Skip to main content
Log in

Autophagy: A critical regulator of cellular metabolism and homeostasis

  • Minireview
  • Published:
Molecules and Cells

Abstract

Autophagy is a dynamic process by which cytosolic material, including organelles, proteins, and pathogens, are sequestered into membrane vesicles called autophagosomes, and then delivered to the lysosome for degradation. By recycling cellular components, this process provides a mechanism for adaptation to starvation. The regulation of autophagy by nutrient signals involves a complex network of proteins that include mammalian target of rapamycin, the class III phosphatidylinositol-3 kinase/Beclin 1 complex, and two ubiquitin-like conjugation systems. Additionally, autophagy, which can be induced by multiple forms of chemical and physical stress, including endoplasmic reticulum stress, and hypoxia, plays an integral role in the mammalian stress response. Recent studies indicate that, in addition to bulk assimilation of cytosol, autophagy may proceed through selective pathways that target distinct cargoes to autophagosomes. The principle homeostatic functions of autophagy include the selective clearance of aggregated protein to preserve proteostasis, and the selective removal of dysfunctional mitochondria (mitophagy). Additionally, autophagy plays a central role in innate and adaptive immunity, with diverse functions such as regulation of inflammatory responses, antigen presentation, and pathogen clearance. Autophagy can preserve cellular function in a wide variety of tissue injury and disease states, however, maladaptive or pro-pathogenic outcomes have also been described. Among the many diseases where autophagy may play a role include proteopathies which involve aberrant accumulation of proteins (e.g., neurodegenerative disorders), infectious diseases, and metabolic disorders such as diabetes and metabolic syndrome. Targeting the autophagy pathway and its regulatory components may eventually lead to the development of therapeutics.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  • Bachar-Wikstrom, E., Wikstrom, J.D., Ariav, Y., Tirosh, B., Kaiser, N., Cerasi, E., and Leibowitz, G. (2013). Stimulation of autophagy improves endoplasmic reticulum stress-induced diabetes. Diabetes 62, 1227–1237.

    Article  PubMed  CAS  Google Scholar 

  • Bodas, M., Tran, I., and Vij, N. (2012). Therapeutic strategies to correct proteostasis-imbalance in chronic obstructive lung diseases. Curr. Mol. Med. 12, 807–814.

    Article  PubMed  CAS  Google Scholar 

  • Boya, P., González-Polo, R.A., Casares, N., Perfettini, J.L., Dessen, P., Larochette, N., Métivier, D., Meley, D., Souquere, S., Yoshimori, T., et al. (2005). Inhibition of macroautophagy triggers apoptosis. Mol. Cell. Biol. 25, 1025–1040.

    Article  PubMed  CAS  Google Scholar 

  • Campbell, G.R., and Spector, S.A. (2011). Hormonally active vitamin D3 (1alpha, 25-dihydroxycholecalciferol) triggers autophagy in human macrophages that inhibits HIV-1 infection. J. Biol. Chem. 286, 18890–18902.

    Article  PubMed  CAS  Google Scholar 

  • Chan, E.Y. (2012). Regulation and function of uncoordinated-51 like kinase proteins. Antioxid. Redox Signal. 17, 775–785.

    Article  PubMed  CAS  Google Scholar 

  • Checroun, C., Wehrly, T.D., Fischer, E.R., Hayes, S.F., and Celli, J. (2006). Autophagy-mediated reentry of Francisella tularensis into the endocytic compartment after cytoplasmic replication. Proc. Natl. Acad. Sci. USA 103, 14578–14583.

    Article  PubMed  CAS  Google Scholar 

  • Chen, Z.H., Kim, H.P., Sciurba, F.C., Lee, S.J., Feghali-Bostwick, C., Stolz, D.B., Dhir, R., Landreneau, R.J., Schuchert, M.J., Yousem, S.A, et al. (2008). Egr-1 regulates autophagy in cigarette smoke-induced chronic obstructive pulmonary disease. PLoS One 3, e3316.

    Article  PubMed  CAS  Google Scholar 

  • Choi, A.M., Ryter, S.W., and Levine, B. (2013). Autophagy in human health and disease. N. Engl. J. Med. 368, 651–662.

    Article  PubMed  CAS  Google Scholar 

  • Clausen, T.H., Lamark, T., Isakson, P., Finley, K., Larsen, K.B., Brech, A., Øvervatn, A., Stenmark, H., Bjørkøy, G., Simonsen, A., et al. (2010). p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy. Autophagy 6, 330–344.

    Article  PubMed  CAS  Google Scholar 

  • Dagda, R.K., Cherra, S.J., Kulich, S.M., Tandon, A., Park, D., and Chu, C.T. (2009). Loss of PINK1 function promotes mitophagy through effects on oxidative stress and mitochondrial fission. J. Biol. Chem. 284, 13843–13855.

    Article  PubMed  CAS  Google Scholar 

  • Deretic, V., and Levine, B. (2009). Autophagy, immunity, and microbial adaptations. Cell Host Microbe. 5, 527–549.

    Article  PubMed  CAS  Google Scholar 

  • Elliott, P.R., Bilton, D., and Lomas, D.A. (1998). Lung polymers in Z alpha1-antitrypsin deficiency-related emphysema. Am. J. Respir. Cell Mol. Biol. 18, 670–674.

    Article  PubMed  CAS  Google Scholar 

  • Ganley, I.G., Lam, D.H., Wang, J., Ding, X., Chen, S., and Jiang, X. (2009). ULK1.ATG13.FIP200 complex mediates mTOR signaling and is essential for autophagy. J. Biol. Chem. 284, 12297–12305.

    Article  PubMed  CAS  Google Scholar 

  • Geisler, S., Holmström, K.M., Skujat, D., Fiesel, F.C., Rothfuss, O.C., Kahle, P.J., and Springer, W. (2010). PINK1/Parkin-mediated mitophagy is dependent on VDAC1 and p62/SQSTM1. Nat. Cell Biol. 12, 119–131.

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez, C.D., Lee, M.S., Marchetti, P., Pietropaolo, M., Towns, R., Vaccaro, M.I., Watada, H., and Wiley, J.W. (2011). The emerging role of autophagy in the pathophysiology of diabetes mellitus. Autophagy 7, 2–11.

    Article  PubMed  CAS  Google Scholar 

  • Granell, S., Baldini, G., Mohammad, S., Nicolin, V., Narducci, P., Storrie, B., and Baldini, G. (2008). Sequestration of mutated alpha1-antitrypsin into inclusion bodies is a cell-protective mechanism to maintain endoplasmic reticulum function. Mol. Biol. Cell 19, 572–586.

    Article  PubMed  CAS  Google Scholar 

  • Gutierrez, M.G., Vazquez, C.L., Munafo, D.B., Zoppino, F.C., Berón, W., Rabinovitch, M., and Colombo, M.I. (2005). Autophagy induction favours the generation and maturation of the Coxiellareplicative vacuoles. Cell. Microbiol. 7, 981–993.

    Article  PubMed  CAS  Google Scholar 

  • Hara, T., Nakamura, K., Matsui, M., Yamamoto, A., Nakahara, Y., Suzuki-Migishima, R., Yokoyama, M., Mishima, K., Saito, I., Okano, H., et al. (2006). Suppression of basal autophagy in neural cells causes neurodegenerative disease in mice. Nature 44, 885–889.

    Article  CAS  Google Scholar 

  • He, C., and Levine, B. (2010). The Beclin 1 interactome. Curr. Opin. Cell Biol. 22, 140–149.

    Article  PubMed  CAS  Google Scholar 

  • He, C., Bassik, M.C., Moresi, V., Sun, K., Wei, Y., Zou, Z., An, Z., Loh, J., Fisher, J., Sun, Q., et al. (2012). Exercise-induced BCL2-regulated autophagy is required for muscle glucose homeostasis. Nature 481, 511–515.

    Article  PubMed  CAS  Google Scholar 

  • Hidvegi, T., Ewing, M., Hale, P., Dippold, C., Beckett, C., Kemp, C., Maurice, N., Mukherjee, A., Goldbach, C., Watkins, S., et al. (2010). An autophagy-enhancing drug promotes degradation of mutant alpha1-antitrypsin Z and reduces hepatic fibrosis. Science 329, 229–232.

    Article  PubMed  CAS  Google Scholar 

  • Hosokawa, N., Hara, T., Kaizuka, T., Kishi, C., Takamura, A., Miura, Y., Iemura, S., Natsume, T., Takehana, K., Yamada, N., et al. (2009). Nutrient-dependent mTORC1 association with the ULK1-Atg13-FIP200 complex required for autophagy. Mol. Biol. Cell 20, 1981–1991.

    Article  PubMed  CAS  Google Scholar 

  • Hsu, L.J., Hsu, L.J., Sagara, Y., Arroyo, A., Rockenstein, E., Sisk, A., Mallory, M., Wong, J., Takenouchi, T., Hashimoto, M., et al. (2000). alpha-synuclein promotes mitochondrial deficit and oxidative stress. Am. J. Pathol. 157, 401–410.

    Article  PubMed  CAS  Google Scholar 

  • Ichimura, Y., and Komatsu, M. (2010). Selective degradation of p62 by autophagy. Semin. Immunopathol. 32, 431–436.

    Article  PubMed  Google Scholar 

  • Inoki, K., Zhu, T., and Guan, K.L. (2003). TSC2 mediates cellular energy response to control cell growth and survival. Cell 115, 577–590.

    Article  PubMed  CAS  Google Scholar 

  • Imarisio, S., Carmichael, J., Korolchuk, V., Chen, C.W., Saiki, S., Rose, C., Krishna, G., Davies, J.E., Ttofi, E., Underwood, B.R., et al. (2008). Huntington’s disease: from pathology and genetics to potential therapies. Biochem. J. 412, 191–209.

    Article  PubMed  CAS  Google Scholar 

  • Itakura, E., Kishi, C., Inoue, K., and Mizushima, N. (2008). Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol. Biol. Cell 19, 5360–5372.

    Article  PubMed  CAS  Google Scholar 

  • Jellinger, K.A. (2010). Basic mechanisms of neurodegeneration: a critical update. J. Cell. Mol. Med. 14, 457–487.

    Article  PubMed  CAS  Google Scholar 

  • Johansen, T., and Lamark, T. (2011). Selective autophagy mediated by autophagic adapter proteins. Autophagy 7, 279–296.

    Article  PubMed  CAS  Google Scholar 

  • Jung, H.S., and Lee, M.S. (2010). Role of autophagy in diabetes and mitochondria. Ann. N Y Acad. Sci. 1201, 79–83.

    Article  PubMed  CAS  Google Scholar 

  • Jung, C.H., Jun, C.B., Ro, S.H., Kim, Y.M., Otto, N.M., Cao, J., Kundu, M., and Kim, D.H. (2009). ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol. Biol. Cell 20, 1992–2003.

    Article  PubMed  CAS  Google Scholar 

  • Jung, C.H., Ro, S.H., Cao, J., Otto, N.M., and Kim, D.H. (2010). mTOR regulation of autophagy. FEBS Lett. 584, 1287–1295.

    Article  PubMed  CAS  Google Scholar 

  • Kabeya, Y., Mizushima, N., Ueno, T., Yamamoto, A., Kirisako, T., Noda, T., Kominami, E., Ohsumi, Y., and Yoshimori, T. (2000). LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J. 19, 5720–5728.

    Article  PubMed  CAS  Google Scholar 

  • Kabeya, Y., Mizushima, N., Yamamoto, A., Oshitani-Okamoto, S., Ohsumi, Y., and Yoshimori T. (2004). LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. J. Cell Sci. 117, 2805–2812.

    Article  PubMed  CAS  Google Scholar 

  • Kamimoto, T., Shoji, S., Hidvegi, T., Mizushima, N., Umebayashi, K., Perlmutter, D.H., and Yoshimori, T. (2006). Intracellular inclusions containing mutant alpha1-antitrypsin Z are propagated in the absence of autophagic activity. J. Biol. Chem. 281, 4467–4476.

    Article  PubMed  CAS  Google Scholar 

  • Kaushik, S., Bandyopadhyay, U., Sridhar, S., Kiffin, R., Martinez-Vicente, M. Kon, M., Orenstein, S.J., Wong, E., and Cuervo, A.M. (2011a). Chaperone-mediated autophagy at a glance. J. Cell Sci. 124, 495–499.

    Article  PubMed  CAS  Google Scholar 

  • Kaushik, S., Rodriguez-Navarro, J.A., Arias, E., Kiffin, R., Sahu, S., Schwartz, G.J., Cuervo, A.M., and Singh, R. (2011b). Autophagy in hypothalamic AgRP neurons regulates food intake and energy balance. Cell Metab. 14, 173–183.

    Article  PubMed  CAS  Google Scholar 

  • Kawaguchi, Y., Kovacs, J.J., McLaurin, A., Vance, J.M., Ito, A., and Yao, T.P. (2003). The deacetylase HDAC6 regulates aggresome formation and cell viability in response to misfolded protein stress. Cell 115, 727–738.

    Article  PubMed  CAS  Google Scholar 

  • Ke, P.Y., and Chen, S.S. (2011). Activation of the unfolded protein response and autophagy after hepatitis C virus infection suppresses innate antiviral immunity in vitro. J. Clin. Invest. 121, 37–56.

    Article  PubMed  CAS  Google Scholar 

  • Kim, J., Kundu, M., Viollet, B., and Guan, K.L. (2011). AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat. Cell Biol. 13, 132–141.

    Article  PubMed  CAS  Google Scholar 

  • Kirkin, V., Lamark, T., Sou, Y.S., Bjørkøy, G., Nunn, J.L., Bruun, J.A., Shvets, E., McEwan, D.G., Clausen, T.H., Wild, P., et al. (2009). A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol. Cell 33, 505–516.

    Article  PubMed  CAS  Google Scholar 

  • Komatsu, M., Waguri, S., Chiba, T., Murata, S., Iwata, J., Tanida, I., Ueno, T., Koike, M., Uchiyama, Y., Kominami, E., et al. (2006). Loss of autophagy in the central nervous system causes neurodegeneration in mice. Nature 441, 880–884.

    Article  PubMed  CAS  Google Scholar 

  • Kroemer, G., Mariño, G., and Levine, B. (2010). Autophagy and the integrated stress response. Mol. Cell 40, 280–293.

    Article  PubMed  CAS  Google Scholar 

  • Kyei, G.B., Dinkins, C., Davis, A.S., Roberts, E., Singh, S.B., Dong, C., Wu, L., Kominami, E., Ueno, T., Yamamoto, A., et al. (2009). Autophagy pathway intersects with HIV-1 biosynthesis and regulates viral yields in macrophages. J. Cell Biol. 186, 255–268.

    Article  PubMed  CAS  Google Scholar 

  • Lamark, T., and Johansen, T. (2012). Aggrephagy: selective disposal of protein aggregates by macroautophagy. Int. J. Cell Biol. 2012, 736905.

    PubMed  Google Scholar 

  • Lee, J.Y., Koga, H., Kawaguchi, Y., Tang, W., Wong, E., Gao, Y.S., Pandey, U.B., Kaushik, S., Tresse, E., Lu, J., et al. (2010). HDAC6 controls autophagosome maturation essential for ubiquitinselective quality-control autophagy. EMBO J. 29, 969–980.

    Article  PubMed  CAS  Google Scholar 

  • Levine, B., and Kroemer, G. (2008). Autophagy in the pathogenesis of disease. Cell 132, 27–42.

    Article  PubMed  CAS  Google Scholar 

  • Levine, B., Mizushima, N., and Virgin, H.W. (2011). Autophagy in immunity and inflammation. Nature 469, 323–335.

    Article  PubMed  CAS  Google Scholar 

  • Li, J., Liu, Y., Wang, Z., Liu, K., Wang, Y., Liu, J., Ding, H., and Yuan, Z. (2011). Subversion of cellular autophagy machinery by hepatitis B virus for viral envelopment. J. Virol. 85, 6319–6333.

    Article  PubMed  CAS  Google Scholar 

  • Liang, X.H., Jackson, S., Seaman, M., Brown, K., Kempkes, B., Hibshoosh, H., and Levine, B. (1999). Induction of autophagy and inhibition of tumorigenesis by beclin 1. Nature 402, 672–676.

    Article  PubMed  CAS  Google Scholar 

  • Liu, K., and Czaja, M.J. (2013). Regulation of lipid stores and metabolism by lipophagy. Cell Death Differ. 20, 3–11.

    Article  PubMed  CAS  Google Scholar 

  • Liu, L., Feng, D., Chen, G., Chen, M., Zheng, Q., Song, P., Ma, Q., Zhu, C., Wang, R., Qi, W., et al. (2012). Mitochondrial outermembrane protein FUNDC1 mediates hypoxia-induced mitophagy in mammalian cells. Nat. Cell Biol. 14, 177–185.

    Article  PubMed  CAS  Google Scholar 

  • Luciani, A., Villella, V.R., Esposito, S., Brunetti-Pierri, N., Medina, D., Settembre, C., Gavina, M., Pulze, L., Giardino, I., Pettoello-Mantovani, M., et al. (2010). Defective CFTR induces aggresome formation and lung inflammation in cystic fibrosis through ROS-mediated autophagy inhibition. Nat. Cell Biol. 12, 863–875.

    Article  PubMed  CAS  Google Scholar 

  • Ma, J.F., Huang, Y., Chen, S.D., and Halliday, G. (2010). Immunohistochemical evidence for macroautophagy in neurones and endothelial cells in Alzheimer’s disease. Neuropathol. Appl. Neurobiol. 36, 312–319.

    Article  PubMed  CAS  Google Scholar 

  • Maiuri, M.C., Zalckvar, E., Kimchi, A., and Kroemer, G. (2007). Selfeating and self-killing: crosstalk between autophagy and apoptosis. Nat. Rev. Mol. Cell Biol. 8, 741–752.

    Article  PubMed  CAS  Google Scholar 

  • Marciniak, S.J., and Lomas, D.A. (2010). Alpha1-antitrypsin deficiency and autophagy. N. Engl. J. Med. 363, 1863–1864.

    Article  PubMed  CAS  Google Scholar 

  • Martinez-Vicente, M., Talloczy, Z., Wong, E., Tang, G., Koga, H., Kaushik, S., de Vries, R., Arias, E., Harris, S., Sulzer, D., et al. (2010). Cargo recognition failure is responsible for inefficient autophagy in Huntington’s disease. Nat. Neurosci. 13, 567–576.

    Article  PubMed  CAS  Google Scholar 

  • Metcalf, D.J., García-Arencibia, M., Hochfeld, W.E., and Rubinsztein, D.C. (2012). Autophagy and misfolded proteins in neurodegeneration. Exp. Neurol. 238, 22–28.

    Article  PubMed  CAS  Google Scholar 

  • Mihaylova, M.M., and Shaw, R.J. (2011). The AMPK signalling pathway coordinates cell growth, autophagy and metabolism. Nat. Cell Biol. 13, 1016–1023.

    Article  PubMed  CAS  Google Scholar 

  • Min, T., Bodas, M., Mazur, S., and Vij, N. (2011). Critical role of proteostasis-imbalance in pathogenesis of COPD and severe emphysema. J. Mol. Med. (Berl.) 89, 577–593.

    Article  CAS  Google Scholar 

  • Mizushima, N. (2010). The role of the Atg1/ULK1 complex in autophagy regulation. Curr. Opin. Cell Biol. 22, 132–139.

    Article  PubMed  CAS  Google Scholar 

  • Mizushima, N., and Komatsu, M. (2011). Autophagy: renovation of cells and tissues. Cell 147, 728–741.

    Article  PubMed  CAS  Google Scholar 

  • Mizushima, N., Levine, B., Cuervo, A.M., and Klionsky, D.J. (2008). Autophagy fights disease through cellular self-digestion. Nature 451, 1069–2075.

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Mornex, J.F., Chytil-Weir, A., Martinet, Y., Courtney, M., LeCocq, J.P., and Crystal, R.G. (1986). Expression of the alpha-1-antitrypsin gene in mononuclear phagocytes of normal and alpha-1-antitrypsin-deficient individuals. J. Clin. Invest. 77, 1952–1961.

    Article  PubMed  CAS  Google Scholar 

  • Morris, H.R. (2005). Genetics of Parkinson’s disease. Ann. Med. 37, 86–96.

    Article  PubMed  CAS  Google Scholar 

  • Nakahira, K., Haspel, J.A., Rathinam, V.A., Lee, S.J., Dolinay, T., Lam, H.C., Englert, J.A., Rabinovitch, M., Cernadas, M., Kim, H.P., et al. (2011). Autophagy proteins regulate innate immune responses by inhibiting the release of mitochondrial DNA mediated by the NALP3 inflammasome. Nat. Immunol. 12, 222–230.

    Article  PubMed  CAS  Google Scholar 

  • Narendra, D., Tanaka, A., Suen, D.F., and Youle, R.J. (2008). Parkin is recruited selectively to impaired mitochondria and promotes their autophagy. J. Cell Biol. 183, 795–803.

    Article  PubMed  CAS  Google Scholar 

  • Orvedahl, A., Sumpter, R., Xiao, G., Ng, A., Zou, Z., Tang, Y., Narimatsu, M., Gilpin, C., Sun, Q., Roth, M., et al. (2011). Imagebased genome-wide siRNA screen identifies selective autophagy factors. Nature 480, 113–117.

    Article  PubMed  CAS  Google Scholar 

  • Pattingre, S., Tassa, A., Qu, X., Garuti, R., Liang, X.H., Mizushima, N., Packer, M., Schneider, M.D., and Levine, B. (2005). Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell 122, 927–939.

    Article  PubMed  CAS  Google Scholar 

  • Pickford, F., Masliah, E., Britschgi, M., Lucin, K., Narasimhan, R., Jaeger, P.A., Small, S., Spencer, B., Rockenstein, E., and Levine, B. (2008). The autophagy-related protein beclin 1 shows reduced expression in early Alzheimer disease and regulates amyloid beta accumulation in mice. J. Clin. Invest. 118, 2190.

    PubMed  CAS  Google Scholar 

  • Ranes, J., and Stoller, J.K. (2005). A review of alpha-1 antitrypsin deficiency. Semin. Respir. Crit. Care Med. 26, 154–166.

    Article  PubMed  Google Scholar 

  • Ravikumar, B., Duden, R., and Rubinsztein, D.C. (2002). Aggregateprone proteins with polyglutamine and polyalanine expansions are degraded by autophagy. Hum. Mol. Genet. 11, 107–117

    Article  Google Scholar 

  • Ravikumar, B., Vacher, C., Berger, Z., Davies, J.E., Luo, S., Oroz, L.G., Scaravilli, F., Easton, D.F., Duden, R., O’Kane, C.J., et al. (2004). Inhibition of mTOR induces autophagy and reduces toxicity of polyglutamine expansions in fly and mouse models of Huntington disease. Nat. Genet. 36, 585–595.

    Article  PubMed  CAS  Google Scholar 

  • Ravikumar, B., Sarkar, S., Davies, J.E., Futter, M., Garcia-Arencibia, M., Green-Thompson, Z.W., Jimenez-Sanchez, M., Korolchuk, V.I., Lichtenberg, M., Luo, S., et al. (2010). Regulation of mammalian autophagy in physiology and pathophysiology. Physiol. Rev. 90, 1383–1435.

    Article  PubMed  CAS  Google Scholar 

  • Rubinsztein, D.C., Codogno, P., and Levine, B. (2012). Autophagy modulation as a potential therapeutic target for diverse diseases. Nat. Rev. Drug Discov. 11, 709–730.

    Article  PubMed  CAS  Google Scholar 

  • Santambrogio, L., and Cuervo, A.M. (2011). Chasing the elusive mammalian microautophagy. Autophagy 7, 652–654.

    Article  PubMed  Google Scholar 

  • Satoo, K., Noda, N.N., Kumeta, H., Fujioka, Y., Mizushima, N., Ohsumi, Y., and Inagaki, F. (2009). The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. EMBO J. 28, 1341–1350.

    Article  PubMed  CAS  Google Scholar 

  • Schaeffer, V., Lavenir, I., Ozcelik, S., Tolnay, M., Winkler, D.T., and Goedert, M. (2012). Stimulation of autophagy reduces neurodegeneration in a mouse model of human tauopathy. Brain 135, 2169–2177.

    Article  PubMed  Google Scholar 

  • Schreiber, A., and Peter, M. (2013). Substrate recognition in selective autophagy and the ubiquitin-proteasome system. Biochim. Biophys. Acta pii: S0167-4889(13)00120-1.

    Google Scholar 

  • Shaid, S., Brandts, C.H., Serve, H., and Dikic, I. (2013). Ubiquitination and selective autophagy. Cell Death Differ. 20, 21–30.

    Article  PubMed  CAS  Google Scholar 

  • Shibata, M., Lu, T., Furuya, T., Degterev, A., Mizushima, N., Yoshimori, T., MacDonald, M., Yankner, B., and Yuan, J. (2006). Regulation of intracellular accumulation of mutant Huntingtin by Beclin 1. J. Biol. Chem. 281, 14474–14485.

    Article  PubMed  CAS  Google Scholar 

  • Singh, R., Kaushik, S., Wang, Y., Xiang, Y., Novak, I., Komatsu, M., Tanaka, K., Cuervo, A.M., and Czaja, M.J. (2009a). Autophagy regulates lipid metabolism. Nature 458, 1131–11135.

    Article  PubMed  CAS  Google Scholar 

  • Singh, R., Xiang, Y., Wang, Y., Baikati, K., Cuervo, A.M., Luu, Y.K., Tang, Y., Pessin, J.E., Schwartz, G.J., and Czaja, M.J. (2009b). Autophagy regulates adipose mass and differentiation in mice. J. Clin. Invest. 119, 3329–3339.

    Article  PubMed  CAS  Google Scholar 

  • Spencer, B., Potkar, R., Trejo, M., Rockenstein, E., Patrick, C., Gindi, R., Adame, A., Wyss-Coray, T., and Masliah, E. (2009). Beclin1 gene transfer activates autophagy and ameliorates the neurodegenerative pathology in α-synuclein models of Parkinson’s and Lewy body diseases. J. Neurosci. 29, 13578–13588.

    Article  PubMed  CAS  Google Scholar 

  • Starr, T., Child, R., Wehrly, T.D., Hansen, B., Hwang, S., López-Otin, C., Virgin, H.W., and Celli, J. (2012). Selective subversion of autophagy complexes facilitates completion of the Brucella intracellular cycle. Cell Host Microbe 11, 33–45.

    Article  PubMed  CAS  Google Scholar 

  • Thurston, T.L., Ryzhakov, G., Bloor, S., von Muhlinen, N., and Randow, F. (2009). The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat. Immunol. 10, 1215–1221.

    Article  PubMed  CAS  Google Scholar 

  • Tian, Y., Sir, D., Kuo, C.F., Ann, D.K., and Ou, J.H. (2011). Autophagy required for hepatitis B virus replication in transgenic mice. J. Virol. 85, 13453–13456.

    Article  PubMed  CAS  Google Scholar 

  • Trancikova, A., Tsika, E., and Moore, D.J. (2012). Mitochondrial dysfunction in genetic animal models of Parkinson’s disease. Antioxid. Redox Signal. 216, 896–919.

    Article  CAS  Google Scholar 

  • Vander Haar, E., Lee, S.I., Bandhakavi, S., Griffin, T.J., and Kim, D.H. (2007). Insulin signalling to mTOR mediated by the Akt/PKB substrate PRAS40. Nat. Cell Biol. 9, 316–323.

    Article  CAS  Google Scholar 

  • Vives-Bauza, C., Zhou, C., Huang, Y., Cui, M., de Vries, R.L., Kim, J., May, J., Tocilescu, M.A., Liu, W., Ko, H.S., et al. (2010). PINK1-dependent recruitment of Parkin to mitochondria in mitophagy. Proc. Natl. Acad. Sci. USA 107, 378–383.

    Article  PubMed  CAS  Google Scholar 

  • Wang, R.C., Wei, Y., An, Z., Zou, Z., Xiao, G., Bhagat, G., White, M., Reichelt, J., and Levine, B. (2012). Akt-mediated regulation of autophagy and tumorigenesis through Beclin 1 phosphorylation. Science 338, 956–959.

    Article  PubMed  CAS  Google Scholar 

  • Wild, P., Farhan, H., McEwan, D.G., Wagner, S., Rogov, V.V., Brady, N.R., Richter, B., Korac, J., Waidmann, O., Choudhary, C., et al. (2011). Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science 333, 228–233.

    Article  PubMed  CAS  Google Scholar 

  • Winslow, A.R., Chen, C.W., Corrochano, S., Acevedo-Arozena, A., Gordon, D.E., Peden, A.A., Lichtenberg, M., Menzies, F.M., Ravikumar, B., Imarisio, S., et al. (2010). α-Synuclein impairs macroautophagy: implications for Parkinson’s disease. J. Cell Biol. 190, 1023–1037.

    Article  PubMed  CAS  Google Scholar 

  • Wong, E., and Cuervo, A.M. (2010). Autophagy gone awry in neurodegenerative diseases. Nat. Neurosci. 13, 805–811.

    Article  PubMed  CAS  Google Scholar 

  • Wong, P.M., Puente, C., Ganley, I.G., and Jiang, X. (2013). The ULK1 complex: sensing nutrient signals for autophagy activation. Autophagy 9, 124–137.

    Article  PubMed  CAS  Google Scholar 

  • Yamamoto, A., and Simonsen, A. (2011). The elimination of accumulated and aggregated proteins: a role for aggrephagy in neurodegeneration. Neurobiol. Dis. 43, 17–28.

    Article  PubMed  CAS  Google Scholar 

  • Yamamoto, H., Kakuta, S., Watanabe, T.M., Kitamura, A., Sekito, T., Kondo-Kakuta, C., Ichikawa, R., Kinjo, M., and Ohsumi, Y. (2012). Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J. Cell Biol. 198, 219–233.

    Article  PubMed  CAS  Google Scholar 

  • Yang, Z., and Klionsky, D.J. (2010a). Eaten alive: a history of macroautophagy. Nat. Cell Biol. 12, 814–822.

    Article  PubMed  CAS  Google Scholar 

  • Yang, Z., and Klionsky, D.J. (2010b). Mammalian autophagy: core molecular machinery and signaling regulation. Curr. Opin. Cell Biol. 22, 124–131.

    Article  PubMed  CAS  Google Scholar 

  • Yang, L., Li, P., Fu, S., Calay, E.S., and Hotamisligil, G.S. (2010). Defective hepatic autophagy in obesity promotes ER stress and causes insulin resistance. Cell Metab. 11, 467–478.

    Article  PubMed  CAS  Google Scholar 

  • Yano, T., and Kurata, S. (2011). Intracellular recognition of pathogens and autophagy as an innate immune host defence. J. Biochem. 150, 143–149.

    Article  PubMed  CAS  Google Scholar 

  • Youle, R.J., and Narendra, D.P. (2011). Mechanisms of mitophagy. Nat. Rev. Mol. Cell Biol. 12, 9–14.

    Article  PubMed  CAS  Google Scholar 

  • Young, A.R., Chan, E.Y., Hu, X.W., Köchl, R., Crawshaw, S.G., High, S., Hailey, D.W., Lippincott-Schwartz, J., and Tooze, S.A. (2006). Starvation and ULK1-dependent cycling of mammalian Atg9 between the TGN and endosomes. J. Cell Sci. 119, 3888–3900.

    Article  PubMed  CAS  Google Scholar 

  • Yu, W.H., Cuervo, A.M., Kumar, A., Peterhoff, C.M., Schmidt, S.D., Lee, J.H., Mohan, P.S., Mercken, M., Farmery, M.R., Tjernberg, L.O., et al. (2005). Macroautophagy-a novel Beta-amyloid peptide-generating pathway activated in Alzheimer’s disease. J. Cell Biol. 171, 87–98.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, H., Bosch-Marce, M., Shimoda, L.A., Tan, Y.S., Baek, J.H., Wesley, J.B., Gonzalez, F.J., and Semenza, G.L. (2008). Mitochondrial autophagy is an HIF-1-dependent adaptive metabolic response to hypoxia. J. Biol. Chem. 283, 10892–10903.

    Article  PubMed  CAS  Google Scholar 

  • Zhou, Z., Wu, S., Li, X., Xue, Z., and Tong, J. (2010). Rapamycin induces autophagy and exacerbates metabolism associated complications in a mouse model of type 1 diabetes. Indian J. Exp. Biol. 48, 31–38.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Stefan W. Ryter.

About this article

Cite this article

Ryter, S.W., Cloonan, S.M. & Choi, A.M.K. Autophagy: A critical regulator of cellular metabolism and homeostasis. Mol Cells 36, 7–16 (2013). https://doi.org/10.1007/s10059-013-0140-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10059-013-0140-8

Keywords

Navigation