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Shatz O, Fraiberg M, Isola D, Das S, Gogoi O, Polyansky A, Shimoni E, Dadosh T, Dezorella N, Wolf SG, Elazar Z. Rim aperture of yeast autophagic membranes balances cargo inclusion with vesicle maturation. Dev Cell 2024; 59:911-923.e4. [PMID: 38447569 DOI: 10.1016/j.devcel.2024.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/28/2023] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Autophagy eliminates cytoplasmic material by engulfment in membranous vesicles targeted for lysosome degradation. Nonselective autophagy coordinates sequestration of bulk cargo with the growth of the isolation membrane (IM) in a yet-unknown manner. Here, we show that in the budding yeast Saccharomyces cerevisiae, IMs expand while maintaining a rim sufficiently wide for sequestration of large cargo but tight enough to mature in due time. An obligate complex of Atg24/Snx4 with Atg20 or Snx41 assembles locally at the rim in a spatially extended manner that specifically depends on autophagic PI(3)P. This assembly stabilizes the open rim to promote autophagic sequestration of large cargo in correlation with vesicle expansion. Moreover, constriction of the rim by the PI(3)P-dependent Atg2-Atg18 complex and clearance of PI(3)P by Ymr1 antagonize rim opening to promote autophagic maturation and consumption of small cargo. Tight regulation of membrane rim aperture by PI(3)P thus couples the mechanism and physiology of nonselective autophagy.
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Affiliation(s)
- Oren Shatz
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Milana Fraiberg
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Damilola Isola
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Shubhankar Das
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Olee Gogoi
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Alexandra Polyansky
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Nili Dezorella
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Sharon G Wolf
- Chemical Research Support, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Zvulun Elazar
- Departments of Biomolecular Sciences, The Weizmann Institute of Science, 76100 Rehovot, Israel.
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Tziouvara O, Petsana M, Kourounis D, Papadaki A, Basdra E, Braliou GG, Boleti H. Characterization of the First Secreted Sorting Nexin Identified in the Leishmania Protists. Int J Mol Sci 2024; 25:4095. [PMID: 38612903 PMCID: PMC11012638 DOI: 10.3390/ijms25074095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/19/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024] Open
Abstract
Proteins of the sorting nexin (SNX) family present a modular structural architecture with a phox homology (PX) phosphoinositide (PI)-binding domain and additional PX structural domains, conferring to them a wide variety of vital eukaryotic cell's functions, from signal transduction to membrane deformation and cargo binding. Although SNXs are well studied in human and yeasts, they are poorly investigated in protists. Herein, is presented the characterization of the first SNX identified in Leishmania protozoan parasites encoded by the LdBPK_352470 gene. In silico secondary and tertiary structure prediction revealed a PX domain on the N-terminal half and a Bin/amphiphysin/Rvs (BAR) domain on the C-terminal half of this protein, with these features classifying it in the SNX-BAR subfamily of SNXs. We named the LdBPK_352470.1 gene product LdSNXi, as it is the first SNX identified in Leishmania (L.) donovani. Its expression was confirmed in L. donovani promastigotes under different cell cycle phases, and it was shown to be secreted in the extracellular medium. Using an in vitro lipid binding assay, it was demonstrated that recombinant (r) LdSNXi (rGST-LdSNXi) tagged with glutathione-S-transferase (GST) binds to the PtdIns3P and PtdIns4P PIs. Using a specific a-LdSNXi antibody and immunofluorescence confocal microscopy, the intracellular localization of endogenous LdSNXi was analyzed in L. donovani promastigotes and axenic amastigotes. Additionally, rLdSNXi tagged with enhanced green fluorescent protein (rLdSNXi-EGFP) was heterologously expressed in transfected HeLa cells and its localization was examined. All observed localizations suggest functions compatible with the postulated SNX identity of LdSNXi. Sequence, structure, and evolutionary analysis revealed high homology between LdSNXi and the human SNX2, while the investigation of protein-protein interactions based on STRING (v.11.5) predicted putative molecular partners of LdSNXi in Leishmania.
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Affiliation(s)
- Olympia Tziouvara
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Marina Petsana
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2–4 Papasiopoulou Str., 35131 Lamia, Greece;
| | - Drosos Kourounis
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
| | - Amalia Papadaki
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
| | - Efthimia Basdra
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | - Georgia G. Braliou
- Department of Computer Science and Biomedical Informatics, University of Thessaly, 2–4 Papasiopoulou Str., 35131 Lamia, Greece;
| | - Haralabia Boleti
- Intracellular Parasitism Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (O.T.); (M.P.); (D.K.); (A.P.)
- Bioimaging Unit, Hellenic Pasteur Institute, 11521 Athens, Greece
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Characterization of Protein-Membrane Interactions in Yeast Autophagy. Cells 2022; 11:cells11121876. [PMID: 35741004 PMCID: PMC9221364 DOI: 10.3390/cells11121876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/03/2022] [Accepted: 06/07/2022] [Indexed: 02/06/2023] Open
Abstract
Cells rely on autophagy to degrade cytosolic material and maintain homeostasis. During autophagy, content to be degraded is encapsulated in double membrane vesicles, termed autophagosomes, which fuse with the yeast vacuole for degradation. This conserved cellular process requires the dynamic rearrangement of membranes. As such, the process of autophagy requires many soluble proteins that bind to membranes to restructure, tether, or facilitate lipid transfer between membranes. Here, we review the methods that have been used to investigate membrane binding by the core autophagy machinery and additional accessory proteins involved in autophagy in yeast. We also review the key experiments demonstrating how each autophagy protein was shown to interact with membranes.
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