Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-seq of Clostridium acetobutylicum ATCC 55025, histidine kinase Cac3319 and Cac0437 inactivated strains.

ABSTRACT: 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)

INSTRUMENT(S): RNeasy Mini Kit, Eppendorf Centrifuge, ABI PCR Instruments, Illumina HiSeq 2000

ORGANISM(S): Clostridium acetobutylicum

SUBMITTER: Chuang Xue

PROVIDER: E-MTAB-7341 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Furfural is the prevalent microbial inhibitor generated during pretreatment and hydrolysis of lignocellulosic biomass to monomeric sugars, but the molecular response of Clostridium beijerinckii NCIMB 8052 to this compound is unknown. To discern the effect of furfural on C. beijerinckii and to gain insights into the molecular mechanisms of action and detoxification, we studied the physiological changes of furfural-stressed cultures during acetone-butanol-ethanol (ABE) fermentation, and profiled differentially expressed genes by genome-wide transcriptional analysis. C. beijerinckii exposed to furfural stress during the acidogenic growth phase produced 13% more ABE than the unstressed control. The growth and ABE by C. beijerinckii ceased following exposure to furfural stress during the solventogenic growth phase. By comparing gene expression of furfural-stressed cultures to that of the unstressed control, at both the acidogenic and solventogenic phases, we ascertained that furfural induces expression of several genes including those that code for heat shock proteins, redox enzymes and cofactor associated proteins, and ATP-binding cassette transporters, and represses genes belonging to the phosphotransferase system, two-component system, chemotaxis and cell motility. Based on these results, we discuss the underpinning for furfural-mediated change in ABE fermentation by the solventogenic Clostridium species. C. beijerinckii 8052 pre-culture was incubated anaerobically to attain acidogenic or solventogenic growth phase. The culture was then subdivided into two bottles. One bottle was challenged with furfural and the other bottle was left unchallenged. After 3 h growth, C. beijerinckii 8052 samples were collected, during which the original concentration of furfural in the growth medium was reduced to more than half. Total RNA was isolated, purified, converted to enriched mRNA, and dye-coupled (Alexa Fluor 555) complementary cRNA. This was followed by hybridization and microarray data analysis.

Dataset Information

RNA-seq of Clostridium acetobutylicum ATCC 55025, histidine kinase Cac3319 and Cac0437 inactivated strains.

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