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Eukaryotic cells have two major protein degradation systems. One is the ubiquitin-proteasome system, which accounts for the selective degradation of most short-lived proteins. The other is the lysosomal system. Autophagy is the primary means for the degradation of cytoplasmic constituents in the lysosome. Although autophagy has been thought to be non-selective, recent studies revealed that autophagy can also be selective.

Figure 1. Intracellular protein degradation systems.
In the autophagy pathway, a small portion of the cytoplasm is enclosed by the isolation membrane (also called phagophore), resulting in the formation of an autophagosome. The outer membrane of the autophagosome fuses with the lysosome where the cytoplasm-derived materials are degraded. In the ubiquitin-proteasome pathway, polyubiquitinated proteins are selectively degraded by the 26S proteasome.

Figure 2. Autophagy detected by electron microscopy.
(Top) Embryonic stem cells under starvation conditions (by Dr. Akitsugu Yamamoto).
(Bottom) Mouse embryonic fibroblasts under starvation conditions (by Dr. Chieko Kishi-Itakura).

Research Directions

1. Molecular Mechanisms of Autophagy

Yeast genetic studies have identified 40 autophagy-related (ATG) genes. Approximately a half of these genes are required for autophagosome formation and conserved in higher eukaryotes. We are currently addressing some of the central questions remaining in the autophagy field and trying to elucidate the mechanisms of (1) regulation of autophagy, (2) initiation of autophagosome formation, (3) elongation of the autophagic membrane, (4) fusion between the autophagosome and lysosome, and (5) recognition of selective substrates.

Figure 3. Molecular mechanisms of autophagosome formation and maturation.

2. Development of methods for monitoring autophagy

To monitor autophagy in vivo, we have generated transgenic mice expressing the autophagosome marker GFP-LC3B. Using this autophagy-indicator mouse model, we have observed that autophagy is induced in various tissues following food withdrawal, during the early neonatal periods, and under some disease settings.

Figure 4. Monitoring autophagy using GFP-LC3.
(Top) Mouse embryonic fibroblasts stably expressing GFP-LC3B after starvation treatment. (Bottom) Autophagy induction in GFP-LC3B transgenic mice (available from RIKEN BRC)

3. Pathophysiological roles of autophagy in mammals

Using the autophagosome-indicator GFP-LC3 mice and various autophagy-deficient mouse models, we have shown that autophagy is important for maintenance of the amino acid pool during starvation and neonatal periods, and preimplantation development as an amino acid supplying system. Autophagy is also important for intracellular protein and organellar quality control to prevent neurodegeneration and tumorigenesis. More recently, we identified a human neurodegenerative disease (SENDA/BPAN), in which one of the core autophagy genes WDR45/WIPI4 (an Atg18 homolog) is mutated. Thus, autophagy plays important roles in various physiological and pathological processes.


Figure 5. Physiological roles of autophagy in mice.

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Mizushima Lab Materials

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For more details

Molecular mechanisms of autophagy

Mizushima, N., Yoshimori, T., Ohsumi, Y. The Role of Atg Proteins in Autophagosome Formation. Annu. Rev. Cell Dev. Biol. 27:107-32 (2011).

Pathophysiological roles of autophagy

Mizushima, N., Komatsu, M. Autophagy: renovation of cells and tissues. Cell 147:728-41 (2011).

Autophagy methods

Mizushima, N., Yoshimori, T. and Levine, B. Methods in mammalian autophagy research. Cell 140; 313-326 (2010)

Autophagy protocols



Selected publications

  1. Suzuki, H., Kaizuka, T., *Mizushima, N., *Noda, N. N. Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in mammalian autophagy initiation. Nat. Struct. Mol. Biol. 22: 572?580 (2015).
  2. Saitsu, H., Nishimura, T., Muramatsu, K., Kodera, H., Kumada, S., Sugai, K., Kasai-Yoshida, E., Sawaura, N., Nishida, H., Hoshino, A., Ryujin, F., Yoshioka, S., Nishiyama, K., Kondo, Y., Tsurusaki, Y., Nakashima, M., Miyake, N., Arakawa, H., Kato, M., *Mizushima, N., *Matsumoto, N. De novo mutations in the autophagy gene encoding WDR45 (WIPI4) cause static encephalopathy of childhood with neurodegeneration in adulthood. Nat. Genet. 45: 445-449 (2013).
  3. Itakura, E., Kishi-Itakura, C., Mizushima, N. The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes. Cell 151: 1256-1269 (2012).
  4. Takamura, A., Komatsu, M., Hara, T., Sakamoto, A., Kishi, C., Waguri, S., Eishi, Y., Hino, O., Tanaka, K., Mizushima, N. Autophagy-deficient mice develop multiple liver tumors. Genes Dev. 25: 795-800 (2011)
  5. Itakura, E., Mizushima, N. p62 targeting to the autophagosome formation site requires self-oligomerization but not LC3-binding. J. Cell Biol. 192: 17-27 (2011).
  6. Tsukamoto, S., Kuma, A., Murakami, M., Kishi, C., Yamamoto, A., Mizushima, N. Autophagy is essential for preimplantation development of mouse embryos. Science 321: 117-120 (2008)
  7. Hara, T., Takamura, A., Kishi, C., Iemura, S., Natsume, T., Guan, J.L., Mizushima, N. FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J. Cell Biol. 181: 497-510 (2008)
  8. Hara, T., Nakamura, K., Matsui, M., Yamamoto, A., Nakahara, Y., Suzuki-Migishima, R. Yokoyama, M., Mishima, K., Saito, I., Okano, H., Mizushima, N. Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 441, 885-889 (2006).
  9. Kuma, A., Hatano, M., Matsui, M., Yamamoto, A., Nakaya, H., Yoshimori, T., Ohsumi, Y., Tokuhisa, T., Mizushima, N. The role of autophagy during the early neonatal starvation period. Nature. 432, 1032-1036 (2004).
  10. Mizushima, N., Yamamoto, A., Matsui, M., Yoshimori, T. and Ohsumi, Y. In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol. Biol. Cell 15, 1101-1111 (2004).
  11. Mizushima, N., Yamamoto, A., Hatano, M., Kobayashi, Y., Kabeya, Y., Suzuki, K., Tokuhisa, T., Ohsumi, Y. and Yoshimori, T. Dissection of Autophagosome Formation using Apg5-Deficient Mouse Embryonic Stem Cells J. Cell Biol. 152, 657-667. (2001)
  12. Mizushima, N., Noda, T., Yoshimori, T., Tanaka, Y., Ishii, T., George, M. D., Klionsky, D. J., Ohsumi, M. and Ohsumi, Y. A protein conjugation system essential for autophagy Nature 395, 395-398. (1998)

Review articles

  1. Mizushima, N., Komatsu, M. Autophagy: renovation of cells and tissues. Cell. 147:728-41 (2011).
  2. Mizushima, N., Levine B. Autophagy in mammalian development and differentiation. Nat. Cell Biol. 12:823-830 (2010).
  3. Mizushima, N., Yoshimori, T. and Levine, B. Methods in mammalian autophagy research. Cell 140; 313-326 (2010)
  4. Mizushima, N., Levine, B., Cuervo, A.M., Klionsky, D.J. Autophagy fights disease through cellular self-digestion Nature 451:1069-1075 (2008)
  5. Mizushima, N. Autophagy: process and function Genes Dev. 21: 2861-2873 (2007)


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