Genome-scale model of Rhodotorula toruloides metabolism
Journal article, 2019

The basidiomycete red yeast Rhodotorula toruloides is a promising platform organism for production of biooils. We present rhto-GEM, the first genome-scale model (GEM) of R. toruloides metabolism, that was largely reconstructed using RAVEN toolbox. The model includes 852 genes, 2,731 reactions, and 2,277 metabolites, while lipid metabolism is described using the SLIMEr formalism allowing direct integration of lipid class and acyl chain experimental distribution data. The simulation results confirmed that the R. toruloides model provides valid growth predictions on glucose, xylose, and glycerol, while prediction of genetic engineering targets to increase production of linolenic acid, triacylglycerols, and carotenoids identified genes-some of which have previously been engineered to successfully increase production. This renders rtho-GEM valuable for future studies to improve the production of other oleochemicals of industrial relevance including value-added fatty acids and carotenoids, in addition to facilitate system-wide omics-data analysis in R. toruloides. Expanding the portfolio of GEMs for lipid-accumulating fungi contributes to both understanding of metabolic mechanisms of the oleaginous phenotype but also uncover particularities of the lipid production machinery in R. toruloides.

yeast

genome-scale model

metabolism

Rhodotorula toruloides

Author

Ievgeniia Tiukova

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Sylvain Prigent

University of Bordeaux

Jens B Nielsen

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Mats Sandgren

Swedish University of Agricultural Sciences (SLU)

Eduard Kerkhoven

Chalmers, Biology and Biological Engineering, Systems and Synthetic Biology

Biotechnology and Bioengineering

0006-3592 (ISSN) 1097-0290 (eISSN)

Vol. 116 12 3396-3408

Subject Categories

Bioinformatics and Systems Biology

Genetics

DOI

10.1002/bit.27162

PubMed

31502665

More information

Latest update

12/3/2019