Rabaptin5 targets autophagy to damaged endosomes and Salmonella vacuoles via FIP200 and ATG16L1

Abstract

Selective autophagy of damaged organelles is important to maintain cellular homeostasis. The mechanisms how autophagy selects specific targets is often poorly understood. Rabaptin5 was previously known as a major regulator of early endosome identity and maturation. Here, we identify two novel Rabaptin5 interactors: FIP200, a subunit of the ULK1 autophagy initiator complex, and ATG16L1, a central component of the E3-like enzyme in LC3 lipidation. Autophagy of early endosomes damaged by chloroquine or monensin treatment requires Rabaptin5 and particularly a short sequence motif that binds to the WD domain of ATG16L1. Rabapt-in5 and its interaction with ATG16L1 further contributes to the autophagic elimination of Salmonella enterica early after infection, when it resides in phagosomes with early endosomal characteristics. Our results demonstrate a novel function of Rabaptin5 in quality control of early endosomes in the selective targeting of autophagy to damaged early endosomes and phagosomes.

ESCRT disruption provides evidence against signaling functions for synaptic exosomes

“…Many organelles are selectively targeted for macroautophagy via compartment-specific receptors (Lamark and Johansen, 2021), but such a process has not been specifically described for neuronal endosomes/MVEs. Our data suggest that synapses use a proteostatic mechanism called endosomophagy or simaphagy that has been previously observed in cell culture (Migliano et al, 2023;Millarte et al, 2022;Wang et al, 2022;Zellner et al, 2021), adding to the numerous intersections between endolysosomal traffic and autophagy in neurons (Boecker and Holzbaur, 2019). We found that autophagy is induced in ESCRT mutant synapses, presumably to dispose of aberrant endosomes, with different outcomes in Tsg101 KD versus Hrs mutants: Tsg101 KD led to aberrant autophagic vacuoles and reduced autophagic flux, perhaps due to a secondary role for ESCRT-1/Tsg101 in phagophore closure or another step of autophagy (Takahashi et al, 2018).…”

“…Our data also raise the possibility of a novel synaptic proteostasis mechanism which might be termed "endosomophagy", as has been seen in cell culture (Millarte et al, 2022;Wang et al, 2022;Zellner et al, 2021), and adds to the numerous intersections between endolysosomal traffic and autophagy in neurons (Boecker and Holzbaur, 2019). Many organelles are selectively targeted for macroautophagy via compartment-specific receptors (Lamark and Johansen, 2021), but such a process has not been specifically described for neuronal endosomes/MVEs.…”

“…Since autophagy is normally rare at wild-type Drosophila NMJ synapses (Soukup et al, 2016), we hypothesized that ESCRT mutants might activate a compensatory “endosomophagy” or “simaphagy” pathway to degrade ESCRT-deficient endosomes (Migliano et al, 2023; Millarte et al, 2022). However, since Tsg101 is also required for phagophore closure (Takahashi et al, 2018), this process is likely unable to dispose of defective endosomes upon Tsg101 knockdown.…”

Removal of hypersignaling endosomes by simaphagy

“…The protein kinase ULK1 (unc-51 like autophagy activating kinase 1) is found together with RB1CC1/FIP200 (RB1 inducible coiled-coil 1), ATG13 and ATG101 in an initiation complex that mediates the first steps of autophagy [ 40 , 41 ]. RB1CC1 has been shown to interact with the endosomal protein RABEP1/Rabaptin 5 on damaged early endosomes [ 24 ]. We therefore tested if components of the autophagy initiation complex were detectable also on unruptured but HGS-depleted endosomes at early stages of simaphagy.…”

FIP200 Methylation by SETD2 Prevents Trim21-Induced Degradation and Preserves Autophagy Initiation

“…Considering FIP200 as an “assembler” seems to be the reason to overlook its importance. Recent studies continue to exhibit new regulatory roles of FIP200 in autophagy, including promoting the selective degradation of ubiquitin condensates through the interaction of p62, TAX1BP1, CCPG1, and Rab5 [ 10 , 24 , 25 , 26 ]. In this study, we used unbiased mass spectrometry approaches to reveal K1133 methylation at FIP200 and elucidated the biological significance of K1133 methylation.…”