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Volumn 333, Issue 2, 2003, Pages 261-278

Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals

Author keywords

Computational predictions; Escherichia coli; Overlapping signals; Sigma70 promoters

Indexed keywords

RNA POLYMERASE;

EID: 0141758085     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2003.07.017     Document Type: Article
Times cited : (182)

References (57)
  • 1
    • 0343597687 scopus 로고
    • Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter
    • Pribnow D. Nucleotide sequence of an RNA polymerase binding site at an early T7 promoter. Proc. Natl Acad. Sci. USA. 72:1975;784-788.
    • (1975) Proc. Natl Acad. Sci. USA , vol.72 , pp. 784-788
    • Pribnow, D.1
  • 2
    • 0017353007 scopus 로고
    • Interaction of RNA polymerase with promoters from bacteriophage fd
    • Seeburg P.H., Nusslein C., Schaller H. Interaction of RNA polymerase with promoters from bacteriophage fd. Eur. J. Biochem. 74:1977;107-113.
    • (1977) Eur. J. Biochem. , vol.74 , pp. 107-113
    • Seeburg, P.H.1    Nusslein, C.2    Schaller, H.3
  • 3
    • 0021111879 scopus 로고
    • Compilation and analysis of Escherichia coli promoter DNA sequences
    • Hawley D.K., McClure W.R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucl. Acids Res. 11:1983;2237-2255.
    • (1983) Nucl. Acids Res. , vol.11 , pp. 2237-2255
    • Hawley, D.K.1    McClure, W.R.2
  • 4
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli
    • Galas D.J., Eggert M., Waterman M.S. Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Mol. Biol. 186:1985;117-128.
    • (1985) J. Mol. Biol. , vol.186 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2    Waterman, M.S.3
  • 5
    • 0023650609 scopus 로고
    • Analysis of E. coli promoter sequences
    • Harley C.B., Reynolds R.P. Analysis of E. coli promoter sequences. Nucl. Acids Res. 15:1987;2343-2361.
    • (1987) Nucl. Acids Res. , vol.15 , pp. 2343-2361
    • Harley, C.B.1    Reynolds, R.P.2
  • 6
    • 0027230594 scopus 로고
    • Compilation of E. coli mRNA promoter sequences
    • Lisser S., Margalit H. Compilation of E. coli mRNA promoter sequences. Nucl. Acids Res. 21:1993;1507-1516.
    • (1993) Nucl. Acids Res. , vol.21 , pp. 1507-1516
    • Lisser, S.1    Margalit, H.2
  • 8
    • 0023644795 scopus 로고
    • Constitutive function of a positively regulated promoter reveals new sequences essential for activity
    • Keilty S., Rosenberg M. Constitutive function of a positively regulated promoter reveals new sequences essential for activity. J. Biol. Chem. 262:1987;6389-6395.
    • (1987) J. Biol. Chem. , vol.262 , pp. 6389-6395
    • Keilty, S.1    Rosenberg, M.2
  • 9
    • 0027295666 scopus 로고
    • The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "Extended minus 10" promoter
    • Kumar A., Malloch R.A., Fujita N., Smillie D.A., Ishihama A., Hayward R.S. The minus 35-recognition region of Escherichia coli sigma 70 is inessential for initiation of transcription at an "Extended minus 10" promoter. J. Mol. Biol. 232:1993;406-418.
    • (1993) J. Mol. Biol. , vol.232 , pp. 406-418
    • Kumar, A.1    Malloch, R.A.2    Fujita, N.3    Smillie, D.A.4    Ishihama, A.5    Hayward, R.S.6
  • 10
    • 0030965301 scopus 로고    scopus 로고
    • Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters
    • Barne K.A., Bown J., Busby S.J., Minchin S.D. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. EMBO J. 16:1997;4034-4040.
    • (1997) EMBO J. , vol.16 , pp. 4034-4040
    • Barne, K.A.1    Bown, J.2    Busby, S.J.3    Minchin, S.D.4
  • 11
    • 0034192263 scopus 로고    scopus 로고
    • DNA sequence elements located immediately upstream of the -10 hexamer in Escherichiacoli promoters: A systematic study
    • Burr T., Mitchell J., Kolb A., Minchin S., Busby S. DNA sequence elements located immediately upstream of the -10 hexamer in Escherichiacoli promoters: a systematic study. Nucl. Acids Res. 28:2000;1864-1870.
    • (2000) Nucl. Acids Res. , vol.28 , pp. 1864-1870
    • Burr, T.1    Mitchell, J.2    Kolb, A.3    Minchin, S.4    Busby, S.5
  • 12
    • 0141605202 scopus 로고    scopus 로고
    • Identification and analysis of 'extended -10' promoters in Escherichia coli
    • Mitchell J.E., Zheng D., Busby S.J., Minchin S.D. Identification and analysis of 'extended -10' promoters in Escherichia coli. Nucl. Acids Res. 31:2003;4689-4695.
    • (2003) Nucl. Acids Res. , vol.31 , pp. 4689-4695
    • Mitchell, J.E.1    Zheng, D.2    Busby, S.J.3    Minchin, S.D.4
  • 13
    • 0023801563 scopus 로고
    • Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro
    • Makino K., Shinagawa H., Amemura M., Kimura S., Nakata A. Regulation of the phosphate regulon of Escherichia coli. Activation of pstS transcription by PhoB protein in vitro. J. Mol. Biol. 203:1988;85-95.
    • (1988) J. Mol. Biol. , vol.203 , pp. 85-95
    • Makino, K.1    Shinagawa, H.2    Amemura, M.3    Kimura, S.4    Nakata, A.5
  • 14
    • 0033624446 scopus 로고    scopus 로고
    • Recognition of overlapping nucleotides by AraC and the sigma subunit of RNA polymerase
    • Dhiman A., Schleif R. Recognition of overlapping nucleotides by AraC and the sigma subunit of RNA polymerase. J. Bacteriol. 182:2000;5076-5081.
    • (2000) J. Bacteriol. , vol.182 , pp. 5076-5081
    • Dhiman, A.1    Schleif, R.2
  • 15
    • 0020958539 scopus 로고
    • A computer graphics study of sequence-directed bending in DNA
    • Levene S.D., Crothers D.M. A computer graphics study of sequence-directed bending in DNA. J. Biomol. Struct. Dynam. 1:1983;429-435.
    • (1983) J. Biomol. Struct. Dynam. , vol.1 , pp. 429-435
    • Levene, S.D.1    Crothers, D.M.2
  • 16
    • 0027761839 scopus 로고
    • A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase
    • Ross W., Gosink K.K., Salomon J., Igarashi K., Zou C., Ishihama A., et al. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science. 262:1993;1407-1413.
    • (1993) Science , vol.262 , pp. 1407-1413
    • Ross, W.1    Gosink, K.K.2    Salomon, J.3    Igarashi, K.4    Zou, C.5    Ishihama, A.6
  • 17
    • 0033567215 scopus 로고    scopus 로고
    • Bacterial promoter architecture: Subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit
    • Estrem S.T., Ross W., Gaal T., Chen Z.W., Niu W., Ebright R.H., Gourse R.L. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes. Dev. 13:1999;2134-2147.
    • (1999) Genes. Dev. , vol.13 , pp. 2134-2147
    • Estrem, S.T.1    Ross, W.2    Gaal, T.3    Chen, Z.W.4    Niu, W.5    Ebright, R.H.6    Gourse, R.L.7
  • 18
    • 0035979258 scopus 로고    scopus 로고
    • Function of the bacterial TATAAT -10 element as single-stranded DNA during RNA polymerase isomerization
    • Fenton M.S., Gralla J.D. Function of the bacterial TATAAT -10 element as single-stranded DNA during RNA polymerase isomerization. Proc. Natl Acad Sci. USA. 98:2001;9020-9025.
    • (2001) Proc. Natl Acad Sci. USA , vol.98 , pp. 9020-9025
    • Fenton, M.S.1    Gralla, J.D.2
  • 19
    • 0037123659 scopus 로고    scopus 로고
    • Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution
    • Murakami K.S., Masuda S., Darst S.A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science. 296:2002;1280-1284.
    • (2002) Science. , vol.296 , pp. 1280-1284
    • Murakami, K.S.1    Masuda, S.2    Darst, S.A.3
  • 20
    • 0030686456 scopus 로고    scopus 로고
    • Non-canonical sequence elements in the promoter structure. Cluster analysis of promoters recognized by Escherichia coli RNA polymerase
    • Ozoline O.N., Deev A.A., Arkhipova M.V. Non-canonical sequence elements in the promoter structure. Cluster analysis of promoters recognized by Escherichia coli RNA polymerase. Nucl. Acids Res. 25:1997;4703-4709.
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4703-4709
    • Ozoline, O.N.1    Deev, A.A.2    Arkhipova, M.V.3
  • 21
    • 0028587703 scopus 로고
    • Promoter strength prediction based on occurrence frequencies of consensus patterns
    • Weller K., Recknagel R.D. Promoter strength prediction based on occurrence frequencies of consensus patterns. J. Theor. Biol. 171:1994;355-359.
    • (1994) J. Theor. Biol. , vol.171 , pp. 355-359
    • Weller, K.1    Recknagel, R.D.2
  • 22
    • 0026019013 scopus 로고
    • Hierarchies of base pair preferences in P22 ant promoter
    • Moyle H., Waldburger C., Susskind M.M. Hierarchies of base pair preferences in P22 ant promoter. J. Bacteriol. 173:1991;1944-1950.
    • (1991) J. Bacteriol. , vol.173 , pp. 1944-1950
    • Moyle, H.1    Waldburger, C.2    Susskind, M.M.3
  • 25
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics. 16:2000;16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 26
    • 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 A.M., Church G.M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284:1998;241-254.
    • (1998) J. Mol. Biol. , vol.284 , pp. 241-254
    • Robison, K.1    McGuire, A.M.2    Church, G.M.3
  • 27
    • 0029845236 scopus 로고    scopus 로고
    • Escherichia coli promoter sequences: Analysis and prediction
    • Hertz G.Z., Stormo G.D. Escherichia coli promoter sequences: analysis and prediction. Methods Enzymol. 273:1996;30-42.
    • (1996) Methods Enzymol. , vol.273 , pp. 30-42
    • Hertz, G.Z.1    Stormo, G.D.2
  • 28
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz G.Z., Stormo G.D. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics. 15:1999;563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 29
    • 0000661051 scopus 로고    scopus 로고
    • Organization and function of transcription regulatory elements
    • F.C. Neidhart, R. Curtiss, J. Ingraham, E.C.C. Lin, K.B. Low, & B. et al. Magasanik. Washington, DC: American Society for Microbiology
    • Gralla J., Collado-Vides J. Organization and function of transcription regulatory elements. Neidhart F.C., Curtiss R., Ingraham J., Lin E.C.C., Low K.B., Magasanik B., et al. Escherichia coli and Salmonella, Cellular and Molecular Biology. 1996;1232-1246 American Society for Microbiology, Washington, DC.
    • (1996) Escherichia coli and Salmonella, Cellular and Molecular Biology , pp. 1232-1246
    • Gralla, J.1    Collado-Vides, J.2
  • 30
    • 0032544080 scopus 로고    scopus 로고
    • Identification of an UP element consensus sequence for bacterial promoters
    • Estrem S.T., Gaal T., Ross W., Gourse R.L. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl Acad. Sci. USA. 95:1998;9761-9766.
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 9761-9766
    • Estrem, S.T.1    Gaal, T.2    Ross, W.3    Gourse, R.L.4
  • 31
    • 0032032780 scopus 로고    scopus 로고
    • Specificity, free energy and information content in protein-DNA interactions
    • Stormo G.D., Fields D.S. Specificity, free energy and information content in protein-DNA interactions. Trends Biochem. Sci. 23:1998;109-113.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 109-113
    • Stormo, G.D.1    Fields, D.S.2
  • 32
    • 0031801743 scopus 로고    scopus 로고
    • Information processing by RNA polymerase: Recognition of regulatory signals during RNA chain elongation
    • Mooney R.A., Artsimovitch I., Landick R. Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol. 180:1998;3265-3275.
    • (1998) J. Bacteriol. , vol.180 , pp. 3265-3275
    • Mooney, R.A.1    Artsimovitch, I.2    Landick, R.3
  • 36
    • 0027983641 scopus 로고
    • CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending
    • Richet E., Sogaard-Andersen L. CRP induces the repositioning of MalT at the Escherichia coli malKp promoter primarily through DNA bending. EMBO J. 13:1994;4558-4567.
    • (1994) EMBO J. , vol.13 , pp. 4558-4567
    • Richet, E.1    Sogaard-Andersen, L.2
  • 37
    • 0343066722 scopus 로고    scopus 로고
    • Promoter interference in a bacteriophage lambda control region: Effects of a range of inter-promoter distances
    • Strainic M.G. Jr, Sullivan J.J., Collado-Vides J., DeHaseth P.L. Promoter interference in a bacteriophage lambda control region: effects of a range of inter-promoter distances. J. Bacteriol. 182:2000;216-220.
    • (2000) J. Bacteriol. , vol.182 , pp. 216-220
    • Strainic M.G., Jr.1    Sullivan, J.J.2    Collado-Vides, J.3    DeHaseth, P.L.4
  • 38
    • 0026800608 scopus 로고
    • The lactose operon-controlling elements: A complex paradigm
    • Reznikoff W. The lactose operon-controlling elements: a complex paradigm. Mol. Microbiol. 6:1992;2419-2422.
    • (1992) Mol. Microbiol. , vol.6 , pp. 2419-2422
    • Reznikoff, W.1
  • 39
    • 0025342573 scopus 로고
    • Consensus patterns in DNA
    • Stormo G. Consensus patterns in DNA. Methods Enzymol. 183:1990;211-221.
    • (1990) Methods Enzymol. , vol.183 , pp. 211-221
    • Stormo, G.1
  • 40
    • 0037109192 scopus 로고    scopus 로고
    • Additivity on protein-DNA interactions: How good an approximation is it?
    • Benos P.V., Bulyk M.L., Stormo G.D. Additivity on protein-DNA interactions: how good an approximation is it? Nucl. Acids Res. 30:2002;4442-4451.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 41
    • 0037115830 scopus 로고    scopus 로고
    • Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections
    • Silbaq F.S., Ruttenberg S.E., Stormo G.D. Specificity of Mnt 'master residue' obtained from in vivo and in vitro selections. Nucl. Acids Res. 30:2002;5539-5548.
    • (2002) Nucl. Acids Res. , vol.30 , pp. 5539-5548
    • Silbaq, F.S.1    Ruttenberg, S.E.2    Stormo, G.D.3
  • 42
    • 0036110292 scopus 로고    scopus 로고
    • Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods (Erratum in: Genome Res. (2002) 12, 1301)
    • GuhaThakurta D., Palomar L., Stormo G.D., Tedesco P., Johnson T.E., Walker D.W., et al. Identification of a novel cis-regulatory element involved in the heat shock response in Caenorhabditis elegans using microarray gene expression and computational methods (Erratum in: Genome Res. (2002) 12, 1301). Genome Res. 12:2002;701-712.
    • (2002) Genome Res. , vol.12 , pp. 701-712
    • GuhaThakurta, D.1    Palomar, L.2    Stormo, G.D.3    Tedesco, P.4    Johnson, T.E.5    Walker, D.W.6
  • 43
    • 0035130597 scopus 로고    scopus 로고
    • Target gene identification from expression array data by promoter analysis
    • Werner T. Target gene identification from expression array data by promoter analysis. Biomol. Eng. 17:2001;87-94.
    • (2001) Biomol. Eng. , vol.17 , pp. 87-94
    • Werner, T.1
  • 45
    • 0031027098 scopus 로고    scopus 로고
    • The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription
    • Czarniecki D., Noel R.J. Jr, Reznikoff W.S. The -45 region of the Escherichia coli lac promoter: CAP-dependent and CAP-independent transcription. J. Bacteriol. 179:1997;423-429.
    • (1997) J. Bacteriol. , vol.179 , pp. 423-429
    • Czarniecki, D.1    Noel R.J., Jr.2    Reznikoff, W.S.3
  • 46
    • 0035016087 scopus 로고    scopus 로고
    • A novel RNA polymerase binding site upstream of the galactose promoter in Escherichia coli exhibits promoter-like activity
    • Sur R., Debnath D., Mukhopadhyay J., Parrack P. A novel RNA polymerase binding site upstream of the galactose promoter in Escherichia coli exhibits promoter-like activity. Eur. J. Biochem. 268:2001;2344-2350.
    • (2001) Eur. J. Biochem. , vol.268 , pp. 2344-2350
    • Sur, R.1    Debnath, D.2    Mukhopadhyay, J.3    Parrack, P.4
  • 47
    • 0021911806 scopus 로고
    • Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter
    • Mulligan M.E., Brosius J., McClure W.R. Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter. J. Biol. Chem. 260:1985;3529-3538.
    • (1985) J. Biol. Chem. , vol.260 , pp. 3529-3538
    • Mulligan, M.E.1    Brosius, J.2    McClure, W.R.3
  • 48
    • 0031904590 scopus 로고    scopus 로고
    • Demand theory of gene regulation. I. Quantitative development of the theory
    • Savageau M.A. Demand theory of gene regulation. I. Quantitative development of the theory. Genetics. 149:1998;1665-1676.
    • (1998) Genetics , vol.149 , pp. 1665-1676
    • Savageau, M.A.1
  • 49
    • 0029852417 scopus 로고    scopus 로고
    • Towards a unified grammatical model of sigma 70 and sigma 54 bacterial promoters
    • Collado-Vides J. Towards a unified grammatical model of sigma 70 and sigma 54 bacterial promoters. Biochimie. 78:1996;351-363.
    • (1996) Biochimie , vol.78 , pp. 351-363
    • Collado-Vides, J.1
  • 50
    • 0030960672 scopus 로고    scopus 로고
    • Transcriptional activation by recruitment
    • Ptashne M., Gann A. Transcriptional activation by recruitment. Nature. 386:1997;569-577.
    • (1997) Nature , vol.386 , pp. 569-577
    • Ptashne, M.1    Gann, A.2
  • 51
    • 0025012093 scopus 로고
    • The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons
    • Hoover T.R., Santero E., Porter S., Kustu S. The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons. Cell. 63:1990;11-22.
    • (1990) Cell , vol.63 , pp. 11-22
    • Hoover, T.R.1    Santero, E.2    Porter, S.3    Kustu, S.4
  • 54
    • 0026003072 scopus 로고
    • Control site location and transcriptional regulation in Escherichia coli
    • Collado-Vides J., Magasanik B., Gralla J.D. Control site location and transcriptional regulation in Escherichia coli. Microbiol. Rev. 55:1991;371-394.
    • (1991) Microbiol. Rev. , vol.55 , pp. 371-394
    • Collado-Vides, J.1    Magasanik, B.2    Gralla, J.D.3
  • 56
    • 0041620271 scopus 로고    scopus 로고
    • Regulatory sequence analysis tools
    • van Helden J. Regulatory sequence analysis tools. Nucl. Acids Res. 31:2003;3593-3596.
    • (2003) Nucl. Acids Res. , vol.31 , pp. 3593-3596
    • Van Helden, J.1
  • 57
    • 0023410603 scopus 로고
    • Mutations that Create New Promoters Supress the Sigma 54 Dependence of glnaA Transcription in Escherichia coli
    • Reitzer L.J., Bueno R., Cheng W.D., Abrams S.A., Rothstein D.M., Hunt T.M., et al. Mutations that Create New Promoters Supress the Sigma 54 Dependence of glnaA Transcription in Escherichia coli. J. Bacteriol. 169:1987;4279-4284.
    • (1987) J. Bacteriol. , vol.169 , pp. 4279-4284
    • Reitzer, L.J.1    Bueno, R.2    Cheng, W.D.3    Abrams, S.A.4    Rothstein, D.M.5    Hunt, T.M.6


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