Comment[ArrayExpressAccession]	E-GEOD-25236
MAGE-TAB Version	1.1										
Public Release Date	2012-08-16
Investigation Title	The molecular response of Clostridium thermocellum ATCC 27405 to ethanol shock										
Comment[Submitted Name]	The molecular response of Clostridium thermocellum ATCC 27405 to ethanol shock
Experiment 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.										
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl									
Person Last Name	YANG	Yang	Giannone	Tschaplinski	Yang	Engle	Lezlee	Rodriguez	Hettich	Keller	Brown
Person First Name	Shihui	Shihui	Richard	Timothy	Zamin	Nancy	Dice	Miguel	Robert	Martin	Steven
Person Mid Initials			J	J		L			L		D
Person Email	Shihui.Yang@nrel.gov										
Person Affiliation	National Renewable Energy Lab										
Person Phone	3033847825										
Person Address	National Bioenergy Center, National Renewable Energy Lab, 1617 Cole Blvd, Golden, CO, USA										
Person Roles	submitter										
Protocol Name	P-GSE25236-1	P-GSE25236-6	P-GSE25236-5	P-GSE25236-3	P-GSE25236-2	P-GSE25236-4	P-GSE25236-7				
Protocol Description	ID_REF =  VALUE = log2 transformed default Loess normalized intensity	The labeling, hybridization, and scanning following NimbleGen company's protocols.	The labeling, hybridization, and scanning following NimbleGen company's protocols.	RNA was isolated essentially described previously [26]. Briefly, samples were harvested by centrifugation and the TRIzol reagent (Invitrogen, Carlsbad, CA) was used to extract total cellular RNA. Each total RNA preparation was treated with RNase-free DNase I (Ambion, Austin, TX) to digest residual chromosomal DNA and subsequently purified with the Qiagen RNeasy Mini kit in accordance with the instructions from the manufacturer. Total cellular RNA was quantified at OD260 and OD280 with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and the RNA quality was checked with Agilent Bioanalyzer (Agilent, CA). The purified RNA with good quality from each sample was used as the template to generate ds-cDNA using Invitrogen ds-cDNA synthesis kit (Invitrogen, CA).	Batch fermentations were conducted in approximately 5 L of MTC medium in 7.5-L BioFlo110 bioreactors (New Brunswick Scientific, Edison, NJ) fitted with agitation, pH, and temperature probes and controls as described previously (Yang et al., 2008).	The labeling, hybridization, and scanning following NimbleGen company's protocols.	Statistical analysis was done with JMP Genomics 4.0 software (SAS Institute, Cary, NC). The data were subsequently normalized using the standard normalization algorithm within JMP Genomics. An analysis of variance (ANOVA) was performed to determine differential expression levels between conditions and time points using the FDR testing method (p < 0.05).				
Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	grow	labeling	feature_extraction				
Experimental Factor Name	TREATMENT	TIME									
Experimental Factor Type	treatment	time									
Publication Title	Clostridium thermocellum ATCC27405 transcriptomic, metabolomic and proteomic profiles after ethanol stress.										
Publication Author List	Yang S, Giannone RJ, Dice L, Yang ZK, Engle NL, Tschaplinski TJ, Hettich RL, Brown SD										
PubMed ID	22823947										
Publication DOI	10.1186/1471-2164-13-336										
Comment[SecondaryAccession]	GSE25236										
Comment[GEOReleaseDate]	2012-08-16										
Comment[ArrayExpressSubmissionDate]	2010-11-09										
Comment[GEOLastUpdateDate]	2012-08-27										
Comment[AEExperimentType]	transcription profiling by array										
SDRF File	E-GEOD-25236.sdrf.txt