Proteomic analyses of autophagy-related structures in yeast

2013 Fiscal Year Final Research Report

• Project/Area Number: 24770182
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Cell biology
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: YAMAMOTO Hayashi 東京工業大学, フロンティア研究機構, 特任助教 (80551283)
• Project Period (FY): 2012-04-01 – 2014-03-31
• Keywords: オートファジー / オートファゴソーム / 出芽酵母 / 膜動態 / 膜小胞 / プロテオーム解析

Research Abstract

Autophagy is a conserved degradation process, wherein autophagosomes are generated by cooperative actions of multiple autophagy-related (Atg) proteins. Previous studies using yeast Saccharomyces cerevisiae have provided various insights into the molecular basis of autophagy, however, the most intriguing issues in autophagy, namely, the origin of the autophagosomal membranes, remain to be elucidated. In this study, we succeeded to purify the autophagosomal membranes and the Atg9 vesicles, one of the autophagy-related membranes, and subjected them to proteomic analyses. These analyses showed that both the Atg9 vesicles and the autophagosomal membranes contain the TRAPPIII complex and its downstream factor Ypt1. Furthermore, we found that the Atg9 vesicles become part of the autophagosomal membranes, thereby recruiting the TRAPPIII complex and Ypt1 onto the autophagosomal membranes.

Research Products

• [Journal Article] Structural basis of starvation-induced assembly of the autophagy initiation complex (2014)
  • Author(s): Fujioka, Y., Suzuki, S.W., Yamamoto, H., Kondo-Kakuta, C., Kimura, Y., Hirano, H., Akada, R., Inagaki, F., Ohsumi, Y., and Noda, N.N.
  • Journal Title: Nat. Struct. Mol. Biol. Volume: (in press)
  • DOI: 10.1038/nsmb.2822
• [Journal Article] Different phosphatidylinositol 3-phosphate asymmetries in yeast and mammalian autophagosomes revealed by a new electron microscopic technique (2014)
  • Author(s): Fujimoto T., Yamamoto, H., and Ohsumi Y.
  • Journal Title: Autophagy Volume: Vol.10 Pages: 933-935
  • DOI: 10.1038/ncomms4207
• [Journal Article] Yeast and mammalian autophagosomes exhibit distinct phosphatidylinositol 3-phosphate asymmetries (2014)
  • Author(s): Cheng, J., Fujita, A., Yamamoto, H., Tatematsu, T., Kakuta, S., Obara, K., Ohsumi, Y., and Fujimoto, T.
  • Journal Title: Nat. Commun. Volume: Vol.5 Pages: 3207 (1-10)
  • DOI: 10.1038/ncomms4207
  • Peer Reviewed
• [Journal Article] Fine mapping of autophagy-related proteins during autophagosome formation in Saccharomyces cerevisiae (2013)
  • Author(s): Suzuki, K., Akioka, M., Kondo-Kakuta, C., Yamamoto, H., and Ohsumi, Y.
  • Journal Title: J. Cell Sci. Volume: Vol.126 Pages: 2534-2544
  • DOI: 10.1242/jcs.122960
  • Peer Reviewed
• [Journal Article] Atg9 vesicles recruit vesicle- tethering proteins Trs85 and Ypt1 to the autophagosome formation site (2012)
  • Author(s): Kakuta, S., Yamamoto, H., Negishi, L., Kondo-Kakuta, C., Hayashi, N., and Ohsumi, Y.
  • Journal Title: J. Biol. Chem. Volume: Vol.287 Pages: 44261-44269
  • DOI: 10.1074/jbc.M112.411454
  • Peer Reviewed
• [Journal Article] Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7. Nat. Struct (2012)
  • Author(s): Yamaguchi, M., Matoba, K., Sawada, R., Fujioka, Y., Nakatogawa, H., Yamamoto, H., Kobashigawa, Y., Hoshida, H., Akada, R., Ohsumi, Y., Noda, N.N., and Inagaki, F.
  • Journal Title: Mol. Biol. Volume: Vol.19 Pages: 1250-1256
  • DOI: 10.1038/nsmb.2451
  • Peer Reviewed
• [Journal Article] Membrane protein Rim21 plays a central role in sensing ambient pH in Saccharomyces cerevisiae (2012)
  • Author(s): Obara, K., Yamamoto, H., and Kihara, A.
  • Journal Title: J. Biol. Chem. Volume: Vol.287 Pages: 38473-38481
  • DOI: 10.1074/jbc.M112.394205
  • Peer Reviewed
• [Journal Article] Structure-based analyses reveal distinct binding sites for Atg2 and phosphoinositides in Atg18 (2012)
  • Author(s): Watanabe, Y., Kobayashi, T., Yamamoto, H., Hoshida, H., Akada, R., Inagaki, F., Ohsumi, Y., and Noda, N.N.
  • Journal Title: J. Biol. Chem. Volume: Vol.287 Pages: 31681-31690
  • DOI: 10.1074/jbc.M112.397570
  • Peer Reviewed
• [Journal Article] The autophagy-related protein kinase Atg1 interacts with the ubiquitin-like protein Atg8 via the Atg8 family interacting motif to facilitate autophagosome formation (2012)
  • Author(s): Nakatogawa, H., Ohbayashi, S., Sakoh- Nakatogawa, M., Kakuta, S., Suzuki, S.W., Kirisako, H., Kondo-Kakuta, C., Noda, N.N., Yamamoto, H., and Ohsumi, Y.
  • Journal Title: J. Biol. Chem. Volume: Vol.287 Pages: 28503-28507
  • DOI: 10.1074/jbc.C112.387514
  • Peer Reviewed
• [Journal Article] Atg9 vesicles are an important membrane source during early steps of autophagosome formation (2012)
  • Author(s): Yamamoto, H., Kakuta, S., Watanabe, T.M., Kitamura, A., Sekito, T., Kondo- Kakuta, C., Ichikawa, R., Kinjo, M., and Ohsumi, Y.
  • Journal Title: J. Cell Biol. Volume: Vol.198 Pages: 219-233
  • DOI: 10.1083/jcb.201202061
  • Peer Reviewed
• [Journal Article] Structural insights into Atg10-mediated formation of the autophagy-essential Atg12-Atg5 conjugate (2012)
  • Author(s): Yamaguchi, M., Noda, N.N., Yamamoto, H., Shima, T., Kumeta, H., Kobashigawa, Y., Akada, R., Ohsumi, Y., and Inagaki, F.
  • Journal Title: Structure Volume: Vol.20 Pages: 1244-1254
  • DOI: 10.1016/j.str.2012.04.018
  • Peer Reviewed
• [Presentation] Characterization and proteomic analysis of Atg9-containing structures in yeast (2012)
  • Author(s): 山本林、大隅良典
  • Organizer: 6th International Symposium on Autophagy
  • Place of Presentation: 沖縄
  • Year and Date: 20121028-1101
• [Presentation] オートファゴソーム形成に関わるAtg9ベシクルの細胞内動態とプロテオーム解析 (2012)
  • Author(s): 山本林、角田宗一郎、渡邉朋信、北村朗、大隅良典
  • Organizer: 第23回日本生体防御学会学術総会
  • Place of Presentation: 東京
  • Year and Date: 20120709-11
• [Remarks]
  • URL: http://www.ohsumilab.aro.iri.titech.ac.jp