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Local and global regulation of transcription initiation in bacteria

Nature Reviews Microbiology volume 14, pages 638–650 (2016)Cite this article

Subjects

Key Points

  • Transcription initiation involves the interaction of DNA-dependent RNA polymerase with promoters. In bacteria, this is a highly regulated process.

  • Many regulators interact directly with the bacterial DNA-dependent RNA polymerase, whereas other regulators interact directly with promoters.

  • Regulation of transcription initiation occurs in the context of folding and compaction of bacterial chromosomes.

  • A very wide range of different strategies are used to regulate transcription initiation in bacteria and these differ between species.

Abstract

Gene expression in bacteria relies on promoter recognition by the DNA-dependent RNA polymerase and subsequent transcription initiation. Bacterial cells are able to tune their transcriptional programmes to changing environments, through numerous mechanisms that regulate the activity of RNA polymerase, or change the set of promoters to which the RNA polymerase can bind. In this Review, we outline our current understanding of the different factors that direct the regulation of transcription initiation in bacteria, whether by interacting with promoters, with RNA polymerase or with both, and we discuss the diverse molecular mechanisms that are used by these factors to regulate gene expression.

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Figure 1: Transcription of bacterial genes.
Figure 2: Modulation of RNA polymerase activity.
Figure 3: Appropriation of RNA polymerase for specific transcriptional programmes.
Figure 4: Repression or activation at promoters by transcription factors.
Figure 5: Regulation by promoter DNA modification.

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Acknowledgements

The authors were supported by the UK Biotechnology and Biological Sciences Research Council (BBSRC; grant BB/J006076/1) and by the Industrial Biotechnology Catalyst programme (funded by Innovate UK, the BBSRC and the UK Engineering and Physical Sciences Research Council (EPSRC)) to support the translation, development and commercialisation of innovative industrial biotechnology processes.

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  1. Institute of Microbiology and Infection, School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK

    Douglas F. Browning & Stephen J. W. Busby

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Correspondence to Douglas F. Browning or Stephen J. W. Busby.

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PowerPoint slides

Glossary

RNA polymerase core enzyme

The form of bacterial DNA-dependent RNA polymerase that lacks a sigma factor.

Template strand

The strand of the DNA duplex that acts as a template for RNA synthesis.

Open complex

The complex between RNA polymerase and a promoter after DNA duplex unwinding has occurred and the RNA polymerase is ready to start transcription.

Housekeeping sigma factor

The sigma factor in a bacterium that is responsible for the recognition of promoters that control the transcription of most genes.

Chromatin immunoprecipitation

(ChIP). A method whereby antibodies are used to isolate DNA fragments that have been cross-linked to a specific protein.

Stationary phase

The period when bacteria have stopped growing.

Guanosine tetraphosphate

(ppGpp). A small molecule that is synthesized in response to certain stresses. ppGpp is often referred to as 'magic spot', which is a term that also refers to guanosine pentaphosphate (pppGpp).

Actinomycetes

A class of soil bacteria with a particular morphology.

Coiled-coil

An extended motif found in proteins.

Closed complex

The complex between RNA polymerase and a promoter before DNA duplex unwinding has occurred.

Michaelis constant

The concentration of a substrate at which the reaction catalysed by an enzyme proceeds at half of its maximum speed.

Initiating nucleotide

The 5′ nucleotide of a transcript.

Nucleoid

The structure that forms after a bacterial chromosome is compacted inside a bacterium.

Superhelical density

The measure of the degree to which the winding of one DNA strand around the other differs from the periodicity of the Watson–Crick structure.

Enterohaemorrhagic E. coli

A virulent strain of Escherichia coli that causes bloody diarrhoea.

Pervasive transcription

The synthesis of transcripts that seem not to correspond to any functional genetic unit.

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Browning, D., Busby, S. Local and global regulation of transcription initiation in bacteria. Nat Rev Microbiol 14, 638–650 (2016). https://doi.org/10.1038/nrmicro.2016.103

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