Abstract
Budding yeast has been utilized as a model system for studying basic mechanisms of autophagy. The cytoplasm-to-vacuole targeting (Cvt) pathway, which delivers some vacuolar enzymes into the vacuole selectively and constitutively, is one of the most characterized examples of selective autophagy in budding yeast. Here we summarize the methods of X-ray crystallography, NMR, and other biophysical analyses to study the structural basis of the Cvt pathway.
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References
Mizushima N, Yoshimori T, Ohsumi Y (2011) The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 27:107–132
Lynch-Day MA, Klionsky DJ (2010) The Cvt pathway as a model for selective autophagy. FEBS Lett 584:1359–1366
Scott SV, Guan J, Hutchins MU, Kim J, Klionsky DJ (2001) Cvt19 is a receptor for the cytoplasm-to-vacuole targeting pathway. Mol Cell 7:1131–1141
Leber R, Silles E, Sandoval IV, Mazon MJ (2001) Yol082p, a novel CVT protein involved in the selective targeting of aminopeptidase I to the yeast vacuole. J Biol Chem 276:29210–29217
Shintani T, Huang WP, Stromhaug PE, Klionsky DJ (2002) Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway. Dev Cell 3:825–837
Suzuki K, Kamada Y, Ohsumi Y (2002) Studies of cargo delivery to the vacuole mediated by autophagosomes in Saccharomyces cerevisiae. Dev Cell 3:815–824
Noda NN et al (2008) Structural basis of target recognition by Atg8/LC3 during selective autophagy. Genes Cells 13:1211–1218
Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F (2010) Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34. J Biol Chem 285:30026–30033
Yorimitsu T, Klionsky DJ (2005) Atg11 links cargo to the vesicle-forming machinery in the cytoplasm to vacuole targeting pathway. Mol Biol Cell 16:1593–1605
Suzuki K, Kondo C, Morimoto M, Ohsumi Y (2010) Selective transport of alpha-mannosidase by autophagic pathways: identification of a novel receptor, Atg34p. J Biol Chem 285:30019–30025
Shintani T, Klionsky DJ (2004) Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway. J Biol Chem 279:29889–29894
Oda MN, Scott SV, Hefner-Gravink A, Caffarelli AD, Klionsky DJ (1996) Identification of a cytoplasm to vacuole targeting determinant in aminopeptidase I. J Cell Biol 132:999–1010
Yamasaki A et al (2016) Structural basis for receptor-mediated selective autophagy of aminopeptidase I aggregates. Cell Rep 16:19–27
Bertipaglia C et al (2016) Higher-order assemblies of oligomeric cargo receptor complexes form the membrane scaffold of the Cvt vesicle. EMBO Rep 17:1044–1060
Su MY et al (2015) Structure of yeast Ape1 and its role in autophagic vesicle formation. Autophagy 11:1580–1593
Yamasaki A, Noda NN (2017) Structural biology of the Cvt pathway. J Mol Biol 429:531–542
Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277–293
Guntert P (2004) Automated NMR structure calculation with CYANA. Methods Mol Biol 278:353–378
Adachi W, Suzuki NN, Fujioka Y, Suzuki K, Ohsumi Y, Inagaki F (2007) Crystallization of Saccharomyces cerevisiae aminopeptidase 1, the major cargo protein of the Cvt pathway. Acta Crystallogr Sect F Struct Biol Cryst Commun 63:200–203
Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307–326
Kabsch W (2010) Xds. Acta Crystallogr D Biol Crystallogr 66:125–132
Adams PD et al (2010) PHENIX: a comprehensive python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66:213–221
Pape T, Schneider TR (2004) HKL2MAP: a graphical user interface for macromolecular phasing with SHELX programs. J Appl Crystallogr 37:843–844
Sheldrick GM (2010) Experimental phasing with SHELXC/D/E: combining chain tracing with density modification. Acta Crystallogr D Biol Crystallogr 66:479–485
Brunger AT et al (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 54:905–921
Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallogr D Biol Crystallogr 66:486–501
Acknowledgments
This work was supported by Japan Society for the Promotion of Sciences KAKENHI [grant numbers 25111001, 25111004 to N.N.N., 17K18339 to A.Y.], CREST, Japan Science and Technology Agency [grant number JPMJCR13M7 to N.N.N.], and The Naito Foundation [to N.N.N.].
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Yamasaki, A., Watanabe, Y., Noda, N.N. (2019). Structural Studies of Selective Autophagy in Yeast. In: Ktistakis, N., Florey, O. (eds) Autophagy. Methods in Molecular Biology, vol 1880. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8873-0_4
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DOI: https://doi.org/10.1007/978-1-4939-8873-0_4
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