(Q35673712)

9 August 2017

title

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle (English)

1 reference

9 August 2017

Patrick Sobetzko

1

1 reference

9 August 2017

Andrew Travers

series ordinal

2

1 reference

9 August 2017

Georgi Muskhelishvili

series ordinal

3

1 reference

9 August 2017

language of work or name

English

0 references

publication date

19 December 2011

1 reference

Proceedings of the National Academy of Sciences of the United States of America

9 August 2017

published in

1 reference

9 August 2017

volume

109

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9 August 2017

issue

2

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9 August 2017

page(s)

E42-50

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Analog regulation of metabolic demand

9 August 2017

cites work

1 reference

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Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA

27 July 2018

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Pervasive regulation of nucleoid structure and function by nucleoid-associated proteins.

27 July 2018

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RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

27 July 2018

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Spatial organization of the flow of genetic information in bacteria

27 July 2018

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The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters.

27 July 2018

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Coordination of genomic structure and transcription by the main bacterial nucleoid-associated protein HU.

27 July 2018

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TraR, a homolog of a RNAP secondary channel interactor, modulates transcription

27 July 2018

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Dissecting the logical types of network control in gene expression profiles

27 July 2018

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RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.

27 July 2018

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Spiral structure of Escherichia coli HU provides foundation for DNA supercoiling

27 July 2018

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Physiological effects of Crl in Salmonella are modulated by sigmaS level and promoter specificity

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Differential regulation of Escherichia coli topoisomerase I by Fis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Dynamic state of DNA topology is essential for genome condensation in bacteria.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

RNA polymerase and an activator form discrete subcomplexes in a transcription initiation complex

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

A pathway branching in transcription initiation in Escherichia coli

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Nucleoid remodeling by an altered HU protein: reorganization of the transcription program

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

DNA looping-mediated repression by histone-like protein H-NS: specific requirement of Esigma70 as a cofactor for looping

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Fis regulates transcriptional induction of RpoS in Salmonella enterica

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

DNA supercoiling - a global transcriptional regulator for enterobacterial growth?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Macrodomain organization of the Escherichia coli chromosome.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

H-NS: a universal regulator for a dynamic genome

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

The gyr genes of Salmonella enterica serovar Typhimurium are repressed by the factor for inversion stimulation, Fis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Adaptation to famine: a family of stationary-phase genes revealed by microarray analysis

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Promoter protection by a transcription factor acting as a local topological homeostat

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

sigma factor selectivity of Escherichia coli RNA polymerase: role for CRP, IHF and lrp transcription factors

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Regulation of HU alpha and HU beta by CRP and FIS in Escherichia coli.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Purified dnaA protein in initiation of replication at the Escherichia coli chromosomal origin of replication

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

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

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Lethal overproduction of the Escherichia coli nucleoid protein H-NS: ultramicroscopic and molecular autopsy

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Structural coupling between RNA polymerase composition and DNA supercoiling in coordinating transcription: a global role for the omega subunit?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Gene clusters reflecting macrodomain structure respond to nucleoid perturbations.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

DnaA-ATP acts as a molecular switch to control levels of ribonucleotide reductase expression in Escherichia coli.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

General organisational principles of the transcriptional regulation system: a tree or a circle?

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Strong intranucleoid interactions organize the Escherichia coli chromosome into a nucleoid filament.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Control of RpoS in global gene expression of Escherichia coli in minimal media.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Selective repression by Fis and H-NS at the Escherichia coli dps promoter.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Dynamic events of sister chromosomes in the cell cycle of Escherichia coli.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Analysis of promoter targets for Escherichia coli transcription elongation factor GreA in vivo and in vitro

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

DoriC: a database of oriC regions in bacterial genomes

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Antagonistic regulation of Escherichia coli ribosomal RNA rrnB P1 promoter activity by GreA and DksA.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

A two-component phosphotransfer network involving ArcB, ArcA, and RssB coordinates synthesis and proteolysis of sigmaS (RpoS) in E. coli

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Effect of oxygen on the Escherichia coli ArcA and FNR regulation systems and metabolic responses

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Spatial patterns of transcriptional activity in the chromosome of Escherichia coli

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Spatial and temporal organization of replicating Escherichia coli chromosomes.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Functional modulation of Escherichia coli RNA polymerase

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Effects of the Escherichia coli DNA-binding protein H-NS on rRNA synthesis in vivo

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like "stringent" RNA polymerases in Escherichia coli

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Antagonistic involvement of FIS and H-NS proteins in the transcriptional control of hns expression.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

DNA supercoiling depends on the phosphorylation potential in Escherichia coli.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3258614

Parallel Genetic and Phenotypic Evolution of DNA Superhelicity in Experimental Populations of Escherichia coli

25 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1108229109

Expression of variant nuclear Arabidopsis tRNA(Ser) genes and pre-tRNA maturation differ in HeLa, yeast and wheat germ extracts

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1108229109

A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Nucleoid restructuring in stationary-state bacteria

1 reference

12 December 2020

DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP

1 reference

12 December 2020

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

1 reference

12 December 2020

Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.1108229109

1 reference

9 August 2017

0 references

1 reference

9 August 2017

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