Base and acid resistance of B. subtilis associated with transcriptomic responses
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ABSTRACT:
ORGANISM(S): Bacillus subtilis
PROVIDER: GSE11810 | GEO | 2009/01/13
SECONDARY ACCESSION(S): PRJNA105899
REPOSITORIES: GEO
Similar Datasets
Project description:Gene expression profiles of Bacillus subtilis strain AG174 were compared as a function of steady-state external pH during growth with aeration. Aerated overnight cultures were diluted 1:500 and incubated in 250 mL baffled flasks containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 6.0, pH 7.0, and pH 9.0. Tubes were incubated at 37°C with aeration (260 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. Overnight cultures were diluted 1:500 and incubated in 250 mL baffled flasks containing potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 6.0, pH 7.0, and pH 9.0. Cultures were incubated at 37°C with aeration (260 rpm) to an optical density at 600 nm of 0.2. Five replicate cultures were grown at each pH.
2009-01-12 | E-GEOD-11810 | biostudies-arrayexpress
Project description:Bacillus subtilis strain AG174 was grown in the presence and absence of benzoate (30 mM). Benzoate was used in order to equalize the external and internal pH. The cultures were grown at external pH 7.0, and the addition of benzoate did not change the external pH. Microarray analysis was performed on cDNA synthesized from bacterial RNA. Real-time PCR of highly up-regulated genes confirmed the results of the microarray. These data were compared to previous B.subtilis microarray results, where genes regulated by external pH were identified. Overnight cultures were diluted 1:500 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM MOPS at pH 7.0. Bacteria were cultured in baffled flasks (less than 10% volume) with rotation at 220 rpm, incubated at 37 °C to an optical density at 600 nm of 0.2. Four cultures were grown in the presence of 30 mM benzoate and four cultures were grown without benzoate. One sample was taken from each of four replicate cultures of 0 mM benzoate and 30 mM benzoate. RNA was isolated using 10% saturated phenol-ethanol solution and the RNeasy Kit. Gene expression profiles were obtained with standard Affymetrix procedures.
2010-05-19 | E-GEOD-12263 | 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 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:Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Cultures were grown with aeration to an optical density at 600 nm of 0.3 in potassium-modified Luria-Bertani medium buffered at pH 5.0, 7.0, and 8.7. For each of the three pH conditions, cDNA from RNA of five independent cultures was hybridized to Affymetrix E. coli arrays. Analysis of variance with a significance level of 0.001 resulted in 98% power to detect genes showing a twofold difference in expression. Normalized expression indices were calculated for each gene and intergenic region (IG). Differential expression among the three pH classes was observed for 763 genes and 353 IGs. Hierarchical clustering yielded six well-defined clusters of pH profiles, designated Acid High (highest expression at pH 5.0), Acid Low (lowest expression at pH 5.0), Base High (highest at pH 8.7), Base Low (lowest at pH 8.7), Neutral High (highest at pH 7.0, lower in acid or base), and Neutral Low (lowest at pH 7.0, higher at both pH extremes). Flagellar and chemotaxis genes were repressed at pH 8.7 (Base Low cluster), where the cell's transmembrane proton potential is diminished by the maintenance of an inverted pH gradient. High pH also repressed the proton pumps cytochrome o (cyo) and NADH dehydrogenases I and II. By contrast, the proton-importing ATP synthase F1Fo and the microaerophilic cytochrome d (cyd), which minimizes proton export, were induced at pH 8.7. These observations are consistent with a model in which high pH represses synthesis of flagella, which expend proton motive force, while stepping up electron transport and ATPase components that keep protons inside the cell. Acid-induced genes, on the other hand, were coinduced by conditions associated with increased metabolic rate, such as oxidative stress. All six pH-dependent clusters included envelope and periplasmic proteins, which directly experience external pH. Overall, this study showed that (i) low pH accelerates acid consumption and proton export, while coinducing oxidative stress and heat shock regulons; (ii) high pH accelerates proton import, while repressing the energy-expensive flagellar and chemotaxis regulons; and (iii) pH differentially regulates a large number of periplasmic and envelope proteins. Experiment Overall Design: Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Overnight cultures were diluted 1:1000 in potassium-modified Luria-Bertani medium (LBK) buffered with 50 mM HOMOPIPES at pH 5.0, pH 7.0, and pH 8.7. Bacteria were cultured in baffled flasks (less than 10% volume filled) with rotation at 240 rpm, incubated at 37°C to an optical density at 600 nm of 0.3. 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).
2007-09-21 | E-GEOD-4511 | 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. 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:Gene expression profiles of Escherichia coli K-12 W3110 were compared as a function of steady-state external pH. Cultures were grown with aeration to an optical density at 600 nm of 0.3 in potassium-modified Luria-Bertani medium buffered at pH 5.0, 7.0, and 8.7. For each of the three pH conditions, cDNA from RNA of five independent cultures was hybridized to Affymetrix E. coli arrays. Analysis of variance with a significance level of 0.001 resulted in 98% power to detect genes showing a twofold difference in expression. Normalized expression indices were calculated for each gene and intergenic region (IG). Differential expression among the three pH classes was observed for 763 genes and 353 IGs. Hierarchical clustering yielded six well-defined clusters of pH profiles, designated Acid High (highest expression at pH 5.0), Acid Low (lowest expression at pH 5.0), Base High (highest at pH 8.7), Base Low (lowest at pH 8.7), Neutral High (highest at pH 7.0, lower in acid or base), and Neutral Low (lowest at pH 7.0, higher at both pH extremes). Flagellar and chemotaxis genes were repressed at pH 8.7 (Base Low cluster), where the cell's transmembrane proton potential is diminished by the maintenance of an inverted pH gradient. High pH also repressed the proton pumps cytochrome o (cyo) and NADH dehydrogenases I and II. By contrast, the proton-importing ATP synthase F1Fo and the microaerophilic cytochrome d (cyd), which minimizes proton export, were induced at pH 8.7. These observations are consistent with a model in which high pH represses synthesis of flagella, which expend proton motive force, while stepping up electron transport and ATPase components that keep protons inside the cell. Acid-induced genes, on the other hand, were coinduced by conditions associated with increased metabolic rate, such as oxidative stress. All six pH-dependent clusters included envelope and periplasmic proteins, which directly experience external pH. Overall, this study showed that (i) low pH accelerates acid consumption and proton export, while coinducing oxidative stress and heat shock regulons; (ii) high pH accelerates proton import, while repressing the energy-expensive flagellar and chemotaxis regulons; and (iii) pH differentially regulates a large number of periplasmic and envelope proteins. Keywords: Steady State
2006-03-23 | GSE4511 | 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 “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:Our research describe the influence of aeration conditions in petri dishes for A. thaliana growth. We analyze the difference between plants grown in standard Petri dish (Non-aerated) and modified Petri dish that include aeration (Aerated). To characterize the differences between those conditions the gene expression analysis was performed. We also wanted to analyze the effect of using a micropore filter, so we designed another experiment with Aerated, Non-aerated and Micropore filter conditions.
2019-03-20 | GSE120840 | GEO
Project description:Transcription profile of Escherichia coli cells in biofilms under static batch culture was compared to that of E. coli cells in planktonic cultures. Both E. coli biofilm and planktonic cultures were cultivated for 18 h in 10% Luria-Bertani broth at room temperature (20 degree Celsius). Biofilms were grown in static batch culture in petri dishes. Both planktonic culture and biofilms were homogenized and run through a separated protocol.
2013-12-30 | GSE24914 | 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. Keywords: Time Course
2008-02-20 | GSE4778 | GEO