Abstract
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.
Highlights
Saccharomyces cerevisiae, R. toruloides possesses the enzyme ATP:citrate lyase, which is the main source of acetyl-CoA for lipid synthesis
More information on the GitHub repository is provided below. To reconstruct those parts of metabolism that are relatively conserved between fungal species, the wellcurated genome-scale model (GEM) of Saccharomyces cerevisiae (yeast-GEM version 8.2.0, doi:10.5281/zenodo.1495483, 75 (Lu et al, 2019)) and Yarrowia lipolytica (iYali4.1.1, (Kerkhoven, Pomraning, Baker, & Nielsen, 2016)) were taken as template models, while orthologous genes were identified via bi-directional BLASTP (Camacho et al, 2009) against the S. cerevisiae S288c and Y. lipolytica CLIB 122 reference genomes
To support the development of R. toruloides as promising microbial biocatalyst for oleochemical production, we developed a genome-scale model for R. toruloides strain NP11 through a combination 145 of semi-automated reconstruction and manual curation based on literature data (Fig 1A)
Summary
Rhodosporidium toruloides) is a basidiomycetous yeast belonging to the subphylum Pucciniomycotina and occurs naturally in a wide range of habitats including surfaces of leaves, soil and sea water (Sampaio, 2011). The ready scalability and fast rate of lipid production by oleaginous yeasts such as R. toruloides makes this approach a competitive alternative to emerging “third generation”. The R. toruloides lipid fraction contains ω-3 linolenic acid and heptadecenoic acid which makes this yeast a promising organism for the production of pharma- and nutraceuticals at the same time as it is a natural producer of several carotenoid pigments including torularhodin, torulene, γ-carotene and β-carotene (Buzzini et al, 2007)
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