Phagophore closure, autophagosome maturation and autophagosome fusion during macroautophagy in the yeast Saccharomyces cerevisiae

Macroautophagy, hereafter referred to as autophagy, is a complex process in which multiple membrane‐remodeling events lead to the formation of a cisterna known as the phagophore, which then expands and closes into a double‐membrane vesicle termed the autophagosome. During the past decade, enormous progress has been made in understanding the molecular function of the autophagy‐related proteins and their role in generating these phagophores. In this Review, we discuss the current understanding of three membrane remodeling steps in autophagy that remain to be largely characterized; namely, the closure of phagophores, the maturation of the resulting autophagosomes into fusion‐competent vesicles, and their fusion with vacuoles/lysosomes. Our review will mainly focus on the yeast Saccharomyces cerevisiae, which has been the leading model system for the study of molecular events in autophagy and has led to the discovery of the major mechanistic concepts, which have been found to be mostly conserved in higher eukaryotes.

[1]  W. Huh,et al.  Atg1-dependent phosphorylation of Vps34 is required for dynamic regulation of the phagophore assembly site and autophagy in Saccharomyces cerevisiae , 2023, Autophagy.

[2]  C. Kraft,et al.  ULK1-mediated phosphorylation regulates the conserved role of YKT6 in autophagy , 2023, Journal of cell science.

[3]  Fan Zhou,et al.  The entry of unclosed autophagosomes into vacuoles and its physiological relevance , 2022, PLoS genetics.

[4]  Zhiping Xie,et al.  Vps21 Directs the PI3K-PI(3)P-Atg21-Atg16 Module to Phagophores via Vps8 for Autophagy , 2022, International journal of molecular sciences.

[5]  Y. Olmos,et al.  The ESCRT Machinery: Remodeling, Repairing, and Sealing Membranes , 2022, Membranes.

[6]  H. Tamaki,et al.  Essential roles of phosphatidylinositol 4-phosphate phosphatases Sac1p and Sjl3p in yeast autophagosome formation. , 2022, Biochimica et biophysica acta. Molecular and cell biology of lipids.

[7]  C. Kraft,et al.  Spatial control of avidity regulates initiation and progression of selective autophagy , 2021, Nature Communications.

[8]  A. Ballabio,et al.  Autophagy in major human diseases , 2021, The EMBO journal.

[9]  R. Xavier,et al.  SAC1 regulates autophagosomal phosphatidylinositol-4-phosphate for xenophagy-directed bacterial clearance , 2021, Cell reports.

[10]  S. Tooze,et al.  Membrane supply and remodeling during autophagosome biogenesis. , 2021, Current opinion in cell biology.

[11]  C. Kraft,et al.  Atg1 kinase regulates autophagosome‐vacuole fusion by controlling SNARE bundling , 2020, EMBO reports.

[12]  N. Mizushima,et al.  Autophagy in Human Diseases. , 2020, The New England journal of medicine.

[13]  F. Fröhlich,et al.  Function of the SNARE Ykt6 on autophagosomes requires the Dsl1 complex and the Atg1 kinase complex , 2020, EMBO reports.

[14]  E. Baehrecke,et al.  A conserved myotubularin-related phosphatase regulates autophagy by maintaining autophagic flux , 2020, The Journal of cell biology.

[15]  H. Nakatogawa Mechanisms governing autophagosome biogenesis , 2020, Nature Reviews Molecular Cell Biology.

[16]  T. Ando,et al.  Phase separation organizes the site of autophagosome formation , 2020, Nature.

[17]  N. Mizushima The ATG conjugation systems in autophagy. , 2019, Current opinion in cell biology.

[18]  Di Chen,et al.  The ER-Localized Transmembrane Protein TMEM39A/SUSR2 Regulates Autophagy by Controlling the Trafficking of the PtdIns(4)P Phosphatase SAC1. , 2019, Molecular cell.

[19]  V. Rogov,et al.  A Diversity of Selective Autophagy Receptors Determines the Specificity of the Autophagy Pathway. , 2019, Molecular cell.

[20]  J. Dengjel,et al.  Multilayered Control of Protein Turnover by TORC1 and Atg1. , 2019, Cell reports.

[21]  Fan Zhou,et al.  Rab5-dependent autophagosome closure by ESCRT , 2019, The Journal of cell biology.

[22]  C. Kraft,et al.  The multi-functional SNARE protein Ykt6 in autophagosomal fusion processes , 2019, Cell cycle.

[23]  J. Haber,et al.  PP2C phosphatases promote autophagy by dephosphorylation of the Atg1 complex , 2019, Proceedings of the National Academy of Sciences.

[24]  G. Kroemer,et al.  Biological Functions of Autophagy Genes: A Disease Perspective , 2019, Cell.

[25]  C. Kraft,et al.  Vac8 spatially confines autophagosome formation at the vacuole in S. cerevisiae , 2019, Journal of Cell Science.

[26]  J. Debnath,et al.  Autophagy and the cell biology of age-related disease , 2018, Nature Cell Biology.

[27]  Y. Ohsumi,et al.  The Atg2-Atg18 complex tethers pre-autophagosomal membranes to the endoplasmic reticulum for autophagosome formation , 2018, Proceedings of the National Academy of Sciences.

[28]  C. Kraft,et al.  Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome–vacuole fusion , 2018, The Journal of cell biology.

[29]  F. Reggiori,et al.  A novel in vitro assay reveals SNARE topology and the role of Ykt6 in autophagosome fusion with vacuoles , 2018, The Journal of cell biology.

[30]  N. Mizushima,et al.  Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17 , 2018, The Journal of cell biology.

[31]  C. Kraft,et al.  Atg9 establishes Atg2-dependent contact sites between the endoplasmic reticulum and phagophores , 2018, The Journal of cell biology.

[32]  D. Klionsky,et al.  A newly characterized vacuolar serine carboxypeptidase, Atg42/Ybr139w, is required for normal vacuole function and the terminal steps of autophagy in the yeast Saccharomyces cerevisiae , 2018, Molecular biology of the cell.

[33]  F. Reggiori,et al.  Coordination of Autophagosome–Lysosome Fusion by Atg8 Family Members , 2018, Current Biology.

[34]  G. Juhász,et al.  Non-canonical role of the SNARE protein Ykt6 in autophagosome-lysosome fusion , 2018, PLoS genetics.

[35]  F. Reggiori,et al.  Molecular mechanism to target the endosomal Mon1-Ccz1 GEF complex to the pre-autophagosomal structure , 2018, eLife.

[36]  A. Mayer,et al.  A tethering complex drives the terminal stage of SNARE-dependent membrane fusion , 2017, Nature.

[37]  Fan Zhou,et al.  A Rab5 GTPase module is important for autophagosome closure , 2017, PLoS genetics.

[38]  C. Kraft,et al.  Atg4 proteolytic activity can be inhibited by Atg1 phosphorylation , 2017, Nature Communications.

[39]  J. Jones,et al.  A reversible phospho-switch mediated by ULK1 regulates the activity of autophagy protease ATG4B , 2017, Nature Communications.

[40]  T. Yoshimori,et al.  New insights into autophagosome–lysosome fusion , 2017, Journal of Cell Science.

[41]  M. Peter,et al.  Conserved Atg8 recognition sites mediate Atg4 association with autophagosomal membranes and Atg8 deconjugation , 2017, EMBO reports.

[42]  F. Reggiori,et al.  Autophagosome Maturation and Fusion. , 2017, Journal of molecular biology.

[43]  S. Martens,et al.  Mechanisms of Selective Autophagy , 2016, Journal of molecular biology.

[44]  D. Klionsky,et al.  The Atg17-Atg31-Atg29 Complex Coordinates with Atg11 to Recruit the Vam7 SNARE and Mediate Autophagosome-Vacuole Fusion , 2016, Current Biology.

[45]  R. Lipowsky,et al.  Autophagosome closure requires membrane scission , 2015, Autophagy.

[46]  P. Jeffrey,et al.  A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly , 2015, Science.

[47]  S. Raunser,et al.  The Habc Domain of the SNARE Vam3 Interacts with the HOPS Tethering Complex to Facilitate Vacuole Fusion* , 2015, The Journal of Biological Chemistry.

[48]  L. Björn,et al.  A Vps21 endocytic module regulates autophagy , 2014, Molecular biology of the cell.

[49]  S. Mitani,et al.  PI3P phosphatase activity is required for autophagosome maturation and autolysosome formation , 2014, EMBO reports.

[50]  Ruedi Aebersold,et al.  Early Steps in Autophagy Depend on Direct Phosphorylation of Atg9 by the Atg1 Kinase , 2014, Molecular cell.

[51]  D. Klionsky,et al.  Estimating the size and number of autophagic bodies by electron microscopy , 2014, Autophagy.

[52]  Y. Ohsumi,et al.  Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae , 2013, Journal of Cell Science.

[53]  D. Klionsky,et al.  Phosphatidylinositol 4-Kinases Are Required for Autophagic Membrane Trafficking* , 2012, The Journal of Biological Chemistry.

[54]  D. Klionsky,et al.  Phosphatidylinositol-3-Phosphate Clearance Plays a Key Role in Autophagosome Completion , 2012, Current Biology.

[55]  Rie Ichikawa,et al.  Atg9 vesicles are an important membrane source during early steps of autophagosome formation , 2012, The Journal of cell biology.

[56]  D. Klionsky,et al.  A role for Atg8–PE deconjugation in autophagosome biogenesis , 2012, Autophagy.

[57]  R. Goody,et al.  GTPases involved in vesicular trafficking: structures and mechanisms. , 2011, Seminars in cell & developmental biology.

[58]  Cahir J. O'Kane,et al.  Lysosomal positioning coordinates cellular nutrient responses , 2011, Nature Cell Biology.

[59]  H. Takematsu,et al.  Identification of Ypk1 as a Novel Selective Substrate for Nitrogen Starvation-triggered Proteolysis Requiring Autophagy System and Endosomal Sorting Complex Required for Transport (ESCRT) Machinery Components* , 2010, The Journal of Biological Chemistry.

[60]  D. Klionsky,et al.  The Cvt pathway as a model for selective autophagy , 2010, FEBS letters.

[61]  Zhijian Li,et al.  The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy , 2010, The Journal of cell biology.

[62]  D. Klionsky,et al.  Atg8 controls phagophore expansion during autophagosome formation. , 2008, Molecular biology of the cell.

[63]  C. Ostrowicz,et al.  The CORVET tethering complex interacts with the yeast Rab5 homolog Vps21 and is involved in endo-lysosomal biogenesis. , 2007, Developmental cell.

[64]  D. Klionsky,et al.  Atg17 regulates the magnitude of the autophagic response. , 2005, Molecular biology of the cell.

[65]  C. Ungermann,et al.  The vacuolar kinase Yck3 maintains organelle fragmentation by regulating the HOPS tethering complex , 2005, The Journal of cell biology.

[66]  S. Emr,et al.  Essential role for the myotubularin-related phosphatase Ymr1p and the synaptojanin-like phosphatases Sjl2p and Sjl3p in regulation of phosphatidylinositol 3-phosphate in yeast. , 2004, Molecular biology of the cell.

[67]  Daniel J Klionsky,et al.  Early stages of the secretory pathway, but not endosomes, are required for Cvt vesicle and autophagosome assembly in Saccharomyces cerevisiae. , 2004, Molecular biology of the cell.

[68]  J. Bonifacino,et al.  The Mechanisms of Vesicle Budding and Fusion , 2004, Cell.

[69]  D. Klionsky,et al.  Autophagy in the Eukaryotic Cell , 2002, Eukaryotic Cell.

[70]  Takeshi Noda,et al.  Two Distinct Vps34 Phosphatidylinositol 3–Kinase Complexes Function in Autophagy and Carboxypeptidase Y Sorting inSaccharomyces cerevisiae , 2001, The Journal of cell biology.

[71]  S. Emr,et al.  Cytoplasm to vacuole trafficking of aminopeptidase I requires a t‐SNARE–Sec1p complex composed of Tlg2p and Vps45p , 1999, The EMBO journal.

[72]  Takeshi Noda,et al.  Formation Process of Autophagosome Is Traced with Apg8/Aut7p in Yeast , 1999, The Journal of cell biology.

[73]  D. Klionsky,et al.  Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway , 1995, The Journal of cell biology.

[74]  S. Emr,et al.  A new vital stain for visualizing vacuolar membrane dynamics and endocytosis in yeast , 1995, The Journal of cell biology.

[75]  M. Schlumpberger,et al.  Isolation of autophagocytosis mutants of Saccharomyces cerevisiae , 1994, FEBS letters.

[76]  Y. Ohsumi,et al.  Isolation and characterization of autophagy‐defective mutants of Saccharomyces cerevisiae , 1993, FEBS letters.

[77]  S. Tsuboi,et al.  Autophagy in yeast demonstrated with proteinase-deficient mutants and conditions for its induction , 1992, The Journal of cell biology.

[78]  T. Noda,et al.  Dynein-dependent movement of autophagosomes mediates efficient encounters with lysosomes. , 2008, Cell structure and function.