A heterodimeric SNX4­–SNX7 SNX-BAR autophagy complex coordinates ATG9A trafficking for efficient autophagosome assembly

Abstract

The sorting nexins (SNXs) are a family of peripheral membrane proteins that direct protein trafficking decisions within the endocytic network. Emerging evidence in yeast and mammalian cells implicates a subgroup of SNXs in selective and non-selective forms of autophagy. Using siRNA and CRISPR-Cas9, we demonstrate that the SNX-BAR protein SNX4 is needed for efficient LC3 (also known as MAP1LC3) lipidation and autophagosome assembly in mammalian cells. SNX-BARs exist as homo- and hetero-dimers, and we show that SNX4 forms functional heterodimers with either SNX7 or SNX30 that associate with tubulovesicular endocytic membranes. Detailed image-based analysis during the early stages of autophagosome assembly reveals that SNX4–SNX7 is an autophagy-specific SNX-BAR heterodimer, required for efficient recruitment and/or retention of core autophagy regulators at the nascent isolation membrane. SNX4 partially colocalises with juxtanuclear ATG9A-positive membranes, with our data linking the autophagy defect upon SNX4 disruption to the mis-trafficking and/or retention of ATG9A in the Golgi region. Taken together, our findings show that the SNX4–SNX7 heterodimer coordinates ATG9A trafficking within the endocytic network to establish productive autophagosome assembly sites, thus extending knowledge of SNXs as positive regulators of autophagy.

Protein complexes and neighborhoods driving autophagy

“…However, upon a physiological stress stimulus leading to activation of autophagy, a BECN1 monomer can interact strongly with ATG14 (K d = 3.2 µM) to form an active hetero-oligomeric PtdIns3K class-III complex [51]. Weak transient interactions are continuously broken and formed and difficult to capture by Under certain physiological conditions such as autophagy, SNX4 can form a hetero-oligomeric complex with SNX7 to mediate autophagosome assembly and maturation [55][56][57]. Overall, the above examples highlight the variety of affinities of protein-protein interactions important for autophagy.…”

Retromer dependent changes in cellular homeostasis and Parkinson's disease

“…The ATG9A trafficking is disrupted in the cells expressing Vps35 D620N variant, with ATG9A remaining localised within the TGN after autophagy induction [53]. Several retromer accessory proteins, including TBC1D5, DNAJC13 (RME8), and SNX4 -a SNX-BAR protein, have been shown to regulate ATG9A trafficking [66,67]. However, it is not known if ATG9A is a retromer cargo, hence the effect of Vps35 D620N variant on ATG9A trafficking could be indirect.…”

Sorting Nexins in Protein Homeostasis

“…Current models suggest that endosome–to–plasma membrane recycling is aided by SNX-BAR association with SNX27 and the retromer, with the PDZ domain of SNX27 as the predominant cargo recognition module [ 54 ]. Lastly, SNX-BAR proteins, have retromer-independent roles in autophagic processes, which is discussed in more detail below ( Section 6 ) [ 60 , 61 ].…”

“…Sorting nexins also interact with cargos outside of endo-lysosomal-TGN pathways (see Figure 1 and Section 6 of this review). Here they play significant roles in autophagy pathways in yeast and mammalian cells [ 61 , 84 , 85 , 86 ]. Taken together, this serves to emphasize the diverse roles sorting nexins play in maintaining protein homeostasis.…”

“…They revealed that the PX-BAR-containing protein SNX18 recruits Dynamin-2 to induce budding of ATG9A and ATG16L1 containing membranes from recycling endosomes to sites of autophagosome formation ( Figure 4 A) [ 149 , 150 ]. More recently, the SNX4-SNX7 heterodimer has been shown to play a role in phagophore biogenesis and ATG9A distribution, although the precise molecular mechanisms remain unknown [ 61 ]. Given the dynamic nature between organelles during autophagosome biogenesis, it is likely that future studies may reveal similar roles for other sorting nexins.…”