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

Abstract

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.

Atg39 selectively captures inner nuclear membrane into lumenal vesicles for delivery to the autophagosome

“…S4 D ). Gratifyingly, concurrent work performed by others suggests a similar model ( Mochida et al, 2021 , Preprint ). At the ONM, Atg39 can engage with the cytosolic autophagy machinery through its cytosolically exposed N-terminal domain while connecting to the INM through its lumenal domain.…”

ER-phagy: mechanisms, regulation, and diseases connected to the lysosomal clearance of the endoplasmic reticulum

“…Engagement of Atg11 and FIP200 also takes place during yeast and mammalian macro-ER-phagy driven by the ER-phagy receptors CCPG1 ( 163 ), Atg39, and Atg40 ( 164 , 165 ) (sects. 3.2.1.1.4 and 3.2.2.1), Atg39-mediated macro-nucleophagy in yeast ( 164 , 166 ), and Nup159-mediated selective macro-autophagic degradation of nucleoporins and nuclear pore complexes ( 167 , 168 ). The cross talk between the autophagy receptors and the Atg1/ULK kinase complex involves kinases such as Hrr25 in yeast and TBK1 in mammals, which phosphorylate the autophagy receptors, thereby increasing their binding affinity for the Atg8/LC3 proteins ( 161 , 162 , 169 – 171 ).…”

“…As such, Atg39 should be considered both an ER-phagy and a nucleophagy receptor ( 164 ). Recent data defining the role of Atg39 in nucleophagy reveal that the COOH-terminal region of the protein contains short amphipathic helices that may tether the outer and the inner nuclear membrane directly ( 166 ) or via interaction with inner nuclear membrane proteins ( 289 ). This would promote the vesiculation of the nuclear envelope and its capture by autophagosomes.…”

ER ‐phagy: selective autophagy of the endoplasmic reticulum

“…Cells lacking Atg39 or expressing Atg39 mutants defective in the interaction with Atg11 and/or Atg8 exhibit abnormal nuclear morphology and cause cell death under nitrogen starvation, suggesting that Atg39‐mediated macroautophagy is important for nuclear homeostasis under the condition (Mochida et al , 2015). In addition, a recent work suggests that Atg39 is involved in the selection of nuclear proteins for autophagic degradation (also see below; Chandra et al , 2021; Mochida et al , 2022). By contrast, there is no evidence for a role of Atg39 in the maintenance or regulation of perinuclear ER function and mass.…”

“…Atg39 is a single membrane‐spanning protein and contains the AIM and Atg11‐binding sequence in its N‐terminal region in the cytoplasm (Fig 2A; Mochida et al , 2022, Mochida et al , 2015; Chandra et al , 2021). While Atg39 is anchored to the outer nuclear membrane via the transmembrane segment, it also binds to the inner nuclear membrane via amphipathic helices in the perinuclear space region, linking these membranes and preventing Atg39 from leaking into the ER which is continuous with the nuclear envelope (Chandra et al , 2021; Mochida et al , 2022). Overexpression of Atg39 leads to the formation of protrusions or blebs from the nuclear envelope, which are likely to represent intermediate structures in the formation of NDVs to be sequestered within autophagosomes (Chandra et al , 2021; Mochida et al , 2022).…”