Architecture and Dynamics of the Autophagic Phosphatidylinositol 3-kinase Complex

Overview

Journal Elife

Specialty Biology

Date 2014 Dec 10

PMID 25490155

Citations 93

Authors

Sulochanadevi Baskaran

Lars-Anders Carlson

Goran Stjepanovic

Lindsey N Young

Do Jin Kim

Patricia Grob

Robin E Stanley

Eva Nogales

James H Hurley

Affiliations

Soon will be listed here.

Abstract

The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) that functions in early autophagy consists of the lipid kinase VPS34, the scaffolding protein VPS15, the tumor suppressor BECN1, and the autophagy-specific subunit ATG14. The structure of the ATG14-containing PI3KC3-C1 was determined by single-particle EM, revealing a V-shaped architecture. All of the ordered domains of VPS34, VPS15, and BECN1 were mapped by MBP tagging. The dynamics of the complex were defined using hydrogen-deuterium exchange, revealing a novel 20-residue ordered region C-terminal to the VPS34 C2 domain. VPS15 organizes the complex and serves as a bridge between VPS34 and the ATG14:BECN1 subcomplex. Dynamic transitions occur in which the lipid kinase domain is ejected from the complex and VPS15 pivots at the base of the V. The N-terminus of BECN1, the target for signaling inputs, resides near the pivot point. These observations provide a framework for understanding the allosteric regulation of lipid kinase activity.

Citing Articles

Beclin 1-Mediated Autophagy Is Potentiated by an Interaction with the Neuronal Adaptor FE65.

Chan W, Chow J, Chau D, Zhai Y, Lau K Biology (Basel). 2025; 14(1.

PMID: 39857327 PMC: 11763304. DOI: 10.3390/biology14010097.

Regulatory Mechanisms Governing the Autophagy-Initiating VPS34 Complex and Its inhibitors.

Lee Y, Tuan N, Lee G, Kim B, Park J, Lee C Biomol Ther (Seoul). 2024; 32(6):723-735.

PMID: 39370737 PMC: 11535298. DOI: 10.4062/biomolther.2024.094.

Inhibition of the cGAS-STING pathway: contributing to the treatment of cerebral ischemia-reperfusion injury.

Yang H, Xia Y, Ma Y, Gao M, Hou S, Xu S Neural Regen Res. 2024; 20(7):1900-1918.

PMID: 38993125 PMC: 11691458. DOI: 10.4103/NRR.NRR-D-24-00015.

Renin-angiotensin system inhibitors positively impact on multiple aging regulatory pathways: Could they be used to protect against human aging?.

de Cavanagh E, Inserra F, Ferder L Physiol Rep. 2024; 12(12):e16094.

PMID: 38924381 PMC: 11200104. DOI: 10.14814/phy2.16094.

contributes to copper stress tolerance by enhancing the antioxidant ability in transgenic grape calli.

Xia J, Wang Z, Liu S, Fang X, Hakeem A, Fang J Physiol Mol Biol Plants. 2024; 30(1):137-152.

PMID: 38435851 PMC: 10902227. DOI: 10.1007/s12298-024-01415-y.

References

Ogura T, Iwasaki K, Sato C . Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking. J Struct Biol. 2003; 143(3):185-200. DOI: 10.1016/j.jsb.2003.08.005. View

Fogel A, Dlouhy B, Wang C, Ryu S, Neutzner A, Hasson S . Role of membrane association and Atg14-dependent phosphorylation in beclin-1-mediated autophagy. Mol Cell Biol. 2013; 33(18):3675-88. PMC: 3753860. DOI: 10.1128/MCB.00079-13. View

Huang W, Choi W, Hu W, Mi N, Guo Q, Ma M . Crystal structure and biochemical analyses reveal Beclin 1 as a novel membrane binding protein. Cell Res. 2012; 22(3):473-89. PMC: 3292424. DOI: 10.1038/cr.2012.24. View

Ludtke S, Baldwin P, Chiu W . EMAN: semiautomated software for high-resolution single-particle reconstructions. J Struct Biol. 1999; 128(1):82-97. DOI: 10.1006/jsbi.1999.4174. View

Graef M, Friedman J, Graham C, Babu M, Nunnari J . ER exit sites are physical and functional core autophagosome biogenesis components. Mol Biol Cell. 2013; 24(18):2918-31. PMC: 3771953. DOI: 10.1091/mbc.E13-07-0381. View

Ge L, Baskaran S, Schekman R, Hurley J . The protein-vesicle network of autophagy. Curr Opin Cell Biol. 2014; 29:18-24. DOI: 10.1016/j.ceb.2014.02.005. View

Mindell J, Grigorieff N . Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol. 2003; 142(3):334-47. DOI: 10.1016/s1047-8477(03)00069-8. View

He C, Levine B . The Beclin 1 interactome. Curr Opin Cell Biol. 2010; 22(2):140-9. PMC: 2854269. DOI: 10.1016/j.ceb.2010.01.001. View

Rosenthal P, Henderson R . Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. J Mol Biol. 2003; 333(4):721-45. DOI: 10.1016/j.jmb.2003.07.013. View

10.

Hurley J, Schulman B . Atomistic autophagy: the structures of cellular self-digestion. Cell. 2014; 157(2):300-311. PMC: 4038036. DOI: 10.1016/j.cell.2014.01.070. View

11.

Matsunaga K, Morita E, Saitoh T, Akira S, Ktistakis N, Izumi T . Autophagy requires endoplasmic reticulum targeting of the PI3-kinase complex via Atg14L. J Cell Biol. 2010; 190(4):511-21. PMC: 2928018. DOI: 10.1083/jcb.200911141. View

12.

Furuya N, Yu J, Byfield M, Pattingre S, Levine B . The evolutionarily conserved domain of Beclin 1 is required for Vps34 binding, autophagy and tumor suppressor function. Autophagy. 2006; 1(1):46-52. DOI: 10.4161/auto.1.1.1542. View

13.

Funderburk S, Wang Q, Yue Z . The Beclin 1-VPS34 complex--at the crossroads of autophagy and beyond. Trends Cell Biol. 2010; 20(6):355-62. PMC: 3781210. DOI: 10.1016/j.tcb.2010.03.002. View

14.

Russell R, Tian Y, Yuan H, Park H, Chang Y, Kim J . ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat Cell Biol. 2013; 15(7):741-50. PMC: 3885611. DOI: 10.1038/ncb2757. View

15.

Scheres S . RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 2012; 180(3):519-30. PMC: 3690530. DOI: 10.1016/j.jsb.2012.09.006. View

16.

Itakura E, Kishi C, Inoue K, Mizushima N . Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG. Mol Biol Cell. 2008; 19(12):5360-72. PMC: 2592660. DOI: 10.1091/mbc.e08-01-0080. View

17.

Scheres S, Nunez-Ramirez R, S Sorzano C, Carazo J, Marabini R . Image processing for electron microscopy single-particle analysis using XMIPP. Nat Protoc. 2008; 3(6):977-90. PMC: 2778070. DOI: 10.1038/nprot.2008.62. View

18.

Chalmers M, Pascal B, Willis S, Zhang J, Iturria S, Dodge J . Methods for the Analysis of High Precision Differential Hydrogen Deuterium Exchange Data. Int J Mass Spectrom. 2011; 302(1-3):59-68. PMC: 3081588. DOI: 10.1016/j.ijms.2010.08.002. View

19.

Shaikh T, Gao H, Baxter W, Asturias F, Boisset N, Leith A . SPIDER image processing for single-particle reconstruction of biological macromolecules from electron micrographs. Nat Protoc. 2009; 3(12):1941-74. PMC: 2737740. DOI: 10.1038/nprot.2008.156. View

20.

Matsunaga K, Saitoh T, Tabata K, Omori H, Satoh T, Kurotori N . Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat Cell Biol. 2009; 11(4):385-96. DOI: 10.1038/ncb1846. View