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Mukhopadhyay S, Subedi S, Hopkins JB, Ugrinov A, Chakravarthy S, Colbert CL, Sinha SC. Invariant BECN1 CXXC motifs bind Zn 2+ and regulate structure and function of the BECN1 intrinsically disordered region. Autophagy 2024; 20:380-396. [PMID: 37791766 PMCID: PMC10813572 DOI: 10.1080/15548627.2023.2259707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 09/12/2023] [Indexed: 10/05/2023] Open
Abstract
ABBREVIATIONS AFM: aromatic finger mutant; BH3D: BCL2 homology 3 domain; CCD: coiled-coil domain; CD: circular dichroism spectroscopy; [CysDM1]: C18S and C21S double mutant; [CysDM2]: C137S, and C140S double mutant; [CysTM], C18S, C21S, C137S, and C140S tetrad mutant; Dmax: maximum particle diameter; dRI, differential refractive index; EFA: evolving factor analysis; FHD: flexible helical domain; FL: full length; GFP: green fluorescent protein; HDX-MS: hydrogen/deuterium exchange mass spectrometry; ICP-MS: inductively coupled plasma mass spectrometry; IDR: intrinsically disordered region; ITC, isothermal titration calorimetry; MALS, multi angle light scattering; MBP: maltose-binding protein; MoRFs: molecular recognition features; P(r): pairwise-distance distribution; PtdIns3K: class III phosphatidylinositol 3-kinase; Rg: radius of gyration; SASBDB: small angle scattering biological data bank; SEC: size-exclusion chromatography; SEC-SAXS: size-exclusion chromatography in tandem with small angle X-ray scattering; TEV: tobacco-etch virus; TFE: 2,2,2-trifluoroethanol; TPEN: N,N,N,N-tetrakis(2-pyridinylmethyl)-1,2-ethanediamine; Vc: volume of correlation; WT: wild-type.
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Affiliation(s)
- Shreya Mukhopadhyay
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Subeksha Subedi
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Jesse B. Hopkins
- The Biophysics Collaborative Access Team, Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Angel Ugrinov
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
| | - Srinivas Chakravarthy
- The Biophysics Collaborative Access Team, Departments of Biology and Physics, Illinois Institute of Technology, Chicago, IL, USA
| | | | - Sangita C. Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, USA
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2
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Kaur S, Vashistt J, Changotra H. Identification of molecular signatures and molecular dynamics simulation of highly deleterious missense variants of key autophagy regulator beclin 1: a computational based approach. J Biomol Struct Dyn 2023:1-14. [PMID: 37640005 DOI: 10.1080/07391102.2023.2252097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Beclin 1 is a key autophagy regulator that also plays significant roles in other intracellular processes such as vacuolar protein sorting. Beclin 1 protein functions as a scaffold in the formation of a multiprotein assemblage during autophagy. Beclin 1 is involved in various diseases such as cancers, neurodegenerative and autophagy-related disorders. In this study, we have used various in silico tools to scan beclin 1 at the molecular level to find its molecular signatures. We have predicted and analysed deleterious non-synonymous single nucleotide polymorphisms (nsSNPs) of beclin 1 causing alterations in its structure and also affecting its interactions with other proteins. In total, twelve coding region deleterious variants were predicted using sequence-based tools and nine were predicted using various structure-based tools. The molecular dynamics (MD) simulations revealed an altered stability of the native structure due to the introduction of mutations. Destabilization of beclin 1 ECD domain was observed due to nsSNPs W300R and E302K. Beclin 1 deleterious nsSNPs were predicted to show significant effects on beclin 1 interactions with ATG14L1, UVRAG and VPS34 proteins and were also predicted to alter the protein-protein interface of beclin 1 complexes. Additionally, beclin 1 was predicted to have thirty-one potential phosphorylation and three ubiquitination sites. In conclusion, the molecular details of beclin 1 could help in the better understanding of its functioning. The study of nsSNPs and their effect on beclin 1 and its interactions might aid in understanding the basis of anomalies caused due to beclin 1 dysfunction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sargeet Kaur
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Jitendraa Vashistt
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, India
| | - Harish Changotra
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India
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3
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Molecular Mechanism and Regulation of Autophagy and Its Potential Role in Epilepsy. Cells 2022; 11:cells11172621. [PMID: 36078029 PMCID: PMC9455075 DOI: 10.3390/cells11172621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/14/2022] [Accepted: 08/22/2022] [Indexed: 01/18/2023] Open
Abstract
Autophagy is an evolutionally conserved degradation mechanism for maintaining cell homeostasis whereby cytoplasmic components are wrapped in autophagosomes and subsequently delivered to lysosomes for degradation. This process requires the concerted actions of multiple autophagy-related proteins and accessory regulators. In neurons, autophagy is dynamically regulated in different compartments including soma, axons, and dendrites. It determines the turnover of selected materials in a spatiotemporal control manner, which facilitates the formation of specialized neuronal functions. It is not surprising, therefore, that dysfunctional autophagy occurs in epilepsy, mainly caused by an imbalance between excitation and inhibition in the brain. In recent years, much attention has been focused on how autophagy may cause the development of epilepsy. In this article, we overview the historical landmarks and distinct types of autophagy, recent progress in the core machinery and regulation of autophagy, and biological roles of autophagy in homeostatic maintenance of neuronal structures and functions, with a particular focus on synaptic plasticity. We also discuss the relevance of autophagy mechanisms to the pathophysiology of epileptogenesis.
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4
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Maheshwari C, Vidoni C, Titone R, Castiglioni A, Lora C, Follo C, Isidoro C. Isolation, Characterization, and Autophagy Function of BECN1-Splicing Isoforms in Cancer Cells. Biomolecules 2022; 12:biom12081069. [PMID: 36008963 PMCID: PMC9405542 DOI: 10.3390/biom12081069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 01/27/2023] Open
Abstract
Alternative splicing allows the synthesis of different protein variants starting from a single gene. Human Beclin 1 (BECN1) is a key autophagy regulator that acts as haploinsufficient tumor suppressor since its decreased expression correlates with tumorigenesis and poor prognosis in cancer patients. Recent studies show that BECN1 mRNA undergoes alternative splicing. Here, we report on the isolation and molecular and functional characterization of three BECN1 transcript variants (named BECN1-α, -β and -γ) in human cancer cells. In ovarian cancer NIHOVCAR3, these splicing variants were found along with the canonical wild-type. BECN1-α lacks 143 nucleotides at its C-terminus and corresponds to a variant previously described. BECN1-β and -γ lack the BCL2 homology 3 domain and other regions at their C-termini. Following overexpression in breast cancer cells MDA-MB231, we found that BECN1-α stimulates autophagy. Specifically, BECN1-α binds to Parkin and stimulates mitophagy. On the contrary, BECN1-β reduces autophagy with a dominant negative effect over the endogenous wild-type isoform. BECN1-γ maintains its ability to interact with the vacuolar protein sorting 34 and only has a slight effect on autophagy. It is possible that cancer cells utilize the alternative splicing of BECN1 for modulating autophagy and mitophagy in response to environmental stresses.
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Affiliation(s)
| | | | | | | | | | - Carlo Follo
- Correspondence: (C.F.); (C.I.); Tel.: +39-0321660507 (C.I.); Fax: +39-0321620421 (C.I.)
| | - Ciro Isidoro
- Correspondence: (C.F.); (C.I.); Tel.: +39-0321660507 (C.I.); Fax: +39-0321620421 (C.I.)
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5
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Tran S, Fairlie WD, Lee EF. BECLIN1: Protein Structure, Function and Regulation. Cells 2021; 10:cells10061522. [PMID: 34204202 PMCID: PMC8235419 DOI: 10.3390/cells10061522] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023] Open
Abstract
BECLIN1 is a well-established regulator of autophagy, a process essential for mammalian survival. It functions in conjunction with other proteins to form Class III Phosphoinositide 3-Kinase (PI3K) complexes to generate phosphorylated phosphatidylinositol (PtdIns), lipids essential for not only autophagy but other membrane trafficking processes. Over the years, studies have elucidated the structural, biophysical, and biochemical properties of BECLIN1, which have shed light on how this protein functions to allosterically regulate these critical processes of autophagy and membrane trafficking. Here, we review these findings and how BECLIN1’s diverse protein interactome regulates it, as well as its impact on organismal physiology.
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Affiliation(s)
- Sharon Tran
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
| | - W. Douglas Fairlie
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (W.D.F.); (E.F.L.)
| | - Erinna F. Lee
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC 3084, Australia;
- School of Cancer Medicine, La Trobe University, Bundoora, VIC 3086, Australia
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC 3086, Australia
- Correspondence: (W.D.F.); (E.F.L.)
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6
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Hu YJ, Zhong JT, Gong L, Zhang SC, Zhou SH. Autophagy-Related Beclin 1 and Head and Neck Cancers. Onco Targets Ther 2020; 13:6213-6227. [PMID: 32669852 PMCID: PMC7335767 DOI: 10.2147/ott.s256072] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Beclin 1, a positive regulator of autophagy, behaves as a double-edged sword in tumorigenesis. Beclin 1 contributes to tumor suppression by removing defective or damaged organelles and other cellular components; however, its activity can also stimulate cancer initiation and progression. In head and neck cancer, Beclin 1 overexpression promotes autophagy, which limits DNA damage and chromosomal instability and increases necrosis and inflammation by impacting apoptotic and autophagic pathways. This paper reviews the relationship between Beclin 1, carcinogenesis and head and neck cancer prognosis.
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Affiliation(s)
- Yang-Jie Hu
- Department of Otolaryngology, The Affiliated Cixi Hospital of Wenzhou Medical University, Cixi 315300, Zhejiang, People's Republic of China.,Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, People's Republic of China
| | - Jiang-Tao Zhong
- Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, People's Republic of China
| | - Liang Gong
- Department of Otolaryngology, The Affiliated Cixi Hospital of Wenzhou Medical University, Cixi 315300, Zhejiang, People's Republic of China
| | - Si-Cong Zhang
- Department of Otolaryngology, The Affiliated Cixi Hospital of Wenzhou Medical University, Cixi 315300, Zhejiang, People's Republic of China
| | - Shui-Hong Zhou
- Department of Otolaryngology, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, People's Republic of China
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7
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Popelka H. Dancing while self-eating: Protein intrinsic disorder in autophagy. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 174:263-305. [PMID: 32828468 DOI: 10.1016/bs.pmbts.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Autophagy is a major catabolic pathway that must be tightly regulated to maintain cellular homeostasis. Protein intrinsic disorder provides a very suitable conformation for regulation; accordingly, the molecular machinery of autophagy is significantly enriched in intrinsically disordered proteins and protein regions (IDPs/IDPRs). Despite experimental challenges that the characterization of IDPRs encounters, remarkable progress has been made in recent years in revealing various roles of IDPs/IDPRs in autophagy. This chapter describes the autophagy pathway from a specific point of view, that of IDPRs. It focuses in detail on structural and mechanistic functions in autophagy that are executed by disordered regions. Via a description of autophagosome biogenesis, linking the cargo to the autophagy machinery, as well as a discussion of certain post-translational regulations, this review reveals many indispensable roles of IDPRs in the functional autophagy pathway. Devastating pathologies such as neurodegeneration, cancer, or diabetes have been linked to a malfunction in IDPs/IDPRs. The same pathologies are associated with dysfunctional autophagy, indicating that autophagic IDPRs may be a paramount causative factor. Several disease-related mechanisms of the autophagy pathway involving protein intrinsic disorder are reported in this chapter, to illustrate a wide-ranging potential of IDPRs in the therapeutic modulation of autophagy.
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Affiliation(s)
- Hana Popelka
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, United States.
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8
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The Bcl-2 Family: Ancient Origins, Conserved Structures, and Divergent Mechanisms. Biomolecules 2020; 10:biom10010128. [PMID: 31940915 PMCID: PMC7022251 DOI: 10.3390/biom10010128] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 12/18/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022] Open
Abstract
Intrinsic apoptosis, the response to intracellular cell death stimuli, is regulated by the interplay of the B-cell lymphoma 2 (Bcl-2) family and their membrane interactions. Bcl-2 proteins mediate a number of processes including development, homeostasis, autophagy, and innate and adaptive immune responses and their dysregulation underpins a host of diseases including cancer. The Bcl-2 family is characterized by the presence of conserved sequence motifs called Bcl-2 homology motifs, as well as a transmembrane region, which form the interaction sites and intracellular location mechanism, respectively. Bcl-2 proteins have been recognized in the earliest metazoans including Porifera (sponges), Placozoans, and Cnidarians (e.g., Hydra). A number of viruses have gained Bcl-2 homologs and subvert innate immunity and cellular apoptosis for their replication, but they frequently have very different sequences to their host Bcl-2 analogs. Though most mechanisms of apoptosis initiation converge on activation of caspases that destroy the cell from within, the numerous gene insertions, deletions, and duplications during evolution have led to a divergence in mechanisms of intrinsic apoptosis. Currently, the action of the Bcl-2 family is best understood in vertebrates and nematodes but new insights are emerging from evolutionarily earlier organisms. This review focuses on the mechanisms underpinning the activity of Bcl-2 proteins including their structures and interactions, and how they have changed over the course of evolution.
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9
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Fairlie WD, Tran S, Lee EF. Crosstalk between apoptosis and autophagy signaling pathways. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2020; 352:115-158. [DOI: 10.1016/bs.ircmb.2020.01.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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10
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Vega-Rubín-de-Celis S. The Role of Beclin 1-Dependent Autophagy in Cancer. BIOLOGY 2019; 9:biology9010004. [PMID: 31877888 PMCID: PMC7168252 DOI: 10.3390/biology9010004] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
Autophagy (self-eating) is an intracellular degradation process used by cells to keep a “clean house”; as it degrades abnormal or damaged proteins and organelles, it helps to fight infections and also provides energy in times of fasting or exercising. Autophagy also plays a role in cancer, although its precise function in each cancer type is still obscure, and whether autophagy plays a protecting (through the clearing of damaged organelles and protein aggregates and preventing DNA damage) or a promoting (by fueling the already stablished tumor) role in cancer remains to be fully characterized. Beclin 1, the mammalian ortholog of yeast Atg6/Vps30, is an essential autophagy protein and has been shown to play a role in tumor suppression. Here, an update of the tumorigenesis regulation by Beclin 1-dependent autophagy is provided.
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Affiliation(s)
- Silvia Vega-Rubín-de-Celis
- Institute for Cell Biology (Tumorforschung), University Hospital Essen, 45122 Essen, Germany; ; Tel.: +49-0201-723-3941
- German Cancer Consortium (DKTK) at Essen-Düsseldorf, 445122 Essen, Germany
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11
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Wen J, Mai Z, Zhao M, Wang X, Chen T. Full anti-apoptotic function of Bcl-XL complexed with Beclin-1 verified by live-cell FRET assays. Biochem Biophys Res Commun 2019; 511:700-704. [PMID: 30827509 DOI: 10.1016/j.bbrc.2019.02.107] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 02/20/2019] [Indexed: 10/27/2022]
Abstract
Binding of Bcl-XL to Beclin-1 reduces Beclin-1's capacity to induce autophagy. This report aims to explore whether this interaction affects Bcl-XL's anti-apoptotic function. Using fluorescence resonance energy transfer (FRET) two-hybrid assay to quantify the stoichiometry of Bcl-XL-Beclin-1 complex in living cells coexpressing Bcl-XL-CFP and Beclin-1-YFP, we showed that Bcl-XL bond to Beclin-1 to form hetero-oligomers whose stoichiometry increases from 1:1 to 2:1 or higher with the increasing relative expression level of Bcl-XL, indicating the multiple binding sites of Beclin-1 with Bcl-XL. Co-expression of Bcl-XL and Beclin-1 exhibited consistent anti-apoptotic ability against staurosporine (STS)-induced apoptosis with expression of Bcl-XL alone irrespective of the relative expression level between Beclin-1 and Bcl-XL. Collectively, Bcl-XL complexed with Beclin-1 maintains full anti-apoptotic ability independent of the stoichiometry of Bcl-XL-Beclin-1 complex.
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Affiliation(s)
- Junlin Wen
- Department of Pain Management, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Zihao Mai
- College of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Mengxin Zhao
- Department of Pain Management, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China
| | - Xiaoping Wang
- Department of Pain Management, The First Affiliated Hospital, Jinan University, Guangzhou, 510632, China.
| | - Tongsheng Chen
- College of Life Science, South China Normal University, Guangzhou, 510631, China
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12
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Lee EF, Smith NA, Soares da Costa TP, Meftahi N, Yao S, Harris TJ, Tran S, Pettikiriarachchi A, Perugini MA, Keizer DW, Evangelista M, Smith BJ, Fairlie WD. Structural insights into BCL2 pro-survival protein interactions with the key autophagy regulator BECN1 following phosphorylation by STK4/MST1. Autophagy 2019; 15:785-795. [PMID: 30626284 DOI: 10.1080/15548627.2018.1564557] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BECN1/Beclin 1 is a critical protein in the initiation of autophagosome formation. Recent studies have shown that phosphorylation of BECN1 by STK4/MST1 at threonine 108 (T108) within its BH3 domain blocks macroautophagy/autophagy by increasing BECN1 affinity for its negative regulators, the anti-apoptotic proteins BCL2/Bcl-2 and BCL2L1/Bcl-xL. It was proposed that this increased binding is due to formation of an electrostatic interaction with a conserved histidine residue on the anti-apoptotic molecules. Here, we performed biophysical studies which demonstrated that a peptide corresponding to the BECN1 BH3 domain in which T108 is phosphorylated (p-T108) does show increased affinity for anti-apoptotic proteins that is significant, though only minor (<2-fold). We also determined X-ray crystal structures of BCL2 and BCL2L1 with T108-modified BECN1 BH3 peptides, but only showed evidence of an interaction between the BH3 peptide and the conserved histidine residue when the histidine flexibility was restrained due to crystal contacts. These data, together with molecular dynamics studies, indicate that the histidine is highly flexible, even when complexed with BECN1 BH3. Binding studies also showed that detergent can increase the affinity of the interaction. Although this increase was similar for both the phosphorylated and non-phosphorylated peptides, it suggests factors such as membranes could impact on the interaction between BECN1 and BCL2 proteins, and therefore, on the regulation of autophagy. Hence, we propose that phosphorylation of BECN1 by STK4/MST1 can increase the affinity of the interaction between BECN1 and anti-apoptotic proteins and this interaction can be stabilized by local environmental factors. Abbreviations: asu: asymmetric unit; BH3: BCL2/Bcl-2 homology 3; DAPK: death associated protein kinase; MD: molecular dynamics; MST: microscale thermophoresis; NMR: nuclear magnetic resonance; PDB: protein data bank; p-T: phosphothreonine; SPR: surface plasmon resonance; STK4/MST1: serine/threonine kinase 4.
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Affiliation(s)
- Erinna F Lee
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia.,b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
| | - Nicholas A Smith
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | | | - Nastaran Meftahi
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - Shenggen Yao
- d Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Australia
| | - Tiffany J Harris
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia
| | - Sharon Tran
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
| | - Anne Pettikiriarachchi
- e Structural Biology Division , The Walter and Eliza Hall Institute of Medical Research , Parkville , Australia
| | - Matthew A Perugini
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - David W Keizer
- d Bio21 Molecular Science and Biotechnology Institute , The University of Melbourne , Parkville , Australia
| | - Marco Evangelista
- b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia
| | - Brian J Smith
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia
| | - W Douglas Fairlie
- a La Trobe Institute for Molecular Science , La Trobe University , Melbourne , Australia.,b Cell Death and Survival Group , Olivia Newton-John Cancer Research Institute , Heidelberg , Australia.,c School of Cancer Medicine , La Trobe University , Melbourne , Australia
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13
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Hill SM, Wrobel L, Rubinsztein DC. Post-translational modifications of Beclin 1 provide multiple strategies for autophagy regulation. Cell Death Differ 2018; 26:617-629. [PMID: 30546075 DOI: 10.1038/s41418-018-0254-9] [Citation(s) in RCA: 151] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/19/2018] [Accepted: 11/28/2018] [Indexed: 01/07/2023] Open
Abstract
Autophagy is a conserved intracellular degradation pathway essential for protein homeostasis, survival and development. Defects in autophagic pathways have been connected to a variety of human diseases, including cancer and neurodegeneration. In the process of macroautophagy, cytoplasmic cargo is enclosed in a double-membrane structure and fused to the lysosome to allow for digestion and recycling of material. Autophagosome formation is primed by the ULK complex, which enables the downstream production of PI(3)P, a key lipid signalling molecule, on the phagophore membrane. The PI(3)P is generated by the PI3 kinase (PI3K) complex, consisting of the core components VPS34, VPS15 and Beclin 1. Beclin 1 is a central player in autophagy and constitutes a molecular platform for the regulation of autophagosome formation and maturation. Post-translational modifications of Beclin 1 affect its stability, interactions and ability to regulate PI3K activity, providing the cell with a plethora of strategies to fine-tune the levels of autophagy. Being such an important regulator, Beclin 1 is a potential target for therapeutic intervention and interfering with the post-translational regulation of Beclin 1 could be one way of manipulating the levels of autophagy. In this review, we provide an overview of the known post-translational modifications of Beclin 1 that govern its role in autophagy and how these modifications are maintained by input from several upstream signalling pathways. ▓.
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Affiliation(s)
- Sandra M Hill
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - Lidia Wrobel
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK. .,UK Dementia Research Institute, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, UK.
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14
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Ranaghan MJ, Durney MA, Mesleh MF, McCarren PR, Garvie CW, Daniels DS, Carey KL, Skepner AP, Levine B, Perez JR. The Autophagy-Related Beclin-1 Protein Requires the Coiled-Coil and BARA Domains To Form a Homodimer with Submicromolar Affinity. Biochemistry 2017; 56:6639-6651. [PMID: 29185708 DOI: 10.1021/acs.biochem.7b00936] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Beclin-1 (BECN1) is an essential component of macroautophagy. This process is a highly conserved survival mechanism that recycles damaged cellular components or pathogens by encasing them in a bilayer vesicle that fuses with a lysosome to allow degradation of the vesicular contents. Mutations or altered expression profiles of BECN1 have been linked to various cancers and neurodegenerative diseases. Viruses, including HIV and herpes simplex virus 1 (HSV-1), are also known to specifically target BECN1 as a means of evading host defense mechanisms. Autophagy is regulated by the interaction between BECN1 and Bcl-2, a pro-survival protein in the apoptotic pathway that stabilizes the BECN1 homodimer. Disruption of the homodimer by phosphorylation or competitive binding promotes autophagy through an unknown mechanism. We report here the first recombinant synthesis (3-5 mg/L in an Escherichia coli culture) and characterization of full-length, human BECN1. Our analysis reveals that full-length BECN1 exists as a soluble homodimer (KD ∼ 0.45 μM) that interacts with Bcl-2 (KD = 4.3 ± 1.2 μM) and binds to lipid membranes. Dimerization is proposed to be mediated by a coiled-coil region of BECN1. A construct lacking the C-terminal BARA domain but including the coiled-coil region exhibits a homodimer KD 3.5-fold weaker than that of full-length BECN1, indicating that both the BARA domain and the coiled-coil region of BECN1 contribute to dimer formation. Using site-directed mutagenesis, we show that residues at the C-terminus of the coiled-coil region previously shown to interact with the BARA domain play a key role in dimerization and mutations weaken the interface by ∼5-fold.
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Affiliation(s)
- Matthew J Ranaghan
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Michael A Durney
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Michael F Mesleh
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Patrick R McCarren
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Colin W Garvie
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Douglas S Daniels
- Department of Chemistry, University of Dayton , 300 College Park, Dayton, Ohio 45469, United States
| | - Kimberly L Carey
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Adam P Skepner
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center , Dallas, Texas 75390, United States
| | - Jose R Perez
- Center for the Development of Therapeutics, Broad Institute of MIT and Harvard , 415 Main Street, Cambridge, Massachusetts 02142, United States
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15
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Glover K, Li Y, Mukhopadhyay S, Leuthner Z, Chakravarthy S, Colbert CL, Sinha SC. Structural transitions in conserved, ordered Beclin 1 domains essential to regulating autophagy. J Biol Chem 2017; 292:16235-16248. [PMID: 28798234 DOI: 10.1074/jbc.m117.804195] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 07/20/2017] [Indexed: 01/10/2023] Open
Abstract
Beclin 1 (BECN1) is a key regulator of autophagy, a critical catabolic homeostasis pathway that involves sequestration of selected cytoplasmic components by multilayered vesicles called autophagosomes, followed by lysosomal fusion and degradation. BECN1 is a core component of class III phosphatidylinositol-3-kinase complexes responsible for autophagosome nucleation. Without heterologous binding partners, BECN1 forms an antiparallel homodimer via its coiled-coil domain (CCD). However, the last 16 CCD residues, composing an "overlap helix" (OH), have been crystallized in two mutually exclusive states: either as part of the CCD or packed against the C-terminal β-α repeated, autophagy-specific domain (BARAD). Here, using CD spectroscopy, isothermal titration calorimetry, and small-angle X-ray scattering, we show that in the homodimeric state, the OH transitions between these two different packing states, with the predominant state comprising the OH packed against the BARAD, contrary to expectations based on known BECN1 interactions with heterologous partners. We confirmed this observation by comparing the impact of mutating four residues that mediate packing of the OH against both the CCD and BARAD on structure and stability of the CCD, the OH+BARAD, and the two-domain CCD-BARAD. Last, we used cellular assays to demonstrate that mutation of these OH-interface residues abrogates starvation-induced up-regulation of autophagy but does not affect basal autophagy. In summary, we have identified a BECN1 helical region that transitions between packing as part of either one of two conserved domains (i.e. the CCD or the BARAD). Our findings have important implications for the relative stability of autophagy-inactive and autophagy-active BECN1 complexes.
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Affiliation(s)
- Karen Glover
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Yue Li
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Shreya Mukhopadhyay
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Zoe Leuthner
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | | | - Christopher L Colbert
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
| | - Sangita C Sinha
- From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050 and
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16
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Su M, Li Y, Wyborny S, Neau D, Chakravarthy S, Levine B, Colbert CL, Sinha SC. BECN2 interacts with ATG14 through a metastable coiled-coil to mediate autophagy. Protein Sci 2017; 26:972-984. [PMID: 28218432 DOI: 10.1002/pro.3140] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/19/2022]
Abstract
ATG14 binding to BECN/Beclin homologs is essential for autophagy, a critical catabolic homeostasis pathway. Here, we show that the α-helical, coiled-coil domain (CCD) of BECN2, a recently identified mammalian BECN1 paralog, forms an antiparallel, curved homodimer with seven pairs of nonideal packing interactions, while the BECN2 CCD and ATG14 CCD form a parallel, curved heterodimer stabilized by multiple, conserved polar interactions. Compared to BECN1, the BECN2 CCD forms a weaker homodimer, but binds more tightly to the ATG14 CCD. Mutation of nonideal BECN2 interface residues to more ideal pairs improves homodimer self-association and thermal stability. Unlike BECN1, all BECN2 CCD mutants bind ATG14, although more weakly than wild type. Thus, polar BECN2 CCD interface residues result in a metastable homodimer, facilitating dissociation, but enable better interactions with polar ATG14 residues stabilizing the BECN2:ATG14 heterodimer. These structure-based mechanistic differences in BECN1 and BECN2 homodimerization and heterodimerization likely dictate competitive ATG14 recruitment.
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Affiliation(s)
- Minfei Su
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Yue Li
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Shane Wyborny
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - David Neau
- Department of Chemistry and Chemical Biology, Cornell University, Northeastern Collaborative Access Team, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Srinivas Chakravarthy
- Biophysics Collaborative Access Team/Illinois Institute of Technology, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois, 60439
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine and Howard Hughes Medical Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, 75390
| | - Christopher L Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Sangita C Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
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17
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Qian X, Li X, Cai Q, Zhang C, Yu Q, Jiang Y, Lee JH, Hawke D, Wang Y, Xia Y, Zheng Y, Jiang BH, Liu DX, Jiang T, Lu Z. Phosphoglycerate Kinase 1 Phosphorylates Beclin1 to Induce Autophagy. Mol Cell 2017; 65:917-931.e6. [PMID: 28238651 DOI: 10.1016/j.molcel.2017.01.027] [Citation(s) in RCA: 192] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 10/28/2016] [Accepted: 01/17/2017] [Indexed: 12/13/2022]
Abstract
Autophagy is crucial for maintaining cell homeostasis. However, the precise mechanism underlying autophagy initiation remains to be defined. Here, we demonstrate that glutamine deprivation and hypoxia result in inhibition of mTOR-mediated acetyl-transferase ARD1 S228 phosphorylation, leading to ARD1-dependent phosphoglycerate kinase 1 (PGK1) K388 acetylation and subsequent PGK1-mediated Beclin1 S30 phosphorylation. This phosphorylation enhances ATG14L-associated class III phosphatidylinositol 3-kinase VPS34 activity by increasing the binding of phosphatidylinositol to VPS34. ARD1-dependent PGK1 acetylation and PGK1-mediated Beclin1 S30 phosphorylation are required for glutamine deprivation- and hypoxia-induced autophagy and brain tumorigenesis. Furthermore, PGK1 K388 acetylation levels correlate with Beclin1 S30 phosphorylation levels and poor prognosis in glioblastoma patients. Our study unearths an important mechanism underlying cellular-stress-induced autophagy initiation in which the protein kinase activity of the metabolic enzyme PGK1 plays an instrumental role and reveals the significance of the mutual regulation of autophagy and cell metabolism in maintaining cell homeostasis.
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Affiliation(s)
- Xu Qian
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xinjian Li
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qingsong Cai
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chuanbao Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China
| | - Qiujing Yu
- The Institute of Cell Metabolism and Diseases, Shanghai Key Laboratory of Pancreatic Cancer, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China
| | - Yuhui Jiang
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Institute of Cell Metabolism and Diseases, Shanghai Key Laboratory of Pancreatic Cancer, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China
| | - Jong-Ho Lee
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - David Hawke
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yugang Wang
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yan Xia
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Institute of Cell Metabolism and Diseases, Shanghai Key Laboratory of Pancreatic Cancer, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China
| | - Yanhua Zheng
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The Institute of Cell Metabolism and Diseases, Shanghai Key Laboratory of Pancreatic Cancer, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200080, China
| | - Bing-Hua Jiang
- State Key Lab of Reproductive Medicine, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Cancer Center, Department of Pathology, Nanjing Medical University, Nanjing 210029, China
| | - David X Liu
- Department of Pharmaceutical Sciences, Washington State University College of Pharmacy, Spokane, WA 99202, USA
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing 100050, China
| | - Zhimin Lu
- Brain Tumor Center and Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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18
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Chen Y, Wang X, Wang G, Li Z, Wang J, Huang L, Qin Z, Yuan X, Cheng Z, Zhang S, Yin Y, He J. Integrating multiple omics data for the discovery of potential Beclin-1 interactions in breast cancer. MOLECULAR BIOSYSTEMS 2017; 13:991-999. [PMID: 28401970 DOI: 10.1039/c6mb00653a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The genes and their three omics are computed to related to breast cancer using LASSO, a method for integrating multiple data.
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19
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Mei Y, Glover K, Su M, Sinha SC. Conformational flexibility of BECN1: Essential to its key role in autophagy and beyond. Protein Sci 2016; 25:1767-85. [PMID: 27414988 DOI: 10.1002/pro.2984] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/09/2016] [Accepted: 07/12/2016] [Indexed: 01/16/2023]
Abstract
BECN1 (Beclin 1), a highly conserved eukaryotic protein, is a key regulator of autophagy, a cellular homeostasis pathway, and also participates in vacuolar protein sorting, endocytic trafficking, and apoptosis. BECN1 is important for embryonic development, the innate immune response, tumor suppression, and protection against neurodegenerative disorders, diabetes, and heart disease. BECN1 mediates autophagy as a core component of the class III phosphatidylinositol 3-kinase complexes. However, the exact mechanism by which it regulates the activity of these complexes, or mediates its other diverse functions is unclear. BECN1 interacts with several diverse protein partners, perhaps serving as a scaffold or interaction hub for autophagy. Based on extensive structural, biophysical and bioinformatics analyses, BECN1 consists of an intrinsically disordered region (IDR), which includes a BH3 homology domain (BH3D); a flexible helical domain (FHD); a coiled-coil domain (CCD); and a β-α-repeated autophagy-specific domain (BARAD). Each of these BECN1 domains mediates multiple diverse interactions that involve concomitant conformational changes. Thus, BECN1 conformational flexibility likely plays a key role in facilitating diverse protein interactions. Further, BECN1 conformation and interactions are also modulated by numerous post-translational modifications. A better structure-based understanding of the interplay between different BECN1 conformational and binding states, and the impact of post-translational modifications will be essential to elucidating the mechanism of its multiple biological roles.
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Affiliation(s)
- Yang Mei
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Karen Glover
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Minfei Su
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050
| | - Sangita C Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota, 58108-6050.
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20
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Characterisation of the conformational preference and dynamics of the intrinsically disordered N-terminal region of Beclin 1 by NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1128-1137. [PMID: 27288992 DOI: 10.1016/j.bbapap.2016.06.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/23/2016] [Accepted: 06/07/2016] [Indexed: 11/21/2022]
Abstract
Beclin 1 is a 450 amino acid protein that plays critical roles in the early stages of autophagosome formation. We recently reported the successful expression, purification and structural characterisation of the entire N-terminal region of Beclin 1 (residues 1-150), including its backbone NMR chemical shift assignments. Based on assigned backbone NMR chemical shifts, it has been established that the N-terminal region of Beclin 1 (1-150), including the BH3 domain (112-123), is intrinsically disordered in the absence of its interaction partners. Here, a detailed study of its conformational preference and backbone dynamics obtained from an analysis of its secondary structure populations using the δ2D method, and the measurements of effective hydrodynamic radius as well as (1)H temperature coefficients, (1)H solvent exchange rates, and (15)N relaxation parameters of backbone amides using NMR spectroscopy is reported. These data provide further evidence for the intrinsically disordered nature of the N-terminal region of Beclin 1 and support the view that the helical conformation adopted by the Beclin 1 BH3 domain upon interaction with binding partners such as BCL-2 pro-survival proteins is likely induced rather than pre-existing.
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