All you can eat yeast: substitution of major hexose transporters by AtSWEET7 in Saccharomyces cerevisiae enables simultaneous utilization of multiple sugars
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ABSTRACT:
ORGANISM(S): Saccharomyces cerevisiae
PROVIDER: GSE238127 | GEO | 2024/07/31
REPOSITORIES: GEO
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Project description:In the developing seeds of all higher plants, filial cells are symplastically isolated from the maternal tissue supplying photosynthate to the reproductive structure. Photoassimilates must be transported apoplastically, crossing several membrane barriers; a process facilitated by sugar transporters. Sugars Will Eventually be Exported Transporters (SWEETs) have been proposed to play a crucial role in apoplastic sugar transport during phloem unloading and the post-phloem pathway in sink tissues. Evidence for this is presented here for developing seeds of the C4 model grass Setaria viridis. Using immunolocalisation, SvSWEET4 was detected in various maternal and filial tissues within the seed along the sugar transport pathway, in the vascular parenchyma of the pedicel and the xylem parenchyma of the stem. Expression of SvSWEET4a in Xenopus laevis oocytes indicated that they function as high-capacity glucose and sucrose transporters. Carbohydrate and transcriptional profiling of Setaria seed heads showed that there were some developmental shifts in hexose and sucrose levels and consistent expression of SvSWEET4 homologues. Collectively, these results provide evidence for the involvement of SWEETs in the apoplastic transport pathway of sink tissues and allow a pathway for post-phloem sugar transport into the seed to be proposed.
2022-04-28 | GSE131540 | GEO
Project description:Though highly efficient at fermenting hexose sugars, the ethanologenic yeast Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomasses is the five carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars. Here we combined classical candidate gene approach with systems biology to develop xylose-utilising S. cerevisiae strains. The introduction of an exogenous xylose isomerase (XYLA) and an additional copy of the endogenous xylulokinase gene (XKS1) results in the significant improvement of xylose consumption. Microarray studies reveal that the introduction of XYLA and XKS1 results in the dramatic transcriptional remodelling of the cell under both glucose and xylose conditions. To further investigate the cellular processes impacted by the introduction of XYLA and XKS1, using genome-wide chemical and synthetic lethal screens we identified greater than 40 deletion mutants that impact xylose utilization. We identified four genes, ALP1, ISC1, RPL20B and BUD21, that when individually deleted allow S. cerevisiae to utilize xylose as the sole carbon source. When these mutants are combined with XYLA and XKS1, it results in strains with significant improvement in xylose consumption. We have demonstrated that systems biology techniques combined with candidate gene approaches can successfully lead to novel genetic strategies for the improvement of xylose utilization
2012-07-15 | GSE27325 | GEO
Project description:Sulfolobus acidocaldarius has been previously reported to grow on a broad range of sugars, but there is limited information on the ability of the organism to metabolize multiple sugars simultaneously. We report here the ability of S. acidocaldarius to utilize glucose and xylose simultaneously without di-auxie effect. The organism utilized a mixture of 1 g/L glucose and 1 g/L xylose with a growth rate of 0.079 h-1 compared to 0.074 h-1 and 0.22 h-1 when the organism was grown on xylose 2 g/L and 2 g/L glucose respectively as sole carbon sources. An increase in xylose concentration to 2 and 4 g/L in a medium containing 1 g/L glucose resulted in a growth rate of 0.082 and 0.085 h-1. However, increasing glucose concentration by 2 and 4 g/L when xylose concentration was maintained at 1 g/L decreased the growth rate to 0.062 and 0.052 h-1 respectively. S. acidocaldarius appeared to be utilizing the sugars at a rate roughly proportional to their concentration in the medium, resulting in complete utilization of these sugars at same time. The organism did not show preference for either glucose or xylose when it was grown on both sugars. Similar results were obtained with a combination of glucose, arabinose and galactose. These observations strongly suggest that S. acidocaldarius does not regulate utilization of the sugars tested herein using carbon catabolite repression (CCR) commonly found in most bacteria. The mechanism by which the organism utilized a mixture of sugar is yet to be elucidated. However, we were able to identify genes encoding for the putative glucose ABC transporters; but the putative xylose transporter was not identified. A study of S. acidocaldarius grown in glucose, xylose, or the two carbon sources combined in mid-log. Analyzed on Nimblegen 4-plex S. acidocaldarius DSM 639 array weblink: http://microbesonline.org/cgi-bin/microarray/viewExp.cgi?expId=1723
2010-07-31 | E-GEOD-21695 | biostudies-arrayexpress
Project description:Sulfolobus acidocaldarius has been previously reported to grow on a broad range of sugars, but there is limited information on the ability of the organism to metabolize multiple sugars simultaneously. We report here the ability of S. acidocaldarius to utilize glucose and xylose simultaneously without di-auxie effect. The organism utilized a mixture of 1 g/L glucose and 1 g/L xylose with a growth rate of 0.079 h-1 compared to 0.074 h-1 and 0.22 h-1 when the organism was grown on xylose 2 g/L and 2 g/L glucose respectively as sole carbon sources. An increase in xylose concentration to 2 and 4 g/L in a medium containing 1 g/L glucose resulted in a growth rate of 0.082 and 0.085 h-1. However, increasing glucose concentration by 2 and 4 g/L when xylose concentration was maintained at 1 g/L decreased the growth rate to 0.062 and 0.052 h-1 respectively. S. acidocaldarius appeared to be utilizing the sugars at a rate roughly proportional to their concentration in the medium, resulting in complete utilization of these sugars at same time. The organism did not show preference for either glucose or xylose when it was grown on both sugars. Similar results were obtained with a combination of glucose, arabinose and galactose. These observations strongly suggest that S. acidocaldarius does not regulate utilization of the sugars tested herein using carbon catabolite repression (CCR) commonly found in most bacteria. The mechanism by which the organism utilized a mixture of sugar is yet to be elucidated. However, we were able to identify genes encoding for the putative glucose ABC transporters; but the putative xylose transporter was not identified.
2010-07-31 | GSE21695 | GEO
Project description:Though highly efficient at fermenting hexose sugars, the ethanologenic yeast Saccharomyces cerevisiae has limited ability to ferment five-carbon sugars. As a significant portion of sugars found in cellulosic biomasses is the five carbon sugar xylose, S. cerevisiae must be engineered to metabolize pentose sugars. Here we combined classical candidate gene approach with systems biology to develop xylose-utilising S. cerevisiae strains. The introduction of an exogenous xylose isomerase (XYLA) and an additional copy of the endogenous xylulokinase gene (XKS1) results in the significant improvement of xylose consumption. Microarray studies reveal that the introduction of XYLA and XKS1 results in the dramatic transcriptional remodelling of the cell under both glucose and xylose conditions. To further investigate the cellular processes impacted by the introduction of XYLA and XKS1, using genome-wide chemical and synthetic lethal screens we identified greater than 40 deletion mutants that impact xylose utilization. We identified four genes, ALP1, ISC1, RPL20B and BUD21, that when individually deleted allow S. cerevisiae to utilize xylose as the sole carbon source. When these mutants are combined with XYLA and XKS1, it results in strains with significant improvement in xylose consumption. We have demonstrated that systems biology techniques combined with candidate gene approaches can successfully lead to novel genetic strategies for the improvement of xylose utilization For this experiment samples (2 reference and 2 test samples), consisting of at least 3 biological reps were hybridized. Cy3 one-color labelling was used for each sample.
2012-07-14 | E-GEOD-27325 | biostudies-arrayexpress
Project description:The co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait for in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus (Csac) growing on individual monosaccharides (arabinose, fructose, galactose, glucose, mannose and xylose), mixtures of these sugars. Based on the whole-genome transcriptional response analysis and comparative genomics, carbohydrate specificities for transport systems could be proposed for most of the 24 putative carbohydrate ATP-binding cassette (ABC) transporters in the C. saccharolyticus genome. Transcriptome contrasts for monosacchride growth showed that minimal changes were observed in some cases (e.g., 31 ORFs changed ï³ 2-fold for glucose/galactose) while substantial changes occurred for cases involving mannose (e.g., 363 ORFs ï³ 2-fold for glucose/mannose). No evidence for catabolite repression was noted for either growth on multi-sugar mixtures or in the corresponding transcriptomes. C. saccharolyticus was subcultured (overnight) seven times on the substrate of interest in modified DSMZ 640 medium before inoculating a 1-liter batch containing 0.5 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (3-5*107) and harvested by rapid cooling to 4 °C and centrifugation and then stored at -80 °C. To elucidate the transporters plus the central carbon metabolic pathways and their regulation utilized on the different sugars, transcriptome analysis was performed after growth on arabinose, fructose, galactose, glucose, mannose, xylose and a mixture of all six substrates.
2010-05-16 | E-GEOD-17425 | 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
Project description:The co-utilization of hexoses and pentoses derived from lignocellulose is an attractive trait for in microorganisms considered for consolidated biomass processing to biofuels. This issue was examined for the H2-producing, extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus growing on oligosaccharides (composed of glucose and xylose) compared to monosaccharides. Based on the whole-genome transcriptional response analysis and comparative genomics, carbohydrate specificities for transport systems could be proposed for a number of the 24 putative carbohydrate ATP-binding cassette (ABC) transporters in the C. saccharolyticus genome. Transcriptome analysis showed different transporters were utilized for uptake of oligosaccharides than those used for monosaccharides uptake. No evidence for catabolite repression was noted for either growth on multi-sugar mixtures or in the corresponding transcriptomes. C. saccharolyticus was subcultured (overnight) seven times on the substrate of interest in modified DSMZ 640 medium before inoculating a 1-liter batch containing 0.5 gram substrate per liter. Cells were grown at 70 °C until mid-logarithmic phase (3-5*107) and harvested by rapid cooling to 4 °C and centrifugation and then stored at -80 °C. To elucidate the transporters plus the central carbon metabolic pathways and their regulation utilized on the different sugars, transcriptome analysis was performed after growth on xylan (oat spelt), xyloglucan, xylogluco-oligosaccharides, glucose and xylose.
2010-05-16 | E-GEOD-17427 | biostudies-arrayexpress
Project description:Saccharomyces cerevisiae cannot metabolize non-glucose sugars including cellobiose, xylose, xylodextrins in nature, which are prevalent in plant cell wall. Here, one engineered S. cerevisiae strain, which expresses a cellodextrin transporter gene (cdt-1) and an intracellular β-glucosidase gene (codon-optimized gh1-1) from Neurospora crassa; XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, as well as cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa, can utilize the above non-glucose sugars. We sequenced mRNA from exponential cultures of the engineered S. cerevisiae grown on glucose, cellobiose, xylose or xylodextrins as a single carbon source in both aerobic and anaerobic conditions in biological triplicate. Differences in gene expression between non-glucose sugar and glucose metabolism revealed by RNA deep sequencing indicated that non-glucose sugar metabolism induced mitochondrial activation and reduced amino acid and protein biosynthesis under fermentation conditions.
2021-05-27 | GSE69404 | GEO
Project description:Sugars modulate expression of hundreds of genes in plants. Previous studies on sugar signaling, using intact plants or plant tissues, were hampered by tissue heterogeneity, uneven sugar transport and/or inter-conversions of the applied sugars. This, in turn, could obscure the identity of a specific sugar that acts as a signal affecting expression of given gene in a given tissue or cell-type. To bypass those biases, we have developed a novel biological system, based on stem-cell-like Arabidopsis suspension culture. The cells were grown in a hormone-free medium and were sustained on xylose as the only carbon source. The functional genomics approach was used to identify sugar responsive genes, which rapidly (within 1 h) respond specifically to low concentration (1 mM) of glucose, fructose and/or sucrose.
2014-05-16 | GSE57751 | GEO