PXD037281

PXD037281 is an original dataset announced via ProteomeXchange.

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

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.

Dataset with its publication pending

submitter keyword: proteomics,Rhodotorula toruloides, metabolic fluxes, multiple substrates, genome-scale model

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

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PRIDE project URI

• PRIDE
  1. PXD037281
     1. Label: PRIDE project
     2. Name: Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides