A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data

Background: Rhodosporidium toruloides is a basidiomycetes yeast that can accumulate large amount of lipids and natively produce carotenoids. To better assess this non-model yeast′s metabolic capabilities, we reconstruct a genome-scale model of R. toruloides IFO0880′s metabolic network (iRhto1108) using recent functional genomics and phenotypic data in literature or generated herein. Results: The model iRhto1108 accounts for 2,203 reactions, 1,985 metabolites and 1,108 genes. In this work, we integrate and supplement the current knowledge with in-house generated biomass composition and experimental measurements pertaining to the organism9s metabolic capabilities. Phenotype-genotype relationship predictions were improved through manual curation of gene-protein-reaction rules for 543 reactions and validations with gene essentiality data leading to correct recapitulations of 84.5% of gene essentiality data (sensitivity of 94.3% and specificity of 53.8%). Organism-specific macromolecular composition and ATP maintenance requirements were experimentally measured for two separate growth conditions: (i) carbon and (ii) nitrogen limitations. Overall, iRhto1108 reproduced R. toruloides′s utilization capabilities for 18 alternate substrates, matched measured wild-type growth yield, and recapitulated the viability of 772 out of 819 deletion mutants. As a demonstration to the model′s fidelity in guiding engineering interventions, the OptForce procedure was applied on iRhto1108 for the overproduction of triacylglycerol. Suggested interventions recapitulated many of the previously successfully implemented genetic modifications and put forth a few new ones. Conclusion: iRhto1108 offers a highly curated model for a non-model yeast supported by multiple layers of experimental data that can be used to inform genetic interventions. Keywords: Genome-scale model, Non-model yeast, Rhodosporidium toruloides, Triacylglycerol production