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PXD037281

PXD037281 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleGenome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
DescriptionRhodotorula 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.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:58:14.412.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterAlina Rekena
SpeciesList scientific name: Rhodotorula toruloides; NCBI TaxID: 5286;
ModificationListNo PTMs are included in the dataset
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-10-10 08:25:35ID requested
12023-03-13 03:48:54announced
22023-04-11 05:48:16announced2023-04-11: Updated project metadata.
32023-11-14 08:58:14announced2023-11-14: 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 affiliationFood Tech and Bioengineering Lab, Department of Chemistry and Biotechnology, Tallinn University of Technology, Estonia
contact emaillahtvee@taltech.ee
lab head
Alina Rekena
contact affiliationTallinn University of Technology
contact emailalina.rekena@taltech.ee
dataset submitter
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Dataset FTP location
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