Leary, K. A. | bioRxiv Science

bioRxiv2025

Atg23 Interacts With Both the N- and C-termini of Atg9 Via a Hydrophobic Binding Pocket

Macroautophagy is a cellular process where cytosolic material is captured in double membrane vesicles, termed autophagosomes, which fuse with the vacuole or lysosomes leading to the degradation of the captured contents. In yeast, the biogenesis of autophagosomes is initiated by the fusion of a few small vesicles which contain the integral membrane protein Atg9. Atg9 vesicle trafficking is in part regulated by the peripheral membrane protein Atg23. However, the structure of Atg23 and the mechanism by which Atg23 interacts with Atg9 are currently unknown. Therefore, we determined the crystal structure for a monomeric form of Atg23 and characterized the interaction between Atg23 and Atg9. This work reveals that Atg23 contains a novel fold which is consistent with the AlphaFold 3 prediction except that the helices running towards the dimerization region have a bend giving a more curved global architecture than the prediction. In addition, we demonstrate that conserved sequences in both the N and C-terminal regions of Atg9 bind to a hydrophobic cavity on Atg23.

biochemistry↗

bioRxiv2020

The third coiled coil domain of Atg11 is required for shaping mitophagy initiation sites

Selective autophagy is the capture of specific cytosolic contents in double membrane vesicles that subsequently fuse with the vacuole or lysosome, thereby delivering cargo for degradation. Selective autophagy receptors (SARs) mark the cargo for degradation and, in yeast, recruit Atg11, the scaffolding protein for selective autophagy initiation. The mitochondrial protein Atg32 is the yeast SAR that mediates mitophagy, the selective autophagic capture of mitochondria. Atg11- Atg32 interactions concentrate Atg32 into puncta that are thought to represent sites of mitophagy initiation. However, it is unclear how Atg11 concentrates Atg32 to generate mitophagy initiation sites. We show here that the coiled coil 3 (CC3) domain of Atg11 is required for concentrating Atg32 into puncta. We determined the structure of the majority of the CC3, demonstrating that the CC3 forms a parallel homodimer whose dimer interface is formed by a small number of hydrophobic residues. We further show that the CC3 dimerization interface is required for shaping Atg32 into functional mitophagy initiation sites and for delivery of mitochondria to the vacuole. Our findings suggest that Atg11 self-interactions help concentrate SARs as a necessary precondition for cargo capture.

cell biology↗