메뉴 건너뛰기




Volumn 9, Issue 12, 2014, Pages

The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli

Author keywords

[No Author keywords available]

Indexed keywords

RNA; RNA POLYMERASE; TRANSCRIPTION FACTOR; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN;

EID: 84920138690     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0114347     Document Type: Article
Times cited : (34)

References (91)
  • 1
    • 79959994529 scopus 로고    scopus 로고
    • Quantitative dissection of the simple repression input-output function
    • Garcia HG, Phillips R (2011) Quantitative dissection of the simple repression input-output function. Proc Natl Acad Sci U S A 108: 12173-8.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 12173-12178
    • Garcia, H.G.1    Phillips, R.2
  • 2
    • 0025343547 scopus 로고
    • The three operators of the lac operon cooperate in repression
    • Oehler S, Eismann ER, Kramer H, Muller-Hill B (1990) The three operators of the lac operon cooperate in repression. EMBO J 9: 973-9.
    • (1990) EMBO J , vol.9 , pp. 973-979
    • Oehler, S.1    Eismann, E.R.2    Kramer, H.3    Muller-Hill, B.4
  • 3
    • 67649826220 scopus 로고    scopus 로고
    • From DNA sequence to transcriptional behaviour: A quantitative approach
    • Segal E, Widom J (2009) From DNA sequence to transcriptional behaviour: A quantitative approach. Nat Rev Genet 10: 443-56.
    • (2009) Nat Rev Genet , vol.10 , pp. 443-456
    • Segal, E.1    Widom, J.2
  • 4
    • 84875149194 scopus 로고    scopus 로고
    • Regulation of nucleosome dynamics by histone modifications
    • Zentner GE, Henikoff S (2013) Regulation of nucleosome dynamics by histone modifications. Nat Struct Mol Biol 20: 259-266.
    • (2013) Nat Struct Mol Biol , vol.20 , pp. 259-266
    • Zentner, G.E.1    Henikoff, S.2
  • 5
    • 84876543942 scopus 로고    scopus 로고
    • RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
    • Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muniz-Rascado L, et al. (2013) RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res 41: D203-213.
    • (2013) Nucleic Acids Res , vol.41 , pp. D203-D213
    • Salgado, H.1    Peralta-Gil, M.2    Gama-Castro, S.3    Santos-Zavaleta, A.4    Muniz-Rascado, L.5
  • 7
    • 0001422329 scopus 로고
    • Quantitative model for gene regulation by lambda phage repressor
    • Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulation by lambda phage repressor. Proc Natl Acad Sci U S A 79: 1129-33.
    • (1982) Proc Natl Acad Sci U S A , vol.79 , pp. 1129-1133
    • Ackers, G.K.1    Johnson, A.D.2    Shea, M.A.3
  • 8
    • 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: 21-9.
    • (1996) J Mol Biol , vol.257 , pp. 21-29
    • Müller, J.1    Oehler, S.2    Müller-Hill, B.3
  • 9
    • 84864318077 scopus 로고    scopus 로고
    • Operator sequence alters gene expression independently of transcription factor occupancy in bacteria
    • Garcia HG, Sanchez A, Boedicker JQ, Osborne M, Gelles J, et al. (2012) Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Cell Rep 2: 150-161.
    • (2012) Cell Rep , vol.2 , pp. 150-161
    • Garcia, H.G.1    Sanchez, A.2    Boedicker, J.Q.3    Osborne, M.4    Gelles, J.5
  • 11
    • 0032569960 scopus 로고    scopus 로고
    • GalR-mediated repression and activation of hybrid lacUV5 promoter: Differential contacts with RNA polymerase
    • Ryu S, Fujita N, Ishihama A, Adhya S (1998) GalR-mediated repression and activation of hybrid lacUV5 promoter: differential contacts with RNA polymerase. Gene 223: 235-45.
    • (1998) Gene , vol.223 , pp. 235-245
    • Ryu, S.1    Fujita, N.2    Ishihama, A.3    Adhya, S.4
  • 12
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • Johnson DS, Mortazavi A, Myers RM, Wold B (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-502.
    • (2007) Science , vol.316 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 13
    • 77952706498 scopus 로고    scopus 로고
    • Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
    • Kinney JB, Murugan A, Callan CG, Cox EC (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci USA 107: 9158-9163.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 9158-9163
    • Kinney, J.B.1    Murugan, A.2    Callan, C.G.3    Cox, E.C.4
  • 16
    • 84861120417 scopus 로고    scopus 로고
    • Thermodynamic state ensemble models of cis-regulation
    • Sherman MS, Cohen BA (2012) Thermodynamic state ensemble models of cis-regulation. PLoS Computational Biology 8: e1002407.
    • (2012) PLoS Computational Biology , vol.8 , pp. e1002407
    • Sherman, M.S.1    Cohen, B.A.2
  • 20
    • 0037440734 scopus 로고    scopus 로고
    • Evolution of transcription factors and the gene regulatory network in Escherichia coli
    • Madan Babu M, Teichmann SA (2003) Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Res 31: 1234-1244.
    • (2003) Nucleic Acids Res , vol.31 , pp. 1234-1244
    • Madan Babu, M.1    Teichmann, S.A.2
  • 21
    • 0032716841 scopus 로고    scopus 로고
    • Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid
    • Ali Azam T, Iwata A, Nishimura A, Ueda S, Ishihama A (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol 181: 6361-6370.
    • (1999) J Bacteriol , vol.181 , pp. 6361-6370
    • Ali Azam, T.1    Iwata, A.2    Nishimura, A.3    Ueda, S.4    Ishihama, A.5
  • 26
    • 84872019085 scopus 로고    scopus 로고
    • Tuning promoter strength through RNA polymerase binding site design in Escherichia coli
    • Brewster RC, Jones DL, Phillips R (2012) Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLoS Comput Biol 8: e1002811.
    • (2012) PLoS Comput Biol , vol.8 , pp. e1002811
    • Brewster, R.C.1    Jones, D.L.2    Phillips, R.3
  • 27
    • 0021760063 scopus 로고
    • Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity
    • Mulligan ME, Hawley DK, Entriken R, McClure WR (1984) Escherichia coli promoter sequences predict in vitro RNA polymerase selectivity. Nucleic Acids Research 12: 789-800.
    • (1984) Nucleic Acids Research , vol.12 , pp. 789-800
    • Mulligan, M.E.1    Hawley, D.K.2    Entriken, R.3    McClure, W.R.4
  • 28
    • 0023425487 scopus 로고
    • Promoter recognition and promoter strength in the Escherichia coli system
    • Brunner M, Bujard H (1987) Promoter recognition and promoter strength in the Escherichia coli system. Embo J 6: 3139-44.
    • (1987) Embo J , vol.6 , pp. 3139-3144
    • Brunner, M.1    Bujard, H.2
  • 29
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo GD (2000) DNA binding sites: Representation and discovery. Bioinformatics 16: 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 31
    • 0027048626 scopus 로고
    • Genetics and biogenesis of bacterial flagella
    • Macnab RM (1992) Genetics and biogenesis of bacterial flagella. Annu Rev Genet 26: 131-158.
    • (1992) Annu Rev Genet , vol.26 , pp. 131-158
    • Macnab, R.M.1
  • 32
    • 84861216569 scopus 로고    scopus 로고
    • The copper-inducible ComR (YcfQ) repressor regulates expression of ComC (YcfR), which affects copper permeability of the outer membrane of Escherichia coli
    • Mermod M, Magnani D, Solioz M, Stoyanov JV (2012) The copper-inducible ComR (YcfQ) repressor regulates expression of ComC (YcfR), which affects copper permeability of the outer membrane of Escherichia coli. Biometals 25: 33-43.
    • (2012) Biometals , vol.25 , pp. 33-43
    • Mermod, M.1    Magnani, D.2    Solioz, M.3    Stoyanov, J.V.4
  • 33
    • 0016266070 scopus 로고
    • Cell-free synthesis of a specific lipoprotein of the Escherichia coli outer membrane directed by purified messenger RNA
    • Hirashima A, Wang S, Inouye M (1974) Cell-free synthesis of a specific lipoprotein of the Escherichia coli outer membrane directed by purified messenger RNA. Proc Natl Acad Sci USA 71: 4149-4153.
    • (1974) Proc Natl Acad Sci USA , vol.71 , pp. 4149-4153
    • Hirashima, A.1    Wang, S.2    Inouye, M.3
  • 34
    • 0018291009 scopus 로고
    • The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III
    • Takahashi S, Hours C, Chu A, Denhardt DT (1979) The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III. Can J Biochem 57: 855-866.
    • (1979) Can J Biochem , vol.57 , pp. 855-866
    • Takahashi, S.1    Hours, C.2    Chu, A.3    Denhardt, D.T.4
  • 35
    • 0011100093 scopus 로고
    • Osmotic control of kdp operon expression in Escherichia coli
    • Laimins LA, Rhoads DB, Epstein W (1981) Osmotic control of kdp operon expression in Escherichia coli. Proc Natl Acad Sci USA 78: 464-468.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 464-468
    • Laimins, L.A.1    Rhoads, D.B.2    Epstein, W.3
  • 36
    • 0026075706 scopus 로고
    • Characterization and mapping of a major Na+/H+ antiporter gene of Escherichia coli
    • Thelen P, Tsuchiya T, Goldberg EB (1991) Characterization and mapping of a major Na+/H+ antiporter gene of Escherichia coli. J Bacteriol 173: 6553-6557.
    • (1991) J Bacteriol , vol.173 , pp. 6553-6557
    • Thelen, P.1    Tsuchiya, T.2    Goldberg, E.B.3
  • 37
    • 54249135920 scopus 로고    scopus 로고
    • GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: Transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites
    • Tramonti A, De Canio M, De Biase D (2008) GadX/GadW-dependent regulation of the Escherichia coli acid fitness island: Transcriptional control at the gadY-gadW divergent promoters and identification of four novel 42 bp GadX/GadW-specific binding sites. Mol Microbiol 70: 965-982.
    • (2008) Mol Microbiol , vol.70 , pp. 965-982
    • Tramonti, A.1    De Canio, M.2    De Biase, D.3
  • 38
    • 0029561748 scopus 로고
    • Expression of two csg operons is required for production of fibronectin- and congo red-binding curli polymers in Escherichia coli K-12
    • Hammar M, Arnqvist A, Bian Z, Olsen A, Normark S (1995) Expression of two csg operons is required for production of fibronectin- and congo red-binding curli polymers in Escherichia coli K-12. Mol Microbiol 18: 661-670.
    • (1995) Mol Microbiol , vol.18 , pp. 661-670
    • Hammar, M.1    Arnqvist, A.2    Bian, Z.3    Olsen, A.4    Normark, S.5
  • 39
    • 84890603570 scopus 로고
    • Phosphorus Assimilation and Its Control of Gene-Expression in Escherichia-Coli
    • Wanner BL (1990) Phosphorus Assimilation and Its Control of Gene-Expression in Escherichia-Coli. Biological Chemistry Hoppe-Seyler 371: 180-180.
    • (1990) Biological Chemistry Hoppe-Seyler , vol.371 , pp. 180-180
    • Wanner, B.L.1
  • 40
    • 0027507211 scopus 로고
    • Effect of glpT and glpD mutations on expression of the phoA gene in Escherichia coli
    • Rao NN, Roberts MF, Torriani A, Yashphe J (1993) Effect of glpT and glpD mutations on expression of the phoA gene in Escherichia coli. J Bacteriol 175: 74-79.
    • (1993) J Bacteriol , vol.175 , pp. 74-79
    • Rao, N.N.1    Roberts, M.F.2    Torriani, A.3    Yashphe, J.4
  • 42
    • 0028023175 scopus 로고
    • Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: A mechanism for differential promoter selection
    • Toledano MB, Kullik I, Trinh F, Baird PT, Schneider TD, et al. (1994) Redox-dependent shift of OxyR-DNA contacts along an extended DNA-binding site: A mechanism for differential promoter selection. Cell 78: 897-909.
    • (1994) Cell , vol.78 , pp. 897-909
    • Toledano, M.B.1    Kullik, I.2    Trinh, F.3    Baird, P.T.4    Schneider, T.D.5
  • 43
    • 0026654183 scopus 로고
    • Binding of the arginine repressor of Escherichia coli K12 to its operator sites
    • Tian G, Lim D, Carey J, Maas WK (1992) Binding of the arginine repressor of Escherichia coli K12 to its operator sites. J Mol Biol 226: 387-397.
    • (1992) J Mol Biol , vol.226 , pp. 387-397
    • Tian, G.1    Lim, D.2    Carey, J.3    Maas, W.K.4
  • 44
    • 0031786214 scopus 로고    scopus 로고
    • Integration host factor and cyclic AMP receptor protein are required for TyrR-mediated activation of tpl in Citrobacter freundii
    • Bai Q, Somerville RL (1998) Integration host factor and cyclic AMP receptor protein are required for TyrR-mediated activation of tpl in Citrobacter freundii. J Bacteriol 180: 6173-6186.
    • (1998) J Bacteriol , vol.180 , pp. 6173-6186
    • Bai, Q.1    Somerville, R.L.2
  • 45
    • 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
  • 46
    • 0035945265 scopus 로고    scopus 로고
    • An architectural role of the Escherichia coli chromatin protein FIS in organising DNA
    • Schneider R, Lurz R, Luder G, Tolksdorf C, Travers A, et al. (2001) An architectural role of the Escherichia coli chromatin protein FIS in organising DNA. Nucleic Acids Res 29: 5107-5114.
    • (2001) Nucleic Acids Res , vol.29 , pp. 5107-5114
    • Schneider, R.1    Lurz, R.2    Luder, G.3    Tolksdorf, C.4    Travers, A.5
  • 47
    • 84894515074 scopus 로고    scopus 로고
    • Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration
    • Rydenfelt M, Cox RS, Garcia H, Phillips R (2014) Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration. Phys Rev E 89: 012702.
    • (2014) Phys Rev e , vol.89 , pp. 012702
    • Rydenfelt, M.1    Cox, R.S.2    Garcia, H.3    Phillips, R.4
  • 48
    • 84896392369 scopus 로고    scopus 로고
    • The transcription factor titration effect dictates level of gene expression
    • Brewster RC, Weinert FM, Garcia HG, Song D, Rydenfelt M, et al. (2014) The transcription factor titration effect dictates level of gene expression. Cell 156: 1312-1323.
    • (2014) Cell , vol.156 , pp. 1312-1323
    • Brewster, R.C.1    Weinert, F.M.2    Garcia, H.G.3    Song, D.4    Rydenfelt, M.5
  • 49
    • 77955102352 scopus 로고    scopus 로고
    • Quantifying E. coli proteome and rranscriptome with single-molecule sensitivity in single cells
    • Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, et al. (2010) Quantifying E. coli proteome and rranscriptome with single-molecule sensitivity in single cells. Science 329: 533-538.
    • (2010) Science , vol.329 , pp. 533-538
    • Taniguchi, Y.1    Choi, P.J.2    Li, G.W.3    Chen, H.4    Babu, M.5
  • 50
    • 33846165487 scopus 로고    scopus 로고
    • Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation
    • Lu P, Vogel C, Wang R, Yao X, Marcotte EM (2007) Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nat Biotechnol 25: 117-24.
    • (2007) Nat Biotechnol , vol.25 , pp. 117-124
    • Lu, P.1    Vogel, C.2    Wang, R.3    Yao, X.4    Marcotte, E.M.5
  • 51
    • 84899550455 scopus 로고    scopus 로고
    • Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources
    • Li GW, Burkhardt D, Gross C, Weissman JS (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157: 624-35.
    • (2014) Cell , vol.157 , pp. 624-635
    • Li, G.W.1    Burkhardt, D.2    Gross, C.3    Weissman, J.S.4
  • 52
    • 0002344794 scopus 로고
    • Bootstrap methods: Another look at the jackknife
    • Efron B (1979) Bootstrap methods: Another look at the jackknife. Ann Statistics 7: 1-26.
    • (1979) Ann Statistics , vol.7 , pp. 1-26
    • Efron, B.1
  • 53
    • 54249116230 scopus 로고
    • Genetic regulatory mechanisms in the synthesis of proteins
    • Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318-356.
    • (1961) J Mol Biol , vol.3 , pp. 318-356
    • Jacob, F.1    Monod, J.2
  • 54
    • 0027419613 scopus 로고
    • Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli
    • Cohen SP, Hachler H, Levy SB (1993) Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli. J Bacteriol 175: 1484-1492.
    • (1993) J Bacteriol , vol.175 , pp. 1484-1492
    • Cohen, S.P.1    Hachler, H.2    Levy, S.B.3
  • 55
    • 0032746803 scopus 로고    scopus 로고
    • Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: Sequence, orientation and spatial relationship to the core promoter
    • Martin RG, Gillette WK, Rhee S, Rosner JL (1999) Structural requirements for marbox function in transcriptional activation of mar/sox/rob regulon promoters in Escherichia coli: sequence, orientation and spatial relationship to the core promoter. Mol Microbiol 34: 431-441.
    • (1999) Mol Microbiol , vol.34 , pp. 431-441
    • Martin, R.G.1    Gillette, W.K.2    Rhee, S.3    Rosner, J.L.4
  • 56
    • 0031026282 scopus 로고    scopus 로고
    • Functional characterization of roles of GalR and GalS as regulators of the gal regulon
    • Geanacopoulos M, Adhya S (1997) Functional characterization of roles of GalR and GalS as regulators of the gal regulon. J Bacteriol 179: 228-34.
    • (1997) J Bacteriol , vol.179 , pp. 228-234
    • Geanacopoulos, M.1    Adhya, S.2
  • 57
    • 15944366483 scopus 로고    scopus 로고
    • Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses
    • Levanon SS, San KY, Bennett GN (2005) Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses. Biotechnol Bioeng 89: 556-564.
    • (2005) Biotechnol Bioeng , vol.89 , pp. 556-564
    • Levanon, S.S.1    San, K.Y.2    Bennett, G.N.3
  • 58
    • 0027251261 scopus 로고
    • Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12
    • Rabin RS, Stewart V (1993) Dual response regulators (NarL and NarP) interact with dual sensors (NarX and NarQ) to control nitrate- and nitrite-regulated gene expression in Escherichia coli K-12. J Bacteriol 175: 3259-3268.
    • (1993) J Bacteriol , vol.175 , pp. 3259-3268
    • Rabin, R.S.1    Stewart, V.2
  • 59
    • 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
  • 60
    • 32544461820 scopus 로고    scopus 로고
    • Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: New insights into microbial physiology
    • Overton TW, Griffiths L, Patel MD, Hobman JL, Penn CW, et al. (2006) Microarray analysis of gene regulation by oxygen, nitrate, nitrite, FNR, NarL and NarP during anaerobic growth of Escherichia coli: New insights into microbial physiology. Biochem Soc Trans 34: 104-107.
    • (2006) Biochem Soc Trans , vol.34 , pp. 104-107
    • Overton, T.W.1    Griffiths, L.2    Patel, M.D.3    Hobman, J.L.4    Penn, C.W.5
  • 61
    • 84879620270 scopus 로고    scopus 로고
    • Genome-scale analysis of Escherichia coli FNR reveals complex features of transcription factor binding
    • Myers KS, Yan H, Ong IM, Chung D, Liang K, et al. (2013) Genome-scale analysis of Escherichia coli FNR reveals complex features of transcription factor binding. PLoS Genet 9: e1003565.
    • (2013) PLoS Genet , vol.9 , pp. e1003565
    • Myers, K.S.1    Yan, H.2    Ong, I.M.3    Chung, D.4    Liang, K.5
  • 62
    • 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
  • 63
    • 80054719570 scopus 로고    scopus 로고
    • The Fur regulon in anaerobically grown Salmonella enterica sv. Typhimurium: Identification of new Fur targets
    • Troxell B, Fink RC, Porwollik S, McClelland M, Hassan HM (2011) The Fur regulon in anaerobically grown Salmonella enterica sv. Typhimurium: Identification of new Fur targets. BMC Microbiol 11: 236.
    • (2011) BMC Microbiol , vol.11 , pp. 236
    • Troxell, B.1    Fink, R.C.2    Porwollik, S.3    McClelland, M.4    Hassan, H.M.5
  • 64
    • 0026682712 scopus 로고
    • Isorepressor of the gal regulon in Escherichia coli
    • Weickert MJ, Adhya S (1992) Isorepressor of the gal regulon in Escherichia coli. J Mol Biol 226: 69-83.
    • (1992) J Mol Biol , vol.226 , pp. 69-83
    • Weickert, M.J.1    Adhya, S.2
  • 65
    • 0030907304 scopus 로고    scopus 로고
    • Activation of prokaryotic transcription through arbitrary protein-protein contacts
    • Dove SL, Joung JK, Hochschild A (1997) Activation of prokaryotic transcription through arbitrary protein-protein contacts. Nature 386: 627-630.
    • (1997) Nature , vol.386 , pp. 627-630
    • Dove, S.L.1    Joung, J.K.2    Hochschild, A.3
  • 66
    • 0004211673 scopus 로고    scopus 로고
    • New York: Cold Spring Harbor Laboratory Press
    • Ptashne M, Gann A (2002) Genes and Signals. New York: Cold Spring Harbor Laboratory Press.
    • (2002) Genes and Signals
    • Ptashne, M.1    Gann, A.2
  • 67
    • 70349873824 scopus 로고    scopus 로고
    • Comprehensive mapping of long-range interactions reveals folding principles of the human genome
    • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, et al. (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326: 289-293.
    • (2009) Science , vol.326 , pp. 289-293
    • Lieberman-Aiden, E.1    Van Berkum, N.L.2    Williams, L.3    Imakaev, M.4    Ragoczy, T.5
  • 68
    • 0032698634 scopus 로고    scopus 로고
    • Transcription activation by catabolite activator protein (CAP)
    • Busby S, Ebright RH (1999) Transcription activation by catabolite activator protein (CAP). J Mol Biol 293: 199-213.
    • (1999) J Mol Biol , vol.293 , pp. 199-213
    • Busby, S.1    Ebright, R.H.2
  • 69
    • 0032489504 scopus 로고    scopus 로고
    • Protein-protein contacts that activate and repress prokaryotic transcription
    • Hochschild A, Dove SL (1998) Protein-protein contacts that activate and repress prokaryotic transcription. Cell 92: 597-600.
    • (1998) Cell , vol.92 , pp. 597-600
    • Hochschild, A.1    Dove, S.L.2
  • 70
    • 0025309753 scopus 로고
    • Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein
    • Pavco PA, Steege DA (1990) Elongation by Escherichia coli RNA polymerase is blocked in vitro by a site-specific DNA binding protein. J Biol Chem 265: 9960-9969.
    • (1990) J Biol Chem , vol.265 , pp. 9960-9969
    • Pavco, P.A.1    Steege, D.A.2
  • 71
    • 0025832198 scopus 로고
    • Characterization of elongating T7 and SP6 RNA polymerases and their response to a roadblock generated by a site-specific DNA binding protein
    • Pavco PA, Steege DA (1991) Characterization of elongating T7 and SP6 RNA polymerases and their response to a roadblock generated by a site-specific DNA binding protein. Nucleic Acids Res 19: 4639-4646.
    • (1991) Nucleic Acids Res , vol.19 , pp. 4639-4646
    • Pavco, P.A.1    Steege, D.A.2
  • 72
    • 0032955002 scopus 로고    scopus 로고
    • Repression of transcription initiation in bacteria
    • Rojo F (1999) Repression of transcription initiation in bacteria. J Bacteriol 181: 2987-2991.
    • (1999) J Bacteriol , vol.181 , pp. 2987-2991
    • Rojo, F.1
  • 73
    • 33847164986 scopus 로고    scopus 로고
    • Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity
    • Garcia HG, Grayson P, Han L, Inamdar M, Kondev J, et al. (2007) Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity. Biopolymers 85: 115-30.
    • (2007) Biopolymers , vol.85 , pp. 115-130
    • Garcia, H.G.1    Grayson, P.2    Han, L.3    Inamdar, M.4    Kondev, J.5
  • 74
    • 0028298256 scopus 로고
    • Promoters responsive to DNA bending: A common theme in prokaryotic gene expression
    • Pérez-Martín J, Rojo F, De Lorenzo V (1994) Promoters responsive to DNA bending: A common theme in prokaryotic gene expression. Microbiological Reviews 58: 268-290.
    • (1994) Microbiological Reviews , vol.58 , pp. 268-290
    • Pérez-Martín, J.1    Rojo, F.2    De Lorenzo, V.3
  • 75
    • 0024814234 scopus 로고
    • Bending of DNA by gene-regulatory proteins: Construction and use of a DNA bending vector
    • Kim J, Zwieb C, Wu C, Adhya S (1989) Bending of DNA by gene-regulatory proteins: Construction and use of a DNA bending vector. Gene 85: 15-23.
    • (1989) Gene , vol.85 , pp. 15-23
    • Kim, J.1    Zwieb, C.2    Wu, C.3    Adhya, S.4
  • 76
    • 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
  • 77
    • 84877355212 scopus 로고    scopus 로고
    • Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology
    • Ruths T, Nakhleh L (2013) Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology. Proc Natl Acad Sci USA 110: 7754-7759.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 7754-7759
    • Ruths, T.1    Nakhleh, L.2
  • 78
    • 78449268845 scopus 로고    scopus 로고
    • Interdependence of cell growth and gene expression: Origins and consequences
    • Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T (2010) Interdependence of cell growth and gene expression: origins and consequences. Science 330: 1099-102.
    • (2010) Science , vol.330 , pp. 1099-1102
    • Scott, M.1    Gunderson, C.W.2    Mateescu, E.M.3    Zhang, Z.4    Hwa, T.5
  • 81
    • 84887642503 scopus 로고    scopus 로고
    • Efficient transcription initiation in bacteria: An interplay of protein-DNA interaction parameters
    • Djordjevic M (2013) Efficient transcription initiation in bacteria: An interplay of protein-DNA interaction parameters. Integr Biol (Camb) 5: 796-806.
    • (2013) Integr Biol (Camb) , vol.5 , pp. 796-806
    • Djordjevic, M.1
  • 82
    • 17644369311 scopus 로고    scopus 로고
    • Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites
    • Gershenzon NI, Stormo GD, Ioshikhes IP (2005) Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res 33: 2290-2301.
    • (2005) Nucleic Acids Res , vol.33 , pp. 2290-2301
    • Gershenzon, N.I.1    Stormo, G.D.2    Ioshikhes, I.P.3
  • 83
    • 0242574990 scopus 로고    scopus 로고
    • A biophysical approach to transcription factor binding site discovery
    • Djordjevic M, Sengupta AM, Shraiman BI (2003) A biophysical approach to transcription factor binding site discovery. Genome Res 13: 2381-2390.
    • (2003) Genome Res , vol.13 , pp. 2381-2390
    • Djordjevic, M.1    Sengupta, A.M.2    Shraiman, B.I.3
  • 84
    • 1842383693 scopus 로고
    • Rate-limiting steps in RNA chain initiation
    • McClure WR (1980) Rate-limiting steps in RNA chain initiation. Proc Natl Acad Sci USA 77: 5634-5638.
    • (1980) Proc Natl Acad Sci USA , vol.77 , pp. 5634-5638
    • McClure, W.R.1
  • 85
    • 0021891874 scopus 로고
    • Mechanism and control of transcription initiation in prokaryotes
    • McClure WR (1985) Mechanism and control of transcription initiation in prokaryotes. Annu Rev Biochem 54: 171-204.
    • (1985) Annu Rev Biochem , vol.54 , pp. 171-204
    • McClure, W.R.1
  • 86
    • 0141758085 scopus 로고    scopus 로고
    • Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals
    • Huerta AM, Collado-Vides J (2003) Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J Mol Biol 333: 261-78.
    • (2003) J Mol Biol , vol.333 , pp. 261-278
    • Huerta, A.M.1    Collado-Vides, J.2
  • 87
    • 79960264362 scopus 로고    scopus 로고
    • Full-length transcriptome assembly from RNA-Seq data without a reference genome
    • Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652.
    • (2011) Nat Biotechnol , vol.29 , pp. 644-652
    • Grabherr, M.G.1    Haas, B.J.2    Yassour, M.3    Levin, J.Z.4    Thompson, D.A.5
  • 88
    • 72249097352 scopus 로고    scopus 로고
    • Growth-rate dependent global effects on gene expression in bacteria
    • Klumpp S, Zhang Z, Hwa T (2009) Growth-rate dependent global effects on gene expression in bacteria. Cell.
    • (2009) Cell
    • Klumpp, S.1    Zhang, Z.2    Hwa, T.3
  • 89
    • 36249017917 scopus 로고    scopus 로고
    • Programming gene expression with combinatorial promoters
    • Cox RS, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3: 145.
    • (2007) Mol Syst Biol , vol.3 , pp. 145
    • Cox, R.S.1    Surette, M.G.2    Elowitz, M.B.3
  • 90
    • 0242386460 scopus 로고    scopus 로고
    • Identifying global regulators in transcriptional regulatory networks in bacteria
    • Martinez-Antonio A, Collado-Vides J (2003) Identifying global regulators in transcriptional regulatory networks in bacteria. Curr Opin Microbiol 6: 482-9.
    • (2003) Curr Opin Microbiol , vol.6 , pp. 482-489
    • Martinez-Antonio, A.1    Collado-Vides, J.2
  • 91
    • 61449254451 scopus 로고    scopus 로고
    • Principles of transcriptional regulation and evolution of the metabolic system in E. coli
    • Seshasayee AS, Fraser GM, Babu MM, Luscombe NM (2009) Principles of transcriptional regulation and evolution of the metabolic system in E. coli. Genome Res 19: 79-91.
    • (2009) Genome Res , vol.19 , pp. 79-91
    • Seshasayee, A.S.1    Fraser, G.M.2    Babu, M.M.3    Luscombe, N.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.