Experimental determination and mathematical modeling of standard shapes of forming autophagosomes

Autophagy is an intracellular degradation process mediated by autophagosomes. The formation of autophagosomes involves dynamic morphological changes of the precursor phagophore, in which a disk-shaped membrane cisterna grows, bends into a cup-shaped intermediate, and finally becomes a spherical autophagosome. However, the physical mechanism behind these morphological changes remains elusive. This is in part because the shapes of phagophores (i.e., forming autophagosomes) are highly variable, and their standard shapes have not been characterized precisely. Here, we first determined the average shapes of phagophores by statistically investigating three-dimensional electron micrographs of more than 100 phagophores. The results showed that the cup-shaped structures adopted a characteristic morphology; they were longitudinally elongated, and the rim was catenoidal with an outwardly recurved shape. From the characteristic shape of the rim, we estimated the Gaussian modulus that determines the elastic properties of the phagophore membrane. Using the Gaussian modulus, we established a theoretical model of the shape of entire phagophores. The model quantitatively reproduced the average morphology observed by electron microscopy and revealed that the characteristic shape of phagophores (i.e., an elongated shape with a catenoidal rim) was primarily determined by the relative size of the open rim to the total surface area. These results suggest that autophagosomal membranes are highly flexible and that the morphological changes during autophagosome formation follow a stable path determined by elastic bending energy minimization. Significance statement Autophagy is an intracellular degradation process mediated by autophagosomes. The formation of autophagosomes involves dynamic morphological changes; a disk-shaped membrane cisterna grows, becomes a cup-shaped structure, and finally develops into a spherical autophagosome. However, since these characteristic morphological changes have never been quantitatively described, the physical mechanism behind these morphological changes remains elusive. Here, we determined the average shapes of forming autophagosomes by statistically investigating three-dimensional electron microscopy images and showed that the rim is catenoidal. Next, we established a theoretical model based on the elastic bending energy, which quantitatively reproduced the experimental results. These results suggest that autophagosomal membranes are highly flexible, and the characteristic morphological changes are primarily determined by elastic bending energy minimization.