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Cited by 659Autophagy in Disease and TherapyCellular transport and secretionFungal and yeast genetics research

Atg9 vesicles are an important membrane source during early steps of autophagosome formation

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Yamamoto, Hayashi, Kakuta, Soichiro, Watanabe, Tomonobu M., Kitamura, Akira, Sekito, Takayuki, Kondo-Kakuta, Chika, Ichikawa, Rie, Kinjo, Masataka +1 more·2012·Journal of Cell Biology
DOI 10.1083/jcb.201202061PMC PMC3410421
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Abstract

During the process of autophagy, cytoplasmic materials are sequestered by double-membrane structures, the autophagosomes, and then transported to a lytic compartment to be degraded. One of the most fundamental questions about autophagy involves the origin of the autophagosomal membranes. In this study, we focus on the intracellular dynamics of Atg9, a multispanning membrane protein essential for autophagosome formation in yeast. We found that the vast majority of Atg9 existed on cytoplasmic mobile vesicles (designated Atg9 vesicles) that were derived from the Golgi apparatus in a process involving Atg23 and Atg27. We also found that only a few Atg9 vesicles were required for a single round of autophagosome formation. During starvation, several Atg9 vesicles assembled individually into the preautophagosomal structure, and eventually, they are incorporated into the autophagosomal outer membrane. Our findings provide conclusive linkage between the cytoplasmic Atg9 vesicles and autophagosomal membranes and offer new insight into the requirement for Atg9 vesicles at the early step of autophagosome formation.

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  • ATG9A-positive vesicles are thought to represent a major membrane source for autophagosome biogenesis.

    “ATG9A-positive vesicles are thought to represent a major membrane source for autophagosome biogenesis [49].”

    From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [49]

    The Discussion says that Atg9 vesicles contribute membrane during early autophagosome formation, but explicitly calls them unlikely to be major lipid suppliers and says other lipid sources must be considered. The paper studies yeast Atg9 vesicles, not specifically ATG9A-positive vesicles. (LLM, conf=0.88)

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References 52 · Cited by 659

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  1. Anderson C.M. Georgiou G.N. Morrison I.E. Stevenson G.V. Cherry R.J. 1992 Tracking of cell surface receptors by fluorescence digital imaging microscopy using a charge-coupled device camera. Low-density lipoprotein and influenza virus receptor mobility at 4 degrees C. J. Cell Sci. 101: 415– 425 1629253
  2. Babst M. Sato T.K. Banta L.M. Emr S.D. 1997 Endosomal transport function in yeast requires a novel AAA-type ATPase, Vps4p. EMBO J. 16: 1820– 1831 10.1093/emboj/16.8.1820 9155008 PMC1169785 · DOI
  3. Cheong H. Nair U. Geng J. Klionsky D.J. 2008 The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae. Mol. Biol. Cell. 19: 668– 681 10.1091/mbc.E07-08-0826 18077553 PMC2230592 · DOI
  4. Coffman V.C. Wu P. Parthun M.R. Wu J.Q. 2011 CENP-A exceeds microtubule attachment sites in centromere clusters of both budding and fission yeast. J. Cell Biol. 195: 563– 572 10.1083/jcb.201106078 22084306 PMC3257534 · DOI
  5. Elsner M. Hashimoto H. Simpson J.C. Cassel D. Nilsson T. Weiss M. 2003 Spatiotemporal dynamics of the COPI vesicle machinery. EMBO Rep. 4: 1000– 1004 10.1038/sj.embor.embor942 14502225 PMC1326400 · DOI
  6. Hailey D.W. Rambold A.S. Satpute-Krishnan P. Mitra K. Sougrat R. Kim P.K. Lippincott-Schwartz J. 2010 Mitochondria supply membranes for autophagosome biogenesis during starvation. Cell. 141: 656– 667 10.1016/j.cell.2010.04.009 20478256 PMC3059894 · DOI
  7. Hayashi-Nishino M. Fujita N. Noda T. Yamaguchi A. Yoshimori T. Yamamoto A. 2009 A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Nat. Cell Biol. 11: 1433– 1437 10.1038/ncb1991 19898463 · DOI
  8. He C. Song H. Yorimitsu T. Monastyrska I. Yen W.L. Legakis J.E. Klionsky D.J. 2006 Recruitment of Atg9 to the preautophagosomal structure by Atg11 is essential for selective autophagy in budding yeast. J. Cell Biol. 175: 925– 935 10.1083/jcb.200606084 17178909 PMC2064702 · DOI
  9. Ichimura Y. Kirisako T. Takao T. Satomi Y. Shimonishi Y. Ishihara N. Mizushima N. Tanida I. Kominami E. Ohsumi M. 2000 A ubiquitin-like system mediates protein lipidation. Nature. 408: 488– 492 10.1038/35044114 11100732 · DOI
  10. Ishihara N. Hamasaki M. Yokota S. Suzuki K. Kamada Y. Kihara A. Yoshimori T. Noda T. Ohsumi Y. 2001 Autophagosome requires specific early Sec proteins for its formation and NSF/SNARE for vacuolar fusion. Mol. Biol. Cell. 12: 3690– 3702 11694599 PMC60286
  11. Janke C. Magiera M.M. Rathfelder N. Taxis C. Reber S. Maekawa H. Moreno-Borchart A. Doenges G. Schwob E. Schiebel E. Knop M. 2004 A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast. 21: 947– 962 10.1002/yea.1142 15334558 · DOI
  12. Joglekar A.P. Bouck D.C. Molk J.N. Bloom K.S. Salmon E.D. 2006 Molecular architecture of a kinetochore-microtubule attachment site. Nat. Cell Biol. 8: 581– 585 10.1038/ncb1414 16715078 PMC2867088 · DOI
  13. Kaiser C. Michaelis S. Mitchell A. 1994 Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York 234 pp
  14. Kawamata T. Kamada Y. Kabeya Y. Sekito T. Ohsumi Y. 2008 Organization of the pre-autophagosomal structure responsible for autophagosome formation. Mol. Biol. Cell. 19: 2039– 2050 10.1091/mbc.E07-10-1048 18287526 PMC2366851 · DOI
  15. Kim J. Dalton V.M. Eggerton K.P. Scott S.V. Klionsky D.J. 1999 Apg7p/Cvt2p is required for the cytoplasm-to-vacuole targeting, macroautophagy, and peroxisome degradation pathways. Mol. Biol. Cell. 10: 1337– 1351 10233148 PMC25275
  16. Klionsky D.J. 2005 The molecular machinery of autophagy: unanswered questions. J. Cell Sci. 118: 7– 18 10.1242/jcs.01620 15615779 PMC1828869 · DOI
  17. Klionsky D.J. 2007 Autophagy: from phenomenology to molecular understanding in less than a decade. Nat. Rev. Mol. Cell Biol. 8: 931– 937 10.1038/nrm2245 17712358 · DOI
  18. Kusumi A. Sako Y. Yamamoto M. 1993 Confined lateral diffusion of membrane receptors as studied by single particle tracking (nanovid microscopy). Effects of calcium-induced differentiation in cultured epithelial cells. Biophys. J. 65: 2021– 2040 10.1016/S0006-3495(93)81253-0 8298032 PMC1225938 · DOI
  19. Lang T. Reiche S. Straub M. Bredschneider M. Thumm M. 2000 Autophagy and the cvt pathway both depend on AUT9. J. Bacteriol. 182: 2125– 2133 10.1128/JB.182.8.2125-2133.2000 10735854 PMC111260 · DOI
  20. Lawrimore J. Bloom K.S. Salmon E.D. 2011 Point centromeres contain more than a single centromere-specific Cse4 (CENP-A) nucleosome. J. Cell Biol. 195: 573– 582 10.1083/jcb.201106036 22084307 PMC3257525 · DOI
  21. Legakis J.E. Yen W.L. Klionsky D.J. 2007 A cycling protein complex required for selective autophagy. Autophagy. 3: 422– 432 17426440
  22. Levine B. Klionsky D.J. 2004 Development by self-digestion: molecular mechanisms and biological functions of autophagy. Dev. Cell. 6: 463– 477 10.1016/S1534-5807(04)00099-1 15068787 · DOI
  23. Lynch-Day M.A. Bhandari D. Menon S. Huang J. Cai H. Bartholomew C.R. Brumell J.H. Ferro-Novick S. Klionsky D.J. 2010 Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc. Natl. Acad. Sci. USA. 107: 7811– 7816 10.1073/pnas.1000063107 20375281 PMC2867920 · DOI
  24. Mizushima N. 2005 The pleiotropic role of autophagy: from protein metabolism to bactericide. Cell Death Differ. 12(Suppl. 2): 1535– 1541 10.1038/sj.cdd.4401728 16247501 · DOI
  25. Monastyrska I. He C. Geng J. Hoppe A.D. Li Z. Klionsky D.J. 2008 Arp2 links autophagic machinery with the actin cytoskeleton. Mol. Biol. Cell. 19: 1962– 1975 10.1091/mbc.E07-09-0892 18287533 PMC2366845 · DOI
  26. Nair U. Jotwani A. Geng J. Gammoh N. Richerson D. Yen W.L. Griffith J. Nag S. Wang K. Moss T. 2011 SNARE proteins are required for macroautophagy. Cell. 146: 290– 302 10.1016/j.cell.2011.06.022 21784249 PMC3143362 · DOI
  27. Nakatogawa H. Ichimura Y. Ohsumi Y. 2007 Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell. 130: 165– 178 10.1016/j.cell.2007.05.021 17632063 · DOI
  28. Nakatogawa H. Suzuki K. Kamada Y. Ohsumi Y. 2009 Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nat. Rev. Mol. Cell Biol. 10: 458– 467 10.1038/nrm2708 19491929 · DOI
  29. Noda T. Kim J. Huang W.P. Baba M. Tokunaga C. Ohsumi Y. Klionsky D.J. 2000 Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. J. Cell Biol. 148: 465– 480 10.1083/jcb.148.3.465 10662773 PMC2174799 · DOI
  30. Ohashi Y. Munro S. 2010 Membrane delivery to the yeast autophagosome from the Golgi-endosomal system. Mol. Biol. Cell. 21: 3998– 4008 10.1091/mbc.E10-05-0457 20861302 PMC2982105 · DOI
  31. Orsi A. Razi M. Dooley H.C. Robinson D. Weston A.E. Collinson L.M. Tooze S.A. 2012 Dynamic and transient interactions of Atg9 with autophagosomes, but not membrane integration, are required for autophagy. Mol. Biol. Cell. 23: 1860– 1873 10.1091/mbc.E11-09-0746 22456507 PMC3350551 · DOI
  32. Reggiori F. Tucker K.A. Stromhaug P.E. Klionsky D.J. 2004 The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Dev. Cell. 6: 79– 90 10.1016/S1534-5807(03)00402-7 14723849 · DOI · Paper page
  33. Reggiori F. Monastyrska I. Shintani T. Klionsky D.J. 2005b The actin cytoskeleton is required for selective types of autophagy, but not nonspecific autophagy, in the yeast Saccharomyces cerevisiae. Mol. Biol. Cell. 16: 5843– 5856 10.1091/mbc.E05-07-0629 16221887 PMC1289426 · DOI · Paper page
  34. Seaman M.N.J. 2008 Endosome protein sorting: motifs and machinery. Cell. Mol. Life Sci. 65: 2842– 2858 10.1007/s00018-008-8354-1 18726175 PMC11131859 · DOI
  35. Sekito T. Kawamata T. Ichikawa R. Suzuki K. Ohsumi Y. 2009 Atg17 recruits Atg9 to organize the pre-autophagosomal structure. Genes Cells. 14: 525– 538 10.1111/j.1365-2443.2009.01299.x 19371383 · DOI
  36. Shintani T. Klionsky D.J. 2004 Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway. J. Biol. Chem. 279: 29889– 29894 10.1074/jbc.M404399200 15138258 PMC1712665 · DOI
  37. Sikorski R.S. Hieter P. 1989 A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics. 122: 19– 27 2659436 PMC1203683
  38. Suzuki K. Kirisako T. Kamada Y. Mizushima N. Noda T. Ohsumi Y. 2001 The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J. 20: 5971– 5981 10.1093/emboj/20.21.5971 11689437 PMC125692 · DOI
  39. Suzuki K. Kubota Y. Sekito T. Ohsumi Y. 2007 Hierarchy of Atg proteins in pre-autophagosomal structure organization. Genes Cells. 12: 209– 218 10.1111/j.1365-2443.2007.01050.x 17295840 · DOI
  40. Tokunaga M. Imamoto N. Sakata-Sogawa K. 2008 Highly inclined thin illumination enables clear single-molecule imaging in cells. Nat. Methods. 5: 159– 161 10.1038/nmeth1171 18176568 · DOI
  41. Tooze S.A. Yoshimori T. 2010 The origin of the autophagosomal membrane. Nat. Cell Biol. 12: 831– 835 10.1038/ncb0910-831 20811355 · DOI
  42. van Werven F.J. Timmers H.T. 2006 The use of biotin tagging in Saccharomyces cerevisiae improves the sensitivity of chromatin immunoprecipitation. Nucleic Acids Res. 34: e33 10.1093/nar/gkl003 16500888 PMC1383622 · DOI
  43. Yen W.L. Legakis J.E. Nair U. Klionsky D.J. 2007 Atg27 is required for autophagy-dependent cycling of Atg9. Mol. Biol. Cell. 18: 581– 593 10.1091/mbc.E06-07-0612 17135291 PMC1783788 · DOI
  44. Yildiz A. Forkey J.N. McKinney S.A. Ha T. Goldman Y.E. Selvin P.R. 2003 Myosin V walks hand-over-hand: single fluorophore imaging with 1.5-nm localization. Science. 300: 2061– 2065 10.1126/science.1084398 12791999 · DOI
  45. Ylä-Anttila P. Vihinen H. Jokitalo E. Eskelinen E.L. 2009 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy. 5: 1180– 1185 10.4161/auto.5.8.10274 19855179 · DOI
  46. Young A.R. Chan E.Y. Hu X.W. Köchl R. Crawshaw S.G. High S. Hailey D.W. Lippincott-Schwartz J. Tooze S.A. 2006 Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J. Cell Sci. 119: 3888– 3900 10.1242/jcs.03172 16940348 · DOI · Paper page

Authors
Yamamoto, H., Kakuta, S., Watanabe, T. M., Kitamura, A., Sekito, T., Kondo-Kakuta, C., Ichikawa, R., Kinjo, M., & Ohsumi, Y.
Affiliations
  • Tokyo Institute of Technology (JP)
  • RIKEN (JP)
  • Hokkaido University (JP)
  • Frontier Research Center, Tokyo Institute of Technology, Yokohama 226-8503, Japan 1
Corresponding author
Ohsumi, Yoshinori
ORCID
Venue
Journal of Cell Biology
Publisher
Rockefeller University Press
Published
2012-07-23
Volume
198
Issue
2
Pages
219-233
ISSN
  • 0021-9525 (ISSN-L)
  • 1540-8140
DOI
10.1083/jcb.201202061
PMC
PMC3410421
OpenAlex
W2017828774
Cited by
659
References
52
Citations by year
2026: 28 · 2025: 37 · 2024: 44 · 2023: 59 · 2022: 44 · 2021: 54 · 2020: 71 · 2019: 51 · 2018: 39 · 2017: 47 · 2016: 56 · 2015: 40 · 2014: 35 · 2013: 45 · 2012: 9
FWCI
30.89
Type
journal article
Language
en
Open access
Licence
cc-by-nc-sa
Locations
  • The Journal of Cell Biology (publishedVersion, cc-by-nc-sa)
  • PubMed Central (publishedVersion, cc-by-nc-sa)
  • PubMed (publishedVersion)
  • Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
Funders
Japan Society for the Promotion of Science (24770182, 23370072)
Topics
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
Keywords
Atg9, autophagosome formation, Golgi apparatus, starvation, yeast autophagy, membrane trafficking
MeSH terms
Autophagy-Related Proteins, Autophagy, Carrier Proteins, Golgi Apparatus, Intracellular Membranes, Membrane Proteins, Phagosomes, Saccharomyces cerevisiae, Starvation, Saccharomyces cerevisiae Proteins

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