![]() ![]() 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. Interference with these relaxation processes can result in undesirable outcomes, such as R-loop formation (Fig. Instead, DNA gyrase will remove the positive supercoils while the negative ones are relaxed by DNA topoisomerases I and/or IV. ![]() 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. 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). Core RNA polymerase is engaged in transcript elongation: mRNA, ribosomes and nascent polypeptide are omitted for clarity. This is the model proposed by Liu and Wang (1987) and supported by numerous independent experiments. This requirement provides one mechanistic link between transcription and DNA supercoiling. The breakage of hydrogen bonds between pairs of bases due to torsional stress assists such processes as transcription, where the generation of single-stranded bubbles in the double-stranded DNA is essential. At any given time in the growth cycle, about 40% of the DNA in the bacterial genome is free of protein and can participate in supercoiling through the formation of DNA plectonemes, segments of interwound, or braided, double-stranded DNA (Fig. DNA binds a variety of proteins that can constraint supercoils and nucleoid-associated proteins have a special role in providing this function. In living bacteria, all three solutions are employed. Underwound DNA experiences torsional stress that is usually neutralised by wrapping the DNA around proteins to constrain supercoils, by allowing the DNA duplex to writhe and/or by allowing some of the pairs of hydrogen-bonded bases to unpair. If the DNA is neither under- nor overwound, it adopts a relaxed conformation. Removing turns through underwinding the duplex has the opposite effect, causing the duplex to writhe negatively. Increasing the frequency of turning tightens the duplex and results in positive writhing as the axis of the double helix coils around itself in search of a minimal energy conformation. In its B form, the strands of the DNA duplex make one complete turn every 10.5 base pairs. DNA is usually negatively supercoiled in bacterial cells because it contains a deficit of helical turns. Variable DNA supercoiling is a fundamental principle in the control of gene expression in bacteria. These insights into fundamental molecular processes reveal mechanisms by which bacteria can prevail in unpredictable and often hostile environments by becoming unpredictable themselves. 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. ![]() 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. 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. ![]()
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