CoChat
Sign Up
Cited by 90

The DOI matches its Crossref record; 4 of the 4 references it cites were found in a registry or an index.

A novel in vitro assay reveals SNARE topology and the role of Ykt6 in autophagosome fusion with vacuoles

Gao, Jieqiong, Reggiori, Fulvio, Ungermann, Christian·2018·Journal of Cell Biology
DOI 10.1083/jcb.201804039PMC PMC6168247
Open this paper in CoChat — free account

Abstract

Autophagy is a catabolic pathway that delivers intracellular material to the mammalian lysosomes or the yeast and plant vacuoles. The final step in this process is the fusion of autophagosomes with vacuoles, which requires SNARE proteins, the homotypic vacuole fusion and protein sorting tethering complex, the RAB7-like Ypt7 GTPase, and its guanine nucleotide exchange factor, Mon1-Ccz1. Where these different components are located and function during fusion, however, remains to be fully understood. Here, we present a novel in vitro assay to monitor fusion of intact and functional autophagosomes with vacuoles. This process requires ATP, physiological temperature, and the entire fusion machinery to tether and fuse autophagosomes with vacuoles. Importantly, we uncover Ykt6 as the autophagosomal SNARE. Our assay and findings thus provide the tools to dissect autophagosome completion and fusion in a test tube.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1083/jcb.201804039

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Show all 4 references

Research works printed but not linked: 78

  1. Arasaki, 2015, A role for the ancient SNARE syntaxin 17 in regulating mitochondrial division, Dev. Cell., 32, 304, 10.1016/j.devcel.2014.12.011 · DOI
  2. Baba, 1994, Ultrastructural analysis of the autophagic process in yeast: detection of autophagosomes and their characterization, J. Cell Biol., 124, 903, 10.1083/jcb.124.6.903 · DOI
  3. Baker, 2015, A direct role for the Sec1/Munc18-family protein Vps33 as a template for SNARE assembly, Science., 349, 1111, 10.1126/science.aac7906 · DOI
  4. Balderhaar, 2013, CORVET and HOPS tethering complexes - coordinators of endosome and lysosome fusion, J. Cell Sci., 126, 1307, 10.1242/jcs.107805 · DOI
  5. Barth, 2001, Autophagy and the cytoplasm to vacuole targeting pathway both require Aut10p, FEBS Lett., 508, 23, 10.1016/S0014-5793(01)03016-2 · DOI · Paper page
  6. Bas, 2018, Reconstitution reveals Ykt6 as the autophagosomal SNARE in autophagosome–vacuole fusion, J. Cell Biol., 10.1083/jcb.201804028 · DOI · Paper page
  7. Brett, 2008, Efficient termination of vacuolar Rab GTPase signaling requires coordinated action by a GAP and a protein kinase, J. Cell Biol., 182, 1141, 10.1083/jcb.200801001 · DOI
  8. Bröcker, 2012, Molecular architecture of the multisubunit homotypic fusion and vacuole protein sorting (HOPS) tethering complex, Proc. Natl. Acad. Sci. USA., 109, 1991, 10.1073/pnas.1117797109 · DOI
  9. Cebollero, 2012, Phosphatidylinositol-3-phosphate clearance plays a key role in autophagosome completion, Curr. Biol., 22, 1545, 10.1016/j.cub.2012.06.029 · DOI
  10. Cheever, 2001, Phox domain interaction with PtdIns(3)P targets the Vam7 t-SNARE to vacuole membranes, Nat. Cell Biol., 3, 613, 10.1038/35083000 · DOI · Paper page
  11. Chen, 2016, Multiple ER-Golgi SNARE transmembrane domains are dispensable for trafficking but required for SNARE recycling, Mol. Biol. Cell., 27, 2633, 10.1091/mbc.e16-05-0277 · DOI
  12. D’Agostino, 2017, A tethering complex drives the terminal stage of SNARE-dependent membrane fusion, Nature., 551, 634, 10.1038/nature24469 · DOI
  13. Darsow, 1997, A multispecificity syntaxin homologue, Vam3p, essential for autophagic and biosynthetic protein transport to the vacuole, J. Cell Biol., 138, 517, 10.1083/jcb.138.3.517 · DOI
  14. Darsow, 1998, Acidic di-leucine motif essential for AP-3-dependent sorting and restriction of the functional specificity of the Vam3p vacuolar t-SNARE, J. Cell Biol., 142, 913, 10.1083/jcb.142.4.913 · DOI
  15. Dietrich, 2005, ATP-independent control of Vac8 palmitoylation by a SNARE subcomplex on yeast vacuoles, J. Biol. Chem., 280, 15348, 10.1074/jbc.M410582200 · DOI
  16. Dilcher, 2001, Genetic interactions with the yeast Q-SNARE VTI1 reveal novel functions for the R-SNARE YKT6, J. Biol. Chem., 276, 34537, 10.1074/jbc.M101551200 · DOI
  17. Fischer von Mollard, 1999, The Saccharomyces cerevisiae v-SNARE Vti1p is required for multiple membrane transport pathways to the vacuole, Mol. Biol. Cell., 10, 1719, 10.1091/mbc.10.6.1719 · DOI
  18. Fukasawa, 2004, Localization and activity of the SNARE Ykt6 determined by its regulatory domain and palmitoylation, Proc. Natl. Acad. Sci. USA., 101, 4815, 10.1073/pnas.0401183101 · DOI
  19. Gao, 2018, Molecular mechanism to target the endosomal Mon1-Ccz1 GEF complex to the pre-autophagosomal structure, eLife., 7, 765, 10.7554/eLife.31145 · DOI
  20. Ge, 2014, The protein-vesicle network of autophagy, Curr. Opin. Cell Biol., 29, 18, 10.1016/j.ceb.2014.02.005 · DOI
  21. Goody, 2017, Mechanisms of action of Rab proteins, key regulators of intracellular vesicular transport, Biol. Chem., 398, 565, 10.1515/hsz-2016-0274 · DOI
  22. Haas, 1995, A quantitative assay to measure homotypic vacuole fusion in vitro, Methods Cell Sci., 17, 283, 10.1007/BF00986234 · DOI
  23. Haas, 1994, G-protein ligands inhibit in vitro reactions of vacuole inheritance, J. Cell Biol., 126, 87, 10.1083/jcb.126.1.87 · DOI
  24. Hasegawa, 2003, Mammalian ykt6 is a neuronal SNARE targeted to a specialized compartment by its profilin-like amino terminal domain, Mol. Biol. Cell., 14, 698, 10.1091/mbc.e02-09-0556 · DOI
  25. Hegedüs, 2016, The Ccz1-Mon1-Rab7 module and Rab5 control distinct steps of autophagy, Mol. Biol. Cell., 27, 3132, 10.1091/mbc.e16-03-0205 · DOI
  26. Hickey, 2010, HOPS initiates vacuole docking by tethering membranes before trans-SNARE complex assembly, Mol. Biol. Cell., 21, 2297, 10.1091/mbc.e10-01-0044 · DOI
  27. Ho, 2015, The HOPS/class C Vps complex tethers membranes by binding to one Rab GTPase in each apposed membrane, Mol. Biol. Cell., 26, 2655, 10.1091/mbc.e14-04-0922 · DOI
  28. Ishihara, 2001, Autophagosome requires specific early Sec proteins for its formation and NSF/SNARE for vacuolar fusion, Mol. Biol. Cell., 12, 3690, 10.1091/mbc.12.11.3690 · DOI
  29. Itakura, 2012, The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes, Cell., 151, 1256, 10.1016/j.cell.2012.11.001 · DOI
  30. Janke, 2004, A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes, Yeast., 21, 947, 10.1002/yea.1142 · DOI
  31. Karim, 2018, The Na+(K+)/H+ exchanger Nhx1 controls multivesicular body-vacuolar lysosome fusion, Mol. Biol. Cell., 29, 317, 10.1091/mbc.e17-08-0496 · DOI
  32. Karim, 2018, Distinct features of multivesicular body-lysosome fusion revealed by a new cell-free content-mixing assay, Traffic., 19, 138, 10.1111/tra.12543 · DOI
  33. Kumar, 2018, Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins, J. Cell Biol., 217, 997, 10.1083/jcb.201708039 · DOI
  34. Kweon, 2003, Ykt6p is a multifunctional yeast R-SNARE that is required for multiple membrane transport pathways to the vacuole, Mol. Biol. Cell., 14, 1868, 10.1091/mbc.e02-10-0687 · DOI
  35. Lai, 2017, Molecular Mechanisms of Synaptic Vesicle Priming by Munc13 and Munc18, Neuron., 95, 591, 10.1016/j.neuron.2017.07.004 · DOI
  36. Lamb, 2013, Endocytosis and autophagy: Shared machinery for degradation, BioEssays., 35, 34, 10.1002/bies.201200130 · DOI
  37. Lamb, 2013, The autophagosome: origins unknown, biogenesis complex, Nat. Rev. Mol. Cell Biol., 14, 759, 10.1038/nrm3696 · DOI
  38. Langemeyer, 2018, A guanine nucleotide exchange factor (GEF) limits Rab GTPase-driven membrane fusion, J. Biol. Chem., 293, 731, 10.1074/jbc.M117.812941 · DOI
  39. Linder, 2013, Mechanism and function of DHHC S-acyltransferases, Biochem. Soc. Trans., 41, 29, 10.1042/BST20120328 · DOI
  40. Lobingier, 2012, Sec1/Munc18 protein Vps33 binds to SNARE domains and the quaternary SNARE complex, Mol. Biol. Cell, 23, 4611, 10.1091/mbc.e12-05-0343 · DOI
  41. Lürick, 2017, Multivalent Rab interactions determine tether-mediated membrane fusion, Mol. Biol. Cell., 28, 322, 10.1091/mbc.e16-11-0764 · DOI
  42. Mari, 2010, Atg9 reservoirs, a new organelle of the yeast endomembrane system?, Autophagy., 6, 1221, 10.4161/auto.6.8.13792 · DOI
  43. Matsui, 2018, Autophagosomal YKT6 is required for fusion with lysosomes independently of syntaxin 17, J. Cell Biol., 217, 2633, 10.1083/jcb.201712058 · DOI · Paper page
  44. McNew, 1997, Ykt6p, a prenylated SNARE essential for endoplasmic reticulum-Golgi transport, J. Biol. Chem., 272, 17776, 10.1074/jbc.272.28.17776 · DOI
  45. McNew, 2000, Compartmental specificity of cellular membrane fusion encoded in SNARE proteins, Nature., 407, 153, 10.1038/35025000 · DOI
  46. Meiringer, 2008, Depalmitoylation of Ykt6 prevents its entry into the multivesicular body pathway, Traffic, 9, 1510, 10.1111/j.1600-0854.2008.00778.x · DOI
  47. Meiringer, 2011, The Dsl1 protein tethering complex is a resident endoplasmic reticulum complex, which interacts with five soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptors (SNAREs): implications for fusion and fusion regulation, J. Biol. Chem., 286, 25039, 10.1074/jbc.M110.215327 · DOI
  48. Mitchell, 2006, Protein palmitoylation by a family of DHHC protein S-acyltransferases, J. Lipid Res., 47, 1118, 10.1194/jlr.R600007-JLR200 · DOI
  49. Nair, 2011, SNARE proteins are required for macroautophagy, Cell., 146, 290, 10.1016/j.cell.2011.06.022 · DOI
  50. Noda, 1995, Novel system for monitoring autophagy in the yeast Saccharomyces cerevisiae, Biochem. Biophys. Res. Commun., 210, 126, 10.1006/bbrc.1995.1636 · DOI
  51. Nordmann, 2010, The Mon1-Ccz1 complex is the GEF of the late endosomal Rab7 homolog Ypt7, Curr. Biol., 20, 1654, 10.1016/j.cub.2010.08.002 · DOI
  52. Ohashi, 2010, Membrane delivery to the yeast autophagosome from the Golgi-endosomal system, Mol. Biol. Cell., 21, 3998, 10.1091/mbc.e10-05-0457 · DOI
  53. Orr, 2017, HOPS catalyzes the interdependent assembly of each vacuolar SNARE into a SNARE complex, Mol. Biol. Cell., 28, 975, 10.1091/mbc.e16-10-0743 · DOI
  54. Peterson, 2001, The class C Vps complex functions at multiple stages of the vacuolar transport pathway, Traffic., 2, 476, 10.1034/j.1600-0854.2001.20705.x · DOI
  55. Puig, 1998, New constructs and strategies for efficient PCR-based gene manipulations in yeast, Yeast., 14, 1139, 10.1002/(SICI)1097-0061(19980915)14:12<1139::AID-YEA306>3.0.CO;2-B · DOI
  56. Reggiori, 2017, Autophagosome Maturation and Fusion, J. Mol. Biol., 429, 486, 10.1016/j.jmb.2017.01.002 · DOI
  57. Rieter, 2013, Atg18 function in autophagy is regulated by specific sites within its β-propeller, J. Cell Sci., 126, 593, 10.1242/jcs.115725 · DOI
  58. Rohde, 2003, The transmembrane domain of Vam3 affects the composition of cis- and trans-SNARE complexes to promote homotypic vacuole fusion, J. Biol. Chem., 278, 1656, 10.1074/jbc.M209522200 · DOI
  59. Roth, 2006, Global analysis of protein palmitoylation in yeast, Cell, 125, 1003, 10.1016/j.cell.2006.03.042 · DOI
  60. Seals, 2000, A Ypt/Rab effector complex containing the Sec1 homolog Vps33p is required for homotypic vacuole fusion, Proc. Natl. Acad. Sci. USA., 97, 9402, 10.1073/pnas.97.17.9402 · DOI
  61. Shibutani, 2014, A current perspective of autophagosome biogenesis, Cell Res., 24, 58, 10.1038/cr.2013.159 · DOI
  62. Takáts, 2013, Autophagosomal Syntaxin17-dependent lysosomal degradation maintains neuronal function in Drosophila, J. Cell Biol., 201, 531, 10.1083/jcb.201211160 · DOI
  63. Takáts, 2014, Interaction of the HOPS complex with Syntaxin 17 mediates autophagosome clearance in Drosophila, Mol. Biol. Cell., 25, 1338, 10.1091/mbc.e13-08-0449 · DOI
  64. Takáts, 2018, Non-canonical role of the SNARE protein Ykt6 in autophagosome-lysosome fusion, PLoS Genet., 14, e1007359, 10.1371/journal.pgen.1007359 · DOI
  65. Torggler, 2017, Assays to Monitor Autophagy in Saccharomyces cerevisiae, Cells., 6, 23, 10.3390/cells6030023 · DOI
  66. Tsui, 2000, Yeast Golgi SNARE interactions are promiscuous, J. Cell Sci., 113, 145, 10.1242/jcs.113.1.145 · DOI
  67. Ungermann, 1998, Vam7p, a vacuolar SNAP-25 homolog, is required for SNARE complex integrity and vacuole docking and fusion, EMBO J., 17, 3269, 10.1093/emboj/17.12.3269 · DOI
  68. Ungermann, 1998, A vacuolar v-t-SNARE complex, the predominant form in vivo and on isolated vacuoles, is disassembled and activated for docking and fusion, J. Cell Biol., 140, 61, 10.1083/jcb.140.1.61 · DOI
  69. Ungermann, 1999, Three v-SNAREs and two t-SNAREs, present in a pentameric cis-SNARE complex on isolated vacuoles, are essential for homotypic fusion, J. Cell Biol., 145, 1435, 10.1083/jcb.145.7.1435 · DOI
  70. Veit, 2004, The human SNARE protein Ykt6 mediates its own palmitoylation at C-terminal cysteine residues, Biochem. J., 384, 233, 10.1042/BJ20041474 · DOI
  71. von Mollard, 1997, The yeast v-SNARE Vti1p mediates two vesicle transport pathways through interactions with the t-SNAREs Sed5p and Pep12p, J. Cell Biol., 137, 1511, 10.1083/jcb.137.7.1511 · DOI
  72. Wickner, 2010, Membrane fusion: five lipids, four SNAREs, three chaperones, two nucleotides, and a Rab, all dancing in a ring on yeast vacuoles, Annu. Rev. Cell Dev. Biol., 26, 115, 10.1146/annurev-cellbio-100109-104131 · DOI
  73. Wickner, 2017, A cascade of multiple proteins and lipids catalyzes membrane fusion, Mol. Biol. Cell., 28, 707, 10.1091/mbc.e16-07-0517 · DOI
  74. Xu, 2011, A lipid-anchored SNARE supports membrane fusion, Proc. Natl. Acad. Sci. USA., 108, 17325, 10.1073/pnas.1113888108 · DOI
  75. Yamamoto, 2012, Atg9 vesicles are an important membrane source during early steps of autophagosome formation, J. Cell Biol., 198, 219, 10.1083/jcb.201202061 · DOI · Paper page
  76. Zick, 2012, Phosphorylation of the effector complex HOPS by the vacuolar kinase Yck3p confers Rab nucleotide specificity for vacuole docking and fusion, Mol. Biol. Cell., 23, 3429, 10.1091/mbc.e12-04-0279 · DOI
  77. Zick, 2013, The tethering complex HOPS catalyzes assembly of the soluble SNARE Vam7 into fusogenic trans-SNARE complexes, Mol. Biol. Cell., 24, 3746, 10.1091/mbc.e13-07-0419 · DOI
  78. Zick, 2016, Improved reconstitution of yeast vacuole fusion with physiological SNARE concentrations reveals an asymmetric Rab(GTP) requirement, Mol. Biol. Cell., 27, 2590, 10.1091/mbc.e16-04-0230 · DOI

Cited by

Sorted by citations

See all 90

Metadata

Authors
Gao, J., Reggiori, F., & Ungermann, C.
Affiliations
  • Biochemistry Section, Department of Biology/Chemistry, University of Osnabrück, Osnabrück, Germany 1
  • Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands 2
ORCID
Venue
Journal of Cell Biology
Publisher
Rockefeller University Press
Published
2018-08-10
Volume
217
Issue
10
Pages
3670-3682
ISSN
  • 0021-9525
  • 1540-8140
DOI
10.1083/jcb.201804039
PMC
PMC6168247
Cited by
90
References
4
Language
en
Licence
Funders
  • ALW (822.02.014)
  • Deutsche Forschungsgemeinschaft (UN111/7-3)
  • Netherlands Organisation for Scientific Research (DN82-303)
  • Swiss National Science Foundation (CRSII3_154421)
  • Marie Skłodowska-Curie (713660)
  • ZonMW (016.130.606)
  • Sonderforschungsbereich (Project P11)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review