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CcpA, a Pleiotropic Key Regulator in Butanol-producing Clostridium acetobutylicum ATCC 824

ABSTRACT: Clostridium acetobutylicum is a typical bacterium of major importance to industrial butanol production. In order to dissect the regulatory network pertaining to the industrial application of this bacterium, catabolite control protein A (CcpA) was investigated for its global function by DNA microarray.It showed that CcpA of C. acetobutylicum controls hundreds of genes, not only carbon metabolism, but also solvent production and sporulation in the life cycle.The results here demonstrated that CcpA is an important pleiotropic regulator related to some specific physiological and biochemical process in butanol-producing C. acetobutylicum.

ORGANISM(S): Clostridium acetobutylicum

PROVIDER: GSE33364 | GEO | 2012/08/30

SECONDARY ACCESSION(S): PRJNA148997

REPOSITORIES: GEO

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CcpA, a Pleiotropic Key Regulator in Butanol-producing Clostridium acetobutylicum ATCC 824

Project description:Clostridium acetobutylicum is a typical bacterium of major importance to industrial butanol production. In order to dissect the regulatory network pertaining to the industrial application of this bacterium, catabolite control protein A (CcpA) was investigated for its global function by DNA microarray.It showed that CcpA of C. acetobutylicum controls hundreds of genes, not only carbon metabolism, but also solvent production and sporulation in the life cycle.The results here demonstrated that CcpA is an important pleiotropic regulator related to some specific physiological and biochemical process in butanol-producing C. acetobutylicum. In order to enable a global understanding of the regulatory roles of CcpA when fermenting mixed sugars, which is of great significance in utilization of lignocellulosic hydrolysates, D-glucose plus D-xylose were used as the carbon sources in fermentation for microarray analysis. Microarray analysis was performed at four time points:the time point M and L were chosen both in acidogenic phase, while the time point T and S were chosen in shift phase (from acidogenesis to solventogenesis) and solventogenic phase, respectively.One-color microarray assays were performed.Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The ratio of transcript level between wildtype and mutant can been achieved using the formula: 2^(value of wildtype)/2^(value of ccpA mutant).

2012-08-30 | E-GEOD-33364 | biostudies-arrayexpress

Metabolite stress response to butanol in Clostridium acetobutylicum ATCC 824

2013-08-20 | GSE48031 | GEO

Clostridium acetobutylicum ATCC 824 butanol stress (50 mM)

Project description:Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, but such effects are not well understood at the genomic level. Using DNA microarrays, the Clostridium acetobutylicum transcriptional stress response to butanol was analyzed. Keywords: stress response

2007-12-29 | GSE5008 | GEO

Metabolite stress response to butanol in Clostridium acetobutylicum ATCC 824

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

Metabolite stress response to butyric acid in Clostridium acetobutylicum ATCC 824

2013-08-20 | GSE48039 | GEO

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum following a single n-butanol pulse

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

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum following a single n-butanol pulse_Exp2

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-3265 | biostudies-arrayexpress

Clostridium acetobutylicum ATCC 824 (pLib1) butanol stresses with repeated transfers

Project description:Metabolite accumulation has pleiotropic, including toxic, effects on cellular physiology, with a variety of genetic resistance mechanisms previously identified. Using random genomic libraries and DNA microarrays, library inserts were preferentially enriched by culturing in media containing butanol, with successive transfers into fresh media containing incrementally increasing butanol concentrations. Keywords: genomic library preferential enrichment

2007-12-29 | GSE6289 | GEO

A transcriptional study of acidogenic chemostat cells of Clostridium acetobutylicum - cellular behavior in adaptation to n-butanol

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

Metabolite stress response to butyric acid in Clostridium acetobutylicum ATCC 824

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

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