PXD037281 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides |
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. |
HostingRepository | PRIDE |
AnnounceDate | 2023-11-14 |
AnnouncementXML | Submission_2023-11-14_08:58:14.412.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Alina Rekena |
SpeciesList | scientific name: Rhodotorula toruloides; NCBI TaxID: 5286; |
ModificationList | No PTMs are included in the dataset |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-10-10 08:25:35 | ID requested | |
1 | 2023-03-13 03:48:54 | announced | |
2 | 2023-04-11 05:48:16 | announced | 2023-04-11: Updated project metadata. |
⏵ 3 | 2023-11-14 08:58:14 | announced | 2023-11-14: Updated project metadata. |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: proteomics,Rhodotorula toruloides, metabolic fluxes, multiple substrates, genome-scale model |
Contact List
Petri-Jaan Lahtvee |
contact affiliation | Food Tech and Bioengineering Lab, Department of Chemistry and Biotechnology, Tallinn University of Technology, Estonia |
contact email | lahtvee@taltech.ee |
lab head | |
Alina Rekena |
contact affiliation | Tallinn University of Technology |
contact email | alina.rekena@taltech.ee |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/03/PXD037281 |
PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD037281
- Label: PRIDE project
- Name: Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides