Expression analysis of an enrofloxacin and a tetracline resistant Escherichia coli strain
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ABSTRACT:
ORGANISM(S): Escherichia coli Escherichia coli str. K-12 substr. MG1655
PROVIDER: GSE57084 | GEO | 2014/04/26
SECONDARY ACCESSION(S): PRJNA245408
REPOSITORIES: GEO
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Project description:Comparison of the whole genome gene expression level of an enrofloxacin and tetracycline resistant E. coli strain with the wildtype it was derived from. The process of drug adaptation of E. coli MG1655 wildtype cells is further descibed in van der Horst, M, J.M. Schuurmans, M. C. Smid, B. B. Koenders, and B. H. ter Kuile (2011) in Microb. Drug Resist. 17:141-147. Resistance to amoxicillin was induced in E. coli by growth in the presence of stepwise increasing antibiotic concentrations. To investigate consequences of the aquisition of amoxicillin resistance the transcriptomic profile of sensitive and resistant cells was compared in the absence and presence of sub-inhibitory (0.25xMIC) amoxicillin concentrations was compared. Total RNA of 3 biological replicates of E. coli MG1655 wildtype cells and drug resistant cells cultured with (0.25xMIC) or without the drug was hybridized on a 12x135k custom designed microarraychip against one common reference.
2014-04-26 | E-GEOD-57084 | biostudies-arrayexpress
Project description:Comparison of the whole genome gene expression level of an amoxicillin resistant E. coli strain with the wildtype it was derived from. The process of amoxicillin adaptation of E. coli MG1655 wildtype cells is further descibed in van der Horst, M, J.M. Schuurmans, M. C. Smid, B. B. Koenders, and B. H. ter Kuile (2011) in Microb. Drug Resist. 17:141-147. Resistance to amoxicillin was induced in E. coli by growth in the presence of stepwise increasing antibiotic concentrations. To investigate consequences of the aquisition of amoxicillin resistance the transcriptomic profile of sensitive and resistant cells was compared in the absence and presence of sub-inhibitory (0.25xMIC) amoxicillin concentrations was compared.
2013-05-27 | GSE47221 | GEO
Project description:Comparison of the whole genome gene expression level of an amoxicillin resistant E. coli strain with the wildtype it was derived from. The process of amoxicillin adaptation of E. coli MG1655 wildtype cells is further descibed in van der Horst, M, J.M. Schuurmans, M. C. Smid, B. B. Koenders, and B. H. ter Kuile (2011) in Microb. Drug Resist. 17:141-147. Resistance to amoxicillin was induced in E. coli by growth in the presence of stepwise increasing antibiotic concentrations. To investigate consequences of the aquisition of amoxicillin resistance the transcriptomic profile of sensitive and resistant cells was compared in the absence and presence of sub-inhibitory (0.25xMIC) amoxicillin concentrations was compared. Total RNA of 3 biological replicates of E. coli MG1655 wildtype cells and amoxicillin resistant cells cultured with (0.25xMIC) or without amoxicillin was hybridized on a 12x135k custom designed microarraychip against one common reference.
2013-05-27 | E-GEOD-47221 | biostudies-arrayexpress
Project description:We studied the effects of three classes of antibiotics (amoxicillin, chlortetracycline and enrofloxacin ) on P. multocida transcriptome using custom oligonucleotide microarrays from Nimblegen systems. All the 2015 genes of Pm70 were spotted on the array and hybridizations were carried out with RNA isolated from three independent cultures of Pm70 grown in the presence or absence of sub-minimum inhibitory (sub-MIC) doses of antibiotics. Differentially expressed genes were identified by ANOVA and Dunnett’s test. Biological modeling of the differentially expressed genes (DE) was carried out based on Clusters of Orthologous (COG) groups and network analysis in Pathway Studio. Keywords: Response to sub-MIC antibiotics
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Project description:Escherichia coli (E. coli) urinary tract infections (UTIs) are becoming a serious problem both for pets and humans (zoonosis) due to the close contact and to the increasing resistance to antibiotics. Great progress has been made in the discovery of novel antibiotics to counteract E. coli pathogens. However, this huge progress has been undercut by the evolution of bacteria in the way of drug resistance. Enrofloxacin is one of the most efficient antibiotics against E. coli pathogens and there is considerable evidence that documents how this microorganism is becoming more resistant to this antibiotic and is developing multidrug resistance. This study has been performed in order to unravel the mechanism of induced enrofloxacin resistance in canine E. coli isolates that represent a good tool to study this pathology. For a comprehensive investigation about antibiotic resistance mechanisms, an E. coli isolate from urinary tract infection (UTI) was induced to grow under a concentration of 10 µg/ml of enrofloxacin. Proteins represent the main contributors to the mechanisms involved in antibiotic resistance in bacteria. Their abundance profile provides reliable information about the mechanisms involved in this process. Three biological replicates of control and resistant isolate have been analyzed both through 2D DIGE and shotgun proteomics. In our case, prior to perform the proteomics analysis, the screening with MS profiling of control and resistant isolates was performed highlighting the differences among strains and successfully clustering experimental strains according to PC analysis (PCA). The results clearly demonstrate differential profiles in peptide expression among clusters and between isolate and reference strain. According to these preliminary results, the protein profile of the resistant group was compared with the one of its sensitive counterpart by a proteomic analysis based on 2D-DIGE to separate proteins combined to MALDI MS analysis and database search to identify differentially expressed proteins. This analysis showed the modulation of 19 proteins between the two conditions. At the same time, another comparative proteomics investigation was also carried out by free-label nLC-MSE. This method has allowed the qualitative and quantitative analysis of total protein extracts of the two groups for the simultaneous screening of a larger number of proteins. A total of 57 differentially expressed proteins were identified and a comprehensive study on the proteins associated with enrofloxacin resistance was carried out. We classified these modulated proteins by their molecular functions and pathways where they are principally involved. This approach allowed to highlight some pathways that can be involved in an increased antibiotic resistance. Two major mechanisms were discovered. The first one was related to the stabilization of DNA structure through the up-regulation of Dsp protein. The second one was the downregulation of outer membrane protein W in order to reduce the membrane permeability to enrofloxacin. Discovered differentilally expressed proteins are principally involved in antibiotic resistance and linked to the oxidative stress response, to DNA protection and in membrane permeability. Moreover, since enrofloxacin is an inhibitor of DNA gyrase, the overexpression of DNA starvation/stationary phase protection protein (Dsp) could be a central point to discover the mechanism of this clone to counteract the effects of enrofloxacin. In parallel, the dramatic decrease of the synthesis of the outer membrane protein W, which represents one of the main gates for enrofloxacin entrance, could explain additional mechanism of E. coli defense against this antibiotic. The proteins differentially expressed could represent putative targets for the development of new strategies to counteract drug and multidrug resistance.
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Project description:We examined the chromosomal distribution of GFP-tagged Tus (Tus-GFP) in exponentially growing E. coli (KRX) using chromosome immunoprecipitation (ChIP)-Seq. Our ChIP-seq allowed delineation of a refined minimal replication fork trap within E. coli comprising two clusters of three Ter sites
2021-12-01 | GSE163680 | GEO
Project description:We studied the effects of three classes of antibiotics (amoxicillin, chlortetracycline and enrofloxacin ) on P. multocida transcriptome using custom oligonucleotide microarrays from Nimblegen systems. All the 2015 genes of Pm70 were spotted on the array and hybridizations were carried out with RNA isolated from three independent cultures of Pm70 grown in the presence or absence of sub-minimum inhibitory (sub-MIC) doses of antibiotics. Differentially expressed genes were identified by ANOVA and Dunnett’s test. Biological modeling of the differentially expressed genes (DE) was carried out based on Clusters of Orthologous (COG) groups and network analysis in Pathway Studio. Keywords: Response to sub-MIC antibiotics The experimental design included three biological replicate cultures of P. multocida grown in the absence or presence of sub-MIC antibiotics. Effects of antibiotics on the transcriptome with each antibiotic were determined by comparing the growth in the presence of antibiotic (treatment) to growth in the absence of antibiotic (control).
2009-09-01 | E-GEOD-12779 | biostudies-arrayexpress
Project description:The gut microbiota has been implicated in obesity and cardiometabolic diseases, although evidence in humans is scarce. We investigated how gut microbiota manipulation by antibiotics (7-day administration of amoxicillin, vancomycin, or placebo) affects host metabolism in 57 obese, prediabetic men. Vancomycin, but not amoxicillin, decreased bacterial diversity and reduced Firmicutes involved in short-chain fatty acid and bile acid metabolism, concomitant with altered plasma and/or fecal metabolite concentrations. Adipose tissue gene expression of oxidative pathways was upregulated by antibiotics, whereas immune-related pathways were downregulated by vancomycin. Antibiotics did not affect tissue-specific insulin sensitivity, energy/substrate metabolism, postprandial hormones and metabolites, systemic inflammation, gut permeability, and adipocyte size. Importantly, energy harvest, adipocyte size, and whole-body insulin sensitivity were not altered at 8-week follow-up, despite a still considerably altered microbial composition, indicating that interference with adult microbiota by 7-day antibiotic treatment has no clinically relevant impact on metabolic health in obese humans. This randomized, placebo-controlled, double-blind study had a 3-armed parallel design. Overweight/obese participants were randomized to oral intake of amoxicillin, vancomycin or placebo for 7 consecutive days. After an overnight fast, subcutaneous adipose tissue biopsies were taken that were subjected to gene expression profiling by array.
2016-07-15 | E-GEOD-76003 | biostudies-arrayexpress
Project description:As in Eukaryotes, bacterial genomes are not randomly folded. Bacterial genetic information is generally carried on a circular chromosome with a single origin of replication from which two replication forks proceed bidirectionaly towards the opposite terminus region. Here we investigate the higher-order architecture of the Escherichia coli genome, showing its partition into two structuraly distinct entities by a complex and intertwined network of contacts: the replication terminus (ter) region and the rest of the chromosome. Outside ter, the condensin MukBEF and the ubiquitous nucleoid-associated protein (NAP) HU promote DNA contacts in the megabase range. Within ter, the MatP protein prevents MukBEF activity and contacts are restricted to ~280 kb creating a domain with distinct structural properties. We also show how other NAPs contribute to nucleoid organization, such as H-NS that restricts short-range interactions. Combined, these results reveal the contributions of major, evolutionary conserved proteins in a bacterial chromosome organization.
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Project description:Paper abstract : The Escherichia coli SMC complex, MukBEF, interacts with the ParC subunit of topoisomerase IV (TopoIV), consistent with sequential roles in chromosome unlinking and segregation. Although clusters of MukBEF molecules are normally associated with the chromosome replication origin region (ori), we demonstrate their association with the replication termination region (ter), which is enhanced when ATP hydrolysis by MukB is impaired. We show that MukBEF interacts in vivo and in vitro with MatP, which binds matS sites in ter. The MatP-MukBEF interaction limits the stable association of MukBEF complexes with ter and the availability of functional TopoIV during decatenation of sister ters. The MukBEF-TopoIV interaction is influenced by the nucleotide state of MukBEF. The combined action of MukBEF and MatP helps position MukBEF clusters in relation to the chromosome, thereby, influencing chromosome organization and segregation. Finally, we demonstrate that the regulated sequential action of TopoIV and MukBEF promotes chromosome decatenation and segregation.
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