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Peroxisomes pp 249–255Cite as

Experimental Systems to Study Yeast Pexophagy

Part of the Methods in Molecular Biology book series (MIMB,volume 1595)

Abstract

Peroxisome abundance is tightly regulated according to the physiological contexts, through regulations of both proliferation and degradation of the organelles. Here, we describe detailed methods to analyze processes for autophagic degradation of peroxisomes, termed pexophagy, in yeast organisms. The assay systems include a method for biochemical detection of pexophagy completion, and one for microscopic visualization of specialized membrane structures acting in pexophagy. As a model yeast organism utilized in studies of pexophagy, the methylotrophic yeast Komagataella phaffii (Pichia pastoris) is referred to in this chapter and related information on the studies with baker’s yeast (Saccharomyces cerevisiae) is also included. The described techniques facilitate elucidation of molecular machineries for pexophagy and understanding of peroxisome-selective autophagic pathways.

Key words

  • Autophagy
  • Atg8
  • Peroxisome
  • Pexophagy
  • Vacuole

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References

  1. Nazarko TY, Farre JC, Subramani S (2009) Peroxisome size provides insights into the function of autophagy-related proteins. Mol Biol Cell 20:3828–3839

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  2. Motley AM, Nuttall JM, Hettema EH (2012) Pex3-anchored Atg36 tags peroxisomes for degradation in Saccharomyces cerevisiae. EMBO J 31:2852–2868

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  3. Tanaka C, Tan LJ, Mochida K, Kirisako H, Koizumi M, Asai E, Sakoh-Nakatogawa M, Ohsumi Y, Nakatogawa H (2014) Hrr25 triggers selective autophagy-related pathways by phosphorylating receptor proteins. J Cell Biol 207:91–105

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  4. Kirisako T, Baba M, Ishihara N, Miyazawa K, Ohsumi M, Yoshimori T, Noda T, Ohsumi Y (1999) Formation process of autophagosome is traced with Apg8/Aut7p in yeast. J Cell Biol 147:435–446

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  5. Nazarko TY, Ozeki K, Till A, Ramakrishnan G, Lotfi P, Yan M, Subramani S (2014) Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy. J Cell Biol 204:541–557

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  6. Nazarko VY, Nazarko TY, Farre JC, Stasyk OV, Warnecke D, Ulaszewski S, Cregg JM, Sibirny AA, Subramani S (2011) Atg35, a micropexophagy-specific protein that regulates micropexophagic apparatus formation in Pichia pastoris. Autophagy 7:375–385

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  7. Yamashita S, Oku M, Wasada Y, Ano Y, Sakai Y (2006) PI4P-signaling pathway for the synthesis of a nascent membrane structure in selective autophagy. J Cell Biol 173:709–717

    CAS  CrossRef  PubMed  PubMed Central  Google Scholar 

  8. Markie D (2006) Markers, selection, and media in yeast artificial chromosome cloning. Methods Mol Biol (Clifton, NJ) 349:1–12

    CAS  Google Scholar 

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Acknowledgments

We thank K. Shimizu for Figure illustrations. This work was supported in part by Grants-in-Aid for Scientific Research (24247038, 25112518, 25116717, 26116007, and 15K14511 to Y.F.; 15K18501 to S.Y.; 16K07689 to M.O.; 16H01200 to Y.S.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and grants from the Takeda Science Foundation, the Naito Foundation, and the Japan Foundation for Applied Enzymology.

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Correspondence to Yukio Fujiki .

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Yamashita, Si., Oku, M., Sakai, Y., Fujiki, Y. (2017). Experimental Systems to Study Yeast Pexophagy. In: Schrader, M. (eds) Peroxisomes. Methods in Molecular Biology, vol 1595. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6937-1_24

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  • DOI: https://doi.org/10.1007/978-1-4939-6937-1_24

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6935-7

  • Online ISBN: 978-1-4939-6937-1

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