1
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Orr A, Wickner W. Sec18 binds the tethering/SM complex HOPS to engage the Qc-SNARE for membrane fusion. Mol Biol Cell 2024; 35:ar71. [PMID: 38536444 PMCID: PMC11151092 DOI: 10.1091/mbc.e24-02-0060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/18/2024] Open
Abstract
Membrane fusion is regulated by Rab GTPases, their tethering effectors such as HOPS, SNARE proteins on each fusion partner, SM proteins to catalyze SNARE assembly, Sec17 (SNAP), and Sec18 (NSF). Though concentrated HOPS can support fusion without Sec18, we now report that fusion falls off sharply at lower HOPS levels, where direct Sec18 binding to HOPS restores fusion. This Sec18-dependent fusion needs adenine nucleotide but neither ATP hydrolysis nor Sec17. Sec18 enhances HOPS recognition of the Qc-SNARE. With high levels of HOPS, Qc has a Km for fusion of a few nM. Either lower HOPS levels, or substitution of a synthetic tether for HOPS, strikingly increases the Km for Qc to several hundred nM. With dilute HOPS, Sec18 returns the Km for Qc to low nM. In contrast, HOPS concentration and Sec18 have no effect on Qb-SNARE recognition. Just as Qc is required for fusion but not for the initial assembly of SNAREs in trans, impaired Qc recognition by limiting HOPS without Sec18 still allows substantial trans-SNARE assembly. Thus, in addition to the known Sec18 functions of disassembling SNARE complexes, oligomerizing Sec17 for membrane association, and allowing Sec17 to drive fusion without complete SNARE zippering, we report a fourth Sec18 function, the Sec17-independent binding of Sec18 to HOPS to enhance functional Qc-SNARE engagement.
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Affiliation(s)
- Amy Orr
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755-3844
| | - William Wickner
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755-3844
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2
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Jahn R, Cafiso DC, Tamm LK. Mechanisms of SNARE proteins in membrane fusion. Nat Rev Mol Cell Biol 2024; 25:101-118. [PMID: 37848589 DOI: 10.1038/s41580-023-00668-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2023] [Indexed: 10/19/2023]
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of small conserved eukaryotic proteins that mediate membrane fusion between organelles and with the plasma membrane. SNAREs are directly or indirectly anchored to membranes. Prior to fusion, complementary SNAREs assemble between membranes with the aid of accessory proteins that provide a scaffold to initiate SNARE zippering, pulling the membranes together and mediating fusion. Recent advances have enabled the construction of detailed models describing bilayer transitions and energy barriers along the fusion pathway and have elucidated the structures of SNAREs complexed in various states with regulatory proteins. In this Review, we discuss how these advances are yielding an increasingly detailed picture of the SNARE-mediated fusion pathway, leading from first contact between the membranes via metastable non-bilayer intermediates towards the opening and expansion of a fusion pore. We describe how SNARE proteins assemble into complexes, how this assembly is regulated by accessory proteins and how SNARE complexes overcome the free energy barriers that prevent spontaneous membrane fusion.
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Affiliation(s)
- Reinhard Jahn
- Laboratory of Neurobiology, Max-Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
| | - David C Cafiso
- Department of Chemistry, University of Virginia, Charlottesville, VA, USA
| | - Lukas K Tamm
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA
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3
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Zhang J, Ding W, Zhao M, Liu J, Xu Y, Wan J, Wang M. Mechanisms of efferocytosis in determining inflammation resolution: Therapeutic potential and the association with cardiovascular disease. Br J Pharmacol 2022; 179:5151-5171. [PMID: 36028471 DOI: 10.1111/bph.15939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/29/2022] Open
Abstract
Efferocytosis is defined as the clearance of apoptotic cells (ACs) in physiological and pathological states and is performed by efferocytes, such as macrophages. Efferocytosis can lead to the resolution of inflammation and restore tissue homoeostasis; however, the mechanisms of efferocytosis in determining inflammation resolution are still not completely understood, and the effects of efferocytosis on other proresolving properties need to be explored and explained. In this review, the process of efferocytosis will be summarized briefly, and then these mechanisms and effects will be thoroughly discussed. In addition, the association between the mechanisms of efferocytosis in determining inflammation resolution and cardiovascular diseases will also be reviewed, as an understanding of this association may provide information on novel treatment targets.
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Affiliation(s)
- Jishou Zhang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Wen Ding
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China.,department of radiology, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Mengmeng Zhao
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jianfang Liu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Yao Xu
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Jun Wan
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
| | - Menglong Wang
- Department of Cardiology, Renmin Hospital of Wuhan University, Wuhan, China.,Cardiovascular Research Institute, Wuhan University, Wuhan, China.,Hubei Key Laboratory of Cardiology, Wuhan, China
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4
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Khan YA, White KI, Brunger AT. The AAA+ superfamily: a review of the structural and mechanistic principles of these molecular machines. Crit Rev Biochem Mol Biol 2021; 57:156-187. [PMID: 34632886 DOI: 10.1080/10409238.2021.1979460] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
ATPases associated with diverse cellular activities (AAA+ proteins) are a superfamily of proteins found throughout all domains of life. The hallmark of this family is a conserved AAA+ domain responsible for a diverse range of cellular activities. Typically, AAA+ proteins transduce chemical energy from the hydrolysis of ATP into mechanical energy through conformational change, which can drive a variety of biological processes. AAA+ proteins operate in a variety of cellular contexts with diverse functions including disassembly of SNARE proteins, protein quality control, DNA replication, ribosome assembly, and viral replication. This breadth of function illustrates both the importance of AAA+ proteins in health and disease and emphasizes the importance of understanding conserved mechanisms of chemo-mechanical energy transduction. This review is divided into three major portions. First, the core AAA+ fold is presented. Next, the seven different clades of AAA+ proteins and structural details and reclassification pertaining to proteins in each clade are described. Finally, two well-known AAA+ proteins, NSF and its close relative p97, are reviewed in detail.
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Affiliation(s)
- Yousuf A Khan
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Center for Biomedical Informatics Research, Stanford University, Stanford, CA, USA
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA.,Department of Structural Biology, Stanford University, Stanford, CA, USA.,Department of Photon Science, Stanford University, Stanford, CA, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
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5
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Sauvola CW, Littleton JT. SNARE Regulatory Proteins in Synaptic Vesicle Fusion and Recycling. Front Mol Neurosci 2021; 14:733138. [PMID: 34421538 PMCID: PMC8377282 DOI: 10.3389/fnmol.2021.733138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/20/2021] [Indexed: 01/01/2023] Open
Abstract
Membrane fusion is a universal feature of eukaryotic protein trafficking and is mediated by the soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) family. SNARE proteins embedded in opposing membranes spontaneously assemble to drive membrane fusion and cargo exchange in vitro. Evolution has generated a diverse complement of SNARE regulatory proteins (SRPs) that ensure membrane fusion occurs at the right time and place in vivo. While a core set of SNAREs and SRPs are common to all eukaryotic cells, a specialized set of SRPs within neurons confer additional regulation to synaptic vesicle (SV) fusion. Neuronal communication is characterized by precise spatial and temporal control of SNARE dynamics within presynaptic subdomains specialized for neurotransmitter release. Action potential-elicited Ca2+ influx at these release sites triggers zippering of SNAREs embedded in the SV and plasma membrane to drive bilayer fusion and release of neurotransmitters that activate downstream targets. Here we discuss current models for how SRPs regulate SNARE dynamics and presynaptic output, emphasizing invertebrate genetic findings that advanced our understanding of SRP regulation of SV cycling.
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Affiliation(s)
- Chad W Sauvola
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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6
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Extreme parsimony in ATP consumption by 20S complexes in the global disassembly of single SNARE complexes. Nat Commun 2021; 12:3206. [PMID: 34050166 PMCID: PMC8163800 DOI: 10.1038/s41467-021-23530-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/30/2021] [Indexed: 11/08/2022] Open
Abstract
Fueled by ATP hydrolysis in N-ethylmaleimide sensitive factor (NSF), the 20S complex disassembles rigid SNARE (soluble NSF attachment protein receptor) complexes in single unraveling step. This global disassembly distinguishes NSF from other molecular motors that make incremental and processive motions, but the molecular underpinnings of its remarkable energy efficiency remain largely unknown. Using multiple single-molecule methods, we found remarkable cooperativity in mechanical connection between NSF and the SNARE complex, which prevents dysfunctional 20S complexes that consume ATP without productive disassembly. We also constructed ATP hydrolysis cycle of the 20S complex, in which NSF largely shows randomness in ATP binding but switches to perfect ATP hydrolysis synchronization to induce global SNARE disassembly, minimizing ATP hydrolysis by non-20S complex-forming NSF molecules. These two mechanisms work in concert to concentrate ATP consumption into functional 20S complexes, suggesting evolutionary adaptations by the 20S complex to the energetically expensive mechanical task of SNARE complex disassembly. Fueled by ATP hydrolysis in N-ethylmaleimide sensitive factor (NSF), the 20S complex disassembles SNARE complexes in a single unravelling step. Here authors use single-molecule methods to show cooperativity between the NSF and SNARE complex, which prevents ATP consumption without productive disassembly.
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7
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Jäpel M, Gerth F, Sakaba T, Bacetic J, Yao L, Koo SJ, Maritzen T, Freund C, Haucke V. Intersectin-Mediated Clearance of SNARE Complexes Is Required for Fast Neurotransmission. Cell Rep 2021; 30:409-420.e6. [PMID: 31940485 DOI: 10.1016/j.celrep.2019.12.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022] Open
Abstract
The rapid replenishment of release-ready synaptic vesicles (SVs) at a limiting number of presynaptic release sites is required to sustain high-frequency neurotransmission in CNS neurons. Failure to clear release sites from previously exocytosed material has been shown to impair vesicle replenishment and, therefore, fast neurotransmission. The identity of this material and the machinery that removes it from release sites have remained enigmatic. Here we show that the endocytic scaffold protein intersectin 1 clears release sites by direct SH3 domain-mediated association with a non-canonical proline-rich segment of synaptobrevin assembled into the SNARE complex for neuroexocytosis. Acute structure-based or sustained genetic interference with SNARE complex recognition by intersectin 1 causes a rapid stimulation frequency-dependent depression of neurotransmission due to impaired replenishment of release-ready SVs. These findings identify a key molecular mechanism that underlies exo-endocytic coupling during fast neurotransmitter release at central synapses.
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Affiliation(s)
- Maria Jäpel
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Molecular Pharmacology & Cell Biology, 13125 Berlin, Germany
| | - Fabian Gerth
- Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany
| | - Takeshi Sakaba
- Doshisha University, Graduate School of Brain Science, Kyoto 610-0394, Japan
| | - Jelena Bacetic
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Molecular Pharmacology & Cell Biology, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany
| | - Lijun Yao
- Max-Planck-Institute for Biophysical Chemistry, Department of Membrane Biophysics, 37077 Göttingen, Germany
| | - Seong-Joo Koo
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Molecular Pharmacology & Cell Biology, 13125 Berlin, Germany
| | - Tanja Maritzen
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Molecular Pharmacology & Cell Biology, 13125 Berlin, Germany
| | - Christian Freund
- Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Molecular Pharmacology & Cell Biology, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, Pharmacy, 14195 Berlin, Germany; NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, 10117 Berlin, Germany.
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8
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Escobar-Henriques M, Anton V. Mitochondrial Surveillance by Cdc48/p97: MAD vs. Membrane Fusion. Int J Mol Sci 2020; 21:E6841. [PMID: 32961852 PMCID: PMC7555132 DOI: 10.3390/ijms21186841] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 11/16/2022] Open
Abstract
Cdc48/p97 is a ring-shaped, ATP-driven hexameric motor, essential for cellular viability. It specifically unfolds and extracts ubiquitylated proteins from membranes or protein complexes, mostly targeting them for proteolytic degradation by the proteasome. Cdc48/p97 is involved in a multitude of cellular processes, reaching from cell cycle regulation to signal transduction, also participating in growth or death decisions. The role of Cdc48/p97 in endoplasmic reticulum-associated degradation (ERAD), where it extracts proteins targeted for degradation from the ER membrane, has been extensively described. Here, we present the roles of Cdc48/p97 in mitochondrial regulation. We discuss mitochondrial quality control surveillance by Cdc48/p97 in mitochondrial-associated degradation (MAD), highlighting the potential pathologic significance thereof. Furthermore, we present the current knowledge of how Cdc48/p97 regulates mitofusin activity in outer membrane fusion and how this may impact on neurodegeneration.
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Affiliation(s)
- Mafalda Escobar-Henriques
- Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine Cologne (CMMC), University of Cologne, Joseph-Stelzmann-Straße 26, 50931 Cologne, Germany;
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9
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Brunger AT, Choi UB, Lai Y, Leitz J, White KI, Zhou Q. The pre-synaptic fusion machinery. Curr Opin Struct Biol 2019; 54:179-188. [PMID: 30986753 PMCID: PMC6939388 DOI: 10.1016/j.sbi.2019.03.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/02/2019] [Accepted: 03/06/2019] [Indexed: 11/26/2022]
Abstract
Here, we review recent insights into the neuronal presynaptic fusion machinery that releases neurotransmitter molecules into the synaptic cleft upon stimulation. The structure of the pre-fusion state of the SNARE/complexin-1/synaptotagmin-1 synaptic protein complex suggests a new model for the initiation of fast Ca2+-triggered membrane fusion. Functional studies have revealed roles of the essential factors Munc18 and Munc13, demonstrating that a part of their function involves the proper assembly of synaptic protein complexes. Near-atomic resolution structures of the NSF/αSNAP/SNARE complex provide first glimpses of the molecular machinery that disassembles the SNARE complex during the synaptic vesicle cycle. These structures show how this machinery captures the SNARE substrate and provide clues as to a possible processing mechanism.
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Affiliation(s)
- Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA; Department of Structural Biology, Stanford University, Stanford, USA; Department of Photon Science, Stanford University, Stanford, USA; Howard Hughes Medical Institute, Stanford University, Stanford, USA.
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA; Department of Structural Biology, Stanford University, Stanford, USA; Department of Photon Science, Stanford University, Stanford, USA; Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Ying Lai
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA; Department of Structural Biology, Stanford University, Stanford, USA; Department of Photon Science, Stanford University, Stanford, USA; Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Jeremy Leitz
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA; Department of Structural Biology, Stanford University, Stanford, USA; Department of Photon Science, Stanford University, Stanford, USA; Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Kristopher Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA; Department of Structural Biology, Stanford University, Stanford, USA; Department of Photon Science, Stanford University, Stanford, USA; Howard Hughes Medical Institute, Stanford University, Stanford, USA
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, USA; Department of Neurology and Neurological Sciences, Stanford University, Stanford, USA; Department of Structural Biology, Stanford University, Stanford, USA; Department of Photon Science, Stanford University, Stanford, USA; Howard Hughes Medical Institute, Stanford University, Stanford, USA
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10
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Sharma G, Guardia CM, Roy A, Vassilev A, Saric A, Griner LN, Marugan J, Ferrer M, Bonifacino JS, DePamphilis ML. A family of PIKFYVE inhibitors with therapeutic potential against autophagy-dependent cancer cells disrupt multiple events in lysosome homeostasis. Autophagy 2019; 15:1694-1718. [PMID: 30806145 DOI: 10.1080/15548627.2019.1586257] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
High-throughput screening identified 5 chemical analogs (termed the WX8-family) that disrupted 3 events in lysosome homeostasis: (1) lysosome fission via tubulation without preventing homotypic lysosome fusion; (2) trafficking of molecules into lysosomes without altering lysosomal acidity, and (3) heterotypic fusion between lysosomes and autophagosomes. Remarkably, these compounds did not prevent homotypic fusion between lysosomes, despite the fact that homotypic fusion required some of the same machinery essential for heterotypic fusion. These effects varied 400-fold among WX8-family members, were time and concentration dependent, reversible, and resulted primarily from their ability to bind specifically to the PIKFYVE phosphoinositide kinase. The ability of the WX8-family to prevent lysosomes from participating in macroautophagy/autophagy suggested they have therapeutic potential in treating autophagy-dependent diseases. In fact, the most potent family member (WX8) was 100-times more lethal to 'autophagy-addicted' melanoma A375 cells than the lysosomal inhibitors hydroxychloroquine and chloroquine. In contrast, cells that were insensitive to hydroxychloroquine and chloroquine were also insensitive to WX8. Therefore, the WX8-family of PIKFYVE inhibitors provides a basis for developing drugs that could selectively kill autophagy-dependent cancer cells, as well as increasing the effectiveness of established anti-cancer therapies through combinatorial treatments. Abbreviations: ACTB: actin beta; Baf: bafilomycin A1; BECN1: beclin 1; BODIPY: boron-dipyrromethene; BORC: BLOC-1 related complex; BRAF: B-Raf proto-oncogene, serine/threonine kinase; BSA: bovine serum albumin; CTSD: cathepsin D; CQ: chloroquine; DNA: deoxyribonucleic acid; EC50: half maximal effective concentration; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; GFP: green fluorescent protein; HCQ: hydroxychloroquine; HOPS complex: homotypic fusion and protein sorting complex; Kd: equilibrium binding constant; IC50: half maximal inhibitory concentration; KO: knockout; LAMP1: lysosomal associated membrane protein 1; MAP1LC3A: microtubule associated protein 1 light chain 3 alpha; MES: 2-(N-morpholino)ethanesulphonic acid; MTOR: mechanistic target of rapamycin kinase; μM: micromolar; NDF: 3-methylbenzaldehyde (2,6-dimorpholin-4-ylpyrimidin-4-yl)hydrazine;NEM: N-ethylmaleimide; NSF: N-ethylmaleimide sensitive factor; PBS: phosphate-buffered saline; PIKFYVE: phosphoinositide kinase, FYVE-type zinc finger containing; PIP4K2C: phosphatidylinositol-5-phosphate 4-kinase type 2 gamma; PtdIns3P: phosphatidylinositol 3-phosphate; PtdIns(3,5)P2: phosphatidylinositol 3,5-biphosphate; RFP: red fluorescent protein; RPS6: ribosomal protein S6; RPS6KB1: ribosomal protein S6 kinase B1; SQSTM1: sequestosome 1; TWEEN 20: polysorbate 20; V-ATPase: vacuolar-type H+-translocating ATPase; VPS39: VPS39 subunit of HOPS complex; VPS41: VPS41 subunit of HOPS complex; WWL: benzaldehyde [2,6-di(4-morpholinyl)-4-pyrimidinyl]hydrazone; WX8: 1H-indole-3-carbaldehyde [4-anilino-6-(4-morpholinyl)-1,3,5-triazin-2-yl]hydrazine; XBA: N-(3-chloro-4-fluorophenyl)-4,6-dimorpholino-1,3,5-triazin-2-amine hydrochloride; XB6: N-(4-ethylphenyl)-4,6-dimorpholino-1,3,5-triazin-2-amine hydrochloride.
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Affiliation(s)
- Gaurav Sharma
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Carlos M Guardia
- Cell Biology and Neurobiology Branch, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Ajit Roy
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Alex Vassilev
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Amra Saric
- Cell Biology and Neurobiology Branch, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Lori N Griner
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Juan Marugan
- Division of Pre-Clinical Innovation, NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville , MD , USA
| | - Marc Ferrer
- Division of Pre-Clinical Innovation, NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health , Rockville , MD , USA
| | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
| | - Melvin L DePamphilis
- Division of Developmental Biology, National Institute of Child Health & Human Development, National Institutes of Health , Bethesda , MD , USA
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11
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White KI, Zhao M, Choi UB, Pfuetzner RA, Brunger AT. Structural principles of SNARE complex recognition by the AAA+ protein NSF. eLife 2018; 7:38888. [PMID: 30198481 PMCID: PMC6160233 DOI: 10.7554/elife.38888] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/26/2018] [Indexed: 12/13/2022] Open
Abstract
The recycling of SNARE proteins following complex formation and membrane fusion is an essential process in eukaryotic trafficking. A highly conserved AAA+ protein, NSF (N-ethylmaleimide sensitive factor) and an adaptor protein, SNAP (soluble NSF attachment protein), disassemble the SNARE complex. We report electron-cryomicroscopy structures of the complex of NSF, αSNAP, and the full-length soluble neuronal SNARE complex (composed of syntaxin-1A, synaptobrevin-2, SNAP-25A) in the presence of ATP under non-hydrolyzing conditions at ~3.9 Å resolution. These structures reveal electrostatic interactions by which two αSNAP molecules interface with a specific surface of the SNARE complex. This interaction positions the SNAREs such that the 15 N-terminal residues of SNAP-25A are loaded into the D1 ring pore of NSF via a spiral pattern of interactions between a conserved tyrosine NSF residue and SNAP-25A backbone atoms. This loading process likely precedes ATP hydrolysis. Subsequent ATP hydrolysis then drives complete disassembly.
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Affiliation(s)
- K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - Ucheor B Choi
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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12
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Choi UB, Zhao M, White KI, Pfuetzner RA, Esquivies L, Zhou Q, Brunger AT. NSF-mediated disassembly of on- and off-pathway SNARE complexes and inhibition by complexin. eLife 2018; 7:36497. [PMID: 29985126 PMCID: PMC6130971 DOI: 10.7554/elife.36497] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/06/2018] [Indexed: 12/24/2022] Open
Abstract
SNARE complex disassembly by the ATPase NSF is essential for neurotransmitter release and other membrane trafficking processes. We developed a single-molecule FRET assay to monitor repeated rounds of NSF-mediated disassembly and reassembly of individual SNARE complexes. For ternary neuronal SNARE complexes, disassembly proceeds in a single step within 100 msec. We observed short- (<0.32 s) and long-lived (≥0.32 s) disassembled states. The long-lived states represent fully disassembled SNARE complex, while the short-lived states correspond to failed disassembly or immediate reassembly. Either high ionic strength or decreased αSNAP concentration reduces the disassembly rate while increasing the frequency of short-lived states. NSF is also capable of disassembling anti-parallel ternary SNARE complexes, implicating it in quality control. Finally, complexin-1 competes with αSNAP binding to the SNARE complex; addition of complexin-1 has an effect similar to that of decreasing the αSNAP concentration, possibly differentially regulating cis and trans SNARE complexes disassembly.
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Affiliation(s)
- Ucheor B Choi
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Minglei Zhao
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States
| | - K Ian White
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Richard A Pfuetzner
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Luis Esquivies
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
| | - Axel T Brunger
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Department of Structural Biology, Stanford University, Stanford, United States.,Department of Photon Science, Stanford University, Stanford, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States
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13
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Ciampa E, Li Y, Dillon S, Lecarpentier E, Sorabella L, Libermann TA, Karumanchi SA, Hess PE. Cerebrospinal Fluid Protein Changes in Preeclampsia. Hypertension 2018; 72:219-226. [PMID: 29844151 DOI: 10.1161/hypertensionaha.118.11153] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 03/15/2018] [Accepted: 05/06/2018] [Indexed: 01/21/2023]
Abstract
The molecular mechanisms underlying seizure susceptibility in preeclampsia are unknown. We hypothesized that altered expression of distinct proteins in the cerebrospinal fluid (CSF) may reflect pathophysiological changes in the central nervous system that contribute to the neurological manifestations of severe preeclampsia. We obtained CSF samples from 13 patients with preeclampsia and 14 control patients during spinal anesthesia before delivery and analyzed them by SOMAscan, an aptamer-based proteomics platform for alterations in 1310 protein levels. Ingenuity Pathway Analysis was conducted to highlight relationships between preeclampsia-specific proteins found to be significantly altered. For 2 of the target proteins, we validated the difference in CSF concentrations by ELISA. SOMAscan revealed 82 proteins, whose expression levels were significantly different (P<0.05) in CSF from patients with preeclampsia versus controls. Principal component analysis achieved perfect separation of the preeclampsia and control groups in 2 dimensions. The differentially expressed proteins converge around 4 signaling molecules: TGF-β (transforming growth factor-β), VEGFA (vascular endothelial growth factor A), angiotensinogen, and IL-6 (interleukin-6). Within the TGF-β pathway, upregulation of activin A (301.6±47.4 versus 151.6±20.5 pg/mL; P=0.0074) and follistatin-related gene (5129±347 versus 3016±188 pg/mL; P<0.0001) in preeclampsia was confirmed by ELISA. In summary, signaling pathways important for vascular remodeling, inflammation, and neuronal growth, signaling, and electrophysiology were well represented among the proteins found to be altered in CSF in patients with preeclampsia.
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Affiliation(s)
- Erin Ciampa
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.)
| | - Yunping Li
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.)
| | - Simon Dillon
- Medicine (S.D., E.L., T.A.L., S.A.K.).,Genomics, Proteomics, Bioinformatics, and Systems Biology Center (S.D., T.A.L.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - Edouard Lecarpentier
- Medicine (S.D., E.L., T.A.L., S.A.K.).,Faculté de médecine de Créteil Université Paris Est Créteil - Paris XII, and Service de Gynécologie-Obstétrique et Médecine de la Reproduction, Centre Hospitalier Intercommunal de Créteil, France (E.L.)
| | - Laura Sorabella
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.).,Department of Anesthesia, Vanderbilt University Medical Center, Nashville, TN (L.S.)
| | - Towia A Libermann
- Medicine (S.D., E.L., T.A.L., S.A.K.).,Genomics, Proteomics, Bioinformatics, and Systems Biology Center (S.D., T.A.L.), Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA
| | - S Ananth Karumanchi
- Medicine (S.D., E.L., T.A.L., S.A.K.) .,Obstetrics and Gynecology (S.A.K.).,Departments of Medicine and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA (S.A.K.)
| | - Philip E Hess
- From the Departments of Anesthesia (E.C., Y.L., L.S., P.E.H.)
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14
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Zhang Y, Jiao J, Rebane AA. Hidden Markov Modeling with Detailed Balance and Its Application to Single Protein Folding. Biophys J 2017; 111:2110-2124. [PMID: 27851936 DOI: 10.1016/j.bpj.2016.09.045] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/26/2016] [Accepted: 09/27/2016] [Indexed: 12/26/2022] Open
Abstract
Hidden Markov modeling (HMM) has revolutionized kinetic studies of macromolecules. However, results from HMM often violate detailed balance when applied to the transitions under thermodynamic equilibrium, and the consequence of such violation has not been well understood. Here, to our knowledge, we developed a new HMM method that satisfies detailed balance (HMM-DB) and optimizes model parameters by gradient search. We used free energy of stable and transition states as independent fitting parameters and considered both normal and skew normal distributions of the measurement noise. We validated our method by analyzing simulated extension trajectories that mimicked experimental data of single protein folding from optical tweezers. We then applied HMM-DB to elucidate kinetics of regulated SNARE zippering containing degenerate states. For both simulated and measured trajectories, we found that HMM-DB significantly reduced overfitting of short trajectories compared to the standard HMM based on an expectation-maximization algorithm, leading to more accurate and reliable model fitting by HMM-DB. We revealed how HMM-DB could be conveniently used to derive a simplified energy landscape of protein folding. Finally, we extended HMM-DB to correct the baseline drift in single-molecule trajectories. Together, we demonstrated an efficient, versatile, and reliable method of HMM for kinetics studies of macromolecules under thermodynamic equilibrium.
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Affiliation(s)
- Yongli Zhang
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut.
| | - Junyi Jiao
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut
| | - Aleksander A Rebane
- Department of Cell Biology, School of Medicine, Yale University, New Haven, Connecticut; Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut; Department of Physics, Yale University, New Haven, Connecticut; Nanobiology Institute, Yale University, West Haven, Connecticut
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15
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Jakhanwal S, Lee CT, Urlaub H, Jahn R. An activated Q-SNARE/SM protein complex as a possible intermediate in SNARE assembly. EMBO J 2017; 36:1788-1802. [PMID: 28483813 DOI: 10.15252/embj.201696270] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Revised: 03/23/2017] [Accepted: 03/24/2017] [Indexed: 01/15/2023] Open
Abstract
Assembly of the SNARE proteins syntaxin1, SNAP25, and synaptobrevin into a SNARE complex is essential for exocytosis in neurons. For efficient assembly, SNAREs interact with additional proteins but neither the nature of the intermediates nor the sequence of protein assembly is known. Here, we have characterized a ternary complex between syntaxin1, SNAP25, and the SM protein Munc18-1 as a possible acceptor complex for the R-SNARE synaptobrevin. The ternary complex binds synaptobrevin with fast kinetics, resulting in the rapid formation of a fully zippered SNARE complex to which Munc18-1 remains tethered by the N-terminal domain of syntaxin1. Intriguingly, only one of the synaptobrevin truncation mutants (Syb1-65) was able to bind to the syntaxin1:SNAP25:Munc18-1 complex, suggesting either a cooperative zippering mechanism that proceeds bidirectionally or the progressive R-SNARE binding via an SM template. Moreover, the complex is resistant to disassembly by NSF Based on these findings, we consider the ternary complex as a strong candidate for a physiological intermediate in SNARE assembly.
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Affiliation(s)
- Shrutee Jakhanwal
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Chung-Tien Lee
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center, Göttingen, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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16
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Klink VP, Sharma K, Pant SR, McNeece B, Niraula P, Lawrence GW. Components of the SNARE-containing regulon are co-regulated in root cells undergoing defense. PLANT SIGNALING & BEHAVIOR 2017; 12:e1274481. [PMID: 28010187 PMCID: PMC5351740 DOI: 10.1080/15592324.2016.1274481] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 12/14/2016] [Accepted: 12/15/2016] [Indexed: 05/23/2023]
Abstract
The term regulon has been coined in the genetic model plant Arabidopsis thaliana, denoting a structural and physiological defense apparatus defined genetically through the identification of the penetration (pen) mutants. The regulon is composed partially by the soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) syntaxin PEN1. PEN1 has homology to a Saccharomyces cerevisae gene that regulates a Secretion (Sec) protein, Suppressor of Sec 1 (Sso1p). The regulon is also composed of the β-glucosidase (PEN2) and an ATP binding cassette (ABC) transporter (PEN3). While important in inhibiting pathogen infection, limited observations have been made regarding the transcriptional regulation of regulon genes until now. Experiments made using the model agricultural Glycine max (soybean) have identified co-regulated gene expression of regulon components. The results explain the observation of hundreds of genes expressed specifically in the root cells undergoing the natural process of defense. Data regarding additional G. max genes functioning within the context of the regulon are presented here, including Sec 14, Sec 4 and Sec 23. Other examined G. max homologs of membrane fusion genes include an endosomal bromo domain-containing protein1 (Bro1), syntaxin6 (SYP6), SYP131, SYP71, SYP8, Bet1, coatomer epsilon (ϵ-COP), a coatomer zeta (ζ-COP) paralog and an ER to Golgi component (ERGIC) protein. Furthermore, the effectiveness of biochemical pathways that would function within the context of the regulon ave been examined, including xyloglucan xylosyltransferase (XXT), reticuline oxidase (RO) and galactinol synthase (GS). The experiments have unveiled the importance of the regulon during defense in the root and show how the deposition of callose relates to the process.
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Affiliation(s)
- Vincent P. Klink
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Keshav Sharma
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Shankar R. Pant
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Brant McNeece
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Prakash Niraula
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Gary W. Lawrence
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
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17
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Bayless AM, Smith JM, Song J, McMinn PH, Teillet A, August BK, Bent AF. Disease resistance through impairment of α-SNAP-NSF interaction and vesicular trafficking by soybean Rhg1. Proc Natl Acad Sci U S A 2016; 113:E7375-E7382. [PMID: 27821740 PMCID: PMC5127302 DOI: 10.1073/pnas.1610150113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
α-SNAP [soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein] and NSF proteins are conserved across eukaryotes and sustain cellular vesicle trafficking by mediating disassembly and reuse of SNARE protein complexes, which facilitate fusion of vesicles to target membranes. However, certain haplotypes of the Rhg1 (resistance to Heterodera glycines 1) locus of soybean possess multiple repeat copies of an α-SNAP gene (Glyma.18G022500) that encodes atypical amino acids at a highly conserved functional site. These Rhg1 loci mediate resistance to soybean cyst nematode (SCN; H. glycines), the most economically damaging pathogen of soybeans worldwide. Rhg1 is widely used in agriculture, but the mechanisms of Rhg1 disease resistance have remained unclear. In the present study, we found that the resistance-type Rhg1 α-SNAP is defective in interaction with NSF. Elevated in planta expression of resistance-type Rhg1 α-SNAPs depleted the abundance of SNARE-recycling 20S complexes, disrupted vesicle trafficking, induced elevated abundance of NSF, and caused cytotoxicity. Soybean, due to ancient genome duplication events, carries other loci that encode canonical (wild-type) α-SNAPs. Expression of these α-SNAPs counteracted the cytotoxicity of resistance-type Rhg1 α-SNAPs. For successful growth and reproduction, SCN dramatically reprograms a set of plant root cells and must sustain this sedentary feeding site for 2-4 weeks. Immunoblots and electron microscopy immunolocalization revealed that resistance-type α-SNAPs specifically hyperaccumulate relative to wild-type α-SNAPs at the nematode feeding site, promoting the demise of this biotrophic interface. The paradigm of disease resistance through a dysfunctional variant of an essential gene may be applicable to other plant-pathogen interactions.
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Affiliation(s)
- Adam M Bayless
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - John M Smith
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Junqi Song
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Patrick H McMinn
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Alice Teillet
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706
| | - Benjamin K August
- University of Wisconsin School of Medicine and Public Health Electron Microscopy Facility, University of Wisconsin-Madison, Madison, WI 53706
| | - Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI 53706;
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18
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Ma L, Kang Y, Jiao J, Rebane AA, Cha HK, Xi Z, Qu H, Zhang Y. α-SNAP Enhances SNARE Zippering by Stabilizing the SNARE Four-Helix Bundle. Cell Rep 2016; 15:531-539. [PMID: 27068468 DOI: 10.1016/j.celrep.2016.03.050] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/09/2016] [Accepted: 03/11/2016] [Indexed: 01/03/2023] Open
Abstract
Intracellular membrane fusion is mediated by dynamic assembly and disassembly of soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) receptors (SNAREs). α-SNAP guides NSF to disassemble SNARE complexes after membrane fusion. Recent experiments showed that α-SNAP also dramatically enhances SNARE assembly and membrane fusion. How α-SNAP is involved in these opposing activities is not known. Here, we examine the effect of α-SNAP on the stepwise assembly of the synaptic SNARE complex using optical tweezers. We found that α-SNAP destabilized the linker domain (LD) of the SNARE complex but stabilized its C-terminal domain (CTD) through a conformational selection mechanism. In contrast, α-SNAP minimally affected assembly of the SNARE N-terminal domain (NTD), indicating that α-SNAP barely bound the partially assembled trans-SNARE complex. Thus, α-SNAP recognizes the folded CTD for SNARE disassembly with NSF and subtly modulates membrane fusion by altering the stabilities of the SNARE CTD and LD.
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Affiliation(s)
- Lu Ma
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yuhao Kang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Junyi Jiao
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, New Haven, CT 06520, USA
| | - Aleksander A Rebane
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA; Integrated Graduate Program in Physical and Engineering Biology, New Haven, CT 06520, USA; Department of Physics, Yale University, New Haven, CT 06511, USA
| | - Hyo Keun Cha
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Zhiqun Xi
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hong Qu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
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19
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Belluzzi E, Gonnelli A, Cirnaru MD, Marte A, Plotegher N, Russo I, Civiero L, Cogo S, Carrion MP, Franchin C, Arrigoni G, Beltramini M, Bubacco L, Onofri F, Piccoli G, Greggio E. LRRK2 phosphorylates pre-synaptic N-ethylmaleimide sensitive fusion (NSF) protein enhancing its ATPase activity and SNARE complex disassembling rate. Mol Neurodegener 2016; 11:1. [PMID: 26758690 PMCID: PMC4711005 DOI: 10.1186/s13024-015-0066-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 12/22/2015] [Indexed: 11/10/2022] Open
Abstract
Background Lrrk2, a gene linked to Parkinson’s disease, encodes a large scaffolding protein with kinase and GTPase activities implicated in vesicle and cytoskeletal-related processes. At the presynaptic site, LRRK2 associates with synaptic vesicles through interaction with a panel of presynaptic proteins. Results Here, we show that LRRK2 kinase activity influences the dynamics of synaptic vesicle fusion. We therefore investigated whether LRRK2 phosphorylates component(s) of the exo/endocytosis machinery. We have previously observed that LRRK2 interacts with NSF, a hexameric AAA+ ATPase that couples ATP hydrolysis to the disassembling of SNARE proteins allowing them to enter another fusion cycle during synaptic exocytosis. Here, we demonstrate that NSF is a substrate of LRRK2 kinase activity. LRRK2 phosphorylates full-length NSF at threonine 645 in the ATP binding pocket of D2 domain. Functionally, NSF phosphorylated by LRRK2 displays enhanced ATPase activity and increased rate of SNARE complex disassembling. Substitution of threonine 645 with alanine abrogates LRRK2-mediated increased ATPase activity. Conclusions Given that the most common Parkinson’s disease LRRK2 G2019S mutation displays increased kinase activity, our results suggest that mutant LRRK2 may impair synaptic vesicle dynamics via aberrant phosphorylation of NSF. Electronic supplementary material The online version of this article (doi:10.1186/s13024-015-0066-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Belluzzi
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy. .,Present Address: Rheumatology Unit, Department of Medicine - DIMED, University Hospital of Padova, Padova, Italy.
| | - Adriano Gonnelli
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy.
| | | | - Antonella Marte
- Department of Experimental Medicine, University of Genova, Genova, Italy.
| | - Nicoletta Plotegher
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy. .,Present Address: Department of Cell and Developmental Biology, University College London, London, WC1E 6BT, UK.
| | - Isabella Russo
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Laura Civiero
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Susanna Cogo
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Maria Perèz Carrion
- San Raffaele Scientific Park & University Vita-Salute San Raffaele, Milan, Italy.
| | - Cinzia Franchin
- Department of Biomedical Sciences, University of Padova, Padova, Italy. .,Proteomics Center of Padova University, Padova, Italy.
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padova, Italy. .,Proteomics Center of Padova University, Padova, Italy.
| | - Mariano Beltramini
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Luigi Bubacco
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy.
| | - Franco Onofri
- Department of Experimental Medicine, University of Genova, Genova, Italy.
| | - Giovanni Piccoli
- San Raffaele Scientific Park & University Vita-Salute San Raffaele, Milan, Italy. .,IN-CNR Milano, Milano, Italy.
| | - Elisa Greggio
- Department of Biology, University of Padova, via Ugo Bassi 58/B, 35131, Padova, Italy.
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20
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Bekal S, Domier LL, Gonfa B, Lakhssassi N, Meksem K, Lambert KN. A SNARE-Like Protein and Biotin Are Implicated in Soybean Cyst Nematode Virulence. PLoS One 2015; 10:e0145601. [PMID: 26714307 PMCID: PMC4699853 DOI: 10.1371/journal.pone.0145601] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 12/07/2015] [Indexed: 11/24/2022] Open
Abstract
Phytoparasitic nematodes that are able to infect and reproduce on plants that are considered resistant are referred to as virulent. The mechanism(s) that virulent nematodes employ to evade or suppress host plant defenses are not well understood. Here we report the use of a genetic strategy (allelic imbalance analysis) to associate single nucleotide polymorphisms (SNPs) with nematode virulence genes in Heterodera glycines, the soybean cyst nematode (SCN). To accomplish this analysis, a custom SCN SNP array was developed and used to genotype SCN F3-derived populations grown on resistant and susceptible soybean plants. Three SNPs reproducibly showed allele imbalances between nematodes grown on resistant and susceptible plants. Two candidate SCN virulence genes that were tightly linked to the SNPs were identified. One SCN gene encoded biotin synthase (HgBioB), and the other encoded a bacterial-like protein containing a putative SNARE domain (HgSLP-1). The two genes mapped to two different linkage groups. HgBioB contained sequence polymorphisms between avirulent and virulent nematodes. However, the gene encoding HgSLP-1 had reduced copy number in virulent nematode populations and appears to produce multiple forms of the protein via intron retention and alternative splicing. We show that HgSLP-1 is an esophageal-gland protein that is secreted by the nematode during plant parasitism. Furthermore, in bacterial co-expression experiments, HgSLP-1 co-purified with the SCN resistance protein Rhg1 α-SNAP, suggesting that these two proteins physically interact. Collectively our data suggest that multiple SCN genes are involved in SCN virulence, and that HgSLP-1 may function as an avirulence protein and when absent it helps SCN evade host defenses.
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Affiliation(s)
- Sadia Bekal
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Leslie L. Domier
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
| | - Biruk Gonfa
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
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21
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Recent Advances in Deciphering the Structure and Molecular Mechanism of the AAA+ ATPase N-Ethylmaleimide-Sensitive Factor (NSF). J Mol Biol 2015; 428:1912-26. [PMID: 26546278 DOI: 10.1016/j.jmb.2015.10.026] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/24/2015] [Accepted: 10/27/2015] [Indexed: 12/16/2022]
Abstract
N-ethylmaleimide-sensitive factor (NSF), first discovered in 1988, is a key factor for eukaryotic trafficking, including protein and hormone secretion and neurotransmitter release. It is a member of the AAA+ family (ATPases associated with diverse cellular activities). NSF disassembles soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes in conjunction with soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP). Structural studies of NSF and its complex with SNAREs and SNAPs (known as 20S supercomplex) started about 20years ago. Crystal structures of individual N and D2 domains of NSF and low-resolution electron microscopy structures of full-length NSF and 20S supercomplex have been reported over the years. Nevertheless, the molecular architecture of the 20S supercomplex and the molecular mechanism of NSF-mediated SNARE complex disassembly remained unclear until recently. Here we review recent atomic-resolution or near-atomic resolution structures of NSF and of the 20S supercomplex, as well as recent insights into the molecular mechanism and energy requirements of NSF. We also compare NSF with other known AAA+ family members.
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22
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Integrative proteomics to understand the transmission mechanism of Barley yellow dwarf virus-GPV by its insect vector Rhopalosiphum padi. Sci Rep 2015; 5:10971. [PMID: 26161807 PMCID: PMC4498328 DOI: 10.1038/srep10971] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/22/2015] [Indexed: 01/18/2023] Open
Abstract
Barley yellow dwarf virus-GPV (BYDV-GPV) is transmitted by Rhopalosiphum padi and Schizaphis graminum in a persistent nonpropagative manner. To improve our understanding of its transmission mechanism by aphid vectors, we used two approaches, isobaric tags for relative and absolute quantitation (iTRAQ) and yeast two-hybrid (YTH) system, to identify proteins in R. padi that may interact with or direct the spread of BYDV-GPV along the circulative transmission pathway. Thirty-three differential aphid proteins in viruliferous and nonviruliferous insects were identified using iTRAQ coupled to 2DLC-MS/MS. With the yeast two-hybrid system, 25 prey proteins were identified as interacting with the readthrough protein (RTP) and eight with the coat protein (CP), which are encoded by BYDV-GPV. Among the aphid proteins identified, most were involved in primary energy metabolism, synaptic vesicle cycle, the proteasome pathway and the cell cytoskeleton organization pathway. In a systematic comparison of the two methods, we found that the information generated by the two methods was complementary. Taken together, our findings provide useful information on the interactions between BYDV-GPV and its vector R. padi to further our understanding of the mechanisms regulating circulative transmission in aphid vectors.
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23
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Xi Z, Deng W, Wang L, Xiao F, Li J, Wang Z, Wang X, Mi X, Wang N, Wang X. Association of Alpha-Soluble NSF Attachment Protein with Epileptic Seizure. J Mol Neurosci 2015; 57:417-25. [DOI: 10.1007/s12031-015-0596-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/02/2015] [Indexed: 01/02/2023]
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24
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Central presynaptic terminals are enriched in ATP but the majority lack mitochondria. PLoS One 2015; 10:e0125185. [PMID: 25928229 PMCID: PMC4416033 DOI: 10.1371/journal.pone.0125185] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/10/2015] [Indexed: 11/19/2022] Open
Abstract
Synaptic neurotransmission is known to be an energy demanding process. At the presynapse, ATP is required for loading neurotransmitters into synaptic vesicles, for priming synaptic vesicles before release, and as a substrate for various kinases and ATPases. Although it is assumed that presynaptic sites usually harbor local mitochondria, which may serve as energy powerhouse to generate ATP as well as a presynaptic calcium depot, a clear role of presynaptic mitochondria in biochemical functioning of the presynapse is not well-defined. Besides a few synaptic subtypes like the mossy fibers and the Calyx of Held, most central presynaptic sites are either en passant or tiny axonal terminals that have little space to accommodate a large mitochondrion. Here, we have used imaging studies to demonstrate that mitochondrial antigens poorly co-localize with the synaptic vesicle clusters and active zone marker in the cerebral cortex, hippocampus and the cerebellum. Confocal imaging analysis on neuronal cultures revealed that most neuronal mitochondria are either somatic or distributed in the proximal part of major dendrites. A large number of synapses in culture are devoid of any mitochondria. Electron micrographs from neuronal cultures further confirm our finding that the majority of presynapses may not harbor resident mitochondria. We corroborated our ultrastructural findings using serial block face scanning electron microscopy (SBFSEM) and found that more than 60% of the presynaptic terminals lacked discernible mitochondria in the wild-type mice hippocampus. Biochemical fractionation of crude synaptosomes into mitochondria and pure synaptosomes also revealed a sparse presence of mitochondrial antigen at the presynaptic boutons. Despite a low abundance of mitochondria, the synaptosomal membranes were found to be highly enriched in ATP suggesting that the presynapse may possess alternative mechanism/s for concentrating ATP for its function. The potential mechanisms including local glycolysis and the possible roles of ATP-binding synaptic proteins such as synapsins, are discussed.
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25
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Zhang X, Gui L, Zhang X, Bulfer SL, Sanghez V, Wong DE, Lee Y, Lehmann L, Lee JS, Shih PY, Lin HJ, Iacovino M, Weihl CC, Arkin MR, Wang Y, Chou TF. Altered cofactor regulation with disease-associated p97/VCP mutations. Proc Natl Acad Sci U S A 2015; 112:E1705-14. [PMID: 25775548 PMCID: PMC4394316 DOI: 10.1073/pnas.1418820112] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Dominant mutations in p97/VCP (valosin-containing protein) cause a rare multisystem degenerative disease with varied phenotypes that include inclusion body myopathy, Paget's disease of bone, frontotemporal dementia, and amyotrophic lateral sclerosis. p97 disease mutants have altered N-domain conformations, elevated ATPase activity, and altered cofactor association. We have now discovered a previously unidentified disease-relevant functional property of p97 by identifying how the cofactors p37 and p47 regulate p97 ATPase activity. We define p37 as, to our knowledge, the first known p97-activating cofactor, which enhances the catalytic efficiency (kcat/Km) of p97 by 11-fold. Whereas both p37 and p47 decrease the Km of ATP in p97, p37 increases the kcat of p97. In contrast, regulation by p47 is biphasic, with decreased kcat at low levels but increased kcat at higher levels. By deleting a region of p47 that lacks homology to p37 (amino acids 69-92), we changed p47 from an inhibitory cofactor to an activating cofactor, similar to p37. Our data suggest that cofactors regulate p97 ATPase activity by binding to the N domain. Induced conformation changes affect ADP/ATP binding at the D1 domain, which in turn controls ATPase cycling. Most importantly, we found that the D2 domain of disease mutants failed to be activated by p37 or p47. Our results show that cofactors play a critical role in controlling p97 ATPase activity, and suggest that lack of cofactor-regulated communication may contribute to p97-associated disease pathogenesis.
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Affiliation(s)
- Xiaoyi Zhang
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502; College of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Lin Gui
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502; College of Pharmaceutical Sciences, Capital Medical University, Beijing 100069, People's Republic of China
| | - Xiaoyan Zhang
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109-1048
| | - Stacie L Bulfer
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Valentina Sanghez
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - Daniel E Wong
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - YouJin Lee
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110
| | - Lynn Lehmann
- NanoTemper Technologies, Inc., South San Francisco, CA 94080
| | - James Siho Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Pei-Yin Shih
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125
| | - Henry J Lin
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - Michelina Iacovino
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502
| | - Conrad C Weihl
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110
| | - Michelle R Arkin
- Small Molecule Discovery Center, Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94158
| | - Yanzhuang Wang
- Department of Molecular, Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109-1048
| | - Tsui-Fen Chou
- Division of Medical Genetics, Department of Pediatrics, Harbor-UCLA Medical Center, Los Angeles Biomedical Research Institute, Torrance, CA 90502;
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26
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Hunn BHM, Cragg SJ, Bolam JP, Spillantini MG, Wade-Martins R. Impaired intracellular trafficking defines early Parkinson's disease. Trends Neurosci 2015; 38:178-88. [PMID: 25639775 PMCID: PMC4740565 DOI: 10.1016/j.tins.2014.12.009] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 12/17/2014] [Accepted: 12/24/2014] [Indexed: 12/13/2022]
Abstract
Parkinson's disease (PD) is an insidious and incurable neurodegenerative disease, and represents a significant cost to individuals, carers, and ageing societies. It is defined at post-mortem by the loss of dopamine neurons in the substantia nigra together with the presence of Lewy bodies and Lewy neurites. We examine here the role of α-synuclein and other cellular transport proteins implicated in PD and how their aberrant activity may be compounded by the unique anatomy of the dopaminergic neuron. This review uses multiple lines of evidence from genetic studies, human tissue, induced pluripotent stem cells, and refined animal models to argue that prodromal PD can be defined as a disease of impaired intracellular trafficking. Dysfunction of the dopaminergic synapse heralds trafficking impairment.
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Affiliation(s)
- Benjamin H M Hunn
- Oxford Parkinson's Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK; Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Stephanie J Cragg
- Oxford Parkinson's Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK; Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - J Paul Bolam
- Oxford Parkinson's Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK; Medical Research Council Anatomical Neuropharmacology Unit, Department of Pharmacology, University of Oxford, Mansfield Road, Oxford OX1 3QT, UK
| | - Maria-Grazia Spillantini
- Department of Clinical Neurosciences, University of Cambridge, The Clifford Allbutt Building, Hills Road, Cambridge CB2 0QH, UK
| | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre, University of Oxford, South Parks Road, Oxford OX1 3QX, UK; Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK.
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27
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Zhao M, Wu S, Zhou Q, Vivona S, Cipriano DJ, Cheng Y, Brunger AT. Mechanistic insights into the recycling machine of the SNARE complex. Nature 2015; 518:61-7. [PMID: 25581794 PMCID: PMC4320033 DOI: 10.1038/nature14148] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Accepted: 12/10/2014] [Indexed: 12/11/2022]
Abstract
Evolutionarily conserved SNARE (soluble N-ethylmaleimide sensitive factor attachment protein receptors) proteins form a complex that drives membrane fusion in eukaryotes. The ATPase NSF (N-ethylmaleimide sensitive factor), together with SNAPs (soluble NSF attachment protein), disassembles the SNARE complex into its protein components, making individual SNAREs available for subsequent rounds of fusion. Here we report structures of ATP- and ADP-bound NSF, and the NSF/SNAP/SNARE (20S) supercomplex determined by single-particle electron cryomicroscopy at near-atomic to sub-nanometre resolution without imposing symmetry. Large, potentially force-generating, conformational differences exist between ATP- and ADP-bound NSF. The 20S supercomplex exhibits broken symmetry, transitioning from six-fold symmetry of the NSF ATPase domains to pseudo four-fold symmetry of the SNARE complex. SNAPs interact with the SNARE complex with an opposite structural twist, suggesting an unwinding mechanism. The interfaces between NSF, SNAPs, and SNAREs exhibit characteristic electrostatic patterns, suggesting how one NSF/SNAP species can act on many different SNARE complexes.
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Affiliation(s)
- Minglei Zhao
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Shenping Wu
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
| | - Qiangjun Zhou
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Sandro Vivona
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Daniel J Cipriano
- Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
| | - Yifan Cheng
- Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, California 94158, USA
| | - Axel T Brunger
- 1] Department of Molecular and Cellular Physiology, Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA [2] Department of Neurology and Neurological Sciences, Department of Structural Biology, Department of Photon Science, Stanford University, Stanford, California 94305, USA
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28
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Shah N, Colbert KN, Enos MD, Herschlag D, Weis WI. Three αSNAP and 10 ATP molecules are used in SNARE complex disassembly by N-ethylmaleimide-sensitive factor (NSF). J Biol Chem 2014; 290:2175-88. [PMID: 25492864 DOI: 10.1074/jbc.m114.620849] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The fusion of intracellular membranes is driven by the formation of a highly stable four-helix bundle of SNARE proteins embedded in the vesicle and target membranes. N-Ethylmaleimide sensitive factor recycles SNAREs after fusion by binding to the SNARE complex through an adaptor protein, αSNAP, and using the energy of ATP hydrolysis to disassemble the complex. Although only a single molecule of αSNAP binds to a soluble form of the SNARE complex, we find that three molecules of αSNAP are used for SNARE complex disassembly. We describe an engineered αSNAP trimer that supports more efficient SNARE complex disassembly than monomeric αSNAP. Using the trimerized αSNAP, we find that N-ethylmaleimide-sensitive factor hydrolyzes 10 ATP molecules on average to disassemble a single SNARE complex.
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Affiliation(s)
- Niket Shah
- From the Departments of Structural Biology, Molecular and Cellular Physiology, and
| | - Karen N Colbert
- From the Departments of Structural Biology, Molecular and Cellular Physiology, and
| | - Michael D Enos
- From the Departments of Structural Biology, Molecular and Cellular Physiology, and
| | - Daniel Herschlag
- Biochemistry, Stanford University School of Medicine, Stanford, California 94305
| | - William I Weis
- From the Departments of Structural Biology, Molecular and Cellular Physiology, and
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29
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Sousa R. Structural mechanisms of chaperone mediated protein disaggregation. Front Mol Biosci 2014; 1:12. [PMID: 25988153 PMCID: PMC4428496 DOI: 10.3389/fmolb.2014.00012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Accepted: 08/27/2014] [Indexed: 11/13/2022] Open
Abstract
The ClpB/Hsp104 and Hsp70 classes of molecular chaperones use ATP hydrolysis to dissociate protein aggregates and complexes, and to move proteins through membranes. ClpB/Hsp104 are members of the AAA+ family of proteins which form ring-shaped hexamers. Loops lining the pore in the ring engage substrate proteins as extended polypeptides. Interdomain rotations and conformational changes in these loops coupled to ATP hydrolysis unfold and pull proteins through the pore. This provides a mechanism that progressively disrupts local secondary and tertiary structure in substrates, allowing these chaperones to dissociate stable aggregates such as β-sheet rich prions or coiled coil SNARE complexes. While the ClpB/Hsp104 mechanism appears to embody a true power-stroke in which an ATP powered conformational change in one protein is directly coupled to movement or structural change in another, the mechanism of force generation by Hsp70s is distinct and less well understood. Both active power-stroke and purely passive mechanisms in which Hsp70 captures spontaneous fluctuations in a substrate have been proposed, while a third proposed mechanism-entropic pulling-may be able to generate forces larger than seen in ATP-driven molecular motors without the conformational coupling required for a power-stroke. The disaggregase activity of these chaperones is required for thermotolerance, but unrestrained protein complex/aggregate dissociation is potentially detrimental. Disaggregating chaperones are strongly auto-repressed, and are regulated by co-chaperones which recruit them to protein substrates and activate the disaggregases via mechanisms involving either sequential transfer of substrate from one chaperone to another and/or simultaneous interaction of substrate with multiple chaperones. By effectively subjecting substrates to multiple levels of selection by multiple chaperones, this may insure that these potent disaggregases are only activated in the appropriate context.
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Affiliation(s)
- Rui Sousa
- Department of Biochemistry, University of Texas Health Science Center at San Antonio San Antonio, TX, USA
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30
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Lobingier BT, Nickerson DP, Lo SY, Merz AJ. SM proteins Sly1 and Vps33 co-assemble with Sec17 and SNARE complexes to oppose SNARE disassembly by Sec18. eLife 2014; 3:e02272. [PMID: 24837546 PMCID: PMC4060006 DOI: 10.7554/elife.02272] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Secretory and endolysosomal fusion events are driven by SNAREs and cofactors, including Sec17/α-SNAP, Sec18/NSF, and Sec1/Munc18 (SM) proteins. SMs are essential for fusion in vivo, but the basis of this requirement is enigmatic. We now report that, in addition to their established roles as fusion accelerators, SM proteins Sly1 and Vps33 directly shield SNARE complexes from Sec17- and Sec18-mediated disassembly. In vivo, wild-type Sly1 and Vps33 function are required to withstand overproduction of Sec17. In vitro, Sly1 and Vps33 impede SNARE complex disassembly by Sec18 and ATP. Unexpectedly, Sec17 directly promotes selective loading of Sly1 and Vps33 onto cognate SNARE complexes. A large thermodynamic barrier limits SM binding, implying that significant conformational rearrangements are involved. In a working model, Sec17 and SMs accelerate fusion mediated by cognate SNARE complexes and protect them from NSF-mediated disassembly, while mis-assembled or non-cognate SNARE complexes are eliminated through kinetic proofreading by Sec18. DOI:http://dx.doi.org/10.7554/eLife.02272.001 Eukaryotic organisms, from single-celled yeast to humans, divide their cells into membrane-bound compartments (organelles) of distinct function. To move from one compartment to another, or to enter or exit a cell, large molecules like proteins are packaged into small membrane sacs called vesicles. To release its cargo, the membrane of a vesicle must fuse with the membrane of the correct destination compartment. The SNARE family of proteins plays a key role in this fusion process. As the membranes of a vesicle and target compartment come close, SNARE proteins located on each membrane form a SNARE complex that tethers the vesicle in place and causes the two membranes fuse. SNARE proteins do not act alone in this process: the SM family of proteins also plays an essential role in SNARE-mediated membrane fusion. However, it is still not clear exactly why the SM proteins are needed. Lobingier et al. used the yeast model organism and biochemical studies with purified proteins to show that SM proteins help SNARE complexes form at the right time by regulating the delicate balance between SNARE complex formation and disassembly. This is achieved through the interplay of SM proteins and two other proteins (Sec17 and Sec18). Sec17 is known to load Sec18 onto SNARE complexes to break them apart. Lobingier et al. showed that Sec17 can also load SM proteins on SNARE complexes. This hinders Sec18 action, and so helps to keep the SNARE complexes intact. Because each SM protein tested only binds to the SNARE complex that should function at the membrane where the SM protein resides, these findings suggest SM proteins perform quality control at potential sites of membrane fusion. DOI:http://dx.doi.org/10.7554/eLife.02272.002
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Affiliation(s)
- Braden T Lobingier
- Department of Biochemistry, University of Washington School of Medicine, Seattle, United States
| | - Daniel P Nickerson
- Department of Biochemistry, University of Washington School of Medicine, Seattle, United States
| | - Sheng-Ying Lo
- Department of Biochemistry, University of Washington School of Medicine, Seattle, United States
| | - Alexey J Merz
- Department of Biochemistry, University of Washington School of Medicine, Seattle, United States Department of Physiology and Biophysics, University of Washington School of Medicine, Seattle, United States
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31
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Federighi G, Traina G, Macchi M, Ciampini C, Bernardi R, Baldi E, Bucherelli C, Brunelli M, Scuri R. Modulation of gene expression in contextual fear conditioning in the rat. PLoS One 2013; 8:e80037. [PMID: 24278235 PMCID: PMC3837011 DOI: 10.1371/journal.pone.0080037] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Accepted: 09/27/2013] [Indexed: 01/30/2023] Open
Abstract
In contextual fear conditioning (CFC) a single training leads to long-term memory of context-aversive electrical foot-shocks association. Mid-temporal regions of the brain of trained and naive rats were obtained 2 days after conditioning and screened by two-directional suppression subtractive hybridization. A pool of differentially expressed genes was identified and some of them were randomly selected and confirmed with qRT-PCR assay. These transcripts showed high homology for rat gene sequences coding for proteins involved in different cellular processes. The expression of the selected transcripts was also tested in rats which had freely explored the experimental apparatus (exploration) and in rats to which the same number of aversive shocks had been administered in the same apparatus, but temporally compressed so as to make the association between painful stimuli and the apparatus difficult (shock-only). Some genes resulted differentially expressed only in the rats subjected to CFC, others only in exploration or shock-only rats, whereas the gene coding for translocase of outer mitochondrial membrane 20 protein and nardilysin were differentially expressed in both CFC and exploration rats. For example, the expression of stathmin 1 whose transcripts resulted up regulated was also tested to evaluate the transduction and protein localization after conditioning.
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Affiliation(s)
- Giuseppe Federighi
- Dipartimento di Ricerca Traslazionale e Delle Nuove Tecnologie in Medicina e Chirurgia, Unità di Fisiologia, Università di Pisa, Pisa, Italy
| | - Giovanna Traina
- Dipartimento di Scienze Economico-Estimative e degli Alimenti, Sezione di Chimica Bromatologica, Biochimica, Fisiologia e Nutrizione, Università degli Studi di Perugia, Perugia, Italy
| | - Monica Macchi
- Dipartimento di Biologia, Università di Pisa, Pisa, Italy
| | - Cristina Ciampini
- Dipartimento di Ricerca Traslazionale e Delle Nuove Tecnologie in Medicina e Chirurgia, Unità di Fisiologia, Università di Pisa, Pisa, Italy
| | - Rodolfo Bernardi
- Dipartimento di Scienze Agrarie, Genetica Alimentari e Agro-Ambientali, Università di Pisa, Pisa, Italy
| | - Elisabetta Baldi
- Dipartimento di Scienze Fisiologiche, Università di Firenze, Firenze, Italy
| | - Corrado Bucherelli
- Dipartimento di Scienze Fisiologiche, Università di Firenze, Firenze, Italy
| | | | - Rossana Scuri
- Dipartimento di Ricerca Traslazionale e Delle Nuove Tecnologie in Medicina e Chirurgia, Unità di Fisiologia, Università di Pisa, Pisa, Italy
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