Reference health
DNA supercoiling and transcription in bacteria: a two-way street
130/130 checkable references clean · checked 2026-07-22
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.
4 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 130 checked references that resolve
resolves10.1007/s12551-016-0205-y
DNA supercoiling is a fundamental regulatory principle in the control of bacterial gene expression
resolves10.1146/annurev.genet.36.032902.111815
DNA Topology-Mediated Control of Global Gene Expression in <i>Escherichia coli</i>
resolves10.1038/nrmicro1088
DNA supercoiling — a global transcriptional regulator for enterobacterial growth?
resolves10.1038/nrmicro2261
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
resolves10.1016/0022-2836(87)90369-X
Use of site-specific recombination as a probe of DNA structure and metabolism in vivo
resolves10.1093/nar/gky153
Protein-mediated loops in supercoiled DNA create large topological domains
resolves10.1128/jb.170.10.4983-4985.1988
Rifampin and rpoB mutations can alter DNA supercoiling in Escherichia coli
resolves10.1016/j.cell.2012.06.003
RNA Polymerase Backtracking in Gene Regulation and Genome Instability
resolves10.15252/embj.201593561
Transcription rate and transcript length drive formation of chromosomal interaction domain boundaries
resolves10.1046/j.1365-2958.2000.02015.x
Activation and silencing of <i>leu‐500</i> promoter by transcription‐induced DNA supercoiling in the <i>Salmonella</i> chromosome
resolves10.1016/0022-2836(92)90721-U
Direct evidence for the effect of transcription on local DNA supercoiling in vivo
resolves10.1016/0092-8674(89)90989-6
Transcription-driven supercoiling of DNA: Direct biochemical evidence from in vitro studies
resolves10.1016/0092-8674(88)90163-8
Transcription generates positively and negatively supercoiled domains in the template
resolves10.1016/j.gene.2012.11.011
Dependence of transcription-coupled DNA supercoiling on promoter strength in Escherichia coli topoisomerase I deficient strains
resolves10.1073/pnas.75.4.1773
Purification of subunits of
<i>Escherichia coli</i>
DNA gyrase and reconstitution of enzymatic activity
resolves10.1038/nsmb1213
Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque
resolves10.1073/pnas.74.11.4772
Nalidixic acid resistance: A second genetic character involved in DNA gyrase activity
resolves10.1074/jbc.275.11.8103
Roles of Topoisomerases in Maintaining Steady-state DNA Supercoiling in Escherichia coli
resolves10.1073/pnas.1507592112
Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid
resolves10.1371/journal.pgen.1002845
Rates of Gyrase Supercoiling and Transcription Elongation Control Supercoil Density in a Bacterial Chromosome
resolves10.1093/nar/gky1143
Single-molecule imaging of DNA gyrase activity in living
<i>Escherichia coli</i>
resolves10.1093/nar/gkr1237
Topo IV is the topoisomerase that knots and unknots sister duplexes during DNA replication
resolves10.1101/gad.9.22.2859
Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli.
resolves10.1016/j.cell.2017.07.044
Replication-Transcription Conflicts Generate R-Loops that Orchestrate Bacterial Stress Survival and Pathogenesis
resolves10.1016/j.tig.2017.10.007
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
resolves10.1016/j.cell.2011.07.034
Linking RNA Polymerase Backtracking to Genome Instability in E. coli
resolves10.1146/annurev-micro-090817-062514
The Clash of Macromolecular Titans: Replication-Transcription Conflicts in Bacteria
resolves10.1016/S0021-9258(17)42136-3
Hypernegative supercoiling of the DNA template during transcription elongation in vitro.
resolves10.1111/j.1365-2958.2008.06334.x
Depletion of RNase HI activity in <i>Escherichia coli</i> lacking DNA topoisomerase I leads to defects in DNA supercoiling and segregation
resolves10.1101/gr.401003
A Microarray-Based Antibiotic Screen Identifies a Regulatory Role for Supercoiling in the Osmotic Stress Response of
<i>Escherichia coli</i>
resolves10.1186/gb-2004-5-11-r87
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
resolves10.1021/bi030110t
Effect of Varying the Supercoiling of DNA on Transcription and Its Regulation
resolves10.1111/1462-2920.13838
Control of virulence gene transcription by indirect readout in
<i>Vibrio cholerae</i>
and
<i>Salmonella enterica</i>
serovar Typhimurium
resolves10.1371/journal.pgen.1002615
A Fundamental Regulatory Mechanism Operating through OmpR and DNA Topology Controls Expression of Salmonella Pathogenicity Islands SPI-1 and SPI-2
resolves10.1101/sqb.1998.63.337
Mechanistic Model of the Elongation Complex of Escherichia coli RNA Polymerase
resolves10.1016/S0092-8674(00)80180-4
The RNA–DNA Hybrid Maintains the Register of Transcription by Preventing Backtracking of RNA Polymerase
resolves10.1111/j.1365-2958.2004.04481.x
Bacterial transcription elongation factors: new insights into molecular mechanism of action
resolves10.1128/mBio.01373-16
Maintenance of Transcription-Translation Coupling by Elongation Factor P
resolves10.1038/s41598-018-33089-4
Inhibition of the gyrA promoter by transcription-coupled DNA supercoiling in Escherichia coli
resolves10.1016/0092-8674(83)90140-X
Regulation of the genes for E. coli DNA gyrase: Homeostatic control of DNA supercoiling
resolves10.1073/pnas.84.12.4185
Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters.
resolves10.1128/jb.176.19.5999-6006.1994
Mutations in the -10 TATAAT sequence of the gyrA promoter affect both promoter strength and sensitivity to DNA supercoiling
resolves10.1046/j.1365-2443.1999.00296.x
Regulation of DNA gyrase operon in <i>Mycobacterium smegmatis</i>: a distinct mechanism of relaxation stimulated transcription
resolves10.1046/j.1365-2958.2000.02129.x
The expression of the <i>Escherichia coli fis</i> gene is strongly dependent on the superhelical density of DNA
resolves10.1093/nar/gkv1088
Autoregulation of topoisomerase I expression by supercoiling sensitive transcription
resolves10.1016/0022-2836(88)90554-2
Multiple promoters for transcription of the Escherichia coli DNA topoisomerase I gene and their regulation by DNA supercoiling
resolves10.1038/sj.embor.7400729
Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome
resolves10.1016/0092-8674(82)90403-2
Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes
resolves10.1128/jb.171.12.6573-6579.1989
Gyrase inhibitors can increase gyrA expression and DNA supercoiling
resolves10.1016/0092-8674(82)90402-0
Escherichia coli DNA topoisomerase I mutants: Increased supercoiling is corrected by mutations near gyrase genes
resolves10.1046/j.1432-1327.2002.02803.x
DNA supercoiling in <i>Escherichia coli</i> is under tight and subtle homeostatic control, involving gene‐expression and metabolic regulation of both topoisomerase I and DNA gyrase
resolves10.1093/nar/gky1271
Genome-wide mapping of Topoisomerase I activity sites reveal its role in chromosome segregation
resolves10.1006/jmbi.1997.1308
Role of DNA supercoiling and RpoS sigma factor in the osmotic and growth phase-dependent induction of the Gene osmE of Escherichia coli K12
resolves10.1093/nar/4.5.1183
The problems of eukaryotic and prokaryotic DNA packaging and in vivo conformation posed by superhelix density heterogeneity
resolves10.1016/j.resmic.2009.08.014
Proteolysis of σS (RpoS) and the general stress response in Escherichia coli
resolves10.1046/j.1365-2958.2003.03461.x
DNA supercoiling contributes to disconnect σ<sup>S</sup> accumulation from σ<sup>S</sup>‐dependent transcription in <i>Escherichia coli</i>
resolves10.1111/j.1365-2958.2006.05442.x
Acyl carrier protein/SpoT interaction, the switch linking SpoT‐dependent stress response to fatty acid metabolism
resolves10.1073/pnas.90.23.11004
spoT-dependent accumulation of guanosine tetraphosphate in response to fatty acid starvation in Escherichia coli.
resolves10.1111/j.1365-2958.2005.04601.x
Iron limitation induces SpoT‐dependent accumulation of ppGpp in
<i>Escherichia coli</i>
resolves10.1016/0092-8674(85)90146-1
Genetically separable functional elements mediate the optimal expression and stringent regulation of a bacterial tRNA gene
resolves10.1002/j.1460-2075.1985.tb03738.x
Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent control.
resolves10.1128/JB.141.2.973-976.1980
Promoter Sequence for Stringent Control of Bacterial Ribonucleic Acid Synthesis
resolves10.1016/0022-2836(86)90397-9
Alteration of the growth-rate-dependent regulation of Escherichia coli tyrT expression by promoter mutations
resolves10.1002/j.1460-2075.1989.tb08498.x
Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2‐ and tac promoter on growth‐rate control and stringent sensitivity.
resolves10.1016/j.cell.2006.04.034
rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase
resolves10.1006/jmbi.2000.3780
The G+C-rich discriminator region of the tyr T promoter antagonises the formation of stable preinitiation complexes 1 1Edited by M. Yaniv
resolves10.1074/jbc.M113.479998
A Proximal Promoter Element Required for Positive Transcriptional Control by Guanosine Tetraphosphate and DksA Protein during the Stringent Response
resolves10.1128/jb.169.10.4499-4506.1987
Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli
resolves10.1128/jb.173.12.3914-3917.1991
Bacterial DNA supercoiling and [ATP]/[ADP] ratio: changes associated with salt shock
resolves10.1128/jb.177.12.3420-3426.1995
Energy buffering of DNA structure fails when Escherichia coli runs out of substrate
resolves10.1128/jb.177.2.390-400.1995
Isolation and characterization of adenylate kinase (adk) mutations in Salmonella typhimurium which block the ability of glycine betaine to function as an osmoprotectant
resolves10.1016/0092-8674(88)90470-9
A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli
resolves10.1046/j.1365-2958.2002.02937.x
Autoinduction of the <i>ompR</i> response regulator by acid shock and control of the <i>Salmonella enterica</i> acid tolerance response
resolves10.1111/mmi.13911
Negative supercoiling of DNA by gyrase is inhibited in <i>Salmonella enterica</i> serovar Typhimurium during adaptation to acid stress
resolves10.1111/j.1365-2958.1993.tb00905.x
The influence of DNA topology on the environmental regulation of a pH‐regulated locus in <i>Salmonella typhimurium</i>
resolves10.1371/journal.pgen.1004215
Bacterial Regulon Evolution: Distinct Responses and Roles for the Identical OmpR Proteins of Salmonella Typhimurium and Escherichia coli in the Acid Stress Response
resolves10.1111/j.1365-2958.2006.05416.x
Roles for DNA supercoiling and the Fis protein in modulating expression of virulence genes during intracellular growth of <i>Salmonella enterica</i> serovar Typhimurium
resolves10.1111/j.1574-6968.1992.tb05559.x
Potassium ions and changes in bacterial DNA supercoiling under osmotic stress
resolves10.1111/j.1365-2958.1992.tb01423.x
The DNA supercoiling‐sensitive expression of the <i>Salmonella typhimurium his</i> operon requires the <i>his</i> attenuator and is modulated by anaerobiosis and by osmolarity
resolves10.1007/BF00299136
Osmotic and growth-phase dependent regulation of the eta gene of Staphylococcus aureus: a role for DNA supercoiling
resolves10.1046/j.1365-2958.2000.01805.x
<i>Escherichia coli</i> response to hydrogen peroxide: a role for DNA supercoiling, Topoisomerase I and Fis
resolves10.1099/00221287-147-3-591
A role for DNA supercoiling in the regulation of the cytochrome bd oxidase of Escherichia coli
resolves10.1371/journal.pone.0084382
Transmission of an Oxygen Availability Signal at the Salmonella enterica Serovar Typhimurium fis Promoter
resolves10.1007/BF00925689
Altered topoisomerase activities may be involved in the regulation of DNA supercoiling in aerobic-anaerobic transitions inEscherichia coli
resolves10.1093/nar/16.21.9933
DNA supercolling and aerobic regulation of transcription from the<i>Klebsiella pneumoniae nifLA</i>promoter
resolves10.1128/jb.170.6.2816-2826.1988
DNA supercoiling and the anaerobic and growth phase regulation of tonB gene expression
resolves10.1007/BF00269868
A physiological role for DNA supercoiling in the anaerobic regulation of colicin gene expression
resolves10.1073/pnas.82.7.2077
Mechanisms determining aerobic or anaerobic growth in the facultative anaerobe Salmonella typhimurium.
resolves10.1073/pnas.81.13.4046
Regulation of bacterial DNA supercoiling: plasmid linking numbers vary with growth temperature.
resolves10.1371/journal.pgen.1006754
Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase
resolves10.1186/gb-2004-5-11-r86
Spatial patterns of transcriptional activity in the chromosome of Escherichia coli
resolves10.1093/nar/gky1222
Single-nucleotide-resolution mapping of DNA gyrase cleavage sites across the
<i>Escherichia coli</i>
genome
resolves10.1101/559138
Growth Phase Dependent Chromosome Condensation and H-NS Protein Redistribution in
<i>E. coli</i>
Under Osmotic Stress
resolves10.1073/pnas.85.23.8850
DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences.
resolves10.1002/j.1460-2075.1993.tb06195.x
Specific interaction of IHF with RIBs, a class of bacterial repetitive DNA elements located at the 3′ end of transcription units.
resolves10.1111/j.1365-2958.1993.tb00908.x
Integration host factor binds to a unique class of complex repetitive extragenic DNA sequences in <i>Escherichia coli</i>
resolves10.1016/j.molcel.2016.04.027
CRISPR Immunological Memory Requires a Host Factor for Specificity
resolves10.1111/j.1365-2958.2009.06919.x
DNA relaxation‐dependent phase biasing of the <i>fim</i> genetic switch in <i>Escherichia coli</i> depends on the interplay of H‐NS, IHF and LRP
resolves10.1128/JB.00344-06
DNA Supercoiling and the Lrp Protein Determine the Directionality of
<i>fim</i>
Switch DNA Inversion in
<i>Escherichia coli</i>
K-12
resolves10.1016/j.cell.2008.09.050
Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences
The 4 references without a DOI — listed, not checked
no DOI — not checkedBauer WR, Crick FHC, White JH. Supercoiled DNA. Sci Am 1980;243(1):100–113.
no DOI — not checkedSinden RR. DNA Structure and Function. 1994 Academic Press.
no DOI — not checkedFerrándiz MJ, Martín-Galiano AJ, Arnanz C, Camacho-Soguero I, Tirado-Vélez JM, de la Campa AG. An increase in negative supercoiling in bacteria reveals topology-reacting gene clusters and a homeostatic response mediated by the DNA topoisomerase I gene. Nucleic Acids Res. 2016;44(15):7292–303.
no DOI — not checkedYang Y, Ames GF. The family of repetitive Extragenic palindrome sequences: interaction with DNA gyrase and histonelike protein HU. In The Bacterial Chromosome, K Drlica (ed) pp 211–225 1990 American society of microbiology, Washington, DC.
What this badge says. CiteStamped means the CHECKABLE references of this
work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a retraction notice at that time. It says nothing about the quality, findings,
or importance of the work itself, and nothing about references deposited without a DOI.
checked 2026-07-22 — re-checked daily as this page is visited; titles and statuses come from Crossref and DataCite and are not part of the signed record
Embed this badge
Both snippets point at the live badge image and link back to this page. The badge re-renders from the daily check, so an embed never goes stale by more than a day of visits.
<a href="https://citestamp.com/citestamped/10.1186/s12860-019-0211-6"><img src="https://citestamp.com/citestamped/10.1186/s12860-019-0211-6/badge.svg" alt="CiteStamped reference-health badge" width="460" height="64"></a>
[](https://citestamp.com/citestamped/10.1186/s12860-019-0211-6)