E. coli evolution to alternating substrate conditions
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655
PROVIDER: GSE97944 | GEO | 2017/04/19
SECONDARY ACCESSION(S): PRJNA383408
REPOSITORIES: GEO
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Project description:Caldicellulosiruptor saccharolyticus is an extremely thermophilic, Gram-positive anaerobe, which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO2 and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to co-utilize glucose and xylose, make this bacterium an attractive candidate for microbial bioenergy production. Glycolytic pathways and an ABC-type sugar transporter were significantly up-regulated during growth on glucose and xylose, indicating that C. saccharolyticus co-ferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks represents a highly desirable feature of a lignocellulose-utilizing, biofuel-producing bacterium. Keywords: substrate response
2008-04-15 | GSE11153 | GEO
Project description:Rhodobacter sphaeroides produces hydrogen gas (H2) via its nitrogenase enzyme during photoheterotrophic growth under nitrogen-limited conditions. We find that cells produce different amounts of H2 and show different growth rates, depending on the organic substrate provided (lactate, succinate, glucose, xylose, or glycerol). We used global transcript analyses to determine what genes are involved in the onset of H2 production, and those that lead to different H2 production capacities in cells fed different organic substrates.
2011-08-22 | GSE29811 | GEO
Project description:Caldicellulosiruptor saccharolyticus is an extremely thermophilic, Gram-positive anaerobe, which ferments cellulose-, hemicellulose- and pectin-containing biomass to acetate, CO2 and hydrogen. Its broad substrate range, high hydrogen-producing capacity, and ability to co-utilize glucose and xylose, make this bacterium an attractive candidate for microbial bioenergy production. Glycolytic pathways and an ABC-type sugar transporter were significantly up-regulated during growth on glucose and xylose, indicating that C. saccharolyticus co-ferments these sugars unimpeded by glucose-based catabolite repression. The capacity to simultaneously process and utilize a range of carbohydrates associated with biomass feedstocks represents a highly desirable feature of a lignocellulose-utilizing, biofuel-producing bacterium. Keywords: substrate response C. saccharolyticus was subcultured (overnight) 3 times on the substrate of interest in modified DSMZ 640 medium before inoculating a pH-controlled (pH = 7) 1-liter fermentor containing 4 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (~OD660 = 0.3-0.4) and harvested by centrifugation and rapid cooling to 4 °C and stored at -80 °C. To elucidate the central carbon metabolic pathways and their regulation, transcriptome analysis was performed after growth on glucose, xylose and a 1:1 mixture of both substrates. L-Rhamnose, which was likely to follow another pathway, was used as a reference substrate.
2008-04-15 | E-GEOD-11153 | biostudies-arrayexpress
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.
2014-09-08 | E-GEOD-57553 | biostudies-arrayexpress
Project description:Rhodobacter sphaeroides produces hydrogen gas (H2) via its nitrogenase enzyme during photoheterotrophic growth under nitrogen-limited conditions. We find that cells produce different amounts of H2 and show different growth rates, depending on the organic substrate provided (lactate, succinate, glucose, xylose, or glycerol). We used global transcript analyses to determine what genes are involved in the onset of H2 production, and those that lead to different H2 production capacities in cells fed different organic substrates. Growth and real-time H2 production were followed for photoheterotrophically grown Rhodobacter sphaeroides cultures (19 mL test tube cultures) fed one of five different organic substrates (lactate, succinate, glucose, xylose, or glycerol) and provided glutamate as the sole nitrogen source. Cells were harvested for RNA extraction during early post-exponential growth, at points near the maximum H2 production rates of the cultures. Non-H2-producing cells (500 mL cultures) fed succinate and provided NH4+ as nitrogen source were also harvested for RNA extraction as reference samples. At least two samples for every given set of conditions were analyzed.
2011-08-21 | E-GEOD-29811 | biostudies-arrayexpress
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.
2014-09-08 | GSE57553 | GEO
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