Skip to main content
Book cover

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

This is a preview of subscription content, access via your institution.

Protocol
USD   49.95
Price excludes VAT (USA)
  • DOI: 10.1007/978-1-4939-6937-1_24
  • Chapter length: 7 pages
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
eBook
USD   109.00
Price excludes VAT (USA)
  • ISBN: 978-1-4939-6937-1
  • Instant PDF download
  • Readable on all devices
  • Own it forever
  • Exclusive offer for individuals only
  • Tax calculation will be finalised during checkout
Softcover Book
USD   139.99
Price excludes VAT (USA)
Hardcover Book
USD   199.99
Price excludes VAT (USA)
Learn about institutional subscriptions
Fig. 1
Fig. 2
Fig. 3

Springer Nature is developing a new tool to find and evaluate Protocols. Learn more

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 

Download references

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.

Author information

Authors and Affiliations

  1. Department of Cellular Physiology, Graduate School of Medical and Dental Sciences, Niigata University, 1-757 Asahimachi-dori, Chuo-ku, Niigata, 951-8510, Japan

    Shun-ichi Yamashita

  2. Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake, Sakyo-ku, Kyoto, 606-8502, Japan

    Masahide Oku & Yasuyoshi Sakai

  3. Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan

    Yukio Fujiki

Authors
  1. Shun-ichi Yamashita
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Masahide Oku
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Yasuyoshi Sakai
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yukio Fujiki
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Yukio Fujiki .

Editor information

Editors and Affiliations

  1. College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom

    Michael Schrader

Rights and permissions

Reprints and Permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

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

Download citation

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

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6935-7

  • Online ISBN: 978-1-4939-6937-1

  • eBook Packages: Springer Protocols