Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA122555 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: This study aimed to identify the genes regulated by plasmid-encoded regulator C (PerC). Whole transcriptomes of WT typical enteropathogenic E. coli (tEPEC) strains E2348/69 and coisogenic null-perC mutant JPEP22 were analyzed to identify and quantify differentially expressed genes. Methods: RNA was isolated from the WT and null-perC mutant strains and RNA integrity (RIN) was determined to be 10 out of possible 10 for all samples by Aligent Bioanalyzer. rRNA was depleted and resulting mRNA was reverse-transcribed into cDNA. Libraries were multiplexed for discrimination between libraries, barcoded for sequencing, and amplified with random hexamers for 15 PCR cycles. Transcripts were sequenced for 50 bases in single-end fashion within one lane of an Illumina Hiseq 2000 flow cell. This yielded roughly 30 million reads per sample. Results: Differential gene expression (DGE) analysis showed that 157 genes were statistically significantly regulated using a false-discovery rate (FDR) of 10% (q ≤ 0.10). Of these genes, the perC-mutant strain had far greater transcripts for the fim operon genes, fewer transcripts of nitrate reductase genes and anaerobic metabolism genes, and fewer transcripts for Hfq-dependent ncRNAs compared to WT. Conclusions: Differential transcript abundance between the perC-mutant and WT strains indicate PerC's negative regulation of the fim genes and positive regulation of anaerobic metabolism and ncRNA genes.
2017-02-07 | GSE91001 | GEO
Project description:Cyadox(CYA), as a new species of Quinoxaline 1, 4-dioxides and olaquindox(OLA) both showed higher antibacterial activity under anaerobic incubation. Microarray was used for global gene expression studies, which were further confirmed by real-time PCR. Cyadox and olaquindox mainly stimulated the expression of DNA repair genes as a response to the DNA damage. The induced gene sbmC was found to provide partial protection against the antibiotics of gyrase inhibitors like the quinolones and the ruvAB helped remove the topoisomerase IV-DNA cleavage complex caused by some type IIA topoisomerase poison antibiotics. It was inferred that the radical intermediate of cyadox reduction under anaerobic condition was responsible for the poison effect of IIA topoisomerases, which brought about DNA double stand breaks and other DNA damages in E. coli.
2012-07-25 | GSE39607 | GEO
Project description:In Escherichia coli, Lon is an ATP-dependent protease which degrades misfolded proteins and certain rapidly-degraded regulatory proteins. Given that oxidatively damaged proteins are generally degraded rather than repaired, we anticipated that Lon deficient cells would exhibit decreased viability during aerobic, but not anaerobic, carbon starvation. We found that the opposite actually occurs. Wild-type and Lon deficient cells survived equally well under aerobic conditions, but Lon deficient cells died more rapidly than the wild-type under anaerobiosis. Microarray analysis revealed that genes of the Clp family of ATP-dependent proteases were induced during aerobic growth but not during anaerobic growth. Thus, Clp may compensate for loss of Lon when cells are in an oxygen containing atmosphere. Under anaerobic carbon starvation conditions, Lon must be active to support survival. Keywords: Other
2007-11-01 | GSE6609 | GEO
Project description:Propionate is an abundant carboxylic acid in nature. Microorganisms metabolize propionate aerobically via the 2-methylcitrate pathway. This pathway depends on a series of three reactions in the citric acid cycle that leads to the conversion of succinate to oxaloacetate. Interestingly, the gamma-proteobacterium Escherichia coli can use propionate as a carbon and electron source under oxic but not under anoxic conditions. The typical downregulation of the citric acid cycle under anoxic conditions is only partially responsible for the inability to use propionate under anoxic conditions since an arcA mutant shows very limited growth on propionate. RT-PCR and transcriptomic analysis revealed a post-transcriptional regulation of the prp-genecluster encoding the necessary enzymes for propionate metabolism. The polycistronic mRNA was hydrolyzed in the 3`-5` direction under anoxic conditions. This regulatory strategy is highly constructive because the last gene of the operon encodes the first enzyme of the propionate metabolism. Further analysis revealed that RNase R catalyzes the hydrolysis of the prp transcripts. Consequently, an rnr-deletion strain could metabolize propionate under anoxic conditions. To the best of our knowledge, this is the first study describing the influence of RNase R on the anaerobic metabolism of E. coli.
2017-12-14 | GSE78814 | GEO
Project description:We report high-throughput RNA sequencing of WT, Δfnr, ΔarcA and Δihf in the exponential phase under anaerobic fermentative conditions
2021-02-28 | GSE153906 | GEO
Project description:We report genome-wide transcriptome profiles of E. coli obtained in the absence (control) and presence of 20 mM and 70 mM sodium fluoride (NaF) under anaerobic conditions, and assess the impact of fluoride-dependent ATP depletion on RNA turnover. We found that transcripts with increased abundance in response to NaF treatment correspond to genes that control cell envelope and osmotic stress adaptation, signal transduction systems, lipid biosynthesis, amine and polyamine degradation as well as acquisition of iron and iron homeostasis. In contrast, downregulated genes are involved in glycolysis, fatty acid metabolism, amino acid biosynthesis, energy production, cytochrome c biogenesis, protein translocation, translation, translation factors, protein folding/processing factors, transport for amino acid, sugar, or ion, and RNA metabolism. By using a quantile-based K-means clustering approach to identify gene clusters with similar expression profiles, we identified subset (100 genes) of transcriptome whose gene expression was up- and down-regulated under fluoride and diluted fluoride conditions, respectively. In addition, we found that about 40% of the highly abundant transcripts carry repetitive extragenic palindromes (REPs). By determining the mRNA stability of osmC as well as yghA, and addressing their ribonucleases/enzymes required for RNA degradation under anaerobic conditions, we found that fluoride ions slow down RNA degradation by increasing RNA stability, in turn increasing the steady-state level of RNA. Furthermore, our results show that turnover of these REP-containing transcripts is dependent on RNase E. Collectively, our study not only reveal the effects of NaF at the whole transcriptome level under hypoxic growth conditions, but also shows that fluoride can affect gene expression post-transcriptionally by slowing down the ATP-dependent degradation of structured RNAs.
2023-03-10 | GSE211579 | GEO
Project description:Mapping the occupancy of FNR, HNS, and IHF throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anerobic growth conditions. We also mapped the binding of the ß subunit of RNA Polymerase under both aerobic and anaerobic growth conditions. As a control, we also performed ChIP-chip on FNR in a ∆fnr mutant strain of Escherchia coli MG1655 K-12. We also examined FNR immunoprecipitation at various FNR concentrations using IPTG and Ptac::fnr (PK8263). The ∆hns/∆stpA strains were also used. Descirbed in the manuscript Genome-scale Analysis of E. coli FNR Reveals the Complexity of Bacterial Regulon Structure
2013-06-20 | GSE41186 | GEO
Project description:A total of 4388/4385 genes' transcripts (under aerobic/microaerobic condition, respectively) were identified. Among them, 105 and 71 transcripts were confidently determined to be up- or down-regulated by more than 4 folds with false discovery rate (FDR) p value more than 1, respectively. Additionally, 49 known regulatory non-coding small RNAs (sRNAs) were detected, and 18 sRNAs were differentially abundant (more than 1.5 fold-change). Functional characterizations were revealed that the major differential expression genes were involved in (i) acid response/cation homeostasis (ex: gadAXW, and hdeAB-yhiD operons), (ii) cell adhesion/biofilm formation (ex; fimAICDFGH, and csgDEFG operons), (iii) electron transportation (ex: cydAB, and nrdHIEF operons), (iv) ion transporter (ex: efeU, and efeOB operons), (v) Iron-sulfur cluster assembly (ex: iscRSUA and sufABCDSE operons), and (vi) the undoubtable anaerobic respiration/fermentation (ex: hyaABCDEF and hybOABCDEFG operons) & aerobic respiration (ex: sdhDAB and sucABCDSE operons).
2022-03-15 | GSE189154 | GEO
Project description:A strain of UPEC CFT073 lacking the three known NO detoxifiaction mechanisms, Hmp, FlRd and Nrf is used to study the global effect of NO on the pathogen Cultures were anaerobically grown in triplicates under two conditions: Without nitrosative stress or with nitrosative stress, induced by anaerobic growth on nitrate. RNA was extracted from the samples and following rRNA depletion, samples were analyzed by RNA-seq for genome wide transcriptional differences.
2015-06-15 | E-GEOD-69830 | biostudies-arrayexpress