A coarse-grained biophysical model of E. coli and its application to perturbation of the rRNA operon copy number (Q33330861)

25 July 2017

title

A coarse-grained biophysical model of E. coli and its application to perturbation of the rRNA operon copy number (English)

1 reference

25 July 2017

0 references

1 reference

25 July 2017

Arbel D Tadmor

1 reference

25 July 2017

publication date

1 April 2008

1 reference

PLOS Computational Biology

25 July 2017

published in

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25 July 2017

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25 July 2017

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25 July 2017

page(s)

e1000038

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Creative Commons Attribution 4.0 International

25 July 2017

start time

2 May 2008

1 reference

April 2022 Public Data File from Crossref

copyrighted

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cites work

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Life history implications of rRNA gene copy number in Escherichia coli

21 June 2018

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Large changes in cytoplasmic biopolymer concentration with osmolality indicate that macromolecular crowding may regulate protein-DNA interactions and growth rate in osmotically stressed Escherichia coli K-12.

21 June 2018

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Catalytic activation of multimeric RNase E and RNase G by 5'-monophosphorylated RNA

21 June 2018

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Changes in Escherichia coli rRNA Promoter Activity Correlate with Changes in Initiating Nucleoside Triphosphate and Guanosine 5′ Diphosphate 3′-Diphosphate Concentrations after Induction of Feedback Control of Ribosome Synthesis

21 June 2018

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Determination of the catalytic parameters of the N-terminal half of Escherichia coli ribonuclease E and the identification of critical functional groups in RNA substrates

21 June 2018

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Control of rRNA expression in Escherichia coli

21 June 2018

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Coupling the initiation of chromosome replication to cell size in Escherichia coli

21 June 2018

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Degradation of mRNA in Escherichia coli

21 June 2018

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Global RNA half-life analysis in Escherichia coli reveals positional patterns of transcript degradation

21 June 2018

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mRNA decay in Escherichia coli comes of age.

21 June 2018

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The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media

21 June 2018

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Cytoplasmic RNA Polymerase in Escherichia coli

21 June 2018

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Macromolecular crowding: an important but neglected aspect of the intracellular environment

21 June 2018

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In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

21 June 2018

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

21 June 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Regions of RNase E important for 5'-end-dependent RNA cleavage and autoregulated synthesis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

rRNA operon copy number reflects ecological strategies of bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

The feedback response of Escherichia coli rRNA synthesis is not identical to the mechanism of growth rate-dependent control

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Functional genomics: expression analysis of Escherichia coli growing on minimal and rich media

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Increased rrn gene dosage causes intermittent transcription of rRNA in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Construction and initial characterization of Escherichia coli strains with few or no intact chromosomal rRNA operons.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Modulation of the nucleoid, the transcription apparatus, and the translation machinery in bacteria for stationary phase survival

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

An Escherichia coli strain with all chromosomal rRNA operons inactivated: complete exchange of rRNA genes between bacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Protein mobility in the cytoplasm of Escherichia coli.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Initiation and velocity of chromosome replication in Escherichia coli B/r and K-12.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

The decay of bacterial messenger RNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Control of rRNA transcription in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Depletion of functional ribosomal RNA operons in Escherichia coli causes increased expression of the remaining intact copies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Gratuitous overexpression of genes in Escherichia coli leads to growth inhibition and ribosome destruction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Effect of macromolecular crowding upon the structure and function of an enzyme: glyceraldehyde-3-phosphate dehydrogenase

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Macromolecular composition of bacteria.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Deletion of a ribosomal ribonucleic acid operon in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

The Adaptive Responses of Escherichia coli to a Feast and Famine Existence

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Growth rate of polypeptide chains as a function of the cell growth rate in a mutant of Escherichia coli 15

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Relationship between Cell Size and Time of Initiation of DNA Replication

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Chromosome replication and the division cycle of Escherichia coli B/r.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Feedback regulation of rRNA and tRNA synthesis and accumulation of free ribosomes after conditional expression of rRNA genes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Evolution in bacteria: evidence for a universal substitution rate in cellular genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Feedback regulation of rRNA synthesis in Escherichia coli. Requirement for initiation factor IF2.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Guanosine 3'-diphosphate 5'-diphosphate is not required for growth rate-dependent control of rRNA synthesis in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Proteases and protein degradation inEscherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Control of rRNA synthesis in Escherichia coli at increased rrn gene dosage. Role of guanosine tetraphosphate and ribosome feedback

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Metabolic growth rate control in Escherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Transcription and translation initiation frequencies of the Escherichia coli lac operon

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2320978

Dependency on medium and temperature of cell size and chemical composition during balanced grown of Salmonella typhimurium

21 June 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000038

Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements

21 January 2018

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Free RNA polymerase and modeling global transcription in Escherichia coli

21 January 2018

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Synthesis of the beta and beta' subunits of Escherichia coli RNA polymerase is autogenously regulated in vivo by both transcriptional and translational mechanisms

21 January 2018

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Translational standby sites: how ribosomes may deal with the rapid folding kinetics of mRNA.

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000038

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.

21 January 2018

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Robust control of initiation of prokaryotic chromosome replication: essential considerations for a minimal cell.

21 January 2018

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Molecular crowding reduces to a similar extent the diffusion of small solutes and macromolecules: measurement by fluorescence correlation spectroscopy

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000038

Consequences of RNase E scarcity in Escherichia coli.

21 January 2018

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Mechanistic modeling of prokaryotic mRNA decay

21 January 2018

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Control of rRNA expression by small molecules is dynamic and nonredundant

21 January 2018

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Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion.

21 January 2018

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RNase E autoregulates its synthesis by controlling the degradation rate of its own mRNA in Escherichia coli: unusual sensitivity of the rne transcript to RNase E activity.

21 January 2018

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Kinetic properties of rrn promoters in Escherichia coli

21 January 2018

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Plasmid vectors for the selection of promoters

21 January 2018

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https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1000038

Excluded volume as a determinant of macromolecular structure and reactivity

21 January 2018

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Evolution of competitive fitness in experimental populations of E. coli: what makes one genotype a better competitor than another?

21 January 2018

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RIBOSOME CONTENT AND THE RATE OF GROWTH OF SALMONELLA TYPHIMURIUM.

21 January 2018

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Autoregulation allows Escherichia coli RNase E to adjust continuously its synthesis to that of its substrates

31 October 2018

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21 January 2018

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

21 January 2018

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12 December 2020

An examination of the Cooper-Helmstetter theory of DNA replication in bacteria and its underlying assumptions

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12 December 2020

Construction and characterization of the chloramphenicol-resistance gene cartridge: A new approach to the transcriptional mapping of extrachromosomal elements

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12 December 2020

[Copy number of ribosomal operons in prokaryotes and its effect on phylogenic analyses]

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12 December 2020

Relation between growth and replication in bacteria

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12 December 2020

The influence of macromolecular crowding on thermodynamic activity: solubility and dimerization constants for spherical and dumbbell-shaped molecules in a hard-sphere mixture

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12 December 2020

T4 polynucleotide kinase: macromolecular crowding increases the efficiency of reaction at DNA termini

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12 December 2020

Computer model for glucose-limited growth of a single cell of Escherichia coli B/r-A

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12 December 2020

Expression of rRNA and tRNA genes in Escherichia coli: evidence for feedback regulation by products of rRNA operons

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12 December 2020

DNA determinants of rRNA synthesis in E. coli: growth rate dependent regulation, feedback inhibition, upstream activation, antitermination

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12 December 2020

10.1371/JOURNAL.PCBI.1000038

Identifiers

DOI

1 reference

journals/ploscb/TadmorT08

25 July 2017

0 references

1 reference

DBLP Dataset 2021-01-02

release_xif7kz5a6ve5la6hjmwt5ptxta

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/xif7kz5a6ve5la6hjmwt5ptxta

24 November 2022

mapped directly with Wikidata item

PMC publication ID

2320978

1 reference

25 July 2017

1 reference