Quantitative transcriptomic analysis of wild type and metabolic mutants of Clostrdidium acetobutylicum ATCC824 under different physiological conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Clostridium acetobutylicum ATCC 824
PROVIDER: GSE69973 | GEO | 2015/07/01
SECONDARY ACCESSION(S): PRJNA288561
REPOSITORIES: GEO
Similar Datasets
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:Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyrate posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butanol.
2013-08-20 | GSE48031 | GEO
Project description:Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyric acid posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butyric acid.
2013-08-20 | GSE48039 | GEO
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).
2012-01-30 | E-MEXP-3571 | biostudies-arrayexpress
Project description:Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyrate posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butanol. C. acetobutylicum cultures were grown, three biological replicates, to mid-exponential phase and then stressed with four levels of butanol (0 mM - No stress; 30 mM - Low stress; 60 mM - Medium stress; & 90 mM - High stress). Samples were collected following the stress at 0, 15, 30, 45, 60 and 75 min, post stress. These sampling times, which are of the order of the doubling time of these cells, were meant to capture largely the direct and immediate impact of these stresses on gene expression. The RNA extracted from two biological replicates were used for microarray hybridization foloowing cDNA generationa nd labelling using Agilent 44K arrays, while the third was used for q-RT-PCR validation. For each stress level, 6 time points with 2 biological replicates and dye swaps (Cy3/Cy5) were prepared for comparison. The hybridization was perfomed against an equal amount of oppositely labeled cDNA from common reference pool prepared using equal amounts of labeled cDNA from all four stress levels.
2013-08-20 | E-GEOD-48031 | biostudies-arrayexpress
Project description:Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyric acid posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butyric acid. C. acetobutylicum cultures were grown, three biological replicates, to mid-exponential phase and then stressed with four levels of butyric acid (0 mM - No stress; 30 mM - Low stress; 40 mM - Medium stress; & 50 mM - High stress). Butyric acid was pH adjusted with 10M KOH to match the pH of the cultures, prior to addition. Samples were collected following the stress at 0, 15, 30, 45, 60 and 75 min, post stress. These sampling times, which are of the order of the doubling time of these cells, were meant to capture largely the direct and immediate impact of these stresses on gene expression. The RNA extracted from two biological replicates were used for microarray hybridization foloowing cDNA generation and labelling using Agilent 44K arrays, while the third was used for q-RT-PCR validation. For each stress level, 6 time points with 2 biological replicates and dye swaps (Cy3/Cy5) were prepared for comparison. The hybridization was perfomed against an equal amount of oppositely labeled cDNA from common reference pool prepared using equal amounts of labeled cDNA from all four stress levels.
2013-08-20 | E-GEOD-48039 | biostudies-arrayexpress
Project description:The goal of this experiment is compare gene expression profiles between C. acetobutylicum ATCC 55025, histidine kinase cac3319 and cac0437 inactivated strains to determine the pleiotropic and distinctive functions of histidine kinases on cell differentiation and cellular metabolism. Samples for total RNA extraction were collected from fermentation broth at acidogenic phase (8 h) and solventogenic phase (16 h)
2019-05-01 | E-MTAB-7341 | biostudies-arrayexpress
Project description:Lee2008 - Genome-scale metabolic network of
Clostridium acetobutylicum (iJL432)
This model is described in the article:
Genome-scale reconstruction
and in silico analysis of the Clostridium acetobutylicum ATCC
824 metabolic network.
Lee J, Yun H, Feist AM, Palsson
BØ, Lee SY.
Appl. Microbiol. Biotechnol. 2008 Oct;
80(5): 849-862
Abstract:
To understand the metabolic characteristics of Clostridium
acetobutylicum and to examine the potential for enhanced
butanol production, we reconstructed the genome-scale metabolic
network from its annotated genomic sequence and analyzed
strategies to improve its butanol production. The generated
reconstructed network consists of 502 reactions and 479
metabolites and was used as the basis for an in silico model
that could compute metabolic and growth performance for
comparison with fermentation data. The in silico model
successfully predicted metabolic fluxes during the acidogenic
phase using classical flux balance analysis. Nonlinear
programming was used to predict metabolic fluxes during the
solventogenic phase. In addition, essential genes were
predicted via single gene deletion studies. This genome-scale
in silico metabolic model of C. acetobutylicum should be useful
for genome-wide metabolic analysis as well as strain
development for improving production of biochemicals, including
butanol.
This model is hosted on
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MODEL1507180030.
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2015-07-30 | MODEL1507180030 | BioModels
Project description:In this study the transcriptional behavior of the natural solvent producing bacterium Clostridium acetobutylicum was investigated following n-butanol stress using DNA microarray analysis. Therefore, a phosphate-limited chemostat culture was established and n-butanol stress (0.9%) was added to acidogenic cells at pH 5.7.
2012-04-30 | E-MEXP-3264 | biostudies-arrayexpress