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E-GEOD-25236 - The molecular response of Clostridium thermocellum ATCC 27405 to ethanol shock

Status
Released on 16 August 2012, last updated on 2 May 2014
Organism
Clostridium thermocellum ATCC 27405
Samples (30)
Array (1)
Protocols (7)
Description
Clostridium thermocellum is a Gram-positive, anaerobic, thermophilic bacterium that ferments cellulose into ethanol. It is a candidate industrial consolidated bioprocess (CBP) biocatalyst for lignocellulosic bioethanol production. However, C. thermocellum is relatively sensitive to ethanol compared to yeast. Previous studies have investigated the membrane and protein composition of wild-type and ethanol tolerant strains, but relatively little is known about the genome changes associated with the ethanol tolerant C. thermocellum strain. In this study, C. thermocellum cultures were grown to mid-exponential phase and then either shocked with the supplementation of ethanol to a final concentration of 3.95 g/L (equal to 0.5% [v/v]) or were untreated. Samples were taken pre-shock and 2, 12, 30, 60, 120, 240 min post-shock for multiple systems biology analyses. The addition of ethanol dramatically reduced the C. thermocellum growth and the final cell density was approximately half of the control fermentations, with concomitant reductions in substrate consumption in the treated cultures. The response of C. thermocellum to ethanol was dynamic and involved more than six hundred genes that were significantly and differentially expressed between the different conditions over time and every functional category was represented. Cellobiose was accumulated within the ethanol-shocked C. thermocellum cells, as well as the sugar phosphates such as fructose-6-P and cellobiose-6-P. The comparison and correlation among intracellular metabolites, proteomic and transcriptomics profiles as well as the ethanol effects on cellulosome, hydrogenase glycolysis and nitrogen metabolism are discussed, which led us to propose that C. thermocellum may utilize the nitrogen metabolism to bypass the arrested carbon metabolism in responding to ethanol stress shock, and the nitrogen metabolic pathway and redox balance may be the key target for improving ethanol tolerance and production in C. thermocellum. A thirty array study using total RNA recovered from wild-type cultures of Clostridium thermocellum at different time points of 0, 12, 30, 60, 120, and 240 min post-inoculation with 3.95 g/L [0.5% (v/v)] treatment compred to that of control without ethanol supplementation. Two biological replicates for treatment and control condition.
Experiment type
transcription profiling by array 
Contacts
Shihui YANG <Shihui.Yang@nrel.gov>, Dice Lezlee, Martin Keller, Miguel Rodriguez, Nancy L Engle, Richard J Giannone, Robert L Hettich, Shihui Yang, Steven D Brown, Timothy J Tschaplinski, Zamin Yang
Citation
Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress. Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD. , PMID:22823947
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-25236.idf.txt
Sample and data relationshipE-GEOD-25236.sdrf.txt
Raw data (1)E-GEOD-25236.raw.1.zip
Processed data (1)E-GEOD-25236.processed.1.zip
Array designA-GEOD-11186.adf.txt
Links