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Series GSE57553 Query DataSets for GSE57553
Status Public on Sep 08, 2014
Title Insights into acetate toxicity in Zymomonas mobilis 8b using different substrates
Organism Zymomonas mobilis
Experiment type Expression profiling by genome tiling array
Summary Background
Lignocellulosic biomass is a promising renewable feedstock for biofuel production. Acetate is one of the major inhibitors liberated from hemicelluloses during hydrolysis. An understanding of the toxic effects of acetate on the fermentation microorganism and the efficient utilization of mixed sugars of glucose and xylose in the presence of hydrolysate inhibitors is crucial for economic biofuel production.

Results
A new microarray was designed including both coding sequences and intergenic regions to investigate the acetate stress responses of Zymomonas mobilis 8b when using single carbon sources of glucose or xylose, or mixed sugars of both glucose and xylose. With the supplementation of exogenous acetate, 8b can utilize all the glucose with a similar ethanol yield, although the growth, final biomass, and ethanol production rate were reduced. However, xylose utilization was inhibited in both media containing xylose or a mixed sugar of glucose and xylose, although the performance of 8b was better in mixed sugar than xylose-only media. The presence of acetate caused genes related to biosynthesis, the flagellar system, and glycolysis to be downregulated, and genes related to stress responses and energy metabolism to be upregulated. Unexpectedly, xylose seems to pose more stress on 8b, recruiting more genes for xylose utilization, than does acetate. Several gene candidates based on transcriptome results were selected for genetic manipulation, and a TonB-dependent receptor knockout mutant was confirmed to have a slight advantage regarding acetate tolerance.

Conclusions
Our results indicate Z. mobilis utilized a different mechanism for xylose utilization, with an even more severe impact on Z. mobilis than that caused by acetate treatment. Our study also suggests redox imbalance caused by stressful conditions may trigger a metabolic reaction leading to the accumulation of toxic intermediates such as xylitol, but Z. mobilis manages its carbon and energy metabolism through the control of individual reactions to mitigate the stressful conditions. We have thus provided extensive transcriptomic datasets and gained insights into the molecular responses of Z. mobilis to the inhibitor acetate when grown in different sugar sources, which will facilitate future metabolic modeling studies and strain improvement efforts for better xylose utilization and acetate tolerance.
 
Overall design Two series of microarray studies using total RNA extracted from Zymomonas mobilis subsp mobilis 8b (an xylose-utilizing recombinant) were carried out to investigate the effect of carbon source and acetate on Z. mobilis. One study compared the acetate effect in either glucose or xylose at exponential phase and another study investigated the acetate effect in mixed sugar of glucose and xylose at three growth phases of exponential, transition, and stationary. Tthree biological replicates were used for each condition.
 
Contributor(s) Yang S, Franden M, Brown SB, Chou Y, Pienkos PT, Zhang M
Citation(s) 25298783
Submission date May 12, 2014
Last update date Oct 24, 2014
Contact name Shihui YANG
E-mail(s) Shihui.Yang@nrel.gov
Phone 3033847825
Organization name National Renewable Energy Lab
Department National Bioenergy Center
Street address 1617 Cole Blvd
City Golden
State/province CO
ZIP/Postal code 80401
Country USA
 
Platforms (1)
GPL18675 NimbleGen Zymomonas mobilis 8b 100907_Z_mobilis_expr_tiling_HX12
Samples (30)
GSM1384626 8b_Xylose_Acetate_F10
GSM1384627 8b_Glucose_F1
GSM1384628 8b_Glucose_Acetate_F4
Relations
BioProject PRJNA246698

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE57553_RAW.tar 14.8 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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