High resolution chemical-genomics identifies targets for synergistic antibiotics with aztreonam
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PROVIDER: PRJEB51785 | ENA |
REPOSITORIES: ENA
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Project description:A whole genome screen was used to assay every gene of Escherichia coli strain BW25113 to identify genes involved in susceptibility to the monobactam (beta-lactam) antibiotic aztreonam. The methodology has been called TraDIS-Xpress, and is a version of TraDIS or Tn-seq. A transposon mutant library consisting of several hundred thousand mutants was constructed using a Tn5-derived transposon incorporating an inducible outward transcribing promoter. All the mutants were grown in LB broth cultures supplemented with aztreonam at 2 x, 1 x, 0.5 x and 0.25 x MIC with induction of the transposon promoter using 0.2 mM IPTG or 1 mM IPTG or without induction. Following growth, mutants with increased susceptibility show reduced numbers and those with reduced susceptibility show increased numbers. Each condition was performed in duplicate. The methodology enable genes to be assayed by insertional inactivation or by changes in expression. Expression changes result from altered transcription from upstream transposon insertions transcribing into the gene, or downstream insertions transcribing into the gene in the reverse direction leading to RNA interference through the generation of reverse and complementary RNA. Thus, essential genes into which transposon insertions are not tolerated may be assayed also by changes in numbers of upstream or downstream insertion mutants. Changes to high throughput sequencing protocols permit the generation of nucleotide sequence reads from the known transposon sequences into the surrounding insertion site for all the mutants in the mixture simultaneously. Matching the sequence of the reads to the genome nucleotide sequence of E. coli BW25113 then allows the precise locations of all the transposon insertion sites of all the mutants to be mapped simultaneously. The relative changes in mutants between control (without) and selective condition (with aztreonam) then indicates which genes are involved in susceptibility. The numbers of sequence reads that match is reflected by the number of mutants, and so the degree of susceptibility can also be estimated.
2024-07-06 | E-MTAB-11576 | biostudies-arrayexpress
Project description:Microarrays allow us to monitor the change in transcription of every gene in the genome in response to a change in cellular state. We use cDNA microarrays to measure the response of E. coli to 13 different antibiotics and 3 synergistic combinations. Hierarchichal clustering reveals 4 distinct classes of antibiotics distinguished by their modes of action, and allows us to predict the mechanism for promethazine, a drug whose mode of action has not previously been established. The expression profiles of the synergistic combinations exhibit a complex relationship between the two component antibiotics, with similarity to one of the two drugs, as well as a surprising number of new gene responses exhibited by E. coli in response to neither drug alone. The subset of drugs which act in synergy with each other suggests that only very specific combination of mechanisms give rise to synergistic behavior. Keywords: stress response, antibiotic response, synergy
2008-02-12 | GSE10440 | GEO
Project description:Microarrays allow us to monitor the change in transcription of every gene in the genome in response to a change in cellular state. We use cDNA microarrays to measure the response of E. coli to 13 different antibiotics and 3 synergistic combinations. Hierarchichal clustering reveals 4 distinct classes of antibiotics distinguished by their modes of action, and allows us to predict the mechanism for promethazine, a drug whose mode of action has not previously been established. The expression profiles of the synergistic combinations exhibit a complex relationship between the two component antibiotics, with similarity to one of the two drugs, as well as a surprising number of new gene responses exhibited by E. coli in response to neither drug alone. The subset of drugs which act in synergy with each other suggests that only very specific combination of mechanisms give rise to synergistic behavior. Keywords: stress response, antibiotic response, synergy Each array has two spots to monitor the response of E coli to one of the treatments, and two control spots (ie no treatment). These are background corrected, normalized for total intensity, and then the average volume difference is calculated. Each treatment has two replicates, and the result is average across these two replicates. Our final processed data is a relative volume difference, in which the aforementioned volume difference is divided by an estimate of the error in the data. This relative volume difference gives us greater confidence that the changes we see are real. Any relative volume difference >= 2 or <= -2 (ie where the absolute volume difference is twice as much as the estimated error or more) is considered to be significant. Total of 68 hybridizations: 17 samples X 2 replicates for each sample X (1 sample + 1 control for each replicate)
2008-02-12 | E-GEOD-10440 | biostudies-arrayexpress
Project description:Recurrent epidemics of methicillin-resistant Staphylococcus aureus (MRSA) have illustrated that the effectiveness of antibiotics in clinical application is rapidly fading. A feasible approach is to combine natural products with existing antibiotics to achieve an antibacterial effect. In this molecular docking study, we found that theaflavin (TF) preferentially binds the allosteric site of penicillin-binding protein 2a (PBP2a), inducing the PBP2a active site to open, which is convenient for β-lactam antibiotics to treat MRSA infection, instead of directly exerting antibacterial activity at the active site. Subsequent TMT-labeled proteomics analysis showed that TF treatment did not significantly change the landscape of the Staphylococcus aureus (S. aureus) USA300 proteome.Checkerboard dilution tests and kill curve assays were performed to validate the synergistic effect of TF and ceftiofur, and the fractional inhibitory concentration index (FICI) was 0.1875.Our findings provide a potential therapeutic strategy to combine existing antibiotics with natural products to resolve the prevalent infections of multidrug-resistant pathogens.
2022-11-09 | PXD037668 | Pride
Project description:Synergistic chemical combination for cell cycle restoration in senescent cells via FoxM1 and E2F1 activation
| PRJNA737407 | ENA
Project description:Genomics of rapid adaptation to antibiotics: Convergent evolution and scalable sequence amplification.
| PRJEB4687 | ENA
Project description:Impact of antibiotics (T2) or antibiotics in combination with stress (T3) in early life on intestinal functioning in pigs on 8, 55, 176 days in jejunum and ileum (blood only day 8) and control pigs (T1) 4 pools consisting of 16 animals were generated per time-point (day 8, 55, 176 after birth) per treatment (T1;control, T2; antibiotics, T3; antibiotics+stress)
2014-09-01 | E-GEOD-53170 | biostudies-arrayexpress
Project description:The emergence of multidrug resistant tuberculosis and the increasing level of resistance urges the search for alternative drugs in treatment. Several neuroleptics, like thioridazine, reveal activity against Mycobacterium tuberculosis. Thioridazine was even successfully applied in compassionate therapy of extensively drug resistant tuberculosis in patients when added to other second and third line antibiotics. The synergistic effects between thioridazine and other anti-tuberculosis drugs is usually assigned to the inhibition of efflux pumps by thioridazine. Using an unbiased proteomic approach, we set out to unravel the molecular mechanism of this potential new anti-tuberculosis component by examining the impact of continuous thioridazine exposure on the proteome of M. tuberculosis. We discovered that under the influence of thioridazine several proteins involved in the maintenance of the cell wall permeability barrier are differentially regulated, while none of the known mycobacterial efflux pumps was differentially regulated on the protein level. By assessing accumulation of fluorescent dyes in M. tuberculosis over time, we demonstrated that long-term drug exposure of M. tuberculosis indeed affected the mycobacterial cell envelope and increased the permeability towards both hydrophilic and hydrophobic compounds. Furthermore, we demonstrated that treatment of M. tuberculosis with thioridazine altered the composition of the plasma membrane. Thioridazine induced an increase in cell envelope permeability, and thereby the enhanced uptake of compounds, this could explain the previously reported synergistic effects between thioridazine and other anti-tuberculosis drugs. Although the hypothesis of higher intercellular drug concentrations by THZ has not changed in this study, the more exact knowledge on its mode of action is a major step forward. This new insight in the molecular mechanism of this anti-tuberculosis compound could facilitate further development of this class of drugs for application in drug therapy of multidrug resistant tuberculosis. In fact, the efficacy of many existing drugs could be improved significantly.
2016-07-06 | PXD001208 | Pride
Project description:Impact of antibiotics (T2) or antibiotics in combination with stress (T3) in early life on intestinal functioning in pigs on 8, 55, 176 days in jejunum and ileum (blood only day 8) and control pigs (T1)
2014-09-01 | GSE53170 | GEO
Project description:Sequencing used for quality control of a chemical genomics screen in Salmonella enterica
| PRJEB61095 | ENA