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Kauffman KJ, Yu S, Jin J, Mugo B, Nguyen N, O'Brien A, Nag S, Lystad AH, Melia TJ. Delipidation of mammalian Atg8-family proteins by each of the four ATG4 proteases. Autophagy 2018; 14:992-1010. [PMID: 29458288 DOI: 10.1080/15548627.2018.1437341] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
During macroautophagy/autophagy, mammalian Atg8-family proteins undergo 2 proteolytic processing events. The first exposes a COOH-terminal glycine used in the conjugation of these proteins to lipids on the phagophore, the precursor to the autophagosome, whereas the second releases the lipid. The ATG4 family of proteases drives both cleavages, but how ATG4 proteins distinguish between soluble and lipid-anchored Atg8 proteins is not well understood. In a fully reconstituted delipidation assay, we establish that the physical anchoring of mammalian Atg8-family proteins in the membrane dramatically shifts the way ATG4 proteases recognize these substrates. Thus, while ATG4B is orders of magnitude faster at processing a soluble unprimed protein, all 4 ATG4 proteases can be activated to similar enzymatic activities on lipid-attached substrates. The recognition of lipidated but not soluble substrates is sensitive to a COOH-terminal LIR motif both in vitro and in cells. We suggest a model whereby ATG4B drives very fast priming of mammalian Atg8 proteins, whereas delipidation is inherently slow and regulated by all ATG4 homologs.
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Affiliation(s)
- Karlina J Kauffman
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Shenliang Yu
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Jiaxin Jin
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA.,b Lanzhou University Second Hospital , Lanzhou , Gansu Province , China
| | - Brian Mugo
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Nathan Nguyen
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Aidan O'Brien
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Shanta Nag
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
| | - Alf Håkon Lystad
- c Department of Molecular Medicine , Institute of Basic Medical Sciences, University of Oslo , Norway
| | - Thomas J Melia
- a Department of Cell Biology , Yale University School of Medicine , New Haven , CT , USA
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52
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Genetic aberrations in macroautophagy genes leading to diseases. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018. [PMID: 29524522 DOI: 10.1016/j.bbamcr.2018.03.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The catabolic process of macroautophagy, through the rapid degradation of unwanted cellular components, is involved in a multitude of cellular and organismal functions that are essential to maintain homeostasis. Those functions include adaptation to starvation, cell development and differentiation, innate and adaptive immunity, tumor suppression, autophagic cell death, and maintenance of stem cell stemness. Not surprisingly, an impairment or block of macroautophagy can lead to severe pathologies. A still increasing number of reports, in particular, have revealed that mutations in the autophagy-related (ATG) genes, encoding the key players of macroautophagy, are either the cause or represent a risk factor for the development of several illnesses. The aim of this review is to provide a comprehensive overview of the diseases and disorders currently known that are or could be caused by mutations in core ATG proteins but also in the so-called autophagy receptors, which provide specificity to the process of macroautophagy. Our compendium underlines the medical relevance of this pathway and underscores the importance of the eventual development of therapeutic approaches aimed at modulating macroautophagy.
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53
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Gao J, Langemeyer L, Kümmel D, Reggiori F, Ungermann C. Molecular mechanism to target the endosomal Mon1-Ccz1 GEF complex to the pre-autophagosomal structure. eLife 2018; 7:31145. [PMID: 29446751 PMCID: PMC5841931 DOI: 10.7554/elife.31145] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/12/2018] [Indexed: 11/13/2022] Open
Abstract
During autophagy, a newly formed double membrane surrounds its cargo to generate the so-called autophagosome, which then fuses with a lysosome after closure. Previous work implicated that endosomal Rab7/Ypt7 associates to autophagosomes prior to their fusion with lysosomes. Here, we unravel how the Mon1-Ccz1 guanosine exchange factor (GEF) acting upstream of Ypt7 is specifically recruited to the pre-autophagosomal structure under starvation conditions. We find that Mon1-Ccz1 directly binds to Atg8, the yeast homolog of the members of the mammalian LC3 protein family. This requires at least one LIR motif in the Ccz1 C-terminus, which is essential for autophagy but not for endosomal transport. In agreement, only wild-type, but not LIR-mutated Mon1-Ccz1 promotes Atg8-dependent activation of Ypt7. Our data reveal how GEF targeting can specify the fate of a newly formed organelle and provide new insights into the regulation of autophagosome-lysosome fusion. Autophagy is a word derived from the Greek for “self-eating”. It describes a biological process in which a living cell breaks down its own material to release their chemical building blocks that can then be used to make new molecules. Autophagy is often triggered when a cell becomes damaged or when nutrients are in short supply. The hallmark of autophagy is the formation of structures called autophagosomes. These structures capture the cellular material, fuse with other compartments in the cell – namely endosomes in animals and vacuoles in yeast – and then deliver the material inside, ready to be broken down. For an autophagosome to fuse to an endosome or a vacuole, small proteins of the Rab protein family must be located on the surface of the autophagosome. Rab proteins are recruited to this surface by enzymes known as GEFs. However it remains unclear how most GEFs get to the surface of a compartment within the cell to begin with. The Mon1-Ccz1 complex is a GEF that occurs in yeast and animals, including fruit flies and humans. It is found on endosomes, and was recently shown to also localize to autophagosomes. Now, Gao et al. report that, in yeast, the Mon1-Ccz1 complex binds directly to a protein named Atg8. This protein is anchored on to the surface of autophagosomes, and is closely related to other proteins in animal cells. Gao et al. discovered that this specific GEF binds to Atg8 via at least one binding site on its Ccz1 component. This binding site is only needed for the GEF to localize to the autophagosomes; the Mon1-Czz1 complex can still bind to endosomes without it. Blocking the GEF from binding to Atg8 stopped the autophagosomes from fusing with vacuoles. These findings reveal how a GEF can be targeted to two distinct compartments in the cell: endosomes and autophagosomes. Further work is now needed to understand how this process is regulated by the availability of nutrients or damage to the cell, to ensure that autophagy is only triggered under the right conditions. Also, because cancer cells often rely on autophagy to survive, the molecules that regulate this process could represent possible targets for new anticancer drugs.
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Affiliation(s)
- Jieqiong Gao
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Lars Langemeyer
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Daniel Kümmel
- Structural Biology Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
| | - Fulvio Reggiori
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Christian Ungermann
- Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany
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54
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Sánchez-Wandelmer J, Reggiori F. Atg4 in autophagosome biogenesis. Oncotarget 2017; 8:108290-108291. [PMID: 29312531 PMCID: PMC5752444 DOI: 10.18632/oncotarget.22714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/24/2017] [Indexed: 12/26/2022] Open
Affiliation(s)
- Jana Sánchez-Wandelmer
- Fulvio Reggiori: Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Fulvio Reggiori
- Fulvio Reggiori: Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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55
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Kriegenburg F, Reggiori F. LIR and APEAR, two distinct Atg8-binding features within Atg4. Oncotarget 2017; 8:81717-81718. [PMID: 29137209 PMCID: PMC5669835 DOI: 10.18632/oncotarget.17697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2017] [Indexed: 11/26/2022] Open
Affiliation(s)
- Franziska Kriegenburg
- Fulvio Reggiori: Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Fulvio Reggiori
- Fulvio Reggiori: Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
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56
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Maruyama T, Noda NN. Autophagy-regulating protease Atg4: structure, function, regulation and inhibition. J Antibiot (Tokyo) 2017; 71:ja2017104. [PMID: 28901328 PMCID: PMC5799747 DOI: 10.1038/ja.2017.104] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 07/19/2017] [Accepted: 07/27/2017] [Indexed: 12/15/2022]
Abstract
Autophagy is an intracellular degradation system that contributes to cellular homeostasis through degradation of various targets such as proteins, organelles and microbes. Since autophagy is related to various diseases such as infection, neurodegenerative diseases and cancer, it is attracting attention as a new therapeutic target. Autophagy is mediated by dozens of autophagy-related (Atg) proteins, among which Atg4 is the sole protease that regulates autophagy through the processing and deconjugating of Atg8. As the Atg4 activity is essential and highly specific to autophagy, Atg4 is a prospective target for developing autophagy-specific inhibitors. In this review article, we summarize our current knowledge of the structure, function and regulation of Atg4 including efforts to develop Atg4-specific inhibitors.The Journal of Antibiotics advance online publication, 13 September 2017; doi:10.1038/ja.2017.104.
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Affiliation(s)
- Tatsuro Maruyama
- Laboratory of Structural Biology, Institute of Microbial Chemistry, Tokyo, Japan
| | - Nobuo N Noda
- Laboratory of Structural Biology, Institute of Microbial Chemistry, Tokyo, Japan
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57
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Abdollahzadeh I, Schwarten M, Gensch T, Willbold D, Weiergräber OH. The Atg8 Family of Proteins-Modulating Shape and Functionality of Autophagic Membranes. Front Genet 2017; 8:109. [PMID: 28894458 PMCID: PMC5581321 DOI: 10.3389/fgene.2017.00109] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 08/07/2017] [Indexed: 12/23/2022] Open
Abstract
Aging is a multifactorial process involving an accumulation of alterations on various organizational levels, which finally compromises viability and limits the lifespan of organisms. It is now well-established that many aspects of aging can be positively affected by (macro)autophagy, a mechanism of self-digestion found in virtually all eukaryotic cells. A comprehensive understanding of autophagy is thus expected to not only deepen our insight into the mechanisms of aging but to also open up new avenues toward increasing the healthy lifespan in humans. In this review, we focus on the Atg8 family of ubiquitin-like proteins, which play a crucial role in the autophagy process by virtue of their unique mode of reversible membrane association.
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Affiliation(s)
- Iman Abdollahzadeh
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum JülichJülich, Germany.,Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum JülichJülich, Germany
| | - Melanie Schwarten
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum JülichJülich, Germany
| | - Thomas Gensch
- Institute of Complex Systems, Cellular Biophysics (ICS-4), Forschungszentrum JülichJülich, Germany
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum JülichJülich, Germany.,Institut für Physikalische Biologie und Biologisch-Medizinisches Forschungszentrum, Heinrich-Heine-Universität DüsseldorfDüsseldorf, Germany
| | - Oliver H Weiergräber
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum JülichJülich, Germany
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58
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Sánchez-Wandelmer J, Kriegenburg F, Rohringer S, Schuschnig M, Gómez-Sánchez R, Zens B, Abreu S, Hardenberg R, Hollenstein D, Gao J, Ungermann C, Martens S, Kraft C, Reggiori F. Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation. Nat Commun 2017; 8:295. [PMID: 28821724 PMCID: PMC5562703 DOI: 10.1038/s41467-017-00302-3] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 06/19/2017] [Indexed: 11/09/2022] Open
Abstract
The biogenesis of autophagosomes depends on the conjugation of Atg8-like proteins with phosphatidylethanolamine. Atg8 processing by the cysteine protease Atg4 is required for its covalent linkage to phosphatidylethanolamine, but it is also necessary for Atg8 deconjugation from this lipid to release it from membranes. How these two cleavage steps are coordinated is unknown. Here we show that phosphorylation by Atg1 inhibits Atg4 function, an event that appears to exclusively occur at the site of autophagosome biogenesis. These results are consistent with a model where the Atg8-phosphatidylethanolamine pool essential for autophagosome formation is protected at least in part by Atg4 phosphorylation by Atg1 while newly synthesized cytoplasmic Atg8 remains susceptible to constitutive Atg4 processing.The protease Atg4 mediates Atg8 lipidation, required for autophagosome biogenesis, but also triggers Atg8 release from the membranes, however is unclear how these steps are coordinated. Here the authors show that phosphorylation by Atg1 inhibits Atg4 at autophagosome formation sites.
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Affiliation(s)
- Jana Sánchez-Wandelmer
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Franziska Kriegenburg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Sabrina Rohringer
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | | | - Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Bettina Zens
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Susana Abreu
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - David Hollenstein
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Jieqiong Gao
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Christian Ungermann
- University of Osnabrück, Department of Biology/Chemistry, Biochemistry section, Barbarastrasse 13, 49076, Osnabrück, Germany
| | - Sascha Martens
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Claudine Kraft
- Max F. Perutz Laboratories, University of Vienna, 1030, Vienna, Austria
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
- Department of Cell Biology, University Medical Center Utrecht, Heidelberglaan 100, 8564 CX, Utrecht, The Netherlands.
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59
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Abreu S, Kriegenburg F, Gómez-Sánchez R, Mari M, Sánchez-Wandelmer J, Skytte Rasmussen M, Soares Guimarães R, Zens B, Schuschnig M, Hardenberg R, Peter M, Johansen T, Kraft C, Martens S, Reggiori F. Conserved Atg8 recognition sites mediate Atg4 association with autophagosomal membranes and Atg8 deconjugation. EMBO Rep 2017; 18:765-780. [PMID: 28330855 DOI: 10.15252/embr.201643146] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 02/12/2017] [Accepted: 02/20/2017] [Indexed: 12/12/2022] Open
Abstract
Deconjugation of the Atg8/LC3 protein family members from phosphatidylethanolamine (PE) by Atg4 proteases is essential for autophagy progression, but how this event is regulated remains to be understood. Here, we show that yeast Atg4 is recruited onto autophagosomal membranes by direct binding to Atg8 via two evolutionarily conserved Atg8 recognition sites, a classical LC3-interacting region (LIR) at the C-terminus of the protein and a novel motif at the N-terminus. Although both sites are important for Atg4-Atg8 interaction in vivo, only the new N-terminal motif, close to the catalytic center, plays a key role in Atg4 recruitment to autophagosomal membranes and specific Atg8 deconjugation. We thus propose a model where Atg4 activity on autophagosomal membranes depends on the cooperative action of at least two sites within Atg4, in which one functions as a constitutive Atg8 binding module, while the other has a preference toward PE-bound Atg8.
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Affiliation(s)
- Susana Abreu
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Franziska Kriegenburg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rubén Gómez-Sánchez
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Muriel Mari
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jana Sánchez-Wandelmer
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mads Skytte Rasmussen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Rodrigo Soares Guimarães
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Bettina Zens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Ralph Hardenberg
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Matthias Peter
- Department of Biology, Institute of Biochemistry, Swiss Federal Institute of Technology, Zurich, Switzerland
| | - Terje Johansen
- Molecular Cancer Research Group, Institute of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Claudine Kraft
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories (MFPL), Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Fulvio Reggiori
- Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands .,Department of Cell Biology, University Medical Center Utrecht, Utrecht, The Netherlands
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