Biology subjects

Nakatogawa, H.

Publications and source records attributed to Nakatogawa, H..

3 recordsLinked to original sources

bioRxiv2025

Mechanism of bridge-type phospholipid transfer by Atg2 for autophagosome biogenesis

Autophagosome biogenesis requires delivery of millions of phospholipids. In budding yeast, Atg2 and Atg18 couple the ER to the isolation membrane for lipid transport, yet the mechanism is poorly understood. Combining molecular dynamics simulations, in vitro imaging-based lipid transfer assays, and in vivo analyses, we show that Atg1-mediated phosphorylation activates Atg2 as a lipid-transfer bridge. Simulations reveal that Atg2 contains a water-excluding hydrophobic cavity that accommodates [~]25 phospholipids with bilayer-like fluidity. Atg1 phosphorylates an N-terminal helix of Atg2 in vitro and in vivo, thereby opening the ER-facing entrance to the Atg2 cavity and enabling lipid flow between membranes in silico and in vitro. Consistently, phosphodeficient but not phosphomimetic mutations impair autophagy. Cavity narrowing along the conduit disrupts lipid alignment in silico, phosphorylation-activated bridge-type lipid transfer in vitro, and ER-to-isolation-membrane lipophilic dye flow and autophagosome expansion in vivo. These data suggest that Atg1 gates Atg2-mediated bridge-type lipid transport to build autophagosomes.

cell biology↗

bioRxiv2024

Phase separation promotes Atg8 lipidation for autophagy progression

Upon starvation, the autophagy-initiating Atg1 complex undergoes phase separation to organize the pre-autophagosomal structure (PAS) in yeast, from which autophagosome formation is considered to proceed. However, the physiological roles of the PAS as a liquid droplet remain unclear. Here we show that core Atg proteins are recruited into early PAS droplets that are formed by phase separation of the Atg1 complex with different efficiencies in vitro. The Atg12-Atg5-Atg16 E3 ligase complex for Atg8 lipidation is the most efficiently condensed in the droplets via specific Atg12-Atg17 interaction, which is also important for the PAS targeting of the E3 complex in vivo. In vitro reconstitution experiments reveal that E3-enriched early PAS droplets promote Atg8 lipidation and incorporate Atg8-coated vesicles to the interior, thereby protecting them from Atg4-mediated delipidation. These data suggest that the PAS utilizes its liquid-like property to function as an efficient production site for lipidated Atg8 and pool membrane seeds to drive autophagosome formation.

cell biology↗

bioRxiv2021

Atg39 links and deforms the outer and inner nuclear membranes in selective autophagy of the nucleus

In selective autophagy of the nucleus (hereafter nucleophagy), nucleus-derived double membrane vesicles (NDVs) are formed, sequestered within autophagosomes, and delivered to lysosomes or vacuoles for degradation. In Saccharomyces cerevisiae, the nuclear envelope (NE) protein Atg39 acts as a nucleophagy receptor, which interacts with Atg8 to target NDVs to forming autophagosomal membranes. In this study, we revealed that Atg39 is anchored to the outer nuclear membrane (ONM) via its transmembrane domain and also associated with the inner nuclear membrane (INM) via membrane-binding amphipathic helices (APHs) in its perinuclear space region, thereby linking these membranes. We also revealed that overaccumulation of Atg39 causes the NE to protrude towards the cytoplasm, and the tips of the protrusions are pinched off to generate NDVs. The APHs of Atg39 are crucial for Atg39 assembly in the NE and subsequent NE protrusion. These findings suggest that the nucleophagy receptor Atg39 plays pivotal roles in NE deformation during the generation of NDVs to be degraded by nucleophagy.

cell biology↗