Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rhodosporidium toruloides haplotypes IFO0559 and IFO0880 rapamycin treatment

ABSTRACT: Comparison between control groups and rapamycin treatment of both haplotypes of Rhodosporidium toruloides.

INSTRUMENT(S):

ORGANISM(S): Rhodotorula Toruloides

SUBMITTER: Philipp Cavelius

LAB HEAD: Thomas Brück

PROVIDER: PXD052386 | Pride | 2025-05-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	559YNB120h1.d.zip	Other
	559YNB120h1DB559.xml	Xml
	559YNB120h1DB880.xml	Xml
	559YNB120h2.d.zip	Other
	559YNB120h2DB559.xml	Xml

Items per page:

1 - 5 of 144

Publications

Rhodosporidium toruloides-a new surrogate model to study rapamycin induced effects on human aging and cancer.

Cavelius Philipp M PM Haack Martina M Awad Dania D Brueck Thomas B TB Mehlmer Norbert N

Cellular and molecular life sciences : CMLS 20250409 1

The haploid, olegenious yeast Rhodosporidium toruloides accumulates intracellular lipids and carotenoids upon metabolic stress. Target of Rapamycin (TOR) signaling, essential for cell proliferation, is known to affect cellular lipid accumulation. In contrast to the conventional surrugate cell model S. cerevisiae, which harbours two TOR kinases within its TOR complex, R. toruloides only harbours one TOR kinase, mimicking mammalian systems. We used a proteomics centered approach to probe the cellu ...[more]

PMID: 40205123

Similar Datasets

A toolset of constitutive promoters for engineering Rhodosporidium toruloides

Project description:Background: A key prerequisite for pathway engineering is the development of genetic tools and resources. Rhodosporidium toruloides is emerging as a promising host for the production of bioproducts from lignocellulosic biomass. However, there is a lack of characterized promoters to drive expression of heterologous genes for strain engineering in R. toruloides. Results: The resulting data describes a set of native R. toruloides promoters, characterized over time in four media commonly used for this yeast. The promoter sequences were sorted using transcriptional analysis and several of them were found to drive expression bidirectionally. We measured promoter expression by flow cytometry using a dual fluorescent reporter system. From these analyses, we found a total of 20 constitutive promoters (12 monodirectional and 8 bidirectional), that are strong, stable, and can reliably be used for genetic manipulation of this emergent host. Conclusions: We are presenting a list of robust constitutive promoters that are native to the emergent bioconversion host R. toruloides which helps to fulfill the lack of existing tools for this yeast and that can be applied in future metabolic engineering studies.

2020-03-02 | GSE128360 | GEO

Global transcriptional profiling of oleaginous yeast Rhodosporidium toruloides under nitrogen limitation.

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

Genome-wide and enzymatic analysis reveals efficient D- galacturonic acid metabolism in the basidiomycete yeast Rhodosporidium toruloides

Project description:Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range of substrates used in fermentation biorefinery approaches. The red basidiomycete yeast Rhodosporidium toruloides is a promising and robust host for lipid and terpene derived chemicals. Previous studies demonstrated assimilation of a range of substrates, from C5/C6-sugars to aromatic molecules similar to lignin monomers. In the current study, we analyzed R. toruloides potential to assimilate Dgalacturonic acid, a major sugar in many pectin-rich agricultural waste streams, including sugar beet pulp and citrus peels. D-galacturonic acid is not a preferred substrate for many fungi, but its metabolism was found to be on par with D-glucose and D-xylose in R. toruloides. A genome-wide analysis by combined RNAseq/RB-TDNAseq revealed those genes with high relevance for fitness on D-galacturonic acid. While R. toruloides was found to utilize the same non-phosphorylative catabolic pathway known from ascomycetes, the maximal velocities of several enzymes exceeded those previously reported. In addition, an efficient downstream glycerol catabolism and a novel transcription factor were found to be important for D-galacturonic acid utilization. These results set the basis for use of R. toruloides as a potential host for pectin-rich waste conversions and demonstrate its suitability as a model for metabolic studies in basidiomycetes.

2019-11-13 | GSE127536 | GEO

Understanding the impact of integration copy number and genome location on heterologous gene expression in Rhodosporidium toruloides

Project description:Transcriptome sequencing to understand the impact of integration copy number and genome location on heterologous gene expression in R. toruloides

2021-04-28 | GSE156051 | GEO

Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides

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

Global transcriptional profiling of oleaginous yeast Rhodosporidium toruloides under nitrogen limitation.

2012-06-30 | GSE39023 | GEO

RNAseq analysis of Rhodosporidium toruloides BOT-A2 for nitrogen-starvation on glucose or xylose

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

Proteome analysis of xylose metabolism in Rhodotorula toruloides during lipid production

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

Multi-omics driven metabolic network reconstruction and analysis of lignocellulosic carbon utilization in Rhodosporidium toruloides

Project description:Global proteomics datasets to study lignocellulosic carbon utilization in Rhodosporidium Toruloides

2021-09-09 | PXD022377 | Pride

Xylose Metabolism and the Effect of Oxidative Stress on Lipid and Carotenoid Production in Rhodotorula toruloides: Insights for Future Biorefinery

Project description:The use of cell factories to convert sugars from lignocellulosic biomass into chemicals in which oleochemicals and food additives, such as carotenoids, play an important role is essential for the shift towards sustainable processes. Rhodotorula toruloides is a yeast that naturally metabolises a wide range of substrates, including lignocellulosic hydrolysates, and converts them into lipids and carotenoids. In this study, xylose, the main component of hemicellulose, was used as the sole substrate for R. toruloides, and a detailed physiology characterisation combined with absolute proteomics and genome-scale metabolic models was carried out to understand the regulation of lipid and carotenoid production. To improve these productions, oxidative stress was induced by hydrogen peroxide and light irradiation and further enhanced by adaptive laboratory evolution. Based on the online measurements of growth and CO2 excretion, three distinct growth phases were identified during batch cultivations. The intracellular flux estimations correlated well with the measured protein levels and demonstrated improved NADPH regeneration and phosphoketolase activity and reduced beta-oxidation, correlating with increasing lipid yields. Light irradiation conditions resulted in 70% higher carotenoid and 40% higher lipid yields. The presence of hydrogen peroxide did not affect the carotenoid yield but culminated in the highest lipid yield of 0.65 ± 0.06 g/gDCW. The adapted strain showed improved fitness and 130% higher carotenoid yield than the parental strain. This work presented a holistic view of xylose conversion into microbial oil and carotenoids by R. toruloides for further cost-effective and renewable production of these molecules.

2020-07-29 | PXD019305 | Pride