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Hong W. SNAREs and traffic. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2005; 1744:120-44. [PMID: 15893389 DOI: 10.1016/j.bbamcr.2005.03.014] [Citation(s) in RCA: 362] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2004] [Revised: 03/24/2005] [Accepted: 03/28/2005] [Indexed: 01/05/2023]
Abstract
SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) are now generally accepted to be the major players in the final stage of the docking and the subsequent fusion of diverse vesicle-mediated transport events. The SNARE-mediated process is conserved evolutionally from yeast to human, as well as mechanistically and structurally across different transport events in eukaryotic cells. In the post-genomic era, a fairly complete list of "all" SNAREs in several organisms (including human) can now be made. This review aims to summarize the key properties and the mechanism of action of SNAREs in mammalian cells.
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Affiliation(s)
- Wanjin Hong
- Membrane Biology Laboratory, Institute of Molecular and Cell Biology, Proteos, Singapore.
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52
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Dietrich LE, Ungermann C. On the mechanism of protein palmitoylation. EMBO Rep 2005; 5:1053-7. [PMID: 15520806 PMCID: PMC1299172 DOI: 10.1038/sj.embor.7400277] [Citation(s) in RCA: 102] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2004] [Accepted: 08/26/2004] [Indexed: 11/08/2022] Open
Abstract
Protein palmitoylation or, more specifically, S-acylation is a reversible post-translational lipid modification. Despite the identification of several proteins that are altered in this way, our understanding of the enzymology of this process has been hampered by the lack of well-characterized acyltransferases. We now know of three proteins in Saccharomyces cerevisiae that promote palmitoylation: effector of Ras function (Erf2), ankyrin-repeat-containing protein (Akr1) and the SNARE protein Ykt6. Erf2 and Akr1 are integral membrane proteins that contain a cysteine-rich domain and an Asp-His-His-Cys motif, both of which catalyse acylation at the carboxyl terminus of their target proteins. Recently, we discovered that Ykt6 mediates the amino-terminal acylation of the fusion protein Vac8. Even though these three proteins differ in sequence, topology, size and substrate specificity, they might function in a similar manner. In this review, we discuss these observations in the context of a potential general mechanism of acylation.
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Affiliation(s)
- Lars E.P. Dietrich
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Christian Ungermann
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
- Tel: +49 6221 544 180; Fax: +49 6221 544 366;
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53
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Hasegawa H, Yang Z, Oltedal L, Davanger S, Hay JC. Intramolecular protein-protein and protein-lipid interactions control the conformation and subcellular targeting of neuronal Ykt6. J Cell Sci 2005; 117:4495-508. [PMID: 15331663 DOI: 10.1242/jcs.01314] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Although the membrane-trafficking functions of most SNAREs are conserved from yeast to humans, some mammalian SNAREs have evolved specialized functions unique to multicellular life. The mammalian homolog of the prenylated yeast SNARE Ykt6p might be one such example, because rat Ykt6 is highly expressed only in brain neurons. Furthermore, neuronal Ykt6 displayed a remarkably specialized, punctate localization that did not overlap appreciably with conventional compartments of the endomembrane system, suggesting that Ykt6 might be involved in a pathway unique to or specifically modified for neuronal function. Targeting of Ykt6 to its unique subcellular location was directed by its profilin-like longin domain. We have taken advantage of high-resolution structural data available for the yeast Ykt6p longin domain to examine mechanisms by which the mammalian longin domain controls Ykt6 conformation and subcellular targeting. We found that the overall tertiary structure of the longin domain, not sequence-specific surface features, drives direct targeting to the Ykt6 punctate structures. However, several sequence-specific surface features of the longin domain indirectly regulate Ykt6 localization through intramolecular interactions that mask otherwise-dominant targeting signals on the SNARE motif and lipid groups. Specifically, two hydrophobic binding pockets, one on each face of the longin domain, and one mixed hydrophobic/charged surface, participate in protein-protein interactions with the SNARE motif and protein-lipid interactions with the lipid group(s) at the molecule's C-terminus. One of the hydrophobic pockets suppresses protein-palmitoylation-dependent mislocalization of Ykt6 to the plasma membrane. The Ykt6 intramolecular interactions would be predicted to create a compact, closed conformation of the SNARE that prevents promiscuous targeting interactions and premature insertion into membranes. Interestingly, both protein-protein and protein-lipid interactions are required for a tightly closed conformation and normal targeting.
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Affiliation(s)
- Haruki Hasegawa
- University of Michigan, Department of Molecular, Cellular and Developmental Biology, Ann Arbor, MI 48109-1048, USA
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54
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55
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Turnbull AP, Kümmel D, Prinz B, Holz C, Schultchen J, Lang C, Niesen FH, Hofmann KP, Delbrück H, Behlke J, Müller EC, Jarosch E, Sommer T, Heinemann U. Structure of palmitoylated BET3: insights into TRAPP complex assembly and membrane localization. EMBO J 2005; 24:875-84. [PMID: 15692564 PMCID: PMC554119 DOI: 10.1038/sj.emboj.7600565] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Accepted: 01/04/2005] [Indexed: 11/09/2022] Open
Abstract
BET3 is a component of TRAPP, a complex involved in the tethering of transport vesicles to the cis-Golgi membrane. The crystal structure of human BET3 has been determined to 1.55-A resolution. BET3 adopts an alpha/beta-plait fold and forms dimers in the crystal and in solution, which predetermines the architecture of TRAPP where subunits are present in equimolar stoichiometry. A hydrophobic pocket within BET3 buries a palmitate bound through a thioester linkage to cysteine 68. BET3 and yeast Bet3p are palmitoylated in recombinant yeast cells, the mutant proteins BET3 C68S and Bet3p C80S remain unmodified. Both BET3 and BET3 C68S are found in membrane and cytosolic fractions of these cells; in membrane extractions, they behave like tightly membrane-associated proteins. In a deletion strain, both Bet3p and Bet3p C80S rescue cell viability. Thus, palmitoylation is neither required for viability nor sufficient for membrane association of BET3, which may depend on protein-protein contacts within TRAPP or additional, yet unidentified modifications of BET3. A conformational change may facilitate palmitoyl extrusion from BET3 and allow the fatty acid chain to engage in intermolecular hydrophobic interactions.
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Affiliation(s)
- Andrew P Turnbull
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- Protein Structure Factory, c/o BESSY GmbH, Berlin, Germany
| | - Daniel Kümmel
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Bianka Prinz
- Institut für Biotechnologie, FG Mikrobiologie und Genetik, Technische Universität Berlin, Berlin, Germany
- Protein Structure Factory, Heubnerweg, Berlin, Germany
| | - Caterina Holz
- Institut für Biotechnologie, FG Mikrobiologie und Genetik, Technische Universität Berlin, Berlin, Germany
- Protein Structure Factory, Heubnerweg, Berlin, Germany
| | - Jeffrey Schultchen
- Institut für Biotechnologie, FG Mikrobiologie und Genetik, Technische Universität Berlin, Berlin, Germany
- Protein Structure Factory, Heubnerweg, Berlin, Germany
| | - Christine Lang
- Institut für Biotechnologie, FG Mikrobiologie und Genetik, Technische Universität Berlin, Berlin, Germany
- Protein Structure Factory, Heubnerweg, Berlin, Germany
| | - Frank H Niesen
- Protein Structure Factory, Heubnerweg, Berlin, Germany
- Institut für Medizinische Physik und Biophysik, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Klaus-Peter Hofmann
- Institut für Medizinische Physik und Biophysik, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Heinrich Delbrück
- Protein Structure Factory, Heubnerweg, Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Berlin, Germany
| | - Joachim Behlke
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | | | - Ernst Jarosch
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Thomas Sommer
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - Udo Heinemann
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- Institut für Chemie/Kristallographie, Freie Universität Berlin, Berlin, Germany
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56
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Dietrich LEP, LaGrassa TJ, Rohde J, Cristodero M, Meiringer CTA, Ungermann C. ATP-independent control of Vac8 palmitoylation by a SNARE subcomplex on yeast vacuoles. J Biol Chem 2005; 280:15348-55. [PMID: 15701652 DOI: 10.1074/jbc.m410582200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Yeast vacuole fusion requires palmitoylated Vac8. We previously showed that Vac8 acylation occurs early in the fusion reaction, is blocked by antibodies against Sec18 (yeast N-ethylmaleimide-sensitive fusion protein (NSF)), and is mediated by the R-SNARE Ykt6. Here we analyzed the regulation of this reaction on purified vacuoles. We show that Vac8 acylation is restricted to a narrow time window, is independent of ATP hydrolysis by Sec18, and is stimulated by the ion chelator EDTA. Analysis of vacuole protein complexes indicated that Ykt6 is part of a complex distinct from the second R-SNARE, Nyv1. We speculate that during vacuole fusion, Nyv1 is the classical R-SNARE, whereas the Ykt6-containing complex has a novel function in Vac8 palmitoylation.
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Affiliation(s)
- Lars E P Dietrich
- Biochemie-Zentrum der Universität Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
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57
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Kim YG, Sohn EJ, Seo J, Lee KJ, Lee HS, Hwang I, Whiteway M, Sacher M, Oh BH. Crystal structure of bet3 reveals a novel mechanism for Golgi localization of tethering factor TRAPP. Nat Struct Mol Biol 2004; 12:38-45. [PMID: 15608655 DOI: 10.1038/nsmb871] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2004] [Accepted: 11/17/2004] [Indexed: 01/24/2023]
Abstract
Transport protein particle (TRAPP) is a large multiprotein complex involved in endoplasmic reticulum-to-Golgi and intra-Golgi traffic. TRAPP specifically and persistently resides on Golgi membranes. Neither the mechanism of the subcellular localization nor the function of any of the individual TRAPP components is known. Here, the crystal structure of mouse Bet3p (bet3), a conserved TRAPP component, reveals a dimeric structure with hydrophobic channels. The channel entrances are located on a putative membrane-interacting surface that is distinctively flat, wide and decorated with positively charged residues. Charge-inversion mutations on the flat surface of the highly conserved yeast Bet3p led to conditional lethality, incorrect localization and membrane trafficking defects. A channel-blocking mutation led to similar defects. These data delineate a molecular mechanism of Golgi-specific targeting and anchoring of Bet3p involving the charged surface and insertion of a Golgi-specific hydrophobic moiety into the channels. This essential subunit could then direct other TRAPP components to the Golgi.
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Affiliation(s)
- Yeon-Gil Kim
- Center for Biomolecular Recognition, Department of Life Science and Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Korea
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58
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Peters C, Baars TL, Bühler S, Mayer A. Mutual Control of Membrane Fission and Fusion Proteins. Cell 2004; 119:667-78. [PMID: 15550248 DOI: 10.1016/j.cell.2004.11.023] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2004] [Revised: 09/27/2004] [Accepted: 10/20/2004] [Indexed: 11/24/2022]
Abstract
Membrane fusion and fission are antagonistic reactions controlled by different proteins. Dynamins promote membrane fission by GTP-driven changes of conformation and polymerization state, while SNAREs fuse membranes by forming complexes between t- and v-SNAREs from apposed vesicles. Here, we describe a role of the dynamin-like GTPase Vps1p in fusion of yeast vacuoles. Vps1p forms polymers that couple several t-SNAREs together. At the onset of fusion, the SNARE-activating ATPase Sec18p/NSF and the t-SNARE depolymerize Vps1p and release it from the membrane. This activity is independent of the SNARE coactivator Sec17p/alpha-SNAP and of the v-SNARE. Vps1p release liberates the t-SNAREs for initiating fusion and at the same time disrupts fission activity. We propose that reciprocal control between fusion and fission components exists, which may prevent futile cycles of fission and fusion.
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Affiliation(s)
- Christopher Peters
- Département de Biochimie, Université de Lausanne, Chemin des Boveresses 155, 1066 Epalinges, Switzerland.
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59
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Turner MD. Fatty acyl CoA-mediated inhibition of endoplasmic reticulum assembly. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2004; 1693:1-4. [PMID: 15276319 DOI: 10.1016/j.bbamcr.2004.05.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Revised: 03/25/2004] [Accepted: 05/05/2004] [Indexed: 11/20/2022]
Abstract
The protein machinery that mediates homotypic fusion of mammalian endoplasmic reticulum (ER) membranes is becoming increasing well defined. However, little is known of how acylation of constituent membrane components might impact upon this event. This is particularly important as acylation has been shown to promote both fusion and fission of heterotypic membranes. Using a previously characterised cell-free ER fusion assay, I show here that incubation of membranes in the presence of either palmitoyl CoA or myristoyl CoA potently inhibits assembly. Furthermore, inhibition does not occur when membranes are incubated in the constituent palmitate or CoA moieties alone. These findings suggest that not only do palmitoyl CoA and myristoyl CoA inhibit ER assembly, but that they might instead be functioning to actively facilitate ER membrane fission.
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Affiliation(s)
- Mark D Turner
- Centre for Diabetes and Metabolic Medicine, Institute of Cell and Molecular Science, St. Bartholomew's and The Royal London School of Medicine and Dentistry, Queen Mary, University of London, Whitechapel, London, E1 1BB, UK.
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60
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Thorngren N, Collins KM, Fratti RA, Wickner W, Merz AJ. A soluble SNARE drives rapid docking, bypassing ATP and Sec17/18p for vacuole fusion. EMBO J 2004; 23:2765-76. [PMID: 15241469 PMCID: PMC514947 DOI: 10.1038/sj.emboj.7600286] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2004] [Accepted: 06/02/2004] [Indexed: 11/09/2022] Open
Abstract
Membrane fusion requires priming, the disassembly of cis-SNARE complexes by the ATP-driven chaperones Sec18/17p. Yeast vacuole priming releases Vam7p, a soluble SNARE. Vam7p reassociation during docking allows trans-SNARE pairing and fusion. We now report that recombinant Vam7p (rVam7p) enters into complex with other SNAREs in vitro and bypasses the need for Sec17p, Sec18p, and ATP. Thus, the sole essential function of vacuole priming in vitro is the release of Vam7p from cis-SNARE complexes. In 'bypass fusion', without ATP but with added rVam7p, there are sufficient unpaired vacuolar SNAREs Vam3p, Vti1p, and Nyv1p to interact with Vam7p and support fusion. However, active SNARE proteins are not sufficient for bypass fusion. rVam7p does not bypass requirements for Rho GTPases,Vps33p, Vps39p, Vps41p, calmodulin, specific lipids, or Vph1p, a subunit of the V-ATPase. With excess rVam7p, reduced levels of PI(3)P or functional Ypt7p suffice for bypass fusion. High concentrations of rVam7p allow the R-SNARE Ykt6p to substitute for Nyv1p for fusion; this functional redundancy among vacuole SNAREs may explain why nyv1delta strains lack the vacuole fragmentation seen with mutants in other fusion catalysts.
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Affiliation(s)
- Naomi Thorngren
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
| | - Kevin M Collins
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
| | - Rutilio A Fratti
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
| | - William Wickner
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
- Department of Biochemistry, 7200 Vail Building, Room 425 Remsen, Dartmouth Medical School, Hanover, NH 03755-3844, USA. Tel.: +1 603 650 1701; Fax: +1 603 650 1353; E-mail: ; Lab website: http://www.dartmouth.edu/~wickner
| | - Alexey J Merz
- Department of Biochemistry, Dartmouth Medical School, Hanover, NH, USA
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Lowe M, Barr FA. Alpine pathways of membrane traffic. EMBO Rep 2004; 5:561-4. [PMID: 15153935 PMCID: PMC1299081 DOI: 10.1038/sj.embor.7400173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 04/27/2004] [Indexed: 11/09/2022] Open
Affiliation(s)
- Martin Lowe
- School of Biological Sciences, University of Manchester, The Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
- Tel: +44 161 275 5387; Fax: +44 161 275 1505;
| | - Francis A. Barr
- Department of Cell Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Fukasawa M, Varlamov O, Eng WS, Söllner TH, Rothman JE. Localization and activity of the SNARE Ykt6 determined by its regulatory domain and palmitoylation. Proc Natl Acad Sci U S A 2004; 101:4815-20. [PMID: 15044687 PMCID: PMC387331 DOI: 10.1073/pnas.0401183101] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) catalyze compartment-specific membrane fusion. Whereas most SNAREs are bona fide type II membrane proteins, Ykt6 lacks a proteinaceous membrane anchor but contains a prenylation consensus motif (CAAX box) and exists in an inactive cytosolic and an active membrane-bound form. We demonstrate that both forms are farnesylated at the carboxyl-terminal cysteine of the CCAIM sequence. Farnesylation is the prerequisite for subsequent palmitoylation of the upstream cysteine, which permits stable membrane association of Ykt6. The double-lipid modification and membrane association is crucial for intra-Golgi transport in vitro and cell homeostasis/survival in vivo. The membrane recruitment and palmitoylation is controlled by the N-terminal domain of Ykt6, which interacts with the SNARE motif, keeping it in an inactive closed conformation. Together, these results suggest that conformational changes control the lipid modification and function of Ykt6. Considering the essential and central role of Ykt6 in the secretory pathway, this spatial and functional cycle might provide a mechanism to regulate the rate of intracellular membrane flow.
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Affiliation(s)
- Masayoshi Fukasawa
- Cellular Biochemistry and Biophysics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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