Atlastins remodel the endoplasmic reticulum for selective autophagy

Abstract

Specific receptors are required for the autophagic degradation of endoplasmic reticulum (ER), known as ER-phagy. However, little is known about how the ER is remodeled and separated for packaging into autophagosomes. We developed two ER-phagy-specific reporter systems and found that Atlastins are key positive effectors and also targets of ER-phagy. Atlastins are ER-resident GTPases involved in ER membrane morphology, and Atlastin-depleted cells have decreased ER-phagy under starvation conditions. Atlastin's role in ER-phagy requires a functional GTPase domain and proper ER localization, both of which are also involved in ER architecture. The three Atlastin family members functionally compensate for one another during ER-phagy and may form heteromeric complexes with one another. We further find that Atlastins act downstream of the FAM134B ER-phagy receptor, such that depletion of Atlastins represses ER-autophagy induced by the overexpression of FAM134B. We propose that during ER-phagy, Atlastins remodel ER membrane to separate pieces of FAM134B-marked ER for efficient autophagosomal engulfment.

ER‐phagy: shaping up and destressing the endoplasmic reticulum

“…ATL2 binds to FAM134B, localizes with FAM134B at autophagosome biogenesis sites, and is required for FAM134Bdriven ER-phagy. This observation strongly supports a role for receptor-coordinated membrane fragmentation in ER-phagy [61].…”

A genome-wide screen for ER autophagy highlights key roles of mitochondrial metabolism and ER-resident UFMylation

“…Using EBSS as an ER-phagy stimulus, we coupled EATR-based FACS screening with genomewide CRISPR transcriptional inhibition (CRISPRi) to identify novel pathways involved in ER-phagy ( Fig 1A-B) (Gilbert et al, 2014;Horlbeck et al, 2016;Liang et al, 2018). Since autophagy is influenced by the availability of cellular energy, we reasoned that complete knockout of ER-phagy regulators via CRISPR cutting could be detrimental to cells and mask interesting players.…”

“…ER expansion can also be reversed via ER-phagy that is mediated by the SEC62 and CCPG1 LIR-containing ER-phagy receptors (Fumagalli et al, 2016;Smith et al, 2018). The reticular ER network is remodeled for delivery to the lysosome by Atlastin GTPases that are also involved in normal ER morphology (Liang et al, 2018;Rismanchi et al, 2008;Wang et al, 2016;Zhao et al, 2016).…”

“…Failure to execute ER-phagy through mutations in known ER-phagy proteins causes neuropathy in mice, and cross-referencing with ClinVar reveals that mutations in human ER-phagy proteins are linked to hereditary neuropathies and paraplegia (Guelly et al, 2011;Khaminets et al, 2015;Kurth et al, 2009;Liang et al, 2018). But beyond the few receptors and remodelers most proximal to autophagosomal function, relatively little is known about the signals that regulate ER-phagy.…”

“…Our data provide insight into the unique cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.unfolded protein response (UPR) did not cause ER-phagy. Only prolonged starvation (16 hours) using Earl's Buffered Saline Solution (EBSS) robustly induced ER-phagy.Using EBSS as an ER-phagy stimulus, we coupled EATR-based FACS screening with genomewide CRISPR transcriptional inhibition (CRISPRi) to identify novel pathways involved in ER-phagy ( Fig 1A-B) (Gilbert et al, 2014;Horlbeck et al, 2016;Liang et al, 2018). Since autophagy is influenced by the availability of cellular energy, we reasoned that complete knockout of ER-phagy regulators via CRISPR cutting could be detrimental to cells and mask interesting players.…”