Escherichia coli K-12 strain:K12
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ABSTRACT:
PROVIDER: PRJNA1198641 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Decoding the Escherichia coli epitranscriptome
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Project description:Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.
2015-09-30 | GSE65385 | GEO
Project description:Proteomics analysis in Escherichia coli K12 (E. coli K12) at DMP concentrations of 0 mg·kg-1 (CK) and 80 mg·kg-1 (DMP) revealed the toxicity of DMP
2022-01-02 | PXD030690 |
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
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Project description:Transfer RNAs (tRNAs) are essential components of the translation machinery and carry numerous post‑transcriptional modifications that contribute to decoding accuracy, efficiency and cellular fitness. In Escherichia coli K‑12, all tRNA modification pathways have been identified, yet the functional interactions between these pathways remain largely unexplored. Here, we systematically analyses genetic interactions between 29 non‑essential tRNA modification genes using a pairwise synthetic lethal screen based on P1 transduction. Most combinations of tRNA modification gene deletions are tolerated during growth in rich medium; however, we identify five synthetically lethal pairs and fifteen additional combinations that display negative genetic interactions. Deletions of truA, which encodes the pseudouridine synthase responsible for modifications at positions 38–40 of multiple tRNAs, show the highest frequency of negative epistasis. Synthetic lethality associated with truA can be complemented by expression of truA in trans and, in specific cases, partially suppressed by overexpression of its tRNA substrates, indicating substrate‑specific functional dependencies. Analysis of tRNA abundance by northern blotting and AQRNA‑seq demonstrates that loss of individual tRNA modification enzymes does not generally lead to widespread tRNA destabilization. Instead, further phenotypic characterization of viable double mutants reveals condition‑dependent growth defects influenced by carbon source, temperature and metabolic stress, as well as toxicity associated with overexpression of specific tRNAs. Together, these results reveal a limited but distinct set of genetic interactions among bacterial tRNA modification pathways and highlight the importance of physiological context in uncovering their cellular roles.
2026-05-20 | GSE331519 | GEO
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.
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Project description:Transcripitonal profiling of Escherichia coli K-12 comparing luxS mutant LW12 with wild type W3110
2010-11-11 | GSE20606 | GEO
Project description:Genome re-seqeuncing of Escherichia coli K12
| PRJNA339654 | 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