MemPrep, a new technology for isolating organellar membranes provides fingerprints of lipid bilayer stress

Reinhard, J.; Starke, L.; Klose, C.; Haberkant, P.; Hammarén, H.; Stein, F.; Klein, O.; Berhorst, C.; Stumpf, H.; Sáenz, J. P.; Hub, J.; Schuldiner, M.; Ernst, R. (2024) The EMBO Journal, 43(8), 1653–1685. DOI: 10.1038/s44318-024-00063-y

Summary

This study describes MemPrep, a new method for purifying organelle membranes from yeast (Saccharomyces cerevisiae). Combined with quantitative lipidomics and proteomics, MemPrep established the lipid composition of the endoplasmic reticulum (ER) and vacuolar membranes, revealing that the ER membrane composition is significantly distinct from the whole-cell lipidome. The approach uncovered dynamic remodeling of ER membranes under stress and identified distinct molecular fingerprints of lipid bilayer stress: increased membrane thickness and low levels of anionic lipids emerge as common denominators when the unfolded protein response is triggered by lipid perturbation.

Key Findings

• MemPrep provides high-purity organelle membrane preparations validated by proteomics
• The ER membrane lipid composition is significantly distinct from the whole-cell lipidome in yeast
• Lipid metabolic perturbations (e.g., inositol depletion) cause dramatic remodeling of ER membrane composition
• Increased membrane thickness and reduced anionic lipid content are common denominators of lipid bilayer stress
• Inositol depletion and prolonged proteotoxic stress produce distinct lipid fingerprints and membrane proteomes

Our Contribution

Our group contributed lipidomics expertise and data analysis supporting the quantitative characterization of organellar membrane compositions.

Significance

MemPrep enables systematic dissection of how lipid perturbations affect specific organelle membranes, providing the resolution needed to understand lipid bilayer stress at the subcellular level rather than inferring it from whole-cell measurements.