PH-dependent steady states of ABE fermetation in C. acetobutylicum
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SUBMITTER: Thomas Millat
PROVIDER: 66 | FAIRDOMHub | 2014-06-11
REPOSITORIES: FAIRDOMHub
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Project description:Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism. Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908
2016-05-11 | GSE81273 | GEO
Project description:Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism. Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908 Phosphate-limited continuous cultures of C. acetobutylicum were performed under acidogenesis (pH 6.3, 995 mM of carbon from glucose), solventogenesis (pH 4.4, 995 mM of carbon from glucose) and alcohologenesis (pH 6.3, 498 mM of carbon from glucose and 498 mM of carbon from glycerol). Samples were collected for three biological replicates from one control strain and three metabolic mutants, respectively. Total RNA of 36 samples was extracted using an RNeasy Midi kit (Qiagen, Courtaboeuf, France) following the manufacturer's instructions with the supplementation of DNase treatment using RNase-Free DNase Set (Qiagen). Agilent microarray for Clostridium acetobutylicum ATCC 824 (4x44K AMADID 024247) was used. The RNAs were labeled with a Low Input Quick Amp Labeling kit and hybridized following a one-color microarray-based gene expression analysis protocol.
2015-07-01 | E-GEOD-69973 | biostudies-arrayexpress
Project description:Transcriptomic analysis was applied to acidogenic, solventogenic and alcohologenic steady-state C. acetobutylicum cells for understanding the regulation of the metabolism of this organism. Used microarray is Clostridium acetobutylicum ATCC824 transcriptional 44k v4, correspondance to GPL10908
2015-07-01 | GSE69973 | GEO
Project description:Clostridium acetobutylicum is characterized by its acetone-butanol (AB) fermentation which <br>can be reproducibly established under continuous grow conditions in a chemostat. <br>At pH 5.7 cells show typical acidogenic metabolism and mainly produce the acids <br>acetate and butyrate. After lowering and further control the external pH at 4.5 <br>the exponentially growing cells switch towards stable solvent production with the <br>dominating fermentation products acetone and butanol. <br>Here we present a comprehensive comparison of proteome and transcriptome <br>data of continuously growing cells of C. acetobutylicum in a chemostat culture <br>under phosphate limitation at pH 5.7 (acidogenesis) and pH 4.5 (solventogenesis).
2010-11-10 | E-MEXP-2503 | biostudies-arrayexpress
Project description:Clostridium acetobutylicum is well-known for its butanol production. Butanol toxicity is a major drawback for the generation of high-butanol producing strains. Here, the transcriptional response a steady state, acidogenic (pH 6), phosphate-limited Clostridium acetobutylicum chemostat culture to different levels of n-butanol (0.25-1%) was investigated. For the butanol challenge experiments butanol (1-butanol) was added (a) to the supplying medium and (b) to the culture vessel to guarantee an immediate change in the butanol concentration. Addition of butanol to the culture was timed to match the supply of the new medium through the feedlines. The butanol concentration was increased stepwise in intervals of 66.6 h (5 volume changes) to moderate butanol concentrations of 0.25%, 0.5%, 0.75% and 1% (v/v).
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Project description:Clostridium acetobutylicum isolate:Clostridium acetobutylicum Genome sequencing
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Project description:effect of pH on continuous cultures of Clostridium acetobutylicum
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Project description:Clostridium acetobutylicum has been extensively exploited to produce biofuels and solvents and its biofilm could dramatically improve its productivities. However, genetic control of C. acetobutylicum biofilm has not been dissected so far. Here, a total of 24 disruptants were finally obtained over several years of attempts. Biofilm formation and physiological phenotypes were characterized for these disruptants and most of them showed robust biofilm formation still, or showed both impaired biofilm formation and cell growth. Only a mutant with a disputed histidine kinase gene (CA_C2730, designated bfcK in this study) abolished biofilm formation without impaired cell growth or solvent production. Phosphoproteomic analysis revealed that bfcK could control C. acetobutylicum flagellar motility at both translational and post-translational (protein phosphorylation) levels. The bfcK also showed apparent regulation of a serine/threonine protein kinase (encoded by CA_C0404) which was involved in protein secretion. Based on these findings, possible bfcK-based mechanisms for biofilm formation in C. acetobutylicum were proposed.
2021-07-30 | PXD021161 | Pride
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:Clostridium acetobutylicum Proteomic
| PRJNA1033420 | ENA