ATL3 Is a Tubular ER-Phagy Receptor for GABARAP-Mediated Selective Autophagy

The endoplasmic reticulum (ER) consists of the nuclear envelope and both peripheral ER sheets and a peripheral tubular network [1, 2]. In response to physiological or pathological conditions, receptor-mediated selective ER-phagy, engulfing specific ER subdomains or components, is essential for ER turnover and homeostasis [3–6]. Four mammalian receptors for ER-phagy have been reported: FAM134B [7], reticulon 3 (RTN3) [8], SEC62 [9], and CCPG1 [10]. However, these ER-phagy receptors function in subcellular- and tissue- or physiological- and pathological-condition-specific manners, so the diversity of ER-phagy receptors and underlying mechanisms remain largely unknown [3, 4]. Atlastins (ATL1, ATL2, and ATL3), in mammals, are a class of membrane-bound, dynamin-like GTPases that function in ER fusion [11, 12]. ATL1 is expressed mainly in the central nervous system, while ATL2 and ATL3 are more ubiquitously distributed [13]. Recent studies showed that ATL2 mainly affects ER morphology by promoting ER fusion, whereas alterations in ER morphology are hardly detectable after ATL3 depletion [14, 15]. Here, we show that ATL3 functions as a receptor for ER-phagy, promoting tubular ER degradation upon starvation. ATL3 specifically binds to GABARAP, but not LC3, subfamily proteins via 2 GABARAP interaction motifs (GIMs). ATL3-GABARAP interaction is essential for ATL3 to function in ER-phagy. Moreover, hereditary sensory and autonomic neuropathy type I (HSAN I)-associated ATL3 mutations (Y192C and P338R) disrupt ATL3’s association with GABARAP and impair ATL3’s function in ER-phagy, suggesting that defective ER-phagy is involved in HSAN I. Therefore, we reveal a new ATL3 function for GABARAP-mediated ER-phagy in the degradation of tubular ER. [Display omitted] •ATL3 is an ER-phagy receptor and promotes tubular ER degradation•ATL3 specifically binds to GABARAP via 2 GABARAP interaction motifs (GIMs)•Sensory neuropathy-associated ATL3 mutations reduce ATL3-GABARAP binding•Sensory neuropathy-associated ATL3 mutations impair ATL3’s function in ER-phagy Chen et al. show that ATL3, a dynamin-like GTPase commonly believed to promote tubular ER fusion, also functions as an autophagy receptor to mediate ER tubule degradation and that dysfunctional ER-phagy may be involved in sensory neuropathy.