Escherichia coli
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ABSTRACT:
PROVIDER: PRJNA134983 | ENA |
REPOSITORIES: ENA
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Project description:Genomic Library Enrichment to determine the n-Butanol Tolerant related genes in E. coli. The samples involves a series of batch transfers to increasing concentrations of n-butanol and controls (always grew in absence of the solvent)
2012-09-19 | GSE26223 | GEO
Project description:We successfully isolated an E. coli strain harboring rpoD mutant B8 with 2% (v/v) butanol tolerance using global transcriptional machinery engineering approach. DNA microarrays were employed to assess the transcriptome profile of n-butanol tolerance strain B8 and control strain E. coli JM109. The goal of this study is therefore to identify E. coli genes that are involved in n-butanol tolerance.
2016-05-10 | GSE79305 | GEO
Project description:Genomic Library Enrichment to determine the n-Butanol Tolerant related genes in E. coli. The samples involves a series of batch transfers to increasing concentrations of n-butanol and controls (always grew in absence of the solvent) Two technical replicas. Samples 1, 3, 5, and 7 are the serial transfers (samples 15, 13, 11, and 9 are their respective replicas). Samples 2, 4, 6 and 8 are the controls grown in absence of n-butanol (samples 16, 14, 12 and 10 are their respective replicas)
2012-09-19 | E-GEOD-26223 | biostudies-arrayexpress
Project description:n-Butanol has been proposed as an alternative biofuel to ethanol, and both Escherichia coli and Saccharomyces cerevisiae have been engineered to produce it. Unfortunately, n-butanol is more toxic than ethanol to these organisms. To understand the basis for its toxicity, cell wide studies were conducted at the transcript, protein and metabolite levels to obtain a global view of the n-butanol stress response. Analysis of the data indicate that n-butanol stress has components common to other stress responses and includes perturbation in respiratory functions (nuo, cyo operons), oxidative stress (sodC, katG, yqhD), heat shock and cell envelope stress (rpoE, clpB, htpG, degP, cpxPR), metabolite transport (malE, opp operon) and biosynthesis. Inducible expression of the yqhD gene was found to improve the host’s tolerance to exogenous n-butanol and confirms the role of this gene in coping with butanol stress. To survey for other potential candidates that may serve to improve host tolerance, mutant strains in several candidates which show changes at the transcript and protein levels were examined for sensitivity during butanol exposure. Chassis engineering based on these cues may be required in a high production titer, butanol-producing host.
2009-12-31 | GSE16973 | GEO
Project description:Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, with a variety of genetic resistance mechanisms previously identified. Using random genomic libraries and DNA microarrays, library inserts were preferentially enriched by culturing in media containing butanol, with successive transfers into fresh media containing incrementally increasing butanol concentrations. Keywords: genomic library preferential enrichment
2007-12-29 | GSE6289 | GEO
Project description:n-Butanol has been proposed as an alternative biofuel to ethanol, and both Escherichia coli and Saccharomyces cerevisiae have been engineered to produce it. Unfortunately, n-butanol is more toxic than ethanol to these organisms. To understand the basis for its toxicity, cell wide studies were conducted at the transcript, protein and metabolite levels to obtain a global view of the n-butanol stress response. Analysis of the data indicate that n-butanol stress has components common to other stress responses and includes perturbation in respiratory functions (nuo, cyo operons), oxidative stress (sodC, katG, yqhD), heat shock and cell envelope stress (rpoE, clpB, htpG, degP, cpxPR), metabolite transport (malE, opp operon) and biosynthesis. Inducible expression of the yqhD gene was found to improve the hostâs tolerance to exogenous n-butanol and confirms the role of this gene in coping with butanol stress. To survey for other potential candidates that may serve to improve host tolerance, mutant strains in several candidates which show changes at the transcript and protein levels were examined for sensitivity during butanol exposure. Chassis engineering based on these cues may be required in a high production titer, butanol-producing host. This comparison is between E. coli DH1 cells treated with 0.8% n-butanol and untreated cells at 0, 30, 80, and 195 minutes after addition. 3 biological replicates were grown, total RNA was extracted, labeled, and hybridized on 3 slides for each time point. http://www.microbesonline.org/cgi-bin/microarray/viewExp.cgi?expId=1266
2010-05-16 | E-GEOD-16973 | biostudies-arrayexpress
Project description:E. coli butanol-responsive promoter library
| PRJNA787372 | ENA
Project description:Transcriptome analysis of isolated mutants using the method Visualizing Evolution in Real-Time (VERT) for the study of n-butanol tolerance. The samples were isolated from an evolution experiment picking samples at different times based in the evolution dynamics obtained with VERT. Mutants were grown in chemostats at 0.8% (v/v) of n-butanol and compared with the expression of wild-type to the same concentration of solvent. Three biological replicas. Each sample represents an isolated mutant. The reference for each mutant corresponds to wild-type, both exposed to the same concentration of n-butanol (0.8% (v/v)).
2012-03-30 | E-GEOD-30005 | biostudies-arrayexpress
Project description:Transcriptome analysis of isolated mutants using the method Visualizing Evolution in Real-Time (VERT) for the study of n-butanol tolerance. The samples were isolated from an evolution experiment picking samples at different times based in the evolution dynamics obtained with VERT. Mutants were grown in chemostats at 0.8% (v/v) of n-butanol and compared with the expression of wild-type to the same concentration of solvent.
2012-03-31 | GSE30005 | GEO
Project description:Butanol is a bulk chemical feedstock and a promising fuels. Microbial production of butanol is challenging primarily because of its toxicity and low titer of production. Transcript regulator factor Rob plays an important role in butanol-tolerant functional revealed by our previous study. In this study, the mutant strain DTrob (AT686-687 deletion in rob gene) could tolerate 1.25 %(v/v) butanol. And the per unit intracellular butanol concentration and transcriptome of wild-type and DTrob were further compared to understand the regulation mechanism of Rob for butanol tolerance. A total of 285 DEGs (differentially expression genes) were identified by bioinformatic analysis, and they may function in transport and localization according to the GO functional annotations and the functional annotation of gene product in NCBI database. Eighteen DEGs representing different functional categories were selected for real-time quantitative PCR (qPCR) for confirming the dependability of RNA-seq data. The deletion strains of glgS or yibT gene, which were down-regulated by Rob, had butanol-toleranct characteristic, indicating that the deletion or downregulated expression of the two genes down-regulated by Rob could improve the butanol tolerance. This study reveals the transcript regulator factor Rob could regulate and control the expression of the butanol tolerant genes, and its inactivation would result in an improved butanol tolerance.
2019-09-17 | GSE120032 | GEO