Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13912577_1.fastq.gz | Fastqsanger.gz | |||
| SRR13912577_2.fastq.gz | Fastqsanger.gz | |||
| SRR13912578_1.fastq.gz | Fastqsanger.gz | |||
| SRR13912578_2.fastq.gz | Fastqsanger.gz | |||
| SRR13912579_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:RNA-seq was performed on T. maritima wild type, three glucose evolved cultures, and three glycerol adapted cultures. Wild type and glucose evolved strains were grown on glucose minimal media and glycerol evolved cultures were grown on glycerol minimal media. All samples were harvested in exponential phase.
2015-06-09 | GSE63141 | GEO
Project description:The goal of the study is to use Next generation sequencing (RNA-seq) to study the underlying regulation of glycerol metabolism in mixed culture fermentation (glucose and glycerol) of Rhodosporidium toruloides. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) with 2 replicates each. Transcriptional profiles showed that glycerol might be produced intracellularly and glycerol kinase (GUT1) and glycerol 3–phosphate dehydrogenase (GUT2) enzymes were not down-regulated in the presence of glucose at the transcriptional level. It also showed that this yeast has a different regulation compared to S.cerevisiae. Certain insights into lipid biosynthesis on these mixed cultures are provided at systems level. This analysis provides interesting targets for metabolic engineering in this organism growing on glucose and glycerol.
2016-05-12 | GSE74307 | GEO
Project description:Listeria monocytogenes is able to efficiently utilize glycerol as carbon source. In a defined minimal medium the growth rate is similar (during balanced growth) in presence of glycerol as in presence of glucose or cellobiose. Comparative transcriptome analyses of L. monocytogenes showed in the presence of glycerol (compared to glucose and/or cellobiose) high transcriptional upregulation of the known genes involved in glycerol uptake and metabolism (glpFK, glpD). Expression of the genes encoding a second putative glycerol uptake facilitator (GlpF-2) and a second putative glycerol kinase (GlpK-2) was less enhanced under these conditions. GlpK-1 but not GlpK-2 was essential for glycerol catabolism in L. monocytogenes under extracellular conditions, while loss of GlpK-1 affected replication in Caco-2 cells less than loss of GlpK-2 and GlpD. Additional genes whose transcription was higher in presence of glycerol than in presence of glucose and cellobiose included those for two dihydroxyacetone (Dha) kinases and many genes that are under carbon catabolite repression (CCR) control. Transcriptional down-regulation in the presence of glycerol (compared to glucose and cellobiose) was observed for several genes and operons that are positively regulated by glucose, including genes involved in glycolysis, N-metabolism and biosynthesis of branched chain amino acids. The highest transcriptional up-regulation was observed for all PrfA-dependent genes during early and late logarithmic growth in glycerol. Under these conditions a low level of HPr-Ser-P and a high level of HPr-His-P was present in the cells, suggesting that all EIIA (B) components of the PTS permeases expressed will be phosphorylated. These and other data reported suggest that the phosphorylation state of PTS permeases correlates with PrfA activity. Keywords: Response of Listeria monocytogenes to different carbon sources
2008-05-30 | GSE11459 | GEO
Project description:RNA-seq was performed on T. maritima wild type, three glucose evolved cultures, and three glycerol adapted cultures. Wild type and glucose evolved strains were grown on glucose minimal media and glycerol evolved cultures were grown on glycerol minimal media. All samples were harvested in exponential phase. Seven samples are included with two biological replicates for each condition.
2015-06-09 | E-GEOD-63141 | biostudies-arrayexpress
Project description:A proteome and acetylome study under different culture conditions was carried out by quantitative label-free mass spectrometry analysis. E. coli K12 BW25113 strain was grown employing TB7 complex medium or M9 minimal medium, supplemented with glucose 20 mM or glycerol 40 mM as carbon source. Therefore, 4 culture conditions (TB7-glucose, TB7-glycerol, MM9-glucose, and MM9-glycerol) were used. Samples were taken in exponential and in stationary growth phase, resulting in 8 experimental samples: TB7-glucose in exponential phase, TB7-glucose in stationary phase, TB7-glycerol in exponential phase, TB7-glycerol in stationary phase, MM9-glucose in exponential phase, MM9-glucose in stationary phase, MM9-glycerol in exponential phase, and MM9-glycerol in stationary phase, with 4 biological replicates from each. This work emphasises the importance of the culture conditions choice, as they determine both, location of acetylation, and acetylation level, which may have an impact on regulation of the central metabolism.
2024-05-21 | PXD041209 | Pride
Project description:Glucose metabolism has been studied extensively, but the role of glucose-derived excretory glycerol remains unclear. Here, we show that hypoxia induces NADH accumulation to promote glycerol excretion and this pathway consumes NADH continuously, thus attenuating its accumulation and reductive stress. Aldolase B (ALDOB) accounts for glycerol biosynthesis by forming a complex with glycerol-3-phosphate dehydrogenases, GPD1 and GPD1L. Blocking GPD1, GPD1L, or glycerol 3-phosphate phosphatase exacerbates reductive stress and suppresses cell proliferation under hypoxia and tumor growth in vivo. Over-expression of these enzymes increases glycerol excretion but still reduces cell viability under hypoxia and tumor proliferation due to energy stress. AMPK inactivates ALDOB to mitigate glycerol synthesis that dissipates ATP, alleviating NADH accumulation-induced energy crisis. Therefore, glycerol biosynthesis/excretion regulates the trade-off between reductive stress and energy stress. Moreover, this mode of regulation seems to be prevalent in reductive stress-driven transformations, enhancing our understanding of the metabolic complexity and guiding tumor treatment.
2024-09-29 | PXD056351 |
Project description:Investigation of gene expression in ∆glpR mutant strains vs wild type in response to glycerol and glucose.
2017-02-01 | GSE77589 | GEO
Project description:Listeria monocytogenes is able to efficiently utilize glycerol as carbon source. In a defined minimal medium the growth rate is similar (during balanced growth) in presence of glycerol as in presence of glucose or cellobiose. Comparative transcriptome analyses of L. monocytogenes showed in the presence of glycerol (compared to glucose and/or cellobiose) high transcriptional upregulation of the known genes involved in glycerol uptake and metabolism (glpFK, glpD). Expression of the genes encoding a second putative glycerol uptake facilitator (GlpF-2) and a second putative glycerol kinase (GlpK-2) was less enhanced under these conditions. GlpK-1 but not GlpK-2 was essential for glycerol catabolism in L. monocytogenes under extracellular conditions, while loss of GlpK-1 affected replication in Caco-2 cells less than loss of GlpK-2 and GlpD. Additional genes whose transcription was higher in presence of glycerol than in presence of glucose and cellobiose included those for two dihydroxyacetone (Dha) kinases and many genes that are under carbon catabolite repression (CCR) control. Transcriptional down-regulation in the presence of glycerol (compared to glucose and cellobiose) was observed for several genes and operons that are positively regulated by glucose, including genes involved in glycolysis, N-metabolism and biosynthesis of branched chain amino acids. The highest transcriptional up-regulation was observed for all PrfA-dependent genes during early and late logarithmic growth in glycerol. Under these conditions a low level of HPr-Ser-P and a high level of HPr-His-P was present in the cells, suggesting that all EIIA (B) components of the PTS permeases expressed will be phosphorylated. These and other data reported suggest that the phosphorylation state of PTS permeases correlates with PrfA activity. Keywords: Response of Listeria monocytogenes to different carbon sources A total of four independently isolated RNA samples from each condition at each growth phase were used for the analysis. RNA from two isolations were pooled and hybridized onto two microarray slides with dye swap. Another two microarray slides were hybridized using the same principle. In total, we used four RNAs and four microarray slides to generate 16 replicate expression values for each combination except for the comparison between glucose and cellobiose, phase B where data generated from three microarray slides were used for further analysis
2008-05-30 | E-GEOD-11459 | biostudies-arrayexpress
Project description:The goal of the study is to use Next generation sequencing (RNA-seq) and 13C based flux analysis to study the underlying regulation of citric acid metabolism in mixed culture fermentation (glucose and glycerl) of Yarrowia lipolytica. We sequenced the RNA from 4 different samples in the mixed culture (glucose and glycerol) under oxygen excess and limited conditions with 2 replicates each . Transcriptional profiles showed that under oxygen limited conditions, due to deficient mitochondrial activity, citric acid is being consumed back after glycerol exhaustion eventhough glucose is present in excess. Transcriptome and fluxome profiles showed that glucose is mainly directed towards the Pentose phosphate pathway in the dual substrate fermentations.
2017-05-08 | GSE83109 | GEO
Project description:The bloodstream forms of Trypanosoma brucei (BSF), responsible for the sleeping sickness, primarily evaluate in the blood of its mammalian hosts. The skin and the adipose tissues were recently identified as additional major sites for the parasite proliferation and transmission through its insect vector blood ingestion. Glucose is the only carbon source used by the blood parasites to feed its central metabolism, however, the metabolic behavior of the tissue-adapted parasites has not yet been addressed. Since production of glycerol is an important primary function of adipocytes, we have adapted the BSF trypanosomes to glucose-depleted and glycerol-rich growth medium (CMM_Gly/GlcNAc) and compared its metabolism and proteome with standard glucose-rich growth conditions (CMM_Glu). BSF consume 2-times more oxygen per carbon consumed in CMM_Gly/GlcNAc and is 11.5-times more sensitive to SHAM, a specific inhibitor of the alternative oxidase, which is consistent with the expected absolute requirement of the mitochondrial respiratory chain activity to convert glycerol into dihydroxyacetone phosphate. Metabolomic analyses by mass spectrometry showed that 13C-labeled glycerol is incorporated into hexose phosphates through gluconeogenesis. After several weeks of growth in CMM_Gly/GlcNAc, BSF adapt their metabolism by increasing and decreasing the rate of glycerol and glucose consumption, respectively. As expected RNAi-mediated down-regulation of glycerol kinase expression abolished glycerol degradation and is lethal for BSF growth in CMM_Gly/GlcNAc. However, the glycerol kinase activity is 7.8-fold decreased in CMM_Gly/GlcNAc, as confirms by western blotting and proteomic analyses, which suggests that the huge excess of glycerol kinase, which is not necessary for glycerol metabolism, is required for another yet undetermined non-essential function in glucose rich-conditions. Altogether these data shows that BSF trypanosomes are well adapted to glycerol-rich conditions, which could be encountered by the parasite in extravascular niches, such as skin and adipose tissues.
2018-10-22 | PXD009763 | Pride