Escherichia coli K-12
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ABSTRACT:
PROVIDER: PRJNA236751 | ENA |
REPOSITORIES: ENA
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Project description:Cells were grown aerobically at 37 degC in Spizizen minimal medium either supplemented with 1 mM glycine betaine, 1.2 M NaCl or 1.2 M NaCl and 1 mM glycine betaine. Cells were harvested in the exponential growth phase at an OD600nm of 1.0.
Proteome analysis was performed with samples from three biological replicates.
2020-01-08 | MSV000084766 | MassIVE
Project description:We probed the mechanism of cross-regulation of osmotic and heat stress responses by characterizing the effects of high osmolarity (0.3M vs. 0.0M NaCl) and temperature (43oC vs. 30oC) on the transcriptome of Escherichia coli K12 using E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures). Total RNA was extracted using a hot phenol-chloroform method. cDNA synthesis, fragmentation and labeling, and washing and scanning of E. coli GeneChip Arrays were performed according to the instructions of the manufacturer (Affymetrix Technical Manual, Affymetrix, Inc., USA). Labeled cDNA was hybridized to E. coli Genome 2 Array (Affymetrix, Inc.). Independent array hybridizations were carried out for 3 biological replicates (independent cultures) of each condition. A number of genes in the SoxRS and OxyR oxidative stress regulons were up-regulated by high osmolarity, high temperature, and/or by the combination of both stresses. This result could account for cross-protection of osmotic stress against oxidative stress. The trehalose biosynthetic genes were induced by both stresses, in accord with the proposed protective role of this disaccharide against thermal and oxidative damage. Experiment Overall Design: E. coli K12 strain NCM3722 cultures were grown with aeration in K medium containing 10 or 20 mM glucose. To impose osmotic stress, the osmolarity of the medium was increased to 0.64 osm by supplementation with 0.3 M NaCl. Because E. coli is a methionine auxotroph above 42oC the K medium cultures were supplemented with 0.5 mM methionine. Glycine betaine (GB) was added to the high osmolarity media to a final concentration of 1 mM. Cells taken from a single colony on LB agar were inoculated into 1ml liquid LB and grown to saturation at 37oC, then 0.05 ml were inoculated into i) K medium, 0.5 mM methionine, 10 mM glucose; ii) K medium, 0.5 mM methionine, 10 mM glucose, 0.3 M NaCl; and iii) K medium, 0.5 mM methionine, 10 mM glucose, 0.3 M NaCl, 1 mM GB. The cultures were grown to saturation at 30oC and 43oC, and sub-cultured once into the same medium and grown at the same temperatures as before. Exponentially growing cells form these cultures were then inoculated into Erlenmeyer flasks (starting OD600nm 0.05) containing 40 ml of the same medium, and incubated in the same salt and temperature conditions as used previously, except that the glucose concentration was increased to 20 mM. When the cells reached OD600nm of 0.4-0.5 (~3 doublings), 25 ml were added to a 2.5 ml mixture of cold 95% ethanol and 5% phenol to preserve RNA. The cells were cooled briefly on ice, immediately harvested by centrifugation (4oC), and the pellet was frozen on dry ice. The six different growth conditions used were: C1 - 30oC, no NaCl; C2: 30oC, 0.3 M NaCl; C3: 30oC, 0.3 M NaCl, 1 mM GB; C4: 43oC, no NaCl; C5: 43oC, 0.3 M NaCl; C6: 43oC, 0.3 M NaCl, 1 mM GB.
2009-01-14 | E-GEOD-7656 | biostudies-arrayexpress
Project description:Global gene expression profiles of V. parahaemolyticus grown under 2% and 0.66% NaCl were compared to define the minimum low-salt stimulon. The ectABC-lysC operon for synthesis of the compatible solute ectoine, as well as three compatible-solute transport systems, namely ProU (glycine betaine), OpuD1 (glycine betaine) and Pot2 (spermidine), was up-regulated under 2% NaCl in relative to 0.66% NaCl. The 2% NaCl condition favored the inducible expression of OmpW, OmpN and OmpA2, while repressed the expression of OmpA1, OmpU and VP1008. These results indicated that, to master the hyperosmotic stress of saline environments, V. parahaemolyticus might not only accumulate osmoprotectants through uptake or endogenous synthesis of compatible solutes, but also remodel its profiles of outer membrane protein to restore its cell membrane. The above differentially regulated genes will provide novel candidates for the further investigation of the molecular mechanisms of osmoadaptation in V. parahaemolyticus.
2009-07-07 | GSE16530 | GEO
Project description:Glycine betaine (GB) is a potent osmoprotectant for salt stressed Bacillus subtilis cells, which possess three high-affinity uptake systems for GB. OpuA is the dominant transporter for this compatible solute. Northern blot analysis, primer extension experiments and opuA-treA reporter gene fusion studies demonstrated that opuA expression is strongly induced at high osmolality from a single SigA-type promoter. Promoter mutations that improve the match of the opuA promoter to the consensus sequence substantially increase basal-level expression but reduce inducibility by high salinity. Expression of opuA is sensitively controlled by GB, which causes significant repression of opuA transcription at low and high salinity. GB influences the kinetics as well as the final level of high salinity induction of opuA in a concentration-dependent fashion. The repressing effect of GB on opuA transcription requires the intracellular presence of GB, regardless whether it is taken up via OpuA or other transporters or synthesized from choline. Genome-wide transcriptional profiling of salt-stressed B. subtilis cells demonstrated that the repressive effect of GB targets only a subset of high-salinity induced genes. This group of GB-responsive genes comprises in essence the full set of genes with demonstrated functions in either the uptake or synthesis of compatible solutes. Four different samples (untreated, GB, NaCl, and GB + NaCl treated) were analyzed and each sample was hybridized in triplicate.
2010-05-15 | E-GEOD-17435 | biostudies-arrayexpress
Project description:Grow strain 3841 on AMS minimal medium with glucose 10mM and ammonium chloride 10 mM and compare it to the same growth conditions but plus 100 mM NaCl
2007-03-17 | E-MEXP-1041 | biostudies-arrayexpress
Project description:Growth in 0.3 M NaCl M63 minimal medium affects the transcriptome of Dickeya dadantii 3937.in comparison to that of cells grown in M63 medium.
2015-11-01 | GSE64739 | GEO
Project description:The gene expression profile of E. coli K-12 MG1655 grown in minimal medium supplemented with elevated copper concentrations (as copper-glycine) has been analysed using whole genome oligonucleotide microarrays. “Pool” RNA was isolated from five independently grown 50ml DMA cultures of E. coli K-12 MG1655. “Test” RNA was isolated from three independently grown 50ml DMA cultures of E. coli K-12 MG1655, for each growth condition (no added CuSO4, or supplemented with either 0.75mM or 2mM copper glycine). A sample of each culture was taken at mid to late exponential growth phase at OD600 0.8 (measured using a Pharmacia Biotech Ultrospec 2000 in a cuvette with a path length of 10mm). Keywords: dose response
2004-09-22 | GSE1780 | GEO
Project description:Sprobolus virginicus is a halophytic C4 grass found in worldwide from tropical to warm temperate regions. A Japanese genotype showed a salinity tolerance up to 1,500 mM NaCl, a three-fold higher concentration than seawater salinity. To identify key genes involved in the regulation of salt tolerance in S. virginicus, random cDNA libraries were constructed from salt-treated leaves, and were introduced into Arabidopsis for salt tolerant plant screening. Eight independent transgenic lines were found to be more salt tolerant than wild type from the screen of 3011 lines on the medium containing 175 mM NaCl. Among the selected lines, two contained cDNAs encoding glycine-rich RNA-binding proteins (GRPs). To identify transcriptomic change in the GRP-transgenic line, we performed microarray analysis of the transgenic line and WTunder salt stress.
2016-07-12 | GSE84221 | GEO
Project description:The gene expression profile of E. coli K-12 MG1655 grown in minimal medium supplemented with elevated copper concentrations (as copper-glycine) has been analysed using whole genome oligonucleotide microarrays. â??Poolâ?? RNA was isolated from five independently grown 50ml DMA cultures of E. coli K-12 MG1655. â??Testâ?? RNA was isolated from three independently grown 50ml DMA cultures of E. coli K-12 MG1655, for each growth condition (no added CuSO4, or supplemented with either 0.75mM or 2mM copper glycine). A sample of each culture was taken at mid to late exponential growth phase at OD600 0.8 (measured using a Pharmacia Biotech Ultrospec 2000 in a cuvette with a path length of 10mm).
2010-06-05 | E-GEOD-1780 | biostudies-arrayexpress
Project description:mRNA sequencing was performed on E. coli K-12 MG1655 with Glucose supplemented on Glycine and L-Threonine
2017-02-14 | GSE59760 | GEO