Ontology highlight
ABSTRACT:
PROVIDER: PRJNA321129 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR3536780_1.fastq.gz | Fastqsanger.gz | |||
| SRR3536780_2.fastq.gz | Fastqsanger.gz | |||
| SRR3536790_1.fastq.gz | Fastqsanger.gz | |||
| SRR3536790_2.fastq.gz | Fastqsanger.gz | |||
| SRR3536800_1.fastq.gz | Fastqsanger.gz |
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Project description:Rhodotorula toruloides is a non-conventional, oleaginous yeast able to naturally accumulate high amounts of microbial lipids. Constraint-based modeling of R. toruloides has been mainly focused on the comparison of experimentally measured and model predicted growth rates, while the analysis of intracellular flux patterns has been superficial. Hence, the intrinsic metabolic properties of R. toruloides that make lipid synthesis possible are not thoroughly understood. At the same time, the lack of diverse physiological data sets has often been the bottleneck to predict accurate fluxes. In this study, we collected detailed physiology data sets of R. toruloides while growing on glucose, xylose and acetate as the sole carbon source in mineral medium. Regardless of the carbon source, the growth was divided into two phases from which proteomic and lipidomic data were collected. Complemental physiological parameters were collected in these two phases and altogether implemented into metabolic models. Simulated intracellular flux patterns acknowledged the role of phosphoketolase in the generation of acetyl-CoA, one of the main precursors during lipid biosynthesis, while the role of ATP citrate lyase was not confirmed. Metabolic modeling on xylose as a carbon substrate was greatly improved by the detection of chirality of D-arabinitol, which together with D-ribulose were involved in an alternative xylose assimilation pathway. Further, flux patterns pointed to a metabolic trade-offs associated with NADPH allocation between nitrogen assimilation and lipid biosynthetic pathways, which was linked to large-scale differences in protein and lipid content. This work includes the first extensive multi-condition analysis of R. toruloides using enzyme-constrained models and quantitative proteomics. Further, more precise kcat values should extend the application of the newly developed enzyme-constrained models that are publicly available for future studies.
2023-03-13 | PXD037281 | Pride
Project description:Our study is the first investigation of proteome of oleaginous yeast Rhotodorula toruloides during conversion of xylose into lipids. We performed comparative proteomics of R. toruloides during cultivation of two carbon sources: glucose and xylose. Proteome analysis revealed significantly lower levels of ribosomal proteins and translation associated factors in xylose-grown cells as compared to glucose-grown cells. We showed that proteins involved in sugar transport, phospholipid and leucine biosynthesis as well as peroxisomal beta-oxidation and oxidative stress response were differentially regulated in response to carbon source.
2019-08-08 | PXD012332 | Pride
Project description:Oleaginous yeasts are capable of accumulating high levels of intracellular storage lipids from excess carbon during times when other key nutrients are limited. The basidiomycete yeast Rhodosporidium toruloides is an emerging host for microbial cell factory applications thanks to its naturally high lipid and carotenoid production. However, the engineering toolbox in this non-model host is limited and is currently a bottleneck for implementation of metabolic engineering strategies. In this study, we performed differential gene expression analysis with the goal to identify promoters that are strongly induced or repressed by nitrogen-limitation, a condition that is commonly used to induce lipid accumulation in oleaginous yeasts. The genome-wide transcriptional response of R. toruloides BOT-A2 was analysed using RNAseq during exponential growth and nitrogen-starvation, with either glucose or xylose as the sole carbon source. To validate the differential gene expression findings, reporter genes were constructed by placing the candidate promoters in control of a fluorescent protein, integrated in BOT-A2 and evaluated in vivo.
2023-08-23 | GSE217097 | GEO
Project description:Nitrogen limitation is a major regulator to initiate lipid overproduction in oleaginous fungi. To examine the influence of nitrogen starvation, chemiostat cultures of R. toruloides in defined media with abundant ammonium (MM) or minute ammonium (MM-N) were performed to obtain steady-state samples. Then Illumina's digital gene expression (DGE) technology was used for high-throughput transcriptome profiling of these samples. Two samples cultured in minimum media with abundant ammonium (MM) or minute ammonium (MM-N)
2012-06-29 | E-GEOD-39023 | biostudies-arrayexpress
Project description:Cells must sense and respond to available nutrients to utilize available resources and establish fungal colonies. Saprophytic microbes harvest carbon from plant biomass, which contain insoluble, complex carbohydrates that must be degraded extracellularly prior to import into the cell. Filamentous fungi can degrade these complex carbohydrates. However, while many single cellular microbes can utilize the building blocks of these insoluble polysaccharides, they frequently are unable to degrade insoluble carbohydrates. Cellobiose is a disaccharide breakdown product of cellulose, the most abundant component of plant biomass. We investigated the genetic regulation of cellobiose utilization in the oleaginous, basidiomycete yeast Rhodotorula (Rhodosporidium) toruloides using a combination of phylogenetic, genetic, and genomic approaches. We tested the closest R. toruloides homolog of the cellulose degradation regulator CLR-2/ClrB for a role in cellobiose utilization. Deletion of this transcription factor, which we named Cbr1, eliminated the ability of cells to grow on media containing cellobiose as the sole carbon source. Although, the role of CLR-2/ClrB is limited to regulating the expression of genes involved in the utilization of cellulose and hemicellulose, Cbr1 plays a role not only in cellobiose utilization, but also utilization of tricarboxylic acid (TCA) cycle intermediates. Transcriptional profiling revealed that the genes activated by Cbr1 included genes encoding beta-glucosidases and transporters. These beta-glucosidases are secreted and are necessary and sufficient for cellobiose utilization, while one of the transporters is required for utilization of the TCA cycle intermediate, citrate. Additionally, Cbr1 inhibits carbon catabolite repression, specifically during utilization of disaccharides, which may have evolved to limit the repression of genes encoding secreted proteins that cleave disaccharides into glucose extracellularly. The co-regulation of cellobiose and TCA cycle utilization with carbon catabolite repression may shed light on alternative methods of the regulation of carbon catabolite repression in fungi.
2025-04-10 | GSE293943 | GEO
Project description:Insufficient biosynthesis efficiency can be a major obstacle to engineer oleaginous yeasts to overproduce very long-chain fatty acids (VLCFAs) during the lipogenic phase. Taking nervonic acid (NA, C24:1) as an example, we overcame the bottleneck to overproduce NA in engineered Rhodosporidium toruloides by improving the biosynthesis of VLCFAs during the lipogenic phase. First, evaluating the catalytic preferences of three plant-derived ketoacyl-CoA synthases rationally guided reconstructing efficient NA biosynthetic pathway in R. toruloides. More importantly, a genome-wide transcriptional analysis endowed clues to strengthen the fatty acid elongation (FAE) module and identify/use lipogenic phase-activated promoter, collectively addressing the stagnation of NA accumulation during the lipogenic phase. The best-designed strain exhibited a high NA content (major component in total fatty acid [TFA], 46.3%) and produced a titer of 44.2 g/L in a 5 L bioreactor. The strategy developed here provides an engineering framework to establish the microbial process of producing valuable VLCFAs in oleaginous yeasts.
2023-09-14 | GSE241709 | GEO
Project description:Nitrogen limitation is a major regulator to initiate lipid overproduction in oleaginous fungi. To examine the influence of nitrogen starvation, chemiostat cultures of R. toruloides in defined media with abundant ammonium (MM) or minute ammonium (MM-N) were performed to obtain steady-state samples. Then Illumina's digital gene expression (DGE) technology was used for high-throughput transcriptome profiling of these samples.
2012-06-30 | GSE39023 | GEO
Project description:The yeast Rhodotorula mucilaginosa shown the capability to degrade patulin by the intracellular enzymes. However, the enzymes which risponsible for the degradation process was unkonown. Transcriptome change in response to mycotoxin patulin was analyzed. The molecular mechanism of Rhodotorula mucilaginosa withstand patulin was revealed.
2018-12-01 | GSE98937 | GEO