Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of cells carrying Type II Csp231I restriction-modification (RM) system reveal the crosstalk between two unrelated transcription factors - C protein and Rac prophage repressor

ABSTRACT: Transcriptome analysis of cells carrying Type II Csp231I restriction-modification (RM) system reveal the crosstalk between two unrelated transcription factors - C protein and Rac prophage repressor

PROVIDER: PRJNA521391 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8545712_1.fastq.gz	Fastqsanger.gz
	SRR8545712_2.fastq.gz	Fastqsanger.gz
	SRR8545713_1.fastq.gz	Fastqsanger.gz
	SRR8545713_2.fastq.gz	Fastqsanger.gz
	SRR8545714_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Transcriptome analysis of cells carrying Type II Csp231I restriction-modification (RM) system reveal the crosstalk between two unrelated transcription factors - C protein and Rac prophage repressor

Project description:Our transcriptome analysis supported by other in vivo and in vitro assays showed that C protein can directly silence the RacR repressor and thus affect the Rac prophage-related genes.

2019-07-30 | GSE126248 | GEO

A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons

Project description:Bacterial genomes are shaped by cryptic prophages, which are viral genomes integrated into the bacterial chromosome. Escherichia coli genomes have 10 prophages on average. Though usually inactive, prophage genes can profoundly impact host cell physiology. Among the phage genes in the E. coli chromosome, there are several putative transcription factors (TFs). These prophage TFs are predicted to control only phage promoters, however their regulatory functions are not well characterized. The co-habitation of prophages and bacteria has led to conditions under which the majority of prophage genes are unexpressed, at least under normal growth conditions. We characterized a Rac prophage TF, YdaT, expression of which is normally inhibited by Rac TFs and, surprisingly, by the host global regulator OxyR. YdaT, when expressed, leads to a toxic phenotype manifested by drastic cell filamentation and cell death. We determined the binding sites and regulatory action for YdaT, finding two sites within the Rac locus, and one upstream of the host rcsA gene, which codes for the global regulator RcsA. The resulting increase in RcsA strongly impacts the bacterial RcsA/B regulon, which includes operons related to motility, capsule biosynthesis, colanic acid production, biofilm formation and cell division. Our results provide novel insights into the host’s genetic network, which appears to integrate YdaT in a complex manner, favoring its maintenance in the silenced state. The fact that the potentially-toxic YdaT locus remains unmutated suggests its importance and potential benefits for the host, which may appear under stress conditions that are not yet known.

2025-05-07 | PXD059580 | Pride

Transcriptome analyses of cells carrying the Type II Csp231I restriction-modification system reveal cross-talk between two unrelated transcription factors: C protein and the Rac prophage repressor.

Project description:Restriction-modification (R-M) systems represent an effective mechanism of defence against invading bacteriophages, and are widely spread among bacteria and archaea. In acquiring a Type II R-M system via horizontal gene transfer, the new hosts become more resistant to phage infection, through the action of a restriction endonuclease (REase), which recognizes and cleaves specific target DNAs. To protect the host cell's DNA, there is also a methyltransferase (MTase), which prevents DNA cleavage by the cognate REase. In some R-M systems, the host also accepts a cis-acting transcription factor (C protein), which regulates the counteracting activities of REase and MTase to avoid host self-restriction. Our study characterized the unexpected phenotype of Escherichia coli cells, which manifested as extensive cell filamentation triggered by acquiring the Csp231I R-M system from Citrobacter sp. Surprisingly, we found that the cell morphology defect was solely dependent on the C regulator. Our transcriptome analysis supported by in vivo and in vitro assays showed that C protein directly silenced the expression of the RacR repressor to affect the Rac prophage-related genes. The rac locus ydaST genes, when derepressed, exerted a toxicity indicated by cell filamentation through an unknown mechanism. These results provide an apparent example of transcription factor cross-talk, which can have significant consequences for the host, and may represent a constraint on lateral gene transfer.

| S-EPMC6765115 | biostudies-literature

Global transcriptional response of Clostridium difficile carrying the ϕCD38-2 prophage

Project description:We used RNA-seq to conduct a genome-wide transcriptomic analysis of the C. difficile strain R20291 carrying the newly introduced ϕCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and PTS subunits involved in glucose, fructose and glucitol/sorbitol uptake and metabolism. Also of note, the presence of ϕCD38-2 upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was the conserved phase-variable cell wall protein CwpV, which was upregulated by about 20-fold in the lysogen. This is the first study describing the global response of C. difficile to the presence of a newly introduced prophage.

2014-12-22 | GSE56818 | GEO

Rhizobium sp. RM strain:RM

Project description:Rhizobium sp. RM strain:RM Genome sequencing and assembly

| PRJNA641501 | ENA

Deinococcus sp. RM strain:RM

Project description:Deinococcus sp. RM strain:RM Genome sequencing and assembly

| PRJNA489992 | ENA

Global transcriptional response of Clostridium difficile carrying the M-OM-^UCD38-2 prophage

Project description:We used RNA-seq to conduct a genome-wide transcriptomic analysis of the C. difficile strain R20291 carrying the newly introduced M-OM-^UCD38-2 prophage. A total of 39 bacterial genes were differentially expressed in the R20291 lysogen, 26 of them being downregulated. Several of the regulated genes encode transcriptional regulators and PTS subunits involved in glucose, fructose and glucitol/sorbitol uptake and metabolism. Also of note, the presence of M-OM-^UCD38-2 upregulated the expression of a group of regulatory genes located in phi-027, a resident prophage common to most ribotype 027 isolates. The most differentially expressed gene was the conserved phase-variable cell wall protein CwpV, which was upregulated by about 20-fold in the lysogen. This is the first study describing the global response of C. difficile to the presence of a newly introduced prophage. Two strains (WT and lysogen) were subjected for RNA-seq analysis with two biological replicates each.

2014-12-22 | E-GEOD-56818 | biostudies-arrayexpress

Chromatin immunoprecipitation to map nucleosomes and H3 lysine 14 acetylation in two unrelated strains of yeast

Project description:Nucleosome mapping and histone H3 lysine 14 acetylation chromatin immuno-precipitation in two unrelated strains of yeast (BY and RM).

2009-08-29 | E-MEXP-1777 | biostudies-arrayexpress

Prophage Maintenance and mutations

Project description:Environmental Dependence on Prophage Maintenance

| PRJEB60436 | ENA

phi 1720a shiga toxin prophage

Project description:phi 1720a shiga toxin prophage

| PRJEB102386 | ENA