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Autophagy pp 173-188 | Cite as

Formation of Autophagosomes Coincides with Relaxation of Membrane Curvature

  • Jaime Agudo-Canalejo
  • Roland L. KnorrEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1880)

Abstract

Autophagy is an intracellular degradation process that employs complex membrane dynamics to isolate and break down cellular components. However, many unanswered questions remain concerning remodeling of autophagic membranes. Here, we focus on the advantages of theoretical modeling to study the formation of autophagosomes and to understand the origin of autophagosomal membranes. Starting from the well-defined geometry of final autophagosomes, we ask the question of how these organelles can be formed by combining various pre-autophagosomal membranes such as vesicles, membrane tubules, or sheets. We analyze the geometric constraints of autophagosome formation by taking the area of the precursor membranes and their internal volume into account. Our results suggest that vesicle fusion contributes little to the formation of autophagosomes. In the second part, we quantify the curvature of the precursors and report that the formation of autophagosomes is associated with a strong relaxation of membrane curvature energy. This effect we find for a wide range of membrane asymmetries. It is especially strong for small distances between both autophagosomal membranes, as observed in vivo. We quantify the membrane bending energies of all precursors by considering membrane asymmetries. We propose that the generation and supply of pre-autophagosomal membranes is one limiting step for autophagosome formation.

Key words

Reverse autophagy Membrane remodeling Fusion Scission Bending energy Membrane curvature Theory modeling Retrograde autophagy 

Notes

Acknowledgments

We thank Reinhard Lipowsky (MPI of Colloids and Interfaces) for stimulating discussions and institutional and financial support.

References

  1. 1.
    Knorr RL, Mizushima N, Dimova R (2017) Fusion and scission of membranes: ubiquitous topological transformations in cells. Traffic 18:758–761CrossRefGoogle Scholar
  2. 2.
    McMahon HT, Gallop JL (2005) Membrane curvature and mechanisms of dynamic cell membrane remodelling. Nature 438:590–596CrossRefGoogle Scholar
  3. 3.
    Xie Z et al (2009) Indirect estimation of the area density of Atg8 on the phagophore. Autophagy 5:217–220CrossRefGoogle Scholar
  4. 4.
    Knorr RL, Dimova R, Lipowsky R (2012) Curvature of double-membrane organelles generated by changes in membrane size and composition. PLoS One 7:e32753CrossRefGoogle Scholar
  5. 5.
    Lamb CA, Yoshimori T, Tooze SA (2013) The autophagosome: origins unknown, biogenesis complex. Nat Rev Mol Cell Biol 14:nrm3696CrossRefGoogle Scholar
  6. 6.
    Hurley JH, Young LN (2017) Mechanisms of autophagy initiation. Annu Rev Biochem 86:225–244CrossRefGoogle Scholar
  7. 7.
    Hamasaki M et al (2013) Autophagosomes form at ER-mitochondria contact sites. Nature 495:389–393CrossRefGoogle Scholar
  8. 8.
    Axe EL et al (2008) Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 182:685–701CrossRefGoogle Scholar
  9. 9.
    Shibata Y, Hu J, Kozlov MM, Rapoport TA (2009) Mechanisms shaping the membranes of cellular organelles. Annu Rev Cell Dev Biol 25:329–354CrossRefGoogle Scholar
  10. 10.
    Helfrich W (1973) Elastic properties of lipid bilayers: theory and possible experiments. Z Naturforsch C 28:693–703CrossRefGoogle Scholar
  11. 11.
    Lipowsky R (1991) The conformation of membranes. Nature 349:475–481CrossRefGoogle Scholar
  12. 12.
    Seifert U, Berndl K, Lipowsky R (1991) Shape transformations of vesicles: phase diagram for spontaneous- curvature and bilayer-coupling models. Phys Rev A 44:1182–1202CrossRefGoogle Scholar
  13. 13.
    Noda NN, Inagaki F (2015) Mechanisms of autophagy. Annu Rev Biophys 44:101–122CrossRefGoogle Scholar
  14. 14.
    Knorr RL et al (2014) Membrane morphology is actively transformed by covalent binding of the protein Atg8 to PE-lipids. PLoS One 9:e115357CrossRefGoogle Scholar
  15. 15.
    Kaufmann A, Beier V, Franquelim HG, Wollert T (2014) Molecular mechanism of autophagic membrane-scaffold assembly and disassembly. Cell 156:469–481CrossRefGoogle Scholar
  16. 16.
    Stagg SM et al (2008) Structural basis for cargo regulation of COPII coat assembly. Cell 134:474–484CrossRefGoogle Scholar
  17. 17.
    Yamamoto H et al (2012) Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J Cell Biol 198:219–233CrossRefGoogle Scholar
  18. 18.
    Shibata Y et al (2010) Mechanisms determining the morphology of the peripheral ER. Cell 143:774–788CrossRefGoogle Scholar
  19. 19.
    Jin M, Klionsky DJ (2014) Regulation of autophagy: modulation of the size and number of autophagosomes. FEBS Lett 588:2457–2463CrossRefGoogle Scholar
  20. 20.
    Kovács AL, Réz G, Pálfia Z, Kovács J (2000) Autophagy in the epithelial cells of murine seminal vesicle in vitro. Formation of large sheets of nascent isolation membranes, sequestration of the nucleus and inhibition by wortmannin and 3-ethyladenine. Cell Tissue Res 302:253–261CrossRefGoogle Scholar
  21. 21.
    Xie Z, Nair U, Klionsky DJ (2008) Atg8 controls phagophore expansion during autophagosome formation. Mol Biol Cell 19:3290–3298CrossRefGoogle Scholar
  22. 22.
    Biazik J, Vihinen H, Anwar T, Jokitalo E, Eskelinen E-L (2015) The versatile electron microscope: an ultrastructural overview of autophagy. Methods 75:44–53CrossRefGoogle Scholar
  23. 23.
    Biazik J, Ylä-Anttila P, Vihinen H, Jokitalo E, Eskelinen E-L (2015) Ultrastructural relationship of the phagophore with surrounding organelles. Autophagy 11:439–451CrossRefGoogle Scholar
  24. 24.
    Bars RL, Marion J, Borgne RL, Satiat-Jeunemaitre B, Bianchi MW (2014) ATG5 defines a phagophore domain connected to the endoplasmic reticulum during autophagosome formation in plants. Nat Commun 5:4121CrossRefGoogle Scholar
  25. 25.
    Yamaguchi A et al (2009) A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Nat Cell Biol 11:1433CrossRefGoogle Scholar
  26. 26.
    Ylä-Anttila P, Vihinen H, Jokitalo E, Eskelinen E-L (2009) 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 5:1180–1185CrossRefGoogle Scholar
  27. 27.
    Bahrami AH, Lin MG, Ren X, Hurley JH, Hummer G (2017) Scaffolding the cup-shaped double membrane in autophagy. PLoS Comput Biol 13:e1005817CrossRefGoogle Scholar
  28. 28.
    Knorr RL, Lipowsky R, Dimova R (2015) Autophagosome closure requires membrane scission. Autophagy 11:2134–2137CrossRefGoogle Scholar
  29. 29.
    Lipowsky R (2014) Remodeling of membrane compartments: some consequences of membrane fluidity. Biol Chem 395:253–274CrossRefGoogle Scholar
  30. 30.
    Kozlov MM, McMahon HT, Chernomordik LV (2010) Protein-driven membrane stresses in fusion and fission. Trends Biochem Sci 35:699–706CrossRefGoogle Scholar
  31. 31.
    Heinrich V, Svetina S, Žekš B (1993) Nonaxisymmetric vesicle shapes in a generalized bilayer-couple model and the transition between oblate and prolate axisymmetric shapes. Phys Rev E 48:3112–3123CrossRefGoogle Scholar
  32. 32.
    Bahrami AH, Hummer G (2017) Formation and stability of lipid membrane nanotubes. ACS Nano 11:9558–9565CrossRefGoogle Scholar
  33. 33.
    Shemesh T et al (2014) A model for the generation and interconversion of ER morphologies. Proc Natl Acad Sci 111:E5243–E5251CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Rudolf Peierls Centre for Theoretical PhysicsUniversity of OxfordOxfordUK
  2. 2.Department of ChemistryThe Pennsylvania State UniversityUniversity ParkUSA
  3. 3.Department of Theory and Bio-SystemsMax Planck Institute of Colloids and InterfacesPotsdamGermany
  4. 4.Department of Biochemistry and Molecular Biology, Graduate School and Faculty of MedicineThe University of TokyoTokyoJapan

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