Rapid changes in gene expression dynamics in response to superoxide reveal SoxRS-dependent and independent transcriptional networks (Q28471595)

1

0 references

Wei-Yun Wholey

2

0 references

Erin M Conlon

3

0 references

Pablo J Pomposiello

Creative Commons Attribution 4.0 International

4

0 references

language of work or name

English

0 references

publication date

14 November 2007

0 references

published in

PLOS One

0 references

volume

2

0 references

issue

11

0 references

page(s)

e1186

0 references

copyright license

start time

14 November 2007

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Evidence that feedback inhibition of NAD kinase controls responses to oxidative stress

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Escherichia coli K-12: a cooperatively developed annotation snapshot--2005

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

From genomics to chemical genomics: new developments in KEGG

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Hfq-dependent regulation of OmpA synthesis is mediated by an antisense RNA.

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

EcoCyc: a comprehensive database resource for Escherichia coli

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

GadY, a small-RNA regulator of acid response genes in Escherichia coli

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Bioconductor: open software development for computational biology and bioinformatics

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

WebLogo: A Sequence Logo Generator

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

TM4: a free, open-source system for microarray data management and analysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Interaction network containing conserved and essential protein complexes in Escherichia coli

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Culture medium for enterobacteria

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

The small RNA regulators of Escherichia coli: roles and mechanisms*

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Submicromolar hydrogen peroxide disrupts the ability of Fur protein to control free-iron levels in Escherichia coli

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

IscR acts as an activator in response to oxidative stress for the suf operon encoding Fe-S assembly proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O2-regulated genes in Escherichia coli.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Sequence requirements for Lon-dependent degradation of the Escherichia coli transcription activator SoxS: identification of the SoxS residues critical to proteolysis and specific inhibition of in vitro degradation by a peptide comprised of the N-ter

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

GeneMerge—post-genomic analysis, data mining, and hypothesis testing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

High levels of intracellular cysteine promote oxidative DNA damage by driving the fenton reaction

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Global adjustment of microbial physiology during free radical stress

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Genomics of the marA/soxS/rob regulon of Escherichia coli: identification of directly activated promoters by application of molecular genetics and informatics to microarray data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Defining a rob regulon in Escherichia coli by using transposon mutagenesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Redox sensing by prokaryotic transcription factors

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Opening the iron box: transcriptional metalloregulation by the Fur protein.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

OxyR and SoxRS regulation of fur

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Activation of the OxyR transcription factor by reversible disulfide bond formation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Superoxide accelerates DNA damage by elevating free-iron levels

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

SoxR, a [2Fe-2S] transcription factor, is active only in its oxidized form

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Sequence specificity for DNA binding by Escherichia coli SoxS and Rob proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

NADPH: ferredoxin oxidoreductase acts as a paraquat diaphorase and is a member of the soxRS regulon

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Genetic definition of the Escherichia coli zwf "soxbox," the DNA binding site for SoxS-mediated induction of glucose 6-phosphate dehydrogenase in response to superoxide

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Lethal oxidative damage and mutagenesis are generated by iron in delta fur mutants of Escherichia coli: protective role of superoxide dismutase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

L-cysteine biosynthesis in Escherichia coli: nucleotide sequence and expression of the serine acetyltransferase (cysE) gene from the wild-type and a cysteine-excreting mutant

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

A global response induced in Escherichia coli by redox-cycling agents overlaps with that induced by peroxide stress.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

The redox state of the [2Fe-2S] clusters in SoxR protein regulates its activity as a transcription factor.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Binuclear [2Fe-2S] Clusters in the Escherichia coli SoxR Protein and Role of the Metal Centers in Transcription

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2064960

Inhibition of Lon-dependent degradation of the Escherichia coli transcription activator SoxS by interaction with 'soxbox' DNA or RNA polymerase.

2 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

The ykgA gene of Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Promoter discrimination by the related transcriptional activators MarA and SoxS: differential regulation by differential binding.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

A Bayesian network approach to operon prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Effects of hydrogen peroxide upon nicotinamide nucleotide metabolism in Escherichia coli: changes in enzyme levels and nicotinamide nucleotide pools and studies of the oxidation of NAD(P)H by Fe(III).

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Evidence for "pre-recruitment" as a new mechanism of transcription activation in Escherichia coli: the large excess of SoxS binding sites per cell relative to the number of SoxS molecules per cell

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Complex formation between activator and RNA polymerase as the basis for transcriptional activation by MarA and SoxS in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Novel protein--protein interaction between Escherichia coli SoxS and the DNA binding determinant of the RNA polymerase alpha subunit: SoxS functions as a co-sigma factor and redeploys RNA polymerase from UP-element-containing promoters to SoxS-depen

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Regulation of ompA mRNA stability: the role of a small regulatory RNA in growth phase-dependent control.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Global iron-dependent gene regulation in Escherichia coli. A new mechanism for iron homeostasis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

A suf operon requirement for Fe-S cluster assembly during iron starvation in Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

BioOptimizer: a Bayesian scoring function approach to motif discovery

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0001186

Interdependence of the position and orientation of SoxS binding sites in the transcriptional activation of the class I subset of Escherichia coli superoxide-inducible promoters

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18000553

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Overview: biological sources of O2-

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18000553

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0001186

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1912116

ADS bibcode

2007PLoSO...2.1186B

0 references

OpenCitations bibliographic resource ID

1912116

1 reference