Topological insulators inhibit diffusion of transcription‐induced positive supercoils in the chromosome of Escherichia coli

Abstract

SummaryThe double helical nature of DNA implies that progression of transcription machinery that cannot rotate easily around the DNA axis creates waves of positive supercoils ahead of it and negative supercoils behind it. Using topological reporters that detect local variations in DNA supercoiling, we have characterized the diffusion of transcription-induced (TI) positive supercoils in plasmids or in the chromosome of wild type Escherichia coli cells. Transcription-induced positive supercoils were able to diffuse and affect local supercoiling several kilobases away from the site of origin. By testing the effect of various DNA sequences, these reporters enabled us to identify elements that impede supercoil diffusion, i.e. behave as topological insulators. All the elements tested correspond to DNA gyrase catalytic targets. These results correlate the ability of a DNA sequence to be cleaved by DNA gyrase with topological insulator activity. Implications of the asymmetry in supercoil diffusion for the control of DNA topology are discussed.

The regulatory role of DNA supercoiling in nucleoprotein complex assembly and genetic activity

“…Any effects would depend on how far such gradients extend. Current estimates suggest that, depending on the strength of the signal, gradients may extend for up to a few kilobases (Krasilnikov et al 1999;Moulin et al 2005;Kouzine et al 2008), and therefore their influence will be local rather than global (Sobetzko 2016;Meyer and Beslon 2014). Since transcription is a dominant source of the local generation of superhelicity, the relative orientation of neighboring genes determines how transcription of one may affect the activity of its neighbor by supercoilingmediated coupling.…”

The bacterial nucleoid: A highly organized and dynamic structure

“…Topoisomerases are thought to create topological barriers in at least two different ways: on the one hand, they were shown to preferentially bind to juxtaposed DNA helices, which could allow them to generate transient interconnections between different DNA regions [Zechiedrich and Osheroff, 1990]. Accordingly, DNA gyrase was demonstrated to block diffusion of transcription-induced supercoils in E. coli, when associated with its catalytic target sites [Moulin et al, 2005]. On the other hand, topoisomerases are responsible for decatenating entangled DNA and controlling the superhelicity of individual DNA segments.…”

“…The RNA polymerase complex is too large to follow the individual helical turns of DNA. Its movement along the template strand, therefore, transiently generates domains of positive and negative supercoiling, respectively, ahead and behind the transcriptional bubble [Wu et al, 1988;Rahmouni and Wells, 1992;Moulin et al, 2005]. These topological changes are significantly stabilized if the transcript encodes a membrane protein [Liu and Wang, 1987;Lodge et al, 1989;Lynch and Wang, 1993], because transcription and co-transcriptional translation are coupled with the insertion of nascent polypeptides into the membrane in bacteria, thereby tethering RNA polymerase to the site of protein translocation [Binenbaum et al, 1999].…”

REP-elements of the Escherichia coli Genome and Transcription Signals: Positional and Functional Analysis

“…Взаимодействуя с ними, ДНК-гираза может вызывать релаксацию положительных супервитков в ДНК, закономерно накапливающихся в 3'-концевых областях генов в результате транскрипции и ингибирующих считывание следующего гена [10]. Специфически связывающие топоизомеразу REP-элементы, расположенные между последовательными генами, могут снижать это напряжение, стимулируя синтез РНК [11].…”