Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA93109 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RyhB is a non-coding RNA regulated by the Fur repressor. It has previously been shown to cause the rapid degradation of a number of mRNAs that encode proteins that utilize iron. Here we examine the effect of ectopic RyhB production on global gene expression by microarray analysis. Many of the previously identified targets were found, as well as other mRNAs encoding iron-binding proteins, bringing the total number of regulated operons to at least 18, encoding 56 genes. The two major operons involved in Fe-S cluster assembly showed different behavior; the isc operon appears to be a direct target of RyhB action, while the suf operon does not. This is consistent with previous findings suggesting that the suf genes but not the isc genes are important for Fe-S cluster synthesis under iron-limiting conditions, presumably for essential iron-binding proteins. In addition, we observed repression of Fur-regulated genes upon RyhB expression, interpreted as due to intracellular iron-sparing resulting from reduced synthesis of iron-binding proteins. Our results demonstrate the broad effects of a single non-coding RNA on iron homeostasis. Keywords: RNA degradation, iron stavation, RyhB small RNA, iron-using proteins
2005-08-31 | GSE3105 | GEO
Project description:Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. Using this technology, we already revealed the targetome of RyhB, RybB and DsrA, three well-characterized sRNAs in Escherichia coli. In this study, we performed MAPS with CyaR sRNA.
2018-01-03 | GSE90128 | GEO
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
| 2230352 | ecrin-mdr-crc
Project description:Despite the characterization of many aetiologic genetic changes. The specific causative factors in the development of sporadic colorectal cancer remain unclear. This study was performed to detect the possible role of Enteropathogenic Escherichia coli (EPEC) in developing colorectal carcinoma.
| 2184564 | ecrin-mdr-crc
Project description:To get a high resolution understanding of the effect of Fur on global gene expression, we compared by high-resolution RNAseq the transcriptomes of a wild-type E. coli K-12 strain and its Fur deletion derivative grown in minimal medium with or without supplementation of iron. Three independent total RNA extraction and RNAseq assays were performed for each strain in each condition.
2023-06-01 | GSE175957 | GEO
Project description:Aerobic Escherichia coli growth at restricted iron concentrations (≤ 1.75 ± 0.04 mM) is characterized by lower biomass yield, higher acetate accumulation, and higher activation of the siderophore iron-acquisition systems. Although iron homeostasis in E. coli has been studied intensively, these studies focused only on understanding the regulation of the iron import systems and the iron-requiring enzymes. In this study, the effect of iron availability on the energy metabolism of E. coli was investigated. It was established that aerobic cultures growing at limiting iron conditions showed lower ATP yield per glucose, lower growth rate, and lower TCA cycle activity and respiration, and at the same time increased glucose consumption, acetate and pyruvate accumulation, practically mimicking microaerobic growth. However, at excess iron, independently of oxygen availability, the cultures showed high cellular energetics (5.8 ATP/mol of glucose) by using pathways requiring iron-rich complex proteins found in the TCA cycle and respiration chain. At conditions of iron excess, some iron requiring terminal reductases of the respiratory chain, that were supposed to be anaerobic, were used by the E. coli, when in aerobic conditions, to keep high respiration activity. This high respiration activity allowed E. coli to produce more biomass and more reactive oxygen species that were controlled by the higher activity of the antioxidant defenses (SOD, peroxidase, and catalase) and the iron-sulfur cluster repair systems.
2022-06-30 | GSE203540 | GEO
Project description:Purpose: We use the gene expression data to estimate the effects of tetracycline on gene expression and average ribosome density. Methods: The mRNAs were extracted with TRIzol reagent. The mRNAs were fragmented into 280 bp and the sequencing process was conducted on HiSeq 2500 platform. We use cutadapt, bowtie2, Plastid and DEseq2 software to analyze the expression levels of genes in two Escherichia coli strains. Results: The gene expression in EF4 knockout Escherichia coli strain was similar with BW25113 strain under normal condition. Under tetracycline treatment, many genes' expression were differentially regulated. Interestingly, we found that the gene expression of ribosomal proteins was up-regulated in WT strain comparing with EF4 knockout E. coli strain. Conclusions: Our results suggest that EF4 affects the average ribosome density and global gene expression in two Escherichia coli strain under tetracycline treatment.
2021-01-09 | GSE109025 | GEO
Project description:More than half of women will experience a urinary tract infection (UTI) with uropathogenic Escherichia coli (UPEC) causing ~80% of uncomplicated cases. Iron acquisition systems are essential for uropathogenesis, and UPEC encode functionally redundant iron acquisition systems, underlining their importance. However, a recent UPEC clinical isolate, HM7 lacks this functional redundancy and instead encodes a sole siderophore, enterobactin. To determine if E. coli HM7 possesses unidentified iron acquisition systems, we performed RNA-sequencing under iron-limiting conditions and demonstrated the ferric citrate uptake system (fecABCDE and fecIR) was highly upregulated. Importantly, there are high levels of citrate within urine, some of which is bound to iron, and the fec system is highly enriched in UPEC isolates compared to commensal or fecal strains. Therefore, we hypothesized that HM7 and other similar strains use the fec system to acquire iron in the host. Deletion of both enterobactin biosynthesis and ferric citrate uptake (ΔentB/ΔfecA) abrogates use of ferric citrate as an iron source and fecA provides an advantage in pooled human urine in absence of enterobactin. However, in a UTI mouse model, fecA is a fitness factor independent of enterobactin production, likely due to the action of host Lipocalin-2 chelating ferrienterobactin. These findings indicate that ferric citrate uptake is used as an iron source when siderophore efficacy is limited, such as in the host during UTI. Defining these novel compensatory mechanisms and understanding the nutritional hierarchy of preferred iron sources within the urinary tract are important in the search for new approaches to combat UTI.
2021-11-06 | GSE188170 | GEO
Project description:The transcriptional profile of Escherichia coli O157 treated with small molecule inhibitors of type III secretion was determined. Four variations of the small molecule inhibitor were assessed for global changes in transcription by treating cells with 20uM of inhibitor or an equivalent volume of DMSO (inhibitor solvent). Keywords: treatment, dose, Cy3, Cy5, 2-colour
2009-08-11 | GSE10319 | GEO
Project description:We have reported that bicarbonate (NaHCO3) potentiates the activity of aminoglycosides in Escherichia coli, but the action mechanism was not identified. To eventually understand how NaHCO3 can potentiate antibiotics, we thought that a rational first step was to examine the effect of NaHCO3 separately and to inspect initial gene expression changes triggered by it. In this work we started by confirming that NaHCO3 can reduce the number of viable E. coli bacteria. We then investigated, via RNAseq, gene expression changes induced by NaHCO3. There were upregulated and downregulated genes, among the top upregulated genes (~10-fold increase in expression) was tnaA, the gene encoding tryptophanase (TnaA), the enzyme that degrades tryptophan to indole. Considering that higher expression of tnaA likely led to increases in indole, we tested the effect of indole and found both growth inhibition and synergy with NaHCO3. We suggest that indole may participate in growth inhibition of E. coli. The RNAseq analysis also revealed upregulation (≥4-fold) of genes encoding proteins for the acquisition of iron and downregulation (≥16-fold) of genes encoding iron-sulfur-holding proteins, hence NaHCO3 apparently triggered also an iron deficit response. We suggest that iron deficiency may also be involved in growth inhibition by NaHCO3.
2018-11-01 | GSE110493 | GEO