Global analysis of the yeast lipidome by quantitative shotgun mass spectrometry

Abstract

Although the transcriptome, proteome, and interactome of several eukaryotic model organisms have been described in detail, lipidomes remain relatively uncharacterized. Using Saccharomyces cerevisiae as an example, we demonstrate that automated shotgun lipidomics analysis enabled lipidome-wide absolute quantification of individual molecular lipid species by streamlined processing of a single sample of only 2 million yeast cells. By comparative lipidomics, we achieved the absolute quantification of 250 molecular lipid species covering 21 major lipid classes. This analysis provided approximately 95% coverage of the yeast lipidome achieved with 125-fold improvement in sensitivity compared with previous approaches. Comparative lipidomics demonstrated that growth temperature and defects in lipid biosynthesis induce ripple effects throughout the molecular composition of the yeast lipidome. This work serves as a resource for molecular characterization of eukaryotic lipidomes, and establishes shotgun lipidomics as a powerful platform for complementing biochemical studies and other systems-level approaches.

Fig. 1.

The lipid metabolic network of S. cerevisiae. Enzymes are annotated by gene name (essential genes are indicated in red). The lipid metabolic network was compiled using the Saccharomyces Genome Database (www.yeastgenome.org) and references therein. Lipids monitored by absolute quantification are indicated by green circles. Lipids that were only identified are shown by gray circles. CL, cardiolipin; Cer, ceramide; CoA, coenzyme A; CDP-DAG, cytidine diacylglycerol; DAG, diacylglycerol; DMPE, dimethyl-phosphatidylethanolamine; FFA, free fatty acid; IPC, inositolphosphoceramide; LCB, long-chain base; LCBP, long-chain base phosphate; LPA, lysophosphatidic acid; LPC, lysophosphatidylcholine; LPE, lysophosphatidylethanolamine; LPI, lysophosphatidylinositol; LPS, lysophosphatidylserine; M(IP)₂C, mannosyl-diinositolphosphoceramide; MIPC, mannosyl-inositolphosphoceramide; MMPE, monomethyl-phosphatidylethanolamine; PA, phosphatidic acid; PC, phosphatidylcholine; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PGP, phosphatidylglycerolphosphate; PI, phosphatidylinositol; PIP, phosphatidylinositol-phosphate; PIP₂, phosphatidylinositol-bisphosphate; PS, phosphatidylserine; TAG, triacylglycerol.

Fig. 2.

Overview of the quantitative shotgun lipidomics approach. Yeast cell lysates were spiked with internal lipid standards. Samples were processed by 2-step lipid extraction for fractionation of apolar and polar lipids. The lipid extracts were analyzed by automated shotgun lipidomics analysis in negative and positive ion mode. Lipid species were detected by MPIS or MRM analysis on a QSTAR instrument, or by FT MS analysis on a LTQ Orbitrap machine. Quantification of ergosterol was achieved by chemical acetylation followed by MRM analysis. Identification and quantification of detected lipid species were performed by Lipid Profiler and ALEX.

Fig. 3.

Molecular composition of the wild-type S. cerevisiae lipidome. 162 molecular lipid species were quantified. S. cerevisiae BY4741 was cultured in synthetic defined medium at 24 °C. The insert shows TAG species. The abundance of lipid species is depicted in mol% and absolute amount (pmol per 0.2 OD units). Error bars indicate ±SD. (n = 4, 2 independent analyses of lipid extracts from 2 independent cultures).

Fig. 4.

Comparative lipidomics of wild-type BY4741, elo1Δ, elo2Δ, and elo3Δ. (A) Lipid class composition. (B) Molecular composition of sphingolipid species. Error bars indicate ±SD. (n = 4).