메뉴 건너뛰기




Volumn 9, Issue 6, 2013, Pages

Genome-scale Analysis of Escherichia coli FNR Reveals Complex Features of Transcription Factor Binding

Author keywords

[No Author keywords available]

Indexed keywords

ESCHERICHIA COLI PROTEIN; NUCLEOID ASSOCIATED PROTEIN; PROTEIN FNR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

EID: 84879620270     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003565     Document Type: Article
Times cited : (144)

References (160)
  • 1
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • Lieb JD, Liu X, Botstein D, Brown PO, (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28: 327-334.
    • (2001) Nat Genet , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 2
    • 33749381311 scopus 로고    scopus 로고
    • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
    • Liu X, Lee C-K, Granek JA, Clarke ND, Lieb JD, (2006) Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res 16: 1517-1528.
    • (2006) Genome Res , vol.16 , pp. 1517-1528
    • Liu, X.1    Lee, C.-K.2    Granek, J.A.3    Clarke, N.D.4    Lieb, J.D.5
  • 3
    • 68949213578 scopus 로고    scopus 로고
    • Insights from genomic profiling of transcription factors
    • Farnham PJ, (2009) Insights from genomic profiling of transcription factors. Nat Rev Genet 10: 605-616.
    • (2009) Nat Rev Genet , vol.10 , pp. 605-616
    • Farnham, P.J.1
  • 4
    • 79959359483 scopus 로고    scopus 로고
    • Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4
    • Zhou X, O'Shea EK, (2011) Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4. Mol Cell 42: 826-836.
    • (2011) Mol Cell , vol.42 , pp. 826-836
    • Zhou, X.1    O'Shea, E.K.2
  • 5
    • 84865739425 scopus 로고    scopus 로고
    • Architecture of the human regulatory network derived from ENCODE data
    • Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan K-K, et al. (2012) Architecture of the human regulatory network derived from ENCODE data. Nature 489: 91-100.
    • (2012) Nature , vol.489 , pp. 91-100
    • Gerstein, M.B.1    Kundaje, A.2    Hariharan, M.3    Landt, S.G.4    Yan, K.-K.5
  • 7
    • 78649640318 scopus 로고    scopus 로고
    • Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression
    • Browning DF, Grainger DC, Busby SJ, (2010) Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. Curr Opin Microbiol 13: 773-780.
    • (2010) Curr Opin Microbiol , vol.13 , pp. 773-780
    • Browning, D.F.1    Grainger, D.C.2    Busby, S.J.3
  • 8
    • 0033538531 scopus 로고    scopus 로고
    • Fundamentally different logic of gene regulation in eukaryotes and prokaryotes
    • Struhl K, (1999) Fundamentally different logic of gene regulation in eukaryotes and prokaryotes. Cell 98: 1-4.
    • (1999) Cell , vol.98 , pp. 1-4
    • Struhl, K.1
  • 9
    • 34250619055 scopus 로고    scopus 로고
    • Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization
    • Wade JT, Struhl K, Busby SJW, Grainger DC, (2007) Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization. Mol Microbiol 65: 21-26.
    • (2007) Mol Microbiol , vol.65 , pp. 21-26
    • Wade, J.T.1    Struhl, K.2    Busby, S.J.W.3    Grainger, D.C.4
  • 10
    • 27644580858 scopus 로고    scopus 로고
    • Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites
    • Wade JT, Reppas NB, Church GM, Struhl K, (2005) Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev 19: 2619-2630.
    • (2005) Genes Dev , vol.19 , pp. 2619-2630
    • Wade, J.T.1    Reppas, N.B.2    Church, G.M.3    Struhl, K.4
  • 11
    • 84861871818 scopus 로고    scopus 로고
    • Architectural organization in E. coli nucleoid
    • Macvanin M, Adhya S, (2012) Architectural organization in E. coli nucleoid. Biochim Biophys Acta 1819: 830-835.
    • (2012) Biochim Biophys Acta , vol.1819 , pp. 830-835
    • Macvanin, M.1    Adhya, S.2
  • 12
    • 79954579293 scopus 로고    scopus 로고
    • Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins
    • Rimsky S, Travers A, (2011) Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins. Curr Opin Microbiol 14: 136-141.
    • (2011) Curr Opin Microbiol , vol.14 , pp. 136-141
    • Rimsky, S.1    Travers, A.2
  • 13
    • 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 Micro 8: 185-195.
    • (2010) Nat Rev Micro , vol.8 , pp. 185-195
    • Dillon, S.C.1    Dorman, C.J.2
  • 14
    • 0028556430 scopus 로고
    • The FNR family of transcriptional regulators
    • Spiro S, (1994) The FNR family of transcriptional regulators. Antonie Van Leeuwenhoek 66: 23-36.
    • (1994) Antonie Van Leeuwenhoek , vol.66 , pp. 23-36
    • Spiro, S.1
  • 16
    • 79953298366 scopus 로고    scopus 로고
    • Iron-containing transcription factors and their roles as sensors
    • Fleischhacker AS, Kiley PJ, (2011) Iron-containing transcription factors and their roles as sensors. Curr Opin Chem Biol 15: 335-341.
    • (2011) Curr Opin Chem Biol , vol.15 , pp. 335-341
    • Fleischhacker, A.S.1    Kiley, P.J.2
  • 17
    • 0043032584 scopus 로고    scopus 로고
    • Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR
    • Salmon K, Hung S-P, Mekjian K, Baldi P, Hatfield GW, et al. (2003) Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR. J Biol Chem 278: 29837-29855.
    • (2003) J Biol Chem , vol.278 , pp. 29837-29855
    • Salmon, K.1    Hung, S.-P.2    Mekjian, K.3    Baldi, P.4    Hatfield, G.W.5
  • 18
    • 13244289800 scopus 로고    scopus 로고
    • Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function
    • Kang Y, Weber KD, Qiu Y, Kiley PJ, Blattner FR, (2005) Genome-wide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J Bacteriol 187: 1135-1160.
    • (2005) J Bacteriol , vol.187 , pp. 1135-1160
    • Kang, Y.1    Weber, K.D.2    Qiu, Y.3    Kiley, P.J.4    Blattner, F.R.5
  • 19
    • 33646184857 scopus 로고    scopus 로고
    • A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth
    • Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, et al. (2006) A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth. J Biol Chem 281: 4802-4815.
    • (2006) J Biol Chem , vol.281 , pp. 4802-4815
    • Constantinidou, C.1    Hobman, J.L.2    Griffiths, L.3    Patel, M.D.4    Penn, C.W.5
  • 20
    • 1842506160 scopus 로고    scopus 로고
    • Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes
    • Barnard A, Wolfe A, Busby S, (2004) Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. Curr Opin Microbiol 7: 102-108.
    • (2004) Curr Opin Microbiol , vol.7 , pp. 102-108
    • Barnard, A.1    Wolfe, A.2    Busby, S.3
  • 21
    • 1842591130 scopus 로고    scopus 로고
    • The regulation of bacterial transcription initiation
    • Browning DF, Busby SJ, (2004) The regulation of bacterial transcription initiation. Nat Rev Micro 2: 57-65.
    • (2004) Nat Rev Micro , vol.2 , pp. 57-65
    • Browning, D.F.1    Busby, S.J.2
  • 22
    • 0032545186 scopus 로고    scopus 로고
    • Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase σ70 subunit
    • Lonetto MA, Rhodius V, Lamberg K, Kiley P, Busby S, et al. (1998) Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase σ70 subunit. J Mol Biol 284: 1353-1365.
    • (1998) J Mol Biol , vol.284 , pp. 1353-1365
    • Lonetto, M.A.1    Rhodius, V.2    Lamberg, K.3    Kiley, P.4    Busby, S.5
  • 23
    • 0020377789 scopus 로고
    • Requirement of Fnr and NarL functions for nitrate reductase expression in Escherichia coli K-12
    • Stewart V, (1982) Requirement of Fnr and NarL functions for nitrate reductase expression in Escherichia coli K-12. J Bacteriol 151: 1320-1325.
    • (1982) J Bacteriol , vol.151 , pp. 1320-1325
    • Stewart, V.1
  • 24
    • 0027452546 scopus 로고
    • Activation of the Escherichia coli nitrate reductase (narGHJI) operon by NarL and Fnr requires integration host factor
    • Schröder I, Darie S, Gunsalus RP, (1993) Activation of the Escherichia coli nitrate reductase (narGHJI) operon by NarL and Fnr requires integration host factor. J Biol Chem 268: 771-774.
    • (1993) J Biol Chem , vol.268 , pp. 771-774
    • Schröder, I.1    Darie, S.2    Gunsalus, R.P.3
  • 25
    • 0033639260 scopus 로고    scopus 로고
    • FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3
    • Lamberg KE, Kiley PJ, (2000) FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3. Mol Microbiol 38: 817-827.
    • (2000) Mol Microbiol , vol.38 , pp. 817-827
    • Lamberg, K.E.1    Kiley, P.J.2
  • 26
    • 19044394317 scopus 로고    scopus 로고
    • Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions
    • Bearson SMD, Albrecht JA, Gunsalus RP, (2002) Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions. BMC Microbiol 2: 13.
    • (2002) BMC Microbiol , vol.2 , pp. 13
    • Bearson, S.M.D.1    Albrecht, J.A.2    Gunsalus, R.P.3
  • 27
    • 0033818258 scopus 로고    scopus 로고
    • Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly
    • Browning DF, Cole JA, Busby SJW, (2000) Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly. Mol Microbiol 37: 1258-1269.
    • (2000) Mol Microbiol , vol.37 , pp. 1258-1269
    • Browning, D.F.1    Cole, J.A.2    Busby, S.J.W.3
  • 28
    • 0033370108 scopus 로고    scopus 로고
    • Eukaryotic transcriptional control
    • Kornberg RD, (1999) Eukaryotic transcriptional control. Trends Cell Biol 9: M46-M49.
    • (1999) Trends Cell Biol , vol.9
    • Kornberg, R.D.1
  • 29
    • 33846659467 scopus 로고    scopus 로고
    • Transcription factor distribution in Escherichia coli: studies with FNR protein
    • Grainger DC, Aiba H, Hurd D, Browning DF, Busby SJW, (2007) Transcription factor distribution in Escherichia coli: studies with FNR protein. Nucleic Acids Res 35: 269-278.
    • (2007) Nucleic Acids Res , vol.35 , pp. 269-278
    • Grainger, D.C.1    Aiba, H.2    Hurd, D.3    Browning, D.F.4    Busby, S.J.W.5
  • 30
    • 79953676877 scopus 로고    scopus 로고
    • Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli
    • Kahramanoglou C, Seshasayee ASN, Prieto AI, Ibberson D, Schmidt S, et al. (2011) Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res 39: 2073-2091.
    • (2011) Nucleic Acids Res , vol.39 , pp. 2073-2091
    • Kahramanoglou, C.1    Seshasayee, A.S.N.2    Prieto, A.I.3    Ibberson, D.4    Schmidt, S.5
  • 31
    • 33750000118 scopus 로고    scopus 로고
    • Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome
    • Grainger DC, Hurd D, Goldberg MD, Busby SJW, (2006) Association of nucleoid proteins with coding and non-coding segments of the Escherichia coli genome. Nucleic Acids Res 34: 4642-4652.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4642-4652
    • Grainger, D.C.1    Hurd, D.2    Goldberg, M.D.3    Busby, S.J.W.4
  • 32
    • 33750898424 scopus 로고    scopus 로고
    • Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase
    • Oshima T, Ishikawa S, Kurokawa K, Aiba H, Ogasawara N, (2006) Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res 13: 141-153.
    • (2006) DNA Res , vol.13 , pp. 141-153
    • Oshima, T.1    Ishikawa, S.2    Kurokawa, K.3    Aiba, H.4    Ogasawara, N.5
  • 33
    • 84860378352 scopus 로고    scopus 로고
    • Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12
    • Prieto AI, Kahramanoglou C, Ali RM, Fraser GM, Seshasayee ASN, et al. (2012) Genomic analysis of DNA binding and gene regulation by homologous nucleoid-associated proteins IHF and HU in Escherichia coli K12. Nucleic Acids Res 109: 3524-3537.
    • (2012) Nucleic Acids Res , vol.109 , pp. 3524-3537
    • Prieto, A.I.1    Kahramanoglou, C.2    Ali, R.M.3    Fraser, G.M.4    Seshasayee, A.S.N.5
  • 34
    • 35549009343 scopus 로고    scopus 로고
    • High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes
    • Lang B, Blot N, Bouffartigues E, Buckle M, Geertz M, et al. (2007) High-affinity DNA binding sites for H-NS provide a molecular basis for selective silencing within proteobacterial genomes. Nucleic Acids Res 35: 6330-6337.
    • (2007) Nucleic Acids Res , vol.35 , pp. 6330-6337
    • Lang, B.1    Blot, N.2    Bouffartigues, E.3    Buckle, M.4    Geertz, M.5
  • 35
    • 84864150307 scopus 로고    scopus 로고
    • Nucleoprotein filament formation is the structural basis for bacterial protein H-NS gene silencing
    • Lim CJ, Lee SY, Kenney LJ, Yan J, (2012) Nucleoprotein filament formation is the structural basis for bacterial protein H-NS gene silencing. Sci Rep 2: 509.
    • (2012) Sci Rep , vol.2 , pp. 509
    • Lim, C.J.1    Lee, S.Y.2    Kenney, L.J.3    Yan, J.4
  • 36
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz GZ, Stormo GD, (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15: 563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 37
    • 9244247618 scopus 로고    scopus 로고
    • Kinetic analysis of the oxidative conversion of the [4Fe-4S]2+ cluster of FNR to a [2Fe-2S]2+ cluster
    • Sutton VR, Mettert EL, Beinert H, Kiley PJ, (2004) Kinetic analysis of the oxidative conversion of the [4Fe-4S]2+ cluster of FNR to a [2Fe-2S]2+ cluster. J Bacteriol 186: 8018-8025.
    • (2004) J Bacteriol , vol.186 , pp. 8018-8025
    • Sutton, V.R.1    Mettert, E.L.2    Beinert, H.3    Kiley, P.J.4
  • 39
    • 0035076860 scopus 로고    scopus 로고
    • The nucleoid-associated protein StpA binds curved DNA, has a greater DNA-binding affinity than H-NS and is present in significant levels in hns mutants
    • Sonnenfield JM, Burns CM, Higgins CF, Hinton J, (2001) The nucleoid-associated protein StpA binds curved DNA, has a greater DNA-binding affinity than H-NS and is present in significant levels in hns mutants. Biochimie 83: 243-249.
    • (2001) Biochimie , vol.83 , pp. 243-249
    • Sonnenfield, J.M.1    Burns, C.M.2    Higgins, C.F.3    Hinton, J.4
  • 40
    • 64049096202 scopus 로고    scopus 로고
    • Differential binding profiles of StpA in wild-type and hns mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis
    • Uyar E, Kurokawa K, Yoshimura M, Ishikawa S, Ogasawara N, et al. (2009) Differential binding profiles of StpA in wild-type and hns mutant cells: a comparative analysis of cooperative partners by chromatin immunoprecipitation-microarray analysis. J Bacteriol 191: 2388-2391.
    • (2009) J Bacteriol , vol.191 , pp. 2388-2391
    • Uyar, E.1    Kurokawa, K.2    Yoshimura, M.3    Ishikawa, S.4    Ogasawara, N.5
  • 41
    • 0030052038 scopus 로고    scopus 로고
    • Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes
    • Melville SB, Gunsalus RP, (1996) Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes. Proc Natl Acad Sci USA 93: 1226-1231.
    • (1996) Proc Natl Acad Sci USA , vol.93 , pp. 1226-1231
    • Melville, S.B.1    Gunsalus, R.P.2
  • 42
    • 22144488494 scopus 로고    scopus 로고
    • Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression
    • Browning DF, Grainger DC, Beatty CM, Wolfe AJ, Cole JA, et al. (2005) Integration of three signals at the Escherichia coli nrf promoter: a role for Fis protein in catabolite repression. Mol Microbiol 57: 496-510.
    • (2005) Mol Microbiol , vol.57 , pp. 496-510
    • Browning, D.F.1    Grainger, D.C.2    Beatty, C.M.3    Wolfe, A.J.4    Cole, J.A.5
  • 43
    • 0023263331 scopus 로고
    • Regulation of Escherichia coli fumarate reductase (frdABCD) operon expression by respiratory electron acceptors and the fnr gene product
    • Jones HM, Gunsalus RP, (1987) Regulation of Escherichia coli fumarate reductase (frdABCD) operon expression by respiratory electron acceptors and the fnr gene product. J Bacteriol 169: 3340-3349.
    • (1987) J Bacteriol , vol.169 , pp. 3340-3349
    • Jones, H.M.1    Gunsalus, R.P.2
  • 44
    • 0030904024 scopus 로고    scopus 로고
    • Regulation of the Salmonella typhimurium pepT gene by cyclic AMP receptor protein (CRP) and FNR acting at a hybrid CRP-FNR site
    • Lombardo MJ, Lee AA, Knox TM, Miller CG, (1997) Regulation of the Salmonella typhimurium pepT gene by cyclic AMP receptor protein (CRP) and FNR acting at a hybrid CRP-FNR site. J Bacteriol 179: 1909-1917.
    • (1997) J Bacteriol , vol.179 , pp. 1909-1917
    • Lombardo, M.J.1    Lee, A.A.2    Knox, T.M.3    Miller, C.G.4
  • 45
    • 80053905923 scopus 로고    scopus 로고
    • The identification of a novel protein involved in molybdenum cofactor biosynthesis in Escherichia coli
    • Dahl JU, Urban A, Bolte A, Sriyabhaya P, Donahue JL, et al. (2011) The identification of a novel protein involved in molybdenum cofactor biosynthesis in Escherichia coli. J Biol Chem 286: 35801-35812.
    • (2011) J Biol Chem , vol.286 , pp. 35801-35812
    • Dahl, J.U.1    Urban, A.2    Bolte, A.3    Sriyabhaya, P.4    Donahue, J.L.5
  • 46
    • 0017648506 scopus 로고
    • The anaerobic oxidation of dihydroorotate by Escherichia coli K-12
    • Andrews S, Cox GB, Gibson F, (1977) The anaerobic oxidation of dihydroorotate by Escherichia coli K-12. Biochim Biophys Acta 462: 153-160.
    • (1977) Biochim Biophys Acta , vol.462 , pp. 153-160
    • Andrews, S.1    Cox, G.B.2    Gibson, F.3
  • 47
    • 0029920825 scopus 로고    scopus 로고
    • Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli
    • Eichler K, Buchet A, Lemke R, Kleber HP, Mandrand-Berthelot MA, (1996) Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli. J Bacteriol 178: 1248-1257.
    • (1996) J Bacteriol , vol.178 , pp. 1248-1257
    • Eichler, K.1    Buchet, A.2    Lemke, R.3    Kleber, H.P.4    Mandrand-Berthelot, M.A.5
  • 48
    • 77349104885 scopus 로고    scopus 로고
    • Reprogramming of anaerobic metabolism by the FnrS small RNA
    • Durand S, Storz G, (2010) Reprogramming of anaerobic metabolism by the FnrS small RNA. Mol Microbiol 75: 1215-1231.
    • (2010) Mol Microbiol , vol.75 , pp. 1215-1231
    • Durand, S.1    Storz, G.2
  • 49
    • 77349101808 scopus 로고    scopus 로고
    • Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli
    • Boysen A, Moller-Jensen J, Kallipolitis B, Valentin-Hansen P, Overgaard M, (2010) Translational regulation of gene expression by an anaerobically induced small non-coding RNA in Escherichia coli. J Biol Chem 285: 10690-10702.
    • (2010) J Biol Chem , vol.285 , pp. 10690-10702
    • Boysen, A.1    Moller-Jensen, J.2    Kallipolitis, B.3    Valentin-Hansen, P.4    Overgaard, M.5
  • 50
    • 0030764901 scopus 로고    scopus 로고
    • Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation
    • Cotter PA, Melville SB, Albrecht JA, Gunsalus RP, (1997) Aerobic regulation of cytochrome d oxidase (cydAB) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation. Mol Microbiol 25: 605-615.
    • (1997) Mol Microbiol , vol.25 , pp. 605-615
    • Cotter, P.A.1    Melville, S.B.2    Albrecht, J.A.3    Gunsalus, R.P.4
  • 51
    • 0036435479 scopus 로고    scopus 로고
    • Decrease in cell viability in an RMF, σ38, and OmpC triple mutant of Escherichia coli
    • Samuel Raj V, Füll C, Yoshida M, Sakata K, Kashiwagi K, et al. (2002) Decrease in cell viability in an RMF, σ38, and OmpC triple mutant of Escherichia coli. Biochem Biophys Res Commun 299: 252-257.
    • (2002) Biochem Biophys Res Commun , vol.299 , pp. 252-257
    • Samuel Raj, V.1    Füll, C.2    Yoshida, M.3    Sakata, K.4    Kashiwagi, K.5
  • 52
    • 31144454629 scopus 로고    scopus 로고
    • Conserved and variable functions of the σE stress response in related genomes
    • Rhodius VA, Suh WC, Nonaka G, West J, Gross CA, (2006) Conserved and variable functions of the σE stress response in related genomes. PLoS Biol 4: e2.
    • (2006) PLoS Biol , vol.4
    • Rhodius, V.A.1    Suh, W.C.2    Nonaka, G.3    West, J.4    Gross, C.A.5
  • 53
    • 0025012920 scopus 로고
    • Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli
    • Lutz S, Böhm R, Beier A, Böck A, (1990) Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli. Mol Microbiol 4: 13-20.
    • (1990) Mol Microbiol , vol.4 , pp. 13-20
    • Lutz, S.1    Böhm, R.2    Beier, A.3    Böck, A.4
  • 54
    • 6044228192 scopus 로고    scopus 로고
    • σS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of σS-dependent genes and identification of their promoter sequences
    • Lacour S, Landini P, (2004) σS-dependent gene expression at the onset of stationary phase in Escherichia coli: function of σS-dependent genes and identification of their promoter sequences. J Bacteriol 186: 7186-7195.
    • (2004) J Bacteriol , vol.186 , pp. 7186-7195
    • Lacour, S.1    Landini, P.2
  • 55
    • 0031856846 scopus 로고    scopus 로고
    • Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro
    • Darwin AJ, Ziegelhoffer EC, Kiley PJ, Stewart V, (1998) Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. J Bacteriol 180: 4192-4198.
    • (1998) J Bacteriol , vol.180 , pp. 4192-4198
    • Darwin, A.J.1    Ziegelhoffer, E.C.2    Kiley, P.J.3    Stewart, V.4
  • 56
    • 63449141265 scopus 로고    scopus 로고
    • Catabolite repression control of napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12
    • Stewart V, Bledsoe PJ, Chen L-L, Cai A, (2009) Catabolite repression control of napF (periplasmic nitrate reductase) operon expression in Escherichia coli K-12. J Bacteriol 191: 996-1005.
    • (2009) J Bacteriol , vol.191 , pp. 996-1005
    • Stewart, V.1    Bledsoe, P.J.2    Chen, L.-L.3    Cai, A.4
  • 57
    • 0027183315 scopus 로고
    • Co-dependent positive regulation of the ansB promoter of Escherichia coli by CRP and the FNR protein: a molecular analysis
    • Jennings MP, Beacham IR, (1993) Co-dependent positive regulation of the ansB promoter of Escherichia coli by CRP and the FNR protein: a molecular analysis. Mol Microbiol 9: 155-164.
    • (1993) Mol Microbiol , vol.9 , pp. 155-164
    • Jennings, M.P.1    Beacham, I.R.2
  • 58
    • 79959400835 scopus 로고    scopus 로고
    • Genotype and phenotypes of an intestine-adapted Escherichia coli K-12 mutant selected by animal passage for superior colonization
    • Fabich AJ, Leatham MP, Grissom JE, Wiley G, Lai H, et al. (2011) Genotype and phenotypes of an intestine-adapted Escherichia coli K-12 mutant selected by animal passage for superior colonization. Infect Immun 79: 2430-2439.
    • (2011) Infect Immun , vol.79 , pp. 2430-2439
    • Fabich, A.J.1    Leatham, M.P.2    Grissom, J.E.3    Wiley, G.4    Lai, H.5
  • 59
    • 0027487221 scopus 로고
    • Characterization of the ferrous iron uptake system of Escherichia coli
    • Kammler M, Schon C, Hantke K, (1993) Characterization of the ferrous iron uptake system of Escherichia coli. J Bacteriol 175: 6212-6219.
    • (1993) J Bacteriol , vol.175 , pp. 6212-6219
    • Kammler, M.1    Schon, C.2    Hantke, K.3
  • 60
    • 84861909704 scopus 로고    scopus 로고
    • Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli
    • Ogasawara H, Shinohara S, Yamamoto K, Ishihama A, (2012) Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli. Microbiology 158: 1482-1492.
    • (2012) Microbiology , vol.158 , pp. 1482-1492
    • Ogasawara, H.1    Shinohara, S.2    Yamamoto, K.3    Ishihama, A.4
  • 61
    • 0036646484 scopus 로고    scopus 로고
    • NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp
    • Cruz-Ramos H, Crack J, Wu G, Hughes MN, Scott C, et al. (2002) NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp. EMBO J 21: 3235-3244.
    • (2002) EMBO J , vol.21 , pp. 3235-3244
    • Cruz-Ramos, H.1    Crack, J.2    Wu, G.3    Hughes, M.N.4    Scott, C.5
  • 62
    • 0031450904 scopus 로고    scopus 로고
    • The molecular basis for the differential regulation of the hlyE-encoded haemolysin of Escherichia coli by FNR and HlyX lies in the improved activating region 1 contact of HlyX
    • Green J, Baldwin ML, (1997) The molecular basis for the differential regulation of the hlyE-encoded haemolysin of Escherichia coli by FNR and HlyX lies in the improved activating region 1 contact of HlyX. Microbiology 143 (Pt 12):: 3785-3793.
    • (1997) Microbiology , vol.143 , Issue.Pt 12 , pp. 3785-3793
    • Green, J.1    Baldwin, M.L.2
  • 63
    • 77954358334 scopus 로고    scopus 로고
    • A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions
    • Teramoto J, Yoshimura SH, Takeyasu K, Ishihama A, (2010) A novel nucleoid protein of Escherichia coli induced under anaerobiotic growth conditions. Nucleic Acids Res 38: 3605-3618.
    • (2010) Nucleic Acids Res , vol.38 , pp. 3605-3618
    • Teramoto, J.1    Yoshimura, S.H.2    Takeyasu, K.3    Ishihama, A.4
  • 64
    • 84870497149 scopus 로고    scopus 로고
    • Rho and NusG suppress pervasive antisense transcription in Escherichia coli
    • Peters JM, Mooney RA, Grass JA, Jessen ED, Tran F, et al. (2012) Rho and NusG suppress pervasive antisense transcription in Escherichia coli. Genes Dev 26: 2621-2633.
    • (2012) Genes Dev , vol.26 , pp. 2621-2633
    • Peters, J.M.1    Mooney, R.A.2    Grass, J.A.3    Jessen, E.D.4    Tran, F.5
  • 65
    • 84873513423 scopus 로고    scopus 로고
    • Host-derived nitrate boosts growth of E. coli in the inflamed gut
    • Winter SE, Winter MG, Xavier MN, Thiennimitr P, Poon V, et al. (2013) Host-derived nitrate boosts growth of E. coli in the inflamed gut. Science 339: 708-711.
    • (2013) Science , vol.339 , pp. 708-711
    • Winter, S.E.1    Winter, M.G.2    Xavier, M.N.3    Thiennimitr, P.4    Poon, V.5
  • 66
    • 0031827572 scopus 로고    scopus 로고
    • Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12
    • Thieffry D, Salgado H, Huerta AM, Collado-Vides J, (1998) Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12. Bioinformatics 14: 391-400.
    • (1998) Bioinformatics , vol.14 , pp. 391-400
    • Thieffry, D.1    Salgado, H.2    Huerta, A.M.3    Collado-Vides, J.4
  • 67
    • 70449380939 scopus 로고    scopus 로고
    • Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli
    • Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, et al. (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS ONE 4: e7526.
    • (2009) PLoS ONE , vol.4
    • Mendoza-Vargas, A.1    Olvera, L.2    Olvera, M.3    Grande, R.4    Vega-Alvarado, L.5
  • 68
    • 0035051602 scopus 로고    scopus 로고
    • A comparative genomics approach to prediction of new members of regulons
    • Tan K, Moreno-Hagelsieb G, Collado-Vides J, Stormo GD, (2001) A comparative genomics approach to prediction of new members of regulons. Genome Res 11: 566-584.
    • (2001) Genome Res , vol.11 , pp. 566-584
    • Tan, K.1    Moreno-Hagelsieb, G.2    Collado-Vides, J.3    Stormo, G.D.4
  • 69
    • 0032573426 scopus 로고    scopus 로고
    • A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
    • Robison K, McGuire AM, Church GM, (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol 284: 241-254.
    • (1998) J Mol Biol , vol.284 , pp. 241-254
    • Robison, K.1    McGuire, A.M.2    Church, G.M.3
  • 72
    • 79957788648 scopus 로고    scopus 로고
    • Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources
    • Shimada T, Fujita N, Yamamoto K, Ishihama A, (2011) Novel roles of cAMP receptor protein (CRP) in regulation of transport and metabolism of carbon sources. PLoS ONE 6: e20081.
    • (2011) PLoS ONE , vol.6
    • Shimada, T.1    Fujita, N.2    Yamamoto, K.3    Ishihama, A.4
  • 73
    • 29144431508 scopus 로고    scopus 로고
    • Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome
    • Grainger DC, Hurd D, Harrison M, Holdstock J, Busby SJW, (2005) Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc Natl Acad Sci USA 102: 17693-17698.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 17693-17698
    • Grainger, D.C.1    Hurd, D.2    Harrison, M.3    Holdstock, J.4    Busby, S.J.W.5
  • 74
    • 34547640859 scopus 로고    scopus 로고
    • Human body temperature (37°C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12
    • White-Ziegler CA, Malhowski AJ, Young S, (2007) Human body temperature (37°C) increases the expression of iron, carbohydrate, and amino acid utilization genes in Escherichia coli K-12. J Bacteriol 189: 5429-5440.
    • (2007) J Bacteriol , vol.189 , pp. 5429-5440
    • White-Ziegler, C.A.1    Malhowski, A.J.2    Young, S.3
  • 75
    • 45549085296 scopus 로고    scopus 로고
    • Predictive behavior within microbial genetic networks
    • Tagkopoulos I, Liu YC, Tavazoie S, (2008) Predictive behavior within microbial genetic networks. Science 320: 1313-1317.
    • (2008) Science , vol.320 , pp. 1313-1317
    • Tagkopoulos, I.1    Liu, Y.C.2    Tavazoie, S.3
  • 76
    • 33846465923 scopus 로고    scopus 로고
    • H-NS, the genome sentinel
    • Dorman CJ, (2007) H-NS, the genome sentinel. Nat Rev Micro 5: 157-161.
    • (2007) Nat Rev Micro , vol.5 , pp. 157-161
    • Dorman, C.J.1
  • 77
    • 34247628510 scopus 로고    scopus 로고
    • H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing
    • Bouffartigues E, Buckle M, Badaut C, Travers A, Rimsky S, (2007) H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing. Nat Struct Mol Biol 14: 441-448.
    • (2007) Nat Struct Mol Biol , vol.14 , pp. 441-448
    • Bouffartigues, E.1    Buckle, M.2    Badaut, C.3    Travers, A.4    Rimsky, S.5
  • 78
    • 80053951751 scopus 로고    scopus 로고
    • Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS
    • Shimada T, Bridier A, Briandet R, Ishihama A, (2011) Novel roles of LeuO in transcription regulation of E. coli genome: antagonistic interplay with the universal silencer H-NS. Mol Microbiol 82: 378-397.
    • (2011) Mol Microbiol , vol.82 , pp. 378-397
    • Shimada, T.1    Bridier, A.2    Briandet, R.3    Ishihama, A.4
  • 79
    • 84866024286 scopus 로고    scopus 로고
    • LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium
    • Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, et al. (2012) LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium. Mol Microbiol 85: 1072-1089.
    • (2012) Mol Microbiol , vol.85 , pp. 1072-1089
    • Dillon, S.C.1    Espinosa, E.2    Hokamp, K.3    Ussery, D.W.4    Casadesús, J.5
  • 80
    • 80052361721 scopus 로고    scopus 로고
    • Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA
    • Queiroz MH, Madrid C, Paytubi S, Balsalobre C, Juarez A, (2011) Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA. Microbiology 157: 2504-2514.
    • (2011) Microbiology , vol.157 , pp. 2504-2514
    • Queiroz, M.H.1    Madrid, C.2    Paytubi, S.3    Balsalobre, C.4    Juarez, A.5
  • 81
    • 84861211375 scopus 로고    scopus 로고
    • Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria
    • Vasu K, Nagamalleswari E, Nagaraja V, (2012) Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria. Proc Natl Acad Sci USA 109: E1287-E1293.
    • (2012) Proc Natl Acad Sci USA , vol.109
    • Vasu, K.1    Nagamalleswari, E.2    Nagaraja, V.3
  • 82
    • 84875390286 scopus 로고    scopus 로고
    • Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription
    • Dorman CJ, (2013) Co-operative roles for DNA supercoiling and nucleoid-associated proteins in the regulation of bacterial transcription. Biochem Soc Trans 41: 542-547.
    • (2013) Biochem Soc Trans , vol.41 , pp. 542-547
    • Dorman, C.J.1
  • 83
    • 84859235790 scopus 로고    scopus 로고
    • A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2
    • Cameron ADS, Dorman CJ, (2012) A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2. PLoS Genet 8: e1002615.
    • (2012) PLoS Genet , vol.8
    • Cameron, A.D.S.1    Dorman, C.J.2
  • 85
    • 77952742099 scopus 로고    scopus 로고
    • Modulation of Shigella virulence in response to available oxygen in vivo
    • Marteyn B, West NP, Browning DF, Cole JA, Shaw JG, et al. (2010) Modulation of Shigella virulence in response to available oxygen in vivo. Nature 465: 355-358.
    • (2010) Nature , vol.465 , pp. 355-358
    • Marteyn, B.1    West, N.P.2    Browning, D.F.3    Cole, J.A.4    Shaw, J.G.5
  • 86
    • 77955141792 scopus 로고    scopus 로고
    • Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks
    • Ishihama A, (2010) Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks. FEMS Microbiol Rev 34: 628-645.
    • (2010) FEMS Microbiol Rev , vol.34 , pp. 628-645
    • Ishihama, A.1
  • 87
    • 30344484891 scopus 로고    scopus 로고
    • Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli
    • Martínez-Antonio A, Janga SC, Salgado H, Collado-Vides J, (2006) Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. J Mol Biol 14: 22-27.
    • (2006) J Mol Biol , vol.14 , pp. 22-27
    • Martínez-Antonio, A.1    Janga, S.C.2    Salgado, H.3    Collado-Vides, J.4
  • 88
    • 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
  • 89
    • 46849106965 scopus 로고    scopus 로고
    • Functional organisation of Escherichia coli transcriptional regulatory network
    • Martínez-Antonio A, Janga SC, Thieffry D, (2008) Functional organisation of Escherichia coli transcriptional regulatory network. J Mol Biol 381: 238-247.
    • (2008) J Mol Biol , vol.381 , pp. 238-247
    • Martínez-Antonio, A.1    Janga, S.C.2    Thieffry, D.3
  • 90
    • 44849093465 scopus 로고    scopus 로고
    • Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
    • Cho B-K, Knight EM, Barrett CL, Palsson BØ, (2008) Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. Genome Res 18: 900-910.
    • (2008) Genome Res , vol.18 , pp. 900-910
    • Cho, B.-K.1    Knight, E.M.2    Barrett, C.L.3    Palsson, BØ.4
  • 91
    • 77952820341 scopus 로고    scopus 로고
    • Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism
    • Dillon SC, Cameron ADS, Hokamp K, Lucchini S, Hinton JCD, et al. (2010) Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism. Mol Microbiol 76: 1250-1265.
    • (2010) Mol Microbiol , vol.76 , pp. 1250-1265
    • Dillon, S.C.1    Cameron, A.D.S.2    Hokamp, K.3    Lucchini, S.4    Hinton, J.C.D.5
  • 92
    • 0031925159 scopus 로고    scopus 로고
    • Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region
    • Buchet A, Eichler K, Mandrand-Berthelot MA, (1998) Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region. J Bacteriol 180: 2599-2608.
    • (1998) J Bacteriol , vol.180 , pp. 2599-2608
    • Buchet, A.1    Eichler, K.2    Mandrand-Berthelot, M.A.3
  • 93
    • 33646092295 scopus 로고    scopus 로고
    • YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling
    • Domka J, Lee J, Wood TK, (2006) YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling. Appl Environ Microbiol 72: 2449-2459.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 2449-2459
    • Domka, J.1    Lee, J.2    Wood, T.K.3
  • 94
    • 0028913511 scopus 로고
    • Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli
    • Quail MA, Guest JR, (1995) Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli. Mol Microbiol 15: 519-529.
    • (1995) Mol Microbiol , vol.15 , pp. 519-529
    • Quail, M.A.1    Guest, J.R.2
  • 95
    • 34547633841 scopus 로고    scopus 로고
    • PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli
    • Ogasawara H, Ishida Y, Yamada K, Yamamoto K, Ishihama A, (2007) PdhR (pyruvate dehydrogenase complex regulator) controls the respiratory electron transport system in Escherichia coli. J Bacteriol 189: 5534-5541.
    • (2007) J Bacteriol , vol.189 , pp. 5534-5541
    • Ogasawara, H.1    Ishida, Y.2    Yamada, K.3    Yamamoto, K.4    Ishihama, A.5
  • 96
    • 1642514566 scopus 로고    scopus 로고
    • GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli
    • Hommais F, Krin E, Coppée J-Y, Lacroix C, Yeramian E, et al. (2004) GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli. Microbiology 150: 61-72.
    • (2004) Microbiology , vol.150 , pp. 61-72
    • Hommais, F.1    Krin, E.2    Coppée, J.-Y.3    Lacroix, C.4    Yeramian, E.5
  • 97
    • 0028255883 scopus 로고
    • Effects of nitrate respiration on expression of the Arc-controlled operons encoding succinate dehydrogenase and flavin-linked L-lactate dehydrogenase
    • Iuchi S, Aristarkhov A, Dong J, Taylor J, Lin E, (1994) Effects of nitrate respiration on expression of the Arc-controlled operons encoding succinate dehydrogenase and flavin-linked L-lactate dehydrogenase. J Bacteriol 176: 1695-1701.
    • (1994) J Bacteriol , vol.176 , pp. 1695-1701
    • Iuchi, S.1    Aristarkhov, A.2    Dong, J.3    Taylor, J.4    Lin, E.5
  • 99
    • 0027451092 scopus 로고
    • The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state
    • Lazazzera BA, Bates DM, Kiley PJ, (1993) The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. Genes Dev 7: 1993-2005.
    • (1993) Genes Dev , vol.7 , pp. 1993-2005
    • Lazazzera, B.A.1    Bates, D.M.2    Kiley, P.J.3
  • 100
    • 0033983166 scopus 로고    scopus 로고
    • Towards single-copy gene expression systems making gene cloning physiologically relevant: lambda InCh, a simple Escherichia coli plasmid-chromosome shuttle system
    • Boyd D, Weiss DS, Chen JC, Beckwith J, (2000) Towards single-copy gene expression systems making gene cloning physiologically relevant: lambda InCh, a simple Escherichia coli plasmid-chromosome shuttle system. J Bacteriol 182: 842-847.
    • (2000) J Bacteriol , vol.182 , pp. 842-847
    • Boyd, D.1    Weiss, D.S.2    Chen, J.C.3    Beckwith, J.4
  • 101
    • 0027457077 scopus 로고
    • A signal sequence is not required for protein export in prlA mutants of Escherichia coli
    • Derman AI, Puziss JW, Bassford PJ Jr, Beckwith J, (1993) A signal sequence is not required for protein export in prlA mutants of Escherichia coli. EMBO J 12: 879-888.
    • (1993) EMBO J , vol.12 , pp. 879-888
    • Derman, A.I.1    Puziss, J.W.2    Bassford Jr., P.J.3    Beckwith, J.4
  • 102
    • 31544450286 scopus 로고    scopus 로고
    • Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection
    • 2006.0008
    • Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008.
    • (2006) Mol Syst Biol , vol.2
    • Baba, T.1    Ara, T.2    Hasegawa, M.3    Takai, Y.4    Okumura, Y.5
  • 103
    • 0034705144 scopus 로고    scopus 로고
    • An efficient recombination system for chromosome engineering in Escherichia coli
    • Yu D, Ellis HM, Lee EC, Jenkins NA, Copeland NG, et al. (2000) An efficient recombination system for chromosome engineering in Escherichia coli. Proc Natl Acad Sci USA 97: 5978-5983.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 5978-5983
    • Yu, D.1    Ellis, H.M.2    Lee, E.C.3    Jenkins, N.A.4    Copeland, N.G.5
  • 104
    • 0142172058 scopus 로고    scopus 로고
    • Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management
    • Khodursky AB, Bernstein JA, Peter BJ, Rhodius V, Wendisch VF, et al. (2003) Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management. Methods Mol Biol 224: 61-78.
    • (2003) Methods Mol Biol , vol.224 , pp. 61-78
    • Khodursky, A.B.1    Bernstein, J.A.2    Peter, B.J.3    Rhodius, V.4    Wendisch, V.F.5
  • 106
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Article3
    • Smyth GK, (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 107
    • 70449370314 scopus 로고    scopus 로고
    • The transcription unit architecture of the Escherichia coli genome
    • Cho B-K, Zengler K, Qiu Y, Park YS, Knight EM, et al. (2009) The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 27: 1043-1049.
    • (2009) Nat Biotechnol , vol.27 , pp. 1043-1049
    • Cho, B.-K.1    Zengler, K.2    Qiu, Y.3    Park, Y.S.4    Knight, E.M.5
  • 108
    • 67650711615 scopus 로고    scopus 로고
    • SOAP2: an improved ultrafast tool for short read alignment
    • Li R, Yu C, Li Y, Lam T-W, Yiu S-M, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25: 1966-1967.
    • (2009) Bioinformatics , vol.25 , pp. 1966-1967
    • Li, R.1    Yu, C.2    Li, Y.3    Lam, T.-W.4    Yiu, S.-M.5
  • 109
    • 77955298482 scopus 로고    scopus 로고
    • baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data
    • Hardcastle TJ, Kelly KA, (2010) baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics 11: 422.
    • (2010) BMC Bioinformatics , vol.11 , pp. 422
    • Hardcastle, T.J.1    Kelly, K.A.2
  • 110
    • 79957519168 scopus 로고    scopus 로고
    • Mapping E. coli RNA Polymerase and associated transcription factors and identifying promoters genome-wide
    • Davis SE, Mooney RA, Kanin EI, Grass J, Landick R, et al. (2011) Mapping E. coli RNA Polymerase and associated transcription factors and identifying promoters genome-wide. Meth Enzymol 498: 449-471.
    • (2011) Meth Enzymol , vol.498 , pp. 449-471
    • Davis, S.E.1    Mooney, R.A.2    Kanin, E.I.3    Grass, J.4    Landick, R.5
  • 112
    • 11244346557 scopus 로고    scopus 로고
    • Variance stabilization applied to microarray data calibration and to the quantification of differential expression
    • Huber W, Heydebreck von A, Sültmann H, Poustka A, Vingron M, (2002) Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18 Suppl 1: S96-S104.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL.
    • Huber, W.1    Heydebreck von, A.2    Sültmann, H.3    Poustka, A.4    Vingron, M.5
  • 113
    • 52949112607 scopus 로고    scopus 로고
    • Organization and evolution of the biological response to singlet oxygen stress
    • Dufour YS, Landick R, Donohue TJ, (2008) Organization and evolution of the biological response to singlet oxygen stress. J Mol Biol 383: 713-730.
    • (2008) J Mol Biol , vol.383 , pp. 713-730
    • Dufour, Y.S.1    Landick, R.2    Donohue, T.J.3
  • 114
    • 40549114662 scopus 로고    scopus 로고
    • CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure
    • Kuan PF, Chun H, Keleş S, (2008) CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. Pac Symp Biocomput pp. 515-526.
    • (2008) Pac Symp Biocomput , pp. 515-526
    • Kuan, P.F.1    Chun, H.2    Keleş, S.3
  • 115
    • 50849090969 scopus 로고    scopus 로고
    • Genome-wide analysis of transcription factor binding sites based on ChIP-seq data
    • Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, et al. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-seq data. Nat Methods 5: 829-834.
    • (2008) Nat Methods , vol.5 , pp. 829-834
    • Valouev, A.1    Johnson, D.S.2    Sundquist, A.3    Medina, C.4    Anton, E.5
  • 116
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293-1300.
    • (2008) Nat Biotechnol , vol.26 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5
  • 118
    • 84864803359 scopus 로고    scopus 로고
    • Normalization of ChIP-seq data with control
    • Liang K, Keleş S, (2012) Normalization of ChIP-seq data with control. BMC Bioinformatics 13: 199.
    • (2012) BMC Bioinformatics , vol.13 , pp. 199
    • Liang, K.1    Keleş, S.2
  • 119
    • 77951042893 scopus 로고    scopus 로고
    • MochiView: versatile software for genome browsing and DNA motif analysis
    • doi:10.1186/1741-7007-8-49
    • Homann OR, Johnson AD, (2010) MochiView: versatile software for genome browsing and DNA motif analysis. BMC Biol 8: 49 doi: 10.1186/1741-7007-8-49.
    • (2010) BMC Biol , vol.8 , pp. 49
    • Homann, O.R.1    Johnson, A.D.2
  • 120
    • 72949083072 scopus 로고    scopus 로고
    • ChIPing away at the genome: the new frontier travel guide
    • Aleksic J, Russell S, (2009) ChIPing away at the genome: the new frontier travel guide. Mol Biosyst 5: 1421-1428.
    • (2009) Mol Biosyst , vol.5 , pp. 1421-1428
    • Aleksic, J.1    Russell, S.2
  • 123
    • 0036081355 scopus 로고    scopus 로고
    • Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
    • Edgar R, Domrachev M, Lash AE, (2002) Gene Expression Omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res 30: 207-210.
    • (2002) Nucleic Acids Res , vol.30 , pp. 207-210
    • Edgar, R.1    Domrachev, M.2    Lash, A.E.3
  • 124
    • 71049126880 scopus 로고    scopus 로고
    • Visualizing post genomics data-sets on customized pathway maps by ProMeTra - aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example
    • Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, et al. (2009) Visualizing post genomics data-sets on customized pathway maps by ProMeTra- aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. BMC Syst Biol 3: 82.
    • (2009) BMC Syst Biol , vol.3 , pp. 82
    • Neuweger, H.1    Persicke, M.2    Albaum, S.P.3    Bekel, T.4    Dondrup, M.5
  • 125
    • 58149490714 scopus 로고    scopus 로고
    • Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model
    • Li H, Lovci MT, Kwon YS, Rosenfeld MG, Fu XD, et al. (2008) Determination of tag density required for digital transcriptome analysis: application to an androgen-sensitive prostate cancer model. Proc Natl Acad Sci USA 105: 20179-20184.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 20179-20184
    • Li, H.1    Lovci, M.T.2    Kwon, Y.S.3    Rosenfeld, M.G.4    Fu, X.D.5
  • 126
    • 0031974456 scopus 로고    scopus 로고
    • Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co-dependence on two transcription factors
    • Wu H, Tyson KL, Cole JA, Busby SJ, (1998) Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co-dependence on two transcription factors. Mol Microbiol 27: 493-505.
    • (1998) Mol Microbiol , vol.27 , pp. 493-505
    • Wu, H.1    Tyson, K.L.2    Cole, J.A.3    Busby, S.J.4
  • 127
    • 0031031830 scopus 로고    scopus 로고
    • Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition
    • Sawers G, Kaiser M, Sirko A, Freundlich M, (1997) Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition. Mol Microbiol 23: 835-845.
    • (1997) Mol Microbiol , vol.23 , pp. 835-845
    • Sawers, G.1    Kaiser, M.2    Sirko, A.3    Freundlich, M.4
  • 128
    • 0026623120 scopus 로고
    • Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins
    • Sawers G, Suppmann B, (1992) Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins. J Bacteriol 174: 3474-3478.
    • (1992) J Bacteriol , vol.174 , pp. 3474-3478
    • Sawers, G.1    Suppmann, B.2
  • 129
    • 0031815910 scopus 로고    scopus 로고
    • Downregulation of Escherichia coli yfiD expression by FNR occupying a site at -93.5 involves the AR1-containing face of FNR
    • Green J, Baldwin ML, Richardson J, (1998) Downregulation of Escherichia coli yfiD expression by FNR occupying a site at -93.5 involves the AR1-containing face of FNR. Mol Microbiol 29: 1113-1123.
    • (1998) Mol Microbiol , vol.29 , pp. 1113-1123
    • Green, J.1    Baldwin, M.L.2    Richardson, J.3
  • 130
    • 0027452664 scopus 로고
    • Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL
    • Tyson KL, Bell AI, Cole JA, Busby SJ, (1993) Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL. Mol Microbiol 7: 151-157.
    • (1993) Mol Microbiol , vol.7 , pp. 151-157
    • Tyson, K.L.1    Bell, A.I.2    Cole, J.A.3    Busby, S.J.4
  • 131
    • 0026747312 scopus 로고
    • Identification of functional cis-acting sequences involved in regulation of narK gene expression in Escherichia coli
    • Bonnefoy V, DeMoss JA, (1992) Identification of functional cis-acting sequences involved in regulation of narK gene expression in Escherichia coli. Mol Microbiol 6: 3595-3602.
    • (1992) Mol Microbiol , vol.6 , pp. 3595-3602
    • Bonnefoy, V.1    DeMoss, J.A.2
  • 132
    • 39749120541 scopus 로고    scopus 로고
    • Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP
    • Partridge JD, Browning DF, Xu M, Newnham LJ, Scott C, et al. (2008) Characterization of the Escherichia coli K-12 ydhYVWXUT operon: regulation by FNR, NarL and NarP. Microbiology 154: 608-618.
    • (2008) Microbiology , vol.154 , pp. 608-618
    • Partridge, J.D.1    Browning, D.F.2    Xu, M.3    Newnham, L.J.4    Scott, C.5
  • 134
    • 14644406240 scopus 로고    scopus 로고
    • Transcriptional regulation of a hybrid cluster (prismane) protein
    • Filenko NA, Browning DF, Cole JA, (2005) Transcriptional regulation of a hybrid cluster (prismane) protein. Biochem Soc Trans 33: 195-197.
    • (2005) Biochem Soc Trans , vol.33 , pp. 195-197
    • Filenko, N.A.1    Browning, D.F.2    Cole, J.A.3
  • 135
    • 27744565164 scopus 로고    scopus 로고
    • Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions
    • Shalel-Levanon S, San K-Y, Bennett GN, (2005) Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions. Biotechnol Bioeng 92: 147-159.
    • (2005) Biotechnol Bioeng , vol.92 , pp. 147-159
    • Shalel-Levanon, S.1    San, K.-Y.2    Bennett, G.N.3
  • 136
    • 0032436622 scopus 로고    scopus 로고
    • Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli
    • Golby P, Kelly DJ, Guest JR, Andrews SC, (1998) Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli. J Bacteriol 180: 6586-6596.
    • (1998) J Bacteriol , vol.180 , pp. 6586-6596
    • Golby, P.1    Kelly, D.J.2    Guest, J.R.3    Andrews, S.C.4
  • 137
    • 0032588086 scopus 로고    scopus 로고
    • Functioning of DcuC as the C4-dicarboxylate carrier during glucose fermentation by Escherichia coli
    • Zientz E, Janausch IG, Six S, Unden G, (1999) Functioning of DcuC as the C4-dicarboxylate carrier during glucose fermentation by Escherichia coli. J Bacteriol 181: 3716-3720.
    • (1999) J Bacteriol , vol.181 , pp. 3716-3720
    • Zientz, E.1    Janausch, I.G.2    Six, S.3    Unden, G.4
  • 138
    • 34247857563 scopus 로고    scopus 로고
    • Contributions of [4Fe-4S]-FNR and integration host factor to fnr transcriptional regulation
    • Mettert EL, Kiley PJ, (2007) Contributions of [4Fe-4S]-FNR and integration host factor to fnr transcriptional regulation. J Bacteriol 189: 3036-3043.
    • (2007) J Bacteriol , vol.189 , pp. 3036-3043
    • Mettert, E.L.1    Kiley, P.J.2
  • 139
    • 0028276785 scopus 로고
    • Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors
    • Green J, Guest JR, (1994) Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors. Mol Microbiol 12: 433-444.
    • (1994) Mol Microbiol , vol.12 , pp. 433-444
    • Green, J.1    Guest, J.R.2
  • 140
    • 0028177225 scopus 로고
    • The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex
    • Quail MA, Haydon DJ, Guest JR, (1994) The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. Mol Microbiol 12: 95-104.
    • (1994) Mol Microbiol , vol.12 , pp. 95-104
    • Quail, M.A.1    Haydon, D.J.2    Guest, J.R.3
  • 141
    • 0034537304 scopus 로고    scopus 로고
    • Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon
    • Govantes F, Orjalo AV, Gunsalus RP, (2000) Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon. Mol Microbiol 38: 1061-1073.
    • (2000) Mol Microbiol , vol.38 , pp. 1061-1073
    • Govantes, F.1    Orjalo, A.V.2    Gunsalus, R.P.3
  • 142
    • 84866160409 scopus 로고    scopus 로고
    • Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling
    • Kim D, Hong JS-J, Qiu Y, Nagarajan H, Seo J-H, et al. (2012) Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet 8: e1002867.
    • (2012) PLoS Genet , vol.8
    • Kim, D.1    Hong, J.S.-J.2    Qiu, Y.3    Nagarajan, H.4    Seo, J.-H.5
  • 143
    • 0025343878 scopus 로고
    • Cyclic AMP stimulates transcription of the structural gene of the outer-membrane protein OmpA of Escherichia coli
    • Gibert I, Barbé J, (1990) Cyclic AMP stimulates transcription of the structural gene of the outer-membrane protein OmpA of Escherichia coli. FEMS Microbiol Lett 56: 307-311.
    • (1990) FEMS Microbiol Lett , vol.56 , pp. 307-311
    • Gibert, I.1    Barbé, J.2
  • 144
    • 0038013804 scopus 로고    scopus 로고
    • Selective regulation of ptsG expression by Fis. Formation of either activating or repressing nucleoprotein complex in response to glucose
    • Shin D, Cho N, Heu S, Ryu S, (2003) Selective regulation of ptsG expression by Fis. Formation of either activating or repressing nucleoprotein complex in response to glucose. J Biol Chem 278: 14776-14781.
    • (2003) J Biol Chem , vol.278 , pp. 14776-14781
    • Shin, D.1    Cho, N.2    Heu, S.3    Ryu, S.4
  • 145
    • 7444245668 scopus 로고    scopus 로고
    • Identification of the CRP regulon using in vitro and in vivo transcriptional profiling
    • Zheng D, Constantinidou C, Hobman JL, Minchin SD, (2004) Identification of the CRP regulon using in vitro and in vivo transcriptional profiling. Nucleic Acids Res 32: 5874-5893.
    • (2004) Nucleic Acids Res , vol.32 , pp. 5874-5893
    • Zheng, D.1    Constantinidou, C.2    Hobman, J.L.3    Minchin, S.D.4
  • 146
    • 0027291428 scopus 로고
    • Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria
    • Postma PW, Lengeler JW, Jacobson GR, (1993) Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol Rev 57: 543-594.
    • (1993) Microbiol Rev , vol.57 , pp. 543-594
    • Postma, P.W.1    Lengeler, J.W.2    Jacobson, G.R.3
  • 147
    • 0034660020 scopus 로고    scopus 로고
    • Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein
    • Hutchings MI, Drabble WT, (2000) Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein. FEMS Microbiol Lett 187: 115-122.
    • (2000) FEMS Microbiol Lett , vol.187 , pp. 115-122
    • Hutchings, M.I.1    Drabble, W.T.2
  • 148
    • 77956544826 scopus 로고    scopus 로고
    • Overlapping repressor binding sites result in additive regulation of Escherichia coli FadH by FadR and ArcA
    • Feng Y, Cronan JE, (2010) Overlapping repressor binding sites result in additive regulation of Escherichia coli FadH by FadR and ArcA. J Bacteriol 192: 4289-4299.
    • (2010) J Bacteriol , vol.192 , pp. 4289-4299
    • Feng, Y.1    Cronan, J.E.2
  • 149
    • 0028171822 scopus 로고
    • The gene encoding the periplasmic cyclophilin homologue, PPIase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor
    • Nørregaard-Madsen M, Mygind B, Pedersen R, Valentin-Hansen P, Søgaard-Andersen L, (1994) The gene encoding the periplasmic cyclophilin homologue, PPIase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor. Mol Microbiol 14: 989-997.
    • (1994) Mol Microbiol , vol.14 , pp. 989-997
    • Nørregaard-Madsen, M.1    Mygind, B.2    Pedersen, R.3    Valentin-Hansen, P.4    Søgaard-Andersen, L.5
  • 150
    • 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
  • 151
    • 13244291348 scopus 로고    scopus 로고
    • Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli
    • Zhang Z, Gosset G, Barabote R, Gonzalez CS, Cuevas WA, et al. (2005) Functional interactions between the carbon and iron utilization regulators, Crp and Fur, in Escherichia coli. J Bacteriol 187: 980-990.
    • (2005) J Bacteriol , vol.187 , pp. 980-990
    • Zhang, Z.1    Gosset, G.2    Barabote, R.3    Gonzalez, C.S.4    Cuevas, W.A.5
  • 152
    • 36749031105 scopus 로고    scopus 로고
    • Discovery of Fur binding site clusters in Escherichia coli by information theory models
    • Chen Z, Lewis KA, Shultzaberger RK, Lyakhov IG, Zheng M, et al. (2007) Discovery of Fur binding site clusters in Escherichia coli by information theory models. Nucleic Acids Res 35: 6762-6777.
    • (2007) Nucleic Acids Res , vol.35 , pp. 6762-6777
    • Chen, Z.1    Lewis, K.A.2    Shultzaberger, R.K.3    Lyakhov, I.G.4    Zheng, M.5
  • 153
    • 0036415664 scopus 로고    scopus 로고
    • Fur-DNA interactions at the bidirectional fepDGC-entS promoter region in Escherichia coli
    • Lavrrar JL, Christoffersen CA, McIntosh MA, (2002) Fur-DNA interactions at the bidirectional fepDGC-entS promoter region in Escherichia coli. J Mol Biol 322: 983-995.
    • (2002) J Mol Biol , vol.322 , pp. 983-995
    • Lavrrar, J.L.1    Christoffersen, C.A.2    McIntosh, M.A.3
  • 154
    • 0035107832 scopus 로고    scopus 로고
    • Regulatory architecture of the iron-regulated fepD-ybdA bidirectional promoter region in Escherichia coli
    • Christoffersen CA, Brickman TJ, McIntosh MA, (2001) Regulatory architecture of the iron-regulated fepD-ybdA bidirectional promoter region in Escherichia coli. J Bacteriol 183: 2059-2070.
    • (2001) J Bacteriol , vol.183 , pp. 2059-2070
    • Christoffersen, C.A.1    Brickman, T.J.2    McIntosh, M.A.3
  • 155
    • 0025304135 scopus 로고
    • Regulation of divergent transcription from the iron-responsive fepB-entC promoter-operator regions in Escherichia coli
    • Brickman TJ, Ozenberger BA, McIntosh MA, (1990) Regulation of divergent transcription from the iron-responsive fepB-entC promoter-operator regions in Escherichia coli. J Mol Biol 212: 669-682.
    • (1990) J Mol Biol , vol.212 , pp. 669-682
    • Brickman, T.J.1    Ozenberger, B.A.2    McIntosh, M.A.3
  • 156
    • 4644232611 scopus 로고    scopus 로고
    • Multiple site-specific binding of Fis protein to Escherichia coli nuoA-N promoter DNA and its impact on DNA topology visualised by means of scanning force microscopy
    • Zhang J, Zeuner Y, Kleefeld A, Unden G, Janshoff A, (2004) Multiple site-specific binding of Fis protein to Escherichia coli nuoA-N promoter DNA and its impact on DNA topology visualised by means of scanning force microscopy. Chembiochem 5: 1286-1289.
    • (2004) Chembiochem , vol.5 , pp. 1286-1289
    • Zhang, J.1    Zeuner, Y.2    Kleefeld, A.3    Unden, G.4    Janshoff, A.5
  • 157
    • 0028291154 scopus 로고
    • Repression of tonB transcription during anaerobic growth requires Fur binding at the promoter and a second factor binding upstream
    • Young GM, Postle K, (1994) Repression of tonB transcription during anaerobic growth requires Fur binding at the promoter and a second factor binding upstream. Mol Microbiol 11: 943-954.
    • (1994) Mol Microbiol , vol.11 , pp. 943-954
    • Young, G.M.1    Postle, K.2
  • 158
    • 0034532850 scopus 로고    scopus 로고
    • A method for direct cloning of Fur-regulated genes: identification of seven new Fur-regulated loci in Escherichia coli
    • Vassinova N, Kozyrev D, (2000) A method for direct cloning of Fur-regulated genes: identification of seven new Fur-regulated loci in Escherichia coli. Microbiology 146: 3171-3182.
    • (2000) Microbiology , vol.146 , pp. 3171-3182
    • Vassinova, N.1    Kozyrev, D.2
  • 159
    • 0028327173 scopus 로고
    • Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay
    • Stojiljkovic I, Bäumler AJ, Hantke K, (1994) Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay. J Mol Biol 236: 531-545.
    • (1994) J Mol Biol , vol.236 , pp. 531-545
    • Stojiljkovic, I.1    Bäumler, A.J.2    Hantke, K.3
  • 160


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.