Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Nhung Pham; Maarten Reijnders; Maria Suarez-Diez; Bart Nijsse; Jan Springer; Gerrit Eggink; Peter J Schaap

doi:10.1186/s13068-020-01838-1

Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production

Biotechnol Biofuels. 2021 Jan 6;14(1):2. doi: 10.1186/s13068-020-01838-1.

Authors

Nhung Pham¹, Maarten Reijnders^{1

2}, Maria Suarez-Diez¹, Bart Nijsse¹, Jan Springer³, Gerrit Eggink^{3

4}, Peter J Schaap⁵

Affiliations

¹ Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands.
² Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland.
³ Food and Biobased Research and AlgaePARC, Wageningen University and Research, Wageningen, the Netherlands.
⁴ Bioprocess Engineering and AlgaePARC, Wageningen University and Research, Wageningen, the Netherlands.
⁵ Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, the Netherlands. peter.schaap@wur.nl.

Abstract

Background: Cutaneotrichosporon oleaginosus ATCC 20509 is a fast-growing oleaginous basidiomycete yeast that is able to grow in a wide range of low-cost carbon sources including crude glycerol, a byproduct of biodiesel production. When glycerol is used as a carbon source, this yeast can accumulate more than 50% lipids (w/w) with high concentrations of mono-unsaturated fatty acids.

Results: To increase our understanding of this yeast and to provide a knowledge base for further industrial use, a FAIR re-annotated genome was used to build a genome-scale, constraint-based metabolic model containing 1553 reactions involving 1373 metabolites in 11 compartments. A new description of the biomass synthesis reaction was introduced to account for massive lipid accumulation in conditions with high carbon-to-nitrogen (C/N) ratio in the media. This condition-specific biomass objective function is shown to better predict conditions with high lipid accumulation using glucose, fructose, sucrose, xylose, and glycerol as sole carbon source.

Conclusion: Contributing to the economic viability of biodiesel as renewable fuel, C. oleaginosus ATCC 20509 can effectively convert crude glycerol waste streams in lipids as a potential bioenergy source. Performance simulations are essential to identify optimal production conditions and to develop and fine tune a cost-effective production process. Our model suggests ATP-citrate lyase as a possible target to further improve lipid production.

Keywords: Biodiesel production; Crude glycerol; Cutaneotrichosporon oleaginosus ATCC 20509; Flux balance analysis; Genome-scale metabolic model; Lipid accumulation; Oleaginous yeast.