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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from ethanol-tolerant E. coli strain and wild type under ethanol stress

ABSTRACT: Cellular tolerance toward ethanol is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to stresses, including ethanol. In order to elucidate the mechanism for enhancement of ethanol tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of ethanol tolerance, we carried out comparative transcriptomic and proteomic analyses with the representative strains E1 and E0 (harboring the ethanol-tolerant mutant E1 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here. Cells of ethanol-tolerant mutant E1 and wild-type strain E0 were grown in 1.5% ethanol, and the samples for both of these two strains were prepared in triplicate with biological replicates

ORGANISM(S): Escherichia coli

SUBMITTER: Tingjian Chen

PROVIDER: E-GEOD-30441 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from ethanol-tolerant E. coli strain and wild type under ethanol stress

Project description:Cellular tolerance toward ethanol is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to stresses, including ethanol. In order to elucidate the mechanism for enhancement of ethanol tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of ethanol tolerance, we carried out comparative transcriptomic and proteomic analyses with the representative strains E1 and E0 (harboring the ethanol-tolerant mutant E1 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here.

2012-05-01 | GSE30441 | GEO

Expression data from furfural-tolerant E. coli strain and wild type under furfural stress

Project description:Cellular tolerance toward furfural is a complex phenotype involved many genes, and hard to be improved by manipulating individual genes. We previously established exogenous global regulator IrrE mutants that confer Escherichia coli with significantly enhanced tolerance to furfural stress. In order to elucidate the mechanism for enhancement of furfural tolerance in the mutants and to identify new genes and pathways that can be possible targets for engineering of furfural tolerance, we carried out comparative transcriptomic with the representative strains F1-37 and WT (harboring the furfural-tolerant mutant F1-37 of IrrE and the wild type IrrE, respectively). The data from transcriptome analyses were deposited here. Cells of furfural-tolerant mutant F1-37 and wild-type strain WT were grown in LB medium supplemented with furfural, and the cells were harvested in the exponential phase. The samples for both of these two strains were prepared in triplicate with biological replicates.

2012-01-28 | E-GEOD-35100 | biostudies-arrayexpress

Proteomic profiling of ethanol tolerance in yeast

Project description:For yeast cells, tolerance to high levels of ethanol is vital both in their natural environment and in industrially relevant conditions. We recently genotyped experimentally evolved yeast strains, tolerant to high levels of ethanol. In this study, we elucidate how the genotype and phenotype are related to each other on the molecular level through an integrated analysis of mutation data with protein abundance profiles from six evolved, ethanol-tolerant clones. We constructed a protein network of regulatory proteins, mutated and differentially regulated proteins. This resulted in the identification of a rewired regulatory network after adaptation to high levels of ethanol.

2020-12-03 | PXD006631 | Pride

Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Terminator_Readthrough_RNAseq]

Project description:The molecular mechanisms of ethanol toxicity and tolerance in bacteria, while important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and revealed multiple mechanisms of tolerance, but it remains difficult to separate direct and indirect effects of ethanol. We used adaptive evolution to generate spontaneous ethanol-tolerant strains of Escherichia coli, then characterized the mechanisms of toxicity and resistance associated with select mutations. Evolved alleles of metJ, rho, and rpsQ were sufficient to recapitulate much of the observed ethanol tolerance, implicating translation and transcription as key processes affected by ethanol. We found that ethanol induces mistranslation errors during protein synthesis, and that the evolved rpsQ allele protects cells by rendering the ribosome hyper-accurate. Ribosome profiling and RNAseq analyses of the ethanol-tolerant strain versus the wild type established that ethanol negatively affects transcriptional and translational processivity. Ethanol-stressed cells exhibited ribosomal stalling at internal AUG codons, which may be ameliorated by the adaptive inactivation of the MetJ repressor of methionine biosynthesis genes. Ethanol also caused aberrant intragenic transcription termination for mRNAs with low ribosome density, which was reduced in a strain with the adaptive rho mutation. Furthermore, ethanol inhibited transcript elongation by RNA polymerase in vitro. We propose that ethanol-induced inhibition and uncoupling of mRNA and protein synthesis are major contributors to ethanol toxicity in E. coli, and that adaptive mutations in metJ, rho, and rpsQ protect central dogma processes in the presence of ethanol.

2014-06-18 | GSE56407 | GEO

Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]

2014-06-18 | GSE56372 | GEO

Ethanol cellular defense induce unfolded protein response in yeast

Project description:Ethanol is a valuable industrial product and a common metabolite used by many cell types. However, this molecule produces high levels of cytotoxicity affecting cellular performance at several levels. In the presence of ethanol, cells must adjust some of their components, such as the membrane lipids to maintain homeostasis. In the case of microorganism as Saccharomyces cerevisiae, ethanol is one of the principal products of their metabolism and is the main stress factor during fermentation. Although many efforts have been made, mechanisms of ethanol tolerance are not fully understood and very little evidence is available to date for specific signaling by ethanol in the cell. This work studied two Saccharomyces cerevisiae strains, CECT10094 and Temohaya-26, isolated from flor wine and traditional fermentations respectively, which differ in ethanol tolerance, in order to understand the molecular mechanisms underlying the ethanol stress response and the reasons for different ethanol tolerance. The transcriptome was analyzed after ethanol stress and, among others, an increased activation of genes related with the unfolded protein response (UPR) and its transcription factor, Hac1p, was observed in the tolerant strain CECT10094. We observed that this strain also resist more UPR agents than Temohaya-26 and the UPR-ethanol stress correlation was corroborated observing growth of 15 more strains and discarding UPR correlation with other stresses as thermal or oxidative stress. Furthermore, higher activation of UPR pathway in the tolerant strain CECT10094 was observed using a UPR mCherry reporter. Finally, we observed UPR activation in response to ethanol stress in other S. cerevisiae ethanol tolerant strains as the wine strains T73 and EC1118.

2016-02-03 | GSE44863 | GEO

Transcriptomic analysis of two ethanol-tolerant Saccharomyces cerevisiae clones obtained by evolutionary engineering

Project description:Evolutionary engineering strategy was used for selection of ethanol-tolerant Saccharomyces cerevisiae clones under gradually increasing ethanol stress levels. Clones B2 and B8 were selected based on their higher ethanol-tolerance and higher ethanol production levels. Whole genome microarray analysis was used for identifying the gene expression levels of these two evolved clones compared to the reference strain.

2016-03-01 | GSE78759 | GEO

Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Terminator_Readthrough_RNAseq]

2014-06-18 | E-GEOD-56407 | biostudies-arrayexpress

Correcting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]

2014-06-18 | E-GEOD-56372 | biostudies-arrayexpress

Proteomics Analysis of Evolved Escherichia coli Populations from Cyclic Antibiotic Treatment

Project description:When the survivors of antibiotic treatment (persisters) are repeatedly regrown and retreated with the same antibiotic for several cycles, the new population will soon adapt to the treatment condition and become tolerant to the drug. Here, we did evolution experiments on Escherichia coli populations by treating it with daily high concentration of different antibiotics (ampicillin, ciprofloxacin and apramycin) approximating clinical dosage, during the rapid growth-exponential phase. After a few cycles, we observed that the evolved populations exhibit extremely high tolerance to the drug, which are achieved by single point mutations in one of several genes. Interestingly, treatment with different antibiotics led to the selection of different mutants despite the shared persistence phenotype. Here, we applied spectral counting-based quantitative proteomics to study the proteome profile of the evolved E. coli populations from different cyclic antibiotic treatments.

2020-01-10 | PXD013326 | Pride

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