Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Evolutionary Rescue to Lethal Temperatures in Escherichia coli

PROVIDER: PRJNA640188 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12041900.fastq.gz	Fastqsanger.gz
	SRR12041901.fastq.gz	Fastqsanger.gz
	SRR12041902.fastq.gz	Fastqsanger.gz
	SRR12041903.fastq.gz	Fastqsanger.gz
	SRR12041904_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 51

Similar Datasets

Transcriptome analysis of thermal adaptive E. coli (part 1)

Project description:Transcriptome analyses of the Escherichia coli cells acquired in the thermal adaptive evolution (Kishimoto et al, 2010, PLoS Genet) were performed. The ancestor strain (Anc) and the evolved strains (41B, 43B, 45L and 37L) were analyzed. The cells exponetially growing at the regular (37ºC) and/or evolutionary (41~45ºC) temperatures and in response to heat shock at 45ºC were collected for microarray analyses. Multiple transcriptome analyses identified the specific evolutionary direction and bias for thermal adaptation.

2015-10-14 | GSE61749 | GEO

A multi-level understanding of the evolutionary trade-offs in thermal adaptation

Project description:The hypothesis that increased fitness within a selective environment must be accompanied by a loss of fitness in other non-selective environments leads to the notion of evolutionary tradeoffs. Experimental evolution provides an approach to test the existence of evolutionary tradeoffs, characterize their general quality, and reveal their genetic origins. To examine the underlying mechanism for a fitness trade-off, we constructed the evolutionary trajectories of Escherichia coli K-12 at increasing temperatures up to 45.3°C, and found diverging mutational histories that led to adaptive phenotypes with and without fitness trade-offs at low temperatures. We identified genetic changes in cellular respiration, iron metabolism and methionine biosynthesis that regulated gene expression to achieve thermal adaptation and determined the presence and absence of a fitness trade-off. Our results suggested that evolutionary trade-off could be generated by a regulatory protein mutation that was beneficial in the selective conditions but forced suboptimal proteome allocation under non-selective environments.

2020-11-17 | GSE140478 | GEO

Study for investigating the effects of a probiotic on diarrhea caused by chemotherapy in patients with gastric, colon and rectum cancer

Project description:Primary objectives: The study investigates whether a Escherichia coli Nissle-suspenison has a (preventive) antidiarrheal effect in patients with tumors who are treated with chemotherapeutic schemes which are associated with increased occurances of diarrhea. Diarrhea caused by treatment are thought to be reduced in intensity and/or frequency by the treatment with Escherichia coli Nissle-Suspension. Primary endpoints: Common toxicity criteria (CTC) for diarrhea

| 2534265 | ecrin-mdr-crc

GNPS - MS/MS spectra of colipterins produced by E. coli

Project description:High-resolution tandem MS spectra of colipterin metabolites produced by Escherichia coli. These metabolites are stimulated in the presence of sub-lethal levels of sulfamethoxazole antibiotic.

2020-06-22 | MSV000085621 | GNPS

Psychological Evaluation According Colonic Colonization by Escherichia Coli of Patients After Colorectal Surgery

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

Homeoviscous adaptation in Escherichia coli

Project description:All free-living microorganisms homeostatically maintain the fluidity of their membranes by adapting lipid composition to environmental temperatures. A quantitative description of how organisms maintain constant fluidity at all growth temperatures has not been achieved. By quantifying both enzymes and metabolic intermediates of the Escherichia coli fatty acid and phospholipid synthesis pathways, we discover how E. coli measures steady-state temperature and restores optimal membrane fluidity within a single generation after temperature shocks.

2024-10-10 | PXD051802 | Pride

Structure of Escherichia coli heat shock protein Hsp15 in complex with ribosomal 50S sununits bearing peptidyl-tRNA

Project description:In Escherichia coli, the heat shock protein 15 (Hsp15) is part of the cellular response to elevated temperature. Hsp15 interacts with peptidyl-tRNA-50S complexes that arise upon dissociation of translating 70S ribosomes, and is proposed to facilitate their rescue and recycling. A previous structure of E. coli Hsp15 in complex with peptidyl-tRNA-50S complex reported a binding site located at the central protuberance of the 50S subunit. By contrast, recent structures of RqcP, the Hsp15 homolog in Bacillus subtilis, in complex with peptidyl-tRNA-50S complexes have revealed a distinct site positioned between the anticodon-stem-loop (ASL) of the P-site tRNA and H69 of the 23S rRNA. Here we demonstrate that exposure of E. coli cells to heat shock leads to dissociation of 70S ribosomes and accumulation of 50S subunits, thus identifying a natural substrate for Hsp15 binding. Additionally, we have determined a cryo-EM reconstruction of the Hsp15-50S-peptidyl-tRNA complex isolated from heat shocked E. coli cells, revealing that Hsp15 binds to the 50S-peptidyl-tRNA complex analogously to its B. subtilis homolog RqcP. Collectively, our findings support a model where Hsp15 promotes access to the A-site for putative rescue factors to release the aberrant nascent polypeptide chain.

2022-11-15 | GSE216100 | GEO

undefined

Project description:A hard limit on the evolutionary rescue of an Antarctic bacterium from rising temperatures

| PRJEB50060 | ENA

EcoliOrbitrap KO dataset for the validation the SLAW metabolomics processing software

Project description:Escherichia coli wild-type and 180 different deletion mutants from the KEIO knockout collection were grown on glucose minimal medium containing, containing different subtract and at different temperatures. Pooled QCs are the sample including PSS in their name.

2020-11-19 | MSV000086486 | MassIVE

Effects of temperature on specificity and efficiency of a bacterial regulatory RNA

Project description:Bacterial small RNAs (sRNAs) are post-transcriptional regulators of stress response, virulence and more. The activity of sRNAs must be maintained across diverse environmental conditions, including the range of temperatures that defines the thermal niche of the species. Here we characterize the effects of temperature on the specificity and efficiency of sRNA regulation in E. coli. By measuring the activity of a large-scale library of sRNA variants at different temperatures, we found that many mutations have a significant but temperature-independent effect. We identified temperature-sensitive sequence elements using measurements that break from this dominant trend. Features associated with the specificity of sRNA regulation are more sensitive to mutations at high temperatures, and we confirm that specificity is more stringent at these temperatures. In contrast, many mutations in the region responsible for interactions with other targets have a stronger negative impact at low temperatures. Together, our results suggest that sRNAs may be structured such that variation in temperature may enhance their evolutionary plasticity.

2018-09-12 | GSE103732 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data