Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome

Sutormin, Dmitry; Rubanova, Natalia; Logacheva, Maria D.; Ghilarov, Dmitry; Severinov, Konstantin

doi:10.1093/nar/gky1312

Cited by 36 publications

(93 citation statements)

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“…Two enzymatic solutions have been used to remove the adduct, namely CIP and TDP2, the first of which is very inefficient and the second far less commercially accessible. Using a single-strand DNA library preparation kit, as Sutormin and colleagues did when exploring DNA gyrase activity [18], offers another elegant solution by only sequencing the free 3 DNA strand.…”

Section: Discussionmentioning

confidence: 99%

“…This raises questions as to the determinants of topo binding and cleavage sites; how do the factors known to influence binding and activity including DNA topology and sequence play off against protein-mediated recruitment or inhibition in trans, and what other factors may influence topo binding and cleavage in vivo. It is clear the answer is not straightforward, with topo IB being directly recruited as part of the transcriptional machinery [19] and mycobacterial topo IA [48] and prokaryotic DNA gyrase [18] exhibiting more substantial DNA sequence preferences. As with all cellular processes, the mechanisms governing DNA topology maintenance are often not only protein specific but also species specific.…”

Section: Discussionmentioning

confidence: 99%

“…(C) Topo-seq, used to map gyrase cleavage, began with DNA extraction from E. coli cells treated with ciprofloxacin (cfx), oxolinic acid (oxo) or microcin B-17 (MccB17), followed by sonication. Gyrase cleavage complexes were then enriched using the SPA-antibody before proteinase K treatment and use in the Accel NGS 1S kit to generate fragments that can be sequenced using the Illumina Nextseq platform [18]. with the HA-antibody, before the protein is removed using proteinase K. The 3 end is extended using TdT and an adapter is ligated that contains an inverted dT residue.…”

Section: Spo11 Dsb Mappingmentioning

confidence: 99%

“…In 2018, an NGS approach was developed that allowed the precise identification of gyrase cleavage sites genome-wide in E. coli, facilitating in depth analysis of drug driven cleavage in vivo [18]. The method, named Topo-seq ( Figure 2C), involved trapping gyrase cleavage complexes using either oxolinic acid (oxo), ciprofloxacin (cfx), or microcin B-17 (MccB17) and immunoprecipitating the resulting fragments.…”

Section: Dna Gyrasementioning

confidence: 99%

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Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques

McKie

Maxwell

Neuman³

2020

Genes

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Next-generation sequencing (NGS) platforms have been adapted to generate genome-wide maps and sequence context of binding and cleavage of DNA topoisomerases (topos). Continuous refinements of these techniques have resulted in the acquisition of data with unprecedented depth and resolution, which has shed new light on in vivo topo behavior. Topos regulate DNA topology through the formation of reversible single- or double-stranded DNA breaks. Topo activity is critical for DNA metabolism in general, and in particular to support transcription and replication. However, the binding and activity of topos over the genome in vivo was difficult to study until the advent of NGS. Over and above traditional chromatin immunoprecipitation (ChIP)-seq approaches that probe protein binding, the unique formation of covalent protein–DNA linkages associated with DNA cleavage by topos affords the ability to probe cleavage and, by extension, activity over the genome. NGS platforms have facilitated genome-wide studies mapping the behavior of topos in vivo, how the behavior varies among species and how inhibitors affect cleavage. Many NGS approaches achieve nucleotide resolution of topo binding and cleavage sites, imparting an extent of information not previously attainable. We review the development of NGS approaches to probe topo interactions over the genome in vivo and highlight general conclusions and quandaries that have arisen from this rapidly advancing field of topoisomerase research.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Spo11 Dsb Mappingmentioning

confidence: 99%

Section: Dna Gyrasementioning

confidence: 99%

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Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques

McKie

Maxwell

Neuman³

2020

Genes

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“…[ 16 ] Another NGS‐based study on E. coli gyrase also found increased activity downstream of highly transcribed operons. [ 124 ] Recent in vivo single‐molecule imaging data suggest multiple gyrases (∼12) cluster ahead of the DNA replication fork. [ 125 ] This is supported by magnetic tweezers data demonstrating that multiple gyrases were recruited to highly overwound DNA.…”

Section: Type Iia Dna Topoisomerasesmentioning

confidence: 99%

DNA topoisomerases: Advances in understanding of cellular roles and multi‐protein complexes via structure‐function analysis

McKie

Neuman²,

Maxwell

2021

BioEssays

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DNA topoisomerases, capable of manipulating DNA topology, are ubiquitous and indispensable for cellular survival due to the numerous roles they play during DNA metabolism. As we review here, current structural approaches have revealed unprecedented insights into the complex DNA‐topoisomerase interaction and strand passage mechanism, helping to advance our understanding of their activities in vivo. This has been complemented by single‐molecule techniques, which have facilitated the detailed dissection of the various topoisomerase reactions. Recent work has also revealed the importance of topoisomerase interactions with accessory proteins and other DNA‐associated proteins, supporting the idea that they often function as part of multi‐enzyme assemblies in vivo. In addition, novel topoisomerases have been identified and explored, such as topo VIII and Mini‐A. These new findings are advancing our understanding of DNA‐related processes and the vital functions topos fulfil, demonstrating their indispensability in virtually every aspect of DNA metabolism.

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How Structure–Function Relationships of 1,4‐Naphthoquinones Combat Antimicrobial Resistance in Multidrug‐Resistant (MDR) Pathogens

et al. 2022

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Antimicrobial resistance (AMR) is one of the top ten health‐related threats worldwide. Among several antimicrobial agents, naphthoquinones (NQs) of plant/chemical origin possess enormous structural and functional diversity and are effective against multidrug‐resistant (MDR) pathogens. 1,4‐NQs possess alkyl, hydroxyl, halide, and metal groups as side chains on their double‐ring structure, predominantly at the C‐2, C‐3, C‐5, and C‐8 positions. Among 1,4‐NQs, hydroxyl groups at either C‐2 or C‐5 exhibit significant antibacterial activity against Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. (ESKAPE) and MDR categories. 1,4‐NQs exhibit antibacterial activities like plasmids curing, reactive oxygen species generation, efflux pumps inhibition, anti‐DNA gyrase activity, membrane permeabilization, and biofilm inhibition. This review emphasizes the structure‐function relationships of 1,4‐NQs against ESKAPE and MDR pathogens based on a literature review of studies published in the last 15 years. Overall, 1,4‐NQs have great potential for counteracting the antimicrobial resistance of MDR pathogens.

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Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the Escherichia coli genome

Cited by 36 publications

References 1 publication

Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques

Mapping DNA Topoisomerase Binding and Cleavage Genome Wide Using Next-Generation Sequencing Techniques

DNA topoisomerases: Advances in understanding of cellular roles and multi‐protein complexes via structure‐function analysis

How Structure–Function Relationships of 1,4‐Naphthoquinones Combat Antimicrobial Resistance in Multidrug‐Resistant (MDR) Pathogens

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