Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. (Q34789412)

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4 March 2020

title

Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding (English)

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4 March 2020

0 references

1

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4 March 2020

Dongjun Chung

4

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4 March 2020

7

Sündüz Keleş

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4 March 2020

author name string

Huihuang Yan

2

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4 March 2020

Irene M Ong

3

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4 March 2020

Kun Liang

5

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4 March 2020

Frances Tran

6

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4 March 2020

Robert Landick

8

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4 March 2020

Patricia J Kiley

9

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publication date

20 June 2013

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4 March 2020

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4 March 2020

volume

9

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issue

6

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4 March 2020

page(s)

e1003565

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Creative Commons Attribution 4.0 International

4 March 2020

copyright license

start time

20 June 2013

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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8 July 2018

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Multiple site-specific binding of Fis protein to Escherichia coli nuoA-N promoter DNA and its impact on DNA topology visualised by means of scanning force microscopy

8 July 2018

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8 July 2018

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The regulation of bacterial transcription initiation

8 July 2018

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Identifying global regulators in transcriptional regulatory networks in bacteria

8 July 2018

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Bacterial iron homeostasis

8 July 2018

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Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR.

8 July 2018

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Escherichia coli spotted double-strand DNA microarrays: RNA extraction, labeling, hybridization, quality control, and data management

8 July 2018

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Selective regulation of ptsG expression by Fis. Formation of either activating or repressing nucleoprotein complex in response to glucose

8 July 2018

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Summaries of Affymetrix GeneChip probe level data

8 July 2018

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Decrease in cell viability in an RMF, sigma(38), and OmpC triple mutant of Escherichia coli

8 July 2018

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Variance stabilization applied to microarray data calibration and to the quantification of differential expression

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

NO sensing by FNR: regulation of the Escherichia coli NO-detoxifying flavohaemoglobin, Hmp.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

A comparative genomics approach to prediction of new members of regulons

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

The nucleoid-associated protein StpA binds curved DNA, has a greater DNA-binding affinity than H-NS and is present in significant levels in hns mutants

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Regulatory architecture of the iron-regulated fepD-ybdA bidirectional promoter region in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Interplay between three global regulatory proteins mediates oxygen regulation of the Escherichia coli cytochrome d oxidase (cydAB) operon.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Suppression of FNR-dependent transcription activation at the Escherichia coli nir promoter by Fis, IHF and H-NS: modulation of transcription initiation by a complex nucleo-protein assembly.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

An efficient recombination system for chromosome engineering in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Towards single-copy gene expression systems making gene cloning physiologically relevant: lambda InCh, a simple Escherichia coli plasmid-chromosome shuttle system

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Eukaryotic transcriptional control

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Identifying DNA and protein patterns with statistically significant alignments of multiple sequences

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Fundamentally different logic of gene regulation in eukaryotes and prokaryotes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Functioning of DcuC as the C4-dicarboxylate carrier during glucose fermentation by Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase sigma70 subunit

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Downregulation of Escherichia coli yfiD expression by FNR occupying a site at -93.5 involves the AR1-containing face of FNR.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Transcriptional activation by FNR and CRP: reciprocity of binding-site recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Regulation of the Salmonella typhimurium pepT gene by cyclic AMP receptor protein (CRP) and FNR acting at a hybrid CRP-FNR site

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Isolation of an oxygen-sensitive FNR protein of Escherichia coli: interaction at activator and repressor sites of FNR-controlled genes

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

A signal sequence is not required for protein export in prlA mutants of Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Activation of the Escherichia coli nitrate reductase (narGHJI) operon by NarL and Fnr requires integration host factor.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Characterization of the ferrous iron uptake system of Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Effects of nitrate respiration on expression of the Arc-controlled operons encoding succinate dehydrogenase and flavin-linked L-lactate dehydrogenase

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Fur regulon in gram-negative bacteria. Identification and characterization of new iron-regulated Escherichia coli genes by a fur titration assay.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

The FNR family of transcriptional regulators

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

The gene encoding the periplasmic cyclophilin homologue, PPIase A, in Escherichia coli, is expressed from four promoters, three of which are activated by the cAMP-CRP complex and negatively regulated by the CytR repressor

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Requirement of Fnr and NarL functions for nitrate reductase expression in Escherichia coli K-12.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Culture medium for enterobacteria

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Regulation of Escherichia coli fumarate reductase (frdABCD) operon expression by respiratory electron acceptors and the fnr gene product

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Regulation of divergent transcription from the iron-responsive fepB-entC promoter-operator regions in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Anaerobic induction of pyruvate formate-lyase gene expression is mediated by the ArcA and FNR proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Identification of functional cis-acting sequences involved in regulation of narK gene expression in Escherichia coli

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

The anaerobic oxidation of dihydroorotate by Escherichia coli K-12

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

Aerobic regulation of cytochrome d oxidase (cydAB ) operon expression in Escherichia coli: roles of Fnr and ArcA in repression and activation

8 July 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Co-dependent positive regulation of the ansB promoter of Escherichia coli by CRP and the FNR protein: a molecular analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Novel regulation targets of the metal-response BasS-BasR two-component system of Escherichia coli

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

H-NS promotes looped domain formation in the bacterial chromosome

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

H-NS, the genome sentinel

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Integration host factor alleviates H-NS silencing of the Salmonella enterica serovar Typhimurium master regulator of SPI1, hilA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Functional organisation of Escherichia coli transcriptional regulatory network

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Transcriptional regulation of a hybrid cluster (prismane) protein

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Effect of ArcA and FNR on the expression of genes related to the oxygen regulation and the glycolysis pathway in Escherichia coli under microaerobic growth conditions

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

Fur-DNA interactions at the bidirectional fepDGC-entS promoter region in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

A method for direct cloning of fur-regulated genes: identification of seven new fur-regulated loci in Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

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/JOURNAL.PGEN.1003565

Internal-sensing machinery directs the activity of the regulatory network in Escherichia coli.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3688515

GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli

26 October 2018

1 reference

https://api.crossref.org/works/10.1371/JOURNAL.PGEN.1003565

FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3

21 January 2018

1 reference

12 December 2020

Regulation of transcription initiation at the Escherichia coli nir operon promoter: a new mechanism to account for co‐dependence on two transcription factors

1 reference

12 December 2020

H-NS cooperative binding to high-affinity sites in a regulatory element results in transcriptional silencing

1 reference

12 December 2020

Repression of tonB transcription during anaerobic growth requires Fur binding at the promoter and a second factor binding upstream

1 reference

12 December 2020

Purification, characterization and mode of action of PdhR, the transcriptional repressor of the pdhR-aceEF-lpd operon of Escherichia coli

1 reference

12 December 2020

The molecular basis for the differential regulation of the hlyE-encoded haemolysin of Escherichia coli by FNR and HlyX lies in the improved Activating Region 1 contact of HlyX

1 reference

12 December 2020

Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein

1 reference

12 December 2020

Cyclic AMP stimulates transcription of the structural gene of the outer-membrane protein OmpA of Escherichia coli

1 reference

12 December 2020

10.1371/JOURNAL.PGEN.1003565

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23818864 AND SRC:MED&resulttype=core&format=json

4 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23818864 AND SRC:MED&resulttype=core&format=json

4 March 2020

PubMed publication ID

23818864

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23818864 AND SRC:MED&resulttype=core&format=json