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Illustration of how cold shock affects the supercoiling state of the DNA, by blocking the activity of Gyrase. The signs ' − ' and '+' represent negative and positive supercoiling, respectively. Created with BioRender.com. Also shown is a stochastic model of gene expression during cold shock as a function of the global DNA supercoiling state.
The enzyme uses the hydrolysis of ATP to introduce positive supercoils and overwinds DNA, a feature attractive in hyperthermophiles, in which reverse gyrase is known to exist. Rodriguez and Stock have done further work to identify a "latch" that is involved in communicating the hydrolysis of ATP to the introduction of positive supercoils.
Transcription by RNA polymerase also generates positive supercoiling ahead of, and negative supercoiling behind, the transcriptional complex (Fig. 2). This effect is known as the twin-supercoiled domain model, as described by Leroy Liu and James Wang in 1987. [21]
While positive supercoiling is certainly more common in thermophiles, positive supercoiling has been found in mesophilic organisms. For example, telomeres and condensins can both utilize positive supercoiling as a means for contributing to chromosomal structure. [19] Furthermore, the reverse gyrase enzyme is not exclusive to thermophiles.
In nature, most DNA has slight negative supercoiling that is introduced by enzymes called topoisomerases. [44] These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication .
DNA gyrase, or simply gyrase, is an enzyme within the class of topoisomerase and is a subclass of Type II topoisomerases [1] that reduces topological strain in an ATP dependent manner while double-stranded DNA is being unwound by elongating RNA-polymerase [2] or by helicase in front of the progressing replication fork.
While topoisomerase IV does relax positive supercoils like DNA gyrase, it does not introduce further negative supercoiling like the latter enzyme. [ 1 ] Topoisomerase IV can unknot right-handed knots and decatenate right-handed catenanes without acting on right-handed plectonemes in negatively supercoiled DNA molecules, based on geometrical ...
Condensin I purified from Xenopus egg extracts is a DNA-stimulated ATPase and displays the ability to introduce positive superhelical tension into dsDNA in an ATP-hydrolysis-dependent manner (positive supercoiling activity). [35] [36] Similar activities have been detected in condensins from other organisms.