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Escherichia coli K-12

ABSTRACT: Transcriptome analysis of sequence-specific RNA cleavage by Nitrosomonas europaea mazF in E. coli JM109

PROVIDER: PRJDB13096 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR351847_1.fastq.gz	Fastqsanger.gz
	DRR351847_2.fastq.gz	Fastqsanger.gz
	DRR351848_1.fastq.gz	Fastqsanger.gz
	DRR351848_2.fastq.gz	Fastqsanger.gz
	DRR351849_1.fastq.gz	Fastqsanger.gz

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RNA-seq for identifying toxin MazF and MqsR cleavage sites in toxin expression and subsequent recovery cultures of Escherichia coli (mRNA and ncRNA excluding rRNA)

Project description:Bacterial toxin-antitoxin systems are thought to help bacteria to reduce their metabolism in various stressful conditions. Many toxins of the bacterial toxin-antitoxin systems are ribonucleases. Such toxins have been mostly viewed as degraders of mRNA, however recently it was demonstrated that they are also capable of cleaving non-coding RNA. MazF toxin is also hypothesized to reprogram E. colis translational machinery. Current cDNA libraries are part of a project which aims to identify the major RNA cleavage sites (in mRNA, rRNA and regulatory non-coding RNA) of MazF and MqsR toxins in E. coli. We wanted to elaborate on the roles of MazF and MqsR in E. coli: is MazF really involved in reprogramming the translational machinery or is MazF, along with MqsR, just a robust cleaver of RNA? We extracted total RNA from cultures where the expression of MazF or MqsR was induced for 2h and from cultures that had been recovering from toxin production for 30 minutes; RNA from log phase culture was used as the control. We used strand specific random primed paired end RNA sequencing data to locate the major cleavage sites. To map the cleavage sites, we counted 5’ end stacks of forward reads in each genomic position and compared them with total coverage. MazF and MqsR cleave at specific recognition sequences, ˇACA and GˇC respectively, which allowed us to eliminate the false positives. One of our initial aims was also to look for irregular RNA ligation events following toxin expression, thus we used long, 300 base reads in sequencing.

2018-10-11 | E-MTAB-6993 | biostudies-arrayexpress

E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [RNA-seq]

Project description:The purpose of this experiment was to characterize MazF cleavage specificity and locations of cleavage genome-wide in E. coli and also identify any leaderless transcripts .To do this, MazF was expressed in a ΔmazF background and compared to an empty vector. rRNA-subtracted samples were used to assess cleavage in the mRNA, and total RNA samples were used to assess changes in the rRNA.

2017-12-05 | GSE107327 | GEO

DNA Microarray of Global Transcription Factor Mutant Reveals Membrane-Related Proteins Involved in n-Butanol Tolerance in Escherichia coli

Project description:We successfully isolated an E. coli strain harboring rpoD mutant B8 with 2% (v/v) butanol tolerance using global transcriptional machinery engineering approach. DNA microarrays were employed to assess the transcriptome profile of n-butanol tolerance strain B8 and control strain E. coli JM109. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.

2016-05-10 | GSE79305 | GEO

Stress-induced MazF-mediated proteins in Escherichia coli

Project description:Escherichia coli (E. coli) mazEF is an extensively studied stress-induced toxin-antitoxin (TA) system. The toxin MazF is an endoribonuclease that cleaves RNAs at ACA sites. Thereby, under stress the induced MazF generates a Stress induced Translation Machinery (STM), composed of MazF processed mRNAs and selective ribosomes that specifically translate the processed mRNAs. Here we performed a proteomic analysis of all the E. coli stress-induced proteins that are mediated through chromosomally borne mazF gene . We show that the mRNAs of almost all of them is characterized by the presence of an ACA site up to 100 nucleotides upstream to the AUG initiator. Thereby, under stressful conditions the induced MazF is processing mRNAs that are translated by STM. Furthermore, the presence of the ACA site far enough upstream (up to 100 nucleotides) to the AUG initiator may still permit translation by the canonical translation machinery. Thus, such dual translation mechanisms, enable under stress also to prepare proteins for immediate functions while coming back to normal growth conditions.

2019-02-25 | PXD010101 | Pride

Comparison of Escherichia coli K-12 tynA- with wild type Escherichia coli K-12

Project description:Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.

2015-09-30 | GSE65385 | GEO

Transcriptional expressions of Nitrosomonas europae after CeO2 nanoparticle exposure and 12-h recovery

Project description:To further explore the biotoxicity mechanisms of CeO2 nanoparticles (NPs) and the recovery strategies of the according impaired Nitrosomonas europaea (N. europaea, ATCC 19718) cells, a genome-sequenced model ammonia oxidizing bacterium (AOB) commonly detected in the activated sludge of biological wastewater treatment plants, the whole-genome microarray analysis was applied to retrieve the induced transcriptional responses, after their physiological and metabolic activities were evealed.

2018-11-28 | GSE122972 | GEO

Escherichia coli K-12

Project description:Time-series transcriptional profiling of MazF-induced E. coli populations

| PRJNA375104 | ENA

Transcriptome profile of Escherichia coli K12 MG1655 cells lacking selected genes

Project description:The aim of the study was to compare the transcriptome of E. coli K12 MG1655 cells lacking genes known to induce the Rtc RNA repair system, such as gor, mazF and srmB, to wild-type cells. In all cases, less than 1% of the genes were found to be differentially expressed.

2022-11-02 | GSE165008 | GEO

Escherichia coli str. K-12 substr. MG1655

Project description:Growth inhibition after MazF activation through specific alteration of cellular state rather than through near-indiscriminate RNA cleavage.

| PRJDB5742 | ENA

E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [5'OH-seq]

Project description:The purpose of this experiment was to characterize MazF cleavage specificity with single-nucleotide resolution by enriching and sequencing 5’-OH ends (a 5’-OH end is generated by MazF cleavage).

2017-12-05 | GSE107329 | GEO

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