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Bacterial RNA thermometers: molecular zippers and switches

Nature Reviews Microbiology volume 10, pages 255–265 (2012)Cite this article

Subjects

Key Points

  • Structured regions in bacterial mRNAs can act as thermosensors, known as RNA thermometers (RNATs), that control translation efficiency of the transcript.

  • Some RNATs act like zippers that open and close, in a reversible manner, according to the ambient temperature. These RNATs control heat shock and virulence genes.

  • Escherichia coli uses a cascade of hierarchically organized RNATs to monitor any harmful temperature upshifts and to induce the production of protective heat shock proteins when required.

  • Known heat shock RNATs have little if any sequence conservation.

  • Recent biophysical approaches revealed details of RNAT zippers at base pair resolution. Non-Watson–Crick base pairs, internal loops and bulges, Mg2+ and the hydration shell can be crucial for RNAT stability and melting.

  • RNATs that permit translation of cold-shock and phage genes at low temperatures switch between two mutually exclusive structures. The conformation at low temperature favours translation.

  • Synthetic thermosensors inspired by natural RNATs can induce gene expression in response to a temperature upshift and bear potential as tools for large-scale industrial applications without the need for chemical inducers.

Abstract

Bacteria use complex strategies to coordinate temperature-dependent gene expression. Many genes encoding heat shock proteins and virulence factors are regulated by temperature-sensing RNA sequences, known as RNA thermometers (RNATs), in their mRNAs. For these genes, the 5′ untranslated region of the mRNA folds into a structure that blocks ribosome access at low temperatures. Increasing the temperature gradually shifts the equilibrium between the closed and open conformations towards the open structure in a zipper-like manner, thereby increasing the efficiency of translation initiation. Here, we review the known molecular principles of RNAT action and the hierarchical RNAT cascade in Escherichia coli. We also discuss RNA-based thermosensors located upstream of cold shock and other genes, translation of which preferentially occurs at low temperatures and which thus operate through a different, more switch-like mechanism. Finally, we consider the potential biotechnological applications of natural and synthetic RNATs.

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Figure 1: RNA zippers and RNA switches.
Figure 2: Three types of zipper-like RNA thermometer.
Figure 3: RNA thermometers for heat shock control in Escherichia coli.
Figure 4: Interplay between a metabolite-sensing riboswitch and a temperature-sensing RNA thermometer.
Figure 5: RNA thermometer switches that permit translation at low temperature.

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Acknowledgements

RNA-related work in the Narberhaus laboratory is supported by grants from the German Research Foundation (DFG Priority Programme 1258, Sensory and Regulatory RNAs in Prokaryotes). J.K. received a fellowship from the Studienstiftung des Deutschen Volkes.

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  1. Lehrstuhl für Biologie der Mikroorganismen, Ruhr-Universität Bochum, Universittsstrasse 150, NDEF 06/783, 44780, Bochum, Germany

    Jens Kortmann & Franz Narberhaus

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Correspondence to Franz Narberhaus.

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Overview of experimentally-characterized RNATs (PDF 190 kb)

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Glossary

Feed-forward systems

Modules within control networks; feed-forward systems sense external perturbations (for example, a temperature up- or downshift) before the actual impact on the network occurs.

Ribosome-binding site

The part of an mRNA with which the 30S ribosome interacts to initiate translation. It contains the Shine–Dalgarno sequence and the AUG start codon.

Riboswitches

Regulatory elements within an mRNA that directly affect gene expression through specific binding of a ligand which induces structural alterations.

Aptamer

An oligonucleotide that specifically binds a target molecule. RNA-based aptamers form the ligand-binding domains of riboswitches.

Shine–Dalgarno sequence

The primary ribosome-binding site of bacterial mRNAs, located 6–10 nucleotides upstream of the AUG start codon, in the 5′ untranslated region. It is complementary to the 3′ end of the 16S ribosomal RNA of the 30S ribosome. The Escherichia coli consensus sequence is AGGAGG.

tRNAfMet

The initiating tRNA, charged with a methionine that has the amino terminus blocked by a formyl group, thus defining the start and synthesis direction of the nascent polypeptide chain.

syn–anti base pairing

Non-Watson–Crick base pairing, in which one base is rotated from the typical anti position (relative to the ribose ring) to a syn position.

Hydration shell

A layer of water molecules that is formed around intracellular macromolecules (for example, DNA, RNA and proteins), with a possible effect on their functionality.

Toeprinting

A primer extension method that uses inhibition of reverse transcription to probe the interaction between an mRNA and the 30S ribosome.

Pseudoknot

A knot-shaped tertiary RNA structure that, in its simplest form, is built by two helical structures. The loop of the first hairpin contributes to the stem of the second hairpin. Pseudoknots are a structurally diverse group with important effects in many biological processes.

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Kortmann, J., Narberhaus, F. Bacterial RNA thermometers: molecular zippers and switches. Nat Rev Microbiol 10, 255–265 (2012). https://doi.org/10.1038/nrmicro2730

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