RNA-Seq of Escherichia coli after anaerobic-aerobic transition
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ABSTRACT:
ORGANISM(S): Escherichia coli
PROVIDER: GSE71562 | GEO | 2016/07/01
SECONDARY ACCESSION(S): PRJNA291519
REPOSITORIES: GEO
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Project description:E. coli K12 strain W3110 was used in this study. Cells were grown anaerobically in defined medium at pH7 and 37°C in a stirred 3-liter bioreactor until the culture reached an OD (600nm) of 3. At that point the first sample was drawn and aeration was started subsequently at 1l/min. 0.5, 1, 2, 5, and 10 min after the onset of aeration additional samples were drawn. 3 replicates of anaerobic culture and 0.5, 1, 2, 5, and 10 min after aeration
2016-07-01 | E-GEOD-71562 | biostudies-arrayexpress
Project description:In Escherichia coli, pH-dependent gene expression varies with oxygen level. Anaerobic pH-dependent expression ratios were analyzed and compared to the published analysis of aerated cultures (Maurer et al, 2005). E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Gene expression profiles were obtained by cDNA hybridization to Affymetrix arrays. pH-dependent expression was seen for 1,394 genes, of which 1,002 show no pH dependence under aeration. Four intergenic regions containing regulatory sRNAs were up-regulated by acid anaerobically (ryeA, csrB, gadY, rybC) and one sRNA (ryhA) by acid with aeration. Acid and anaerobiosis co-regulated the gad regulon; drug transporters (mdtEF, mdtL); catabolism of sugar derivatives whose fermentation minimized acid production; and all hydrogenases (hya, hyb, hyc, hyf, hyp). The hydrogenases however were up-regulated at high pH under aeration (observed by real-time PCR). Acid with anaerobiosis down-regulated penicillin-binding proteins (dacACD, mreBC) and ribosome biosynthesis. Ribosome down-regulation may be caused by restriction of anaerobic metabolism at low pH. A core group of 236 genes showed similar pH response with or without aeration. Core genes up-regulated by acid included fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), the “constitutive” Na+/H+ antiporter (nhaB), and over thirty unidentified proteins. Core genes at high pH included maltodextrin transport (lamB, malEFGKMPQT), ATP synthase, and DNA repair (recA and mutL). Overall, pH and anaerobiosis co-regulated metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm. Keywords: Steady State
2006-10-01 | GSE4556 | GEO
Project description:In Escherichia coli, pH-dependent gene expression varies with oxygen level. Anaerobic pH-dependent expression ratios were analyzed and compared to the published analysis of aerated cultures (Maurer et al, 2005). E. coli K-12 strain W3110 was cultured in closed tubes containing LBK broth buffered at pH 5.7, pH 7.0, and pH 8.5. Gene expression profiles were obtained by cDNA hybridization to Affymetrix arrays. pH-dependent expression was seen for 1,394 genes, of which 1,002 show no pH dependence under aeration. Four intergenic regions containing regulatory sRNAs were up-regulated by acid anaerobically (ryeA, csrB, gadY, rybC) and one sRNA (ryhA) by acid with aeration. Acid and anaerobiosis co-regulated the gad regulon; drug transporters (mdtEF, mdtL); catabolism of sugar derivatives whose fermentation minimized acid production; and all hydrogenases (hya, hyb, hyc, hyf, hyp). The hydrogenases however were up-regulated at high pH under aeration (observed by real-time PCR). Acid with anaerobiosis down-regulated penicillin-binding proteins (dacACD, mreBC) and ribosome biosynthesis. Ribosome down-regulation may be caused by restriction of anaerobic metabolism at low pH. A core group of 236 genes showed similar pH response with or without aeration. Core genes up-regulated by acid included fimbriae (fimAC), periplasmic chaperones (hdeAB), cyclopropane fatty acid synthase (cfa), the â??constitutiveâ?? Na+/H+ antiporter (nhaB), and over thirty unidentified proteins. Core genes at high pH included maltodextrin transport (lamB, malEFGKMPQT), ATP synthase, and DNA repair (recA and mutL). Overall, pH and anaerobiosis co-regulated metabolism and transport so as to maximize alternative catabolic options while minimizing acidification or alkalinization of the cytoplasm. Experiment Overall Design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH during growth without aeration. The experiment was designed for direct comparison with the pH profile under aerobic conditions reported previously (GSE4511). Non-aerated overnight cultures were diluted 1:1000 and incubated in closed tubes containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.7, pH 7.0, and pH 8.5. Tubes were incubated at37°C with slow rotation (8 rpm) to an optical density at 600 nm of 0.2. For each of the three pH conditions, RNA was isolated from five independent cultures. Labeled cDNA was hybridized to Affymetrix antisense arrays according to standard procedures. To analyze the expression levels, Dchip software was used to generate model-based expression indices normalized to sample pH 7 replicate 1. ANOVA was used to identify genes with sitnificant expression differences among the three pH classes (p = 0.001). For genes showing significant differences, the Log2 expression ratios were determined for each pair of pH classes, and significance was determined by Tukey's test (p = 0.001).
2008-06-13 | E-GEOD-4556 | biostudies-arrayexpress
Project description:Global transcriptome analyses at growth before and after 10 min of photooxidative stress were applied to monitor stress dependent gene expression in the alpha-proteobacterium Rhodobacter capsulatus. Transcriptome profiles of pigmented cultures with high aeration were monitored before and after the onset of singlet oxygen stress.
2020-01-24 | GSE134200 | GEO
Project description:The effect of an extracellular acid shift on gene expression profiles of Escherichia coli K-12 W3110 was observed using Affymetrix E. coli arrays. In order to maximize aeration and maintain logarithmic growth, the overnight culture (LBK broth medium) was diluted 500-fold into a 250-ml baffled flask containing 55 ml of 20mM HOMOPIPES buffered medium (pH 7.6). Cultures were grown to OD600=0.2. A shift to acid external pH was conducted by rapid addition of 840 µl 1M HCl, which lowered the pH of the medium to pH 5.5. For each of five biological replicates, 10-ml samples were taken at times 0, 1, 5, and 10 min post addition of HCl. Each sample was added to 1 ml 10% phenol-ethanol stop solution in <5 sec. For each sample, cDNA synthesized from total RNA was hybridized onto Affymetrix E. coli arrays. Model-based gene expression intensities were determined using GCOS software. Gene-by-gene temporal differential expression was analyzed as a mixed-effects model using polynomial time functions as fixed effects and flask variation as a random effect. Experiment Overall Design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of time versus change in external pH. Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 20 mM HOMOPIPES at 7.6. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 225 rpm, incubated at 37°C to an optical density at 600 nm of 0.2. External pH was lowered to pH 5.5 by adding 840 µl of 1M HCl to 40 mls of culture within 5 seconds. Four samples were taken from each of five replicate cultures, corresponding to time 0 (before HCl addition),1, 5, and 10 min post HCl addition.
2008-04-07 | E-GEOD-4778 | biostudies-arrayexpress
Project description:The effect of an extracellular acid shift on gene expression profiles of Escherichia coli K-12 W3110 was observed using Affymetrix E. coli arrays. In order to maximize aeration and maintain logarithmic growth, the overnight culture (LBK broth medium) was diluted 500-fold into a 250-ml baffled flask containing 55 ml of 20mM HOMOPIPES buffered medium (pH 7.6). Cultures were grown to OD600=0.2. A shift to acid external pH was conducted by rapid addition of 840 µl 1M HCl, which lowered the pH of the medium to pH 5.5. For each of five biological replicates, 10-ml samples were taken at times 0, 1, 5, and 10 min post addition of HCl. Each sample was added to 1 ml 10% phenol-ethanol stop solution in <5 sec. For each sample, cDNA synthesized from total RNA was hybridized onto Affymetrix E. coli arrays. Model-based gene expression intensities were determined using GCOS software. Gene-by-gene temporal differential expression was analyzed as a mixed-effects model using polynomial time functions as fixed effects and flask variation as a random effect. Keywords: Time Course
2008-02-20 | GSE4778 | GEO
Project description:Whole genome gene expression level changes in E. coli DH1 exposed to 150 mM [C2mim]Cl in mid exponential growth, and compared to a non-exposed strain. Total RNA was isolated from three biological replicates for each condition: 150 mM [C2mim]Cl exposed at OD(600nm) 0.6, after 30 and 60 min, no exposure to [C2mim]Cl at OD(600 nm) 0.6 after 30 and 60 min.
2014-05-01 | E-GEOD-51731 | biostudies-arrayexpress
Project description:Here we report a metatranscriptomic analysis of gene expression and regulation of “Candidatus Accumulibacter”-enriched lab-scale sludge during enhanced biological phosphorus removal (EBPR). Medium density oligonucleotide microarrays were generated with probes targeting most predicted genes hypothesized to be important for the EBPR phenotype. The objectives were to investigate which genes were expressed during EBPR and which genes were differentially expressed between the early stage of anaerobic and aerobic phases (defined as 15 min after acetate addition and 15 min after switching to aeration respectively).
2009-12-31 | GSE17857 | GEO
Project description:To understand cell responses against high succinate stress, a continuous culture was performed for 9 months using a wild Escherichia coli under gradually increasing succinate stress. The final adapted strain against high succinate stress, named DST160, was able to grow with no lag phase in medium containing 1.35 M of succinate stress while wild W3110 showed more than 38 h lag phase. The maximum growth rate and growth yield of DST160 under the stress condition were 0.20 h-1 and 0.192 g-cell/g-glucose, which were 53.8 % and 12.3 % higher than those of W3110 (0.13 h-1 and 0.171 g-cell/g-glucose, respectively). A single colony of E. coli W3110 was inoculated into a 15-mL tube containing 4 mL of LB medium. After 12 h cultivation in a shaking incubator at 37℃ and 220 rpm, pre-culture (1 mL) was transferred to a 250 mL-fermentor (Mini-chemostat fermentor; Biotron Inc., Bucheon, Korea) containing 100 mL medium consisted of M9-glucose minimal medium (3 g glucose , 0.8 g NH4Cl, 0.5 g NaCl, 7.5 g Na2HPO4•2H2O, 3 g KH2PO4 with separately added trace elements of 0.2 g MgSO4•7H2O, 0.1 g CaCl2, 1 mg thiamine) per liter supplemented with 254 mmole of succinate (30 g succinic acid) per liter. The initial pH of the medium was set to be pH 7.5 by adding 6N NaOH. The fermentor was operated at 37℃, 350 rpm with air flushing (100 mL/min.). After 12 h batch mode growth, feeding and outlet pumps were turned on at flow rate of 0.167 mL/min (Dilution rate=0.1 h-1). The fresh medium reservoir (10 L) contained the same contents and pH with the initial medium. Every 10 turnover time (100 h), the reservoir was changed with the same medium composition except succinate concentration. The succinate concentration of the reservoir was gradually increased by 25.4 ~ 84.7 mM (3 ~ 10 g/L of succinic acid) at a time than previous states depending on the cell concentrations at the outlet. When the cell concentration was reduced below O.D.=0.2, succinate feeding pump was temporarily stopped to go back to the slightly lower succinate concentration. The continuous culture was performed until the steady state when succinate in the reservoir reached 1.35 M (160 g/L in succinic acid form). The final adapted cells in 100 mL culture were harvested by centrifuge and frozen rapidly in a liquid nitrogen tank for further analyses including DNA microarray. To understand the change of up/down regulations in the high-succinate adapted E. coli, total mRNAs of control cells and the adapted E. coli cells were extracted using a RNA extraction kit (RNeasy mini kit; Quiagen, Hilden, Germany), and the transcriptomes were compared using DNA microarray. Hybridization and washing were accomplished by a facility of Digital Genomics Co (Seoul, Korea). DNA microarray were scanned using an Axon GenePix 4000B Scanner (Axon Instruments, Union City, CA, USA), and the scanned images were analyzed with GenePix Pro 3.0 software to obtain gene expression ratios.
2009-10-29 | E-GEOD-17991 | biostudies-arrayexpress
Project description:Gene expression in E coli W3110 strains with either ybaO over-expression (W3110/pcutR) or ybaO deletion (W3110/ΔcutR) were measured with cysteine challenge.
2017-06-13 | GSE90066 | GEO