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Assessing Pexophagy in Mammalian Cells

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Peroxisomes

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

Abstract

In mammalian cells several hundred peroxisomes are maintained by a balance between the biogenesis and turnover by peroxisome homeostasis. Pexophagy, a form of autophagy specific for peroxisomes, is the main pathway for peroxisome degradation, but molecular mechanisms of mammalian pexophagy are largely unknown. This is due to the lack of well-established pexophagy-inducing conditions in mammalian cells. Recently, several conditions that induce pexophagy were described for mammalian cells, involving ubiquitin and adaptor proteins of autophagy. In this chapter, we describe the protocol for Pex3-induced pexophagy, the more readable and highly inducible pexophagy condition in mammalian cells.

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References

  1. de Duve C, Baudhuin P (1966) Peroxisomes (microbodies and related particles). Physiol Rev 46:323–357

    PubMed  Google Scholar 

  2. van den Bosch H, Schutgens RBH, Wanders RJA, Tager JM (1992) Biochemistry of peroxisomes. Annu Rev Biochem 61:157–197

    Article  PubMed  Google Scholar 

  3. Wanders RJA (2004) Metabolic and molecular basis of peroxisomal disorders: a review. Am J Med Genet A 126A:355–375

    Article  PubMed  Google Scholar 

  4. Fujiki Y (2000) Peroxisome biogenesis and peroxisome biogenesis disorders. FEBS Lett 476:42–46

    Article  CAS  PubMed  Google Scholar 

  5. Gould SJ, Valle D (2000) Peroxisome biogenesis disorders: genetics and cell biology. Trends Genet 16:340–345

    Article  CAS  PubMed  Google Scholar 

  6. Yokota S, Haraguchi CM, Oda T (2008) Induction of peroxisomal Lon protease in rat liver after di-(2-ethylhexyl)phthalate treatment. Histochem Cell Biol 129:73–83

    Article  CAS  PubMed  Google Scholar 

  7. Yokota S, Oda T, Fahimi HD (2001) The role of 15-lipoxygenase in disruption of the peroxisomal membrane and in programmed degradation of peroxisomes in normal rat liver. J Histochem Cytochem 49:613–622

    Article  CAS  PubMed  Google Scholar 

  8. Iwata J, Ezaki J, Komatsu M, Yokota S, Ueno T, Tanida I, Chiba T, Tanaka K, Kominami E (2006) Excess peroxisomes are degraded by autophagic machinery in mammals. J Biol Chem 281:4035–4041

    Article  CAS  PubMed  Google Scholar 

  9. Komatsu M, Waguri S, Ueno T, Iwata J, Murata S, Tanida I, Ezaki J, Mizushima N, Ohsumi Y, Uchiyama Y, Kominami E, Tanaka K, Chiba T (2005) Impairment of starvation-induced and constitutive autophagy in Atg7-deficient mice. J Cell Biol 169:425–434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Till A, Lakhani R, Burnett SF, Subramani S (2012) Pexophagy: the selective degradation of peroxisomes. Int J Cell Biol 2012:512721

    Article  PubMed  PubMed Central  Google Scholar 

  11. Farre J-C, Manjithaya R, Mathewson RD, Subramani S (2008) PpAtg30 tags peroxisomes for turnover by selective autophagy. Dev Cell 14:365–376

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Hara-Kuge S, Fujiki Y (2008) The peroxin Pex14p is involved in LC3-dependent degradation of mammalian peroxisomes. Exp Cell Res 314:3531–3541

    Article  CAS  PubMed  Google Scholar 

  14. Jiang L, Hara-Kuge S, Yamashita S, Fujiki Y (2015) Peroxin Pex14p is the key component for coordinated autophagic degradation of mammalian peroxisomes by direct binding to LC3-II. Genes Cells 20:36–49

    Article  CAS  PubMed  Google Scholar 

  15. Kim PK, Hailey DW, Mullen RT, Lippincott-Schwartz J (2008) Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes. Proc Natl Acad Sci U S A 105:20567–20574

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Deosaran E, Larsen KB, Hua R, Sargent G, Wang Y, Kim S, Lamark TM, Jauregui M, Law K, Lippincott-Schwartz J, Brech A, Johansen T, Kim PK (2013) NBR1 acts as an autophagy receptor for peroxisomes. J Cell Sci 126:939–952

    Article  CAS  PubMed  Google Scholar 

  17. Yamashita S, Abe K, Tatemichi Y, Fujiki Y (2014) The membrane peroxin PEX3 induces peroxisome-ubiquitination-linked pexophagy. Autophagy 10:1549–1564

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Nordgren M, Francisco T, Lismont C, Hennebel L, Brees C, Wang B, Van Veldhoven PP, Azevedo JE, Fransen M (2015) Export-deficient monoubiquitinated PEX5 triggers peroxisome removal in SV40 large T antigen-transformed mouse embryonic fibroblasts. Autophagy 11:1326–1340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Zhang J, Tripathi DN, Jing J, Alexander A, Kim J, Powell RT, Dere R, Tait-Mulder J, Lee J-H, Paull TT, Pandita RK, Charaka VK, Pandita TK, Kastan MB, LynWalker C (2015) ATM functions at the peroxisome to induce pexophagy in response to ROS. Nat Cell Biol 17:1259–1269

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Shimizu N, Itoh R, Hirono Y, Otera H, Ghaedi K, Tateishi K, Tamura S, Okumoto K, Harano T, Mukai S, Fujiki Y (1999) The peroxin Pex14p: cDNA cloning by functional complementation on a Chinese hamster ovary cell mutant, characterization, and functional analysis. J Biol Chem 274:12593–12604

    Article  CAS  PubMed  Google Scholar 

  21. Tsukamoto T, Yokota S, Fujiki Y (1990) Isolation and characterization of Chinese hamster ovary cell mutants defective in assembly of peroxisomes. J Cell Biol 110:651–660

    Article  CAS  PubMed  Google Scholar 

  22. Honsho M, Tamura S, Shimozawa N, Suzuki Y, Kondo N, Fujiki Y (1998) Mutation in PEX16 is causal in the peroxisome-deficient Zellweger syndrome of complementation group D. Am J Hum Genet 63:1622–1630

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgments

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.) 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., Fujiki, Y. (2017). Assessing Pexophagy in Mammalian Cells. 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_23

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  • DOI: https://doi.org/10.1007/978-1-4939-6937-1_23

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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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