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The discriminator sequence is a primary determinant in the supercoiling response of bacterial promoters

https://doi.org/10.1101/2020.10.01.322149

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Evolution of global regulatory networks during a long‐term experiment withEscherichia coli

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Supercoiling response of a bacterial tRNA gene.

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The G+C-rich discriminator region of the tyr T promoter antagonises the formation of stable preinitiation complexes 1 1Edited by M. Yaniv

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Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro

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Identification of DNA topoisomerases involved in immediate and transient DNA relaxation induced by heat shock inEscherichia coli

inferredcites →https://doi.org/10.1007/s12551-016-0238-2openalex-snapshot

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

inferredcites →https://doi.org/10.1016/0022-2836(78)90061-xopenalex-snapshot

Superhelical Escherichia coli DNA: Relaxation by coumermycin

inferredcites →https://doi.org/10.1016/0022-2836(85)90305-5openalex-snapshot

Supercoiling response of the lac ps promoter in vitro

inferredcites →https://doi.org/10.1016/0022-2836(91)90185-9openalex-snapshot

Bacterial DNA supercoiling and

inferredcites →https://doi.org/10.1016/0092-8674(89)90574-6openalex-snapshot

DNA supercoiling and prokaryotic transcription

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Modulation of firefly luciferase stability and impact on studies of gene regulation

inferredcites →https://doi.org/10.1016/b978-0-08-099387-4.00001-6openalex-snapshot

High-resolution temporal analysis of global promoter activity in Bacillus subtilis

inferredcites →https://doi.org/10.1016/j.cell.2006.04.034openalex-snapshot

rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase

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Insights into the Mechanisms of Basal Coordination of Transcription Using a Genome-Reduced Bacterium

inferredcites →https://doi.org/10.1016/j.cels.2019.07.001openalex-snapshot

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

inferredcites →https://doi.org/10.1016/j.csbj.2019.07.013openalex-snapshot

DNA Supercoiling: an Ancestral Regulator of Gene Expression in Pathogenic Bacteria?

inferredcites →https://doi.org/10.1016/j.dib.2020.105297openalex-snapshot

Transcriptomic data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S treated with novobiocin

inferredcites →https://doi.org/10.1016/j.gde.2005.02.006openalex-snapshot

Transcriptional regulation by the numbers: applications

inferredcites →https://doi.org/10.1016/j.molcel.2020.02.017openalex-snapshot

Stepwise Promoter Melting by Bacterial RNA Polymerase

inferredcites →https://doi.org/10.1016/s0021-9258(18)90844-6openalex-snapshot

Effect of supercoiling on the abortive initiation kinetics of the RNA-I promoter of ColE1 plasmid DNA.

inferredcites →https://doi.org/10.1016/s0021-9258(19)88626-xopenalex-snapshot

DNA melting within stable closed complexes at the Escherichia coli rrnB P1 promoter.

inferredcites →https://doi.org/10.1016/s0022-2836(03)00727-7openalex-snapshot

Mechanism of Transcriptional Activation by FIS: Role of Core Promoter Structure and DNA Topology

inferredcites →https://doi.org/10.1016/s0022-2836(61)80072-7openalex-snapshot

Genetic regulatory mechanisms in the synthesis of proteins

inferredcites →https://doi.org/10.1016/s0022-2836(80)80030-1openalex-snapshot

A tRNATyr promoter with an altered in vitro response to ppGpp

inferredcites →https://doi.org/10.1017/s0033583500005825openalex-snapshot

DNA supercoiling and transcription: topological coupling of promoters

inferredcites →https://doi.org/10.1038/msb.2010.18openalex-snapshot

Metabolomic and transcriptomic stress response of Escherichia coli

inferredcites →https://doi.org/10.1038/nature18959openalex-snapshot

Tempo and mode of genome evolution in a 50,000-generation experiment

inferredcites →https://doi.org/10.1038/ncomms11055openalex-snapshot

Genome scale patterns of supercoiling in a bacterial chromosome

inferredcites →https://doi.org/10.1038/nrmicro1088openalex-snapshot

DNA supercoiling — a global transcriptional regulator for enterobacterial growth?

inferredcites →https://doi.org/10.1038/sj.embor.7400729openalex-snapshot

Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

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Increase in negative supercoiling of plasmid DNA in Escherichia coli exposed to cold shock

inferredcites →https://doi.org/10.1046/j.1365-2958.2000.01805.xopenalex-snapshot

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

inferredcites →https://doi.org/10.1046/j.1365-2958.2000.02129.xopenalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.0334340100openalex-snapshot

Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli

inferredcites →https://doi.org/10.1073/pnas.0804953105openalex-snapshot

Growth-rate-dependent partitioning of RNA polymerases in bacteria

inferredcites →https://doi.org/10.1073/pnas.0912673106openalex-snapshot

Oscillations in supercoiling drive circadian gene expression in cyanobacteria

inferredcites →https://doi.org/10.1073/pnas.1618675114openalex-snapshot

Mechanism of transcription initiation and promoter escape by E . coli RNA polymerase

inferredcites →https://doi.org/10.1073/pnas.1819682116openalex-snapshot

Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase

inferredcites →https://doi.org/10.1073/pnas.200365097openalex-snapshot

An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled

inferredcites →https://doi.org/10.1073/pnas.84.12.4185openalex-snapshot

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

inferredcites →https://doi.org/10.1073/pnas.84.20.7024openalex-snapshot

Supercoiling of the DNA template during transcription.

inferredcites →https://doi.org/10.1074/jbc.275.11.8103openalex-snapshot

Roles of Topoisomerases in Maintaining Steady-state DNA Supercoiling in Escherichia coli

inferredcites →https://doi.org/10.1093/bioinformatics/btt415openalex-snapshot

Twist-DNA: computing base-pair and bubble opening probabilities in genomic superhelical DNA

inferredcites →https://doi.org/10.1093/bioinformatics/btw629openalex-snapshot

bTSSfinder: a novel tool for the prediction of promoters in cyanobacteria and Escherichia coli

inferredcites →https://doi.org/10.1093/emboj/17.8.2359openalex-snapshot

The supercoiling sensitivity of a bacterial tRNA promoter parallels its responsiveness to stringent control

inferredcites →https://doi.org/10.1093/nar/gks014openalex-snapshot

The nucleoid-associated proteins H-NS and FIS modulate the DNA supercoiling response of the pel genes, the major virulence factors in the plant pathogen bacterium Dickeya dadantii

inferredcites →https://doi.org/10.1093/nar/gkw1003openalex-snapshot

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

inferredcites →https://doi.org/10.1093/nar/gkz300openalex-snapshot

Bacterial genome architecture shapes global transcriptional regulation by DNA supercoiling

inferredcites →https://doi.org/10.1098/rsta.2015.0069openalex-snapshot

Bacteria differently regulate mRNA abundance to specifically respond to various stresses

inferredcites →https://doi.org/10.1103/physreve.84.031912openalex-snapshot

Bubble statistics and positioning in superhelically stressed DNA

inferredcites →https://doi.org/10.1111/j.1365-2958.1992.tb01486.xopenalex-snapshot

Control of bacterial DNA supercoiling

inferredcites →https://doi.org/10.1111/j.1365-2958.2011.07560.xopenalex-snapshot

DNA supercoiling is differentially regulated by environmental factors and FIS in Escherichia coli and Salmonella enterica

inferredcites →https://doi.org/10.1111/j.1365-2958.2011.07718.xopenalex-snapshot

Regulation of transcription by DNA supercoiling in Mycoplasma genitalium: global control in the smallest known self‐replicating genome

inferredcites →https://doi.org/10.1128/ecosalplus.esp-0016-2019openalex-snapshot

Chromosomal Organization and Regulation of Genetic Function in Escherichia coli Integrates the DNA Analog and Digital Information

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Promoter Sequence for Stringent Control of Bacterial Ribonucleic Acid Synthesis

inferredcites →https://doi.org/10.1128/jb.169.10.4431-4435.1987openalex-snapshot

Estimation of the effect of coumermycin A1 on Salmonella typhimurium promoters by using random operon fusions

inferredcites →https://doi.org/10.1128/jb.170.6.2816-2826.1988openalex-snapshot

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

inferredcites →https://doi.org/10.1128/mbio.00353-15openalex-snapshot

Chromosomal “Stress-Response” Domains Govern the Spatiotemporal Expression of the Bacterial Virulence Program

inferredcites →https://doi.org/10.1128/mbio.00524-22openalex-snapshot

Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii

inferredcites →https://doi.org/10.1146/annurev-micro-092412-155737openalex-snapshot

Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective

inferredcites →https://doi.org/10.1146/annurev.genet.36.032902.111815openalex-snapshot

DNA Topology-Mediated Control of Global Gene Expression in Escherichia coli

inferredcites →https://doi.org/10.1186/1471-2164-14-73openalex-snapshot

Genomic analysis of the regulatory elements and links with intrinsic DNA structural properties in the shrunken genome of Buchnera

inferredcites →https://doi.org/10.1186/gb-2004-5-11-r87openalex-snapshot

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

inferredcites →https://doi.org/10.1186/s12860-019-0211-6openalex-snapshot

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

inferredcites →https://doi.org/10.1371/journal.pcbi.1002484openalex-snapshot

Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA

inferredcites →https://doi.org/10.1371/journal.pone.0165306openalex-snapshot

Supercoiling Effects on Short-Range DNA Looping in E. coli

inferredcites →https://doi.org/10.1534/genetics.104.035717openalex-snapshot

Long-Term Experimental Evolution in Escherichia coli. XII. DNA Topology as a Key Target of Selection

inferredcites →https://doi.org/10.3389/fmolb.2016.00073openalex-snapshot

Bacterial RNA Polymerase-DNA Interaction—The Driving Force of Gene Expression and the Target for Drug Action

inferredcites →https://doi.org/10.3390/biom5021035openalex-snapshot

Initial Events in Bacterial Transcription Initiation

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.jbc.2021.101446openalex-snapshot

Carbon catabolite repression in pectin digestion by the phytopathogen Dickeya dadantii

inferred← citeshttps://doi.org/10.1038/s41598-021-03817-4openalex-snapshot

The bacterial promoter spacer modulates promoter strength and timing by length, TG-motifs and DNA supercoiling sensitivity

inferred← citeshttps://doi.org/10.1093/nar/gkac579openalex-snapshot

Quantitative contribution of the spacer length in the supercoiling-sensitivity of bacterial promoters

inferred← citeshttps://doi.org/10.1093/nar/gkac679openalex-snapshot

What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii

inferred← citeshttps://doi.org/10.3389/fmolb.2023.1335409openalex-snapshot

Alteration of the −35 and −10 sequences and deletion the upstream sequence of the −35 region of the promoter A1 of the phage T7 in dsDNA confirm the contribution of non-specific interactions with E. coli RNA polymerase to the transcription initiation process

inferred← citeshttps://doi.org/10.70675/121231b7zf5eez4064zaf52zd8b8e6e71fd3openalex-snapshot

Modelling transcriptional regulation by DNA supercoiling in bacteria

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