Analysis of the stress response after induction of the dormancy-inducing membrane toxin TisB in Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA1076485 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27966600.fastq.gz | Fastqsanger.gz | |||
| SRR27966601.fastq.gz | Fastqsanger.gz | |||
| SRR27966602.fastq.gz | Fastqsanger.gz | |||
| SRR27966603.fastq.gz | Fastqsanger.gz | |||
| SRR27966604.fastq.gz | Fastqsanger.gz |
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Project description:Protein aggregates occur in all living cells due to misfolding of proteins. In bacteria, protein aggregation is associated with cellular inactivity, which is related to dormancy and tolerance to stressful conditions, including the exposure to antibiotics. In Escherichia coli, the membrane toxin TisB is an important factor for dormancy and antibiotic tolerance upon DNA damage mediated by the fluoroquinolone antibiotic ciprofloxacin. Here, we show that TisB provokes protein aggregation in response to ciprofloxacin. The stress response and TisB-dependent protein aggregates are analyzed by LC-MS.
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Project description:Bacterial antibiotic resistance is as a serious health problem. Antibiotic resistance appears either because of mutations or as a result of a bacteria dormant state without heritable genetic change. This non-growing state allows bacteria to survive antibiotic treatment. The mechanisms of entrance to the bacterial dormant state are unknown. It has been suggested that toxin-antitoxin systems (TASs) are possible controlling factors for cell dormancy. In Staphylococcus aureus, the role of TASs genome-wide and their link to the dormancy induction mechanisms has not been investigated in detail. In this study, we analyzed the role of MazF toxin on transcriptome, translatome and proteome of S. aureus using RNA-Seq, Ribo-Seq and quantitative proteomics. We characterized the correlation between transcription, translation, and protein levels, and demonstrated that the MazF endonuclease decreases translation directly by cleaving mRNA, and indirectly, by decreasing translation factors and by promoting ribosome hibernation. Thus, MazF represses transcription and translation of many genes rather than a particular set of genes. Nevertheless, several specific pathways affected by MazF were identified: we demonstrated that cell wall thickness is increased and cell division is decreased upon MazF induction. MazF cleaves mRNA in vivo, creating stop-less transcripts and stalled ribosomes. These stalled ribosomes are rescued by SsrA-system, which is activated upon MazF induction. Finally, we described the overall impact of MazF on S. aureus metabolism, and propose one of the mechanisms by which MazF may induce bacterial dormancy.
2020-12-28 | GSE155036 | GEO
Project description:We assume that adaptation to tisB expression is driven by cellular stress responses. It has already been observed that expression of type I toxins leads to up-regulation of several stress-related genes. To reveal the response to TisB on a global scale, transcriptome analysis of MG1655 p0SD-tisB was performed.
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Project description:Solid cancers frequently relapse with distant metastasis, despite local and systemic treatment. Cellular dormancy has been identified as an important mechanism underlying drug resistance enabling late relapse. Therefore, relapse from invisible, minimal residual cancer of seemingly disease-free patients call for in vitro models of dormant cells suited for drug discovery. Here, we explore dormancy-inducing 3D engineered matrices, which generate mechanical confinement and induce growth arrest and survival against chemotherapy in cancer cells. We characterized the dormant phenotype of solitary cells by P-ERKlow:P-p38high dormancy signaling ratio, along with Ki67− expression. As underlying mechanism, we identified stiffness-dependent nuclear localization of the four-and-a-half LIM domain 2 (FHL2) protein, leading to p53-independent high p21Cip1/Waf1 nuclear expression, validated in murine and human tissue. Suggestive of a resistance-causing role, cells in the dormancy-inducing matrix became sensitive against chemotherapy upon FHL2 down-regulation. Thus, our biomaterial-based approach will enable systematic screens for previously unidentified compounds suited to eradicate potentially relapsing dormant cancer cells.
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Project description:Mycobacterium tuberculosis is the causative agent of tuberculosis, a disease that affects one-third of the world’s population. The sole extant vaccine for tuberculosis is the live attenuated Mycobacterium bovis bacille Calmette-Guerin (BCG). We examined 13 representative BCG strains from around the world to ascertain their ability to express DosR-regulated dormancy antigens. These are known to be recognized by T-cells of M. tuberculosis infected individuals, especially those harboring latent infections. Differences in expression of these antigens could be valuable for use as diagnostic markers to distinguish BCG vaccination from latent tuberculosis. We determined that all BCG strains were defective for induction of two dormancy genes, narK2 (Rv1737c) and narX (Rv1736c). NarK2 is known to be necessary for nitrate respiration during anaerobic dormancy. Analysis of the narK2/X promoter region revealed a base substitution mutation in all tested BCG strains and M. bovis in comparison to the M. tuberculosis sequence. We also show that nitrate reduction by BCG strains during dormancy was greatly reduced compared to M. tuberculosis and varied between tested strains. Several dormancy regulon transcriptional differences were also identified among the strains, as well as variation in their growth and survival. These findings demonstrate defects in DosR regulon expression during dormancy and phenotypic variation between commonly used BCG vaccine strains. Keywords: Comparison of induction of a subset of genes between various mycobacterial strains.
2008-05-03 | GSE11315 | GEO
Project description:Bacterial antibiotic resistance is as a serious health problem. Antibiotic resistance appears either because of mutations or as a result of a bacteria dormant state without heritable genetic change. This non-growing state allows bacteria to survive antibiotic treatment. The mechanisms of entrance to the bacterial dormant state are unknown. It has been suggested that toxin-antitoxin systems (TASs) are possible controlling factors for cell dormancy. In Staphylococcus aureus, the role of TASs genome-wide and their link to the dormancy induction mechanisms has not been investigated in detail. In this study, we analyzed the role of MazF toxin on transcriptome, translatome and proteome of S. aureus using RNA-Seq, Ribo-Seq and quantitative proteomics. We characterized the correlation between transcription, translation, and protein levels, and demonstrated that the MazF endonuclease decreases translation directly by cleaving mRNA, and indirectly, by decreasing translation factors and by promoting ribosome hibernation. Thus, MazF represses transcription and translation of many genes rather than a particular set of genes. Nevertheless, several specific pathways affected by MazF were identified: we demonstrated that cell wall thickness is increased and cell division is decreased upon MazF induction. MazF cleaves mRNA in vivo, creating stop-less transcripts and stalled ribosomes. These stalled ribosomes are rescued by SsrA-system, which is activated upon MazF induction. Finally, we described the overall impact of MazF on S. aureus metabolism, and propose one of the mechanisms by which MazF may induce bacterial dormancy.
Samples in dupicates RNA-Seq and Ribo-Seq of WT with pRAB11 vector, DELTAmazEF with pRAB11, and DELTAmazEF with pRAB11 vector expressing inducible MazF. All samples submited to RNA-Seq and Ribo-Seq.
ATc induction was done for 10 min. For total protein extraction 25 ml of cultures with OD600 of 0.7 were collected and washed 3 times with 1 ml of Phosphate-buffered saline (PBS) buffer. Cells were lysed in the presence of 400 microl of lysis buffer (LB) (PBS, 200 microg/ml lysostaphin (AMBI, LLC), 200 microg/ml DNAse I, protease inhibitors (Roche)) for 20 min at 37 C, chilled on ice, and sonicated 10 times with 30-sec cycles using Cell Disrupter B-30 (Branson). Extracts were clarified by centrifugation for 10 min at 14000 g 4 C. Total protein concentration was measured in supernatants by the Bradford protein assay. This method permitted to obtain of about 1 mg of total protein with a concentration of about 2.5-3.0 mg/ml. Samples were mixed with Laemmli Sample Buffer (SB) and analyzed by SDS polyacrylamide gel electrophoresis (SDS-PAGE) followed by Coomassie Blue staining or western blot.
Tandem Mass Tags Mass Spectrometry (TMT-MS2) was done at the Proteome Sciences R&D GmbH&Co KG. Samples were digested with trypsin, TMT-labelled, and subjected to Strong Cation Exchange (SCX) chromatography. Each fraction was analyzed by nano LC-MS/MS and MS2 (Thermo LTQ-Orbitrap Velos mass spectrometer). Data were analyzed with the MASCOT and SEQUEST databases. Filtering, normalization and quantification was achieved using Proteome Discoverer (Thermo Scientific).
In the raw data sample with WT with pRAB11 vector expressing inducible MazF is present, which is not used for the analysis.
2020-08-26 | MSV000086018 | MassIVE
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