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High-throughput suppressor selection of a type I toxin-antitoxin system in Helicobacter pylori

ABSTRACT: High-throughput suppressor selection of a type I toxin-antitoxin system in Helicobacter pylori

PROVIDER: PRJNA497299 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8073130_1.fastq.gz	Fastqsanger.gz
	SRR8073130_2.fastq.gz	Fastqsanger.gz
	SRR8073131_1.fastq.gz	Fastqsanger.gz
	SRR8073131_2.fastq.gz	Fastqsanger.gz
	SRR8073132_1.fastq.gz	Fastqsanger.gz

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High-throughput suppressor selection of a type I toxin-antitoxin system in Helicobacter pylori

Project description:As the number of bacterial genomes and transcriptomes increases, so does the number of newly identified toxin–antitoxin (TA) systems. However, their functional characterization remains challenging, often requiring the use of overexpression vectors that can lead to misinterpretations. To fill this gap, we developed a systematic approach called FASTBAC-Seq (Functional AnalysiS of Toxin–Antitoxin Systems in BACteria by Deep Sequencing). Combining life/death phenotypic selection with next-generation sequencing, FASTBAC-Seq allows the rapid identification of loss-of- function (toxicity) mutations in toxin-encoding genes belonging to TA loci with nucleotide resolution. Here, we apply this new tool to study aapA3/IsoA3, a member of a new family of type I TA systems hosted on the chromosome of the major human gastric pathogen Helicobacter pylori.

2019-08-30 | GSE121423 | GEO

Profiling the intragenic toxicity determinants of the hok/Sok toxin-antitoxin system

Project description:Here, we adapted and improved our FASTBAC-Seq method originally designed in Helicobacter pylori to investigate T1TAs in the model organism Escherichia coli. Our approach combines a life and death selection with deep-sequencing to assess the killing capability of a toxin and obtain an overview of single-nucleotide substitutions suppressing the toxin expression or activity in absence of its antitoxin. As a proof of concept, we revisited the regulation of the plasmidic hok/Sok T1TA system.

2022-10-06 | GSE207195 | GEO

E.coli toxin-antitoxin systems

Project description:E.coli toxin-antitoxin systems

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Staphylococcus aureus toxin-antitoxin system

Project description:Type I toxin-antitoxin (TA) systems are widespread genetic modules in bacterial genomes. They express toxic peptides whose overexpression leads to growth arrest or cell death, whereas antitoxins regulate the expression of toxins, acting as labile antisense RNAs. The Staphylococcus aureus (S. aureus) genome contains and expresses several functional type I TA systems, but their biological functions remain unclear. Here we addressed and challenged experimentally, by proteomics, if a type I TA system, the SprF1/SprG1 pair, influences the overall gene expression in S. aureus. Deleted and complemented S. aureus strains were analyzed for their proteomes, both intracellular and extracellular, during growth. Comparison of intracellular proteomes between the strains points on SprF1 antitoxin as an agent downregulating protein expression. In the strain naturally expressing the SprG1 toxin, cytoplasmic proteins are excreted into the medium, but this is not due to unspecific cell leakages. Such toxin-driven release of the cytoplasmic proteins may modulate the host inflammatory response that, in turn, may amplify the S. aureus infection spread.

2021-07-05 | PXD023449 | Pride

Mechanism of phage sensing and abortion by toxin-antitoxin-chaperone systems (HDX-MS)

Project description:Toxin-antitoxins (TAs) are prokaryotic two-gene systems comprised of a toxin neutralised by an antitoxin. Toxin-antitoxin-chaperone (TAC) systems additionally include a SecB-like chaperone that stabilises the antitoxin by recognising its chaperone addiction (ChAD) element. TACs have been shown to mediate antiphage defence, but the mechanisms of viral sensing and restriction are unexplored. Here we tried to find the epitope between SecB and gpV with HDX-MS.

2024-03-14 | PXD050182 | Pride

Growth control switch by a DNA damage-inducible toxin-antitoxin system in Caulobacter

Project description:Bacterial toxin-antitoxin systems (TASs) are thought to respond to various stresses, often inducing growth-arrested (persistent) sub-populations of cells whose housekeeping functions are inhibited. However, it is not always clear whether specific targets of orthologous RNAse toxins are responsible for their phenotypic effect, which has made it difficult to accurately place the multitude of TASs within cellular and adaptive regulatory networks. Here we show that the TAS HigBA can promote and inhibit bacterial growth dependent on the dosage of HigB, a toxin regulated by the DNA damage (SOS) repressor LexA in addition to its antitoxin HigA, and the target selectivity of HigBâs mRNA cleavage activity. HigB reduced the expression of an efflux pump that is toxic to a polarity control mutant, cripples the growth of cells lacking LexA and targets the cell cycle circuitry. Thus, TASs can have outcome switching activity in bacterial adaptive (stress) and systemic (cell cycle) networks. DNA binding of the antitoxin HigA and the SOS regulator LexA was analysed by chromatin immunoprecipitation-deep sequencing, and found to overlap at only one locus, the HigBA TA system promoter

2016-02-17 | E-GEOD-76721 | biostudies-arrayexpress

HipBA toxin-antitoxin system Caulobacter crescentus.

Project description:Antibiotic persistence is a transient phenotypic state during which a bacterium can withstand otherwise lethal antibiotic exposure or environmental stresses. In Escherichia coli, persistence is promoted by the HipBA toxin-antitoxin system. The HipA toxin functions as a serine/threonine kinase that inhibits cell growth, while the HipB antitoxin neutralizes the toxin. E. coli HipA inactivates the glutamyl-tRNA synthetase GltX, which inhibits translation and triggers the highly conserved stringent response. Although hipBA operons are widespread in bacterial genomes, it is unknown if this mechanism is conserved in other species. Here we describe the functions of three hipBA modules in the alpha-proteobacterium Caulobacter crescentus. The HipA toxins have different effects on growth and macromolecular syntheses, and they phosphorylate distinct substrates. HipA1 and HipA2 contribute to antibiotic persistence during stationary phase by phosphorylating the aminoacyl-tRNA synthetases GltX and TrpS. The stringent response regulator SpoT is required for HipA-mediated antibiotic persistence, but persister cells can form in the absence of all hipBA operons or spoT, indicating that multiple pathways lead to persister cell formation in C. crescentus.

2020-02-06 | PXD015525 | Pride

Global analysis of the specificities and targets of endoribonucleases from E. coli toxin-antitoxin systems

Project description:The purpose of this study was to identify the RNA cleavage targets and specificities of 9 endoribonuclease toxins from toxin-antitoxin systems in E. coli MG1655.

2021-07-13 | GSE179607 | GEO

Growth control switch by a DNA damage-inducible toxin-antitoxin system in Caulobacter

Project description:Bacterial toxin-antitoxin systems (TASs) are thought to respond to various stresses, often inducing growth-arrested (persistent) sub-populations of cells whose housekeeping functions are inhibited. However, it is not always clear whether specific targets of orthologous RNAse toxins are responsible for their phenotypic effect, which has made it difficult to accurately place the multitude of TASs within cellular and adaptive regulatory networks. Here we show that the TAS HigBA can promote and inhibit bacterial growth dependent on the dosage of HigB, a toxin regulated by the DNA damage (SOS) repressor LexA in addition to its antitoxin HigA, and the target selectivity of HigB’s mRNA cleavage activity. HigB reduced the expression of an efflux pump that is toxic to a polarity control mutant, cripples the growth of cells lacking LexA and targets the cell cycle circuitry. Thus, TASs can have outcome switching activity in bacterial adaptive (stress) and systemic (cell cycle) networks.

2016-02-17 | GSE76721 | GEO

Stress induces the transcription of toxin-antitoxin systems but does not activate toxin

Project description:Stress induces the transcription of toxin-antitoxin systems but does not activate toxin

| PRJNA593049 | ENA