models
    • Morozov AV, Havranek JJ, Baker D, Siggia ED. 2005. Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res. 33:5781-5798.
    • (2005) Nucleic Acids Res , vol.33 , pp. 5781-5798
    • Morozov, A.V.1    Havranek, J.J.2    Baker, D.3    Siggia, E.D.4
  • 46
    • 0032029574 scopus 로고    scopus 로고
    • DNA bending and expression of the divergent nagE-B operons
    • Plumbridge J, Kolb A. 1998. DNA bending and expression of the divergent nagE-B operons. Nucleic Acids Res. 26:1254-1260.
    • (1998) Nucleic Acids Res , vol.26 , pp. 1254-1260
    • Plumbridge, J.1    Kolb, A.2
  • 47
    • 0033585029 scopus 로고    scopus 로고
    • Designed hyperstable Lac repressor DNA loop topologies suggest alternative loop geometries
    • Mehta RA, Kahn JD. 1999. Designed hyperstable Lac repressor.DNA loop topologies suggest alternative loop geometries. J. Mol. Biol. 294: 67-77.
    • (1999) J. Mol. Biol. , vol.294 , pp. 67-77
    • Mehta, R.A.1    Kahn, J.D.2
  • 48
    • 0033607486 scopus 로고    scopus 로고
    • Hemiplegic mutations in AraC protein
    • Reed WL, Schleif RF. 1999. Hemiplegic mutations in AraC protein. J. Mol. Biol. 294:417-425.
    • (1999) J. Mol. Biol. , vol.294 , pp. 417-425
    • Reed, W.L.1    Schleif, R.F.2
  • 49
    • 0030072556 scopus 로고    scopus 로고
    • Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by Gal repressor
    • Aki T, Choy HE, Adhya S. 1996. Histone-like protein HU as a specific transcriptional regulator: co-factor role in repression of gal transcription by Gal repressor. Genes Cells 1:179-188.
    • (1996) Genes Cells , vol.1 , pp. 179-188
    • Aki, T.1    Choy, H.E.2    Adhya, S.3
  • 51
    • 0025361357 scopus 로고
    • A bacterial enhancer functions to tether a transcriptional activator near a promoter
    • Wedel A, Weiss DS, Popham D, Dröge P, Kustu S. 1990. A bacterial enhancer functions to tether a transcriptional activator near a promoter. Science 248:486-490.
    • (1990) Science , vol.248 , pp. 486-490
    • Wedel, A.1    Weiss, D.S.2    Popham, D.3    Dröge, P.4    Kustu, S.5
  • 52
    • 0022545056 scopus 로고
    • DNA loops induced by cooperative binding of lambda repressor
    • Griffith J, Hochschild A, Ptashne M. 1986. DNA loops induced by cooperative binding of lambda repressor. Nature 322:750-752.
    • (1986) Nature , vol.322 , pp. 750-752
    • Griffith, J.1    Hochschild, A.2    Ptashne, M.3
  • 53
    • 0025867008 scopus 로고
    • Transcription by single molecules of RNA polymerase observed by light microscopy
    • Schafer DA, Gelles J, Sheetz MP, Landick R. 1991. Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 352:444-448.
    • (1991) Nature , vol.352 , pp. 444-448
    • Schafer, D.A.1    Gelles, J.2    Sheetz, M.P.3    Landick, R.4
  • 54
    • 68349150612 scopus 로고    scopus 로고
    • First-principles calculation of DNA looping in tethered particle experiments
    • doi:10.1088/1478-3975/6/2/025001
    • Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC. 2009. First-principles calculation of DNA looping in tethered particle experiments. Phys. Biol. 6:25001. doi:10.1088/1478-3975/6/2/025001.
    • (2009) Phys. Biol. , vol.6 , pp. 25001
    • Towles, K.B.1    Beausang, J.F.2    Garcia, H.G.3    Phillips, R.4    Nelson, P.C.5
  • 57
  • 59
    • 0031871889 scopus 로고    scopus 로고
    • The function of auxiliary operators
    • Müller-Hill B. 1998. The function of auxiliary operators. Mol. Microbiol. 29:13-18.
    • (1998) Mol. Microbiol. , vol.29 , pp. 13-18
    • Müller-Hill, B.1
  • 60
    • 33645323777 scopus 로고    scopus 로고
    • What is life? The paradigm of DNA and protein cooperation at high local concentrations
    • Müller-Hill B. 2006. What is life? The paradigm of DNA and protein cooperation at high local concentrations. Mol. Microbiol. 60:253-255.
    • (2006) Mol. Microbiol. , vol.60 , pp. 253-255
    • Müller-Hill, B.1
  • 61
    • 73149092964 scopus 로고    scopus 로고
    • High local concentration: a fundamental strategy of life
    • Oehler S, Müller-Hill B. 2010. High local concentration: a fundamental strategy of life. J. Mol. Biol. 395:242-253.
    • (2010) J. Mol. Biol. , vol.395 , pp. 242-253
    • Oehler, S.1    Müller-Hill, B.2
  • 62
    • 0015101706 scopus 로고
    • Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect
    • Page MI, Jencks WP. 1971. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. Proc. Natl. Acad. Sci. U. S. A. 68:1678-1683.
    • (1971) Proc. Natl. Acad. Sci. U. S. A. , vol.68 , pp. 1678-1683
    • Page, M.I.1    Jencks, W.P.2
  • 63
    • 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
  • 65
    • 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
  • 67
    • 79955613183 scopus 로고    scopus 로고
    • Impact of gene expression noise on organismal fitness and the efficacy of natural selection
    • Wang Z, Zhang J. 2011. Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc. Natl. Acad. Sci. U. S. A. 108:E67-E76.
    • (2011) Proc. Natl. Acad. Sci. U. S. A. , vol.108
    • Wang, Z.1    Zhang, J.2
  • 68
    • 15744393452 scopus 로고    scopus 로고
    • DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise
    • Vilar JMG, Saiz L. 2005. DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise. Curr. Opin. Genet. Dev. 15:136-144.
    • (2005) Curr. Opin. Genet. Dev. , vol.15 , pp. 136-144
    • Vilar, J.M.G.1    Saiz, L.2
  • 69
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D. 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.1
  • 70
    • 12144259350 scopus 로고    scopus 로고
    • Gene regulation at-a-distance in Escherichia coli: new insights
    • Amouyal M. 2005. Gene regulation at-a-distance in Escherichia coli: new insights. C. R. Biol. 328:1-9.
    • (2005) C. R. Biol. , vol.328 , pp. 1-9
    • Amouyal, M.1
  • 71
    • 0034212551 scopus 로고    scopus 로고
    • Engineering stability in gene networks by autoregulation
    • Becskei A, Serrano L. 2000. Engineering stability in gene networks by autoregulation. Nature 405:590-593.
    • (2000) Nature , vol.405 , pp. 590-593
    • Becskei, A.1    Serrano, L.2
  • 73
    • 63849284078 scopus 로고    scopus 로고
    • Effects of macromolecular crowding and DNA looping on gene regulation kinetics
    • Li GW, Berg OG, Elf J. 2009. Effects of macromolecular crowding and DNA looping on gene regulation kinetics. Nat. Phys. 5:294-297.
    • (2009) Nat. Phys. , vol.5 , pp. 294-297
    • Li, G.W.1    Berg, O.G.2    Elf, J.3
  • 74
    • 27644460480 scopus 로고    scopus 로고
    • Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA
    • Gowers DM, Wilson GG, Halford SE. 2005. Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. Proc. Natl. Acad. Sci. U. S. A. 102:15883-15888.
    • (2005) Proc. Natl. Acad. Sci. U. S. A. , vol.102 , pp. 15883-15888
    • Gowers, D.M.1    Wilson, G.G.2    Halford, S.E.3
  • 77
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner TS, Cantor CR, Collins JJ. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403:339-342.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 79
    • 0345359924 scopus 로고    scopus 로고
    • A positive-feedback-based bistable "memory module" that governs a cell fate decision
    • Xiong W, Ferrell JE. 2003. A positive-feedback-based bistable "memory module" that governs a cell fate decision. Nature 426:460-465.
    • (2003) Nature , vol.426 , pp. 460-465
    • Xiong, W.1    Ferrell, J.E.2
  • 80
    • 0035582202 scopus 로고    scopus 로고
    • Multistationarity, the basis of cell differentiation and memory. ii. logical analysis of regulatory networks in terms of feedback circuits
    • Thomas R, Kaufman M. 2001. Multistationarity, the basis of cell differentiation and memory. ii. logical analysis of regulatory networks in terms of feedback circuits. Chaos 11:180-195.
    • (2001) Chaos , vol.11 , pp. 180-195
    • Thomas, R.1    Kaufman, M.2
  • 81
    • 32644439362 scopus 로고    scopus 로고
    • Induction of the lac promoter in the absence ofDNAloops and the stoichiometry of induction
    • Oehler S, Alberti S, Müller-Hill B. 2006. Induction of the lac promoter in the absence ofDNAloops and the stoichiometry of induction. Nucleic Acids Res. 34:606-612.
    • (2006) Nucleic Acids Res , vol.34 , pp. 606-612
    • Oehler, S.1    Alberti, S.2    Müller-Hill, B.3
  • 84
    • 33748058888 scopus 로고    scopus 로고
    • Bistability in bacteria
    • Dubnau D, Losick R. 2006. Bistability in bacteria. Mol. Microbiol. 61:564-572.
    • (2006) Mol. Microbiol. , vol.61 , pp. 564-572
    • Dubnau, D.1    Losick, R.2
  • 85
    • 0038241770 scopus 로고    scopus 로고
    • Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
    • Atkinson MR, Savageau MA, Myers JT, Ninfa AJ. 2003. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 113:597-607.
    • (2003) Cell , vol.113 , pp. 597-607
    • Atkinson, M.R.1    Savageau, M.A.2    Myers, J.T.3    Ninfa, A.J.4
  • 86
    • 66249124272 scopus 로고    scopus 로고
    • DNA looping provides stability and robustness to the bacteriophage lambda switch
    • Morelli MJ, Wolde PRT, Allen RJ. 2009. DNA looping provides stability and robustness to the bacteriophage lambda switch. Proc. Natl. Acad. Sci. U. S. A. 106:8101-8106.
    • (2009) Proc. Natl. Acad. Sci. U. S. A. , vol.106 , pp. 8101-8106
    • Morelli, M.J.1    Wolde, P.R.T.2    Allen, R.J.3
  • 87
    • 0033517148 scopus 로고    scopus 로고
    • Robustness of a gene regulatory circuit
    • Little JW, Shepley DP, Wert DW. 1999. Robustness of a gene regulatory circuit. EMBO J. 18:4299-4307.
    • (1999) EMBO J , vol.18 , pp. 4299-4307
    • Little, J.W.1    Shepley, D.P.2    Wert, D.W.3
  • 89
    • 0029975889 scopus 로고    scopus 로고
    • Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
    • Müller J, Oehler S, Müller-Hill B. 1996. Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J. Mol. Biol. 257:21-29.
    • (1996) J. Mol. Biol. , vol.257 , pp. 21-29
    • Müller, J.1    Oehler, S.2    Müller-Hill, B.3
  • 94
    • 33745595880 scopus 로고    scopus 로고
    • Modeling the lac repressoroperator assembly: the influence of DNA looping on Lac repressor conformation
    • Swigon D, Coleman BD, Olson WK. 2006. Modeling the lac repressoroperator assembly: the influence of DNA looping on Lac repressor conformation. Proc. Natl. Acad. Sci. U. S. A. 103:9879-9884.
    • (2006) Proc. Natl. Acad. Sci. U. S. A. , vol.103 , pp. 9879-9884
    • Swigon, D.1    Coleman, B.D.2    Olson, W.K.3
  • 95
    • 20444411150 scopus 로고    scopus 로고
    • The lac repressor
    • Lewis M. 2005. The lac repressor. C. R. Biol. 328:521-548.
    • (2005) C. R. Biol. , vol.328 , pp. 521-548
    • Lewis, M.1
  • 96
    • 0037223124 scopus 로고    scopus 로고
    • Two different modes of transcription repression of the Escherichia coli acetate operon by IclR
    • Yamamoto K, Ishihama A. 2003. Two different modes of transcription repression of the Escherichia coli acetate operon by IclR. Mol. Microbiol. 47:183-194.
    • (2003) Mol. Microbiol. , vol.47 , pp. 183-194
    • Yamamoto, K.1    Ishihama, A.2
  • 97
    • 1242342950 scopus 로고    scopus 로고
    • Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in Nacetylgalactosamine metabolism in Escherichia coli K-12
    • Ray WK, Larson TJ. 2004. Application of AgaR repressor and dominant repressor variants for verification of a gene cluster involved in Nacetylgalactosamine metabolism in Escherichia coli K-12. Mol. Microbiol. 51:813-826.
    • (2004) Mol. Microbiol. , vol.51 , pp. 813-826
    • Ray, W.K.1    Larson, T.J.2
  • 98
    • 1942501133 scopus 로고    scopus 로고
    • Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC
    • Plumbridge J, Pellegrini O. 2004. Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP. Mol. Microbiol. 52:437-449.
    • (2004) ChbR and CAP. Mol. Microbiol. , vol.52 , pp. 437-449
    • Plumbridge, J.1    Pellegrini, O.2
  • 100
    • 33744729365 scopus 로고    scopus 로고
    • A complex transcription network controls the early stages of biofilm development by Escherichia coli
    • Prüss BM, Besemann C, Denton A, Wolfe AJ. 2006. A complex transcription network controls the early stages of biofilm development by Escherichia coli. J. Bacteriol. 188:3731-3739.
    • (2006) J. Bacteriol. , vol.188 , pp. 3731-3739
    • Prüss, B.M.1    Besemann, C.2    Denton, A.3    Wolfe, A.J.4
  • 101
    • 0029130181 scopus 로고
    • Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR
    • Shin S, Park C. 1995. Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR. J. Bacteriol. 177: 4696-4702.
    • (1995) J. Bacteriol. , vol.177 , pp. 4696-4702
    • Shin, S.1    Park, C.2
  • 102
    • 58149117729 scopus 로고    scopus 로고
    • Repression of galP, the galactose transporter in Escherichia coli, requires the specific regulator of N-acetylglucosamine metabolism
    • El Qaidi S, Allemand F, Oberto J, Plumbridge J. 2009. Repression of galP, the galactose transporter in Escherichia coli, requires the specific regulator of N-acetylglucosamine metabolism. Mol. Microbiol. 71:146-157.
    • (2009) Mol. Microbiol. , vol.71 , pp. 146-157
    • El Qaidi, S.1    Allemand, F.2    Oberto, J.3    Plumbridge, J.4
  • 103
    • 0031748313 scopus 로고    scopus 로고
    • Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli
    • Stauffer LT, Stauffer GV. 1998. Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli. Microbiology 144(Pt 5):1417-1422.
    • (1998) Microbiology , vol.144 , Issue.PART 5 , pp. 1417-1422
    • Stauffer, L.T.1    Stauffer, G.V.2
  • 104
    • 0029145921 scopus 로고
    • Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites
    • Plumbridge J. 1995. Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites. EMBO J. 14:3958-3965.
    • (1995) EMBO J , vol.14 , pp. 3958-3965
    • Plumbridge, J.1
  • 105
    • 0030463126 scopus 로고    scopus 로고
    • Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12
    • Yang B, Larson TJ. 1996. Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12. J. Bacteriol. 178:7090-7098.
    • (1996) J. Bacteriol. , vol.178 , pp. 7090-7098
    • Yang, B.1    Larson, T.J.2
  • 106
    • 0026702038 scopus 로고
    • Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12
    • Weissenborn DL, Wittekindt N, Larson TJ. 1992. Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12. J. Biol. Chem. 267:6122-6131.
    • (1992) J. Biol. Chem. , vol.267 , pp. 6122-6131
    • Weissenborn, D.L.1    Wittekindt, N.2    Larson, T.J.3
  • 107
    • 0030914635 scopus 로고    scopus 로고
    • Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12
    • Yang B, Gerhardt SG, Larson TJ. 1997. Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12. Mol. Microbiol. 24:511-521.
    • (1997) Mol. Microbiol. , vol.24 , pp. 511-521
    • Yang, B.1    Gerhardt, S.G.2    Larson, T.J.3
  • 108
    • 0031897881 scopus 로고    scopus 로고
    • Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex
    • Peekhaus N, Conway T. 1998. Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex. J. Bacteriol. 180:1777-1785.
    • (1998) J. Bacteriol. , vol.180 , pp. 1777-1785
    • Peekhaus, N.1    Conway, T.2
  • 109
    • 0031046248 scopus 로고    scopus 로고
    • Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism
    • Porco A, Peekhaus N, Bausch C, Tong S, Isturiz T, Conway T. 1997. Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism. J. Bacteriol. 179:1584-1590.
    • (1997) J. Bacteriol. , vol.179 , pp. 1584-1590
    • Porco, A.1    Peekhaus, N.2    Bausch, C.3    Tong, S.4    Isturiz, T.5    Conway, T.6
  • 110
    • 41949098532 scopus 로고    scopus 로고
    • Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli
    • Aguilera L, Campos E, Giménez R, Badía J, Aguilar J, Baldoma L. 2008. Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli. J. Bacteriol. 190:2997-3005.
    • (2008) J. Bacteriol. , vol.190 , pp. 2997-3005
    • Aguilera, L.1    Campos, E.2    Giménez, R.3    Badía, J.4    Aguilar, J.5    Baldoma, L.6
  • 111
    • 0031973888 scopus 로고    scopus 로고
    • Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS
    • Plumbridge J. 1998. Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS. Mol. Microbiol. 27:369-380.
    • (1998) Mol. Microbiol. , vol.27 , pp. 369-380
    • Plumbridge, J.1
  • 112
    • 33646266716 scopus 로고    scopus 로고
    • Mutational analysis of the Escherichia coli melR gene suggests a two-state concerted model to explain transcriptional activation and repression in the melibiose operon
    • Kahramanoglou C, Webster CL, El-Robh MS, Belyaeva TA, Busby SJW. 2006. Mutational analysis of the Escherichia coli melR gene suggests a two-state concerted model to explain transcriptional activation and repression in the melibiose operon. J. Bacteriol. 188:3199-3207.
    • (2006) J. Bacteriol. , vol.188 , pp. 3199-3207
    • Kahramanoglou, C.1    Webster, C.L.2    El-Robh, M.S.3    Belyaeva, T.A.4    Busby, S.J.W.5
  • 114
    • 0028222516 scopus 로고
    • The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation
    • Rampersaud A, Harlocker SL, Inouye M. 1994. The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation. J. Biol. Chem. 269:12559-12566.
    • (1994) J. Biol. Chem. , vol.269 , pp. 12559-12566
    • Rampersaud, A.1    Harlocker, S.L.2    Inouye, M.3
  • 115
    • 0028325749 scopus 로고
    • A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene
    • Huang KJ, Schieberl JL, Igo MM. 1994. A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene. J. Bacteriol. 176:1309-1315.
    • (1994) J. Bacteriol. , vol.176 , pp. 1309-1315
    • Huang, K.J.1    Schieberl, J.L.2    Igo, M.M.3
  • 116
    • 0032458848 scopus 로고    scopus 로고
    • Hierarchical and co-operative binding of OmpR to a fusion construct containing the ompC and ompF upstream regulatory sequences of Escherichia coli
    • Bergstrom LC, Qin L, Harlocker SL, Egger LA, Inouye M. 1998. Hierarchical and co-operative binding of OmpR to a fusion construct containing the ompC and ompF upstream regulatory sequences of Escherichia coli. Genes Cells 3:777-788.
    • (1998) Genes Cells , vol.3 , pp. 777-788
    • Bergstrom, L.C.1    Qin, L.2    Harlocker, S.L.3    Egger, L.A.4    Inouye, M.5
  • 117
    • 46049110706 scopus 로고    scopus 로고
    • Switching control of expression of ptsG from the Mlc regulon to the NagC regulon
    • El Qaidi S, Plumbridge J. 2008. Switching control of expression of ptsG from the Mlc regulon to the NagC regulon. J. Bacteriol. 190:4677-4686.
    • (2008) J. Bacteriol. , vol.190 , pp. 4677-4686
    • El Qaidi, S.1    Plumbridge, J.2
  • 118
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martínez-Antonio A, Collado-Vides J. 2003. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6:482-489.
    • (2003) Curr. Opin. Microbiol. , vol.6 , pp. 482-489
    • Martínez-Antonio, A.1    Collado-Vides, J.2
  • 120
    • 0023113779 scopus 로고
    • Longrange cooperativity between gene regulatory sequences in a prokaryote
    • Dandanell G, Valentin-Hansen P, Larsen JE, Hammer K. 1987. Longrange cooperativity between gene regulatory sequences in a prokaryote. Nature 325:823-826.
    • (1987) Nature , vol.325 , pp. 823-826
    • Dandanell, G.1    Valentin-Hansen, P.2    Larsen, J.E.3    Hammer, K.4
  • 121
    • 3242812952 scopus 로고    scopus 로고
    • Periodic transcriptional organization of the Escherichia coli genome
    • Képès F. 2004. Periodic transcriptional organization of the Escherichia coli genome. J. Mol. Biol. 340:957-964.
    • (2004) J. Mol. Biol. , vol.340 , pp. 957-964
    • Képès, F.1
  • 122
    • 11344293422 scopus 로고    scopus 로고
    • Spatial patterns of transcriptional activity in the chromosome of Escherichia coli
    • doi:10.1186/gb-2004-5-11-r86
    • Jeong KS, Ahn J, Khodursky AB. 2004. Spatial patterns of transcriptional activity in the chromosome of Escherichia coli. Genome Biol. 5:R86. doi:10.1186/gb-2004-5-11-r86.
    • (2004) Genome Biol , vol.5
    • Jeong, K.S.1    Ahn, J.2    Khodursky, A.B.3
  • 123
    • 33847205083 scopus 로고    scopus 로고
    • What are the molecular ties that maintain genomic loops?
    • Marenduzzo D, Faro-Trindade I, Cook PR. 2007. What are the molecular ties that maintain genomic loops? Trends Genet. 23:126-133.
    • (2007) Trends Genet , vol.23 , pp. 126-133
    • Marenduzzo, D.1    Faro-Trindade, I.2    Cook, P.R.3
  • 125
    • 0036842123 scopus 로고    scopus 로고
    • Predicting three-dimensional genome structure from transcriptional activity
    • Cook PR. 2002. Predicting three-dimensional genome structure from transcriptional activity. Nat. Genet. 32:347-352.
    • (2002) Nat. Genet. , vol.32 , pp. 347-352
    • Cook, P.R.1
  • 126
    • 70450222694 scopus 로고    scopus 로고
    • A model for all genomes: the role of transcription factories
    • Cook PR. 2010. A model for all genomes: the role of transcription factories. J. Mol. Biol. 395:1-10.
    • (2010) J. Mol. Biol. , vol.395 , pp. 1-10
    • Cook, P.R.1
  • 127
    • 84863117103 scopus 로고    scopus 로고
    • A model for Escherichia coli chromosome packaging supports transcription factorinduced DNA domain formation
    • Fritsche M, Li S, Heermann DW, Wiggins PA. 2012. A model for Escherichia coli chromosome packaging supports transcription factorinduced DNA domain formation. Nucleic Acids Res. 40:972-980.
    • (2012) Nucleic Acids Res , vol.40 , pp. 972-980
    • Fritsche, M.1    Li, S.2    Heermann, D.W.3    Wiggins, P.A.4
  • 130
    • 40349098663 scopus 로고    scopus 로고
    • Chromosome conformation capture carbon copy technology
    • Chapter 21:Unit 21. 14. doi:10.1002/0471142727.mb2114s80
    • Dostie J, Zhan Y, Dekker J. 2007. Chromosome conformation capture carbon copy technology. Curr. Protoc. Mol. Biol. Chapter 21:Unit 21.14. doi:10.1002/0471142727.mb2114s80.
    • (2007) Curr. Protoc. Mol. Biol
    • Dostie, J.1    Zhan, Y.2    Dekker, J.3
  • 131
    • 80052643394 scopus 로고    scopus 로고
    • Chromosome organization by a nucleoid-associated protein in live bacteria
    • Wang W, Li GW, 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
  • 136
    • 41349089522 scopus 로고    scopus 로고
    • Gene regulation in the third dimension
    • Dekker J. 2008. Gene regulation in the third dimension. Science 319: 1793-1794.
    • (2008) Science , vol.319 , pp. 1793-1794
    • Dekker, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.