1887

Abstract

The gene is transcribed from four known and differently regulated promoters: P1, P3, P4 and P5. This study demonstrates that the conserved consensus sequence of the promoter in the regulatory region of the gene, described previously, is a functional promoter, P6. The evidence for this conclusion is: (i) the specific binding of the –RNAP holoenzyme to P6, (ii) the location of the transcription start site at the predicted position (C, 30 nt upstream of ATG) and (iii) the dependence of transcription on and on an ATP-dependent activator. Nitrogen starvation, heat shock, ethanol and CCCP treatment did not activate transcription from P6 under the conditions examined. Two activators of promoters, PspF and NtrC, were tested but neither of them acted specifically. Therefore, PspFΔHTH, a derivative of PspF, devoid of DNA binding capability but retaining its ATPase activity, was used for transcription , taking advantage of the relaxed specificity of ATP-dependent activators acting in solution. In experiments overexpression of PspFΔHTH from a plasmid was employed. Thus, the -dependent transcription capability of the P6 promoter was demonstrated both and , although the specific conditions inducing initiation of the transcription remain to be elucidated. The results clearly indicate that the closed –RNAP–promoter initiation complex was formed and and needed only an ATP-dependent activator to start transcription.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2006/000463-0
2007-01-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/153/1/111.html?itemId=/content/journal/micro/10.1099/mic.0.2006/000463-0&mimeType=html&fmt=ahah

References

  1. Allen S. P., Polazzi J. O., Gierse J. K., Easton A. M. 1992; Two novel heat shock genes encoding proteins produced in response to heterologous protein expression in Escherichia coli . J Bacteriol 174:6938–6947
    [Google Scholar]
  2. Arsène F. Tomoyasu T., Bukau B. 2000; The heat shock response of Escherichia coli . Int J Food Microbiol 55:3–9 [CrossRef]
    [Google Scholar]
  3. Barrios H., Valderrama B., Morett E. 1999; Compilation and analysis of σ 54-dependent promoter sequences. Nucleic Acids Res 27:4305–4313 [CrossRef]
    [Google Scholar]
  4. Belitsky B. R., Sonenshein A. L. 1999; An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis . Proc Natl Acad Sci U S A 96:10290–10295 [CrossRef]
    [Google Scholar]
  5. Beloin C., Valle J., Latour-Lambert P., Faure P., Krzeminski P., Balestrino D., Haagensen J. A., Molin S., Prensier G. other authors 2004; Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression. Mol Microbiol 51:659–674
    [Google Scholar]
  6. Blattner F. R., Plunkett G. 3rd, Bloch C. A., Perna T. A., Burland V., Riley M., Collado-Vides J., Glasner J. D., Rode C. K. other authors 1997; The complete genome sequence of Escherichia coli K-12. Science 277:1453–1474 [CrossRef]
    [Google Scholar]
  7. Brissette J. L., Weiner L., Ripmaster T. L., Model P. 1991; Characterization and sequence of the Escherichia coli stress-induced psp operon. J Mol Biol 220:35–48 [CrossRef]
    [Google Scholar]
  8. Buck M., Cannon W. 1992; Specific binding of the transcription factor sigma-54 to promoter DNA. Nature 358:422–424 [CrossRef]
    [Google Scholar]
  9. Cannon W., Bordes P., Wigneshweraraj S. R., Buck M. 2003; Nucleotide-dependent triggering of RNA polymerase-DNA interactions by an AAA regulator of transcription. J Biol Chem 278:19815–19825 [CrossRef]
    [Google Scholar]
  10. Carmona M., Claverie-Martin F., Magasanik B. 1997; DNA bending and the initiation of transcription at σ 54-dependent bacterial promoters. Proc Natl Acad Sci U S A 94:9568–9572 [CrossRef]
    [Google Scholar]
  11. Connolly L., Yura T., Gross C. A. 1999; Autoregulation of the heat shock response in prokaryotes. In Molecular Chaperones and Folding Catalysts: Regulation, Cellular Function and Mechanisms pp 13–33 Edited by Bukau B. Amsterdam: Harwood Academic Publishers;
    [Google Scholar]
  12. Craig N. L., Nash H. A. 1984; E. coli integration host factor binds to specific sites in DNA. Cell 39:707–716 [CrossRef]
    [Google Scholar]
  13. Darwin A. J. 2005; The phage-shock-response. Mol Microbiol 57:621–628 [CrossRef]
    [Google Scholar]
  14. Dworkin J., Jovanovic G., Model P. 1997; Role of upstream activation sequences and integration host factor in transcriptional activation by the consitutively active prokaryotic enhancer-binding protein PspF. J Mol Biol 273:377–388 [CrossRef]
    [Google Scholar]
  15. Dworkin J., Ninfa A. J., Model P. 1998; A protein induced DNA bend increases the specificity of a prokaryotic enhancer-binding protein. Genes Dev 12:894–900 [CrossRef]
    [Google Scholar]
  16. Elderkin S., Jones S., Schumacher J., Studholme D., Buck M. 2002; Mechanism of action of the Escherichia coli phage shock protein PspA in repression of the AAA family transcription factor PspF. J Mol Biol 320:23–37 [CrossRef]
    [Google Scholar]
  17. Elliott T., Geiduschek E. P. 1984; Defining a bacteriophage T4 late promoter: absence of a “−35” region. Cell 36:211–219 [CrossRef]
    [Google Scholar]
  18. Erickson J. W., Gross C. A. 1989; Identification of the σ E subunit of Escherichia coli RNA polymerase: a second alternative sigma involved in high temperature gene expression. Genes Dev 3:1462–1471 [CrossRef]
    [Google Scholar]
  19. Erickson J. W., Vaughn V., Walter W. A., Neidhardt F. C., Gross C. A. 1987; Regulation of the promoters and transcripts rpoH , the Escherichia coli heat shock regulatory gene. Genes Dev 1:419–432 [CrossRef]
    [Google Scholar]
  20. Filutowicz M., Grimek H., Appelt K. 1994; Purification of the Escherichia coli Integration Host Factor (IHF) in one chromatographic step. Gene 147:149–150 [CrossRef]
    [Google Scholar]
  21. Foster J. E., Holmes S. F., Erie D. A. 2001; Allosteric binding of nucleoside triphosphates to RNA polymerase regulates transcription elongation. Cell 106:243–252 [CrossRef]
    [Google Scholar]
  22. Fu J., Gnatt A. L., Bushnell D. A., Jensen G. J., Thompson J. E., Burgess R. R., David P. R., Kornberg R. D. 2000; Yeast RNA-polymerase II at 5 Å resolution. Cell 98:799–810
    [Google Scholar]
  23. Fujita N., Ishihama A. 1996; Reconstitution of RNA polymerase. Methods Enzymol 273:121–130
    [Google Scholar]
  24. Goodrich J. A., Schwartz M. L., McClure W. R. 1990; Searching for and predicting the activity of sites for DNA binding proteins: compilation and analysis of the binding sites for Escherichia coli integration host factor (IHF. Nucleic Acids Res 18:4993–5000 [CrossRef]
    [Google Scholar]
  25. Gralla J. D., Collado-Vides J. others 1996; Organization and function of transcription regulatory elements. In Escherichia coli and Salmonella: Cellular and Molecular Biology , 2nd edn. pp 1232–1246 Edited by Neidhart F. C. Washington, DC: American Society for Microbiology;
    [Google Scholar]
  26. Granston A. E., Nash H. A. 1993; Characterization of a set of integration host factor mutants deficient for DNA binding. J Mol Biol 234:45–49 [CrossRef]
    [Google Scholar]
  27. Grimm C., Aufsatz W., Panopoulos N. J. 1995; The hrpRS locus of Pseudomonas syringae pv. phaseolicola constitutes a complex regulatory unit. Mol Microbiol 15:155–165 [CrossRef]
    [Google Scholar]
  28. Guo Y., Wang L., Gralla J. D. 1999; A fork junction DNA-protein switch that controls promoter melting by the bacterial enhancer-dependent sigma factor. EMBO J 18:3736–3745 [CrossRef]
    [Google Scholar]
  29. Guo Y., Lew C. M., Gralla J. D. 2000; Promoter opening by the σ 54 and σ 70 RNA polymerases: σ factor-directed alterations in the mechanism and tightness of control. Genes Dev 14:2242–2255 [CrossRef]
    [Google Scholar]
  30. Hanahan D. 1983; Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557–580 [CrossRef]
    [Google Scholar]
  31. Hankamer B. D., Elderkin S. L., Buck M., Nield J. 2004; Organization of the AAA+ adaptor protein PspA is an oligomeric ring. J Biol Chem 279:8862–8866 [CrossRef]
    [Google Scholar]
  32. Jishage M., Kvint K., Shingler V., Nyström T. 2002; Regulation of σ factor competition by the alarmone ppGpp. Genes Dev 16:1260–1270 [CrossRef]
    [Google Scholar]
  33. Jovanovic G., Weiner L., Model P. 1996; Identification, nucleotide sequence and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J Bacteriol 178:1936–1945
    [Google Scholar]
  34. Jovanovic G., Rakonjac J., Model P. 1999; In vivo and in vitro activities of the Escherichia coli σ 54 transcription activator, PspF, and its DNA-binding mutant. PspFΔHTH. J Mol Biol 285:469–483 [CrossRef]
    [Google Scholar]
  35. Kallipolitis B. H., Valentin-Hansen P. 1998; Transcription of rpoH , encoding the Escherichia coli heat-shock regulator σ 54, is negatively controlled by the cAMP-CRP/CytR nucleoprotein complex. Mol Microbiol 29:1091–1099 [CrossRef]
    [Google Scholar]
  36. Kuczyńska-Wiśnik D. Laskowska E., Taylor A. 2001; Transcription of the ibpB heat-shock gene is under control of σ 32 and σ 54-promoters; a third regulon of heat-shock response. Biochem Biophys Res Commun 284:57–64 [CrossRef]
    [Google Scholar]
  37. Laurie A. D., Bernardo L. M. D., Sze C. C., Szalewska-Pałasz A., Shingler V, Skärfstad E., Nyström T. 2003; The role of the alarmone (p)ppGpp in σ N competition for core RNA polymerase. J Biol Chem 278:1494–1503 [CrossRef]
    [Google Scholar]
  38. Leblanc B., Moss T. 2001; DNase I footprinting. Methods Mol Biol 148:31–38
    [Google Scholar]
  39. MacNeil D. 1981; General method, using Mu-Mudl dilysogens, to determine the direction of transcription and generate deletions in the glnA region of Escherichia coli . J Bacteriol 146:260–268
    [Google Scholar]
  40. Maeda H., Fujita N., Ishihama A. 2000; Competition among seven Escherichia coli σ subunits: relative binding affinities to the core RNA polymerase. Nucleic Acids Res 28:3497–3503 [CrossRef]
    [Google Scholar]
  41. Magnusson L. U., Farewell A., Nyström T. 2005; ppGpp: a global regulator in Escherichia coli . Trends Microbiol 13:236–242 [CrossRef]
    [Google Scholar]
  42. Merrick M. J. 1993; In a class of its own – the RNA polymerase sigma factor σ 54. Mol Microbiol 10:903–909 [CrossRef]
    [Google Scholar]
  43. Messer W., Weigel C. 1997; DnaA initiator – also a transcription factor. Mol Microbiol 24:1–6 [CrossRef]
    [Google Scholar]
  44. Missiakas D., Raina S. 1998; The extracytoplasmic function sigma factors: role and regulation. Mol Microbiol 28:1059–1066 [CrossRef]
    [Google Scholar]
  45. Model P., Jovanovic G., Dworkin J. 1997; The Escherichia coli phage-shock-protein ( psp ) operon. Mol Microbiol 24:255–261 [CrossRef]
    [Google Scholar]
  46. Nagai H., Yano R., Erickson J. R., Yura T. 1990; Transcriptional regulation of the heat shock regulatory gene rpoH in Escherichia coli : involvement of a novel catabolite-sensitive promoter. J Bacteriol 172:2710–2271
    [Google Scholar]
  47. Nyström T. 1995; Glucose starvation stimulon of Escherichia coli : role of integration host factor in starvation survival and growth phase-dependent protein synthesis. J Bacteriol 177:5707–5710
    [Google Scholar]
  48. Nyström T. 2004; Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition. Mol Microbiol 54:855–862 [CrossRef]
    [Google Scholar]
  49. Pallen M. 1999; RpoN-dependent transcription of rpoH ?. Mol Microbiol 31:393 [CrossRef]
    [Google Scholar]
  50. Pérez-Martin J. Rojo F., de Lorenzo V. 1994; Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol Rev 58:268–290
    [Google Scholar]
  51. Polyakov A., Severinova E., Darst S. A. 1995; Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83:365–373 [CrossRef]
    [Google Scholar]
  52. Ramírez-Santos J., Collado-Vides J. Garcia-Varela M., Gómez-Eichelman M. C. 2001; Conserved regulatory elements of the promoter sequence of the gene rpoH of enteric bacteria. Nucleic Acids Res 29:380–386 [CrossRef]
    [Google Scholar]
  53. Reitzer L., Schneider B. L. 2001; Metabolic context and possible physiological themes of σ 54-dependent genes in Escherichia coli . Microbiol Mol Biol Rev 65:422–444 [CrossRef]
    [Google Scholar]
  54. Rippe K., Guthgold M., Bustamante C, von Hippel P. H. 1997; Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase- σ 54 holoenzyme by scanning force microscopy. J Mol Biol 270:125–138 [CrossRef]
    [Google Scholar]
  55. Rippe K., Schulz A, Mücke N. 1998; Association states of the transcription activator protein NtrC from E. coli determined by analytical ultracentrifugation. J Mol Biol 278:915–933 [CrossRef]
    [Google Scholar]
  56. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual , 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
    [Google Scholar]
  57. Schembri M. A., Kjaergaard K., Klemm P. 2003; Global gene expression in Escherichia coli biofilms. Mol Microbiol 48:253–267 [CrossRef]
    [Google Scholar]
  58. Severinov K. 2000; RNA polymerase structure-function: insights into points of transcriptional regulation. Curr Opin Microbiol 3:118–125 [CrossRef]
    [Google Scholar]
  59. Shingler V. 1996; Signal sensing by σ 54-dependent regulators: derepression as a control mechanism. Mol Microbiol 19:409–416 [CrossRef]
    [Google Scholar]
  60. Solis-Guzman G., Ramirez-Santos J., Souza V., Gómez-Eichelman M. C. 2001; Analysis of the regulatory region of the heat-shock gene rpoH of Escherichia coli strains isolated from non-human hosts. FEMS Microbiol Lett 205:191–196
    [Google Scholar]
  61. Spiess E., Lurz R. 1988; Electron microscope analysis of nucleic acids and nucleic acids-protein complexes. Methods Microbiol 20:293–323
    [Google Scholar]
  62. Studholme D. J., Dixon R. 2003; Domain architecture of σ 54-dependent transcriptional activators. J Bacteriol 185:1757–1767 [CrossRef]
    [Google Scholar]
  63. Studier F. W., Moffat B. A. 1986; Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes. J Mol Biol 189:113–130 [CrossRef]
    [Google Scholar]
  64. Su W., Porter S., Kustu S., Echols H. 1990; DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter. Proc Natl Acad Sci U S A 87:5504–5508 [CrossRef]
    [Google Scholar]
  65. Sze C. C., Shingler V. 1999; The alarmone (p)ppGpp mediates physiological-responsive control at the σ 54-dependent Po promoter. Mol Microbiol 31:1217–1228 [CrossRef]
    [Google Scholar]
  66. Sze C. C., Bernardo L. M., Shingler V. 2002; Integration of global regulation of two aromatic-responsive σ 54-dependent systems: a common phenotype by different mechanisms. J Bacteriol 184:760–770 [CrossRef]
    [Google Scholar]
  67. Wang Q., Kaguni J. M. 1989a; A novel sigma factor is involved in expression of the rpoH gene of Escherichia coli . J Bacteriol 171:4248–4253
    [Google Scholar]
  68. Wang Q., Kaguni J. M. 1989b; DnaA protein regulates transcription of the rpoH gene of Escherichia coli . J Biol Chem 264:7338–7344
    [Google Scholar]
  69. Wang Y. P., Kolb A., Buck M., Wen J., O'Gara F., Buc H. 1998; CRP interacts with promoter-bound σ 54-RNAP and blocks transcriptional activation of the dctA promoter. EMBO J 17:786–796 [CrossRef]
    [Google Scholar]
  70. Weigel C., Schmidt A., Ruckert B., Lurz R., Messer W. 1997; DnaA protein binding to individual DnaA boxes in the Escherichia coli replication origin oriC . EMBO J 16:6574–6583 [CrossRef]
    [Google Scholar]
  71. Weiss D. S., Batut J., Klose K. E., Keener J., Kustu S. 1991; The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription. Cell 67:155–167 [CrossRef]
    [Google Scholar]
  72. Weiss V., Claverie-Martin F., Magasanik B. 1992; Phosphorylation of nitrogen regulator I of Escherichia coli induces strong cooperative binding to DNA essential for activation of transcription. Proc Natl Acad Sci U S A 89:5088–5092 [CrossRef]
    [Google Scholar]
  73. Wigneshweraraj S. R., Nechaev S., Bordes P., Jones S., Cannon W., Severinov K., Buck M. 2003; Enhancer-dependent transcription by bacterial RNA polymerase: the β subunit downstream lobe is used by σ 54 during open promoter complex formation. Methods Enzymol 370:646–657
    [Google Scholar]
  74. Wösten M. M. S. M. 1998; Eubacterial sigma factors. FEMS Microbiol Rev 22:127–150 [CrossRef]
    [Google Scholar]
  75. Zhang G., Campbell E. A., Minakhin L., Richter C., Severinov K., Darst S. A. 1999; Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98:811–824 [CrossRef]
    [Google Scholar]
  76. Zhang X., Chaney M., Wigneshweraraj S. R., Schumacher J., Bordes P., Cannon W., Buck M. 2002; Mechanochemical ATPases and transcriptional activation. Mol Microbiol 45:895–903 [CrossRef]
    [Google Scholar]
  77. Zhao K., Liu M., Burgess R. 2005; The global transcriptional response of Escherichia coli to induced σ 32 protein involves σ 32 regulon activation followed by inactivation and degradation of σ 32 in vivo . J Biol Chem 280:17758–17768 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/mic.0.2006/000463-0
Loading
/content/journal/micro/10.1099/mic.0.2006/000463-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error