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Volumn 41, Issue D1, 2013, Pages

RegulonDB v8.0: Omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(27)  Salgado, Heladia a   Peralta Gil, Martin a   Gama Castro, Socorro a   Santos Zavaleta, Alberto a   Muñiz Rascado, Luis a   García Sotelo, Jair S a   Weiss, Verena a   Solano Lira, Hilda a   Martínez Flores, Irma a   Medina Rivera, Alejandra a   Salgado Osorio, Gerardo a   Alquicira Hernández, Shirley a   Alquicira Hernández, Kevin a   López Fuentes, Alejandra a   Porrón Sotelo, Liliana a   Huerta, Araceli M a   Bonavides Martínez, César a   Balderas Martínez, Yalbi I a   Pannier, Lucia a   Olvera, Maricela b   more..


Author keywords

[No Author keywords available]

Indexed keywords

RNA POLYMERASE;

EID: 84876543942     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1201     Document Type: Article
Times cited : (361)

References (46)
  • 4
    • 0035951305 scopus 로고    scopus 로고
    • Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro
    • Barker, M.M., Gaal, T., Josaitis, C.A. and Gourse, R.L. (2001) Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol., 305, 673-688.
    • (2001) J. Mol. Biol. , vol.305 , pp. 673-688
    • Barker, M.M.1    Gaal, T.2    Josaitis, C.A.3    Gourse, R.L.4
  • 5
    • 0035951301 scopus 로고    scopus 로고
    • Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP
    • Barker, M.M., Gaal, T. and Gourse, R.L. (2001) Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J. Mol. Biol., 305, 689-702.
    • (2001) J. Mol. Biol. , vol.305 , pp. 689-702
    • Barker, M.M.1    Gaal, T.2    Gourse, R.L.3
  • 7
    • 33748662456 scopus 로고    scopus 로고
    • DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli
    • Mallik, P., Paul, B.J., Rutherford, S.T., Gourse, R.L. and Osuna, R. (2006) DksA is required for growth phase-dependent regulation, growth rate-dependent control, and stringent control of fis expression in Escherichia coli. J. Bacteriol., 188, 5775-5782.
    • (2006) J. Bacteriol. , vol.188 , pp. 5775-5782
    • Mallik, P.1    Paul, B.J.2    Rutherford, S.T.3    Gourse, R.L.4    Osuna, R.5
  • 8
    • 73349100378 scopus 로고    scopus 로고
    • Transcription from bacteriophage lambda pR promoter is regulated independently and antagonistically by DksA and ppGpp
    • Lyzen, R., Kochanowska, M., Wegrzyn, G. and Szalewska-Palasz, A. (2009) Transcription from bacteriophage lambda pR promoter is regulated independently and antagonistically by DksA and ppGpp. Nucleic Acids Res., 37, 6655-6664.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 6655-6664
    • Lyzen, R.1    Kochanowska, M.2    Wegrzyn, G.3    Szalewska-Palasz, A.4
  • 9
    • 33744962968 scopus 로고    scopus 로고
    • Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA
    • Potrykus, K., Vinella, D., Murphy, H., Szalewska-Palasz, A., D'Ari, R. and Cashel, M. (2006) Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA. J. Biol. Chem., 281, 15238-15248.
    • (2006) J. Biol. Chem. , vol.281 , pp. 15238-15248
    • Potrykus, K.1    Vinella, D.2    Murphy, H.3    Szalewska-Palasz, A.4    D'Ari, R.5    Cashel, M.6
  • 10
    • 0346964255 scopus 로고    scopus 로고
    • Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: Anti-activation by the nucleoid proteins FIS and IHF
    • Browning, D.F., Beatty, C.M., Sanstad, E.A., Gunn, K.E., Busby, S.J. and Wolfe, A.J. (2004) Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF. Mol. Microbiol., 51, 241-254.
    • (2004) Mol. Microbiol. , vol.51 , pp. 241-254
    • Browning, D.F.1    Beatty, C.M.2    Sanstad, E.A.3    Gunn, K.E.4    Busby, S.J.5    Wolfe, A.J.6
  • 11
    • 0042890424 scopus 로고    scopus 로고
    • Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism
    • Beatty, C.M., Browning, D.F., Busby, S.J. and Wolfe, A.J. (2003) Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism. J. Bacteriol., 185, 5148-5157.
    • (2003) J. Bacteriol. , vol.185 , pp. 5148-5157
    • Beatty, C.M.1    Browning, D.F.2    Busby, S.J.3    Wolfe, A.J.4
  • 12
    • 0026003072 scopus 로고
    • Control site location and transcriptional regulation in Escherichia coli
    • Collado-Vides, J., Magasanik, B. and Gralla, J.D. (1991) Control site location and transcriptional regulation in Escherichia coli. Microbiol. Rev., 55, 371-394.
    • (1991) Microbiol. Rev. , vol.55 , pp. 371-394
    • Collado-Vides, J.1    Magasanik, B.2    Gralla, J.D.3
  • 13
    • 0029852417 scopus 로고    scopus 로고
    • Towards a unified grammatical model of sigma 70 and sigma 54 bacterial promoters
    • Collado-Vides, J. (1996) Towards a unified grammatical model of sigma 70 and sigma 54 bacterial promoters. Biochimie, 78, 351-363.
    • (1996) Biochimie , vol.78 , pp. 351-363
    • Collado-Vides, J.1
  • 14
    • 0025185784 scopus 로고
    • Helical phase dependent action of CRP: Effect of the distance between the CRP site and the -35 region on promoter activity
    • Ushida, C. and Aiba, H. (1990) Helical phase dependent action of CRP: effect of the distance between the CRP site and the -35 region on promoter activity. Nucleic Acids Res., 18, 6325-6330.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6325-6330
    • Ushida, C.1    Aiba, H.2
  • 15
    • 0032502838 scopus 로고    scopus 로고
    • Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: Organisation of the RNA polymerase alpha subunits
    • Belyaeva, T.A., Rhodius, V.A., Webster, C.L. and Busby, S.J. (1998) Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: organisation of the RNA polymerase alpha subunits. J. Mol. Biol., 277, 789-804.
    • (1998) J. Mol. Biol. , vol.277 , pp. 789-804
    • Belyaeva, T.A.1    Rhodius, V.A.2    Webster, C.L.3    Busby, S.J.4
  • 16
    • 0030867901 scopus 로고    scopus 로고
    • Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors
    • Murakami, K., Owens, J.T., Belyaeva, T.A., Meares, C.F., Busby, S.J. and Ishihama, A. (1997) Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase at promoters by two transcription factors. Proc. Natl Acad. Sci. USA, 94, 11274-11278.
    • (1997) Proc. Natl Acad. Sci. USA , vol.94 , pp. 11274-11278
    • Murakami, K.1    Owens, J.T.2    Belyaeva, T.A.3    Meares, C.F.4    Busby, S.J.5    Ishihama, A.6
  • 17
    • 0034035345 scopus 로고    scopus 로고
    • Transcription activation at the Escherichia coli melAB promoter: The role of MelR and the cyclic AMP receptor protein
    • Belyaeva, T.A., Wade, J.T., Webster, C.L., Howard, V.J., Thomas, M.S., Hyde, E.I. and Busby, S.J. (2000) Transcription activation at the Escherichia coli melAB promoter: the role of MelR and the cyclic AMP receptor protein. Mol. Microbiol., 36, 211-222.
    • (2000) Mol. Microbiol. , vol.36 , pp. 211-222
    • Belyaeva, T.A.1    Wade, J.T.2    Webster, C.L.3    Howard, V.J.4    Thomas, M.S.5    Hyde, E.I.6    Busby, S.J.7
  • 18
    • 78649640318 scopus 로고    scopus 로고
    • Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression
    • Browning, D.F., Grainger, D.C. and Busby, S.J. (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
  • 19
    • 79954579293 scopus 로고    scopus 로고
    • Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins
    • Rimsky, S. and 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
  • 22
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M. and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 23
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • Park, P.J. (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 669-680
    • Park, P.J.1
  • 30
    • 78149421813 scopus 로고    scopus 로고
    • Bacterial antisense RNAs: How many are there, and what are they doing?
    • Thomason, M.K. and Storz, G. (2010) Bacterial antisense RNAs: how many are there, and what are they doing? Annu. Rev. Genet., 44, 167-188.
    • (2010) Annu. Rev. Genet. , vol.44 , pp. 167-188
    • Thomason, M.K.1    Storz, G.2
  • 31
    • 79958047291 scopus 로고    scopus 로고
    • Cis-antisense RNA, another level of gene regulation in bacteria
    • Georg, J. and Hess, W.R. (2011) cis-antisense RNA, another level of gene regulation in bacteria. Microbiol. Mol. Biol. Rev., 75, 286-300.
    • (2011) Microbiol. Mol. Biol. Rev. , vol.75 , pp. 286-300
    • Georg, J.1    Hess, W.R.2
  • 32
    • 84865728811 scopus 로고    scopus 로고
    • Antisense transcription is pervasive but rarely conserved in enteric bacteria
    • Raghavan, R., Sloan, D.B. and Ochman, H. (2012) Antisense transcription is pervasive but rarely conserved in enteric bacteria. MBio., 3, e00156-12.
    • (2012) MBio. , vol.3
    • Raghavan, R.1    Sloan, D.B.2    Ochman, H.3
  • 34
    • 75949096070 scopus 로고    scopus 로고
    • Using the generic genome browser (GBrowse)
    • Chapter 9, Unit 9.9
    • Donlin, M.J. (2009) Using the generic genome browser (GBrowse). Curr. Protoc. Bioinformatics, Chapter 9, Unit 9.9.
    • (2009) Curr. Protoc. Bioinformatics
    • Donlin, M.J.1
  • 35
    • 38849135019 scopus 로고    scopus 로고
    • Choosing BLAST options for better detection of orthologs as reciprocal best hits
    • Moreno-Hagelsieb, G. and Latimer, K. (2008) Choosing BLAST options for better detection of orthologs as reciprocal best hits. Bioinformatics, 24, 319-324.
    • (2008) Bioinformatics , vol.24 , pp. 319-324
    • Moreno-Hagelsieb, G.1    Latimer, K.2
  • 36
    • 33646540406 scopus 로고    scopus 로고
    • Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes
    • Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005
    • Huerta, A.M., Collado-Vides, J. and Francino, M.P. (2006) Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Positional conservation of clusters of overlapping promoter-like sequences in enterobacterial genomes. Mol. Biol. Evol., 23, 997-1010.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 997-1010
    • Huerta, A.M.1    Collado-Vides, J.2    Francino, M.P.3
  • 37
    • 0141758085 scopus 로고    scopus 로고
    • Sigma70 promoters in Escherichia coli: Specific transcription in dense regions of overlapping promoter-like signals
    • Huerta, A.M. and Collado-Vides, J. (2003) Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals. J. Mol. Biol., 333, 261-278.
    • (2003) J. Mol. Biol. , vol.333 , pp. 261-278
    • Huerta, A.M.1    Collado-Vides, J.2
  • 38
    • 3543068251 scopus 로고    scopus 로고
    • Regulog analysis: Detection of conserved regulatory networks across bacteria: Application to Staphylococcus aureus
    • Alkema, W.B., Lenhard, B. and Wasserman, W.W. (2004) Regulog analysis: detection of conserved regulatory networks across bacteria: application to Staphylococcus aureus. Genome Res., 14, 1362-1373.
    • (2004) Genome Res. , vol.14 , pp. 1362-1373
    • Alkema, W.B.1    Lenhard, B.2    Wasserman, W.W.3
  • 39
    • 30344484891 scopus 로고    scopus 로고
    • Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli
    • Martinez-Antonio, A., Janga, S.C., Salgado, H. and Collado-Vides, J. (2006) Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli. Trends Microbiol., 14, 22-27.
    • (2006) Trends Microbiol. , vol.14 , pp. 22-27
    • Martinez-Antonio, A.1    Janga, S.C.2    Salgado, H.3    Collado-Vides, J.4
  • 41
    • 52749097035 scopus 로고    scopus 로고
    • Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules
    • Turatsinze, J.V., Thomas-Chollier, M., Defrance, M. and van Helden, J. (2008) Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat. Protoc., 3, 1578-1588.
    • (2008) Nat. Protoc. , vol.3 , pp. 1578-1588
    • Turatsinze, J.V.1    Thomas-Chollier, M.2    Defrance, M.3    Van Helden, J.4
  • 42
    • 0027167459 scopus 로고
    • Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli
    • Nygaard, P. and Smith, J.M. (1993) Evidence for a novel glycinamide ribonucleotide transformylase in Escherichia coli. J. Bacteriol., 175, 3591-3597.
    • (1993) J. Bacteriol. , vol.175 , pp. 3591-3597
    • Nygaard, P.1    Smith, J.M.2
  • 43
    • 0026568864 scopus 로고
    • Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase
    • Danielsen, S., Kilstrup, M., Barilla, K., Jochimsen, B. and Neuhard, J. (1992) Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase. Mol. Microbiol., 6, 1335-1344.
    • (1992) Mol. Microbiol. , vol.6 , pp. 1335-1344
    • Danielsen, S.1    Kilstrup, M.2    Barilla, K.3    Jochimsen, B.4    Neuhard, J.5
  • 44
    • 20444463884 scopus 로고    scopus 로고
    • Cloning and functional characterization of two bacterial members of the NAT/NCS2 family in Escherichia coli
    • Karatza, P. and Frillingos, S. (2005) Cloning and functional characterization of two bacterial members of the NAT/NCS2 family in Escherichia coli. Mol. Membr. Biol., 22, 251-261.
    • (2005) Mol. Membr. Biol. , vol.22 , pp. 251-261
    • Karatza, P.1    Frillingos, S.2
  • 45
    • 0023852792 scopus 로고
    • Pore-forming activity of the Tsx protein from the outer membrane of Escherichia coli. Demonstration of a nucleoside-specific binding site
    • Maier, C., Bremer, E., Schmid, A. and Benz, R. (1988) Pore-forming activity of the Tsx protein from the outer membrane of Escherichia coli. Demonstration of a nucleoside-specific binding site. J. Biol. Chem., 263, 2493-2499.
    • (1988) J. Biol. Chem. , vol.263 , pp. 2493-2499
    • Maier, C.1    Bremer, E.2    Schmid, A.3    Benz, R.4
  • 46
    • 0029560257 scopus 로고
    • Regulation of codBA operon expression in Escherichia coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching
    • Qi, F. and Turnbough, C.L. Jr (1995) Regulation of codBA operon expression in Escherichia coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching. J. Mol. Biol., 254, 552-565.
    • (1995) J. Mol. Biol. , vol.254 , pp. 552-565
    • Qi, F.1    Turnbough Jr., C.L.2


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