(Q35315347)

7 August 2017

title

A model for sigma factor competition in bacterial cells (English)

1 reference

7 August 2017

2

0 references

author name string

Marco Mauri

series ordinal

1

1 reference

7 August 2017

publication date

9 October 2014

1 reference

PLOS Computational Biology

7 August 2017

published in

1 reference

7 August 2017

volume

10

1 reference

7 August 2017

issue

10

1 reference

7 August 2017

page(s)

e1003845

1 reference

Creative Commons Attribution 4.0 International

7 August 2017

copyright license

start time

9 October 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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27 July 2018

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Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters

27 July 2018

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Molecular crowding limits translation and cell growth

27 July 2018

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Translational cross talk in gene networks

27 July 2018

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Ultrasensitive response motifs: basic amplifiers in molecular signalling networks

27 July 2018

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Sequestration-based bistability enables tuning of the switching boundaries and design of a latch

27 July 2018

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Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation

27 July 2018

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Queueing up for enzymatic processing: correlated signaling through coupled degradation

27 July 2018

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How molecular competition influences fluxes in gene expression networks

27 July 2018

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Stochastic pulse regulation in bacterial stress response

27 July 2018

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The role of tRNA and ribosome competition in coupling the expression of different mRNAs in Saccharomyces cerevisiae

27 July 2018

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Bistable responses in bacterial genetic networks: designs and dynamical consequences

27 July 2018

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Mechanism of bacterial transcription initiation: RNA polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of RNA synthesis

27 July 2018

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Transcriptional switching in Escherichia coli during stress and starvation by modulation of sigma activity

27 July 2018

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Diverse two-dimensional input functions control bacterial sugar genes

27 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Differential mechanisms of binding of anti-sigma factors Escherichia coli Rsd and bacteriophage T4 AsiA to E. coli RNA polymerase lead to diverse physiological consequences

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Prevalence of RNA polymerase stalling at Escherichia coli promoters after open complex formation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

RNA polymerase is poised for activation across the 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=4191881

Quantitative characteristics of gene regulation by small RNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Mechanisms of physiological regulation of RNA synthesis in bacteria: new discoveries breaking old schemes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Combinatorial transcriptional control of the lactose operon of 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=4191881

Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Real-time kinetics of gene activity in individual 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=4191881

Holoenzyme switching and stochastic release of sigma factors from RNA polymerase in vivo

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

DksA potentiates direct activation of amino acid promoters by ppGpp

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

ppGpp: a global regulator 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=4191881

Transcriptional regulation by the numbers: models.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition?

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Recent insights into the general stress response regulatory network 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=4191881

Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core 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=4191881

Sigma competition: the contest between bacteriophage T4 middle and late transcription

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

The functional and regulatory roles of sigma factors in transcription

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

27 July 2018

The anti-sigma factors.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Negative regulation by RpoS: a case of sigma factor competition

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Promoter selectivity of Escherichia coli RNA polymerase sigmaF holoenzyme involved in transcription of flagellar and chemotaxis genes

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth 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=4191881

Control of rRNA transcription 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=4191881

In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N).

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Autogenous and post-transcriptional regulation of RNA polymerase synthesis.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Competition between sigma factors for core 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=4191881

Release of the sigma subunit of Escherichia coli DNA-dependent RNA polymerase depends mainly on time elapsed after the start of initiation, not on length of product RNA.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

A mutant sigma 32 with a small deletion in conserved region 3 of sigma has reduced affinity for core 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=4191881

How a mutation in the gene encoding sigma 70 suppresses the defective heat shock response caused by a mutation in the gene encoding sigma 32.

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: differences in the binding behavior of core and holoenzyme

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

The transcription factor titration effect dictates level of gene expression

27 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Regulation of alternative sigma factor use.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Interdependence of cell growth and gene expression: origins and consequences.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

A global view of Escherichia coli Rsd protein and its interactions.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Protein sequestration generates a flexible ultrasensitive response in a genetic network

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Growth-rate-dependent partitioning of RNA polymerases in bacteria

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

26 September 2018

(p)ppGpp: still magical?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

ppGpp and DksA likely regulate the activity of the extracytoplasmic stress factor sigmaE in Escherichia coli by both direct and indirect mechanisms.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Properties of RNA polymerase bypass mutants: implications for the role of ppGpp and its co-factor DksA in controlling transcription dependent on sigma54.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Extensive functional overlap between sigma factors in Escherichia coli.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

A bottom-up approach to gene regulation.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Control of rRNA expression by small molecules is dynamic and nonredundant

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Free RNA polymerase and modeling global transcription in Escherichia coli

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

The role of the alarmone (p)ppGpp in sigma N competition for core RNA polymerase.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Mechanochemical ATPases and transcriptional activation.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Regulation of sigma factor competition by the alarmone ppGpp

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Functional modulation of Escherichia coli RNA polymerase

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

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

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Promoter selectivity of Escherichia coli RNA polymerase E sigma 70 and E sigma 38 holoenzymes. Effect of DNA supercoiling.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

A novel bacterial transcription cycle involving sigma 54.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4191881

Effects of reduced amount of RNA polymerase sigma factor on gene expression and growth of Escherichia coli: studies of the rpoD450 (amber) mutation

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25299042

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Stringent response in Escherichia coli induces expression of heat shock proteins

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25299042

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Altering the level and regulation of the major sigma subunit of RNA polymerase affects gene expression and development in Bacillus subtilis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25299042

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1003845

1 reference

7 August 2017

DBLP publication ID

journals/ploscb/MauriK14

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

7 August 2017

1 reference