Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
Ontology highlight
ABSTRACT:
ORGANISM(S): Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Ra
PROVIDER: GSE85357 | GEO | 2017/01/31
SECONDARY ACCESSION(S): PRJNA338794
REPOSITORIES: GEO
Similar Datasets
Project description:Reverse gyrase is a DNA topoisomerase that catalyzes positive DNA supercoiling in an ATP-dependent reaction. The enzyme consists of a helicase and a topoisomerase domain. The isolated helicase-like domain is a DNA-stimulated ATPase, and the isolated topoisomerase domain can relax supercoiled DNA. For positive supercoiling of DNA, the two domains need to cooperate, presumably through conformational changes. Here, we probed conformational changes of Thermotoga maritima reverse gyrase on DNA and nucleotide binding using hydrogen deuterium exchange (HDX). While ADPNP binding does not induce major conformational changes, binding of DNA leads to increased exposure of a region at the helicase-topoisomerase interface, encompassing R501 and E705, the side chains of which engage in electrostatic interactions. Removing the charges in an R501/E705A variant leads to a moderate increase in supercoiling activity, suggesting a slightly inhibitory role of this interactions. A R501/E705C variant, crosslinked to fix the two side chains in a disulphide bond, on the other hand, is inactive. Collectively these data show that rearrangements at the helicase and topoisomerase interface are important for the functional cooperation of the domains and for the enzymatic activity of reverse gyrase.
2026-08-24 | PXD074413 | Pride
Project description:Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
| PRJNA338794 | ENA
Project description:DNA supercoiling is essential for all living cells because it controls all processes involving DNA. In bacteria, global DNA supercoiling results from the opposing activities of topoisomerase I, which relaxes DNA, and DNA gyrase, which compacts DNA. These enzymes are widely conserved, sharing >91% amino acid identity between the closely related species Escherichia coli and Salmonella enterica serovar Typhimurium. Why, then, do E. coli and Salmonella exhibit different DNA supercoiling when experiencing the same conditions? We now report that this surprising difference reflects disparate activation of their DNA gyrases by the polyamine spermidine and its precursor putrescine. In vitro, Salmonella DNA gyrase activity was sensitive to changes in putrescine concentration within the physiological range, whereas activity of the E. coli enzyme was not. In vivo, putrescine activated the Salmonella DNA gyrase and spermidine the E. coli enzyme. High extracellular Mg2+ decreased DNA supercoiling exclusively in Salmonella by reducing the putrescine concentration. Our results establish the basis for the differences in global DNA supercoiling between E. coli and Salmonella, define a signal transduction pathway regulating DNA supercoiling, and identify potential targets for antibacterial agents.
2020-10-30 | GSE150757 | GEO
Project description: Not available
| S-EPMC5433769 | biostudies-literature
Project description:DNA gyrase is an essential enzyme whose activity is required for DNA replication and chromosome maintenance. Inhibition of gyrase results in multiple physiological effects including changes in DNA superhelicity, replication arrest and DNA damage. Using genetic, genomic, statistical and biochemical techniques, we have untangled the contribution of individual effects, assessed their relative significance and concluded that: i) DNA replication is required for the formation of spatial transcriptional domains; ii) transcriptional response to gyrase inhibition is coordinated between at least two modules involved in DNA maintenance, relaxation and damage response; iii) genes whose transcriptional response to gyrase inhibition does not depend on the activity of topoisomerase I can be classified on the basis of the GC excess in their upstream and coding sequences into, respectively, activated and repressed by gyrase inhibition; iv) relaxation by topoisomerase I dominates the transcriptional response upon gyrase inhibition, followed by the effects of replication and RecA. Keywords: time course
2006-03-10 | GSE4408 | GEO
Project description:Various bis-benzimidazole derivatives have been reported to possess activity against Gram-positive pathogens. No mechanism of action has been elucidated to fully account for the antibacterial activity of this class of compounds. A group of symmetric bis-benzimidazoles (BBZ) designed as anticancer agents have previously been shown to possess moderate antiproliferative activity. We sought to assess the antibacterial activity and mechanism of action of BBZ compounds against Staphylococcus aureus. Antibacterial activities were assessed by determination of minimal inhibitory concentrations (MICs), time-kill curves, and scanning electron microscopy. Transcriptional responses to BBZ treatment were determined using whole genome microarrays. Activities against bacterial type II topoisomerases were investigated using in vitro supercoiling, decatenation, DNA binding, and DNA cleavage inhibition assays. MICs for EMRSA-16 were between 0.03 and 0.5 μg/mL. The compounds showed concentration-dependent bactericidal activity and induced cell swelling and lysis. Transcriptional responses to BBZ were consistent with topoisomerase inhibition and DNA damage. A subset of BBZ compounds inhibited S. aureus DNA gyrase supercoiling activity with IC50 values in the range of 5−10 μM. This inhibition was subsequently shown to operate through both inhibition of binding of DNA gyrase to DNA and accumulation of single-stranded DNA breaks. We conclude that BBZ compounds are potent antistaphylococcal agents and operate at least in part through DNA gyrase inhibition, leading to the accumulation of single-stranded DNA breaks, and by preventing the binding of gyrase to DNA. [Data is also available from http://bugs.sgul.ac.uk/E-BUGS-106]
2012-10-14 | E-BUGS-106 | biostudies-arrayexpress
Project description:Type II topoisomerases (topos) are a ubiquitous and essential class of enzymes that form transient enzyme-bound double-stranded breaks on DNA called cleavage complexes. The location and frequency of these cleavage complexes on DNA is important for cellular function, genomic stability, and a number of clinically important anticancer and antibacterial drugs, e.g., quinolones. We developed a simple high-accuracy end-sequencing (SHAN-seq) method to sensitively map type II topo cleavage complexes on DNA in vitro. Using SHAN-seq, we detected Escherichia coli gyrase and topoisomerase IV cleavage complexes at hundreds of sites on supercoiled pBR322 DNA, approximately one site every ten bp, with frequencies that varied by two-to-three orders of magnitude. These sites included previously identified sites and 20-50 fold more new sites. We show that the location and frequency of cleavage complexes at these sites are enzyme-specific and vary substantially in the presence of the quinolone, ciprofloxacin, but not with DNA supercoil chirality, i.e., negative vs. positive supercoiling. SHAN-seq’s exquisite sensitivity provides an unprecedented single-nucleotide resolution view of the distribution of gyrase and topoisomerase IV cleavage complexes on DNA. Moreover, the discovery that these enzymes can cleave DNA at orders of magnitude more sites than the relatively few previously known sites resolves the apparent paradox of how these enzymes resolve topological problems throughout the genome.
2024-08-06 | GSE267149 | GEO
Project description:DNA supercoiling has the potential to alter gene transcription and chromatin topology, yet how its distribution is regulated on a genome-wide level is poorly understood. Here we utilized psoralen crosslinking and sequencing (TMP-seq) to assess the distribution of underwound DNA at high resolution in postmitotic neurons. We report that supercoiling propagates widely (> 200 kb) from the sites of active RNAPII and that its distribution is constrained by chromosome compartments and by specific nucleosome configurations, including H3K27me3-rich regions and broad distributions of active promoter-related chromatin marks. Underwound DNA does not accrue upstream of expressed genes in postmitotic neurons, which could shield them from cumulative torsional stress. Inhibiting either transcription or TOP1 affect underwound DNA levels genome-wide; however, supercoiling at the boundaries of expressed genes is minimally perturbed, indicating that dynamic supercoiling is not locally confined to sites of RNAPII activity at expressed genes. Surprisingly, TOP1 inhibition elevates supercoiling but stimulates nascent transcription at most genes and other sites of transcription, including enhancers, suggesting that torsional stress generally favors transcription, and that topoisomerase activity is not essential for transcription at most genes. We show that the induction of cryptic transcription within gene bodies, and not supercoiling buildup, could underlie the vulnerability of long neuronal genes to topoisomerase inhibition. These observations illuminate how chromatin organization governs the distribution of torsional stress within the genome and how the interplay of supercoiling and topoisomerases regulates transcription.
2026-07-14 | GSE231609 | GEO
Project description:DNA supercoiling has the potential to alter gene transcription and chromatin topology, yet how its distribution is regulated on a genome-wide level is poorly understood. Here we utilized psoralen crosslinking and sequencing (TMP-seq) to assess the distribution of underwound DNA at high resolution in postmitotic neurons. We report that supercoiling propagates widely (> 200 kb) from the sites of active RNAPII and that its distribution is constrained by chromosome compartments and by specific nucleosome configurations, including H3K27me3-rich regions and broad distributions of active promoter-related chromatin marks. Underwound DNA does not accrue upstream of expressed genes in postmitotic neurons, which could shield them from cumulative torsional stress. Inhibiting either transcription or TOP1 affect underwound DNA levels genome-wide; however, supercoiling at the boundaries of expressed genes is minimally perturbed, indicating that dynamic supercoiling is not locally confined to sites of RNAPII activity at expressed genes. Surprisingly, TOP1 inhibition elevates supercoiling but stimulates nascent transcription at most genes and other sites of transcription, including enhancers, suggesting that torsional stress generally favors transcription, and that topoisomerase activity is not essential for transcription at most genes. We show that the induction of cryptic transcription within gene bodies, and not supercoiling buildup, could underlie the vulnerability of long neuronal genes to topoisomerase inhibition. These observations illuminate how chromatin organization governs the distribution of torsional stress within the genome and how the interplay of supercoiling and topoisomerases regulates transcription.
2026-07-14 | GSE231690 | GEO
Project description:DNA supercoiling has the potential to alter gene transcription and chromatin topology, yet how its distribution is regulated on a genome-wide level is poorly understood. Here we utilized psoralen crosslinking and sequencing (TMP-seq) to assess the distribution of underwound DNA at high resolution in postmitotic neurons. We report that supercoiling propagates widely (> 200 kb) from the sites of active RNAPII and that its distribution is constrained by chromosome compartments and by specific nucleosome configurations, including H3K27me3-rich regions and broad distributions of active promoter-related chromatin marks. Underwound DNA does not accrue upstream of expressed genes in postmitotic neurons, which could shield them from cumulative torsional stress. Inhibiting either transcription or TOP1 affect underwound DNA levels genome-wide; however, supercoiling at the boundaries of expressed genes is minimally perturbed, indicating that dynamic supercoiling is not locally confined to sites of RNAPII activity at expressed genes. Surprisingly, TOP1 inhibition elevates supercoiling but stimulates nascent transcription at most genes and other sites of transcription, including enhancers, suggesting that torsional stress generally favors transcription, and that topoisomerase activity is not essential for transcription at most genes. We show that the induction of cryptic transcription within gene bodies, and not supercoiling buildup, could underlie the vulnerability of long neuronal genes to topoisomerase inhibition. These observations illuminate how chromatin organization governs the distribution of torsional stress within the genome and how the interplay of supercoiling and topoisomerases regulates transcription.
2026-07-14 | GSE231610 | GEO