Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (RNA-seq dataset)

ABSTRACT: The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (RNA-seq dataset)

PROVIDER: PRJNA625287 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR11544569.fastq.gz	Fastqsanger.gz
	SRR11544570.fastq.gz	Fastqsanger.gz
	SRR11544571.fastq.gz	Fastqsanger.gz
	SRR11544572.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics

Project description:The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics

| PRJNA625281 | ENA

The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (ChIP-seq dataset)

Project description:The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (ChIP-seq dataset)

| PRJNA625288 | ENA

The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (RNA-seq dataset)

Project description:The regulatory roles of proteins associating with DNA-dependent RNA polymerase (RNAP) during transcription elongation are poorly characterized in bacteria. A forward genetic selection for Caulobacter crescentus cell cycle mutants revealed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR associates with promoters and coding sequences (CDSs) and tracks with active RNAP. Loss of TrcR causes a cell division cycle and growth defect and an insufficiency in the essential cell cycle regulator CtrA. TrcR also protects cells from the quinolone antibiotic nalidixic acid that induces a multi-drug efflux pump and from the RNAP inhibitor rifampicin (Rif) that prevents transcription elongation. TrcR interacts biochemically and genetically with RNAP and no longer associates with chromatin when RNAP is inhibited with Rif. We show that these TrcR functions and its RNAP-dependent chromatin recruitment are conserved in symbiotic Sinorhizobium sp. and pathogenic Brucella sp., indicating that TrcR represents a new antibiotic target.

2021-02-03 | GSE148653 | GEO

The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (ChIP-seq dataset)

2021-02-03 | GSE148652 | GEO

Protection of the human gut microbiome against antibiotics

Project description:Protection of the human gut microbiome against antibiotics

| PRJEB12391 | ENA

The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics

Project description:This SuperSeries is composed of the SubSeries listed below.

2021-02-03 | GSE148654 | GEO

The DUF1013 protein TrcR tracks with RNA polymerase to control the bacterial cell cycle and protect against antibiotics.

Project description:How DNA-dependent RNA polymerase (RNAP) acts on bacterial cell cycle progression during transcription elongation is poorly investigated. A forward genetic selection for Caulobacter crescentus cell cycle mutants unearthed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR promotes the accumulation of the essential cell cycle transcriptional activator CtrA in late S-phase but also affects transcription at a global level to protect cells from the quinolone antibiotic nalidixic acid that induces a multidrug efflux pump and from the RNAP inhibitor rifampicin that blocks transcription elongation. We show that TrcR associates with promoters and coding sequences in vivo in a rifampicin-dependent manner and that it interacts physically and genetically with RNAP. We show that TrcR function and its RNAP-dependent chromatin recruitment are conserved in symbiotic Sinorhizobium sp. and pathogenic Brucella spp Thus, TrcR represents a hitherto unknown antibiotic target and the founding member of the DUF1013 family, an uncharacterized class of transcriptional regulators that track with RNAP during the elongation phase to promote transcription during the cell cycle.

| S-EPMC7923619 | biostudies-literature

Fibroblast-tracks are topographical cues that direct cancer cell migration

Project description:Fibroblasts rely on adhesive structures to migrate. It is generally thought that adhesive structures disassemble once at the rear of the cell to release the cell and allow further movement. However, a significant portion of adhesions is not disassembled and is instead left on the substrate. We observed that virtually all the non-resorbed adhesions remain connected to the substrate by the means of integrin β5. Forward cell migration results in plasma membrane pulling giving rise to tubular structures that are then left on the ground, forming a network of lipid tracks that persist for several days, thus altering substrate’s topography. Cancer cells of different origin exploit fibroblast-tracks as migration railways. The adhesion of cancer cells along tracks is not mediated by focal adhesions, but rather by frustrated clathrin-coated structures (CCSs). Analysis of the composition of track generated by cancer associated fibroblasts allowed to identify integrin αv as the receptor on cancer cells responsible for track recognition. Some cancer cell lines are not able to perform durotaxis (rigidity driven migration), while fibroblasts are very good at it. We thus tested whether, in the presence of fibroblast-tracks, non-durotactic cancer cells would become durotactic by following tracks and this was indeed the case. Hence, fibroblast-tracks are a novel structure capable of physically directing cell migration of different cell types.

2023-09-22 | PXD034091 | Pride

Mode of action characterization of antibiotics using expression profile fingerprints generated by RNA-sequencing technology

Project description:RNA-seq based transcriptome profiling allows a detailed molecular analysis of the E.coli transcriptome (~4200 genes) after perturbation with different antibiotics. Transcriptome fingerprints enable the identification of gene and pathway level responses to treatment to derive a mechanistic understanding of antibiotics mode of action and to differentiate antibiotics. For this goal, treatment has to be performed in a short time period and with sublethal concentrations of the antibiotics. Sublethal concentrations were chosen based on the EC90 concentration of the antibiotic necessary to change the cellular morphology compared to control conditions. Conclusions: Our study represents the first detailed analysis of E.coli transcriptomes after treatment with different antibiotics, with biologic replicates, generated by RNA-seq technology. The experimental design and data analysis reported here should provide a framework for comparative investigations of expression profiles of known and novel antibiotics. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2019-03-25 | GSE110137 | GEO

BAMscale: quantification of DNA sequencing peaks and generation of scaled coverage tracks

Project description:We present a tool for processing NGS DNA-seq BAM files to quantify peaks and create coverage tracks from ChIP-seq, NS-seq, ATAC-seq, OK-seq, END-seq and replication timing data

2020-05-17 | GSE131417 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data