Termination of autophagy and reformation of lysosomes regulated by mTOR

Abstract

Autophagy is an evolutionarily conserved process by which cytoplasmic proteins and organelles are catabolized1,2. During starvation, the protein TOR (target of rapamycin), a nutrient-responsive kinase, is inhibited, and this induces autophagy. In autophagy, double-membrane autophagosomes envelop and sequester intracellular components and then fuse with lysosomes to form autolysosomes, which degrade their contents to regenerate nutrients. Current models of autophagy terminate with the degradation of the autophagosome cargo in autolysosomes3,4,5, but the regulation of autophagy in response to nutrients and the subsequent fate of the autolysosome are poorly understood. Here we show that mTOR signalling in rat kidney cells is inhibited during initiation of autophagy, but reactivated by prolonged starvation. Reactivation of mTOR is autophagy-dependent and requires the degradation of autolysosomal products. Increased mTOR activity attenuates autophagy and generates proto-lysosomal tubules and vesicles that extrude from autolysosomes and ultimately mature into functional lysosomes, thereby restoring the full complement of lysosomes in the cell—a process we identify in multiple animal species. Thus, an evolutionarily conserved cycle in autophagy governs nutrient sensing and lysosome homeostasis during starvation.

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Figure 1: Lysosome homeostasis during starvation.
Figure 2: Proto-lysosome formation and maturation.
Figure 3: Reactivation of mTOR inhibits autophagy and initiates lysosome reformation.
Figure 4: Autophagic lysosome reformation.

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Acknowledgements

We thank the National Institute of Allergy and Infectious Diseases (NIAID) imaging core facility and Olympus China for technical support; O. Schwartz, J. Kabat, L. Koo, M. Czapiga (Bio-imaging facility (BIF), NIAID, NIH) and Q. Dong (Olympus China) for assistance with confocal microscopy and imaging processing; K. Nagashima and M. J. de la Cruz (NCI) for TEM analyses: J. Lippincott-Schwartz, H Bernstein, and J. Bonifacino for helpful discussions; D. Yamamoto, G. Davis and H. Kramer for constructs and fly strains; and M. v. Peski and R. Scriwanek for assistance with the preparation of the EM figures. This research was supported by the Division of Intramural Research of the NIAID, NIH, Department of Health and Human Services and NIH Grant GM079431 to E.B., 973 program 2010CB833704, NSF grant 20091300700, and Tsinghua University grant 20091081391 to Y.L. J.K. is the recipient of VICI grant 918.56.611 of the Netherlands Organisation for Scientific Research (NWO).

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Contributions

L.Y. first observed lysosome reformation at the end of autophagy, autophagy dependent mTOR reactivation and performed the original characterization of the phenomenon. G.A.M. and D.W.H. made critical DNA constructs and designed the live imaging experiments. L.Z. performed the density gradient analyses. C.K.M. performed Drosophila experiments. V.O. performed immuno-TEM analyses. M.J.L. and L.Y. wrote the manuscript and J.P., Y.R., N.M., Y.Z., Z.L. and F.W. helped in the manuscript revision experiments. Most of the experiments were performed by L.Y. and were conceived by L.Y., E.H.B. and M.J.L. J.K. conceived and executed certain E.M. experiments. All authors wrote, discussed and revised the manuscript.

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Correspondence to Michael J. Lenardo.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Figures S1-S19 with legends, full legends for Supplementary Movies 1-3 and Supplementary Methods. (PDF 4940 kb)

41586_2010_BFnature09076_MOESM256_ESM.avi

This movie shows that multiple lysosomes fuse with GFP-LC3-labeled autophagic vesicle (see movie legend S1 in Supplementary Information file). (AVI 5489 kb)

Supplementary Movie 1

This movie shows that multiple lysosomes fuse with GFP-LC3-labeled autophagic vesicle (see movie legend S1 in Supplementary Information file). (AVI 5489 kb)

41586_2010_BFnature09076_MOESM257_ESM.mov

This movie shows tubules extending from autolysosomal membranes (arrow) and small Lamp1-positive vesicles pinching off from the tips of tubules (see movie legend S2 in Supplementary Information file). (MOV 2730 kb)

Supplementary Movie 2

This movie shows tubules extending from autolysosomal membranes (arrow) and small Lamp1-positive vesicles pinching off from the tips of tubules (see movie legend S2 in Supplementary Information file). (MOV 2730 kb)

41586_2010_BFnature09076_MOESM258_ESM.avi

This movie shows tubules breaking away from autolysosomes and condensing into Lamp1-positive vesicles (see movie legend S3 in Supplementary Information file). (AVI 3733 kb)

The Supplementary Information file and this table of contents were updated and replaced on 07 July 2010.

Supplementary Movie 3

This movie shows tubules breaking away from autolysosomes and condensing into Lamp1-positive vesicles (see movie legend S3 in Supplementary Information file). (AVI 3733 kb)

The Supplementary Information file and this table of contents were updated and replaced on 07 July 2010.

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Yu, L., McPhee, C., Zheng, L. et al. Termination of autophagy and reformation of lysosomes regulated by mTOR. Nature 465, 942–946 (2010). https://doi.org/10.1038/nature09076

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