Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomic analysis of glycolaldehyde-treated wild type cells and a synthetic strain

ABSTRACT: A synthetic pathway for (D)-xylose assimilation was stoichiometrically evaluated regarding its potential to produce selected value-added compounds and implemented in Escherichia coli strains. The pathway proceeds via the isomerization of (D)-xylose to (D)-xylulose, the phosphorylation of (D)-xylulose to obtain (D)-xylulose-1-phosphate (Xyl1P), and the aldolase cleavage of the latter to yield glycolaldehyde and DHAP. Both compounds can be further processed via the annotated natural metabolic network. Stoichiometric analyses showed that the synthetic pathway provides an efficient access to the value-added two-carbon (C2) compounds ethylene glycol and glycolic acid, which are either inaccessible via the annotated metabolic network of E. coli or produced at 20 % lower theoretical yield, respectively. The simultaneous expression of xylulose-1 kinase and Xyl1P aldolase activities, which were provided by human ketohexokinase-C and human aldolase-B, respectively, was necessary and sufficient to restore growth of a (D)-xylulose-5-kinase (?xylB) mutant on xylose. In this strain, ethylene glycol was the major metabolic end-product and produced at a molar yield of 0.47. Further metabolic engineering provided strains that assimilated the entire C2 fraction back into the central metabolism, or that produced 4.3 g/l glycolic acid at a molar yield of 0.9 in shake flasks. The wild-type (WT) culture and synthetic strain (PEN205) were used for the microarray analysis. PEN205 is a ?xylB deleted strain that express the synthetic pathway. WT and PEN205 were grown to the logarithmic phase of growth in M9 minimal medium supplemented with xylose. PEN205 culture RNA was extracted when their OD was around 1. WT culture were split into two equal aliquots at the OD of ~1 and further cultivated in the presence or absence of 10 mM glycolaldehyde. After 30 min of incubation, cells were used for RNA extraction as well.

ORGANISM(S): Escherichia coli

SUBMITTER: Ceren Alkim

PROVIDER: E-GEOD-69265 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Background: Lignocellulosic biomass is a promising renewable feedstock for the microbial production of fuels. To release the major fermentable sugars such as glucose and xylose, pretreatment and enzymatic hydrolysis of biomass feedstock are needed. During this process, many toxic compounds are produced or introduced which subsequently inhibit microbial growth and eventually the production rate and yield. Acetate is one of the major inhibitors liberated from hemicelluloses during dilute acid pretreatment. An understanding of the toxic effects of acetate on the fermentation microorganism is critical to improving biofuel yields in the process. In addition, the efficient utilization of mixed sugars of glucose and xylose in the presence of hydrolysate inhibitors is crucial for economic biofuel production. Results: We have observed previously that some pretreatment inhibitors affect growth and performance in Zymomonas mobilis 8b differently when different sugars (e.g. glucose or xylose) are used as substrate. To investigate this phenomenon at the cellular level, microarray technology was used to investigate the acetate stress responses of Z. mobilis 8b when using single carbon sources of glucose or xylose, and mixed sugars of glucose and xylose. We designed a microarray based on the most up-to-date genome annotation for both coding sequences and intergenic regions. In the presence of acetate, 8b still can utilize all the glucose (though xylose utilization was inhibited) with similar ethanol yield although the growth, final biomass, and ethanol production rate were reduced. The presence of acetate caused genes related to biosynthesis, flagellar system, and glycolysis to be downregulated, and genes related to stress responses and energy metabolism to be upregulated. Our result indicates that Z. mobilis utilized different mechanism for xylose utilization compared to that of glucose, with even more dramatic results than those caused by treatment of the culture with the inhibitor acetate. Our study also suggests that redox imbalance caused by stressful conditions may trigger a metabolic reaction that leads to the accumulation of toxic intermediates such as xylitol, but Z. mobilis appears to be capable of managing its carbon and energy metabolism through the control of individual reactions to overcome the inhibition caused by stressful conditions. Several target gene candidates based on transcriptomic result have been selected for genetic manipulation and a TonB-dependent receptor knockout mutant was confirmed to have advantage on acetate tolerance. Conclusions: We have gained insights into the molecular responses of the model ethanologenic bacterium Z. mobilis to the inhibitor acetate when grown in different sugar sources. These insights will facilitate future metabolic modeling studies and help further strain metabolic engineering efforts for better xylose utilization and acetate tolerance. 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.

Project description: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.

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Transcriptomic analysis of glycolaldehyde-treated wild type cells and a synthetic strain

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