Ubiquitination of exposed glycoproteins by SCFFBXO27 directs damaged lysosomes for autophagy Yukiko Yoshidaa,1, Sayaka Yasudab, Toshiharu Fujitac,d, Maho Hamasakic,d, Arisa Murakamia, Junko Kawawakia, Kazuhiro Iwaie, Yasushi Saekib, Tamotsu Yoshimoric,d, Noriyuki Matsudaa, and Keiji Tanakab,1 aUbiquitin Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; bLaboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan; cGraduate School of Frontier Bioscience, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan; dDepartment of Genetics, Graduate School of Medicine, Osaka University, Osaka 565-0871, Japan; and eDepartment of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan Edited by Alfred Lewis Goldberg, Harvard Medical School, Boston, MA, and approved July 5, 2017 (received for review February 17, 2017) Ubiquitination functions as a signal to recruit autophagic machinery in N-glycans to direct unfolded glycoproteins to the ER-associated to damaged organelles and induce their clearance. Here, we report degradation pathway (6, 7). Furthermore, we found that FBXO27, the characterization of FBXO27, a glycoprotein-specific F-box pro- as well as FBXO2 and FBXO6, bind to glycoproteins modified tein that is part of the SCF (SKP1/CUL1/F-box protein) ubiquitin with high-mannose N-glycans (8). However, FBXO27 has also ligase complex, and demonstrate that SCFFBXO27 ubiquitinates gly- been reported to bind some glycoproteins modified with complex- coproteins in damaged lysosomes to regulate autophagic machinery type N-glycans (9), suggesting that the SCF complex containing recruitment. Unlike F-box proteins in other SCF complexes, FBXO27 has the ability to ubiquitinate glycoproteins that have FBXO27 is subject to N-myristoylation, which localizes it to mem- transited from the ER to other organelles or the plasma mem- branes, allowing it to accumulate rapidly around damaged lyso- brane. If FBXO27 recognizes complex-type N-glycans, there must somes. We also screened for proteins that are ubiquitinated upon be a mechanism through which glycoproteins from these other lysosomal damage, and identified two SNARE proteins, VAMP3 and organelles become exposed to cytoplasmic SCFFBXO27. VAMP7, and five lysosomal proteins, LAMP1, LAMP2, GNS, PSAP, Emerging evidence suggests that selective autophagy is used to and TMEM192. Ubiquitination of all glycoproteins identified in this degrade aggregated proteins, invading pathogens, and damaged screen increased upon FBXO27 overexpression. We found that the or surplus organelles, such as peroxisomes, mitochondria, lyso- lysosomal protein LAMP2, which is ubiquitinated preferentially on somes, the nucleus, and the ER (10, 11). In these systems, lysosomal damage, enhances autophagic machinery recruitment ubiquitination often plays a pivotal role in directing the auto- to damaged lysosomes. Thus, we propose that SCFFBXO27 ubiquiti- phagic machinery to substrates (12). It has been shown that nates glycoproteins exposed upon lysosomal damage to induce ubiquitin-positive inclusion bodies are degraded by autophagy lysophagy. via p62, an adaptor protein linking ubiquitin to LC3, an auto- phagosome marker (13). Furthermore, a key signaling step autophagy | FBXO27 | LAMP2 | lysosome | ubiquitin during mitophagy involves ubiquitination of outer membrane proteins of damaged mitochondria by the ubiquitin ligase Parkin, ost cell-surface proteins and secretory proteins are glyco- which is recruited from the cytoplasm by PINK1-mediated Mproteins modified with highly diverse Asn (N)-linked oligo- phosphorylation of ubiquitin (14). In another example, auto- saccharides (N-glycans) that have been implicated in various phagy specifically targets invading bacteria to restrict their growth extracellular processes. N-glycosylation of proteins occurs cotrans- after ubiquitination (15). Furthermore, damaged lysosomes are lationally in the endoplasmic reticulum (ER), and glycoproteins selectively sequestered by autophagosomes through a ubiquitin- transit from the ER through the Golgi, where N-glycans are trim- dependent mechanism called lysophagy (16, 17). Although which med and remodeled before they are delivered to their final desti- proteins and how they are ubiquitinated during xenophagy and nations. This process results in N-glycans facing either out of cells or on the luminal side of organelles in the secretory pathway, in- Significance cluding the ER, Golgi complex, lysosomes, and endosomes. Thus, most molecules that recognize N-glycoproteins are also present in Although lysosomes play a crucial role in autophagy, damaged these organelles or on the cell surface. However, a subset of gly- lysosomes are eliminated by autophagy. The molecular mecha- cosidases or lectins are found either in the cytosol or in nuclei. nisms that recognize lysosomal damage in cells remain poorly Peptide-N-glycanase (PNGase) and glycoprotein-specific ubiquitin understood, but ubiquitination is a known prerequisite for ligases are cytosolic, and function in the ER-associated degradation directing autophagic machinery to damaged lysosomes. FBXO27, pathway in which misfolded glycoproteins are translocated from a substrate-recognition subunit of the SCF (SKP1/CUL1/F-box the ER to the cytosol for degradation by the ubiquitin-proteasome protein) ubiquitin ligase complex, localizes to the cytosolic sur- system (1–4). In another case, galectin 8, a cytosolic β-galactoside– face of endomembranes and binds glycoproteins. This paper binding lectin, detects bacterial invasion by binding host gly- reports that SCFFBXO27 ubiquitinates exposed glycoproteins nor- cans exposed on damaged endosomes and lysosomes, and ac- mally sequestered on the lumenal surface of lysosomes follow- tivates xenophagy through the recruitment autophagy receptor ing lysosomal damage, resulting in accelerated recruitment of NDP52 (5). Thus, the appearance of N-glycan–modified proteins autophagic machinery. in the cytosol likely signals the presence of unwanted proteins or Author contributions: Y.Y., M.H., K.I., T.Y., N.M., and K.T. designed research; Y.Y., T.F., organelles. M.H., A.M., and J.K. performed research; Y.S. contributed new reagents/analytic tools; F-box proteins are receptors for substrates in the SCF (SKP1- Y.Y., S.Y., M.H., and Y.S. analyzed data; and Y.Y., N.M., and K.T. wrote the paper. CUL1-F-box protein-RBX1) ubiquitin ligase complex. F-box The authors declare no conflict of interest. ≈ proteins belong to a large protein family comprised of 70 pro- This article is a PNAS Direct Submission. teins in humans. Among these are FBXO2 and FBXO6, which 1 To whom correspondence may be addressed. Email: [email protected] or bind to glycoproteins modified with high-mannose N-glycans [email protected]. found in the ER (3, 4). Biochemical and structural analyses in- This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. dicate that FBXO2 recognizes the innermost chitobiose structure 1073/pnas.1702615114/-/DCSupplemental. 8574–8579 | PNAS | August 8, 2017 | vol. 114 | no. 32 www.pnas.org/cgi/doi/10.1073/pnas.1702615114 Downloaded by guest on October 5, 2021 lysophagy, before autophagy, remain largely unknown, it is plau- predicted to be unmyristoylated. We subsequently incubated sible that luminal proteins in organelles are exposed to the cytosol the cells with myristic acid-azide, and generated cell lysates that following membrane rupture, which may subsequently lead to were subjected to the Click-iT reaction for in vitro biotinylation. their ubiquitination. FBXO27-FLAG proteins and biotinylated proteins were isolated Here, we demonstrated that FBXO27 is efficiently recruited to from the biotinylated lysate by using either anti-FLAG antibody or lysosomes upon damage, and regulates subsequent accumulation streptavidin (SA) beads, and were analyzed by blotting. Wild-type of autophagic machinery. We analyzed proteins ubiquitinated FBXO27 was biotinylated but not the G2M mutant, indicating that upon lysosomal damage by using the trypsin-resistant tandem FBXO27 is N-myristoylated in cells. ubiquitin-binding entity (TR-TUBE) method, which we recently To determine whether the membranous localization of developed, to identify ubiquitin ligase substrates (18), and found FBXO27 is a result of its N-myristoylation or to its ability to bind that SCFFBXO27 ubiquitinates luminal sites on the lysosomal to N-glycans, we proceeded to compare the localization of the protein LAMP2. G2M mutant and the glycoprotein-binding defective FW/AA mutant (Fig. 1B and Fig. S1A). Although the membranous local- Results ization was retained in the FW/AA mutant, the G2M mutant FBXO27 Recognizes N-Glycoproteins and Is Targeted to Membranes protein was detected in whole cells and recovered in cytosolic via N-Myristoylation. Previous work showed that FBXO2 binds to fraction, indicating that FBXO27 is targeted to membranes via the innermost chitobiose in high-mannose N-glycans, and that the N-myristoylation. We further characterized the subcellular lo- mutation of Y279 and W280 prevent binding (6). To determine calization of FBXO27 by staining with antibodies for organelle whether FBXO27 and FBXO6 also recognize the chitobiose, we marker proteins (Fig. S1B). Interestingly, FBXO27 did not expressed FLAG-tagged wild-type versions of these proteins, as colocalize with TOMM20, a protein marker of mitochondria, but well as versions containing