In situ evidence for systematic membrane thickness variation across cellular organelles

In eukaryotes, membrane-bound organelles create distinct molecular environments. The compartmentalizing lipid bilayer is a dynamic composite material, whose thickness and curvature modulate the structure and function of membrane proteins. In vitro, bilayer thickness correlates with lipid composition. Cellular membranes in situ, however, are continuously remodeled and the spatial variation of their biophysical properties remains understudied. Here, we present a computational approach to measure local membrane thickness in cryo-electron tomograms. Analysis of Chlamydomonas reihardtii and human cells reveals systematic thickness variations within and across organelles. These findings orthogonally support models of hydrophobic matching for differential sorting of proteins based on their transmembrane domain lengths, e.g., across the Golgi apparatus. Our workflow is computationally efficient, public, easy to integrate within existing tomogram analysis pipelines, and enables membrane thickness measurements across experimental conditions. Using this approach, relationships between membrane composition, thickness, and function are explored in situ, with broader applications across membrane biology.