The MemDense project aims to identify how eukaryotic cells control the ratio of proteins and lipid in their membranes. Despite the enormous relevance of these biomolecules for virtually every cellular function, it remains unknown how cells balance the production of proteins and lipids. It has been known for decades that the different organelles (e.g. the endoplasmic reticulum (ER) or mitochondria) feature remarkably distinct protein-to-lipid ratios. Barely anything is known about, how different organelles control the exchange and flux of lipids for maintaining these largely distinct packing densities, and if an overcrowding of proteins in the membrane induces cellular stress.
We pursue the hypothesis that the protein-to-lipid ratio is sensed via the unfolded protein response (UPR), a conserved pathway, which controls the relative rate of lipid and protein production and which serves as a diagnostic marker for ER stress. We study this mechanistic connection in two model systems: The baker's yeast Saccharomyces cerevisiae and cultured, mammalian cells. We aim to understand, how communication and exchange of lipid metabolites between organelles support cell functions during acute, prolonged, and chronic ER stresses.
The MemDense project is important for society, because a large number of chronic inflammatory and complex metabolic diseases, such as type II diabetes and non-alcoholic fatty liver disease have been firmly associated with chronic ER stress, while the molecular basis of ER stress remains unresolved. The MemDense project establishes new experimental pipelines to test the contribution of the ER membrane and its composition to ER stress and UPR activation in health and disease.
Our objectives are
1) Isolating organelles from cells with unprecedented purity,
2) Establishing lipid fingerprints of ER stress (or: What are the characteristic lipid compositions of the stressed ER membrane?),
3) Studying the cooperation of cellular organelles, e.g. the ER, mitochondria, and the vacuole, in dealing with ER stress, and
4) Figuring out how the protein-to-lipid ratio is balanced in healthy cells and how membrane protein overcrowding causes chronic ER stress.
We find that acute and prolonged ER stress signaling is regulated by aberrant biophysical properties of the ER membrane. Surprisingly, we find that negatively charged lipids play a key role as modulators of ER stress. We establish lipid finger prints of ER stress in both yeast and mammalian cells and find that a decreased membrane compressibility is a major determinant of ER stress signaling by UPR transducers from yeast an mammals. We developed new experimental pipelines to quantitatively analyze the protein and lipid composition in ultra-pure organelle-derived preparations. By establishing new paradigms of modulating and exchanging membrane lipid compositions, we can now address - for the first time - the lipid dependency of membrane protein insertion, topology and folding by mammalian membrane protein insertion machineries. By addressing fundamental questions in membrane cell biology, we work towards lipid metabolic perturbations, which may pave the way to new preventive and therapeutic interventions to fight diseases associated with aberrant metabolism, infection, chronic ER stress, and disrupted (membrane) protein folding.
