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Fluoroquinolone-induced gyrase cleavage sites

ABSTRACT: Fluoroquinolone-induced gyrase cleavage sites

PROVIDER: PRJNA851452 | ENA |

REPOSITORIES: ENA

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Genome-wide mapping of fluoroquinolone-induced gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence

Project description:Persisters are rare phenotypic variants that can survive bactericidal doses of antibiotics and resume growth after the conclusion of treatment. They are suspected to be culprits of recurrent infections, and are distinct from resistant mutants because they are genetically identical to bacteria that die from treatment. Persisters to fluoroquinolones (FQs) experience DNA damage from treatment in stationary-phase culture, which suggests that FQs can corrupt their primary target, DNA gyrase, even in these super-tolerant cells. Since DNA damage from FQs originates from its stabilization of DNA gyrase in complexes with cleaved DNA, we hypothesized that the characteristics of FQ-stabilized DNA gyrase cleavage sites (GCS), such as the abundance, and/or location, might be influential to persistence. To test this hypothesis, we measured genome-wide distributions of GCS after treatment with a panel of FQs.We found drug-specific effects on the location and abundances of GCSs and discovered a negative correlation between the number of GCSs and FQ persister levels. Further, additional experiments and analyses suggested that persister levels are not governed by cleavage to a single specific site, but rather survival is a more complex function with respect to GCSs. Together, these findings demonstrate that there are drug specific differences in GCSs that correlate with persister levels, and suggest that the ability of an FQ to stabilize DNA-gyrase complexes at more sites will improve its bactericidal ability.

2022-12-05 | GSE206608 | GEO

Effect of fluoroquinolone-induced gyrase cleavage sites on gene expression during drug treatment period and recovery period on E. coli

2022-12-05 | GSE206609 | GEO

Genome-wide mapping of fluoroquinolone-induced gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence

Project description:Genome-wide mapping of fluoroquinolone-induced gyrase cleavage sites displays drug specific effects that correlate with bacterial persistence

| PRJNA851453 | ENA

Fluoroquinolone-induced gyrase cleavage sites

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-12-05 | GSE206610 | GEO

Effect of fluoroquinolone-induced gyrase cleavage sites on gene expression during drug treatment period and recovery period on E. coli

Project description:Effect of fluoroquinolone-induced gyrase cleavage sites on gene expression during drug treatment period and recovery period on E. coli

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Highly sensitive mapping of type II topoisomerase DNA cleavage sites with SHAN-seq

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.

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Defining Giardia lamblia cleavage sites

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Targeting bacterial gyrase with cystobactamid, fluoroquinolone and aminocoumarin antibiotics induces distinct molecular signatures in Pseudomonas aeruginosa

Project description:The design of novel antibiotics that break antimicrobial resistance relies on a profound understanding of their mechanism of action. While it has been shown that the cellular effects of antibiotics cluster according to their molecular targets, we investigated whether compounds binding to different sites of the same target can be differentiated by their transcriptome or metabolome signatures. The effects of three fluoroquinolones, two aminocoumarins and two cystobactamids, all inhibiting bacterial gyrase, on Pseudomonas aeruginosa at sub-inhibitory concentrations were captured by RNA sequencing.

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Genome-wide strand-specific mapping of cleavage sites induced by topoisomerase I in E. coli

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Topo-Seq application for topoisomerases binding sites identification with a single-nucleotide resolution

Project description:Topo-Seq is a ChIP-Seq-based methodology that allows high-throughput identification of topoisomerases binding (cleavage) sites with a single-base precision. On a first stage of the project DNA-gyrase binding sites on a Escherichia coli DY330 genome are investigated.

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