Rhodotorula toruloides
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA156807 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| DRR032556_1.fastq.gz | Fastqsanger.gz | |||
| DRR032556_2.fastq.gz | Fastqsanger.gz | |||
| DRR032557_1.fastq.gz | Fastqsanger.gz | |||
| DRR032557_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 651 |
Similar Datasets
Project description:Global transcriptional profiling of oleaginous yeast Rhodosporidium toruloides under nitrogen limitation.
| PRJNA169625 | ENA
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:The oleaginous red yeast species Rhodotorula toruloides, a prominent environmental basidiomycetous yeast, has garnered significant interest for its remarkable capacity to utilize main carbon sources present in lignocellulosic hydrolysates, such as glucose, xylose, and acetic acid, and to efficiently produce lipids and carotenoids. This species can also efficiently use other less usual and difficult-to-catabolize C-sources, as is the case of the acid sugar D-galacturonic acid and the neutral sugar L-arabinose, present in hydrolysates from pectin-rich agro-industrial residues. Strain R. toruloides IST536 (alias PYCC 5615) was previously selected in our laboratory for sugar beet pulp valorization based on its ability to produce lipids and carotenoids through the complete catabolism of the major C-sources present in the hydrolysates (1). This strain, whose genome has been recently sequenced in our laboratory, is a conjugated strain derived from IFO 0559 (isolated from wood-pulp; GCA_000988805.1) × IFO 0880 (isolated from air; GCA_001255795.1) (2). Despite its potential, the metabolism of this promising strain can be limited by the presence of acetic acid in the hydrolysates as well as other inhibitors present in lignocellulosic hydrolysates. To increase IST536 (PYCC 5615) strain robustness, an adaptive laboratory evolution (ALE) strategy was used. The selected evolved strain IST536 MM15 exhibits increased tolerance to several inhibitors of biotechnological relevance: methanol and the four main inhibitors present in lignocellulosic hydrolysates: acetic and formic acids, hydroxymethylfurfural (HMF), and furfural (3). The superior performance of this evolved multi-stress tolerant strain for lipid production from non-detoxified lignocellulosic biomass hydrolysates was confirmed. To obtain mechanistic insights underlying such multi-tolerant phenotype, the genomes of the original and the evolved strains, IST536 (PYCC 5615) and IST536 MM15, respectively, were sequenced and the transcriptomic profiling of both strains under non-stressing conditions was performed. References: 1. Martins LC, et, al. Journal of Fungi. 2021; 7(3):215. https://doi.org/10.3390/jof7030215 2. Banno, I. (1967). The Journal of General and Applied Microbiology, 13(2), 167-196. https://doi.org/10.2323/jgam.13.167 3. Fernandes, M. A., Mota, M. N., et al, Journal of Fungi, 2023, 9(11), 1073 https://doi.org/10.3390/jof9111073
2024-05-29 | GSE254308 | GEO
Project description:Genome of the oleaginous yeast Rhodotorula toruloides CBS 14 assembled by a combined approach of long- and short read sequencing
| PRJEB40807 | ENA
Project description:BackgroundResveratrol is a plant-derived phenylpropanoid with diverse biological activities and pharmacological applications. Plant-based extraction could not satisfy ever-increasing market demand, while chemical synthesis is impeded by the existence of toxic impurities. Microbial production of resveratrol offers a promising alternative to plant- and chemical-based processes. The non-conventional oleaginous yeast Rhodotorula toruloides is a potential workhorse for the production of resveratrol that endowed with an efficient and intrinsic bifunctional phenylalanine/tyrosine ammonia-lyase (RtPAL) and malonyl-CoA pool, which may facilitate the resveratrol synthesis when properly rewired.ResultsResveratrol showed substantial stability and would not affect the R. toruloides growth during the yeast cultivation in flasks. The heterologus resveratrol biosynthesis pathway was established by introducing the 4-coumaroyl-CoA ligase (At4CL), and the stilbene synthase (VlSTS) from Arabidopsis thaliana and Vitis labrusca, respectively. Next, The resveratrol production was increased by 634% through employing the cinnamate-4-hydroxylase from A. thaliana (AtC4H), the fused protein At4CL::VlSTS, the cytochrome P450 reductase 2 from A. thaliana (AtATR2) and the endogenous cytochrome B5 of R. toruloides (RtCYB5). Then, the related endogenous pathways were optimized to affect a further 60% increase. Finally, the engineered strain produced a maximum titer of 125.2 mg/L resveratrol in YPD medium.ConclusionThe non-conventional oleaginous yeast R. toruloides was engineered for the first time to produce resveratrol. Protein fusion, co-factor channeling, and ARO4 and ARO7 overexpression were efficient for improving resveratrol production. The results demonstrated the potential of R. toruloides for resveratrol and other phenylpropanoids production.
| S-EPMC9789595 | biostudies-literature
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: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:α-Terpineol is a monoterpenoid alcohol that has been widely used in the flavor, fragrance, and pharmaceutical industries because of its sensory and biological properties. However, few studies have focused on the microbial production of α-terpineol. The oleaginous yeast Rhodotorula toruloides is endowed with a natural mevalonate pathway and is a promising host in synthetic biology and biorefinery. The primary objective of this work was to engineer R. toruloides for the direct biosynthesis of α-terpineol. The improvement in monoterpenoid production was achieved through the implementation of modular engineering strategies, which included the enhancement of precursor supply, blocking of downstream pathways, and disruption of competing pathways. The results of these three methods showed varying degrees of favorable outcomes in enhancing α-terpineol production. The engineered strain 5L6HE5, with competitive pathway disruption and increased substrate supply, reached the highest product titer of 1.5 mg/L, indicating that reducing lipid accumulation is an efficient method in R. toruloides engineering for terpenoid synthesis. This study reveals the potential of R. toruloides as a host platform for the synthesis of α-terpineol as well as other monoterpenoid compounds.
| S-EPMC10835275 | biostudies-literature
Project description:BackgroundRhodotorula toruloides is a robust producer of triacylglycerol owing to its fast growth rate and strong metabolic flux under conditions of high cell density fermentation. However, the molecular basis of fatty acid biosynthesis, desaturation and regulation remains elusive.ResultsWe present the molecular characterization of four fatty acid desaturase (FAD) genes in R. toruloides. Biosynthesis of oleic acid (OA) and palmitoleic acid (POA) was conferred by a single-copy ∆9 Fad (Ole1) as targeted deletion of which abolished the biosynthesis of all unsaturated fatty acids. Conversion of OA to linoleic acid (LA) and α-linolenic acid (ALA) was predominantly catalyzed by the bifunctional ∆12/∆15 Fad2. FAD4 was found to encode a trifunctional ∆9/∆12/∆15 FAD, playing important roles in lipid and biomass production as well as stress resistance. Furthermore, an abundantly transcribed OLE1-related gene, OLE2 encoding a 149-aa protein, was shown to regulate Ole1 regioselectivity. Like other fungi, the transcription of FAD genes was controlled by nitrogen levels and fatty acids in the medium. A conserved DNA motif, (T/C)(G/A)TTGCAGA(T/C)CCCAG, was demonstrated to mediate the transcription of OLE1 by POA/OA. The applications of these FAD genes were illustrated by engineering high-level production of OA and γ-linolenic acid (GLA).ConclusionOur work has gained novel insights on the transcriptional regulation of FAD genes, evolution of FAD enzymes and their roles in UFA biosynthesis, membrane stress resistance and, cell mass and total fatty acid production. Our findings should illuminate fatty acid metabolic engineering in R. toruloides and beyond.
| S-EPMC7977280 | biostudies-literature