Organelle packing interactions in yeast revealed by high-resolution, isotropic soft X-ray tomography and 3D morphometric modeling

To what extent is cell anatomy a reflection of organelle confinement within the limited space of the crowded cytoplasm? Soft X-ray tomography of budding yeast and custom autosegmentation enabled reconstruction of hundreds of whole cells, including nucleus and vacuole. 3D morphometric analysis showed that vacuole enlargement progressively breaks the linear scaling of the nucleus, and drives nuclear displacement and flattening. Joint 3D shape analysis of meshed vacuole-nucleus pairs shows correlated curvature at the interface. These results suggest that asymmetric deformations may arise due to organelle packing. Dimensionality reduction of joint spherical harmonics-based shape representations of cell-nucleus-vacuole complexes pointed to relative organelle size, positioning, shape, and orientation as principal components of anatomical variation in wild-type and large-vacuole mutant cells. We propose that packing of organelles within the cytoplasm plays a significant role in establishing organelle morphology and global cell patterning. Further analyses of these co-varying features and biophysical deformation simulations based on observed organelle shapes are in progress. This work will provide the basis to quantify disorganization in a highly packed cytoplasm and characterize the impacts of physical interdependencies between organelles on global cell anatomy.