Sphingolipids have been shown to play important roles in physiology and cell biology, but a systematic examination of their functions is lacking. We performed a genome-wide CRISPRi screen in sphingolipid-depleted cells and identified hypersensitive mutants in genes of membrane trafficking and lipid biosynthesis, including ether lipid synthesis. Systematic lipidomic analysis showed a coordinate regulation of ether lipids with sphingolipids, where depletion of one of these lipid types resulted in increases in the other, suggesting an adaptation and functional compensation. Biophysical experiments on model membranes show common properties of these structurally diverse lipids that also share a known function as GPI anchors in different kingdoms of life. Molecular dynamics simulations show a selective enrichment of ether phosphatidylcholine around p24 proteins, which are receptors for the export of GPI-anchored proteins and have been shown to bind a specific sphingomyelin species. Our results support a model of convergent evolution of proteins and lipids, based on their physico-chemical properties, to regulate GPI-anchored protein transport and maintain homeostasis in the early secretory pathway.
INTRODUCTIONThe maintenance of membrane lipid homeostasis is an energetically expensive yet necessary process in cells. Lipid diversity has evolved together with cell complexity to give rise to thousands of different lipids species with specific functions, many of which are still unexplored 1, 2 . Moreover, different lipid metabolic pathways are interconnected, and cells show a high phenotypic plasticity when adapting to changes in membrane lipid composition, which makes it difficult to disentangle the function of individual lipid species 3 . A systematic analysis of the cellular responses to perturbation of specific synthetic pathways is thus needed to reveal co-regulated lipid networks and uncover new lipid functions. Sphingolipids (SL) are a class of lipids that contain a sphingoid-base backbone, in contrast to the more commonly found glycerol backbone in glycerophospholipids (GPL). These bioactive lipids have been extensively studied in the last decades, revealing distinctive physico-chemical properties and connections to diseases 4,5 . SL have been implicated in diabetes 6 , cancer 7 and inflammation 8 , and mutations in SL synthetic or metabolic enzymes are associated with severe genetic disorders [9][10][11] . SL species sphingosine (So) and ceramide (Cer) can permeabilize membranes 12,13 ; Cer induces the flip-flop of neighbouring lipids 14 and can phase-separate to form membrane platforms important for signalling 15 . The most abundant SL species, sphingomyelin (SM), has been shown to modulate membrane properties and regulate signalling pathways 16,17 . Besides direct phosphorylation of ceramide synthases [18][19][20] , the only direct regulators of sphingolipid synthesis identified are Orm proteins (ORMDL in mammalian cells), that associate with serine palmitoyl transferase (SPT), the first enzyme of the sphingolipi...