Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA104853 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcription profiles in BL21, BL21/pOri1 and BL21/pOri2 were analysed using DNA microarray technology. BL21, BL21/pOri1 or BL21/pOri2 strains were cultured at chemostat status and harvested after the cultivation arrived steady status. Keywords: Effects of plasmid DNA on Escherichia coli metabolism
2006-07-07 | GSE5239 | GEO
Project description:Cinnamaldehyde is a natural antimicrobial and has been found to be effective against many foodborne pathogens including Escherichia coli O157:H7. Although its antimicrobial effects have been well investigated, limited information is available on its effects at the molecular level. Sublethal treatment at 200 mg/l cinnamaldehyde inhibited growth of E. coli O157:H7 at 37oC and for ≤ 2 h caused cell elongation, but from 2 to 4 h growth resumed and cells reverted to normal length. To understand this transient behaviour, genome-wide transcriptional analysis of E. coli O157:H7 was performed at 2 and 4 h exposure to cinnamaldehyde. Drastically different gene expression profiles were obtained at 2 and 4 h. At 2 h exposure, cinnamaldehyde induced overexpression of many oxidative stress-related genes, reduced DNA replication, and synthesis of protein, O-antigen and fimbriae. At 4 h, many cinnamaldehyde-induced repressive effects on E. coli O157:H7 gene expressions were reversed and oxidatve stress genes were nolonger differentially expressed.
2012-09-08 | GSE40693 | GEO
Project description:Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]
| PRJNA243254 | ENA
Project description:Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Terminator_Readthrough_RNAseq]
| PRJNA243255 | ENA
Project description:PhoP is considered a regulator of virulence despite being conserved in both pathogenic and non-pathogenic Enterobacteriaceae. While Escherichia coli strains represent both non-pathogenic commensal isolates and numerous virulent pathotypes, the PhoP virulence regulator has only been studied in commensal E. coli. To better understand how conserved transcription factors contribute to virulence, we characterized PhoP in pathogenic E. coli. Loss of phoP significantly attenuated E. coli during extraintestinal infection. This was not surprising since we demonstrated that PhoP differentially regulated the transcription of >600 genes. In addition to survival at acidic pH and resistance to polymyxin B, PhoP was required for repression of motility and oxygen-independent changes in the expression of primary dehydrogenase and terminal reductase respiratory chain components. All phenotypes have in common a reliance on an energized membrane. Thus, we hypothesized that PhoP mediated these effects by regulating genes that generate a proton motive force. Indeed, bacteria lacking PhoP exhibited a hyper-polarized membrane, and dissipation of the transmembrane electrochemical gradient increased the susceptibility of the phoP mutant to acidic pH, while inhibiting respiratory generation of the proton gradient restored resistance to antimicrobial peptides independent of lipopolysaccharide modification. These findings demonstrate a connection between PhoP, virulence, and the energized state of the membrane.
2011-07-29 | GSE31029 | GEO
Project description:Cinnamaldehyde is a natural antimicrobial and has been found to be effective against many foodborne pathogens including Escherichia coli O157:H7. Although its antimicrobial effects have been well investigated, limited information is available on its effects at the molecular level. Sublethal treatment at 200 mg/l cinnamaldehyde inhibited growth of E. coli O157:H7 at 37oC and for M-bM-^IM-$ 2 h caused cell elongation, but from 2 to 4 h growth resumed and cells reverted to normal length. To understand this transient behaviour, genome-wide transcriptional analysis of E. coli O157:H7 was performed at 2 and 4 h exposure to cinnamaldehyde. Drastically different gene expression profiles were obtained at 2 and 4 h. At 2 h exposure, cinnamaldehyde induced overexpression of many oxidative stress-related genes, reduced DNA replication, and synthesis of protein, O-antigen and fimbriae. At 4 h, many cinnamaldehyde-induced repressive effects on E. coli O157:H7 gene expressions were reversed and oxidatve stress genes were nolonger differentially expressed. Duplicate E. coli O157:H7 cultures with or without 200 mg/l cinnamaldehyde were incubated at 37M-BM-0C for M-bM-^IM-$ 4 h. Cinnamaldehyde-induced changes in gene expression profiles were compared at 2 and 4 h using Affymetrix Ginechip 2.0 microarrays.
2012-09-08 | E-GEOD-40693 | biostudies-arrayexpress
Project description:Compare the protein acetylation modification levels of the acetyltransferase YhbS overexpression strain and wild-type strain of Escherichia coli
2025-12-27 | PXD072471 |
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