Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA529312 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To understand the mechanism of isopropanol tolerance of Escherichia coli for improvement of isopropanol production, we performed genome re-sequencing and transcriptome analysis of isopropanol tolerant E. coli strains obtained from parallel adaptive laboratory evolution under IPA stress.
2017-06-21 | GSE89685 | GEO
Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints
2011-10-22 | GSE33147 | GEO
Project description:Laboratory adaptive evolution experiments were conducted using serial passage of E. coli in M9 minimal medium supplemented with either 2 g/L of lactate for 60 days or 2 g/L of glycerol for 44 days. 7 parallel evolution strains were generated for growth on lactate and 7 parallel evolution strains were generated for growth on glycerol. Affymetrix arrays were used to study the time-course change in gene expression from unevolved E. coli (day 0) to a midpoint evolved strain (day 20) and evolutionary endpoints Biological replicate arrays were conducted for each of the time points tested for the different evolution strains
2011-10-21 | E-GEOD-33147 | biostudies-arrayexpress
Project description:We have performed adaptive laboratory evolution of E. coli pdhR gene deletion strain to examine the adaptive strategies of E. coli.
2021-03-08 | GSE167389 | GEO
Project description:We have performed adaptive laboratory evolution of E. coli ndh gene deletion strain to examine the adaptive strategies of E. coli.
2023-09-12 | GSE242875 | GEO
Project description:Mapping the occupancy of ArcA throughout the genome of Escherchia coli MG1655 K-12 using an affinity purified antibody under anaerobic and aerobic growth conditions. As a control, we also performed ChIP-chip onArcA in a ∆arcA mutant strain of Escherchia coli MG1655 K-12. Described in the manuscript The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli
2013-10-17 | GSE46413 | GEO
Project description:We obtained pfkAB-deleted E. coli K-12 MG1655 strain that can thrive on glucose minimal medium with adaptive laboratory evolution (pfk_ALE-1 strain). Functional analysis of the mutations detected in the pfk_ALE-1 strain was conducted to elucidate the molecular mechanisms underlying the effects of these mutations. We performed transcriptome analysis with RNA-seq to investigate the transcriptomic effects of mutations involved in the glycolytic pathway and global transcriptional regulation. Transcriptomic analysis revealed the expression levels of 4,497 genes on the chromosome of MG1655 and ALE-1 strains.
2022-11-16 | GSE199153 | GEO
Project description:Using a synthetic biosensor to couple production of a specific metabolite with cell growth, we spontaneously evolved cells under the selective condition toward the acquisition of genotypes that optimally reallocated cellular resources. Using 3-hydroxypropionic acid (3-HP) production from glycerol in Escherichia coli as a model system, we determined that spontaneous mutations in the conserved regions of proteins involved in global transcriptional regulation altered the expression of several genes associated with central carbon metabolism. Our study provides a new perspective on adaptive laboratory evolution (ALE) using synthetic biosensors, thereby supporting future efforts in metabolic pathway optimization.
2021-08-23 | GSE162594 | GEO
Project description:Escherichia coli arbitrarily encompasses facultative anaerobic, rod-shaped bacteria with defined respiratory and fermentative types of metabolism. The species diversification has been further advanced by atypical strains whose features deviate from the essential species-specific morphological and metabolic cut-off. The morphological cut-off is exemplified by bacterial filamentation. E. coli filamentation has been studied from two different perspectives: the first considers filamentation as a result of adaptive strategies and response to stress, while the second is based on findings from the cell division of E. coli’s conditional mutants. Another cut-off is represented by E. coli’s inability to use citrate as a sole carbon and energy source, which can be overcome either by saltational or long-term evolution. In this study, we compared two atypical E. coli strains that belong to the same neuroinvasive ecovar but exhibit either of the two phenotypes that deviate from the species features. While E. coli RS218 exists in the form of filaments incapable of growth on citrate, strain IHE3034 is represented as normal-sized bacteria able to aerobically ferment citrate in the presence of glucose; in this paper we show that these two phenotypes result from a bona fide trade-off. With the help of comparative proteomics and metabolomics, we discovered the proteome required for the upkeep of these phenotypes. The metabolic profiles of both strains reveal that under aerobic conditions, RS218 undergoes oxidative metabolism, while IHE3034 undergoes – anaerobic respiration. Finally, we show that the use of citrate and the filament formation are both linked in a trade-off occurring via a c-di-GMP-dependent phase-variation event.
2022-09-23 | PXD036163 | Pride
Project description:We carried out adaptive laboratory evolution of an E. coli strain lacking four genes (adhE, pta, ldhA, frdA) involved in acetyl-CoA consumption, allowing the efficient utilization of acetate as its sole carbon and energy source. The transcriptomes according to the medium status (M9 aceate, M9 glucose) of the evolved strain (SBA01) and its parent strain (DSM01) were compared using RNA-seq.
2020-09-15 | GSE157942 | GEO