Quantitative Analysis of Proteome and Lipidome Dynamics Reveals Functional Regulation of Global Lipid Metabolism

Abstract

Elucidating how and to what extent lipid metabolism is remodeled under changing conditions is essential for understanding cellular physiology. Here, we analyzed proteome and lipidome dynamics to investigate how regulation of lipid metabolism at the global scale supports remodeling of cellular architecture and processes during physiological adaptations in yeast. Our results reveal that activation of cardiolipin synthesis and remodeling supports mitochondrial biogenesis in the transition from fermentative to respiratory metabolism, that down-regulation of de novo sterol synthesis machinery prompts differential turnover of lipid droplet-associated triacylglycerols and sterol esters during respiratory growth, that sphingolipid metabolism is regulated in a previously unrecognized growth stage-specific manner, and that endogenous synthesis of unsaturated fatty acids constitutes an in vivo upstream activator of peroxisomal biogenesis, via the heterodimeric Oaf1/Pip2 transcription factor. Our work demonstrates the pivotal role of lipid metabolism in adaptive processes and provides a resource to investigate its regulation at the cellular level.

Analyzing and Understanding Lipids of Yeast: A Challenging Endeavor

“…The lipid composition of yeast is rather simple and comprises some 150 distinct molecular species that have been identified to date (Guan and Wenk 2006;Ejsing et al 2009;Guan et al 2010;Klose et al 2012;Casanovas et al 2015). Table 1 summarizes the total lipid composition of various yeast wild-type strains grown in minimal medium supplemented with inositol ).…”

“…Advances in lipid mass spectrometry have significantly facilitated lipid analysis in yeast and other cell types and have unveiled unprecedented insight into the molecular species composition of yeast lipids (Guan and Wenk 2006;Ejsing et al 2009;Guan et al 2010;Shui et al 2010;Klose et al 2012;Casanovas et al 2015). Because lipid molecular masses are typically <1000 Da, they are excellent targets for mass spectrometry approaches.…”

“…Second, various lipid classes differ dramatically in their abundance, ranging from "bulk" lipids such as storage triacylglycerols and membrane phospholipids to less abundant sphingolipids, which are lipid-signaling molecules present only in trace amounts. Third, despite the relative simple lipid composition in yeast (see below), there is a great deal of combinatorial chemistry in terms of variations in acyl chain composition in various phospholipid classes, giving rise to a quite complex set of lipid molecular species even in the "simple" yeast cell (Guan and Wenk 2006;Ejsing et al 2009;Shui et al 2010;Knittelfelder et al 2014;Casanovas et al 2015). Fourth, lipid metabolism is a highly dynamic process, which correlates with cell growth, nutritional supply, and even the cell cycle (Kurat et al 2006(Kurat et al , 2009Zanghellini et al 2008;Klose et al 2012;Chauhan et al 2015).…”

Mga2 Transcription Factor Regulates an Oxygen-responsive Lipid Homeostasis Pathway in Fission Yeast

“…Lipid Extraction-Lipid extraction was performed as described previously (23)(24)(25). Six biological replicate cultures of wild-type and mga2⌬ cells growing exponentially in the presence of oxygen (6.8 ϫ 10 7 -1.3 ϫ 10 8 cells) were pelleted and washed twice in 155 mM ammonium acetate and then frozen under liquid nitrogen.…”

“…The collected lipid extracts were then vacuum-evaporated and dissolved in chloroform/methanol. Shotgun Lipidomics-Mass spectrometry was performed as described previously (23)(24)(25). Extracts were analyzed on a LTQ Orbitrap XL mass spectrometer (Thermo Fisher Scientific) equipped with the robotic nanoflow ion source TriVersa NanoMate (Advion Biosciences).…”