Medina Michaela, Chang Ya-Ting, Rahmani Hamidreza, Fuentes Daniel, Barad Benjamin A, Grotjahn Danielle A
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Department of Chemical Physiology and Biochemistry, School of Medicine, Oregon Health & Science University, Portland, OR 97239, USA.
bioRxiv. 2025 May 1:2025.04.30.651574. doi: 10.1101/2025.04.30.651574.
Lipid bilayers form the basis of organellar architecture, structure, and compartmentalization in the cell. Decades of biophysical, biochemical, and imaging studies on purified or reconstituted liposomes have shown that variations in lipid composition influence the physical properties of membranes, such as thickness and curvature. However, similar studies characterizing these membrane properties within the native cellular context have remained technically challenging. Recent advancements in cellular cryo-electron tomography (cryo-ET) imaging enable high-resolution, three-dimensional views of native organellar membrane architecture preserved in near-native conditions. We previously developed a 'Surface Morphometrics' pipeline that generates surface mesh reconstructions to model and quantify cellular membrane ultrastructure from cryo-ET data. Here, we expand this pipeline to measure the distance between the phospholipid head groups (PHG) of the membrane bilayer as a readout of membrane thickness. Using this approach, we demonstrate thickness variations both within and between distinct organellar membranes. We also demonstrate that membrane thickness positively correlates with other features, such as membrane curvedness. Further, we show that subcompartments of the mitochondrial inner membrane exhibit varying membrane thicknesses that are independent of network morphology (i.e., fragmented versus elongated networks). Finally, we demonstrate that large membrane-associated macromolecular complexes exhibit distinct density profiles that correlate with local variations in membrane thickness. Overall, our updated Surface Morphometrics pipeline provides a framework for investigating how changes in membrane composition in various cellular and disease contexts affect organelle ultrastructure and function.
脂质双层构成了细胞内细胞器结构、构造和区室化的基础。数十年来，针对纯化或重构脂质体开展的生物物理、生化及成像研究表明，脂质组成的变化会影响膜的物理性质，如厚度和曲率。然而，在天然细胞环境中表征这些膜性质的类似研究在技术上仍具有挑战性。细胞冷冻电子断层扫描（cryo-ET）成像技术的最新进展能够提供在近天然条件下保存的天然细胞器膜结构的高分辨率三维视图。我们之前开发了一种“表面形态计量学”流程，该流程可生成表面网格重建，以便根据cryo-ET数据对细胞膜超微结构进行建模和量化。在此，我们扩展该流程，以测量膜双层中磷脂头部基团（PHG）之间的距离，作为膜厚度的一种读数。利用这种方法，我们展示了不同细胞器膜内部以及之间的厚度变化。我们还证明膜厚度与其他特征（如膜曲率）呈正相关。此外，我们表明线粒体内膜的亚区室呈现出不同的膜厚度，且这些厚度与网络形态（即碎片化与伸长的网络）无关。最后，我们证明大型膜相关大分子复合物呈现出与膜厚度局部变化相关的独特密度分布。总体而言，我们更新后的表面形态计量学流程为研究在各种细胞和疾病背景下膜组成的变化如何影响细胞器超微结构和功能提供了一个框架。
