Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica

Abstract

Yarrowia lipolytica is a promising microbial cell factory for the production of lipids to be used as fuels and chemicals, but there are few studies on regulation of its metabolism. Here we performed the first integrated data analysis of Y. lipolytica grown in carbon and nitrogen limited chemostat cultures. We first reconstructed a genome-scale metabolic model and used this for integrative analysis of multilevel omics data. Metabolite profiling and lipidomics was used to quantify the cellular physiology, while regulatory changes were measured using RNAseq. Analysis of the data showed that lipid accumulation in Y. lipolytica does not involve transcriptional regulation of lipid metabolism but is associated with regulation of amino-acid biosynthesis, resulting in redirection of carbon flux during nitrogen limitation from amino acids to lipids. Lipid accumulation in Y. lipolytica at nitrogen limitation is similar to the overflow metabolism observed in many other microorganisms, e.g. ethanol production by Sacchromyces cerevisiae at nitrogen limitation.

Figure 1

Experimental design. Triplicate chemostats were run at steady-state, after which various samples were taken. Strain-specific GEMs were generated using the experimental data and the predicted flux changes were compared with differentially expressed transcripts, indicating potential transcriptional regulation.

Figure 2

Lipid and total fatty acid composition. Error bars are s.d. of three independent biological replicates. CL, cardiolipin; ES, ergosterol; FFA, free fatty acid; PA, phosphatidate; PC, phosphatidyl-choline; PE, phosphatidylethanolamine; PI, phosphatidyl-inositol; PS, phosphatidyl-serine; SE, steryl ester; TAG, triacylglycerol.

Figure 3

Gene-set analysis of nitrogen over carbon limitation. Carbon limitation functioned as reference condition. Gene sets are defined by GO terms, and for significantly enriched GO terms (adjusted P<0.01) is shown what percentage of genes are either up- or downregulated at nitrogen limitation. The top GO terms are upregulated while the lower GO terms are downregulated.

Figure 4

Schematic overview of changes in flux and transcript levels. Arrows can represent multiple reactions. Z-scores indicate changes on the levels of metabolic flux or RNA, TR score indicates a correlation between metabolix flux and RNA, suggesting transcriptional regulation. (a) Central carbon metabolism including lipid metabolism. (b) Nitrogen metabolism. (c) Amino acid biosynthetic pathways.

Figure 5

Schematic overview of regulation that occurs during nitrogen limitation in a high-lipid producing strain.