Replication-transcription conflicts in bacteria. (Q36307709)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22669220 AND SRC:MED&resulttype=core&format=json

3 February 2020

title

Replication-transcription conflicts in bacteria (English)

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3 February 2020

4

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3 February 2020

author name string

Houra Merrikh

series ordinal

1

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3 February 2020

Yan Zhang

series ordinal

2

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3 February 2020

Alan D Grossman

series ordinal

3

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3 February 2020

language of work or name

English

0 references

publication date

6 June 2012

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Nature Reviews Microbiology

3 February 2020

published in

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3 February 2020

volume

10

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3 February 2020

issue

7

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3 February 2020

page(s)

449-458

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22669220 AND SRC:MED&resulttype=core&format=json

Replication fork reversal after replication-transcription collision.

3 February 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

R-loop-mediated genomic instability is caused by impairment of replication fork progression

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Linking RNA polymerase backtracking to genome instability in E. coli

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Genome-wide function of THO/TREX in active genes prevents R-loop-dependent replication obstacles

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

DNA Replicases from a Bacterial Perspective

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Co-directional replication-transcription conflicts lead to replication restart

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Transcription termination maintains chromosome integrity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

PcrA helicase dismantles RecA filaments by reeling in DNA in uniform steps

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

What happens when replication and transcription complexes collide?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

A NusE:NusG complex links transcription and translation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Co-orientation of replication and transcription preserves genome integrity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Rep provides a second motor at the replisome to promote duplication of protein-bound DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

CarD is an essential regulator of rRNA transcription required for Mycobacterium tuberculosis persistence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

30 September 2017

(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=3467967

Chromosome structuring limits genome plasticity in Escherichia coli.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

UvrD controls the access of recombination proteins to blocked replication forks

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Avoiding and resolving conflicts between DNA replication and transcription

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Transcription-associated mutagenesis in yeast is directly proportional to the level of gene expression and influenced by the direction of DNA replication

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Genome-wide coorientation of replication and transcription reduces adverse effects on replication in Bacillus subtilis.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

UvrD limits the number and intensities of RecA-green fluorescent protein structures in Escherichia coli K-12

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Roles of Pif1-like helicases in the maintenance of genomic stability.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Cotranscriptional processes and their influence on genome stability.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Transcription regulatory elements are punctuation marks for DNA replication

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Interruptions in gene expression drive highly expressed operons to the leading strand of DNA replication

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Mechanisms of transcription-replication collisions in bacteria

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

UvrD helicase, unlike Rep helicase, dismantles RecA nucleoprotein filaments in Escherichia coli.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Why is transcription coupled to translation in bacteria?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Backtracking by single RNA polymerase molecules observed at near-base-pair resolution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Transcript cleavage factors GreA and GreB act as transient catalytic components of RNA polymerase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Gene essentiality determines chromosome organisation in bacteria

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

A salvage pathway for protein structures: tmRNA and trans-translation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Rho-dependent termination and ATPases in transcript termination

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

E. coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Essential bacterial helicases that counteract the toxicity of recombination proteins

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

An expanded view of bacterial DNA replication.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

GreA and GreB proteins revive backtracked RNA polymerase in vivo by promoting transcript trimming

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Effect of DNA lesions on transcription elongation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Base composition skews, replication orientation, and gene orientation in 12 prokaryote genomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

The complete genome sequence of the gram-positive bacterium Bacillus subtilis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Bacteriophage phi29 DNA replication arrest caused by codirectional collisions with the transcription machinery

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

The complete genome sequence of Escherichia coli K-12

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3' end of the RNA intact and extruded

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Escherichia coli RNA polymerase mutants that enhance or diminish the SOS response constitutively expressed in the absence of RNase HI activity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

The RecF pathway of homologous recombination can mediate the initiation of DNA damage-inducible replication of the Escherichia coli chromosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Crystal structure of the GreA transcript cleavage factor from Escherichia coli

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Formation of an RNA primer for initiation of replication of ColE1 DNA by ribonuclease H

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

When polymerases collide: replication and the transcriptional organization of the E. coli chromosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Effects of chromosomal inversion on cell fitness in Escherichia coli K-12.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Molecular cloning and DNA sequence analysis of Escherichia coli priA, the gene encoding the primosomal protein replication factor Y.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Consequences of replication fork movement through transcription units in vivo

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Enzyme-catalyzed DNA unwinding: Studies on Escherichia coli rep protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Localization of an accessory helicase at the replisome is critical in sustaining efficient genome duplication

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

RNA polymerase mutations that facilitate replication progression in the rep uvrD recF mutant lacking two accessory replicative helicases

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Cooperation between translating ribosomes and RNA polymerase in transcription elongation

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

The helicases DinG, Rep and UvrD cooperate to promote replication across transcription units in vivo

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

UvrD and UvrD252 counteract RecQ, RecJ, and RecFOR in a rep mutant of Escherichia coli.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

DNA helicase activity of PcrA is not required for the displacement of RecA protein from DNA or inhibition of RecA-mediated strand exchange.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Escherichia coli DNA topoisomerase I inhibits R-loop formation by relaxing transcription-induced negative supercoiling.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

PcrA is an essential DNA helicase of Bacillus subtilis fulfilling functions both in repair and rolling-circle replication.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Molecular mechanism of transcription-repair coupling.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

Requirement for E. coli NusG protein in factor-dependent transcription termination

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

The rep mutation. IV. Slower movement of replication forks in Escherichia coli rep strains

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3467967

RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription

29 June 2018

1 reference

The transcription factor DksA prevents conflicts between DNA replication and transcription machinery

21 January 2018

1 reference

YabA of Bacillus subtilis controls DnaA-mediated replication initiation but not the transcriptional response to replication stress

21 January 2018

1 reference

The replicase sliding clamp dynamically accumulates behind progressing replication forks in Bacillus subtilis cells.

21 January 2018

1 reference

DNA knotting caused by head-on collision of transcription and replication

21 January 2018

1 reference

The replisome uses mRNA as a primer after colliding with RNA polymerase

21 January 2018

1 reference

Essentiality, not expressiveness, drives gene-strand bias in bacteria.

21 January 2018

1 reference

Genometric analyses of the organization of circular chromosomes: a universal pressure determines the direction of ribosomal RNA genes transcription relative to chromosome replication.

21 January 2018

1 reference

The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase.

21 January 2018

1 reference

Transcript cleavage factors from E. coli.

21 January 2018

1 reference

The DinG protein from Escherichia coli is a structure-specific helicase.

21 January 2018

1 reference

The Escherichia coli UvrD helicase is essential for Tus removal during recombination-dependent replication restart from Ter sites.

21 January 2018

1 reference

A fork-clearing role for UvrD.

21 January 2018

1 reference

The dynamic protein partnership of RNA polymerase inBacillus subtilis

21 January 2018

1 reference

Functionality of essential genes drives gene strand-bias in bacterial genomes.

21 January 2018

1 reference

Properties of the T4 bacteriophage DNA replication apparatus: The T4 dda DNA helicase is required to pass a bound RNA polymerase molecule

21 January 2018

1 reference

Regulation through the Secondary Channel—Structural Framework for ppGpp-DksA Synergism during Transcription

21 January 2018

1 reference

Transcription-induced deletions in Escherichia coli plasmids

21 January 2018

1 reference

Transcription-induced deletions in plasmid vectors: M13 DNA replication as a source of instability

31 March 2020

1 reference

DNA replication fork pause sites dependent on transcription

31 March 2020

1 reference

Direct restart of a replication fork stalled by a head-on RNA polymerase

31 March 2020

1 reference

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

31 March 2020

1 reference

Function of transcription cleavage factors GreA and GreB at a regulatory pause site

31 March 2020

1 reference

Host factor titration by chromosomal R-loops as a mechanism for runaway plasmid replication in transcription termination-defective mutants of Escherichia coli

31 March 2020

1 reference

31 March 2020

Identifiers

DOI

10.1038/NRMICRO2800

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22669220 AND SRC:MED&resulttype=core&format=json

3 February 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22669220 AND SRC:MED&resulttype=core&format=json

3 February 2020

PubMed publication ID

22669220

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22669220 AND SRC:MED&resulttype=core&format=json