Bidirectional Control of Autophagy by BECN1 BARA Domain Dynamics

• Published in: Molecular cell 2019-01, Vol.73 (2), p.339-353.e6
• Main Authors: Chang, Chunmei, Young, Lindsey N., Morris, Kyle L., von Bülow, Sören, Schöneberg, Johannes, Yamamoto-Imoto, Hitomi, Oe, Yukako, Yamamoto, Kentaro, Nakamura, Shuhei, Stjepanovic, Goran, Hummer, Gerhard, Yoshimori, Tamotsu, Hurley, James H.
• Format: Article
• Language: English
• Subjects: 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; Human immunodeficiency virus 1; Humans; Intracellular Signaling Peptides and Proteins - genetics; Intracellular Signaling Peptides and Proteins - metabolism; molecular dynamics; Molecular Dynamics Simulation; nef Gene Products, Human Immunodeficiency Virus - genetics; nef Gene Products, Human Immunodeficiency Virus - metabolism; peptides; phosphatidylinositol 3-kinase; Phosphatidylinositol Phosphates - metabolism; Protein Binding; Protein Conformation, beta-Strand; protein engineering; Protein Interaction Domains and Motifs; Signal Transduction; Structure-Activity Relationship
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2018.10.035

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. [Display omitted] •Structural mapping of Rubicon binding to PI3KC3-C2•Rubicon stabilizes BECN1 BARA β sheet-1 and blocks membrane docking•BECN1 autophagy-activating peptide promotes BARA membrane binding•HIV-1 Nef modulates PI3KC3-C2 by a similar mechanism as Rubicon A structural, biochemical, and biophysical study of PI 3-kinase regulation by Rubicon, HIV-1 Nef, and an autophagy-activating peptide shows how BECN1 BARA domain is switched on and off in both physiology and infection, and how it can be targeted for therapeutic induction of autophagy.