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Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

ABSTRACT: 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

ORGANISM(S): Escherichia coli K-12 Escherichia coli

PROVIDER: GSE33147 | GEO | 2011/10/22

SECONDARY ACCESSION(S): PRJNA149373

REPOSITORIES: GEO

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Expression data from laboratory evolution of Escherichia coli on lactate or glycerol

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

Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol

Project description:The aim of this study is to investigate the changes of global gene expression in E. coli during a carbon source shift. Expression profiling of an evolved strain of E. coli K12 MG1655 grown in M9 minimal media supplemented with propylene glycol or glycerol.

2012-06-01 | GSE34631 | GEO

Transcriptome analysis of E. coli in M9 minimal media supplemented with propylene glycol or glycerol

2012-05-31 | E-GEOD-34631 | biostudies-arrayexpress

Transcription profiling of Escherichia coli K12 HUalpha, HUbeta and HUalphabeta K12 to identification the HU regulon

Project description:The physiological role of the various nucleoid-associated proteins in bacteria and HU in particular has been addressed in a number of studies but remains so far not fully understood. In this work, a genome-wide microarray hybridization approach, combined with in vivo genetic experimentation, has been performed in order to compare and evaluate the effect of HUalpha, HUbeta and HUalphabeta on the transcription of the Escherichia coli K12 genes as a function of growth phase. The histone-like protein HU is present in the E. coli cell under three dimeric forms (HUalphabeta, HUalpha2 and HUbeta2) in a ratio that varies with growth phase. The experimental protocol is designed to handle strain genotype and growth phase as independent variables. Experiment Overall Design: We used microarrays to investigate global bacterial gene expression in five genotypes of E. coli C600: WT (JO2057), hupA (JO2081), hupB (JO2083), hupAB (JO3020) and rpoS (MW30) at three growth growth phases: exponential, transition and stationary and in three growth media: LB, M9 minimal Glucose and M9 minimal Glycerol. The most relevant experiments were carried out in duplicate: the wild type (JO2057) and the hupAB (JO3020) strains were tested in the exponential and stationary phase, in LB. Wild type and hupAB strains were also tested in single experiments at the transition phase in LB. The single hupA (JO2081) and single hupB (JO2083) mutants were tested at the three growth phases in LB. Wild type and hupAB strains were compared in single experiments both in M9 Minimal Glucose and M9 Minimal Glycerol at the exponential and stationary phase. The last chips were used to test respectively the rpoS mutant at the at the exponential and stationary phase in LB.

2009-01-14 | E-GEOD-11183 | biostudies-arrayexpress

Improvement of isopropanol tolerance of Escherichia coli using adaptive laboratory evolution and omics technologies

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

Balanced growth of Ecoli MG1655/pTrc99a(NOX-) at different growth rates

Project description:Responses of Escherichia coli MG1655/pTrc99a(NOX-) grown at different growth rates in chemostat in M9 + salts Keywords: different growth rates in parallel

2006-03-08 | GSE4366 | GEO

Syntrophic glycerol fermentation

Project description:Enhanced glycerol conversion by Thermoanaerobacter strains by cocultivation with a methanogenic partner

| PRJEB30535 | ENA

Transcriptome analysis of E. coli MG1655

Project description:Expression profiling of wild type and purR deletion strains of E. coli K-12 MG1655 under both M9 minimal media and addition of adenine.

2011-06-14 | GSE26588 | GEO

Escherichia coli K-12 grown in the presence of glycerol exhibits upregulation in genes for acid stress chaperones and concomitant downregulation in genes involved in generation of acidic metabolites

Project description:This study explores the effects of glycerol, on whole genome expression of Escherichia coli. DNA microarray analysis imply that E. coli in the presence of glycerol generates acidic metabolites to which it adapts by upregulation of genes involved in acid stress and by simultaneously downregulating genes involved in high pH stress.

2011-12-09 | GSE34275 | GEO

E. coli ATCC 8739 transcriptomics under culture medium optimization and adaptive laboratory evolution for glycerol consumption

Project description:Biotechnology suggests that microorganisms can be used as chemical factories that transform renewable feedstock into value-added chemicals. Conversion of glycerol, using direct transformation or fermentation, into valuable products such as polymers, surfactants, solvents, and chemical intermediates has attained growing interest in recent years due to the dramatic growth of the biodiesel industry. However, the use of cell factories could be limited by low growth and uptake rates under certain environmental conditions, thus understanding microbial nutritional requirements is a critical point to use them as cell factories. Here, we compared E. coli ATCC 8739 transcriptomic responses to glycerol under aerobic conditions in an optimized culture medium (Condition 3) and one evolved strain in glycerol using as a reference a glycerol-based medium (Condition 11). Our analyses revealed 478 and 431 differentially expressed genes (DEGs) with log2 fold change (FC) > |2| and p Adjusted value < 0.05, for the bacteria growing in the optimized culture medium and the evolved strain, respectively. Among the DEGs, glp operon was found to be up-regulated as a response to glycerol uptake. Interestingly, between them, it was found genes that requires the use of phosphorous to ovoid the toxicity during glycerol consumption. Previously, we identified using a computational approach that phosphorous and nitrogen are essential compound that support high glycerol consumption in E. coli.

2019-11-23 | GSE140847 | GEO

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