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Autophagy machinery mediates macroendocytic processing and entotic cell death by targeting single membranes

Abstract

Autophagy normally involves the formation of double-membrane autophagosomes that mediate bulk cytoplasmic and organelle degradation. Here we report the modification of single-membrane vacuoles in cells by autophagy proteins. LC3 (Light chain 3) a component of autophagosomes, is recruited to single-membrane entotic vacuoles, macropinosomes and phagosomes harbouring apoptotic cells, in a manner dependent on the lipidation machinery including ATG5 and ATG7, and the class III phosphatidylinositol-3-kinase VPS34. These downstream components of the autophagy machinery, but not the upstream mammalian Tor (mTor)-regulated ULK–ATG13–FIP200 complex, facilitate lysosome fusion to single membranes and the degradation of internalized cargo. For entosis, a live-cell-engulfment program, the autophagy-protein-dependent fusion of lysosomes to vacuolar membranes leads to the death of internalized cells. As pathogen-containing phagosomes can be targeted in a similar manner, the death of epithelial cells by this mechanism mimics pathogen destruction. These data demonstrate that proteins of the autophagy pathway can target single-membrane vacuoles in cells in the absence of pathogenic organisms.

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Figure 1: Entotic cell death involves recruitment of LC3 to a single-membrane vacuole.
Figure 2: Autophagy machinery in host cells controls the fate of starving internalized cells.
Figure 3: Inhibition of apoptosis and entotic cell death promotes anchorage-independent growth.
Figure 4: LC3 recruits to single-membrane vacuoles containing apoptotic cells to facilitate corpse degradation.
Figure 5: LC3 is recruited to macropinosomes independently of macroautophagy.
Figure 6: LGG-1 recruitment to apoptotic phagosomes during C. elegans embryonic development.

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References

  1. Kumari, S., Mg, S. & Mayor, S. Endocytosis unplugged: multiple ways to enter the cell. Cell Res. 20, 256–275 (2010).

    Article  CAS  Google Scholar 

  2. Kawane, K. et al. Requirement of DNase II for definitive erythropoiesis in the mouse fetal liver. Science 292, 1546–1549 (2001).

    Article  CAS  Google Scholar 

  3. Broadie, K. Axon pruning: an active role for glial cells. Curr. Biol. 14, R302–R304 (2004).

    Article  CAS  Google Scholar 

  4. Elliott, M. R. & Ravichandran, K. S. Clearance of apoptotic cells: implications in health and disease. J. Cell Biol. 189, 1059–1070 (2010).

    Article  CAS  Google Scholar 

  5. Savina, A. & Amigorena, S. Phagocytosis and antigen presentation in dendritic cells. Immunol. Rev. 219, 143–156 (2007).

    Article  CAS  Google Scholar 

  6. Haas, A. The phagosome: compartment with a license to kill. Traffic 8, 311–330 (2007).

    Article  CAS  Google Scholar 

  7. Steinberg, B. E. & Grinstein, S. Pathogen destruction versus intracellular survival: the role of lipids as phagosomal fate determinants. J. Clin. Invest. 118, 2002–2011 (2008).

    Article  CAS  Google Scholar 

  8. Kinchen, J. M. et al. A pathway for phagosome maturation during engulfment of apoptotic cells. Nat. Cell Biol. 10, 556–566 (2008).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  11. Jin, S. & White, E. Tumor suppression by autophagy through the management of metabolic stress. Autophagy 4, 563–566 (2008).

    Article  CAS  Google Scholar 

  12. Burman, C. & Ktistakis, N. T. Autophagosome formation in mammalian cells. Semin. Immunopathol. 32, 397–413 (2010).

    Article  CAS  Google Scholar 

  13. Levine, B. & Yuan, J. Autophagy in cell death: an innocent convict? J. Clin. Invest. 115, 2679–2688 (2005).

    Article  CAS  Google Scholar 

  14. Rich, K. A., Burkett, C. & Webster, P. Cytoplasmic bacteria can be targets for autophagy. Cell Microbiol. 5, 455–468 (2003).

    Article  CAS  Google Scholar 

  15. Yano, T. et al. Autophagic control of listeria through intracellular innate immune recognition in Drosophila. Nat. Immunol. 9, 908–916 (2008).

    Article  CAS  Google Scholar 

  16. Gutierrez, M. G. et al. Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages. Cell 119, 753–766 (2004).

    Article  CAS  Google Scholar 

  17. Nakagawa, I. et al. Autophagy defends cells against invading group A Streptococcus. Science 306, 1037–1040 (2004).

    Article  CAS  Google Scholar 

  18. Ogawa, M. et al. Escape of intracellular Shigella from autophagy. Science 307, 727–731 (2005).

    Article  CAS  Google Scholar 

  19. Ling, Y. M. et al. Vacuolar and plasma membrane stripping and autophagic elimination of Toxoplasma gondii in primed effector macrophages. J. Exp. Med. 203, 2063–2071 (2006).

    Article  CAS  Google Scholar 

  20. Sanjuan, M. A., Milasta, S. & Green, D. R. Toll-like receptor signaling in the lysosomal pathways. Immunol. Rev. 227, 203–220 (2009).

    Article  CAS  Google Scholar 

  21. Sanjuan, M. A. et al. Toll-like receptor signalling in macrophages links the autophagy pathway to phagocytosis. Nature 450, 1253–1257 (2007).

    Article  CAS  Google Scholar 

  22. Overholtzer, M. et al. A nonapoptotic cell death process, entosis, that occurs by cell-in-cell invasion. Cell 131, 966–979 (2007).

    Article  CAS  Google Scholar 

  23. Overholtzer, M. & Brugge, J. S. The cell biology of cell-in-cell structures. Nat. Rev. Mol. Cell Biol. 9, 796–809 (2008).

    Article  CAS  Google Scholar 

  24. Seglen, P. O. & Gordon, P. B. 3-methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes. Proc. Natl Acad. Sci. USA 79, 1889–1892 (1982).

    Article  CAS  Google Scholar 

  25. Ichimura, Y. et al. A ubiquitin-like system mediates protein lipidation. Nature 408, 488–492 (2000).

    Article  CAS  Google Scholar 

  26. Hanada, T. et al. The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. J. Biol. Chem. 282, 37298–37302 (2007).

    Article  CAS  Google Scholar 

  27. Petiot, A., Ogier-Denis, E., Blommaart, E. F., Meijer, A. J. & Codogno, P. Distinct classes of phosphatidylinositol 3’-kinases are involved in signaling pathways that control macroautophagy in HT-29 cells. J. Biol. Chem. 275, 992–998 (2000).

    Article  CAS  Google Scholar 

  28. Jung, C. H. et al. ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol. Biol. Cell 20, 1992–2003 (2009).

    Article  CAS  Google Scholar 

  29. Hosokawa, N. et al. Nutrient-dependent mTORC1 association with theULK1-Atg13-FIP200 complex required for autophagy. Mol. Biol. Cell 20, 1981–1991 (2009).

    Article  CAS  Google Scholar 

  30. Ganley, I. G. et al. ULK1.ATG13.FIP200 complex mediates mTOR signaling and is essential for autophagy. J. Biol. Chem. 284, 12297–12305 (2009).

    Article  CAS  Google Scholar 

  31. Stenmark, H., Aasland, R., Toh, B. H. & D’Arrigo, A. Endosomal localization of the autoantigen EEA1 is mediated by a zinc-binding FYVE finger. J. Biol. Chem. 271, 24048–24054 (1996).

    Article  CAS  Google Scholar 

  32. Eskelinen, E. L. et al. Inhibition of autophagy in mitotic animal cells. Traffic 3, 878–893 (2002).

    Article  CAS  Google Scholar 

  33. Kimura, S., Noda, T. & Yoshimori, T. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 3, 452–460 (2007).

    Article  CAS  Google Scholar 

  34. Sulston, J. E. & Horvitz, H. R. Post-embryonic cell lineages of the nematode, Caenorhabditis elegans. Dev. Biol. 56, 110–156 (1977).

    Article  CAS  Google Scholar 

  35. Sulston, J. E., Schierenberg, E., White, J. G. & Thomson, J. N. The embryonic cell lineage of the nematode Caenorhabditis elegans. Dev. Biol. 100, 64–119 (1983).

    Article  CAS  Google Scholar 

  36. Ruck, A. et al. The Atg6/Vps30/Beclin1 ortholog BEC-1 mediates endocytic retrograde transport in addition to autophagy in C. elegans. Autophagy 7, 386–400 (2011).

    Article  CAS  Google Scholar 

  37. Zhou, Z., Hartwieg, E. & Horvitz, H. R. CED-1 is a transmembrane receptor that mediates cell corpse engulfment in C. elegans. Cell 104, 43–56 (2001).

    Article  CAS  Google Scholar 

  38. Kamada, Y., Sekito, T. & Ohsumi, Y. Autophagy in yeast: a TOR-mediated response to nutrient starvation. Curr. Top. Microbiol. Immunol. 279, 73–84 (2004).

    CAS  PubMed  Google Scholar 

  39. Kim, D. H. et al. mTOR interacts with raptor to form a nutrient-sensitive complex that signals to the cell growth machinery. Cell 110, 163–175 (2002).

    Article  CAS  Google Scholar 

  40. Mizushima, N. et al. A protein conjugation system essential for autophagy. Nature 395, 395–398 (1998).

    Article  CAS  Google Scholar 

  41. Mizushima, N., Sugita, H., Yoshimori, T. & Ohsumi, Y. A new protein conjugation system in human. The counterpart of the yeast Apg12p conjugation system essential for autophagy. J. Biol. Chem. 273, 33889–33892 (1998).

    Article  CAS  Google Scholar 

  42. Hara, T. et al. FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells. J. Cell Biol. 181, 497–510 (2008).

    Article  CAS  Google Scholar 

  43. Cheong, H. et al. Atg17 regulates the magnitude of the autophagic response. Mol. Biol. Cell 16, 3438–3453 (2005).

    Article  CAS  Google Scholar 

  44. Kabeya, Y. et al. Atg17 functions in cooperation with Atg1 and Atg13 in yeast autophagy. Mol. Biol. Cell 16, 2544–2553 (2005).

    Article  CAS  Google Scholar 

  45. Kamada, Y. et al. Tor-mediated induction of autophagy via an Apg1 protein kinase complex. J. Cell Biol. 150, 1507–1513 (2000).

    Article  CAS  Google Scholar 

  46. Zhao, Z. et al. Autophagosome-independent essential function for the autophagy protein Atg5 in cellular immunity to intracellular pathogens. Cell Host Microbe 4, 458–469 (2008).

    Article  CAS  Google Scholar 

  47. Lee, H. K. et al. In vivo requirement for Atg5 in antigen presentation by dendritic cells. Immunity 32, 227–239 (2010).

    Article  CAS  Google Scholar 

  48. Qu, X. et al. Autophagy gene-dependent clearance of apoptotic cells during embryonic development. Cell 128, 931–946 (2007).

    Article  CAS  Google Scholar 

  49. Huang, J. et al. Activation of antibacterial autophagy by NADPH oxidases. Proc. Natl Acad. Sci. USA 106, 6226–6231 (2009).

    Article  CAS  Google Scholar 

  50. Shui, W. et al. Membrane proteomics of phagosomes suggests a connection to autophagy. Proc. Natl Acad. Sci. USA 105, 16952–16957 (2008).

    Article  CAS  Google Scholar 

  51. Kabeya, Y. et al. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J. 19, 5720–5728 (2000).

    Article  CAS  Google Scholar 

  52. Weidberg, H. et al. LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis. EMBO J. 29, 1792–1802 (2010).

    Article  CAS  Google Scholar 

  53. Fujita, N. et al. An Atg4B mutant hampers the lipidation of LC3 paralogues and causes defects in autophagosome closure. Mol. Biol. Cell 19, 4651–4659 (2008).

    Article  CAS  Google Scholar 

  54. Morvan, J. et al. In vitro reconstitution of fusion between immature autophagosomes and endosomes. Autophagy 5, 676–689 (2009).

    Article  CAS  Google Scholar 

  55. Nakatogawa, H., Ichimura, Y. & Ohsumi, Y. Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell 130, 165–178 (2007).

    Article  CAS  Google Scholar 

  56. Weidberg, H. et al. LC3 and GATE-16 N termini mediate membrane fusion processes required for autophagosome biogenesis. Dev. Cell 20, 444–454.

    Article  CAS  Google Scholar 

  57. Nair, U. et al. SNARE proteins are required for macroautophagy. Cell 146, 290–302.

    Article  CAS  Google Scholar 

  58. Behrends, C., Sowa, M. E., Gygi, S. P. & Harper, J. W. Network organization of the human autophagy system. Nature 466, 68–76 (2010).

    Article  CAS  Google Scholar 

  59. Krajcovic, M. et al. A non-genetic route to aneuploidy in human cancers. Nat. Cell Biol. 13, 324–330 (2011).

    Article  CAS  Google Scholar 

  60. Horbinski, C., Mojesky, C. & Kyprianou, N. Live free or die: tales of homeless (cells) in cancer. Am. J. Pathol. 177, 1044–1052 (2010).

    Article  CAS  Google Scholar 

  61. Debnath, J. et al. The role of apoptosis in creating and maintaining luminal space within normal and oncogene-expressing mammary acini. Cell 111, 29–40 (2002).

    Article  CAS  Google Scholar 

  62. Debnath, J., Muthuswamy, S. K. & Brugge, J. S. Morphogenesis and oncogenesis of MCF-10A mammary epithelial acini grown in three-dimensional basement membrane cultures. Methods 30, 256–268 (2003).

    Article  CAS  Google Scholar 

  63. Kamath, R. S., Martinez-Campos, M., Zipperlen, P., Fraser, A. G. & Ahringer, J. Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biol. 2, 1–10 (2000).

    Article  Google Scholar 

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Acknowledgements

We thank J. Durgan, I. Ganley, X. Jiang, G. Mouneimne, E. Yao, A. Spencer and members of the Overholtzer laboratory for helpful discussions, reagents and for reading the manuscript. We also thank N. Lampen of the Memorial Sloan Kettering Cancer Center Electron Microscopy Facility for processing of electron microscopy samples. This work was financially supported by a grant from the National Cancer Institute (CA154649; M.O.), The Geoffrey Beene Cancer Research Center at MSKCC (M.O.), the Louis V. Gerstner, Jr. Young Investigators Fund (M.O. and C.M.H.) and the Alfred W. Bressler Scholar Fund (C.M.H.).

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O.F. and M.O. designed, carried out experiments and wrote the paper. S.E.K. and C.P.S. contributed experimental assistance and data. C.M.H. provided worm strains and carried out RNAi feeding of C. elegans.

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Correspondence to Michael Overholtzer.

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Florey, O., Kim, S., Sandoval, C. et al. Autophagy machinery mediates macroendocytic processing and entotic cell death by targeting single membranes. Nat Cell Biol 13, 1335–1343 (2011). https://doi.org/10.1038/ncb2363

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