101
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Suzuki H, Osawa T, Fujioka Y, Noda NN. Structural biology of the core autophagy machinery. Curr Opin Struct Biol 2016; 43:10-17. [PMID: 27723509 DOI: 10.1016/j.sbi.2016.09.010] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 09/13/2016] [Accepted: 09/21/2016] [Indexed: 02/08/2023]
Abstract
In autophagy, which is an intracellular degradation system that is conserved among eukaryotes, degradation targets are sequestered through the de novo synthesis of a double-membrane organelle, the autophagosome, which delivers them to the lysosomes for degradation. The core autophagy machinery comprising 18 autophagy-related (Atg) proteins in yeast plays an essential role in autophagosome formation; however, the molecular role of each Atg factor and the mechanism of autophagosome formation remain elusive. Recent years have seen remarkable progress in structural biological studies on the core autophagy machinery, opening new avenues for autophagy research. This review summarizes recent advances in structural biological and mechanistic studies on the core autophagy machinery and discusses the molecular mechanisms of autophagosome formation.
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Affiliation(s)
- Hironori Suzuki
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Takuo Osawa
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Yuko Fujioka
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Nobuo N Noda
- Institute of Microbial Chemistry, Microbial Chemistry Research Foundation, 3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan.
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102
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Takizawa Y, Binshtein E, Erwin AL, Pyburn TM, Mittendorf KF, Ohi MD. While the revolution will not be crystallized, biochemistry reigns supreme. Protein Sci 2016; 26:69-81. [PMID: 27673321 DOI: 10.1002/pro.3054] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 09/22/2016] [Indexed: 12/14/2022]
Abstract
Single-particle cryo-electron microscopy (EM) is currently gaining attention for the ability to calculate structures that reach sub-5 Å resolutions; however, the technique is more than just an alternative approach to X-ray crystallography. Molecular machines work via dynamic conformational changes, making structural flexibility the hallmark of function. While the dynamic regions in molecules are essential, they are also the most challenging to structurally characterize. Single-particle EM has the distinct advantage of being able to directly visualize purified molecules without the formation of ordered arrays of molecules locked into identical conformations. Additionally, structures determined using single-particle EM can span resolution ranges from very low- to atomic-levels (>30-1.8 Å), sometimes even in the same structure. The ability to accommodate various resolutions gives single-particle EM the unique capacity to structurally characterize dynamic regions of biological molecules, thereby contributing essential structural information needed for the development of molecular models that explain function. Further, many important molecular machines are intrinsically dynamic and compositionally heterogeneous. Structures of these complexes may never reach sub-5 Å resolutions due to this flexibility required for function. Thus, the biochemical quality of the sample, as well as, the calculation and interpretation of low- to mid-resolution cryo-EM structures (30-8 Å) remains critical for generating insights into the architecture of many challenging biological samples that cannot be visualized using alternative techniques.
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Affiliation(s)
- Yoshimasa Takizawa
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Elad Binshtein
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Amanda L Erwin
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Tasia M Pyburn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
| | - Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center Vanderbilt University Medical Center, Nashville, Tennessee, 37232
| | - Melanie D Ohi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, 37232.,Center for Structural Biology Vanderbilt University, Nashville, Tennessee, 37232
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103
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Ohashi Y, Soler N, García Ortegón M, Zhang L, Kirsten ML, Perisic O, Masson GR, Burke JE, Jakobi AJ, Apostolakis AA, Johnson CM, Ohashi M, Ktistakis NT, Sachse C, Williams RL. Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex. Autophagy 2016; 12:2129-2144. [PMID: 27630019 PMCID: PMC5103362 DOI: 10.1080/15548627.2016.1226736] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with these assemblies. Combining hydrogen-deuterium exchange mass spectrometry (HDX-MS), X-ray crystallography and electron microscopy (EM), we have characterized Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human). HDX-MS shows that Atg38 binds the Vps30-Atg14 subcomplex of complex I, using mainly its N-terminal MIT domain and bridges the coiled-coil I regions of Atg14 and Vps30 in the base of complex I. The Atg38 C-terminal domain is important for localization to the phagophore assembly site (PAS) and homodimerization. Our 2.2 Å resolution crystal structure of the Atg38 C-terminal homodimerization domain shows 2 segments of α-helices assembling into a mushroom-like asymmetric homodimer with a 4-helix cap and a parallel coiled-coil stalk. One Atg38 homodimer engages a single complex I. This is in sharp contrast to human NRBF2, which also forms a homodimer, but this homodimer can bridge 2 complex I assemblies.
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Affiliation(s)
- Yohei Ohashi
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - Nicolas Soler
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | | | - Lufei Zhang
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - Marie L Kirsten
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Olga Perisic
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - Glenn R Masson
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | - John E Burke
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Arjen J Jakobi
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany.,c European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany
| | | | | | - Maki Ohashi
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
| | | | - Carsten Sachse
- b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany
| | - Roger L Williams
- a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom
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104
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Hurley JH, Nogales E. Next-generation electron microscopy in autophagy research. Curr Opin Struct Biol 2016; 41:211-216. [PMID: 27614295 DOI: 10.1016/j.sbi.2016.08.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Revised: 08/25/2016] [Accepted: 08/25/2016] [Indexed: 12/24/2022]
Abstract
Autophagy is the process whereby cytosol, organelles, and inclusions are taken up in a double-membrane vesicle known as the autophagosome, and transported to the lysosome for destruction and recycling. Electron microscopy (EM) led to the discovery of autophagy in the 1950s and has been a central part of its characterization ever since. New capabilities in single particle EM studies of the autophagy machinery are beginning to provide exciting insights into the mechanisms of autophagosome initiation, growth, and substrate targeting. These include EM structures at various resolutions of part of the Atg1 protein kinase complex and all of the class III phosphatidylinositol 3-phosphate complex I that initiate autophagy; the mTORC1 complex that regulates autophagy initiation; the Ape1 particle, a major substrate for selective autophagy in yeast; and p62, a mammalian selective autophagy adaptor. Equally exciting are the prospects for increased resolution and insight into autophagosome formation in cells from advances in cryo-EM tomography and focused ion beam-scanning electron microscopy (FIB-SEM). This review considers recent accomplishments, prospects for progress, and remaining obstacles that still need to be overcome.
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Affiliation(s)
- James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, CA 94720, USA.
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105
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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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106
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Deretic V. Autophagy in leukocytes and other cells: mechanisms, subsystem organization, selectivity, and links to innate immunity. J Leukoc Biol 2016; 100:969-978. [PMID: 27493243 DOI: 10.1189/jlb.4mr0216-079r] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 07/06/2016] [Indexed: 12/20/2022] Open
Abstract
Autophagy is a fundamental biologic process that fulfills general and specialized roles in cytoplasmic homeostasis. The cell-autonomous antimicrobial functions of autophagy have been established in the macrophage. These cells and other leukocytes continue to be the cells of choice in studying autophagy in immunity and inflammation. This review uses several model examples that will be of interest to leukocyte and cell biologists alike. Furthermore, it comprehensively covers the subsystems in autophagy as they apply to all mammalian cells and incorporates the recent progress in our understanding of how these modules come together-a topic that should be of interest to all readers.
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Affiliation(s)
- Vojo Deretic
- Department of Molecular Genetics and Microbiology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
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107
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Mei Y, Su M, Sanishvili R, Chakravarthy S, Colbert CL, Sinha SC. Identification of BECN1 and ATG14 Coiled-Coil Interface Residues That Are Important for Starvation-Induced Autophagy. Biochemistry 2016; 55:4239-53. [PMID: 27383850 PMCID: PMC5116031 DOI: 10.1021/acs.biochem.6b00246] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Autophagy, an essential eukaryotic homeostasis pathway, allows the sequestration of unwanted, damaged, or harmful cytoplasmic components in vesicles called autophagosomes, permitting subsequent lysosomal degradation and nutrient recycling. Autophagosome nucleation is mediated by class III phosphatidylinositol-3-kinase complexes that include two key autophagy proteins, BECN1/Beclin 1 and ATG14/BARKOR, which form parallel heterodimers via their coiled-coil domains (CCDs). Here we present the 1.46 Å X-ray crystal structure of the antiparallel, human BECN1 CCD homodimer, which represents BECN1 oligomerization outside the autophagosome nucleation complex. We use circular dichroism and small-angle X-ray scattering (SAXS) to show that the ATG14 CCD is significantly disordered but becomes more helical in the BECN1:ATG14 heterodimer, although it is less well-folded than the BECN1 CCD homodimer. SAXS also indicates that the BECN1:ATG14 heterodimer is more curved than other BECN1-containing CCD dimers, which has important implications for the structure of the autophagosome nucleation complex. A model of the BECN1:ATG14 CCD heterodimer that agrees well with the SAXS data shows that BECN1 residues at the homodimer interface are also responsible for heterodimerization, allowing us to identify ATG14 interface residues. Finally, we verify the role of BECN1 and ATG14 interface residues in binding by assessing the impact of point mutations of these residues on co-immunoprecipitation of the partner and demonstrate that these mutations abrogate starvation-induced upregulation of autophagy but do not impact basal autophagy. Thus, this research provides insights into structures of the BECN1 CCD homodimer and the BECN1:ATG14 CCD heterodimer and identifies interface residues that are important for BECN1:ATG14 heterodimerization and for autophagy.
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Affiliation(s)
- Yang Mei
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Minfei Su
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Srinivas Chakravarthy
- Bio-CAT, Advanced Photon Source, 9700 South Cass Avenue, Bldg. 435B, Argonne, IL 60439, USA
| | - Christopher L. Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
| | - Sangita C. Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108-6050, USA
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108
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Ktistakis NT, Tooze SA. Digesting the Expanding Mechanisms of Autophagy. Trends Cell Biol 2016; 26:624-635. [PMID: 27050762 DOI: 10.1016/j.tcb.2016.03.006] [Citation(s) in RCA: 264] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/03/2016] [Accepted: 03/14/2016] [Indexed: 12/17/2022]
Abstract
Autophagy is a catabolic 'self-eating' pathway that is emerging as a crucial integration point in cell physiology. With its own set of genes, the autophagy pathway communicates with virtually all signalling networks and organelles. Recent advances have been made in understanding the origin of the autophagosomal membrane, novel regulators, and the mechanisms by which specific intracellular membranes become autophagy substrates. New studies on noncanonical autophagy, mediated by subsets of autophagy proteins, and the role of autophagy proteins in non-autophagy pathways are also emerging in many different biological contexts. Our understanding of canonical autophagy, including membrane origin and autophagy proteins, needs to be considered together with emerging noncanonical pathways.
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Affiliation(s)
| | - Sharon A Tooze
- Molecular Cell Biology of Autophagy, Francis Crick Institute, London, UK.
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109
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Dynamics and architecture of the NRBF2-containing phosphatidylinositol 3-kinase complex I of autophagy. Proc Natl Acad Sci U S A 2016; 113:8224-9. [PMID: 27385829 DOI: 10.1073/pnas.1603650113] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The class III phosphatidylinositol 3-kinase complex I (PI3KC3-C1) is central to autophagy initiation. We previously reported the V-shaped architecture of the four-subunit version of PI3KC3-C1 consisting of VPS (vacuolar protein sorting) 34, VPS15, BECN1 (Beclin 1), and ATG (autophagy-related) 14. Here we show that a putative fifth subunit, nuclear receptor binding factor 2 (NRBF2), is a tightly bound component of the complex that profoundly affects its activity and architecture. NRBF2 enhances the lipid kinase activity of the catalytic subunit, VPS34, by roughly 10-fold. We used hydrogen-deuterium exchange coupled to mass spectrometry and negative-stain electron microscopy to map NRBF2 to the base of the V-shaped complex. NRBF2 interacts primarily with the N termini of ATG14 and BECN1. We show that NRBF2 is a homodimer and drives the dimerization of the larger PI3KC3-C1 complex, with implications for the higher-order organization of the preautophagosomal structure.
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110
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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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111
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Turco E, Martens S. Insights into autophagosome biogenesis from in vitro reconstitutions. J Struct Biol 2016; 196:29-36. [PMID: 27251905 PMCID: PMC5039013 DOI: 10.1016/j.jsb.2016.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/11/2016] [Accepted: 04/12/2016] [Indexed: 01/01/2023]
Abstract
Macro-autophagy (autophagy) is a conserved catabolic pathway for the degradation of cytoplasmic material in the lysosomal system. This is achieved by the sequestration of the cytoplasmic cargo material within double membrane-bound vesicles that fuse with lysosomes, wherein the vesicle’s inner membrane and the cargo are degraded. Autophagosomes form in a de novo manner and their precursors are initially detected as small membrane structures that are referred to as isolation membranes. The isolation membranes gradually expand and subsequently close to give rise to autophagosomes. Many proteins required to form autophagosomes have been identified but how they act mechanistically is still enigmatic. Here we critically review reconstitution approaches employed to decipher the inner working of the fascinating autophagy machinery.
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Affiliation(s)
- Eleonora Turco
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
| | - Sascha Martens
- Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohr-Gasse 9, 1030 Vienna, Austria.
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112
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Advances in Autophagy Regulatory Mechanisms. Cells 2016; 5:cells5020024. [PMID: 27187479 PMCID: PMC4931673 DOI: 10.3390/cells5020024] [Citation(s) in RCA: 96] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 04/20/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
Autophagy plays a critical role in cell metabolism by degrading and recycling internal components when challenged with limited nutrients. This fundamental and conserved mechanism is based on a membrane trafficking pathway in which nascent autophagosomes engulf cytoplasmic cargo to form vesicles that transport their content to the lysosome for degradation. Based on this simple scheme, autophagy modulates cellular metabolism and cytoplasmic quality control to influence an unexpectedly wide range of normal mammalian physiology and pathophysiology. In this review, we summarise recent advancements in three broad areas of autophagy regulation. We discuss current models on how autophagosomes are initiated from endogenous membranes. We detail how the uncoordinated 51-like kinase (ULK) complex becomes activated downstream of mechanistic target of rapamycin complex 1 (MTORC1). Finally, we summarise the upstream signalling mechanisms that can sense amino acid availability leading to activation of MTORC1.
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113
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Mei Y, Ramanathan A, Glover K, Stanley C, Sanishvili R, Chakravarthy S, Yang Z, Colbert CL, Sinha SC. Conformational Flexibility Enables the Function of a BECN1 Region Essential for Starvation-Mediated Autophagy. Biochemistry 2016; 55:1945-58. [PMID: 26937551 DOI: 10.1021/acs.biochem.5b01264] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BECN1 is essential for autophagy, a critical eukaryotic cellular homeostasis pathway. Here we delineate a highly conserved BECN1 domain located between previously characterized BH3 and coiled-coil domains and elucidate its structure and role in autophagy. The 2.0 Å sulfur-single-wavelength anomalous dispersion X-ray crystal structure of this domain demonstrates that its N-terminal half is unstructured while its C-terminal half is helical; hence, we name it the flexible helical domain (FHD). Circular dichroism spectroscopy, double electron-electron resonance-electron paramagnetic resonance, and small-angle X-ray scattering (SAXS) analyses confirm that the FHD is partially disordered, even in the context of adjacent BECN1 domains. Molecular dynamic simulations fitted to SAXS data indicate that the FHD transiently samples more helical conformations. FHD helicity increases in 2,2,2-trifluoroethanol, suggesting it may become more helical upon binding. Lastly, cellular studies show that conserved FHD residues are required for starvation-induced autophagy. Thus, the FHD likely undergoes a binding-associated disorder-to-helix transition, and conserved residues critical for this interaction are essential for starvation-induced autophagy.
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Affiliation(s)
- Yang Mei
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108-6050, United States
| | - Arvind Ramanathan
- Health Data Sciences Institute, Computational Science and Engineering Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | - Karen Glover
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108-6050, United States
| | - Christopher Stanley
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Ruslan Sanishvili
- GMCA@APS, X-ray Science Division, Advanced Photon Source, Argonne National Laboratory , Argonne, Illinois 60439, United States
| | - Srinivas Chakravarthy
- Bio-CAT, Advanced Photon Source , 9700 South Cass Avenue, Building 435B, Argonne, Illinois 60439, United States
| | - Zhongyu Yang
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108-6050, United States
| | - Christopher L Colbert
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108-6050, United States
| | - Sangita C Sinha
- Department of Chemistry and Biochemistry, North Dakota State University , Fargo, North Dakota 58108-6050, United States
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114
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Mechanistically Dissecting Autophagy: Insights from In Vitro Reconstitution. J Mol Biol 2016; 428:1700-13. [PMID: 26946034 DOI: 10.1016/j.jmb.2016.02.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Revised: 02/19/2016] [Accepted: 02/19/2016] [Indexed: 12/13/2022]
Abstract
Autophagy is a fundamental cellular mechanism responsible for bulk turnover of cytoplasmic components. It is broadly related to many cellular activities, physiological processes, and pathological conditions. Autophagy entails a spatiotemporal interaction between cytosolic factors and membranes that are remodeled to encapsulate autophagic cargo within an autophagosome. Although majority of the factors [autophagy-related gene (Atg) proteins] involved in autophagy have been identified by genetic studies, the mechanism accounting for how these factors act upon the membrane to remodel it and efficiently recruit cargo for degradation is unclear. In vitro reconstitution of several different aspects of autophagy has provided important insights into the understanding of the mechanistic details underlying autophagic membrane remodeling and cargo recruitment. Here, we highlight these efforts toward studying autophagy through in vitro approaches.
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115
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Structure and function of the ULK1 complex in autophagy. Curr Opin Cell Biol 2016; 39:61-8. [PMID: 26921696 DOI: 10.1016/j.ceb.2016.02.010] [Citation(s) in RCA: 163] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 02/03/2016] [Accepted: 02/04/2016] [Indexed: 12/30/2022]
Abstract
The ULK1 complex initiates autophagosome formation, linking cellular nutrient status to downstream events in autophagy. Recent work suggests that the ULK1 complex might also be activated in selective autophagy independent of nutrient or energy status. In this review we will discuss our current understanding of how the ULK1 complex is regulated by different signals, as well as how this complex then regulates other components of the autophagy machinery. Recently obtained structural data both on ULK1 and the orthologous yeast Atg1 complex are beginning to shed light on the higher-order organization of ULK1 complex. Ultimately, these insights might make it possible to understand how cargo organization and structure recruits and regulates ULK1 in selective autophagy initiation.
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116
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Bento CF, Renna M, Ghislat G, Puri C, Ashkenazi A, Vicinanza M, Menzies FM, Rubinsztein DC. Mammalian Autophagy: How Does It Work? Annu Rev Biochem 2016; 85:685-713. [PMID: 26865532 DOI: 10.1146/annurev-biochem-060815-014556] [Citation(s) in RCA: 500] [Impact Index Per Article: 62.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Autophagy is a conserved intracellular pathway that delivers cytoplasmic contents to lysosomes for degradation via double-membrane autophagosomes. Autophagy substrates include organelles such as mitochondria, aggregate-prone proteins that cause neurodegeneration and various pathogens. Thus, this pathway appears to be relevant to the pathogenesis of diverse diseases, and its modulation may have therapeutic value. Here, we focus on the cell and molecular biology of mammalian autophagy and review the key proteins that regulate the process by discussing their roles and how these may be modulated by posttranslational modifications. We consider the membrane-trafficking events that impact autophagy and the questions relating to the sources of autophagosome membrane(s). Finally, we discuss data from structural studies and some of the insights these have provided.
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Affiliation(s)
- Carla F Bento
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Maurizio Renna
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Ghita Ghislat
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Claudia Puri
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Avraham Ashkenazi
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Mariella Vicinanza
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - Fiona M Menzies
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
| | - David C Rubinsztein
- Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge Biomedical Campus, Cambridge CB2 0XY, United Kingdom;
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117
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Lee EF, Perugini MA, Pettikiriarachchi A, Evangelista M, Keizer DW, Yao S, Fairlie WD. The BECN1 N-terminal domain is intrinsically disordered. Autophagy 2016; 12:460-71. [PMID: 27046249 PMCID: PMC4836020 DOI: 10.1080/15548627.2016.1140292] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/16/2015] [Accepted: 01/04/2016] [Indexed: 10/22/2022] Open
Abstract
BECN1/Beclin 1 has a critical role in the early stages of autophagosome formation. Recently, structures of its central and C-terminal domains were reported, however, little structural information is available on the N-terminal domain, comprising a third of the protein. This lack of structural information largely stems from the inability to produce this region in a purified form. Here, we describe the expression and purification of the N-terminal domain of BECN1 (residues 1 to 150) and detailed biophysical characterization, including NMR spectroscopy. Combined, our studies demonstrated at the atomic level that the BECN1 N-terminal domain is intrinsically disordered, and apart from the BH3 subdomain, remains disordered following interaction with a binding partner, BCL2L1/BCL-XL. In addition, the BH3 domain α-helix induced upon interaction with BCL2L1 reverts to a disordered state when the complex is dissociated by exposure to a competitive inhibitor. No significant interactions between N- and C-terminal domains were detected.
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Affiliation(s)
- Erinna F. Lee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
| | - Matthew A. Perugini
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | | | - Marco Evangelista
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
| | - David W. Keizer
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Shenggen Yao
- Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - W. Douglas Fairlie
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Victoria, Australia
- Department of Chemistry and Physics, La Trobe Institute for Molecular Science, Melbourne, Victoria, Australia
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118
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Wesselborg S, Stork B. Autophagy signal transduction by ATG proteins: from hierarchies to networks. Cell Mol Life Sci 2015; 72:4721-57. [PMID: 26390974 PMCID: PMC4648967 DOI: 10.1007/s00018-015-2034-8] [Citation(s) in RCA: 169] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 08/13/2015] [Accepted: 08/31/2015] [Indexed: 02/07/2023]
Abstract
Autophagy represents an intracellular degradation process which is involved in both cellular homeostasis and disease settings. In the last two decades, the molecular machinery governing this process has been characterized in detail. To date, several key factors regulating this intracellular degradation process have been identified. The so-called autophagy-related (ATG) genes and proteins are central to this process. However, several additional molecules contribute to the outcome of an autophagic response. Several review articles describing the molecular process of autophagy have been published in the recent past. In this review article we would like to add the most recent findings to this knowledge, and to give an overview of the network character of the autophagy signaling machinery.
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Affiliation(s)
- Sebastian Wesselborg
- Institute of Molecular Medicine I, Heinrich-Heine-University, Universitätsstr. 1, Building 23.12, 40225, Düsseldorf, Germany
| | - Björn Stork
- Institute of Molecular Medicine I, Heinrich-Heine-University, Universitätsstr. 1, Building 23.12, 40225, Düsseldorf, Germany.
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119
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Morris DH, Yip CK, Shi Y, Chait BT, Wang QJ. BECLIN 1-VPS34 COMPLEX ARCHITECTURE: UNDERSTANDING THE NUTS AND BOLTS OF THERAPEUTIC TARGETS. ACTA ACUST UNITED AC 2015; 10:398-426. [PMID: 26692106 DOI: 10.1007/s11515-015-1374-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Autophagy is an important lysosomal degradation pathway that aids in the maintenance of cellular homeostasis by breaking down and recycling intracellular contents. Dysregulation of autophagy is linked to a growing number of human diseases. The Beclin 1-Vps34 protein-protein interaction network is critical for autophagy regulation and is therefore essential to cellular integrity. Manipulation of autophagy, in particular via modulation of the action of the Beclin 1-Vps34 complexes, is considered a promising route to combat autophagy-related diseases. Here we summarize recent findings on the core components and structural architecture of the Beclin 1-Vps34 complexes, and how these findings provide valuable insights into the molecular mechanisms that underlie the multiple functions of these complexes and for devising therapeutic strategies.
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Affiliation(s)
- Deanna H Morris
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536
| | - Calvin K Yip
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC, Canada V6T1Z3
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY 10065
| | - Qing Jun Wang
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536 ; Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY 40536, USA ; Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
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120
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Rostislavleva K, Soler N, Ohashi Y, Zhang L, Pardon E, Burke JE, Masson GR, Johnson C, Steyaert J, Ktistakis NT, Williams RL. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science 2015; 350:aac7365. [PMID: 26450213 DOI: 10.1126/science.aac7365] [Citation(s) in RCA: 174] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphatidylinositol 3-kinase Vps34 complexes regulate intracellular membrane trafficking in endocytic sorting, cytokinesis, and autophagy. We present the 4.4 angstrom crystal structure of the 385-kilodalton endosomal complex II (PIK3C3-CII), consisting of Vps34, Vps15 (p150), Vps30/Atg6 (Beclin 1), and Vps38 (UVRAG). The subunits form a Y-shaped complex, centered on the Vps34 C2 domain. Vps34 and Vps15 intertwine in one arm, where the Vps15 kinase domain engages the Vps34 activation loop to regulate its activity. Vps30 and Vps38 form the other arm that brackets the Vps15/Vps34 heterodimer, suggesting a path for complex assembly. We used hydrogen-deuterium exchange mass spectrometry (HDX-MS) to reveal conformational changes accompanying membrane binding and identify a Vps30 loop that is critical for the ability of complex II to phosphorylate giant liposomes on which complex I is inactive.
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Affiliation(s)
| | - Nicolas Soler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Yohei Ohashi
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Lufei Zhang
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Els Pardon
- Structural Biology Research Center, VIB, B-1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussel, Belgium
| | - John E Burke
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Glenn R Masson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Chris Johnson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Jan Steyaert
- Structural Biology Research Center, VIB, B-1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, B-1050 Brussel, Belgium
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121
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Qi S, Kim DJ, Stjepanovic G, Hurley JH. Structure of the Human Atg13-Atg101 HORMA Heterodimer: an Interaction Hub within the ULK1 Complex. Structure 2015; 23:1848-1857. [PMID: 26299944 PMCID: PMC4598286 DOI: 10.1016/j.str.2015.07.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Revised: 07/13/2015] [Accepted: 07/20/2015] [Indexed: 01/01/2023]
Abstract
The ULK1 complex, consisting of the ULK1 protein kinase itself, FIP200, Atg13, and Atg101, controls the initiation of autophagy in animals. We determined the structure of the complex of the human Atg13 HORMA (Hop1, Rev7, Mad2) domain in complex with the full-length HORMA domain-only protein Atg101. The two HORMA domains assemble with an architecture conserved in the Mad2 conformational heterodimer and the S. pombe Atg13-Atg101 HORMA complex. The WF finger motif that is essential for function in human Atg101 is sequestered in a hydrophobic pocket, suggesting that the exposure of this motif is regulated. Benzamidine molecules from the crystallization solution mark two hydrophobic pockets that are conserved in, and unique to, animals, and are suggestive of sites that could interact with other proteins. These features suggest that the activity of the animal Atg13-Atg101 subcomplex is regulated and that it is an interaction hub for multiple partners.
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Affiliation(s)
- Shiqian Qi
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Do Jin Kim
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Goran Stjepanovic
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James H Hurley
- Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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122
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Shi Y, Pellarin R, Fridy PC, Fernandez-Martinez J, Thompson MK, Li Y, Wang QJ, Sali A, Rout MP, Chait BT. A strategy for dissecting the architectures of native macromolecular assemblies. Nat Methods 2015; 12:1135-8. [PMID: 26436480 DOI: 10.1038/nmeth.3617] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 08/20/2015] [Indexed: 02/07/2023]
Abstract
It remains particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here we present a strategy for isolating complexes at endogenous levels from GFP-tagged transgenic cell lines. Using cross-linking mass spectrometry, we extracted distance restraints that allowed us to model the complexes' molecular architectures.
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Affiliation(s)
- Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA.,Institut Pasteur, Paris, France
| | - Peter C Fridy
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | | | - Mary K Thompson
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Yinyin Li
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | | | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.,Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, California, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
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123
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Ciferri C, Lander GC, Nogales E. Protein domain mapping by internal labeling and single particle electron microscopy. J Struct Biol 2015; 192:159-62. [PMID: 26431894 DOI: 10.1016/j.jsb.2015.09.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Revised: 09/26/2015] [Accepted: 09/28/2015] [Indexed: 11/30/2022]
Abstract
In recent years, electron microscopy (EM) and single particle analysis have emerged as essential tools for investigating the architecture of large biological complexes. When high resolution is achievable, crystal structure docking and de-novo modeling allows for precise assignment of individual protein domain sequences. However, the achievable resolution may limit the ability to do so, especially when small or flexible complexes are under study. In such cases, protein labeling has emerged as an important complementary tool to characterize domain architecture and elucidate functional mechanistic details. All labeling strategies proposed to date are either focused on the identification of the position of protein termini or require multi-step labeling strategies, potentially interfering with the final labeling efficiency. Here we describe a strategy for determining the position of internal protein domains within EM maps using a recombinant one-step labeling approach named Efficient Mapping by Internal Labeling (EMIL). EMIL takes advantage of the close spatial proximity of the GFP's N- and C-termini to generate protein chimeras containing an internal GFP at desired locations along the main protein chain. We apply this method to characterize the subunit domain localization of the human Polycomb Repressive Complex 2.
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Affiliation(s)
- Claudio Ciferri
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.
| | - Gabriel C Lander
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, United States; Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States; Howard Hughes Medical Institute, UC Berkeley, Berkeley, United States
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124
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Levine B, Liu R, Dong X, Zhong Q. Beclin orthologs: integrative hubs of cell signaling, membrane trafficking, and physiology. Trends Cell Biol 2015; 25:533-44. [PMID: 26071895 PMCID: PMC4554927 DOI: 10.1016/j.tcb.2015.05.004] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/04/2015] [Accepted: 05/07/2015] [Indexed: 12/25/2022]
Abstract
Beclin orthologs are crucial regulators of autophagy and related membrane-trafficking pathways. Multiple signaling pathways converge on Beclin 1 to regulate cellular stress responses, membrane trafficking, and physiology.
The Beclin family, including yeast Atg6 (autophagy related gene 6), its orthologs in higher eukaryotic species, and the more recently characterized mammalian-specific Beclin 2, are essential molecules in autophagy and other membrane-trafficking events. Extensive studies of Beclin orthologs have provided considerable insights into the regulation of autophagy, the diverse roles of autophagy in physiology and disease, and potential new strategies to modulate autophagy in a variety of clinical diseases. In this review we discuss the functions of Beclin orthologs, the regulation of such functions by diverse cellular signaling pathways, and the effects of such regulation on downstream cellular processes including tumor suppression and metabolism. These findings suggest that Beclin orthologs serve as crucial molecules that integrate diverse environmental signals with membrane trafficking events to ensure optimal responses of the cell to stressful stimuli.
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Affiliation(s)
- Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Rong Liu
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiaonan Dong
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Zhong
- Center for Autophagy Research, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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125
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Wei Y, An Z, Zou Z, Sumpter R, Su M, Zang X, Sinha S, Gaestel M, Levine B. The stress-responsive kinases MAPKAPK2/MAPKAPK3 activate starvation-induced autophagy through Beclin 1 phosphorylation. eLife 2015; 4:e05289. [PMID: 25693418 PMCID: PMC4337728 DOI: 10.7554/elife.05289] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 01/26/2015] [Indexed: 12/18/2022] Open
Abstract
Autophagy is a fundamental adaptive response to amino acid starvation orchestrated by conserved gene products, the autophagy (ATG) proteins. However, the cellular cues that activate the function of ATG proteins during amino acid starvation are incompletely understood. Here we show that two related stress-responsive kinases, members of the p38 mitogen-activated protein kinase (MAPK) signaling pathway MAPKAPK2 (MK2) and MAPKAPK3 (MK3), positively regulate starvation-induced autophagy by phosphorylating an essential ATG protein, Beclin 1, at serine 90, and that this phosphorylation site is essential for the tumor suppressor function of Beclin 1. Moreover, MK2/MK3-dependent Beclin 1 phosphorylation (and starvation-induced autophagy) is blocked in vitro and in vivo by BCL2, a negative regulator of Beclin 1. Together, these findings reveal MK2/MK3 as crucial stress-responsive kinases that promote autophagy through Beclin 1 S90 phosphorylation, and identify the blockade of MK2/3-dependent Beclin 1 S90 phosphorylation as a mechanism by which BCL2 inhibits the autophagy function of Beclin 1.
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Affiliation(s)
- Yongjie Wei
- Center for Autophagy Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, United States
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
| | - Zhenyi An
- Center for Autophagy Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, United States
| | - Zhongju Zou
- Center for Autophagy Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, United States
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
| | - Rhea Sumpter
- Center for Autophagy Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, United States
| | - Minfei Su
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, United States
| | - Xiao Zang
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas, United States
| | - Sangita Sinha
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, United States
| | - Matthias Gaestel
- Institute of Physiological Chemistry, Hannover Medical School, Hannover, Germany
| | - Beth Levine
- Center for Autophagy Research, Department of Internal Medicine, UT Southwestern Medical Center, Dallas, United States
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, United States
- Department of Microbiology, UT Southwestern Medical Center, Dallas, United States
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126
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Yu X, Long YC, Shen HM. Differential regulatory functions of three classes of phosphatidylinositol and phosphoinositide 3-kinases in autophagy. Autophagy 2015; 11:1711-28. [PMID: 26018563 PMCID: PMC4824607 DOI: 10.1080/15548627.2015.1043076] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/11/2015] [Accepted: 04/14/2015] [Indexed: 02/06/2023] Open
Abstract
Autophagy is an evolutionarily conserved and exquisitely regulated self-eating cellular process with important biological functions. Phosphatidylinositol 3-kinases (PtdIns3Ks) and phosphoinositide 3-kinases (PI3Ks) are involved in the autophagic process. Here we aim to recapitulate how 3 classes of these lipid kinases differentially regulate autophagy. Generally, activation of the class I PI3K suppresses autophagy, via the well-established PI3K-AKT-MTOR (mechanistic target of rapamycin) complex 1 (MTORC1) pathway. In contrast, the class III PtdIns3K catalytic subunit PIK3C3/Vps34 forms a protein complex with BECN1 and PIK3R4 and produces phosphatidylinositol 3-phosphate (PtdIns3P), which is required for the initiation and progression of autophagy. The class II enzyme emerged only recently as an alternative source of PtdIns3P and autophagic initiator. However, the orthodox paradigm is challenged by findings that the PIK3CB catalytic subunit of class I PI3K acts as a positive regulator of autophagy, and PIK3C3 was thought to be an amino acid sensor for MTOR, which curbs autophagy. At present, a number of PtdIns3K and PI3K inhibitors, including specific PIK3C3 inhibitors, have been developed for suppression of autophagy and for clinical applications in autophagy-related human diseases.
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Affiliation(s)
- Xinlei Yu
- a Department of Biochemistry; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
| | - Yun Chau Long
- a Department of Biochemistry; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
| | - Han-Ming Shen
- b Department of Physiology; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
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