Sugar-dependent gene expression in xylose grown A. thaliana cell suspension culture
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE57751 | GEO | 2014/05/16
SECONDARY ACCESSION(S): PRJNA248001
REPOSITORIES: GEO
Similar Datasets
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. A habituated A. thaliana cell culture grown in a hormone free full strength MS media in the dark was adapted to growth on xylose as the only carbon source in the media.The cells were subjected to a 1 hour treatment with 1 mM of either Fru, Glc, Suc or Xyl (control). The experiments were carried out in 3 biological repeats per treatment. Whole genome expression analysis was conducted by hybridization of the extracted RNA to the Affymetrix Arabidopsis ATH1 Genome Array.
2014-05-16 | E-GEOD-57751 | biostudies-arrayexpress
Project description:The molecular basis for glucose and xylose fermentation by industrial Saccharomyces cerevisiae is of interest to promote bioethanol production We used microarrays to investigate the transcriptional difference of a industrial strain cultured in both single sugar media and a mixed sugar medium of glucose and xylose
2016-04-28 | GSE80748 | 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.
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: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:This proposed study is designed to investigate the specific uptake of fructose by human colorectal tumors. In this study, subjects with colorectal cancer undergoing surgery will receive an oral sugar solution containing fructose or xylose prior to surgery. The tumor will then be resected, and a portion of the tissue will be used to measure the abundance of fructose and xylose. The study hypothesis is that the tumors will take up fructose sugar but not xylose sugar. A comparison of the sugar uptake between the tumor and normal tissues from the adjacent intestinal epithelium and smooth muscle and the liver will be conducted. This proposal will confirm that human colorectal cancer tumors can directly absorb dietary sugars, which has never been demonstrated.
| 2396702 | ecrin-mdr-crc
Project description:Herbaspirillum seropedicae are β-proteobacteria that establish as endophytes in various plants. They are able to consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolism pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that D-xylose is the second most abundant sugar in nature. Furthermore, it is found in some potential raw materials such as lignocellulosic biomass. In this work we present a study of D-xylose catabolism pathways in H. seropedicae strain Z69, using RNA-seq analysis and the subsequent study of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB, encodes a NAD+- dependent D-xylose dehydrogenase. Mutant Z69∆xylB was still able to grow on D-xylose, although at a reduced rate. This is due to expression of an L-arabinose dehydrogenase encoded by G5B88_05250 gene, and was thus able to use D-xylose as substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize D-xylose. The lower portion of metabolism involves co-expression of two routes: Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that produces pyruvate and glycolate. This novel pathway seems to be essential since a mutant in the last step of this pathway, Z69∆G5B88_06410, was unable to grow on D‑xylose.
2021-03-01 | GSE162430 | GEO
Project description:The ascomycetes Saccharomyces cerevisiae, Candida albicans and Scheffersomyces stipitis metabolize the pentose sugar xylose very differently. S. cerevisiae fails to grow on xylose, while C. albicans can grow, and S. stipitis can both grow and ferment xylose to ethanol. However, all three species contain highly similar genes that encode xylose reductase and xylitol dehydrogenase required to convert xylose to xylulose, on which all three fungi grow. We have created C. albicans strains deleted for either or both the xylose reductase gene GRE3, and the xylitol dehydrogenase gene XYL2. As expected, all the mutant strains cannot grow on xylose, while the gre3 mutant can grow on xylitol. The gre3 and xyl2 mutants are complemented efficiently by the XYL1 and XYL2 from S. stipitis respectively. Intriguingly, the S. cerevisiae GRE3 and SOR1 genes can complement the gre3 and xyl2 mutants respectively, showing that S. cerevisiae contains the enzymatic capacity for converting xylose to xylulose. In addition, the gre3 xyl2 double mutant is effectively rescued by the xylose isomerase (XI) gene of either Piromyces or Orpinomyces, suggesting that the XI provides an alternative to the missing oxido-reductase functions in the mutant required for the xylose-xylulose conversion. Overall this work establishes that C. albicans strains engineered to lack essential steps for xylose metabolism provide a platform for the analysis of xylose metabolism enzymes from a variety of species, and confirms that S. cerevisiae has the genetic potential to convert xylose to xylulose, although non-engineered strains cannot proliferate on xylose as the sole carbon source. Transcription profile of cells in xylose compared to glucose. Two sets: Candida albicans, 1 condition ; Saccharomyces cerevisiae 2 conditions / in xylose (SX) or no sugar (S) (replicates with dye-swap)
2013-10-30 | E-GEOD-50476 | biostudies-arrayexpress
Project description:As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation by the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutation in the gene encoding the cyclic AMP receptor protein, Crp*, has been shown to disable CCR and improve co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site specific crp* chromosomal mutant in E. coli BL21 starTM (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomic analysis further showed that cells link xylose consumption to energy production through the de novo nucleotide synthesis pathway, explaining the relatively slower growth of the crp* mutant strain. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.
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