Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics

Mol Cell. 2019 Jan 17;73(2):339-353.e6. doi: 10.1016/j.molcel.2018.10.035. Epub 2018 Dec 20.


Membrane targeting of the BECN1-containing class III PI 3-kinase (PI3KC3) complexes is pivotal to the regulation of autophagy. The interaction of PI3KC3 complex II and its ubiquitously expressed inhibitor, Rubicon, was mapped to the first β sheet of the BECN1 BARA domain and the UVRAG BARA2 domain by hydrogen-deuterium exchange and cryo-EM. These data suggest that the BARA β sheet 1 unfolds to directly engage the membrane. This mechanism was confirmed using protein engineering, giant unilamellar vesicle assays, and molecular simulations. Using this mechanism, a BECN1 β sheet-1 derived peptide activates both PI3KC3 complexes I and II, while HIV-1 Nef inhibits complex II. These data reveal how BECN1 switches on and off PI3KC3 binding to membranes. The observations explain how PI3KC3 inhibition by Rubicon, activation by autophagy-inducing BECN1 peptides, and inhibition by HIV-1 Nef are mediated by the switchable ability of the BECN1 BARA domain to partially unfold and insert into membranes.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Video-Audio Media

MeSH terms

  • Autophagy*
  • Autophagy-Related Proteins
  • Beclin-1 / chemistry
  • Beclin-1 / genetics
  • Beclin-1 / metabolism*
  • Binding Sites
  • Class III Phosphatidylinositol 3-Kinases / chemistry
  • Class III Phosphatidylinositol 3-Kinases / genetics
  • Class III Phosphatidylinositol 3-Kinases / metabolism*
  • Cryoelectron Microscopy
  • Enzyme Activation
  • Gene Expression Regulation
  • HEK293 Cells
  • HeLa Cells
  • Humans
  • Intracellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / metabolism
  • Molecular Dynamics Simulation
  • Phosphatidylinositol Phosphates / metabolism
  • Protein Binding
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Signal Transduction
  • Structure-Activity Relationship
  • nef Gene Products, Human Immunodeficiency Virus / genetics
  • nef Gene Products, Human Immunodeficiency Virus / metabolism


  • Autophagy-Related Proteins
  • BECN1 protein, human
  • Beclin-1
  • Intracellular Signaling Peptides and Proteins
  • Phosphatidylinositol Phosphates
  • RUBCN protein, human
  • nef Gene Products, Human Immunodeficiency Virus
  • nef protein, Human immunodeficiency virus 1
  • phosphatidylinositol 3-phosphate
  • Class III Phosphatidylinositol 3-Kinases