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Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies

Nature Reviews Microbiology volume 11, pages 303–315 (2013)Cite this article

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Key Points

  • Recent advances have improved the range of measurements that can be made using fluorescence-based single-molecule in vitro techniques, and these tools are now being used to monitor the assembly of macromolecular complexes, which has provided new mechanistic insights for the processes of DNA replication, transcription and translation in bacteria.

  • Fluorescence-based studies have revealed that the DNA polymerase holoenzyme complex contains an 'extra' core polymerase. This core polymerase, in addition to the leading-strand and lagging-strand core polymersases, can be exchanged with others from the cytosolic pool, and the complex as a whole maintains a stable association with the replication fork.

  • Using single-molecule studies, it has been shown that transcription initiation progresses through a well-ordered molecular pathway with a single rate-limiting step, providing a physical basis for the tight control of gene expression.

  • Single-molecule techniques have also demonstrated that throughout transcription, the bacterial RNA polymerase holoenzyme (RNAP HE)–DNA complex transitions between open and closed states, which appear to correspond to paused and processive forms of RNAP HE, respectively.

  • These technologies have also been used to investigate the dynamics of bacterial translation and have revealed that the initial stages of translation do not necessarily progress through a single series of events, but can instead follow multiple pathways.

  • In addition, a novel checkpoint has been discovered that governs the stable binding of the first non-initiator tRNA during translation initiation. This checkpoint seems to play a part in promoting a faithful transition to the elongation stage of translation.

Abstract

Decades of research have resulted in a remarkably detailed understanding of the molecular mechanisms of bacterial DNA replication, transcription and translation. Our understanding of the kinetics and physical mechanisms that drive these processes forward has been expanded by the ability of single-molecule in vitro techniques, such as force spectroscopy and single-molecule Förster (fluorescence) resonance energy transfer (smFRET), to capture short-lived intermediate states in complex pathways. Furthermore, these technologies have revealed novel mechanisms that support enzyme processivity and govern the assembly of large multicomponent complexes. Here, we summarize the application of in vitro single-molecule studies to the analysis of fundamental bacterial processes, with a focus on the most recent functional insights that have been gained from fluorescence-based methods.

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Figure 1: Initiation of DNA replication in Escherichia coli.
Figure 2: Mechanism of core-polymerase exchange in the T7 and Escherichia coli systems.
Figure 3: Binding and conformational changes of RNA polymerase during transcription at a σ54-dependent promoter.
Figure 4: Monitoring translational events using a single-molecule approach.

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Acknowledgements

A.M.v.O. is supported by grants from the Netherlands Organisation for Scientific Research (NWO; Vici 680-47-607) and the European Research Council (ERC 281098).

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  1. Zernike Institute for Advanced Materials, University of Groningen, Groningen, 9747 AG, The Netherlands

    Andrew Robinson & Antoine M. van Oijen

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Glossary

Derivatized glass coverslip

A microscope coverslip that has been coated or chemically treated to allow site-specific attachment of biomolecules.

Flow cell

A microscopy sample environment that allows liquid flow over surface-immobilized particles.

Drag

A force that acts on solid objects placed in a liquid flow. Drag acts in the same direction as the flow.

Brownian motion

Random movement of particles in suspension, resulting from bombardment by solvent molecules.

EMCCD camera

(Electron-multiplying charge-coupled device camera). A camera that can be used to capture low-level light emanating from a microscopy sample, for example.

Fluorophore

A compound that is capable of producing fluorescence, such as an organic dye or a fluorescent protein.

Förster (fluorescence) resonance energy transfer

A phenomenon whereby energy induced by light excitation is transferred from one fluorophore to another in a distance-dependent manner.

Okazaki fragments

Regions of double-stranded DNA that are produced during discontinuous synthesis of the lagging strand.

DNA curtain

A tethered-particle technique in which DNA molecules are trapped along a diffusion barrier within a flow cell and stretched parallel to the glass surface by drag.

Rolling-circle replication

A mode of DNA replication of a circular substrate to yield a linear, double-stranded product of theoretically infinite length.

Brownian ratchet

In the context of this article: a mechanism whereby particles undergoing Brownian motion are driven in a certain direction by selecting for only those motions that occur in the desired direction.

Zero-mode waveguides

Nanostructures that are used in microscopy; in these nanostructures, light is guided through compartments that are smaller than the wavelength of the light.

Photoswitchable fluorescent probes

Molecules that change from being non-fluorescent to fluorescent, or vice versa, in response to light.

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Robinson, A., van Oijen, A. Bacterial replication, transcription and translation: mechanistic insights from single-molecule biochemical studies. Nat Rev Microbiol 11, 303–315 (2013). https://doi.org/10.1038/nrmicro2994

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