Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA119813 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model.
2009-07-25 | GSE17074 | GEO
Project description:Conventional prokaryotic RNA labeling method usually requires large amounts of starting materials and tends to generate high background signals. Recently, two novel methods based on amplification systems were introduced. Here, we compared three alternative strategies: direct labeling method, ployadenylation-involved oligo-dT priming amplification method and random priming amplification method (hereafter referred to as DL, PAOD and RPA method in this article) for prokaryotic RNA labeling employing the expression profiling investigation in Escherichia coli (E. coli) heat shock model. To identify an optimal RNA labeling method for prokaryotic microarray analysis, experiments were performed with starting RNA obtained from E.coli growing at control (37°C) or heat shock (43°C) condition. We employed 0.5 μg of total RNA for a single round of amplification using PAOD and RPA methods coupling to IVT to generate cDNA targets. In addition, an approach using DL method was also performed. Three types of cDNA mixtures containing Cy5-labeled (or Cy3-labeled) control DNA and Cy3-labeled (or Cy5-labeled) DNA targets were hybridized with E.coli microarrays in a dye-swap strategy. Replicate experiments were conducted from the same batch of total RNA to assess technique reproducibility of each approach.
2010-05-15 | E-GEOD-17074 | biostudies-arrayexpress
Project description:Prokaryotic expression profiling analysis for single or combined chaperones deletion
| PRJNA287227 | ENA
Project description:Modifications of RNA, known as the epitranscriptome, affect mRNA stability, translation, and splicing in eukaryotes and have implications for developmental processes, cancer, and viral infections. In prokaryotes, however, the landscape of the epitranscriptome is still poorly understood. To address this knowledge gap, we used direct RNA sequencing with Nanopore technology to study RNA modifications in the model bacterium Escherichia coli. With a single sequencing reaction, we were able to simultaneously identify and map most of the known modification types in rRNA, tRNA, and mRNA. Subsequently, a multifaceted approach integrating different algorithms for data analysis, deletion mutants, mass spectrometry, qPCR, and in vitro methylation was implemented to evaluate the presence of m5C and m6A in E. coli. Known m5C and m6A sites in rRNA were confirmed, but these modifications could not be localized in the mRNA. Nevertheless, based on the sequencing data, modifications were found to be enriched in the coding regions of genes associated with general metabolism and RNA processing. This study provides a useful resource for experimental and bioinformatic approaches to gain new insights into post-transcriptional regulation in a prokaryotic model.
2025-02-21 | GSE271571 | GEO
Project description:Digital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes
| PRJNA151211 | ENA
Project description:Increasing numbers of small proteins with diverse physiological roles are being identified and characterized in both prokaryotic and eukaryotic systems, but the origins and evolution of these proteins remain unclear. Recent genomic sequence analyses in several organisms suggest that new functions encoded by small open reading frames (sORFs) may emerge de novo from noncoding sequences. However, experimental data demonstrating if and how randomly generated sORFs can confer beneficial effects to cells are limited. Here we show that by up-regulating hisB expression, de novo small proteins (≤ 50 amino acids in length) selected from random sequence libraries can rescue Escherichia coli cells that lack the conditionally essential SerB enzyme. The recovered small proteins are hydrophobic and confer their rescue effect by binding to the 5’ end regulatory region of the his operon mRNA, suggesting that protein binding promotes structural rearrangements of the RNA that allow increased hisB expression. This study adds RNA regulatory elements as another interacting partner for de novo proteins isolated from random sequence libraries, and provides further experimental evidence that small proteins with selective benefits can originate from the expression of nonfunctional sequences.
2023-03-31 | PXD040161 | Pride
Project description:Total transcript amplification (TTA) from single eukaryotic cells for transcriptome analysis is established, but TTA from a single prokaryotic cell presents additional challenges with much less starting material and lack of poly(A)-tails. We described, here, a novel method for single bacterium TTA, using a Burkholderia thailandensis model exposed to subinhibitory concentration of the antibacterial agent, glyphosate. Utilizing B. thialandensis microarray to assess the TTA method showed little gene bias (< 2 fold-change) and absence (~5-6%) when compared to the larger scale non-amplified RNA samples. B. thailandensis genes important to possibly recuperate and balance the intracellular amino acid pool were induced (or repressed) by the aromatic amino acid biosynthesis inhibitor, glyphosate. We validated our single-cell microarray data at the multi-cells and single-cell levels with lacZ and gfp reporter-gene fusions, respectively. This novel method will rejuvenate and expand the prokaryotic transcriptomic field.
2010-08-05 | GSE23419 | GEO
Project description:YajL is the most closely related Escherichia coli homolog of Parkinsonism-associated protein DJ-1, a protein with a yet undefined function in the oxidative stress response. YajL protects cells against oxidative stress-induced protein aggregation and functions as a covalent chaperone for the thiol proteome, including FeS proteins. To clarify the cellular responses to YajL deficiency, transcriptional profiling of the yajL mutant was performed. As compared to the parental strain, the yajL mutant overexpressed genes coding for chaperones, proteases, chemical chaperone transporters, superoxide dismutases, catalases, peroxidases, components of thioredoxin and glutaredoxin systems, iron transporters, ferritins and FeS cluster biogenesis enzymes, DNA-repair proteins, RNA chaperones and small regulatory RNAs. It also overexpressed the RNA polymerase stress sigma factors sigma S (multiple stresses) and sigma 32 (protein stress) and activated the OxyR and SoxRS oxidative stress transcriptional regulators, which together trigger the global stress response. The yajL mutant also overexpressed genes involved in septation and adopted a shorter and rounder shape characteristic of stressed bacteria. Biochemical experiments showed that this upregulation of many stress genes resulted in increased expression of stress proteins and improved biochemical function. Thus, protein defects resulting from the yajL mutation trigger the onset of a robust and global stress response in a prokaryotic model of DJ-1-associated Parkinsonism.
2012-12-04 | GSE42702 | GEO
Project description:Purpose: the goals of this study was to find the differential genes of spleen in chickens infected with Escherichia coli Methods: The spleen samples from control group and the spleen samples from infection group were generated by deep sequencing using Illumina system with 9 biological repetitions and 2 technical repetitions, respectively. Results: Using an optimized data analysis workflow, we mapped about 68-91 million sequence reads per sample to the chicken spleens from the infection and control group by Hisat2. Approximately a quarter of the transcripts showed differential expression between the infection and control group, with a 5x SD fold change and p value <0.05.
2023-01-11 | GSE182967 | GEO
Project description:B-methylthiolation of the Escherichia coli Ribosomal Protein S12 Regulates Anaerobic Gene Expression. B-methylthiolation is a unique post-translational modification (PTM) that maps to a conserved Asp 88 of the bacterial ribosomal protein S12. This modification is phylogenetically conserved in several bacteria yet has not been identified on other proteins. We use microarrays to delineate the association of prokaryotic ribosomal protein PTM to the regulation of genes.
2010-05-27 | E-GEOD-21551 | biostudies-arrayexpress