Transcriptomic response of a genetically modifed Escherichia coli strain at higher growth temperatures
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ABSTRACT:
ORGANISM(S): Escherichia coli K-12 Escherichia coli
PROVIDER: GSE309788 | GEO | 2025/11/18
REPOSITORIES: GEO
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Project description:Transcriptomic response of a genetically modifed Escherichia coli strain at higher growth temperatures
| PRJNA1363177 | ENA
Project description:We have shown the quorum-sensing signals acylhomoserine lactones (AHLs), autoinducer-2 (AI-2), and indole influence the biofilm formation of Escherichia coli. Here, we investigate how the environment, i.e., temperature, affects indole and AI-2 signaling in E. coli. We show in biofilms that indole addition leads to more extensive differential gene expression at 30°C (186 genes) than at 37°C (59 genes), that indole reduces biofilm formation (without affecting growth) more significantly at 25°C and 30°C than at 37°C, and that the effect is associated with the quorum-sensing protein SdiA. The addition of indole at 30°C compared to 37°C most significantly repressed genes involved in uridine monophosphate (UMP) biosynthesis (carAB, pyrLBI, pyrC, pyrD pyrF, and upp) and uracil transport (uraA). These uracil-related genes are also repressed at 30°C by SdiA, which confirms SdiA is involved in indole signaling. Also, compared to 37°C, indole more significantly decreased flagella-related qseB, flhD, and fliA promoter activity, enhanced antibiotic resistance, and inhibited cell division at 30°C. In contrast to indole and SdiA, the addition of (S)-4,5-dihydroxy-2,3-pentanedione (the AI-2 precursor) leads to more extensive differential gene expression at 37°C (63 genes) than at 30°C (11 genes), and, rather than repressing UMP synthesis genes, AI-2 induces them at 37°C (but not at 30°C). Also, the addition of AI-2 induces the transcription of virulence genes in enterohemorrhagic E. coli O157:H7 at 37°C but not at 30°C. Hence, cell signals cause diverse responses at different temperatures, and indole- and AI-2-based signaling are intertwined.
2008-06-05 | GSE9923 | GEO
Project description:The heat-shock response is a cellular protection mechanism against sudden temperature upshifts extensively studied in Escherichia coli. However, the effects of thermal evolution on this response remain largely unknown. In this study, we investigated the early and late physiological and transcriptional responses to temperature upshift in a thermotolerant strain under continuous culture conditions. Adaptive laboratory evolution was performed on a metabolically engineered E. coli strain (JU15), designed for D-lactic acid production, to enable cellular growth and fermentation of glucose at 45 °C in batch cultures. The resulting homofermentative strain, ECL45, successfully adapted to 45 °C in a glucose-mineral medium at pH 7 under non-aerated conditions. The thermal-adapted ECL45 retained the parental strain’s high volumetric productivity and product/substrate yield. Genomic sequencing of ECL45 revealed eight mutations, including one in a non-coding region and six within the coding regions of genes associated with metabolic, transport, and regulatory functions. Transcriptomic analysis comparing the evolved strain with its parental counterpart under early and late temperature upshifts indicated that the adaptation involved an inactive stringent response. This mechanism likely contributes to the strain’s ability to maintain growth capacity at high temperatures.
2025-05-29 | GSE289056 | GEO
Project description:The bacterial cell envelope is a primary defense mechanism, protecting cells from environmental and intrinsic stressors and ensuring homeostasis. Understanding the molecular pathways involved in envelope biology is critical for both basic and translational research. Peptidoglycan (PG), a key structural component of the envelope, protects bacteria from mechanical and osmotic stress, and maintains cell shape and integrity. We previously identified the Escherichia coli ElyC protein, which contains a conserved domain of unknown function, as essential for envelope integrity at low temperatures. ElyC is required for PG assembly at 21°C and for lipid carrier metabolism in the membrane-associated biosynthesis of PG and other envelope polysaccharides. In ElyC-defective cells at 21°C, PG assembly is blocked, leading to cell lysis. The physiological role of ElyC at 37°C remained unexplored. We performed phenotypic characterization and transcriptomic profiling of ΔelyC mutant cells grown at 37°C and 21°C, compared to wild-type cells. Although ΔelyC mutants grow similarly to wild-type cells at 37°C, they exhibit altered morphology. PG quantification revealed significant inhibition of PG biosynthesis in the absence of ElyC at 37°C. Moreover, these cells show increased sensitivity to PG-targeting β-lactam antibiotics. RNA-Seq analysis revealed that the loss of ElyC leads to a defective cellular envelope at 21°C, whereas at 37°C, the response is more moderate. While PG defects in ElyC-deficient cells are lethal at 21°C, these cells retain sufficient PG integrity at 37°C to survive. However, they are morphologically defective, under envelope stress, and more sensitive to antibiotics. Our findings highlight ElyC’s critical role in the metabolic regulation of PG biosynthesis at both optimal and suboptimal temperatures. These results underscore the importance of ElyC in maintaining cell envelope integrity and its potential as a target for antibiotic development.
2020-03-20 | GSE141694 | GEO
Project description:These E. coli strains were grown with various signaling molecules and the expression profiles were determined. Keywords: addition of quorum and host hormone signals
2007-09-20 | GSE7439 | GEO
Project description:The food enzyme, a maltogenic amylase (glucan 1,4-α-maltohydrolase; EC 3.2.1.133), is produced with a genetically modified Escherichia coli strain BLASC by Advanced Enzyme Technologies Ltd. The genetic modifications do not give rise to safety concerns. The food enzyme is free from viable cells of the production organism and recombinant DNA. This maltogenic amylase is intended to be used in baking and brewing processes and starch processing for the production of glucose syrups. Residual amounts of total organic solids (TOS) are removed by the purification steps applied during the production of glucose syrups; consequently, dietary exposure was not calculated for this food process. For baking and brewing processes, based on the maximum use levels recommended for food processes and individual data from the EFSA Comprehensive European Food Database, dietary exposure to the food enzyme-TOS was estimated to be up to 0.107 mg TOS/kg body weight (bw) per day. Genotoxicity tests did not raise a safety concern. The systemic toxicity was assessed by means of a repeated dose 90-day oral toxicity study in rats. The Panel identified a no observed adverse effect level at the highest dose tested of 838 mg TOS/kg bw per day that, compared with the estimated dietary exposure, resulted in a sufficiently high margin of exposure (at least 7,800). Similarity of the amino acid sequence to those of known allergens was searched and one match was found with respiratory allergen produced by Aspergillus oryzae. The Panel considered that, under the intended conditions of use, the risk for allergic sensitisation and elicitation reactions by dietary exposure cannot be excluded, but the likelihood of such reaction to occur is considered to be low. Based on the data provided, the Panel concluded that this food enzyme does not raise safety concerns under the intended conditions of use.
| S-EPMC7009224 | biostudies-literature
Project description:Toxin/antitoxin (TA) systems reduce metabolism under stress; for example, toxin YafQ of the YafQ/DinJ Escherichia coli TA system reduces growth by cleaving transcripts with in-frame 5'-AAA-G/A-3' sites, and antitoxin DinJ is a global regulator that represses its locus as well as controls levels of the stationary sigma factor RpoS. Here we investigated the influence on cell growth at various temperatures and found that deletion of the antitoxin gene, dinJ, resulted in both reduced metabolism and slower growth at 18°C but not at 37°C. The reduction in growth could be complemented by producing DinJ from a plasmid. Using a transposon screen to reverse the effect of the absence of DinJ, two mutations were found that inactivated the toxin YafQ; hence, the toxin caused the slower growth only at low temperatures rather than DinJ acting as a global regulator. Corroborating this result, a clean deletion of yafQ in the ΔdinJ ΔKmR strain restored both metabolism and growth at 18°C. In addition, production of YafQ was more toxic at 18°C compared to 37°C. Furthermore, by overproducing all the E. coli proteins, the global transcription repressor Mlc was found that counteracts YafQ toxicity only at 18°C. Therefore, YafQ is more effective at reducing metabolism at low temperatures, and Mlc is its putative target.
| S-EPMC4996492 | biostudies-literature
Project description:All free-living microorganisms homeostatically maintain the fluidity of their membranes by adapting lipid composition to environmental temperatures. A quantitative description of how organisms maintain constant fluidity at all growth temperatures has not been achieved. By quantifying both enzymes and metabolic intermediates of the Escherichia coli fatty acid and phospholipid synthesis pathways, we discover how E. coli measures steady-state temperature and restores optimal membrane fluidity within a single generation after temperature shocks.
2024-10-10 | PXD051802 | Pride
Project description:We report the effect of oxygenation state in lactose grown escherichia coli producing recombinant proteins. To shed more light on the mechanistic correlation between the uptake of lactose and dissolved oxygen, a comprehensive study has been undertaken with the E. coli BL21 (DE3) strain. Differences in consumption pattern of lactose, metabolites, biomass and product formation due to aerobiosis have been investigated. Transcriptomic profiling of metabolic changes due to aerobic process and microaerobic process during protein formation phase has been studied and the results provide a deeper understanding of protein production in E. coli BL21 (DE3) strains with lactose based promoter expression systems.This study also provides a scientific understanding of escherichia coli metabolism upon oxygen fluctuations.
2020-05-18 | GSE135698 | GEO
Project description:L-5-Methyltetrahydrofolate (L-5-MTHF) is the only biologically active form of folate in the human body. Production of L-5-MTHF by using microbes is an emerging consideration for green synthesis. However, microbes naturally produce only a small amount of L-5-MTHF. Here, Escherichia coli BL21(DE3) was engineered to increase the production of L-5-MTHF by overexpressing the intrinsic genes of dihydrofolate reductase and methylenetetrahydrofolate (methylene-THF) reductase, introducing the genes encoding formate-THF ligase, formyl-THF cyclohydrolase and methylene-THF dehydrogenase from the one-carbon metabolic pathway of Methylobacterium extorquens or Clostridium autoethanogenum and disrupting the gene of methionine synthase involved in the consumption and synthesis inhibition of the target product. Thus, upon its native pathway, an additional pathway for L-5-MTHF synthesis was developed in E. coli, which was further analysed and confirmed by qRT-PCR, enzyme assays and metabolite determination. After optimizing the conditions of induction time, temperature, cell density and concentration of IPTG and supplementing exogenous substances (folic acid, sodium formate and glucose) to the culture, the highest yield of 527.84 μg g-1 of dry cell weight for L-5-MTHF was obtained, which was about 11.8 folds of that of the original strain. This study paves the way for further metabolic engineering to improve the biosynthesis of L-5-MTHF in E. coli.
| S-EPMC9618320 | biostudies-literature