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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

ABSTRACT: 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.

ORGANISM(S): Escherichia coli

PROVIDER: GSE34275 | GEO | 2011/12/09

SECONDARY ACCESSION(S): PRJNA149955

REPOSITORIES: GEO

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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. E.coli was grown in the presence and absence of glycerol. RNA was extracted from these samples, cDNA was prepared, fragmented cDNA was labled with labeling reagent and hybridized with Affymetrix E.coli2.0 genome array chips.Data was analysed to get the effect of glycerol on E.coli gene expression

2011-12-09 | E-GEOD-34275 | biostudies-arrayexpress

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

2011-10-22 | GSE33147 | GEO

Pseudomonas aerugionsa PAO1 transcriptome cultured in MOPS Glycerol, MOPS Acetate

Project description:Drastic alterations in transcripts associated with central carbon metabolism and associated processes have been repeatedly observed a common expression program as P. aeruginosa adapts to the cystic fibrosis lung when compared to standard laboratory conditions. However, we have limited knowledge of how well these transcriptomic changes correlate with actual alterations in metabolic flux; the rate of turnover of molecules through metabolic pathways. We have compared the transcriptome of Pseudomonas aeruginosa PAO1 during growth on the carbon sources acetate and glycerol.

2019-10-05 | E-MTAB-8374 | 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

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

Pseudomonas aerugionsa PAO1 transcriptome cultured in MOPS Glycerol and MOPS Acetate

Project description:Drastic alterations in transcripts associated with central carbon metabolism and associatedprocesses have been repeatedly observed a common expression program as P. aeruginosa adapts to the cystic fibrosis lung when compared to standard laboratory conditions. However, we have limited knowledge of how well these transcriptomic changes correlate with actual alterations in metabolic flux; the rate of turnover of molecules through metabolic pathways. We have compared the proteome of Pseudomonas aeruginosa PAO1 during growth on the carbon sources acetate and glycerol.

2020-02-17 | PXD015615 | Pride

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

2011-10-21 | E-GEOD-33147 | biostudies-arrayexpress

Metabolome and proteome analyses of glycerol overproducing E. coli unravel transcriptional misregulation of glycolysis and guide optimization strategies

Project description:Feedback-regulation of gene expression in synthetic metabolic pathways can improve production titers and yields. However, the dynamic nature of metabolism makes it difficult to engineer such regulation on a rational basis. Here, we expressed enzymes in a synthetic glycerol production pathway with static or feedback-regulated promoters, and explored the consequences for E. coli metabolism. Expressing the synthetic glycerol pathway with static promoters caused a strong growth burden, resulting in low biomass-levels and low glycerol titers. We show that the growth burden is due to a regulatory interaction between fructose-1,6-bisphoshate (FBP) and the transcription factor Cra, which switches between glycolysis and gluconeogenesis in E. coli. This regulation activated gluconeogenesis at higher induction of the glycerol pathway, because FBP levels were low. Feedback-regulated promoters, in contrast, stabilized FBP levels and enabled robust expression of the synthetic glycerol pathway. We show the broad utility of this approach by engineering different feedback-regulated promoters (pBAD, pTet, pConstitutive) and by applying one of them to carotenoid production in E. coli.

2021-07-21 | PXD022965 | Pride

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

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

Glycerol metabolism and PrfA activity in Listeria monocytogenes

Project description:Listeria monocytogenes is able to efficiently utilize glycerol as carbon source. In a defined minimal medium the growth rate is similar (during balanced growth) in presence of glycerol as in presence of glucose or cellobiose. Comparative transcriptome analyses of L. monocytogenes showed in the presence of glycerol (compared to glucose and/or cellobiose) high transcriptional upregulation of the known genes involved in glycerol uptake and metabolism (glpFK, glpD). Expression of the genes encoding a second putative glycerol uptake facilitator (GlpF-2) and a second putative glycerol kinase (GlpK-2) was less enhanced under these conditions. GlpK-1 but not GlpK-2 was essential for glycerol catabolism in L. monocytogenes under extracellular conditions, while loss of GlpK-1 affected replication in Caco-2 cells less than loss of GlpK-2 and GlpD. Additional genes whose transcription was higher in presence of glycerol than in presence of glucose and cellobiose included those for two dihydroxyacetone (Dha) kinases and many genes that are under carbon catabolite repression (CCR) control. Transcriptional down-regulation in the presence of glycerol (compared to glucose and cellobiose) was observed for several genes and operons that are positively regulated by glucose, including genes involved in glycolysis, N-metabolism and biosynthesis of branched chain amino acids. The highest transcriptional up-regulation was observed for all PrfA-dependent genes during early and late logarithmic growth in glycerol. Under these conditions a low level of HPr-Ser-P and a high level of HPr-His-P was present in the cells, suggesting that all EIIA (B) components of the PTS permeases expressed will be phosphorylated. These and other data reported suggest that the phosphorylation state of PTS permeases correlates with PrfA activity. Keywords: Response of Listeria monocytogenes to different carbon sources

2008-05-30 | GSE11459 | GEO

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