Figure 4.

Examples for the three shape categories (A,D: U-shape; B,E: circle; C,F: ellipse). Structures in A, B, and C are from EYFP-GABARAP expressing cells, structures in D,E, and F are from EYFP-LC3B expressing cells (scale bars: 100 nm). In G, the presumed roles of GABARAP and LC3B at distinct stages of the autophagy pathway (phagophore initiation, elongation, closure, and fusion of the mature autophagosome with a lysosome to yield an autolysosome) are depicted. Steps that are assumed to require GABARAP and LC3B on the convex face of the isolation membrane (not drawn for clarity reasons) are highlighted in blue and red, respectively. As shown, GABARAP and LC3B can both link cargo materials to the concave face of the isolation membrane during selective autophagy in a cargo receptor-mediated manner. The various autophagic structures drawn as cross-sections are assigned to the respective 2D projections as anticipated in SMLM reconstructions (with a marked direction-dependence in the case of an early phagophore). Note, however, that SMLM cannot strictly distinguish between these membrane-bound autophagic organelles and other (vesicular or non-vesicular) structures populated by Atg8 proteins (see Discussion).