PNNL

Abstract

The Lipomyces clade contains oleaginous yeast species with advantageous metabolic features for biochemical and biofuel production. Limited knowledge on the metabolic networks of the species and limited tools for genetic engineering have led to a relatively small amounts of research on the microbes. Here, a genome-scale metabolic model (GSM) of Lipomyces starkeyi NRRL Y-11557 was built using ortholog protein mappings to model yeast species. Phenotypic growth assays were used to validate the GSM (66% accuracy) and indicated that NRRL Y-11557 ready utilized diverse carbohydrates but had limited catabolism of organic acids. The final GSM (iLst996) predicted a flux distribution in line with oleaginous yeast measurements and was utilized to predict theoretical lipid yields. iLst996 contained 96 of the annotated carbohydrate-active enzymes. 26 other yeasts in the Lipomyces clade were then genome sequenced and annotated. 16 of the sequenced species had orthologs for more than 97% of the iLst996 genes, demonstrating the usefulness of iLst996 as a broad GSM for Lipomyces metabolism. Pathways that diverged from iLst996 mainly revolved around alternate carbon metabolism, with ortholog groups excluding NRRL Y-11557 annotated to be involved in transport, glycerolipid, and starch metabolism among others. More specific analysis revealed 15 of the 26 species had predicted 3-oxoacyl-acyl-carrier protein reductases that had no orthologs in NRRL Y-11557. Overall, this study provides a useful modeling tool and data for analyzing and understanding Lipomyces species metabolism and will assist further engineering efforts in Lipomyces.