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The regulation of bacterial transcription initiation

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.

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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.

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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.

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Correspondence to Stephen J. W. Busby.

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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.

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

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