Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 3 February 1989:
Vol. 243. no. 4891, pp. 629 - 635
DOI: 10.1126/science.2563595
Prev | Table of Contents | Next

Articles

Science, Vol 243, Issue 4891, 629-635
Copyright © 1989 by American Association for the Advancement of Science

articles

Function of a bacterial activator protein that binds to transcriptional enhancers

DL Popham, D Szeto, J Keener, and S Kustu

Department of Microbiology and Immunology, University of California, Berkley 94720.

The nitrogen regulatory (NtrC) protein of enteric bacteria, which binds to sites that have the properties of transcriptional enhancers, is known to activate transcription by a form of RNA polymerase that contains the NtrA protein (sigma 54) as sigma factor (referred to as sigma 54-holoenzyme). In the presence of adenosine triphosphate, the NtrC protein catalyzes isomerization of closed recognition complexes between sigma 54-holoenzyme and the glnA promoter to open complexes in which DNA in the region of the transcription start site is locally denatured. NtrC is not required subsequently for maintenance of open complexes or initiation of transcription.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Comparative analysis of activator-E{sigma}54 complexes formed with nucleotide-metal fluoride analogues.
P. C. Burrows, N. Joly, B. T. Nixon, and M. Buck (2009)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Construction and functional analyses of a comprehensive {sigma}54 site-directed mutant library using alanine-cysteine mutagenesis.
Y. Xiao, S. R. Wigneshweraraj, R. Weinzierl, Y.-P. Wang, and M. Buck (2009)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Rrp2, a {sigma}54-Dependent Transcriptional Activator of Borrelia burgdorferi, Activates rpoS in an Enhancer-Independent Manner.
J. S. Blevins, H. Xu, M. He, M. V. Norgard, L. Reitzer, and X. F. Yang (2009)
J. Bacteriol. 191, 2902-2905
   Abstract »    Full Text »    PDF »
Causes and Consequences of Increased Glucose Metabolism of Cancers.
R. J. Gillies, I. Robey, and R. A. Gatenby (2008)
J. Nucl. Med. 49, 24S-42S
   Abstract »    Full Text »    PDF »
An Intramolecular Route for Coupling ATPase Activity in AAA+ Proteins for Transcription Activation.
N. Joly, P. C. Burrows, and M. Buck (2008)
J. Biol. Chem. 283, 13725-13735
   Abstract »    Full Text »    PDF »
The dynamic interplay between a cell fate determinant and a lysozyme homolog drives the asymmetric division cycle of Caulobacter crescentus.
S. K. Radhakrishnan, M. Thanbichler, and P. H. Viollier (2008)
Genes & Dev. 22, 212-225
   Abstract »    Full Text »    PDF »
A negative feedback loop involving small RNAs accelerates Vibrio cholerae's transition out of quorum-sensing mode.
S. L. Svenningsen, C. M. Waters, and B. L. Bassler (2008)
Genes & Dev. 22, 226-238
   Abstract »    Full Text »    PDF »
Two-Component Response Regulators of Vibrio fischeri: Identification, Mutagenesis, and Characterization.
E. A. Hussa, T. M. O'Shea, C. L. Darnell, E. G. Ruby, and K. L. Visick (2007)
J. Bacteriol. 189, 5825-5838
   Abstract »    Full Text »    PDF »
Evidence that RpoS ({sigma}S) in Borrelia burgdorferi Is Controlled Directly by RpoN ({sigma}54/{sigma}N).
A. H. Smith, J. S. Blevins, G. N. Bachlani, X. F. Yang, and M. V. Norgard (2007)
J. Bacteriol. 189, 2139-2144
   Abstract »    Full Text »    PDF »
Chromatin structure can strongly facilitate enhancer action over a distance.
M. A. Rubtsov, Y. S. Polikanov, V. A. Bondarenko, Y.-H. Wang, and V. M. Studitsky (2006)
PNAS 103, 17690-17695
   Abstract »    Full Text »    PDF »
Evolution of sensory complexity recorded in a myxobacterial genome.
B. S. Goldman, W. C. Nierman, D. Kaiser, S. C. Slater, A. S. Durkin, J. A. Eisen, C. M. Ronning, W. B. Barbazuk, M. Blanchard, C. Field, et al. (2006)
PNAS 103, 15200-15205
   Abstract »    Full Text »    PDF »
Transcriptional Specificity of RpoN1 and RpoN2 Involves Differential Recognition of the Promoter Sequences and Specific Interaction with the Cognate Activator Proteins.
S. Poggio, A. Osorio, G. Dreyfus, and L. Camarena (2006)
J. Biol. Chem. 281, 27205-27215
   Abstract »    Full Text »    PDF »
The structural basis for regulated assembly and function of the transcriptional activator NtrC.
S. De Carlo, B. Chen, T. R. Hoover, E. Kondrashkina, E. Nogales, and B. T. Nixon (2006)
Genes & Dev. 20, 1485-1495
   Abstract »    Full Text »    PDF »
Stable Accumulation of {sigma}54 in Helicobacter pylori Requires the Novel Protein HP0958.
L. Pereira and T. R. Hoover (2005)
J. Bacteriol. 187, 4463-4469
   Abstract »    Full Text »    PDF »
Characterization of Enhancer Binding by the Vibrio cholerae Flagellar Regulatory Protein FlrC.
N. E. Correa and K. E. Klose (2005)
J. Bacteriol. 187, 3158-3170
   Abstract »    Full Text »    PDF »
Structural Insights into the Activity of Enhancer-Binding Proteins.
M. Rappas, J. Schumacher, F. Beuron, H. Niwa, P. Bordes, S. Wigneshweraraj, C. A. Keetch, C. V. Robinson, M. Buck, and X. Zhang (2005)
Science 307, 1972-1975
   Abstract »    Full Text »    PDF »
Enhancer-binding proteins with a forkhead-associated domain and the {sigma}54 regulon in Myxococcus xanthus fruiting body development.
L. Jelsbak, M. Givskov, and D. Kaiser (2005)
PNAS 102, 3010-3015
   Abstract »    Full Text »    PDF »
Bacterial Transcriptional Regulators for Degradation Pathways of Aromatic Compounds.
D. Tropel and J. R. van der Meer (2004)
Microbiol. Mol. Biol. Rev. 68, 474-500
   Abstract »    Full Text »    PDF »
Mutations Altering the N-Terminal Receiver Domain of NRI (NtrC) That Prevent Dephosphorylation by the NRII-PII Complex in Escherichia coli.
A. A. Pioszak and A. J. Ninfa (2004)
J. Bacteriol. 186, 5730-5740
   Abstract »    Full Text »    PDF »
Nucleotide-dependent interactions between a fork junction-RNA polymerase complex and an AAA+ transcriptional activator protein.
W. V. Cannon, J. Schumacher, and M. Buck (2004)
Nucleic Acids Res. 32, 4596-4608
   Abstract »    Full Text »    PDF »
Helicobacter pylori FlgR Is an Enhancer-Independent Activator of {sigma}54-RNA Polymerase Holoenzyme.
P. Brahmachary, M. G. Dashti, J. W. Olson, and T. R. Hoover (2004)
J. Bacteriol. 186, 4535-4542
   Abstract »    Full Text »    PDF »
Purification and Characterization of the AAA+ Domain of Sinorhizobium meliloti DctD, a {sigma}54-Dependent Transcriptional Activator.
H. Xu, B. Gu, B. T. Nixon, and T. R. Hoover (2004)
J. Bacteriol. 186, 3499-3507
   Abstract »    Full Text »    PDF »
Evidence for a Second Interaction between the Regulatory Amino-terminal and Central Output Domains of the Response Regulator NtrC (Nitrogen Regulator I) in Escherichia coli.
A. C. Harrod, X. Yang, M. Junker, and L. Reitzer (2004)
J. Biol. Chem. 279, 2350-2359
   Abstract »    Full Text »    PDF »
Transient XylR binding to the UAS of the Pseudomonas putida {sigma}54 promoter Pu revealed with high intensity UV footprinting in vivo.
M. Valls and V. de Lorenzo (2003)
Nucleic Acids Res. 31, 6926-6934
   Abstract »    Full Text »    PDF »
Nucleotide-Dependent Conformational Changes in the {sigma}54-Dependent Activator DctD.
Y.-K. Wang, S. Park, B. T. Nixon, and T. R. Hoover (2003)
J. Bacteriol. 185, 6215-6219
   Abstract »    Full Text »    PDF »
Mapping {sigma}54-RNA Polymerase Interactions at the -24 Consensus Promoter Element.
P. C. Burrows, K. Severinov, A. Ishihama, M. Buck, and S. R. Wigneshweraraj (2003)
J. Biol. Chem. 278, 29728-29743
   Abstract »    Full Text »    PDF »
Nucleotide-dependent Triggering of RNA Polymerase-DNA Interactions by an AAA Regulator of Transcription.
W. Cannon, P. Bordes, S. R. Wigneshweraraj, and M. Buck (2003)
J. Biol. Chem. 278, 19815-19825
   Abstract »    Full Text »    PDF »
Prokaryotic Development: Emerging Insights.
L. Kroos and J. R. Maddock (2003)
J. Bacteriol. 185, 1128-1146
   Full Text »    PDF »
Genetic and Biochemical Analysis of Phosphatase Activity of Escherichia coli NRII (NtrB) and Its Regulation by the PII Signal Transduction Protein.
A. A. Pioszak and A. J. Ninfa (2003)
J. Bacteriol. 185, 1299-1315
   Abstract »    Full Text »    PDF »
Binding affinity of Escherichia coli RNA polymerase{middle dot}{sigma}54 holoenzyme for the glnAp2, nifH and nifL promoters.
S. K. Vogel, A. Schulz, and K. Rippe (2002)
Nucleic Acids Res. 30, 4094-4101
   Abstract »    Full Text »    PDF »
Correlating protein footprinting with mutational analysis in the bacterial transcription factor {sigma}54 ({sigma}N).
S. R. Wigneshweraraj, P. Casaz, and M. Buck (2002)
Nucleic Acids Res. 30, 1016-1028
   Abstract »    Full Text »    PDF »
Action of prokaryotic enhancer over a distance does not require continued presence of promoter-bound {sigma}54 subunit.
V. Bondarenko, Y. Liu, A. Ninfa, and V. M. Studitsky (2002)
Nucleic Acids Res. 30, 636-642
   Abstract »    Full Text »    PDF »
In vitro roles of invariant helix-turn-helix motif residue R383 in {{sigma}}54 ({{sigma}}N).
S. R. Wigneshweraraj, A. Ishihama, and M. Buck (2001)
Nucleic Acids Res. 29, 1163-1174
   Abstract »    Full Text »    PDF »
Single amino acid substitution mutants of Klebsiella pneumoniae {sigma}54 defective in transcription.
M. Pitt, M.-T. Gallegos, and M. Buck (2000)
Nucleic Acids Res. 28, 4419-4427
   Abstract »    Full Text »    PDF »
Promoter opening by sigma 54 and sigma 70 RNA polymerases: sigma factor-directed alterations in the mechanism and tightness of control.
Y. Guo, C. M. Lew, and J. D. Gralla (2000)
Genes & Dev. 14, 2242-2255
   Abstract »    Full Text »
The Bacterial Enhancer-Dependent sigma 54 (sigma N) Transcription Factor.
M. Buck, M.-T. Gallegos, D. J. Studholme, Y. Guo, and J. D. Gralla (2000)
J. Bacteriol. 182, 4129-4136
   Full Text »
The role of Region II in the RNA polymerase {sigma} factor {sigma}N ({sigma}54).
E. Southern and M. Merrick (2000)
Nucleic Acids Res. 28, 2563-2570
   Abstract »    Full Text »    PDF »
The sigma 70 Transcription Factor TyrR Has Zinc-Stimulated Phosphatase Activity That Is Inhibited by ATP and Tyrosine.
S. Zhao, Q. Zhu, and R. L. Somerville (2000)
J. Bacteriol. 182, 1053-1061
   Abstract »    Full Text »
The Amino Terminus of Salmonella enterica Serovar Typhimurium sigma 54 Is Required for Interactions with an Enhancer-Binding Protein and Binding to Fork Junction DNA.
M. T. Kelly and T. R. Hoover (2000)
J. Bacteriol. 182, 513-517
   Abstract »    Full Text »
"Switch I" mutant forms of the bacterial enhancer-binding protein NtrC that perturb the response to DNA.
D. Yan and S. Kustu (1999)
PNAS 96, 13142-13146
   Abstract »    Full Text »    PDF »
The hydrophobic heptad repeat in Region III of Escherichia coli transcription factor sigma 54 is essential for core RNA polymerase binding.
M. Hsieh, H.-M. Hsu, S.-F. Hwang, F.-C. Wen, J.-S. Yu, C.-C. Wen, and C. Li (1999)
Microbiology 145, 3081-3088
   Abstract »    Full Text »    PDF »
Abortive Initiation by Saccharomyces cerevisiae RNA Polymerase III.
P. Bhargava and G. A. Kassavetis (1999)
J. Biol. Chem. 274, 26550-26556
   Abstract »    Full Text »    PDF »
Functions of the sigma 54 Region I in Trans and Implications for Transcription Activation.
M.-T. Gallegos, W. V. Cannon, and M. Buck (1999)
J. Biol. Chem. 274, 25285-25290
   Abstract »    Full Text »    PDF »
Mutations Affecting Motifs of Unknown Function in the Central Domain of Nitrogen Regulatory Protein C.
J. Li, L. Passaglia, I. Rombel, D. Yan, and S. Kustu (1999)
J. Bacteriol. 181, 5443-5454
   Abstract »    Full Text »
Mutant Forms of Salmonella typhimurium sigma 54 Defective in Transcription Initiation but Not Promoter Binding Activity.
M. T. Kelly and T. R. Hoover (1999)
J. Bacteriol. 181, 3351-3357
   Abstract »    Full Text »
Physical evidence for a phosphorylation-dependent conformational change in the enhancer-binding protein NtrC.
I. Hwang, T. Thorgeirsson, J. Lee, S. Kustu, and Y.-K. Shin (1999)
PNAS 96, 4880-4885
   Abstract »    Full Text »    PDF »
Amino-terminal sequences of sigma N (sigma 54) inhibit RNA polymerase isomerization.
W. Cannon, M.-T. Gallegos, P. Casaz, and M. Buck (1999)
Genes & Dev. 13, 357-370
   Abstract »    Full Text »
Control of Herbaspirillum seropedicae NifA Activity by Ammonium Ions and Oxygen.
E. M. Souza, F. O. Pedrosa, M. Drummond, L. U. Rigo, and M. G. Yates (1999)
J. Bacteriol. 181, 681-684
   Abstract »    Full Text »
Identification of an N-Terminal Region of Sigma 54 Required for Enhancer Responsiveness.
A. Syed and J. D. Gralla (1998)
J. Bacteriol. 180, 5619-5625
   Abstract »    Full Text »
Multiple In Vivo Roles for the -12-Region Elements of Sigma 54 Promoters.
L. Wang and J. D. Gralla (1998)
J. Bacteriol. 180, 5626-5631
   Abstract »    Full Text »
Characterization of the Closed Complex Intermediate Formed during Transcription Initiation by Escherichia coli RNA Polymerase.
X.-Y. Li and W. R. McClure (1998)
J. Biol. Chem. 273, 23549-23557
   Abstract »    Full Text »    PDF »
A bacterial ATP-dependent, enhancer binding protein that activates the housekeeping RNA polymerase.
W. C. Bowman and R. G. Kranz (1998)
Genes & Dev. 12, 1884-1893
   Abstract »    Full Text »
Mutational Analysis of the Phosphate-Binding Loop of Rhizobium meliloti DctD, a sigma 54-Dependent Activator.
Y. Gao, Y.-K. Wang, and T. R. Hoover (1998)
J. Bacteriol. 180, 2792-2795
   Abstract »    Full Text »
DNA strand separation during activation of a developmental promoter by the Bacillus subtilis response regulator Spo0A.
D. A. Rowe-Magnus and G. B. Spiegelman (1998)
PNAS 95, 5305-5310
   Abstract »    Full Text »    PDF »
The Rhizobium etli rpoN Locus: DNA Sequence Analysis and Phenotypical Characterization of rpoN, ptsN, and ptsA Mutants.
J. Michiels, T. Van Soom, I. D'hooghe, B. Dombrecht, T. Benhassine, P. de Wilde, and J. Vanderleyden (1998)
J. Bacteriol. 180, 1729-1740
   Abstract »    Full Text »
A protein-induced DNA bend increases the specificity of a prokaryotic enhancer-binding protein.
J. Dworkin, A. J. Ninfa, and P. Model (1998)
Genes & Dev. 12, 894-900
   Abstract »    Full Text »
In vivo genomic footprinting analysis reveals that the complex Bradyrhizobium japonicum fixRnifA promoter region is differently occupied by two distinct RNA polymerase holoenzymes.
H. Barrios, R. Grande, L. Olvera, and E. Morett (1998)
PNAS 95, 1014-1019
   Abstract »    Full Text »    PDF »
The Bacterial Enhancer-binding Protein NtrC as a Molecular Machine.
I. ROMBEL, A. NORTH, I. HWANG, C. WYMAN, and S. KUSTU (1998)
Cold Spring Harb Symp Quant Biol 63, 157-166
   Abstract »    PDF »
Probing the assembly of transcription initiation complexes through changes in sigma N protease sensitivity.
P. Casaz and M. Buck (1997)
PNAS 94, 12145-12150
   Abstract »    Full Text »    PDF »
Characterization of the Rhodobacter capsulatus Housekeeping RNA Polymerase. IN VITRO TRANSCRIPTION OF PHOTOSYNTHESIS AND OTHER GENES.
P. J. Cullen, C. K. Kaufman, W. C. Bowman, and R. G. Kranz (1997)
J. Biol. Chem. 272, 27266-27273
   Abstract »    Full Text »    PDF »
Multiple pathways to bypass the enhancer requirement of sigma 54 RNA polymerase: Roles for DNA and protein determinants.
J. T. Wang, A. Syed, and J. D. Gralla (1997)
PNAS 94, 9538-9543
   Abstract »    Full Text »    PDF »
Two domains within sigma N (sigma 54) cooperate for DNA binding.
W. V. Cannon, M. K. Chaney, X.-Y. Wang, and M. Buck (1997)
PNAS 94, 5006-5011
   Abstract »    Full Text »    PDF »
sigma 54, a vital protein for Myxococcus xanthus.
I. M. Keseler and D. Kaiser (1997)
PNAS 94, 1979-1984
   Abstract »    Full Text »    PDF »
The Transcription Initiation Pathway of Sigma 54Mutants That Bypass the Enhancer Protein Requirement. IMPLICATIONS FOR THE MECHANISM OF ACTIVATION.
J. T. Wang and J. D. Gralla (1996)
J. Biol. Chem. 271, 32707-32713
   Abstract »    Full Text »    PDF »
In Vitro Reconstitution and Characterization of the Rhodobacter capsulatus NtrB and NtrC Two-component System.
P. J. Cullen, W. C. Bowman, and R. G. Kranz (1996)
J. Biol. Chem. 271, 6530-6536
   Abstract »    Full Text »    PDF »
Converting Escherichia coli RNA Polymerase into an Enhancer-Responsive Enzyme: Role of an NH2-Terminal Leucine Patch in sigma54.
J. T. Wang, A. Syed, M. Hsieh, and J. D. Gralla (1995)
Science 270, 992-994
   Abstract »    PDF »
The Neisseria Transcriptional Regulator PilA Has a GTPase Activity.
C. G. Arvidson and M. So (1995)
J. Biol. Chem. 270, 26045-26048
   Abstract »    Full Text »    PDF »
Abortive Cycling and the Release of Polymerase for Elongation at the [IMAGE]54-dependent glnAp2 Promoter.
Y. Tintut, J. T. Wang, and J. D. Gralla (1995)
J. Biol. Chem. 270, 24392-24398
   Abstract »    Full Text »    PDF »
A novel bacterial transcription cycle involving sigma 54..
Y Tintut, J T Wang, and J D Gralla (1995)
Genes & Dev. 9, 2305-2313
   Abstract »    PDF »
The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation..
A Wedel and S Kustu (1995)
Genes & Dev. 9, 2042-2052
   Abstract »    PDF »
Single Amino Acids Changes in the Signal Receptor Domain of XylR Resulted in Mutants That Stimulate Transcription in the Absence of Effectors.
A.ón Delgado, R. Salto, S. Marqués, and J. L. Ramos (1995)
J. Biol. Chem. 270, 5144-5150
   Abstract »    Full Text »    PDF »
A sigma 54 transcriptional activator also functions as a pole-specific repressor in Caulobacter..
J A Wingrove and J W Gober (1994)
Genes & Dev. 8, 1839-1852
   Abstract »    PDF »
Oligomerization of NTRC at the glnA enhancer is required for transcriptional activation..
S C Porter, A K North, A B Wedel, and S Kustu (1993)
Genes & Dev. 7, 2258-2273
   Abstract »    PDF »
Spatial and temporal phosphorylation of a transcriptional activator regulates pole-specific gene expression in Caulobacter..
J A Wingrove, E K Mangan, and J W Gober (1993)
Genes & Dev. 7, 1979-1992
   Abstract »    PDF »
A temporally controlled sigma-factor is required for polar morphogenesis and normal cell division in Caulobacter..
Y V Brun and L Shapiro (1992)
Genes & Dev. 6, 2395-2408
   Abstract »    PDF »
Polymerase II promoter activation: closed complex formation and ATP-driven start site opening.
W Wang, M Carey, and J. Gralla (1992)
Science 255, 450-453
   Abstract »    PDF »
An RNA polymerase-binding protein that is required for communication between an enhancer and a promoter.
D. Herendeen, K. Williams, G. Kassavetis, and E. Geiduschek (1990)
Science 248, 573-578
   Abstract »    PDF »
A bacterial enhancer functions to tether a transcriptional activator near a promoter.
A Wedel, D. Weiss, D Popham, P Droge, and S Kustu (1990)
Science 248, 486-490
   Abstract »    PDF »
Enhancement of bacteriophage T4 late transcription by components of the T4 DNA replication apparatus.
D. Herendeen, G. Kassavetis, J Barry, B. Alberts, and E. Geiduschek (1989)
Science 245, 952-958
   Abstract »    PDF »
DNA Melting within a Binary sigma 54-Promoter DNA Complex.
W. Cannon, M.-T. Gallegos, and M. Buck (2001)
J. Biol. Chem. 276, 386-394
   Abstract »    Full Text »    PDF »
Roles for the C-terminal Region of Sigma 54 in Transcriptional Silencing and DNA Binding.
L. Wang and J. D. Gralla (2001)
J. Biol. Chem. 276, 8979-8986
   Abstract »    Full Text »    PDF »
A Gal4-sigma 54 Hybrid Protein That Functions as a Potent Activator of RNA Polymerase II Transcription in Yeast.
B.-S. Chen, Z.-W. Sun, and M. Hampsey (2001)
J. Biol. Chem. 276, 23881-23887
   Abstract »    Full Text »    PDF »
DNA supercoiling allows enhancer action over a large distance.
Y. Liu, V. Bondarenko, A. Ninfa, and V. M. Studitsky (2001)
PNAS 98, 14883-14888
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)