Transcriptomics

Dataset Information

6

Metabolite stress response to butyric acid in Clostridium acetobutylicum ATCC 824


ABSTRACT: 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.

ORGANISM(S): Clostridium acetobutylicum ATCC 824  

SUBMITTER: Keerthi P Venkataramanan   Eleftherios T Papoutsakis  Eleftherios Terry Papoutsakis  Shawn W Jones 

PROVIDER: E-GEOD-48039 | ArrayExpress | 2013-08-20

SECONDARY ACCESSION(S): GSE48039PRJNA208745

REPOSITORIES: GEO, ArrayExpress

Dataset's files

Source:
Action DRS
E-GEOD-48039.idf.txt Idf
E-GEOD-48039.processed.1.zip Processed
E-GEOD-48039.raw.1.zip Raw
E-GEOD-48039.raw.2.zip Raw
E-GEOD-48039.raw.3.zip Raw
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