Biochemical and biophysical properties of positively supercoiled DNA

Liu, Yingting; Berrido, Andrea M; Zhang, Hua; Tse‐Dinh, Yuk‐Ching; Leng, Fenfei

doi:10.1016/j.bpc.2017.08.008

Cited by 8 publications

(7 citation statements)

References 16 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It envisions that transcribing RNA polymerase (RNAP) generates downstream positive supercoils, while the same number of negative supercoils is formed upstream. DNA gyrase has an increased affinity for positively supercoiled regions (20) and, according to the model, relaxes DNA downstream of the transcription elongation complex, while Topo I, which prefers negatively supercoiled DNA (21,22), acts upstream. Recent genome-wide studies using ChIP-Seq in Mycobacterium tuberculosis (23) and ChIP-chip in E. coli (24) reveal that global distribution of gyrase and Topo I is generally consistent with the ‘twin supercoiled-domain model’ expectations.…”

Section: Introductionmentioning

confidence: 99%

Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across theEscherichia coligenome

Sutormin

Rubanova

Logacheva

et al. 2018

Nucleic Acids Research

View full text Add to dashboard Cite

An important antibiotic target, DNA gyrase is an essential bacterial enzyme that introduces negative supercoils into DNA and relaxes positive supercoils accumulating in front of moving DNA and RNA polymerases. By altering the superhelical density, gyrase may regulate expression of bacterial genes. The information about how gyrase is distributed along genomic DNA and whether its distribution is affected by drugs is scarce. During catalysis, gyrase cleaves both DNA strands forming a covalently bound intermediate. By exploiting the ability of several topoisomerase poisons to stabilize this intermediate we developed a ChIP-Seq-based approach to locate, with single nucleotide resolution, DNA gyrase cleavage sites (GCSs) throughout the Escherichia coli genome. We identified an extended gyrase binding motif with phased 10-bp G/C content variation, indicating that bending ability of DNA contributes to gyrase binding. We also found that GCSs are enriched in extended regions located downstream of highly transcribed operons. Transcription inhibition leads to redistribution of gyrase suggesting that the enrichment is functionally significant. Our method can be applied for precise mapping of prokaryotic and eukaryotic type II topoisomerases cleavage sites in a variety of organisms and paves the way for future studies of various topoisomerase inhibitors.

show abstract

Section: Introductionmentioning

confidence: 99%

Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across theEscherichia coligenome

Sutormin

Rubanova

Logacheva

et al. 2018

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…8b ). Our results might also be useful to explore DNA dynamics and its interactions in confined space 47 – 49 with other charged molecules, such as chemotherapeutic compounds, intercalating agents, and proteins involved in DNA metabolism.…”

Section: Discussionmentioning

confidence: 91%

Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Bettotti¹,

Visone²,

Lunelli³

et al. 2018

Sci Rep

View full text Add to dashboard Cite

Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated and the supercoiling degree of defined genome regions may change according to physiological and environmental conditions. Elucidation of structural properties of DNA molecules with different topology may thus help to better understand genome functions. Whereas a number of structural studies have been published on highly negatively supercoiled DNA molecules, only preliminary observations of highly positively supercoiled are available, and a description of DNA structural properties over the full range of supercoiling degree is lacking. Atomic Force Microscopy (AFM) is a powerful tool to study DNA structure at single molecule level. We here report a comprehensive analysis by AFM of DNA plasmid molecules with defined supercoiling degree, covering the full spectrum of biologically relevant topologies, under different observation conditions. Our data, supported by statistical and biochemical analyses, revealed striking differences in the behavior of positive and negative plasmid molecules.

show abstract

“…EcTopoI and DNA gyrase have opposite binding preferences and activities: while EcTopoI is attracted to and relaxes negative supercoils, DNA gyrase is attracted to and removes positive supercoils (Terekhova et al, 2012;Ashley et al, 2017;Liu et al, 2017;Sutormin et al, 2019).…”

Section: Ectopoi and Dna Gyrase Have Mutually Exclusive Localization On The E Coli Chromosomementioning

confidence: 99%

“…Topoisomerase I of Escherichia coli (EcTopoI, encoded by the topA gene) belongs to the A class of type I topoisomerases (Maxwell, Bush and Evans-Roberts, 2015). EcTopoI relaxes only negatively supercoiled DNA and is thought to maintain the steady-state level of supercoiling by compensating the activity of another topoisomerase -the DNA gyrase, a IIA type enzyme, which introduces negative supercoiling utilizing the energy of ATP hydrolysis (Menzel and Gellert, 1978;Tse-Dinha, 1985;Liu et al, 2017). Deletion of topA leads to rapid accumulation of suppressor mutations, mostly in genes encoding the DNA gyrase subunits.…”

Section: Introductionmentioning

confidence: 99%

Interaction Between Transcribing RNA Polymerase and Topoisomerase I Prevents R-loop Formation in E. coli

Sutormin

Galivondzhyan

Musharova

et al. 2021

Preprint

View full text Add to dashboard Cite

Bacterial topoisomerase I (TopoI) removes excessive negative supercoiling and is thought to relax DNA molecules during transcription, replication and other processes. Using ChIP-Seq, we show that TopoI of Escherichia coli (EcTopoI) is co-localized, genome-wide, with RNA polymerase (RNAP) in transcription units. Treatment with transcription elongation inhibitor rifampicin leads to EcTopoI relocation to promoter regions, where RNAP also accumulates. When a 14 kDa RNAP-binding EcTopoI C-terminal domain (CTD) is overexpressed, co-localization of EcTopoI and RNAP along the transcription units is reduced. Pull-down experiments directly show that the two enzymes interact in vivo. Using ChIP-Seq and Topo-Seq, we demonstrate that EcTopoI is enriched and in and upstream (within up to 12-15 Kbs) of highly-active transcription units, indicating that EcTopoI relaxes negative supercoiling generated by transcription. Uncoupling of the RNAP-EcTopoI interaction by either overexpression of EcTopoI CTD or deletion of EcTopoI domains involved in the interaction is toxic for cells and leads to excessive negative plasmid supercoiling. Moreover, the CTD overexpression leads to R-loops accumulation genome-wide, indicating that the RNAP-EcTopoI interaction is required for prevention of R-loops formation.Article HighlightsTopoI colocalizes genome-wide and interacts with RNAP in E. coliDisruption of the interaction between TopoI and RNAP decreases cells viability, leads to hypernegative DNA supercoiling, and R-loops accumulationTopoI and DNA gyrase are enriched, respectively, upstream and downstream of transcription units in accordance with twin-domain model of Liu and WangTopoI recognizes its cleavage sites through a specific motif and by sensing negative supercoiling

show abstract

Biochemical and biophysical properties of positively supercoiled DNA

Cited by 8 publications

References 16 publications

Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across theEscherichia coligenome

Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across theEscherichia coligenome

Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Interaction Between Transcribing RNA Polymerase and Topoisomerase I Prevents R-loop Formation in E. coli

Contact Info

Product

Resources

About