Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

The regulation of bacterial transcription initiation

Nature Reviews Microbiology volume 2, pages 57–65 (2004)Cite this article

Key Points

  • The DNA-dependent multi-subunit RNA polymerase is the central component in the regulation of transcription initiation in bacteria. Sigma factors bind to the RNA polymerase to produce a holoenzyme that is competent for transcription. There are multiple factors that determine the level of transcription of a particular gene in a bacterium.

  • The crucial sequence elements of a bacterial promoter are described, including the −35 element, the −10 element, the extended −10 element and the UP element.

  • The role played by sigma factors in bacterial gene regulation is briefly outlined.

  • Small ligands, like ppGpp, can influence the level of transcription of certain genes.

  • Transcription factors can either activate or repress transcription by several mechanisms, but all of these mechanisms involve either optimizing the interaction of the RNA polymerase holoenzyme with the promoter (activation) or preventing the RNA polymerase holoenzyme from binding to the promoter (repression).

  • The organisation of the bacterial chromosome — although still poorly understood — contributes to the regulation of bacterial transcription initiation.

  • Promoters are frequently regulated by changes in environmental or physiological conditions. It is rare for a promoter to be regulated in response to a single environmental or physiological factor. Instead, several signals are often integrated by one (or more) transcriptional regulator by a combination of mechanisms at the promoter.

Abstract

Bacteria use their genetic material with great effectiveness to make the right products in the correct amounts at the appropriate time. Studying bacterial transcription initiation in Escherichia coli has served as a model for understanding transcriptional control throughout all kingdoms of life. Every step in the pathway between gene and function is exploited to exercise this control, but for reasons of economy, it is plain that the key step to regulate is the initiation of RNA-transcript formation.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: RNA polymerase and its interactions at promoters.
Figure 2: The pathway of transcription initiation at bacterial promoters.
Figure 3: Activation at simple promoters.
Figure 4: Mechanisms of repression.
Figure 5: Mechanisms of promoter co-dependence on two activator proteins.

Similar content being viewed by others

References

  1. Ebright, R. H. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304, 687–698 (2000).

    CAS  PubMed  Google Scholar 

  2. Zhang, G. et al. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3Å resolution. Cell 98, 811–824 (1999).

    CAS  PubMed  Google Scholar 

  3. Fu, J. et al. Yeast RNA polymerase II at 5Å resolution. Cell 98, 799–810 (1999).

    CAS  PubMed  Google Scholar 

  4. Korzheva, N. et al. A structural model for transcription elongation. Science 289, 619–625 (2000). A masterful article that explains how to apply intelligent chemistry to supplement structural data to produce a model for the bacterial transcription elongation complex.

    CAS  PubMed  Google Scholar 

  5. Blatter, E. E., Ross, W., Tang, H., Gourse, R. L. & Ebright, R. H. Domain organisation of RNA-polymerase α-subunit: C-terminal 85 amino-acids constitute a domain capable of dimerisation and DNA-binding. Cell 78, 889–896 (1994).

    CAS  PubMed  Google Scholar 

  6. Gourse, R. L., Ross, W. & Gaal T. UPs and downs in bacterial transcription initiation: the role of the α subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37, 687–695 (2000). A nicely written micro-review that summarizes our current understanding about the RNA polymerase α-subunit C-terminal domain.

    CAS  PubMed  Google Scholar 

  7. Hampsey, M. Omega meets its match. Trends Genet. 17, 190–191 (2001).

    CAS  Google Scholar 

  8. Gross, C. et al. in Transcription. Cold Spring Harbor Symposia on Quantitative Biology, LXIII. 141–155 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 1998). Recommended reading for University of Birmingham undergraduates! A gentle introduction to σ factors that quickly leads to outlining the present problems.

    Google Scholar 

  9. Wösten, M. M. S. M. Eubacterial sigma-factors. FEMS Microbiol. Rev. 22, 127–150 (1998).

    PubMed  Google Scholar 

  10. Merrick, M. J. In a class of its own — the RNA polymerase sigma factor, σ54. Mol. Microbiol. 10, 903–909 (1993).

    CAS  PubMed  Google Scholar 

  11. Campbell, E. A. et al. Structure of the bacterial RNA polymerase promoter specificity α subunit. Mol. Cell. 9, 527–539 (2002). Explains the structural basis for the organisation of σ factors.

    CAS  PubMed  Google Scholar 

  12. Murakami, K. S., Masuda, S. & Darst, S. A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4Å resolution. Science 296, 1280–1284 (2002).

    CAS  PubMed  Google Scholar 

  13. Murakami, K. S., Masuda, S., Campbell, E. A., Muzzin, O. & Darst, S. A. Structural basis of transcription initiation: an RNA polymerase holoenzyme–DNA complex. Science 296, 1285–1290 (2002). References 12 and 13 represent a quantum leap in our understanding of RNA polymerase and its interactions with promoters

    CAS  PubMed  Google Scholar 

  14. Vassylyev, D. G. et al. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417, 712–719 (2002).

    CAS  PubMed  Google Scholar 

  15. de Haseth, P. L., Zupancic, M. L. & Record, M. T. Jr. RNA polymerase–promoter interactions: the comings and goings of RNA polymerase. J. Bacteriol. 180, 3019–3025 (1998).

    CAS  Google Scholar 

  16. Busby, S. & Ebright R. H. Promoter structure, promoter recognition, and transcription activation in prokaryotes. Cell 79, 743–746 (1994).

    CAS  PubMed  Google Scholar 

  17. Bown, J., Barne, K., Minchin, S. & Busby, S. in Nucleic Acids and Molecular Biology Vol. 11 (eds Lilley, D. & Eckstein, F.) 41–52 (Springer, New York, 1997).

    Google Scholar 

  18. Sanderson, A., Mitchell, J. E., Minchin, S. D. & Busby, S. J. Substitutions in the Escherichia coli RNA polymerase σ70 factor that affect recognition of extended −10 elements at promoters. FEBS Lett. 544, 199–205 (2003).

    CAS  PubMed  Google Scholar 

  19. Ross, W., Ernst, A. & Gourse, R. L. Fine structure of E. coli RNA polymerase-promoter interactions: α subunit binding to the UP element minor groove. Genes Dev. 15, 491–506 (2001). A great illustration of how clever biochemistry can be used to discover basic information about the ways in which a protein recognizes its DNA target.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Tsujikawa, L., Tsodikov, O. V. & deHaseth, P. L. Interaction of RNA polymerase with forked DNA: evidence for two kinetically significant intermediates on the pathway to the final complex. Proc. Natl Acad. Sci. USA 99, 3493–3498 (2002).

    CAS  PubMed  Google Scholar 

  21. Tomsic, M. et al. Different roles for basic and aromatic amino acids in conserved region 2 of Escherichia coli σ70 in the nucleation and maintenance of the single-stranded DNA bubble in open RNA polymerase-promoter complexes. J. Biol. Chem. 276, 31891–31896 (2001).

    CAS  PubMed  Google Scholar 

  22. Ishihama, A. Functional modulation of Escherichia coli RNA polymerase. Annu. Rev. Microbiol. 54, 499–518 (2000).

    CAS  PubMed  Google Scholar 

  23. Maeda, H., Fujita, N. & Ishihama A. Competition among seven Escherichia coli σ subunits: relative binding affinities to the core RNA polymerase. Nucleic Acids Res. 28, 3497–3503 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  24. Blomfield, I. C. in Signals, Switches, Regulons, and Cascades (eds Hodgson, D. A. and Thomas, C. M.) 57–72 (Cambridge Univ. Press, Cambridge, UK, 2002).

    Google Scholar 

  25. Salgado, H. et al. RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-12. Nucleic Acids Res. 29, 72–74 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Yura, T. & Nakahigashi, K. Regulation of the heat-shock response. Curr. Opin. Microbiol. 2, 153–158 (1999).

    CAS  PubMed  Google Scholar 

  27. Raivio, T. L. & Silhavy, T. J. Periplasmic stress and ECF sigma factors. Annu. Rev. Microbiol. 55, 591–624 (2001).

    CAS  PubMed  Google Scholar 

  28. Hughes, K. & Mathee, K. The anti-sigma factors. Annu. Rev. Microbiol. 52, 231–286 (1998).

    CAS  PubMed  Google Scholar 

  29. Chatterji, D. & Ojha, A. K. Revisiting the stringent response, ppGpp and starvation signaling. Curr. Opin. Microbiol. 4, 160–165 (2001).

    CAS  PubMed  Google Scholar 

  30. Barker, M. M., Gaal, T., Josaitis, C. A. & Gourse, R. L. 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).

    CAS  PubMed  Google Scholar 

  31. Barker, M. M., Gaal, T. & Gourse, R. L. 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).

    CAS  PubMed  Google Scholar 

  32. Gaal, T., Bartlett, M. S., Ross, W., Turnbough, C. L. Jr & Gourse, R. L. Transcription regulation by initiating NTP concentration: rRNA synthesis in bacteria. Science 278, 2092–2097 (1997).

    CAS  PubMed  Google Scholar 

  33. Schneider, D. A., Gaal, T. & Gourse, R. L. NTP-sensing by rRNA promoters in Escherichia coli is direct. Proc. Natl Acad. Sci. USA 99, 8602–8607 (2002).

    CAS  PubMed  Google Scholar 

  34. Schneider, D. A., Ross, W. & Gourse, R. L. Control of rRNA expression in Escherichia coli. Curr. Opin. Microbiol. 6, 151–156 (2003). A nice summary of our present understanding of growth control and of transcription initiation.

    CAS  PubMed  Google Scholar 

  35. Pérez-Rueda, E. & Collado-Vides, J. The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12. Nucleic Acids Res. 28, 1838–1847 (2000).

    PubMed  PubMed Central  Google Scholar 

  36. Babu, M. M. & Teichmann, S. A. Evolution of transcription factors and the gene regulatory network in Escherichia coli K-12. Nucleic Acids Res. 31, 1234–1244 (2003).

    Google Scholar 

  37. Martinez-Antonio, A. & Collado-Vides, J. Identifying global regulators in transcriptional regulatory networks in bacteria. Curr. Opin. Microbiol. 6, 482–489 (2003).

    CAS  PubMed  Google Scholar 

  38. Müller-Hill, B. The Lac Operon: A Short History of a Genetic Paradigm. (Walter de Gruyter, New York, 1996). A beautifully crafted account of the lac system. Although written from a historical perspective, the text probes current issues and is overlaid with the author's personal philosophy.

    Google Scholar 

  39. Stock, A. M., Robinson, V. L. & Goudreau, P. N. Two-component signal transduction. Annu. Rev. Biochem. 69, 183–215 (2000).

    CAS  Google Scholar 

  40. Darwin, A. J. & Stewart, V. in Regulation of Gene Expression in E. coli. (eds Lin, E. C. C. & Lynch, A. S.) 343–359 (R. G. Landes, New York, 1996).

    Google Scholar 

  41. Demple, B. Redox signaling and gene control in the Escherichia coli soxRS oxidative stress regulon — a review. Gene 179, 53–57 (1996).

    CAS  PubMed  Google Scholar 

  42. Plumbridge, J. Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc. Curr. Opin. Microbiol. 5, 187–193 (2002).

    CAS  PubMed  Google Scholar 

  43. Griffith, K. L., Shah, I. M., Myers, T. E., O'Neill, M. C. & Wolf, R. E. Jr. Evidence for 'pre-recruitment' as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell. Biochem. Biophys. Res. Commun. 291, 979–986 (2002).

    CAS  PubMed  Google Scholar 

  44. Martin, R. G., Gillette, W. K., Martin, N. I. & Rosner, J. L. Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli. Mol. Microbiol. 43, 355–370 (2002).

    CAS  PubMed  Google Scholar 

  45. Ebright, R. H. Transcription activation at Class I CAP-dependent promoters. Mol. Microbiol. 8, 797–802 (1993).

    CAS  PubMed  Google Scholar 

  46. Dove, S. L., Darst, S. A. & Hochschild, A. Region 4 of σ as a target for transcription regulation. Mol. Microbiol. 48, 863–874 (2003).

    CAS  PubMed  Google Scholar 

  47. Nickels, B. E., Dove, S. L., Murakami, K. S., Darst, S. A. & Hochschild, A. Protein–protein and protein–DNA interactions of σ70 region 4 involved in transcription activation by λcI. J. Mol. Biol. 324, 17–34 (2002).

    CAS  PubMed  Google Scholar 

  48. Busby, S. & Ebright, R. H. Transcription activation at Class II CAP-dependent promoters. Mol. Microbiol. 23, 853–859 (1997).

    CAS  PubMed  Google Scholar 

  49. Sheridan, S. D., Benham, C. J. & Hatfield, G. W. Activation of gene expression by a novel DNA structural transmission mechanism that requires supercoiling-induced DNA duplex destabilization in an upstream activating sequence. J. Biol. Chem. 273, 21298–21308 (1998).

    CAS  PubMed  Google Scholar 

  50. Sheridan, S. D., Opel, M. L. & Hatfield, G. W. Activation and repression of transcription initiation by a distant DNA structural transition. Mol. Microbiol. 40, 684–690 (2001). Rightly or wrongly, it is said that it is the exception that proves the rule — this article advocates the exceptional cases.

    CAS  PubMed  Google Scholar 

  51. Brown, N. L., Stoyanov, J. V., Kidd, S. P. & Hobman, J. L. The MerR family of transcriptional regulators. FEMS Microbiol. Rev. 27, 145–163 (2003).

    CAS  PubMed  Google Scholar 

  52. Heldwein, E. E. & Brennan, R. G. Crystal structure of the transcription activator BmrR bound to DNA and a drug. Nature 409, 378–382 (2001). Great crystallography, an interesting problem and an unexpected result!

    CAS  PubMed  Google Scholar 

  53. Müller-Hill, B. Some repressors of bacterial transcription. Curr. Opin. Microbiol. 1, 145–151 (1998).

    PubMed  Google Scholar 

  54. Choy, H. & Adhya, S. in Escherichia coli and Salmonella: Cellular and Molecular Biology (ed. Neidhardt, F. C.) 1287–1299 (ASM Press, Washington, 1996).

    Google Scholar 

  55. Shin, M. et al. Repression of deoP2 in Escherichia coli by CytR: conversion of a transcription activator into a repressor. EMBO J. 20, 5392–5399 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  56. Valentin-Hansen, P., Sogaard-Andersen, L. & Pedersen, H. A flexible partnership: the CytR anti-activator and the cAMP-CRP activator protein, comrades in transcription control. Mol. Microbiol. 20, 461–466 (1996).

    CAS  PubMed  Google Scholar 

  57. Azam, T. A. & Ishihama, A. Twelve species of the nucleoid-associated protein from Escherichia coli. J. Biol. Chem. 274, 33105–33113 (1999).

    CAS  PubMed  Google Scholar 

  58. Schnetz, K. Silencing of Escherichia coli bgl promoter by flanking sequence elements. EMBO J. 14, 2545–50 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. Jordi, B. J. A. M. & Higgins, C. F. The downstream regulatory element of the proU operon of Salmonella typhimurium inhibits open complex formation by RNA polymerase at a distance. J. Biol. Chem. 275, 12123–12128 (2000).

    CAS  PubMed  Google Scholar 

  60. Petersen, C., Moller, L. B. & Valentin-Hansen, P. The cryptic adenine deaminase gene of Escherichia coli. Silencing by the nucleoid-associated DNA-binding protein, H-NS, and activation by insertion elements. J. Biol. Chem. 277, 31373–31380 (2002).

    CAS  PubMed  Google Scholar 

  61. McLeod, S. M. & Johnson, R. C. Control of transcription by nucleoid proteins. Curr. Opin. Microbiol. 4, 152–159 (2001). A very clear summary of an interesting and topical subject.

    CAS  PubMed  Google Scholar 

  62. Browning, D. F., Cole, J. A. & Busby, S. J. W. Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription by a complex nucleo-protein assembly. Mol. Microbiol. 37, 1258–1269 (2000).

    CAS  PubMed  Google Scholar 

  63. Gerstel, U., Park, C. & Romling, U. Complex regulation of csgD promoter activity by global regulatory proteins. Mol. Microbiol. 49, 639–654 (2003).

    CAS  PubMed  Google Scholar 

  64. Dixon, R. in Signals, Switches, Regulons, and Cascades (eds Hodgson, D. A. & Thomas C. M.) 212–230 (Cambridge Univ. Press, UK, 2002).

    Google Scholar 

  65. Busby, S. & Kolb, A. in Regulation of Gene Expression in E. coli. (eds Lin, E. C. C. & Lynch, A. S.) 255–279 (R. G. Landes, New York, 1996).

    Google Scholar 

  66. Chahla, M., Wooll, J., Laue, T. M., Nguyen, N. & Senear, D. F. Role of protein-protein bridging interactions on cooperative assembly of DNA-bound CRP-CytR-CRP complex and regulation of the Escherichia coli CytR regulon. Biochemistry 42, 3812–3825 (2003).

    CAS  PubMed  Google Scholar 

  67. Richet, E., Vidal-Ingigliardi, D. & Raibaud, O. A new mechanism for coactivation of transcription initiation: repositioning of an activator triggered by the binding of a second activator. Cell 66, 1185–1195 (1991).

    CAS  PubMed  Google Scholar 

  68. Schroder, I., Darie, S. & Gunsalus, R. P. Activation of the Escherichia coli nitrate reductase (narGHJI) operon by NarL and Fnr requires integration host factor. J. Biol. Chem. 268, 771–774 (1993).

    CAS  PubMed  Google Scholar 

  69. Joung, J. K., Koepp, D. M. & Hochschild, A. Synergistic activation of transcription by bacteriophage lambda cI protein and E. coli cAMP receptor protein. Science 265, 1863–1866 (1994).

    CAS  PubMed  Google Scholar 

  70. Scott, S., Busby, S. & Beacham, I. Transcriptional coactivation at the ansB promoters: involvement of the activating regions of CRP and FNR when bound in tandem. Mol. Microbiol. 18, 521–532 (1995).

    CAS  PubMed  Google Scholar 

  71. McLeod, S. M., Aiyar, S. E., Gourse, R. L. & Johnson, R. C. The C-terminal domains of the RNA polymerase σ subunits: contact site with Fis and localization during co-activation with CRP at the Escherichia coli proP P2 promoter. J. Mol. Biol. 316, 517–529 (2002).

    CAS  PubMed  Google Scholar 

  72. Belyaeva, T., Rhodius, V., Webster, C. & Busby, S. Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein: organisation of the RNA polymerase σ subunits. J. Mol. Biol. 277, 789–804 (1998).

    CAS  PubMed  Google Scholar 

  73. Beatty, C., Browning, D., Busby, S. & Wolfe, A. CRP-dependent activation of the Escherichia coli acsP2 promoter by a synergistic Class III mechanism. J. Bacteriol. 185, 5148–5157 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Tebbutt, J., Rhodius, V., Webster, C. & Busby, S. Architectural requirements for optimal activation by tandem CRP molecules at a Class I CRP-dependent promoter. FEMS Lett. 210, 55–60 (2002).

    CAS  Google Scholar 

  75. Wade, J., Belyaeva, T., Hyde, E. & Busby, S. A simple mechanism for codependence on two activators at an E. coli promoter. EMBO J. 20, 7160–7167 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  76. Wu, H-C., Tyson, K., Cole, J. & Busby, S. Regulation of the E. coli nir operon by two transcription factors: a new mechanism to account for co-dependence on two activators. Mol. Microbiol. 27, 493–505 (1998).

    CAS  PubMed  Google Scholar 

  77. Browning, D. F., Beatty, C. M., Wolfe, A. J., Cole, J. A. & Busby, S. J. W. Independent regulation of the divergent Escherichia coli nrfA and acsP1 promoters by a nucleoprotein assembly at a shared regulatory region. Mol. Microbiol. 43, 687–701 (2002).

    CAS  PubMed  Google Scholar 

  78. Eriksson, S., Lucchini, S., Thompson, A., Rhen, M. & Hinton, J. C. Unravelling the biology of macrophage infection by gene expression profiling of intracellular Salmonella enterica. Mol. Microbiol. 47, 103–118 (2003).

    CAS  PubMed  Google Scholar 

  79. Reisner, A., Haagensen, J. A., Schembri, M. A., Zechner, E. L. & Molin, S. Development and maturation of Escherichia coli K-12 biofilms. Mol. Microbiol. 48, 933–946 (2003).

    CAS  PubMed  Google Scholar 

  80. Burgess, R. R., Travers, A. A., Dunn, J. J. & Bautz, E. K. Factor stimulating transcription by RNA polymerase. Nature 221, 43–46 (1969).

    CAS  Google Scholar 

  81. Gruber, T. M. & Gross, C. A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57, 441–466 (2003).

    CAS  PubMed  Google Scholar 

  82. Jishage, M., Kvint, K., Shingler, V. & Nystrom, T. Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev. 16, 1260–1270 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Helmann, J. D. Anti-sigma factors. Curr. Opin. Microbiol. 2, 135–141 (1999). An informative account of what is known about anti-sigma factors.

    CAS  PubMed  Google Scholar 

  84. Hengge, R. & Bukau, B. Proteolysis in prokaryotes: protein quality control and regulatory principles. Mol. Microbiol. 49, 1451–1462 (2003).

    CAS  PubMed  Google Scholar 

  85. Studemann, A. et al. Sequential recognition of two distinct sites in σS by the proteolytic targeting factor RssB and ClpX. EMBO J. 22, 4111–4120 (2003). Together with Reference 84, this paper describes a series of experiments that tackle a complicated problem with amazing directness. A paper for connoisseurs.

    PubMed  PubMed Central  Google Scholar 

  86. Buck, M., Gallegos, M.-T., Studholme, D. J., Guo, Y. & Gralla, J. D. The bacterial enhancer-dependent σ54 (σN) transcription factor. J. Bacteriol. 182, 4129–4136 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

Work in the authors' laboratory is funded by the Wellcome Trust and the UK Biotechnology and Biological Sciences Research Council. We are grateful to the very many colleagues who have discussed their ideas with us, and we apologise to those whose work we have been unable to cite due to space limitations. We thank A. Barnard and G. Lloyd for critical scrutiny of the manuscript.

Author information

Authors and Affiliations

  1. School of Biosciences, The University of Birmingham, Edgbaston, B15 2TT, Birmingham, UK

    Douglas F. Browning & Stephen J. W. Busby

Authors
  1. Douglas F. Browning
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Stephen J. W. Busby
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Stephen J. W. Busby.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

DATABASES

ColiBase

AraC

ArcA

CRP

CytR

Dps

Fis

FNR

LacI

Lrp

LysR

LysR

MalT

NarL

NarQ

NarX

OmpR

SoxR

SoxS

StpA

SwissProt

GaIR

IHF

MarA

NarP

FURTHER INFORMATION

Stephen J.W. Busby's laboratory

Glossary

CRAB-CLAW STRUCTURE

This is the name given to the structure that is probably common to all multi-subunit RNA polymerases, in which the two largest subunits form a cleft that contains the enzyme active site.

LINKER

In the context of a protein, a linker is a short stretch of amino acids that joins two separately folding domains. Many linkers have a flexible structure that allows the adjacent domains to adopt different juxtapositions with respect to each other.

SIGMA FACTOR

The subunit of RNA polymerase holoenzyme that is required for promoter sequence recognition and ability to initiate transcription.

OPEN COMPLEX

For transcription, the two strands of the DNA duplex must be unwound locally. An open complex is formed when RNA polymerase binds at a promoter, and the duplex around the transcription start is unwound.

UP ELEMENT

This is a DNA sequence element found at some promoters that increases promoter activity by providing a point of contact for the RNA polymerase α subunit C-terminal domains.

ISOMERIZATION

Describes the step in which the DNA segment, in the RNA polymerase-promoter complex, is unwound.

ANTI-SIGMA FACTORS

A negative transcriptional regulator that acts by binding to a sigma factor and preventing its activity. An anti-anti-sigma factor, in turn, counteracts the action of an anti-sigma factor.

RESPONSE REGULATORS

Usually bacterial gene-regulatory proteins that control gene expression in response to external signals. Most response regulators consist of two domains: a DNA-binding domain and a regulatory domain, the activity of which is modulated (indirectly) by the external signal.

SENSOR KINASE

Transmits the external signal to the response regulator.

SUPERCOILING

Describes a state of the DNA in which its conformation deviates from the well-known Watson-Crick double helix, leading to its compaction and favouring local DNA unwinding.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Browning, D., Busby, S. The regulation of bacterial transcription initiation. Nat Rev Microbiol 2, 57–65 (2004). https://doi.org/10.1038/nrmicro787

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro787

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing