Home LiteratureArticle Details
PMID: 22310240 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Crystal structure and biochemical analyses reveal Beclin 1 as a novel membrane binding protein.

Cell research ·Vol. 22 ·No. 3 ·2012-03-00 ·Pages 473-89

Huang W, Choi W, Hu W, Mi N, Guo Q, Ma M, Liu M, Tian Y, Lu P, Wang FL, Deng H, Liu L, Gao N, Yu L, Shi Y

Abstract

The Beclin 1 gene is a haplo-insufficient tumor suppressor and plays an essential role in autophagy. However, the molecular mechanism by which Beclin 1 functions remains largely unknown. Here we report the crystal structure of the evolutionarily conserved domain (ECD) of Beclin 1 at 1.6 Å resolution. Beclin 1 ECD exhibits a previously unreported fold, with three structural repeats arranged symmetrically around a central axis. Beclin 1 ECD defines a novel class of membrane-binding domain, with a strong preference for lipid membrane enriched with cardiolipin. The tip of a surface loop in Beclin 1 ECD, comprising three aromatic amino acids, acts as a hydrophobic finger to associate with lipid membrane, consequently resulting in the deformation of membrane and liposomes. Mutation of these aromatic residues rendered Beclin 1 unable to stably associate with lipid membrane in vitro and unable to fully rescue autophagy in Beclin 1-knockdown cells in vivo. These observations form an important framework for deciphering the biological functions of Beclin 1.

MeSH Terms
Animals Apoptosis Regulatory Proteins/chemistry,genetics,metabolism Beclin-1 Cells, Cultured HeLa Cells Humans Membrane Proteins/chemistry,genetics,metabolism Models, Molecular Protein Conformation Rats
Chemicals
Apoptosis Regulatory Proteins BECN1 protein, human Beclin-1 Membrane Proteins
Authors & Affiliations
15 authors, click to expand affiliations / ORCID
Huang Weijiao
Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
Choi Wooyoung
Hu Wanqiu
Mi Na
Guo Qiang
Ma Meisheng
Liu Mei
Tian Yuan
Lu Peilong
Wang Feng-Liang
Deng Haiteng
Liu Lei
Gao Ning
Yu Li
Shi Yigong
References (52)
52 references, click to expand
  1. pH-dissociation characteristics of cardiolipin and its 2'-deoxy analogue.
    Lipids. 1993 Oct;28(10):877-82 PMID: 8246687
  2. Substructure solution with SHELXD.
    Acta Crystallogr D Biol Crystallogr. 2002 Oct;58(Pt 10 Pt 2):1772-9 PMID: 12351820
  3. Endosome to Golgi retrieval of the vacuolar protein sorting receptor, Vps10p, requires the function of the VPS29, VPS30, and VPS35 gene products.
    J Cell Biol. 1997 Apr 7;137(1):79-92 PMID: 9105038
  4. Phospholipid composition of highly purified mitochondrial outer membranes of rat liver and Neurospora crassa. Is cardiolipin present in the mitochondrial outer membrane?
    Biochim Biophys Acta. 1997 Apr 3;1325(1):108-16 PMID: 9106488
  5. Milk fat globule epidermal growth factor 8 (MFG-E8) binds to oxidized phosphatidylserine: implications for macrophage clearance of apoptotic cells.
    Cell Death Differ. 2004 Aug;11(8):943-5 PMID: 15031725
  6. Purification of human respiratory syncytial virus by ultracentrifugation in iodixanol density gradient.
    J Virol Methods. 2008 Feb;147(2):328-32 PMID: 18029032
  7. Protein structure comparison by alignment of distance matrices.
    J Mol Biol. 1993 Sep 5;233(1):123-38 PMID: 8377180
  8. Interplay of proteins and lipids in generating membrane curvature.
    Curr Opin Cell Biol. 2010 Aug;22(4):430-6 PMID: 20605711
  9. The regulation of autophagy - unanswered questions.
    J Cell Sci. 2011 Jan 15;124(Pt 2):161-70 PMID: 21187343
  10. Identification of Barkor as a mammalian autophagy-specific factor for Beclin 1 and class III phosphatidylinositol 3-kinase.
    Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19211-6 PMID: 19050071
  11. The CCP4 suite: programs for protein crystallography.
    Acta Crystallogr D Biol Crystallogr. 1994 Sep 1;50(Pt 5):760-3 PMID: 15299374
  12. Current knowledge of the pre-autophagosomal structure (PAS).
    FEBS Lett. 2010 Apr 2;584(7):1280-6 PMID: 20138172
  13. Protection against fatal Sindbis virus encephalitis by beclin, a novel Bcl-2-interacting protein.
    J Virol. 1998 Nov;72(11):8586-96 PMID: 9765397
  14. Membrane recognition by phospholipid-binding domains.
    Nat Rev Mol Cell Biol. 2008 Feb;9(2):99-111 PMID: 18216767
  15. Mammalian autophagy: core molecular machinery and signaling regulation.
    Curr Opin Cell Biol. 2010 Apr;22(2):124-31 PMID: 20034776
  16. Mitochondria supply membranes for autophagosome biogenesis during starvation.
    Cell. 2010 May 14;141(4):656-67 PMID: 20478256
  17. Promotion of tumorigenesis by heterozygous disruption of the beclin 1 autophagy gene.
    J Clin Invest. 2003 Dec;112(12):1809-20 PMID: 14638851
  18. Weaning-induced expression of a milk-fat globule protein, MFG-E8, in mouse mammary glands, as demonstrated by the analyses of its mRNA, protein and phosphatidylserine-binding activity.
    Biochem J. 2006 Apr 1;395(1):21-30 PMID: 16401186
  19. Autophagy requires endoplasmic reticulum targeting of the PI3-kinase complex via Atg14L.
    J Cell Biol. 2010 Aug 23;190(4):511-21 PMID: 20713597
  20. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum.
    J Cell Biol. 2008 Aug 25;182(4):685-701 PMID: 18725538
  21. Processing of X-ray diffraction data collected in oscillation mode.
    Methods Enzymol. 1997;276:307-26 PMID: 27754618
  22. Functional and physical interaction between Bcl-X(L) and a BH3-like domain in Beclin-1.
    EMBO J. 2007 May 16;26(10):2527-39 PMID: 17446862
  23. Crystal structures of the membrane-binding C2 domain of human coagulation factor V.
    Nature. 1999 Nov 25;402(6760):434-9 PMID: 10586886
  24. How proteins produce cellular membrane curvature.
    Nat Rev Mol Cell Biol. 2006 Jan;7(1):9-19 PMID: 16365634
  25. Beclin 1 cleavage by caspase-3 inactivates autophagy and promotes apoptosis.
    Protein Cell. 2010 May;1(5):468-77 PMID: 21203962
  26. Beclin 1 contains a leucine-rich nuclear export signal that is required for its autophagy and tumor suppressor function.
    Cancer Res. 2001 Apr 15;61(8):3443-9 PMID: 11309306
  27. Molecular basis of Bcl-xL's target recognition versatility revealed by the structure of Bcl-xL in complex with the BH3 domain of Beclin-1.
    J Mol Biol. 2007 Sep 7;372(1):223-35 PMID: 17659302
  28. Structure of Nampt/PBEF/visfatin, a mammalian NAD+ biosynthetic enzyme.
    Nat Struct Mol Biol. 2006 Jul;13(7):661-2 PMID: 16783373
  29. Crystal structure of the Bcl-XL-Beclin 1 peptide complex: Beclin 1 is a novel BH3-only protein.
    J Biol Chem. 2007 Apr 27;282(17):13123-32 PMID: 17337444
  30. Iodixanol: a nonionic iso-osmotic centrifugation medium for the formation of self-generated gradients.
    Anal Biochem. 1994 Aug 1;220(2):360-6 PMID: 7978279
  31. Bid, Bax, and lipids cooperate to form supramolecular openings in the outer mitochondrial membrane.
    Cell. 2002 Nov 1;111(3):331-42 PMID: 12419244
  32. Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy.
    Cell. 2005 Sep 23;122(6):927-39 PMID: 16179260
  33. Atg14 and UVRAG: mutually exclusive subunits of mammalian Beclin 1-PI3K complexes.
    Autophagy. 2009 May;5(4):534-6 PMID: 19223761
  34. The Buccaneer software for automated model building. 1. Tracing protein chains.
    Acta Crystallogr D Biol Crystallogr. 2006 Sep;62(Pt 9):1002-11 PMID: 16929101
  35. Autophagic and tumour suppressor activity of a novel Beclin1-binding protein UVRAG.
    Nat Cell Biol. 2006 Jul;8(7):688-99 PMID: 16799551
  36. Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation.
    Autophagy. 2010 May;6(4):506-22 PMID: 20505359
  37. Mitochondrial cardiolipin involved in outer-membrane protein biogenesis: implications for Barth syndrome.
    Curr Biol. 2009 Dec 29;19(24):2133-9 PMID: 19962311
  38. Cloning and genomic organization of beclin 1, a candidate tumor suppressor gene on chromosome 17q21.
    Genomics. 1999 Jul 1;59(1):59-65 PMID: 10395800
  39. Beclin-phosphatidylinositol 3-kinase complex functions at the trans-Golgi network.
    EMBO Rep. 2001 Apr;2(4):330-5 PMID: 11306555
  40. Coot: model-building tools for molecular graphics.
    Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2126-32 PMID: 15572765
  41. The Beclin 1-VPS34 complex--at the crossroads of autophagy and beyond.
    Trends Cell Biol. 2010 Jun;20(6):355-62 PMID: 20356743
  42. PHENIX: building new software for automated crystallographic structure determination.
    Acta Crystallogr D Biol Crystallogr. 2002 Nov;58(Pt 11):1948-54 PMID: 12393927
  43. The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8.
    Genes Cells. 2004 Jul;9(7):611-8 PMID: 15265004
  44. Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor.
    Proc Natl Acad Sci U S A. 2003 Dec 9;100(25):15077-82 PMID: 14657337
  45. Cardiolipin microdomains localize to negatively curved regions of Escherichia coli membranes.
    Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6264-9 PMID: 21444798
  46. Beclin 1 forms two distinct phosphatidylinositol 3-kinase complexes with mammalian Atg14 and UVRAG.
    Mol Biol Cell. 2008 Dec;19(12):5360-72 PMID: 18843052
  47. The autophagy effector Beclin 1: a novel BH3-only protein.
    Oncogene. 2008 Dec;27 Suppl 1:S137-48 PMID: 19641499
  48. Caspase-mediated cleavage of Beclin-1 inactivates Beclin-1-induced autophagy and enhances apoptosis by promoting the release of proapoptotic factors from mitochondria.
    Cell Death Dis. 2010;1:e18 PMID: 21364619
  49. Induction of autophagy and inhibition of tumorigenesis by beclin 1.
    Nature. 1999 Dec 9;402(6762):672-6 PMID: 10604474
  50. Apg14p and Apg6/Vps30p form a protein complex essential for autophagy in the yeast, Saccharomyces cerevisiae.
    J Biol Chem. 1998 Aug 28;273(35):22284-91 PMID: 9712845
  51. Phaser crystallographic software.
    J Appl Crystallogr. 2007 Aug 1;40(Pt 4):658-674 PMID: 19461840
  52. The evolutionarily conserved domain of Beclin 1 is required for Vps34 binding, autophagy and tumor suppressor function.
    Autophagy. 2005 Apr;1(1):46-52 PMID: 16874027
Article Info
Journal
Cell research
Abbr.
Cell Res
ISSN
1748-7838
Published
2012-03-00
Epub
2012-00-07
Pages
473-89
Language
English
Region
England
NLM ID
9425763
PMCID
PMC3292424
Subset
IM
Databases
PDB
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com