DNA supercoiling and transcription in bacteria: a two-way street

Abstract

Background: The processes of DNA supercoiling and transcription are interdependent because the movement of a transcription elongation complex simultaneously induces under- and overwinding of the DNA duplex and because the initiation, elongation and termination steps of transcription are all sensitive to the topological state of the DNA.

Results: Policing of the local and global supercoiling of DNA by topoisomerases helps to sustain the major DNA-based transactions by eliminating barriers to the movement of transcription complexes and replisomes. Recent data from whole-genome and single-molecule studies have provided new insights into how interactions between transcription and the supercoiling of DNA influence the architecture of the chromosome and how they create cell-to-cell diversity at the level of gene expression through transcription bursting.

Conclusions: These insights into fundamental molecular processes reveal mechanisms by which bacteria can prevail in unpredictable and often hostile environments by becoming unpredictable themselves.

Fig. 1

Twin supercoiling domain model. This is the model proposed by Liu and Wang (1987) and supported by numerous independent experiments. Core RNA polymerase is engaged in transcript elongation: mRNA, ribosomes and nascent polypeptide are omitted for clarity. As the coupled transcription-translation complex moves from left to right, the DNA template ahead becomes over wound (positively supercoiled plectonemes) while the DNA behind becomes under wound (negatively supercoiled plectonemes). This situation will halt transcription as the machinery jams because: (a) the domains of supercoiled DNA cannot be removed by supercoil diffusion due to the presence of topological barriers (black spheres at the ends of the DNA) and (b) the bulky transcription-translation complex cannot rotate around the DNA to relieve the torsional tension in the duplex DNA. Instead, DNA gyrase will remove the positive supercoils while the negative ones are relaxed by DNA topoisomerases I and/or IV. Interference with these relaxation processes can result in undesirable outcomes, such as R-loop formation (Fig. 2). Topological barriers can arise due to head-to-head transcription complex collisions and by collisions between converging replisomes and transcription complexes; they can be produced by nucleoprotein complexes and by distortions (e.g. sharp bends) in the DNA duplex. The oval arrows at the bottom of the figure represent possible rotational solutions to these topological problems: each of these solutions is ruled out (red lines) because rotation of the DNA and/or the transcription complex cannot occur, for the reasons summarised in (a) and (b) above

Fig. 2

DNA negative supercoiling and R-loop formation during transcription. When RNA polymerase (green) reads a G + C-rich DNA template, stalls and backtracks, it leaves a domain of hyper-negatively supercoiled behind. The associated stalling of transcription may allow the RNA transcript (red) to base pair with its DNA template strand (blue), leaving the non-transcribed strand as a single-stranded bubble. Other impediments to RNA polymerase progression include head-on collisions with other transcription units or with replisomes (the barrier is represented by the red vertical dotted line). Loss of the DNA relaxing activity of topoisomerase I promotes R-loop formation because it encourages the accumulation of hyper-negative-superhelicity in DNA that is being transcribed (or replicated). Failure to process and remove RNA loops can lead to DNA damage, including double-stranded breaks and hyper-recombination. RNase H eliminates R-loops by removing the RNA component of the RNA:DNA hybrid in the R-loop. The Rho transcription terminating helicase can suppress R-loop formation by preventing RNA polymerase backtracking

Fig. 3

Transcription DNA, supercoiling and chromosome architecture. Data from chromosome conformation capture experiments indicate that long, heavily-transcribed transcription units can form barriers to DNA-DNA interaction [16]. The transcribed region (red) has few plectonemes and insulates the flanking regions that are rich in plectonemically interwound DNA. Cessation of transcription in the red zone allows plectonemic wrapping of DNA to be restored, re-establishing DNA-DNA contacts and allowing interactions between the red zone and the flanking regions. Activating and inhibiting transcription in the red region lowers and raises, respectively, the barrier that insulates it from its neighbouring genomic regions. The insulating mechanism does not involve influencing supercoil diffusion, nor is it dependent on translation of the transcripts within the heavily transcribed region