Data-independent acquisition-based lipidomics reveals lipidome alterations associated with growth of Saccharomyces cerevisiae at low temperature

Budding yeast, Saccharomyces cerevisiae, adapts to low-temperature stress by altering the amounts and proportions of phospholipids, as well as the structures of acyl chains. To better understand this process, a data-independent acquisition-based lipidomics using liquid chromatography-quadrupole time-of-flight mass spectrometry method was developed to quantify acyl chain isomers in glycerolipids and phospholipids. This method distinguished lipid molecular species, such as phosphatidylcholine (PC) 16:1_18:0 and PC16:0_18:1, at the level of acyl chain isomers. These species were previously identified only at the total acyl chain level as PC 34:1 using the conventional data-dependent acquisition (DDA) method. Using this approach, 145 diacyl lipid molecular species were identified in S. cerevisiae at 30 °C, compared to only 101 identified using the conventional DDA method. Analysis of S. cerevisiae at 10 °C revealed 121 phospholipid and diacylglycerol (DG) molecular species and 260 triacylglycerol (TG) features as well as other 51 sphingolipids and sterol lipids. The results demonstrated unique increases in phosphatidylinositol (PI), phosphatidylethanolamine (PE), monomethyl (MM) PE, and TG containing both 16:1 and medium-chain fatty acids (MCFAs). The knockout strains ole1Δ and slc1Δ, lacking the desaturase that produces 16:1 and the acyltransferase favoring MCFAs, respectively, exhibited growth defects exclusively while growing at 10 °C. These findings suggest that S. cerevisiae regulates its lipid profiles to address low-temperature stress.