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

ABSTRACT: 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).

ORGANISM(S): Escherichia coli

PROVIDER: GSE107329 | GEO | 2017/12/05

SECONDARY ACCESSION(S): PRJNA419769

REPOSITORIES: GEO

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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

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

Project description:The purpose of this experiment was to assess translation of mRNA after MazF expression to determine if cleavage events resulted in a loss in ribosome footprints.

2017-12-05 | GSE107328 | GEO

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

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

2017-12-05 | GSE107330 | GEO

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

| PRJNA419769 | ENA

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

Project description:E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis

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

Project description:E. coli MazF does not create specialized ribosomes that translate leaderless mRNAs, but instead blocks rRNA maturation and ribosome biogenesis [Ribo-Seq]

| PRJNA419768 | ENA

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

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

| PRJNA419767 | ENA

Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin

Project description:A crucial bacterial strategy to avoid killing by antibiotics is to enter a growth arrested state, yet the molecular mechanisms behind this process remain elusive. The conditional overexpression of MazF, the endoribonuclease toxin of the MazEF toxin-antitoxin system in Staphylococcus aureus, is one approach to induce bacterial growth arrest, but its targets remain largely unknown. We used overexpression of MazF and high-throughput sequence analysis following the exact mapping of non-phosphorylated transcriptome ends (nEMOTE) technique to reveal in vivo toxin cleavage sites on a global scale. We obtained a catalogue of MazF cleavage sites and unearthed an extended MazF cleavage specificity that goes beyond the previously reported one. We correlated transcript cleavage and abundance in a global transcriptomic profiling during mazF overexpression. We observed that MazF affects RNA molecules involved in ribosome biogenesis, cell wall synthesis, cell division and RNA turover and thus deliver a plausible explanation for how mazF overexpression induces stasis. We hypothesize that autoregulation of MazF occurs by directly modulating the MazEF operon, such as the rsbUVW genes that regulate the alternative SigB, including an observed cleavage site on the MazF mRNA that would ultimately play a role in entry and exit from bacterial stasis.

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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