DNA supercoiling and transcription in bacteria: a two-way street (Q91996441)

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26 April 2020

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29 May 2020

19 January 2021

DNA supercoiling and transcription in bacteria: a two-way street (English)

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publication date

18 July 2019

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BMC molecular and cell biology

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20

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Creative Commons Attribution 4.0 International

26 April 2020

copyright license

2 references

29 May 2020

Transcriptional Bursts in a Nonequilibrium Model for Gene Regulation by Supercoiling

19 January 2021

cites work

1 reference

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Genome-wide mapping of Topoisomerase I activity sites reveal its role in chromosome segregation

23 February 2021

1 reference

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DNA sequence encodes the position of DNA supercoils.

23 February 2021

1 reference

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

23 February 2021

1 reference

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Single-molecule imaging of DNA gyrase activity in living Escherichia coli

23 February 2021

1 reference

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Inhibition of the gyrA promoter by transcription-coupled DNA supercoiling in Escherichia coli

23 February 2021

1 reference

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The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria

23 February 2021

1 reference

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Protein-mediated loops in supercoiled DNA create large topological domains.

23 February 2021

1 reference

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Negative supercoiling of DNA by gyrase is inhibited in Salmonella enterica serovar Typhimurium during adaptation to acid stress.

23 February 2021

1 reference

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When DNA Topology Turns Deadly - RNA Polymerases Dig in Their R-Loops to Stand Their Ground: New Positive and Negative (Super)Twists in the Replication-Transcription Conflict.

23 February 2021

1 reference

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Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis

23 February 2021

1 reference

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Structures of the CRISPR genome integration complex

23 February 2021

1 reference

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Control of virulence gene transcription by indirect readout in Vibrio cholerae and Salmonella enterica serovar Typhimurium.

23 February 2021

1 reference

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DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression

23 February 2021

1 reference

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Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase

23 February 2021

1 reference

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23 February 2021

Transcription elongation

1 reference

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Maintenance of Transcription-Translation Coupling by Elongation Factor P.

23 February 2021

1 reference

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An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene.

23 February 2021

1 reference

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Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries.

23 February 2021

1 reference

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CRISPR Immunological Memory Requires a Host Factor for Specificity

23 February 2021

1 reference

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Transcription is regulated by NusA:NusG interaction.

23 February 2021

1 reference

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Autoregulation of topoisomerase I expression by supercoiling sensitive transcription

23 February 2021

1 reference

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Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid

23 February 2021

1 reference

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Regulation of transcription elongation and termination

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Interplay between DNA supercoiling and transcription elongation

23 February 2021

1 reference

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Diversity in (p)ppGpp metabolism and effectors

23 February 2021

1 reference

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Mechanism of transcriptional bursting in bacteria

23 February 2021

1 reference

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Bacterial regulon evolution: distinct responses and roles for the identical OmpR proteins of Salmonella Typhimurium and Escherichia coli in the acid stress response

23 February 2021

1 reference

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UvrD facilitates DNA repair by pulling RNA polymerase backwards

23 February 2021

1 reference

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Transmission of an oxygen availability signal at the Salmonella enterica serovar Typhimurium fis promoter

23 February 2021

1 reference

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RNA polymerase is a powerful torsional motor

23 February 2021

1 reference

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Divergent RNA transcription: a role in promoter unwinding?

23 February 2021

1 reference

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Transcription under torsion

23 February 2021

1 reference

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A proximal promoter element required for positive transcriptional control by guanosine tetraphosphate and DksA protein during the stringent response.

23 February 2021

1 reference

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Dependence of transcription-coupled DNA supercoiling on promoter strength in Escherichia coli topoisomerase I deficient strains

23 February 2021

1 reference

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Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome

23 February 2021

1 reference

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RNA polymerase backtracking in gene regulation and genome instability

23 February 2021

1 reference

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A fundamental regulatory mechanism operating through OmpR and DNA topology controls expression of Salmonella pathogenicity islands SPI-1 and SPI-2

23 February 2021

1 reference

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Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Linking RNA polymerase backtracking to genome instability in E. coli

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

23 February 2021

1 reference

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DNA relaxation-dependent phase biasing of the fim genetic switch in Escherichia coli depends on the interplay of H-NS, IHF and LRP.

23 February 2021

1 reference

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The role of DNA shape in protein-DNA recognition

23 February 2021

1 reference

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Proteolysis of sigmaS (RpoS) and the general stress response in Escherichia coli

23 February 2021

1 reference

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Bacterial DNA topology and infectious disease.

23 February 2021

1 reference

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Nature, nurture, or chance: stochastic gene expression and its consequences

23 February 2021

1 reference

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Depletion of RNase HI activity in Escherichia coli lacking DNA topoisomerase I leads to defects in DNA supercoiling and segregation.

23 February 2021

1 reference

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23 February 2021

(p)ppGpp: still magical?

1 reference

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ppGpp regulation of RpoS degradation via anti-adaptor protein IraP.

23 February 2021

1 reference

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Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque

23 February 2021

1 reference

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Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism

23 February 2021

1 reference

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Roles for DNA supercoiling and the Fis protein in modulating expression of virulence genes during intracellular growth of Salmonella enterica serovar Typhimurium.

23 February 2021

1 reference

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DNA supercoiling and the Lrp protein determine the directionality of fim switch DNA inversion in Escherichia coli K-12.

23 February 2021

1 reference

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Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

23 February 2021

1 reference

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rRNA promoter regulation by nonoptimal binding of sigma region 1.2: an additional recognition element for RNA polymerase.

23 February 2021

1 reference

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Real-time kinetics of gene activity in individual bacteria

23 February 2021

1 reference

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Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli

23 February 2021

1 reference

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Bacterial transcription elongation factors: new insights into molecular mechanism of action

23 February 2021

1 reference

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DNA supercoiling - a global transcriptional regulator for enterobacterial growth?

23 February 2021

1 reference

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Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

23 February 2021

1 reference

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Spatial patterns of transcriptional activity in the chromosome of Escherichia coli

23 February 2021

1 reference

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Coupling DNA supercoiling to transcription in defined protein systems.

23 February 2021

1 reference

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Effect of varying the supercoiling of DNA on transcription and its regulation.

23 February 2021

1 reference

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DNA supercoiling contributes to disconnect sigmaS accumulation from sigmaS-dependent transcription in Escherichia coli

23 February 2021

1 reference

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A microarray-based antibiotic screen identifies a regulatory role for supercoiling in the osmotic stress response of Escherichia coli

23 February 2021

1 reference

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DNA topology-mediated control of global gene expression in Escherichia coli

23 February 2021

1 reference

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Autoinduction of the ompR response regulator by acid shock and control of the Salmonella enterica acid tolerance response

23 February 2021

1 reference

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DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase.

23 February 2021

1 reference

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A role for DNA supercoiling in the regulation of the cytochrome bd oxidase of Escherichia coli.

23 February 2021

1 reference

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The expression of the Escherichia coli fis gene is strongly dependent on the superhelical density of DNA

23 February 2021

1 reference

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Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome

23 February 2021

1 reference

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The G+C-rich discriminator region of the tyrT promoter antagonises the formation of stable preinitiation complexes

23 February 2021

1 reference

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Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, topoisomerase I and Fis

23 February 2021

1 reference

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Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli

23 February 2021

1 reference

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Regulation of DNA gyrase operon in Mycobacterium smegmatis: a distinct mechanism of relaxation stimulated transcription

23 February 2021

1 reference

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Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking.

23 February 2021

1 reference

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Mechanistic model of the elongation complex of Escherichia coli RNA polymerase

23 February 2021

1 reference

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DNA Supercoiling and Osmoresistance in Bacillus subtilis 168

23 February 2021

1 reference

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Role of DNA supercoiling and RpoS sigma factor in the osmotic and growth phase-dependent induction of the Gene osmE of Escherichia coli K12

23 February 2021

1 reference

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The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase.

23 February 2021

1 reference

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Transcript cleavage factors from E. coli.

23 February 2021

1 reference

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Altered topoisomerase activities may be involved in the regulation of DNA supercoiling in aerobic-anaerobic transitions in Escherichia coli.

23 February 2021

1 reference

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Hypernegative supercoiling of the DNA template during transcription elongation in vitro.

23 February 2021

1 reference

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Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3' end of transcription units

23 February 2021

1 reference

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The influence of DNA topology on the environmental regulation of a pH-regulated locus in Salmonella typhimurium

23 February 2021

1 reference

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Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in Escherichia coli

23 February 2021

1 reference

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Isolation and characterization of adenylate kinase (adk) mutations in Salmonella typhimurium which block the ability of glycine betaine to function as an osmoprotectant

23 February 2021

1 reference

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Energy buffering of DNA structure fails when Escherichia coli runs out of substrate

23 February 2021

1 reference

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Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli

23 February 2021

1 reference

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Mutations in the -10 TATAAT sequence of the gyrA promoter affect both promoter strength and sensitivity to DNA supercoiling

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

spoT-dependent accumulation of guanosine tetraphosphate in response to fatty acid starvation in Escherichia coli

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Regulation of bacterial DNA supercoiling: plasmid linking numbers vary with growth temperature

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Regulation of the genes for E. coli DNA gyrase: Homeostatic control of DNA supercoiling

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Escherichia coli DNA topoisomerase I mutants: Increased supercoiling is corrected by mutations near gyrase genes

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Promoter sequence for stringent control of bacterial ribonucleic acid synthesis.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

The twisted circular form of polyoma viral DNA

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Genetically separable functional elements mediate the optimal expression and stringent regulation of a bacterial tRNA gene

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Alteration of the growth-rate-dependent regulation of Escherichia coli tyrT expression by promoter mutations.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

DNA supercoiling and aerobic regulation of transcription from the Klebsiella pneumoniae nifLA promoter

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Use of site-specific recombination as a probe of DNA structure and metabolism in vivo

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent control

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Mechanisms determining aerobic or anaerobic growth in the facultative anaerobe Salmonella typhimurium

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Multiple promoters for transcription of the Escherichia coli DNA topoisomerase I gene and their regulation by DNA supercoiling

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Rifampin and rpoB mutations can alter DNA supercoiling in Escherichia coli

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Transcription generates positively and negatively supercoiled domains in the template.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Supercoiling of the DNA template during transcription

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Gyrase inhibitors can increase gyrA expression and DNA supercoiling

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth-rate control and stringent sensitivity

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

DNA supercoiling by DNA gyrase. A static head analysis

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Structure of plectonemically supercoiled DNA.

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

A physiological role for DNA supercoiling in the anaerobic regulation of colicin gene expression

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Direct evidence for the effect of transcription on local DNA supercoiling in vivo

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Bacterial DNA supercoiling and [ATP]/[ADP]. Changes associated with a transition to anaerobic growth

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Osmotic and growth-phase dependent regulation of the eta gene of Staphylococcus aureus: a role for DNA supercoiling

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Potassium ions and changes in bacterial DNA supercoiling under osmotic stress

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

The DNA supercoiling-sensitive expression of the Salmonella typhimurium his operon requires the his attenuator and is modulated by anaerobiosis and by osmolarity

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Control of bacterial DNA supercoiling

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

Nalidixic acid resistance: A second genetic character involved in DNA gyrase activity

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

A Sign Inversion Mechanism for Enzymatic Supercoiling of DNA

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

DNA gyrase: an enzyme that introduces superhelical turns into DNA

23 February 2021

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6639932

10.1186/S12860-019-0211-6

23 February 2021

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31319794%20AND%20SRC:MED&resulttype=core&format=json

26 April 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:31319794%20AND%20SRC:MED&resulttype=core&format=json

26 April 2020

PubMed publication ID

31319794

1 reference