Project description:Investigation of whole genome gene expression levels in Clostridium acetobutylicum strain 824 grown individually on starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose A 33 array study using total RNA recovered from three separate wild-type cultures of Clostridium acetobutylicum 824 grown on each of the following sugars: starch, galactose, lactose, mannose, fructose, glucose, arabinose, xylose, cellobiose, maltose, sucrose. RNA extraction, cDNA production, and labeling were performed independently on three separate cultures for each carbohydrate. Each independent sample was hybridized to one array equating to one technical replicate for each biological sample and three biological replicates for each condition tested. Each array contains 2 replicates of 9 probes approximately 60 bp in length for each of the 3,842 open reading frames annotated in the C. acetobutylicum 824 genome.
Project description:Clostridium acetobutylicum, the endospore-forming anaerobe best known for its ABE (acetone-butanol-ethanol) fermentation, has received renewed attention recently for the biological production of butanol, both for bulk chemical production and as a potential biofuel. With butanol production in mind, most of the recent research on C. acetobutylicum has focused on increasing butanol production, tolerance to butanol, and optimizing it for various substrates. However, an equally important trait, though less understood, is its sporulation program, which it coupled to solvent formation. The model organism for endospore formation is Bacillus subtilis, but significant physiological, metabolic, and genomic differences exist between the two organisms. Despite these differences, the major sporulation-related transcription/sigma factors are conserved between the two species. These transcription/sigma factors are activated in a cascade manner such that Spo0A becomes active first, followed by σF, then σE, then σG, and finally σK. The goal of this study is to determine the regulons of 4 of these transcription/sigma factors (Spo0A, σF, σE, and σG) and compare them to those in B. subtilis. To accomplish this goal, individual mutant strains were created for Spo0A, σF, σE, and σG, in which the transcription/sigma factor is silenced. These mutants were then compared transcriptionally using microarrays to determine the regulon of each transcription/sigma factor. To help avoid false positives, comparisons were made between strains in which the downstream transcription/sigma factor is silenced (e.g., for the Spo0A regulon, the Spo0A mutant was compared against the σF mutant and the σE mutant, since they are both upregulated by Spo0A) rather than just the WT. For each regulon, 4 timepoints were taken, since it is very difficult to synchronize sporulation in C. acetobutylicum cultures, and dye-swaps were prepared for each timepoint.
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.
