Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon (Q37545645)

20 August 2017

Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon (English)

1 reference

20 August 2017

0 references

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Anne M Stringer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Salvatore Currenti

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Richard P Bonocora

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Catherine Baranowski

1 reference

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8 June 2020

Brianna L Petrone

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Michael J Palumbo

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Andrew A Reilly

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Zhen Zhang

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

language of work or name

English

0 references

publication date

22 November 2013

1 reference

20 August 2017

Journal of Bacteriology

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

volume

196

1 reference

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8 June 2020

issue

1 reference

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8 June 2020

page(s)

660-671

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

Database resources for the tuberculosis community

8 June 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

FRUIT, a scar-free system for targeted chromosomal mutagenesis, epitope tagging, and promoter replacement in Escherichia coli and Salmonella enterica.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

WebGeSTer DB—a transcription terminator database

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

AraC protein, regulation of the l-arabinose operon in Escherichia coli, and the light switch mechanism of AraC action

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Short-term signatures of evolutionary change in the Salmonella enterica serovar typhimurium 14028 genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

The transcription unit architecture of the Escherichia coli genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Furanose-specific Sugar Transport: CHARACTERIZATION OF A BACTERIAL GALACTOFURANOSE-BINDING PROTEIN

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Evolution of a bacterial regulon controlling virulence and Mg(2+) homeostasis

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Small membrane proteins found by comparative genomics and ribosome binding site models.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Technical considerations in using DNA microarrays to define regulons.

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Genomic analysis of protein-DNA interactions in bacteria: insights into transcription and chromosome organization

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

H-NS mediates the silencing of laterally acquired genes in bacteria

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Prediction of transcriptional terminators in Bacillus subtilis and related species

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Interaction network containing conserved and essential protein complexes in Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

WebLogo: A Sequence Logo Generator

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

RraA. a protein inhibitor of RNase E activity that globally modulates RNA abundance in E. coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Growing repertoire of AraC/XylS activators

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Roles of DNA polymerases V and II in SOS-induced error-prone and error-free repair in Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

The complete genome sequence of Escherichia coli K-12

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

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

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

A control element within a structural gene: The gal operon of Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Positive Control of Enzyme Synthesis by Gene C in the l -Arabinose System

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

A Second Transport System for l -Arabinose in Escherichia coli B/r Controlled by the araC Gene

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Information content of binding sites on nucleotide sequences

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Regulation of arabinose and xylose metabolism in Escherichia coli

23 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Transcription factor distribution in Escherichia coli: studies with FNR protein.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Prediction of rho-independent transcriptional terminators in Escherichia coli

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: a systematic study

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Mapping, sequence, and apparent lack of function of araJ, a gene of the Escherichia coli arabinose regulon

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Non-canonical protein-DNA interactions identified by ChIP are not artifacts.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

RNIE: genome-wide prediction of bacterial intrinsic terminators

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Widespread antisense transcription in Escherichia coli.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Evolution of transcriptional regulatory circuits in bacteria

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

The araE low affinity L-arabinose transport promoter. Cloning, sequence, transcription start site and DNA binding sites of regulatory proteins

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

The l-arabinose permease system in Escherichia coli B/r

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Arabinose C protein: regulation of the arabinose operon in vitro

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Characterization of the Escherichia coli araFGH and araJ promoters

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Elevated expression of DNA polymerase II increases spontaneous mutagenesis in Escherichia coli.

25 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

Arabinose-inducible promoter from Escherichia coli. Its cloning from chromosomal DNA, identification as the araFG promoter and sequence

1 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3911152

AraC protein contacts asymmetric sites in the Escherichia coli araFGH promoter

1 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24272778

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Determination of the order of mutational sites governing L-arabinose utilization in Escherichia coli B/r bv transduction with phage Plbt

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24272778

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/JB.01007-13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

PubMed publication ID

24272778

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24272778%20AND%20SRC:MED&resulttype=core&format=json