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DAmico KA, Stanton AE, Shirkey JD, Travis SM, Jeffrey PD, Hughson FM. Structure of a membrane tethering complex incorporating multiple SNAREs. Nat Struct Mol Biol 2024; 31:246-254. [PMID: 38196032 PMCID: PMC10923073 DOI: 10.1038/s41594-023-01164-8] [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: 01/14/2023] [Accepted: 10/26/2023] [Indexed: 01/11/2024]
Abstract
Most membrane fusion reactions in eukaryotic cells are mediated by multisubunit tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial attachment of two membranes. Complementary SNAREs then form membrane-bridging complexes whose assembly draws the membranes together for fusion. Here we present a cryo-electron microscopy structure of the simplest known MTC, the 255-kDa Dsl1 complex of Saccharomyces cerevisiae, bound to the two SNAREs that anchor it to the endoplasmic reticulum. N-terminal domains of the SNAREs form an integral part of the structure, stabilizing a Dsl1 complex configuration with unexpected similarities to the 850-kDa exocyst MTC. The structure of the SNARE-anchored Dsl1 complex and its comparison with exocyst reveal what are likely to be common principles underlying MTC function. Our structure also implies that tethers and SNAREs can work together as a single integrated machine.
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Affiliation(s)
- Kevin A DAmico
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Abigail E Stanton
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Jaden D Shirkey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Sophie M Travis
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
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2
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Khakurel A, Lupashin VV. Role of GARP Vesicle Tethering Complex in Golgi Physiology. Int J Mol Sci 2023; 24:6069. [PMID: 37047041 PMCID: PMC10094427 DOI: 10.3390/ijms24076069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/17/2023] [Accepted: 03/19/2023] [Indexed: 04/14/2023] Open
Abstract
The Golgi associated retrograde protein complex (GARP) is an evolutionarily conserved component of Golgi membrane trafficking machinery that belongs to the Complexes Associated with Tethering Containing Helical Rods (CATCHR) family. Like other multisubunit tethering complexes such as COG, Dsl1, and Exocyst, the GARP is believed to function by tethering and promoting fusion of the endosome-derived small trafficking intermediate. However, even twenty years after its discovery, the exact structure and the functions of GARP are still an enigma. Recent studies revealed novel roles for GARP in Golgi physiology and identified human patients with mutations in GARP subunits. In this review, we summarized our knowledge of the structure of the GARP complex, its protein partners, GARP functions related to Golgi physiology, as well as cellular defects associated with the dysfunction of GARP subunits.
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Affiliation(s)
| | - Vladimir V. Lupashin
- Department of Physiology and Cell Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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3
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DAmico KA, Stanton AE, Shirkey JD, Travis SM, Jeffrey PD, Hughson FM. Structure of a Membrane Tethering Complex Incorporating Multiple SNAREs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.30.526244. [PMID: 36778436 PMCID: PMC9915479 DOI: 10.1101/2023.01.30.526244] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Most membrane fusion reactions in eukaryotic cells are mediated by membrane tethering complexes (MTCs) and SNARE proteins. MTCs are much larger than SNAREs and are thought to mediate the initial attachment of two membranes. Complementary SNAREs then form membrane-bridging complexes whose assembly draws the membranes together for fusion. Here, we present a cryo-EM structure of the simplest known MTC, the 255-kDa Dsl1 complex, bound to the two SNAREs that anchor it to the endoplasmic reticulum. N-terminal domains of the SNAREs form an integral part of the structure, stabilizing a Dsl1 complex configuration with remarkable and unexpected similarities to the 850-kDa exocyst MTC. The structure of the SNARE-anchored Dsl1 complex and its comparison with exocyst reveal what are likely to be common principles underlying MTC function. Our structure also implies that tethers and SNAREs can work together as a single integrated machine.
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Affiliation(s)
- Kevin A DAmico
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Abigail E Stanton
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Jaden D Shirkey
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Sophie M Travis
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
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4
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Wang YH, Chiu WY, Chen YT, Cai PJ, Wu YC, Wu JL, Chen BH, Liu YW, Yu CJ, Lee FJS. Golgin Imh1 and GARP complex cooperate to restore the impaired SNARE recycling transport induced by ER stress. Cell Rep 2022; 38:110488. [PMID: 35320730 DOI: 10.1016/j.celrep.2022.110488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/11/2021] [Accepted: 02/14/2022] [Indexed: 11/03/2022] Open
Abstract
The accumulation of misfolded proteins in the endoplasmic reticulum (ER) induces the unfolded protein response (UPR), which acts through various mechanisms to reduce ER stress. While the UPR has been well studied for its effects on the ER, its impact on the Golgi is less understood. The Golgi complex receives transport vesicles from the endosome through two types of tethering factors: long coiled-coil golgin and the multisubunit Golgi-associated retrograde protein (GARP) complex. Here, we report that ER stress increases the phosphorylation of golgin Imh1 to maintain the GARP-mediated recycling of the SNAREs Snc1 and Tlg1. We also identify a specific function of the Golgi affected by ER stress and elucidate a homeostatic response to restore this function, which involves both an Ire1-dependent and a MAP kinase Slt2/ERK2-dependent mechanism. Furthermore, our findings advance a general understanding of how two different types of tethers act cooperatively to mediate a transport pathway.
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Affiliation(s)
| | | | | | | | - Yu-Chieh Wu
- Institute of Molecular Medicine, Taipei, Taiwan
| | - Jia-Lu Wu
- Institute of Molecular Medicine, Taipei, Taiwan
| | - Bo-Han Chen
- Institute of Molecular Medicine, Taipei, Taiwan
| | - Ya-Wen Liu
- Institute of Molecular Medicine, Taipei, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chia-Jung Yu
- Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Fang-Jen S Lee
- Institute of Molecular Medicine, Taipei, Taiwan; Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan.
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5
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Wang S, Ma C. Neuronal SNARE complex assembly guided by Munc18-1 and Munc13-1. FEBS Open Bio 2022; 12:1939-1957. [PMID: 35278279 PMCID: PMC9623535 DOI: 10.1002/2211-5463.13394] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 02/28/2022] [Accepted: 03/10/2022] [Indexed: 01/25/2023] Open
Abstract
Neurotransmitter release by Ca2+ -triggered synaptic vesicle exocytosis is essential for information transmission in the nervous system. The soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs) syntaxin-1, SNAP-25, and synaptobrevin-2 form the SNARE complex to bring synaptic vesicles and the plasma membranes together and to catalyze membrane fusion. Munc18-1 and Munc13-1 regulate synaptic vesicle priming via orchestrating neuronal SNARE complex assembly. In this review, we summarize recent advances toward the functions and molecular mechanisms of Munc18-1 and Munc13-1 in guiding neuronal SNARE complex assembly, and discuss the functional similarities and differences between Munc18-1 and Munc13-1 in neurons and their homologs in other intracellular membrane trafficking systems.
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Affiliation(s)
- Shen Wang
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
| | - Cong Ma
- Key Laboratory of Molecular Biophysics of the Ministry of EducationCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina
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6
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Ahuja A, Kushwah J, Mathur C, Chauhan K, Dutta TK, Somvanshi VS. Identification of Galtox, a new protein toxin from Photorhabdus bacterial symbionts of Heterorhabditis nematodes. Toxicon 2021; 194:53-62. [PMID: 33610634 DOI: 10.1016/j.toxicon.2021.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 02/02/2021] [Accepted: 02/16/2021] [Indexed: 01/25/2023]
Abstract
The Gram-negative bacteria Photorhabdus lives in a symbiotic relationship with the insect-pathogenic Heterorhabditis nematodes and produces numerous hydrolytic enzymes, secondary metabolites and protein toxins. Seven Photorhabdus strains were previously isolated from the Heterorhabditis nematodes collected from different geographical regions of India. The strains IARI-SGMG3, IARI-SGHR2, IARI-SGHR4, IARI-SGMS1 and IARI-SGGJ2 were identified as P. akhurstii, whereas IARI-SGLDK1 and IARI-SGHP1 were identified as P. laumondii subsp. laumondii and P. laumondii subsp. clarkeii, respectively. A new and previously unreported 35 kDa molecular weight protein toxin 'Galtox' was identified from these Photorhabdus strains. The nucleotide sequences of the toxin gene from seven Photorhabdus strains were PCR amplified, sequenced, cloned into pET protein expression vector, and the protein toxin was expressed and purified. The Galtox sequence from various strains showed variations in sequence and toxicity against Galleria mellonella. The injection of purified Galtox protein into the 4th instar larvae showed median lethal dose (LD50) values of 2.39-26.08 ng toxin/g G. mellonella bodyweight after 48 h. The protein injection killed the insects quickly and exhibited a median lethal time (LT50) of 12-60 h when injected at the rate of 3.1-31.2 ng toxin/g G. mellonella bodyweight. Galtox protein sequence analysis indicated similarity to several bacterial toxin-related protein domains, such as 6rgnA domain of Bordetella membrane targeting toxin BteA, 6gy6 domain of Xenorhabdus α-Xenorhabdolysins, 4mu6A and 4xa9a domains similar to effector protein LegC3 from Legionella pneumophila and 1cv8.1 domain of staphylococcal cysteine proteinase staphopain B. The mode of action of Galtox needs to be understood to enable its use for the management of agricultural insect-pests.
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Affiliation(s)
- Amit Ahuja
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jyoti Kushwah
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Chetna Mathur
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Khushbu Chauhan
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Tushar Kanti Dutta
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vishal Singh Somvanshi
- Division of Nematology, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India.
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7
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Sawa-Makarska J, Baumann V, Coudevylle N, von Bülow S, Nogellova V, Abert C, Schuschnig M, Graef M, Hummer G, Martens S. Reconstitution of autophagosome nucleation defines Atg9 vesicles as seeds for membrane formation. Science 2020; 369:eaaz7714. [PMID: 32883836 PMCID: PMC7610778 DOI: 10.1126/science.aaz7714] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 05/16/2020] [Accepted: 07/06/2020] [Indexed: 12/15/2022]
Abstract
Autophagosomes form de novo in a manner that is incompletely understood. Particularly enigmatic are autophagy-related protein 9 (Atg9)-containing vesicles that are required for autophagy machinery assembly but do not supply the bulk of the autophagosomal membrane. In this study, we reconstituted autophagosome nucleation using recombinant components from yeast. We found that Atg9 proteoliposomes first recruited the phosphatidylinositol 3-phosphate kinase complex, followed by Atg21, the Atg2-Atg18 lipid transfer complex, and the E3-like Atg12-Atg5-Atg16 complex, which promoted Atg8 lipidation. Furthermore, we found that Atg2 could transfer lipids for Atg8 lipidation. In selective autophagy, these reactions could potentially be coupled to the cargo via the Atg19-Atg11-Atg9 interactions. We thus propose that Atg9 vesicles form seeds that establish membrane contact sites to initiate lipid transfer from compartments such as the endoplasmic reticulum.
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Affiliation(s)
- Justyna Sawa-Makarska
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
| | - Verena Baumann
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Nicolas Coudevylle
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Sören von Bülow
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
| | - Veronika Nogellova
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Christine Abert
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martina Schuschnig
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria
| | - Martin Graef
- Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931 Cologne, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Sascha Martens
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, 1030 Vienna, Austria.
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8
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Travis SM, DAmico K, Yu IM, McMahon C, Hamid S, Ramirez-Arellano G, Jeffrey PD, Hughson FM. Structural basis for the binding of SNAREs to the multisubunit tethering complex Dsl1. J Biol Chem 2020; 295:10125-10135. [PMID: 32409579 DOI: 10.1074/jbc.ra120.013654] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/01/2020] [Indexed: 01/02/2023] Open
Abstract
Multisubunit-tethering complexes (MTCs) are large (250 to >750 kDa), conserved macromolecular machines that are essential for soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-mediated membrane fusion in all eukaryotes. MTCs are thought to organize membrane trafficking by mediating the initial long-range interaction between a vesicle and its target membrane and promoting the formation of membrane-bridging SNARE complexes. Previously, we reported the structure of the yeast Dsl1 complex, the simplest known MTC, which is essential for coat protein I (COPI) mediated transport from the Golgi to the endoplasmic reticulum (ER). This structure suggests how the Dsl1 complex might tether a vesicle to its target membrane by binding at one end to the COPI coat and at the other to ER-associated SNAREs. Here, we used X-ray crystallography to investigate these Dsl1-SNARE interactions in greater detail. The Dsl1 complex comprises three subunits that together form a two-legged structure with a central hinge. We found that distal regions of each leg bind N-terminal Habc domains of the ER SNAREs Sec20 (a Qb-SNARE) and Use1 (a Qc-SNARE). The observed binding modes appear to anchor the Dsl1 complex to the ER target membrane while simultaneously ensuring that both SNAREs are in open conformations, with their SNARE motifs available for assembly. The proximity of the two SNARE motifs, and therefore their ability to enter the same SNARE complex, will depend on the relative orientation of the two Dsl1 legs. These results underscore the critical roles of SNARE N-terminal domains in mediating interactions with other elements of the vesicle docking and fusion machinery.
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Affiliation(s)
- Sophie M Travis
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Kevin DAmico
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - I-Mei Yu
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Conor McMahon
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Safraz Hamid
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | | | - Philip D Jeffrey
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Frederick M Hughson
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
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9
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Delgado Cruz M, Kim K. The inner workings of intracellular heterotypic and homotypic membrane fusion mechanisms. J Biosci 2019. [DOI: 10.1007/s12038-019-9913-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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10
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Ungermann C, Kümmel D. Structure of membrane tethers and their role in fusion. Traffic 2019; 20:479-490. [DOI: 10.1111/tra.12655] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/26/2019] [Accepted: 05/03/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Christian Ungermann
- Biochemistry Section, Department of Biology/ChemistryUniversity of Osnabrück Osnabrück Germany
- Center for Cellular Nanoanalytics (CellNanOs)University of Osnabrück Osnabrück Germany
| | - Daniel Kümmel
- Biochemistry & Structural Biology Section, Institute of BiochemistryUniversity of Münster Münster Germany
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11
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Makaraci P, Delgado Cruz M, McDermott H, Nguyen V, Highfill C, Kim K. Yeast dynamin and Ypt6 function in parallel for the endosome-to-Golgi retrieval of Snc1. Cell Biol Int 2018; 43:1137-1151. [PMID: 30080296 DOI: 10.1002/cbin.11042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Protein recycling is an important cellular process required for cell homeostasis. Results from prior studies have shown that vacuolar sorting protein-1 (Vps1), a dynamin homolog in yeast, is implicated in protein recycling from the endosome to the trans-Golgi Network (TGN). However, the function of Vps1 in relation to Ypt6, a master GTPase in the recycling pathway, remains unknown. The present study reveals that Vps1 physically interacts with Ypt6 if at least one of them is full-length. We found that overexpression of full-length Vps1, but not GTP hydrolysis-defective Vps1 mutants, is sufficient to rescue abnormal phenotypes of Snc1 distribution provoked by the loss of Ypt6, and vice versa. This suggests that Vps1 and Ypt6 function in parallel pathways instead of in a sequential pathway and that GTP binding/hydrolysis of Vps1 is required for proper traffic of Snc1 toward the TGN. Additionally, we identified two novel Vps1-binding partners, Vti1 and Snc2, which function for the endosome-derived vesicle fusion at the TGN. Taken together, the present study demonstrates that Vps1 plays a role in later stages of the endosome-to-TGN traffic.
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Affiliation(s)
- Pelin Makaraci
- Department of Biology, Missouri State University, 901S National, Springfield, MO, 65807, USA
| | | | - Hyoeun McDermott
- Department of Biology, Missouri State University, 901S National, Springfield, MO, 65807, USA
| | | | - Chad Highfill
- Department of Biology, Missouri State University, 901S National, Springfield, MO, 65807, USA.,Genetics Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901S National, Springfield, MO, 65807, USA
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12
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Makaraci P, Kim K. trans-Golgi network-bound cargo traffic. Eur J Cell Biol 2018; 97:137-149. [PMID: 29398202 DOI: 10.1016/j.ejcb.2018.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 12/15/2017] [Accepted: 01/16/2018] [Indexed: 12/19/2022] Open
Abstract
Cargo following the retrograde trafficking are sorted at endosomes to be targeted the trans-Golgi network (TGN), a central receiving organelle. Though molecular requirements and their interaction networks have been somewhat established, the complete understanding of the intricate nature of their action mechanisms in every step of the retrograde traffic pathway remains unachieved. This review focuses on elucidating known functions of key regulators, including scission factors at the endosome and tethering/fusion mediators at the receiving dock, TGN, as well as a diverse range of cargo.
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Affiliation(s)
- Pelin Makaraci
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National Ave., Springfield, MO 65807, USA.
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13
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Bonjack-Shterengartz M, Avnir D. The enigma of the near-symmetry of proteins: Domain swapping. PLoS One 2017; 12:e0180030. [PMID: 28708874 PMCID: PMC5510828 DOI: 10.1371/journal.pone.0180030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 06/08/2017] [Indexed: 01/25/2023] Open
Abstract
The majority of proteins form oligomers which have rotational symmetry. Literature has suggested many functional advantages that the symmetric packing offers. Yet, despite these advantages, the vast majority of protein oligomers are only nearly symmetric. A key question in the field of proteins structure is therefore, if symmetry is so advantageous, why do oligomers settle for aggregates that do not maximize that structural property? The answer to that question is apparently multi-parametric, and involves distortions at the interaction zones of the monomer units of the oligomer in order to minimize the free energy, the dynamics of the protein, the effects of surroundings parameters, and the mechanism of oligomerization. The study of this problem is in its infancy: Only the first parameter has been explored so far. Here we focus on the last parameter-the mechanism of formation. To test this effect we have selected to focus on the domain swapping mechanism of oligomerization, by which oligomers form in a mechanism that swaps identical portions of monomeric units, resulting in an interwoven oligomer. We are using continuous symmetry measures to analyze in detail the oligomer formed by this mechanism, and found, that without exception, in all analyzed cases, perfect symmetry is given away, and we are able to identify that the main burden of distortion lies in the hinge regions that connect the swapped portions. We show that the continuous symmetry analysis method clearly identifies the hinge region of swapped domain proteins-considered to be a non-trivial task. We corroborate our conclusion about the central role of the hinge region in affecting the symmetry of the oligomers, by a special probability analysis developed particularly for that purpose.
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Affiliation(s)
- Maayan Bonjack-Shterengartz
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Avnir
- Institute of Chemistry and the Lise Meitner Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
- * E-mail:
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14
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Saimani U, Kim K. Traffic from the endosome towards trans-Golgi network. Eur J Cell Biol 2017; 96:198-205. [PMID: 28256269 DOI: 10.1016/j.ejcb.2017.02.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/24/2017] [Accepted: 02/16/2017] [Indexed: 11/16/2022] Open
Abstract
Retrograde passage of a transport carrier entails cargo sorting at the endosome, generation of a cargo-laden carrier and its movement along cytoskeletal tracks towards trans-Golgi network (TGN), tethering at the TGN, and fusion with the Golgi membrane. Significant advances have been made in understanding this traffic system, revealing molecular requirements in each step and the functional connection between them as well as biomedical implication of the dysregulation of those important traffic factors. This review focuses on describing up-to-date action mechanisms for retrograde transport from the endosomal system to the TGN.
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Affiliation(s)
- Uma Saimani
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65807, United States
| | - Kyoungtae Kim
- Department of Biology, Missouri State University, 901 S National, Springfield, MO 65807, United States.
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15
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Crystal structure of Sec10, a subunit of the exocyst complex. Sci Rep 2017; 7:40909. [PMID: 28098232 PMCID: PMC5241887 DOI: 10.1038/srep40909] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/13/2016] [Indexed: 12/22/2022] Open
Abstract
The exocyst complex is a heterooctameric protein complex composed of Sec3, Sec5, Sec6, Sec8, Sec10, Sec15, Exo70 and Exo84. This complex plays an essential role in trafficking secretory vesicles to the plasma membrane through its interaction with phosphatidylinositol 4,5-bisphosphate and small GTPases. To date, the near-full-length structural information of each subunit has been limited to Exo70, although the C-terminal half structures of Sec6, Sec15 and Exo84 and the structures of the small GTPase-binding domains of Sec3, Sec5 and Exo84 have been reported. Here, we report the crystal structure of the near-full-length zebrafish Sec10 (zSec10) at 2.73 Å resolution. The structure of zSec10 consists of tandem antiparallel helix bundles that form a straight rod, like helical core regions of other exocyst subunits. This structure provides the first atomic details of Sec10, which may be useful for future functional and structural studies of this subunit and the exocyst complex.
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16
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Jimenez-Ruiz E, Morlon-Guyot J, Daher W, Meissner M. Vacuolar protein sorting mechanisms in apicomplexan parasites. Mol Biochem Parasitol 2016; 209:18-25. [PMID: 26844642 PMCID: PMC5154328 DOI: 10.1016/j.molbiopara.2016.01.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 01/14/2016] [Accepted: 01/28/2016] [Indexed: 12/26/2022]
Abstract
The phylum Apicomplexa comprises more than 5000 species including pathogens of clinical and economical importance. These obligate intracellular parasites possess a highly complex endomembrane system to build amongst others three morphologically distinct secretory organelles: rhoptries, micronemes and dense granules. Proteins released by these organelles are essential for invasion and hijacking of the host cell. Due to the complexity of the internal organization of these parasites, a wide panoply of trafficking factors was expected to be required for the correct sorting of proteins towards the various organelles. However, Toxoplasma gondii and other apicomplexan parasites contain only a core set of these factors and several of the vacuolar protein sorting (VPS) homologues found in most eukaryotes have been lost in this phylum. In this review, we will summarise our current knowledge about the role of trafficking complexes in T. gondii, highlighting recent studies focused on complexes formed by VPS proteins. We also present a novel, hypothetical model, suggesting the recycling of parasite membrane and micronemal proteins.
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Gershlick DC, Schindler C, Chen Y, Bonifacino JS. TSSC1 is novel component of the endosomal retrieval machinery. Mol Biol Cell 2016; 27:2867-78. [PMID: 27440922 PMCID: PMC5025273 DOI: 10.1091/mbc.e16-04-0209] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/13/2016] [Indexed: 12/23/2022] Open
Abstract
A previously uncharacterized WD40 domain–containing protein named TSSC1 is shown to interact with the GARP and EARP tethering complexes, promoting retrograde transport of Shiga toxin from endosomes to the TGN, as well as recycling internalized transferrin from endosomes to the plasma membrane. Endosomes function as a hub for multiple protein-sorting events, including retrograde transport to the trans-Golgi network (TGN) and recycling to the plasma membrane. These processes are mediated by tubular-vesicular carriers that bud from early endosomes and fuse with a corresponding acceptor compartment. Two tethering complexes named GARP (composed of ANG2, VPS52, VPS53, and VPS54 subunits) and EARP (composed of ANG2, VPS52, VPS53, and Syndetin subunits) were previously shown to participate in SNARE-dependent fusion of endosome-derived carriers with the TGN and recycling endosomes, respectively. Little is known, however, about other proteins that function with GARP and EARP in these processes. Here we identify a protein named TSSC1 as a specific interactor of both GARP and EARP and as a novel component of the endosomal retrieval machinery. TSSC1 is a predicted WD40/β-propeller protein that coisolates with both GARP and EARP in affinity purification, immunoprecipitation, and gel filtration analyses. Confocal fluorescence microscopy shows colocalization of TSSC1 with both GARP and EARP. Silencing of TSSC1 impairs transport of internalized Shiga toxin B subunit to the TGN, as well as recycling of internalized transferrin to the plasma membrane. Fluorescence recovery after photobleaching shows that TSSC1 is required for efficient recruitment of GARP to the TGN. These studies thus demonstrate that TSSC1 plays a critical role in endosomal retrieval pathways as a regulator of both GARP and EARP function.
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Affiliation(s)
- David C Gershlick
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Christina Schindler
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Yu Chen
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Juan S Bonifacino
- Cell Biology and Neurobiology Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
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18
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Abascal-Palacios G, Schindler C, Rojas AL, Bonifacino JS, Hierro A. Structural basis for the interaction of the Golgi-Associated Retrograde Protein Complex with the t-SNARE Syntaxin 6. Structure 2013; 21:1698-706. [PMID: 23932592 PMCID: PMC4788097 DOI: 10.1016/j.str.2013.06.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Revised: 06/27/2013] [Accepted: 06/27/2013] [Indexed: 01/07/2023]
Abstract
The Golgi-Associated Retrograde Protein (GARP) complex is a tethering factor involved in the fusion of endosome-derived transport vesicles to the trans-Golgi network through interaction with components of the Syntaxin 6/Syntaxin 16/Vti1a/VAMP4 SNARE complex. The mechanisms by which GARP and other tethering factors engage the SNARE fusion machinery are poorly understood. Herein, we report the structural basis for the interaction of the human Ang2 subunit of GARP with the Syntaxin 6 and the closely related Syntaxin 10. The crystal structure of the Syntaxin 6 Habc domain in complex with a peptide from the N terminus of Ang2 shows a binding mode in which a dityrosine motif of Ang2 interacts with a highly conserved groove in Syntaxin 6. Structure-based mutational analyses validate the crystal structure and support the phylogenetic conservation of this interaction.
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Affiliation(s)
| | - Christina Schindler
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Adriana L Rojas
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain
| | - Juan S. Bonifacino
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA,To whom correspondence should be addressed: Aitor Hierro: ; phone: +34-946-572-522; fax: +34-946-572-502. Juan S. Bonifacino: ; phone: +1-301-496-6368; fax: +1-301-402-0078
| | - Aitor Hierro
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain,IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain,To whom correspondence should be addressed: Aitor Hierro: ; phone: +34-946-572-522; fax: +34-946-572-502. Juan S. Bonifacino: ; phone: +1-301-496-6368; fax: +1-301-402-0078
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Arasaki K, Takagi D, Furuno A, Sohda M, Misumi Y, Wakana Y, Inoue H, Tagaya M. A new role for RINT-1 in SNARE complex assembly at the trans-Golgi network in coordination with the COG complex. Mol Biol Cell 2013; 24:2907-17. [PMID: 23885118 PMCID: PMC3771952 DOI: 10.1091/mbc.e13-01-0014] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Yeast Tip20, a subunit of the Dsl1 complex, is implicated in Golgi-to–endoplasmic reticulum retrograde transport. Differing from Tip20, its mammalian counterpart, RINT-1, is required for endosome-to–trans-Golgi network transport. RINT-1 in coordination with the COG complex regulates SNARE complex assembly at the trans-Golgi network. Docking and fusion of transport vesicles/carriers with the target membrane involve a tethering factor–mediated initial contact followed by soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE)–catalyzed membrane fusion. The multisubunit tethering CATCHR family complexes (Dsl1, COG, exocyst, and GARP complexes) share very low sequence homology among subunits despite likely evolving from a common ancestor and participate in fundamentally different membrane trafficking pathways. Yeast Tip20, as a subunit of the Dsl1 complex, has been implicated in retrograde transport from the Golgi apparatus to the endoplasmic reticulum. Our previous study showed that RINT-1, the mammalian counterpart of yeast Tip20, mediates the association of ZW10 (mammalian Dsl1) with endoplasmic reticulum–localized SNARE proteins. In the present study, we show that RINT-1 is also required for endosome-to–trans-Golgi network trafficking. RINT-1 uncomplexed with ZW10 interacts with the COG complex, another member of the CATCHR family complex, and regulates SNARE complex assembly at the trans-Golgi network. This additional role for RINT-1 may in part reflect adaptation to the demand for more diverse transport routes from endosomes to the trans-Golgi network in mammals compared with those in a unicellular organism, yeast. The present findings highlight a new role of RINT-1 in coordination with the COG complex.
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Affiliation(s)
- Kohei Arasaki
- School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan Division of Oral Biochemistry, Niigata University Graduate School of Medical and Dental Sciences, 2-5274 Gakkocho-dori, Chuo-ku, Niigata 951-8514, Japan Department of Cell Biology, Fukuoka University School of Medicine, Jonan-ku, Fukuoka 814-0180, Japan
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20
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Gossing M, Chidambaram S, Fischer von Mollard G. Importance of the N-terminal domain of the Qb-SNARE Vti1p for different membrane transport steps in the yeast endosomal system. PLoS One 2013; 8:e66304. [PMID: 23776654 PMCID: PMC3680383 DOI: 10.1371/journal.pone.0066304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/04/2013] [Indexed: 01/11/2023] Open
Abstract
SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) on transport vesicles and target membranes are crucial for vesicle targeting and fusion. They form SNARE complexes, which contain four α-helical SNARE motifs contributed by three or four different SNAREs. Most SNAREs function only in a single transport step. The yeast SNARE Vti1p participates in four distinct SNARE complexes in transport from the trans Golgi network to late endosomes, in transport to the vacuole, in retrograde transport from endosomes to the trans Golgi network and in retrograde transport within the Golgi. So far, all vti1 mutants investigated had mutations within the SNARE motif. Little is known about the function of the N-terminal domain of Vti1p, which forms a three helix bundle called Habc domain. Here we generated a temperature-sensitive mutant of this domain to study the effects on different transport steps. The secondary structure of wild type and vti1-3 Habc domain was analyzed by circular dichroism spectroscopy. The amino acid exchanges identified in the temperature-sensitive vti1-3 mutant caused unfolding of the Habc domain. Transport pathways were investigated by immunoprecipitation of newly synthesized proteins after pulse-chase labeling and by fluorescence microscopy of a GFP-tagged protein cycling between plasma membrane, early endosomes and Golgi. In vti1-3 cells transport to the late endosome and assembly of the late endosomal SNARE complex was blocked at 37°C. Retrograde transport to the trans Golgi network was affected while fusion with the vacuole was possible but slower. Steady state levels of SNARE complexes mediating these steps were less affected than that of the late endosomal SNARE complex. As different transport steps were affected our data demonstrate the importance of a folded Vti1p Habc domain for transport.
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Affiliation(s)
- Michael Gossing
- Biochemie III, Fakultät für Chemie, Universität Bielefeld, Bielefeld, Germany
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21
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A computational prediction of structure and function of novel homologue of Arabidopsis thaliana Vps51/Vps67 subunit in Corchorus olitorius. Interdiscip Sci 2013; 4:256-67. [PMID: 23354814 DOI: 10.1007/s12539-012-0139-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2011] [Revised: 06/05/2012] [Accepted: 07/29/2012] [Indexed: 10/27/2022]
Abstract
Vps mediated vesicular transport is important for transferring macromolecules trapped inside a vesicle. Although highly abundant, Vps shows tremendous sequence variation among diverse array of species. However, this difference in sequence, which seems to also translate into substantial functional variation, is hardly characterized in Corchorus spp. Here, our computational study investigates structural and functional features of one of the Vps subunit namely Vps51/Vps67 in C. olitorius. Broad scale structural characterization revealed novel information about the overall Vps structure and binding sites. Moreover, functional analyses indicate interaction partners which were unexplored to date. Since membrane trafficking is essentially associated with nutrient uptake and chemical de-toxification, characterization of the Vps subunit can well provide us with better insight into important agronomic traits such as stress response, immune response and phytoremediation capacity.
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22
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Jackson LP, Kümmel D, Reinisch KM, Owen DJ. Structures and mechanisms of vesicle coat components and multisubunit tethering complexes. Curr Opin Cell Biol 2012; 24:475-83. [PMID: 22728063 PMCID: PMC3425711 DOI: 10.1016/j.ceb.2012.05.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 05/23/2012] [Indexed: 11/17/2022]
Abstract
Eukaryotic cells face a logistical challenge in ensuring prompt and precise delivery of vesicular cargo to specific organelles within the cell. Coat protein complexes select cargo and initiate vesicle formation, while multisubunit tethering complexes participate in the delivery of vesicles to target membranes. Understanding these macromolecular assemblies has greatly benefited from their structural characterization. Recent structural data highlight principles in coat recruitment and uncoating in both the endocytic and retrograde pathways, and studies on the architecture of tethering complexes provide a framework for how they might link vesicles to the respective acceptor compartments and the fusion machinery.
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Affiliation(s)
- Lauren P Jackson
- Cambridge Institute for Medical Research, Department of Clinical Biochemistry, University of Cambridge, Cambridge CB2 0XY, UK.
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23
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Abstract
Among thousands of homo-oligomeric protein structures, there is a small but growing subset of ‘domain-swapped’ proteins. The term ‘domain swapping,’ originally coined by D. Eisenberg, describes a scenario in which two or more polypeptide chains exchange identical units for oligomerization. This type of assembly could play a role in disease-related aggregation and amyloid formation or as a specific mechanism for regulating function. This chapter introduces terms and features concerning domain swapping, summarizes ideas about its putative mechanisms, reports on domain-swapped structures collected from the literature, and describes a few notable examples in detail.
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24
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Kümmel D, Reinisch KM. Structure of Golgi transport proteins. Cold Spring Harb Perspect Biol 2011; 3:cshperspect.a007609. [PMID: 21813399 DOI: 10.1101/cshperspect.a007609] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The function of the Golgi has long been recognized to critically depend on vesicular transport from, to, and within its cisternae, involving constant membrane fission and fusion. These processes are mediated by Arf GTPases and coat proteins, and Rabs, tethers and SNARE proteins, respectively. In this article, we describe structural studies of Golgi coats and tethers and their interactions with SNAREs and GTPases as well as insights regarding membrane traffic processes that these have provided.
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Affiliation(s)
- Daniel Kümmel
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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25
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Abstract
Antero- and retrograde cargo transport through the Golgi requires a series of membrane fusion events. Fusion occurs at the cis- and trans-side and along the rims of the Golgi stack. Four functional SNARE complexes have been identified mediating lipid bilayer merger in the Golgi. Their function is tightly controlled by a series of reactions involving vesicle tethering and SM proteins. This network of protein interactions spatially and temporally determines the specificity of transport vesicle targeting and fusion within the Golgi.
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Affiliation(s)
- Jörg Malsam
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
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26
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Wang LC, Tsai MC, Chang KY, Fan YS, Yeh CH, Wu SJ. Involvement of the Arabidopsis HIT1/AtVPS53 tethering protein homologue in the acclimation of the plasma membrane to heat stress. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:3609-3620. [PMID: 21398432 DOI: 10.1093/jxb/err060] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Arabidopsis thaliana hit1-1 is a heat-intolerant mutant. The HIT1 gene encodes a protein that is homologous to yeast Vps53p, which is a subunit of the Golgi-associated retrograde protein (GARP) complex that is involved in retrograde membrane trafficking to the Golgi. To investigate the correlation between the cellular role of HIT1 and its protective function in heat tolerance in plants, it was verified that HIT1 was co-localized with AtVPS52 and AtVPS54, the other putative subunits of GARP, in the Golgi and post-Golgi compartments in Arabidopsis protoplasts. A bimolecular fluorescence complementation assay showed that HIT1 interacted with AtVPS52 and AtVPS54, which indicated their assembly into a protein complex in vivo. Under heat stress conditions, the plasma membrane of hit1-1 was less stable than that of the wild type, as determined by an electrolyte leakage assay, and enhanced leakage occurred before peroxidation injury to the membrane. In addition, the ability of hit1-1 to survive heat stress was not influenced by exposure to light, which suggested that the heat intolerance of hit-1 was a direct outcome of reduced membrane thermostability rather than heat-induced oxidative stress. Furthermore, hit1-1 was sensitive to the duration (sustained high temperature stress at 37 °C for 3 d) but not the intensity (heat shock at 44 °C for 30 min) of exposure to heat. Collectively, these results imply that HIT1 functions in the membrane trafficking that is involved in the thermal adaptation of the plasma membrane for tolerance to long-term heat stress in plants.
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Affiliation(s)
- Lian-Chin Wang
- Department of Life Sciences, National Central University, No. 300, Jhong-da Road, Jhong-li City, Taoyuan 32001, Taiwan
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27
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Luo L, Hannemann M, Koenig S, Hegermann J, Ailion M, Cho MK, Sasidharan N, Zweckstetter M, Rensing SA, Eimer S. The Caenorhabditis elegans GARP complex contains the conserved Vps51 subunit and is required to maintain lysosomal morphology. Mol Biol Cell 2011; 22:2564-78. [PMID: 21613545 PMCID: PMC3135481 DOI: 10.1091/mbc.e10-06-0493] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Functional characterization of the Golgi-associated retrograde protein (GARP) complex in Caenorhabditis elegans has led to the identification of the conserved metazoan Vps51 subunit. It is found that GARP mutants lead to abnormal lysosomal morphology, GARP subunits interact with a distinct set of Golgi SNAREs, and GARP and GOG complexes show functional overlap. In yeast the Golgi-associated retrograde protein (GARP) complex is required for tethering of endosome-derived transport vesicles to the late Golgi. It consists of four subunits—Vps51p, Vps52p, Vps53p, and Vps54p—and shares similarities with other multimeric tethering complexes, such as the conserved oligomeric Golgi (COG) and the exocyst complex. Here we report the functional characterization of the GARP complex in the nematode Caenorhabditis elegans. Furthermore, we identified the C. elegans Vps51 subunit, which is conserved in all eukaryotes. GARP mutants are viable but show lysosomal defects. We show that GARP subunits bind specific sets of Golgi SNAREs within the yeast two-hybrid system. This suggests that the C. elegans GARP complex also facilitates tethering as well as SNARE complex assembly at the Golgi. The GARP and COG tethering complexes may have overlapping functions for retrograde endosome-to-Golgi retrieval, since loss of both complexes leads to a synthetic lethal phenotype.
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Affiliation(s)
- L Luo
- European Neuroscience Institute, 37077 Göttingen, Germany
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28
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Bröcker C, Engelbrecht-Vandré S, Ungermann C. Multisubunit tethering complexes and their role in membrane fusion. Curr Biol 2011; 20:R943-52. [PMID: 21056839 DOI: 10.1016/j.cub.2010.09.015] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Protein trafficking within eukaryotic cells depends on vesicular carriers that fuse with organelles to deliver their lipid and protein content. Cells have developed an elaborate system to capture vesicles at organelles that involves the action of Rab GTPases and tethers. Vesicle fusion then takes place with the help of SNARE proteins. In this review we focus on the role of multisubunit tethering complexes of eukaryotic cells. In particular, we discuss the tethering complexes of the secretory pathway and the endolysosomal system and highlight recent evidence for the role of these complexes in interaction with Rabs, coat recognition and cooperation with SNAREs during the fusion cascade.
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Affiliation(s)
- Cornelia Bröcker
- University of Osnabrück, Department of Biology/Chemistry, Barbarastrasse 13, 49076 Osnabrück, Germany
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29
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Abstract
The trans-Golgi network (TGN) receives a select set of proteins from the endocytic pathway-about 5% of total plasma membrane glycoproteins (Duncan and Kornfeld 1988). Proteins that are delivered include mannose 6-phosphate receptors (MPRs), TGN46, sortilin, and various toxins that hitchhike a ride backward through the secretory pathway to intoxicate cells after they exit into the cytoplasm from the endoplasmic reticulum (ER). This article will review work on the molecular players that drive protein transport from the endocytic pathway to the TGN. Distinct requirements have revealed multiple routes for retrograde transport; in addition, the existence of multiple, potential coat proteins and/or cargo adaptors imply that multiple vesicular transfers are likely involved. Several comprehensive reviews have appeared recently and should be sought for additional details (Bonifacino and Rojas 2006; Johannes and Popoff 2008).
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Affiliation(s)
- Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, California 94305-5307, USA.
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Transport according to GARP: receiving retrograde cargo at the trans-Golgi network. Trends Cell Biol 2010; 21:159-67. [PMID: 21183348 DOI: 10.1016/j.tcb.2010.11.003] [Citation(s) in RCA: 117] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Revised: 10/29/2010] [Accepted: 11/11/2010] [Indexed: 01/05/2023]
Abstract
Tethering factors are large protein complexes that capture transport vesicles and enable their fusion with acceptor organelles at different stages of the endomembrane system. Recent studies have shed new light on the structure and function of a heterotetrameric tethering factor named Golgi-associated retrograde protein (GARP), which promotes fusion of endosome-derived, retrograde transport carriers to the trans-Golgi network (TGN). X-ray crystallography of the Vps53 and Vps54 subunits of GARP has revealed that this complex is structurally related to other tethering factors such as the exocyst, the conserved oligomeric Golgi (COG) and Dsl1 (dependence on SLY1-20) complexes, indicating that they all might work by a similar mechanism. Loss of GARP function compromises the growth, fertility and/or viability of the defective organisms, emphasizing the essential nature of GARP-mediated retrograde transport.
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Dissecting Ent3p: the ENTH domain binds different SNAREs via distinct amino acid residues while the C-terminus is sufficient for retrograde transport from endosomes. Biochem J 2010; 431:123-34. [PMID: 20658963 DOI: 10.1042/bj20100693] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ENTH (epsin N-terminal homology) domain protein Ent3p and the ANTH [AP (adaptor protein)-180 N-terminal homology] domain protein Ent5p serve as partially redundant adaptors in vesicle budding from the TGN (trans-Golgi network) in Saccharomyces cerevisiae. They interact with phosphoinositides, clathrin, adaptor proteins and cargo such as chitin synthase Chs3p and SNAREs (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptors). In the present study, we show that ent3Δent5Δ cells displayed defects in cell separation and bud site selection. Ent3p and Ent5p were also involved in retrograde transport from early endosomes to the TGN because GFP (green fluorescent protein)-Snc1p shifted from a plasma membrane to an intracellular localization in ent3Δent5Δ cells. The C-terminal part of Ent3p was sufficient to restore retrograde transport from early endosomes to the TGN in ent3Δent5Δ cells. In contrast, the ENTH domain and the C-terminus were required for transport from the TGN to late endosomes, demonstrating that both functions are distinct. The ENTH domain of Ent3p is known to bind the N-terminal domains of the SNAREs Vti1p, Pep12p and Syn8p, which are required for fusion with late endosomes. The interaction surface between the Ent3p-related mammalian epsinR and vti1b is known. In the present paper, we show that Vti1p bound to the homologous surface patch of Ent3p. Pep12p and Syn8p interacted with the same surface area of Ent3p. However, different amino acid residues in Ent3p were crucial for the interaction with these SNAREs in two-hybrid assays. This provides the necessary flexibility to bind three SNAREs with little sequence homology but maintains the specificity of the interaction.
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32
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Pérez-Victoria FJ, Schindler C, Magadán JG, Mardones GA, Delevoye C, Romao M, Raposo G, Bonifacino JS. Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex. Mol Biol Cell 2010; 21:3386-95. [PMID: 20685960 PMCID: PMC2947474 DOI: 10.1091/mbc.e10-05-0392] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The Golgi-associated retrograde protein (GARP) complex mediates tethering and fusion of endosome-derived transport carriers to the trans-Golgi network (TGN). In the yeast Saccharomyces cerevisiae, GARP comprises four subunits named Vps51p, Vps52p, Vps53p, and Vps54p. Orthologues of the GARP subunits, except for Vps51p, have been identified in all other eukaryotes. A yeast two-hybrid screen of a human cDNA library yielded a phylogenetically conserved protein, Ang2/Fat-free, which interacts with human Vps52, Vps53 and Vps54. Human Ang2 is larger than yeast Vps51p, but exhibits significant homology in an N-terminal coiled-coil region that mediates assembly with other GARP subunits. Biochemical analyses show that human Ang2, Vps52, Vps53 and Vps54 form an obligatory 1:1:1:1 complex that strongly interacts with the regulatory Habc domain of the TGN SNARE, Syntaxin 6. Depletion of Ang2 or the GARP subunits similarly impairs protein retrieval to the TGN, lysosomal enzyme sorting, endosomal cholesterol traffic¤ and autophagy. These findings indicate that Ang2 is the missing component of the GARP complex in most eukaryotes.
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Affiliation(s)
- F Javier Pérez-Victoria
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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Dual roles of the mammalian GARP complex in tethering and SNARE complex assembly at the trans-golgi network. Mol Cell Biol 2009; 29:5251-63. [PMID: 19620288 DOI: 10.1128/mcb.00495-09] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tethering factors and SNAREs control the last two steps of vesicular trafficking: the initial interaction and the fusion, respectively, of transport vesicles with target membranes. The Golgi-associated retrograde protein (GARP) complex regulates retrograde transport from endosomes to the trans-Golgi network (TGN). Although GARP has been proposed to function as a tethering factor at the TGN, direct evidence for such a role is still lacking. Herein we report novel and specific interactions of the mammalian GARP complex with SNAREs that participate in endosome-to-TGN transport, namely, syntaxin 6, syntaxin 16, and Vamp4. These interactions depend on the N-terminal regions of Vps53 and Vps54 and the SNARE motif of the SNAREs. We show that GARP functions upstream of the SNAREs, regulating their localization and assembly into SNARE complexes. However, interactions of GARP with SNAREs are insufficient to promote retrograde transport, because deletion of the C-terminal region of Vps53 precludes GARP function without affecting GARP-SNARE interactions. Finally, we present in vitro data consistent with a tethering role for GARP, which is disrupted by deletion of the Vps53 C-terminal region. These findings indicate that GARP orchestrates retrograde transport from endosomes to the TGN by promoting vesicle tethering and assembly of SNARE complexes in consecutive, independent steps.
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Theis M, Slabicki M, Junqueira M, Paszkowski-Rogacz M, Sontheimer J, Kittler R, Heninger AK, Glatter T, Kruusmaa K, Poser I, Hyman AA, Pisabarro MT, Gstaiger M, Aebersold R, Shevchenko A, Buchholz F. Comparative profiling identifies C13orf3 as a component of the Ska complex required for mammalian cell division. EMBO J 2009; 28:1453-65. [PMID: 19387489 PMCID: PMC2684023 DOI: 10.1038/emboj.2009.114] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 03/31/2009] [Indexed: 01/01/2023] Open
Abstract
Proliferation of mammalian cells requires the coordinated function of many proteins to accurately divide a cell into two daughter cells. Several RNAi screens have identified previously uncharacterised genes that are implicated in mammalian cell division. The molecular function for these genes needs to be investigated to place them into pathways. Phenotypic profiling is a useful method to assign putative functions to uncharacterised genes. Here, we show that the analysis of protein localisation is useful to refine a phenotypic profile. We show the utility of this approach by defining a function of the previously uncharacterised gene C13orf3 during cell division. C13orf3 localises to centrosomes, the mitotic spindle, kinetochores, spindle midzone, and the cleavage furrow during cell division and is specifically phosphorylated during mitosis. Furthermore, C13orf3 is required for centrosome integrity and anaphase onset. Depletion by RNAi leads to mitotic arrest in metaphase with an activation of the spindle assembly checkpoint and loss of sister chromatid cohesion. Proteomic analyses identify C13orf3 (Ska3) as a new component of the Ska complex and show a direct interaction with a regulatory subunit of the protein phosphatase PP2A. All together, these data identify C13orf3 as an important factor for metaphase to anaphase progression and highlight the potential of combined RNAi screening and protein localisation analyses.
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Affiliation(s)
- Mirko Theis
- Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany
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Yanay C, Morpurgo N, Linial M. Evolution of insect proteomes: insights into synapse organization and synaptic vesicle life cycle. Genome Biol 2008; 9:R27. [PMID: 18257909 PMCID: PMC2374702 DOI: 10.1186/gb-2008-9-2-r27] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2007] [Revised: 12/06/2007] [Accepted: 02/07/2008] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The molecular components in synapses that are essential to the life cycle of synaptic vesicles are well characterized. Nonetheless, many aspects of synaptic processes, in particular how they relate to complex behaviour, remain elusive. The genomes of flies, mosquitoes, the honeybee and the beetle are now fully sequenced and span an evolutionary breadth of about 350 million years; this provides a unique opportunity to conduct a comparative genomics study of the synapse. RESULTS We compiled a list of 120 gene prototypes that comprise the core of presynaptic structures in insects. Insects lack several scaffolding proteins in the active zone, such as bassoon and piccollo, and the most abundant protein in the mammalian synaptic vesicle, namely synaptophysin. The pattern of evolution of synaptic protein complexes is analyzed. According to this analysis, the components of presynaptic complexes as well as proteins that take part in organelle biogenesis are tightly coordinated. Most synaptic proteins are involved in rich protein interaction networks. Overall, the number of interacting proteins and the degrees of sequence conservation between human and insects are closely correlated. Such a correlation holds for exocytotic but not for endocytotic proteins. CONCLUSION This comparative study of human with insects sheds light on the composition and assembly of protein complexes in the synapse. Specifically, the nature of the protein interaction graphs differentiate exocytotic from endocytotic proteins and suggest unique evolutionary constraints for each set. General principles in the design of proteins of the presynaptic site can be inferred from a comparative study of human and insect genomes.
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Affiliation(s)
- Chava Yanay
- Department of Biological Chemistry, Institute of Life Sciences, Givat Ram Campus, Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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Role of the conserved oligomeric Golgi (COG) complex in protein glycosylation. Carbohydr Res 2008; 343:2024-31. [PMID: 18353293 DOI: 10.1016/j.carres.2008.01.034] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2007] [Revised: 01/23/2008] [Accepted: 01/24/2008] [Indexed: 11/20/2022]
Abstract
The Golgi apparatus is a central hub for both protein and lipid trafficking/sorting and is also a major site for glycosylation in the cell. This organelle employs a cohort of peripheral membrane proteins and protein complexes to keep its structural and functional organization. The conserved oligomeric Golgi (COG) complex is an evolutionary conserved peripheral membrane protein complex that is proposed to act as a retrograde vesicle tethering factor in intra-Golgi trafficking. The COG protein complex consists of eight subunits, distributed in two lobes, Lobe A (Cog1-4) and Lobe B (Cog5-8). Malfunctions in the COG complex have a significant impact on processes such as protein sorting, glycosylation, and Golgi integrity. A deletion of Lobe A COG subunits in yeasts causes severe growth defects while mutations in COG1, COG7, and COG8 in humans cause novel types of congenital disorders of glycosylation. These pathologies involve a change in structural Golgi phenotype and function. Recent results indicate that down-regulation of COG function results in the resident Golgi glycosyltransferases/glycosidases to be mislocalized or degraded.
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Shestakova A, Suvorova E, Pavliv O, Khaidakova G, Lupashin V. Interaction of the conserved oligomeric Golgi complex with t-SNARE Syntaxin5a/Sed5 enhances intra-Golgi SNARE complex stability. ACTA ACUST UNITED AC 2008; 179:1179-92. [PMID: 18086915 PMCID: PMC2140037 DOI: 10.1083/jcb.200705145] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tethering factors mediate initial interaction of transport vesicles with target membranes. Soluble N-ethylmaleimide–sensitive fusion protein attachment protein receptors (SNAREs) enable consequent docking and membrane fusion. We demonstrate that the vesicle tether conserved oligomeric Golgi (COG) complex colocalizes and coimmunoprecipitates with intra-Golgi SNARE molecules. In yeast cells, the COG complex preferentially interacts with the SNARE complexes containing yeast Golgi target (t)-SNARE Sed5p. In mammalian cells, hCog4p and hCog6p interact with Syntaxin5a, the mammalian homologue of Sed5p. Moreover, fluorescence resonance energy transfer reveals an in vivo interaction between Syntaxin5a and the COG complex. Knockdown of the mammalian COG complex decreases Golgi SNARE mobility, produces an accumulation of free Syntaxin5, and decreases the steady-state levels of the intra-Golgi SNARE complex. Finally, overexpression of the hCog4p N-terminal Syntaxin5a-binding domain destabilizes intra-Golgi SNARE complexes, disrupting the Golgi. These data suggest that the COG complex orchestrates vesicular trafficking similarly in yeast and mammalian cells by binding to the t-SNARE Syntaxin5a/Sed5p and enhancing the stability of intra-Golgi SNARE complexes.
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Affiliation(s)
- Anna Shestakova
- Department of Physiology and Biophysics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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Swennen D, Beckerich JM. Yarrowia lipolytica vesicle-mediated protein transport pathways. BMC Evol Biol 2007; 7:219. [PMID: 17997821 PMCID: PMC2241642 DOI: 10.1186/1471-2148-7-219] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Accepted: 11/12/2007] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Protein secretion is a universal cellular process involving vesicles which bud and fuse between organelles to bring proteins to their final destination. Vesicle budding is mediated by protein coats; vesicle targeting and fusion depend on Rab GTPase, tethering factors and SNARE complexes. The Génolevures II sequencing project made available entire genome sequences of four hemiascomycetous yeasts, Yarrowia lipolytica, Debaryomyces hansenii, Kluyveromyces lactis and Candida glabrata. Y. lipolytica is a dimorphic yeast and has good capacities to secrete proteins. The translocation of nascent protein through the endoplasmic reticulum membrane was well studied in Y. lipolytica and is largely co-translational as in the mammalian protein secretion pathway. RESULTS We identified S. cerevisiae proteins involved in vesicular secretion and these protein sequences were used for the BLAST searches against Génolevures protein database (Y. lipolytica, C. glabrata, K. lactis and D. hansenii). These proteins are well conserved between these yeasts and Saccharomyces cerevisiae. We note several specificities of Y. lipolytica which may be related to its good protein secretion capacities and to its dimorphic aspect. An expansion of the Y. lipolytica Rab protein family was observed with autoBLAST and the Rab2- and Rab4-related members were identified with BLAST against NCBI protein database. An expansion of this family is also found in filamentous fungi and may reflect the greater complexity of the Y. lipolytica secretion pathway. The Rab4p-related protein may play a role in membrane recycling as rab4 deleted strain shows a modification of colony morphology, dimorphic transition and permeability. Similarly, we find three copies of the gene (SSO) encoding the plasma membrane SNARE protein. Quantification of the percentages of proteins with the greatest homology between S. cerevisiae, Y. lipolytica and animal homologues involved in vesicular transport shows that 40% of Y. lipolytica proteins are closer to animal ones, whereas they are only 13% in the case of S. cerevisiae. CONCLUSION These results provide further support for the idea, previously noted about the endoplasmic reticulum translocation pathway, that Y. lipolytica is more representative of vesicular secretion of animals and other fungi than is S. cerevisiae.
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Affiliation(s)
- Dominique Swennen
- Laboratoire de Microbiologie et Génétique Moléculaire INRA-CNRS-AgroParisTech UMR 1238 CBAI BP01 F-78850 Thiverval Grignon, France.
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A SNARE–adaptor interaction is a new mode of cargo recognition in clathrin-coated vesicles. Nature 2007; 450:570-4. [DOI: 10.1038/nature06353] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2007] [Accepted: 10/03/2007] [Indexed: 11/08/2022]
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Kloepper TH, Kienle CN, Fasshauer D. An elaborate classification of SNARE proteins sheds light on the conservation of the eukaryotic endomembrane system. Mol Biol Cell 2007; 18:3463-71. [PMID: 17596510 PMCID: PMC1951749 DOI: 10.1091/mbc.e07-03-0193] [Citation(s) in RCA: 162] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 06/15/2007] [Accepted: 06/18/2007] [Indexed: 11/11/2022] Open
Abstract
Proteins of the SNARE (soluble N-ethylmalemide-sensitive factor attachment protein receptor) family are essential for the fusion of transport vesicles with an acceptor membrane. Despite considerable sequence divergence, their mechanism of action is conserved: heterologous sets assemble into membrane-bridging SNARE complexes, in effect driving membrane fusion. Within the cell, distinct functional SNARE units are involved in different trafficking steps. These functional units are conserved across species and probably reflect the conservation of the particular transport step. Here, we have systematically analyzed SNARE sequences from 145 different species and have established a highly accurate classification for all SNARE proteins. Principally, all SNAREs split into four basic types, reflecting their position in the four-helix bundle complex. Among these four basic types, we established 20 SNARE subclasses that probably represent the original repertoire of a eukaryotic cenancestor. This repertoire has been modulated independently in different lines of organisms. Our data are in line with the notion that the ur-eukaryotic cell was already equipped with the various compartments found in contemporary cells. Possibly, the development of these compartments is closely intertwined with episodes of duplication and divergence of a prototypic SNARE unit.
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Affiliation(s)
- Tobias H. Kloepper
- *Research Group Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany; and
- Research Group Structural Biochemistry, Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - C. Nickias Kienle
- *Research Group Algorithms in Bioinformatics, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany; and
- Research Group Structural Biochemistry, Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Dirk Fasshauer
- Research Group Structural Biochemistry, Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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Cai H, Reinisch K, Ferro-Novick S. Coats, tethers, Rabs, and SNAREs work together to mediate the intracellular destination of a transport vesicle. Dev Cell 2007; 12:671-82. [PMID: 17488620 DOI: 10.1016/j.devcel.2007.04.005] [Citation(s) in RCA: 501] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Tethering factors have been shown to interact with Rabs and SNAREs and, more recently, with coat proteins. Coat proteins are required for cargo selection and membrane deformation to bud a transport vesicle from a donor compartment. It was once thought that a vesicle must uncoat before it recognizes its target membrane. However, recent findings have revealed a role for the coat in directing a vesicle to its correct intracellular destination. In this review we will discuss the literature that links coat proteins to vesicle targeting events.
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Affiliation(s)
- Huaqing Cai
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06519, USA
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Worrall LJ, Walkinshaw MD. Crystal structure of the C-terminal three-helix bundle subdomain of C. elegans Hsp70. Biochem Biophys Res Commun 2007; 357:105-10. [PMID: 17407764 DOI: 10.1016/j.bbrc.2007.03.107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Accepted: 03/16/2007] [Indexed: 01/21/2023]
Abstract
Hsp70 chaperones are composed of two domains; the 40 kDa N-terminal nucleotide-binding domain (NDB) and the 30 kDa C-terminal substrate-binding domain (SBD). Structures of the SBD from Escherichia coli homologues DnaK and HscA show it can be further divided into an 18 kDa beta-sandwich subdomain, which forms the hydrophobic binding pocket, and a 10 kDa C-terminal three-helix bundle that forms a lid over the binding pocket. Across prokaryotes and eukaryotes, the NBD and beta-sandwich subdomain are well conserved in both sequence and structure. The C-terminal subdomain is, however, more evolutionary variable and the only eukaryotic structure from rat Hsc70 revealed a diverged helix-loop-helix fold. We have solved the crystal structure of the C-terminal 10 kDa subdomain from Caenorhabditis elegans Hsp70 which forms a helical-bundle similar to the prokaryotic homologues. This provides the first confirmation of the structural conservation of this subdomain in eukaryotes. Comparison with the rat structure reveals a domain-swap dimerisation mechanism; however, the C. elegans subdomain exists exclusively as a monomer in solution in agreement with the hypothesis that regions out with the C-terminal subdomain are necessary for Hsp70 self-association.
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Affiliation(s)
- Liam J Worrall
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, UK
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Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins. BMC Evol Biol 2007; 7:29. [PMID: 17319956 PMCID: PMC1810245 DOI: 10.1186/1471-2148-7-29] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2006] [Accepted: 02/23/2007] [Indexed: 12/31/2022] Open
Abstract
Background In membrane trafficking, the mechanisms ensuring vesicle fusion specificity remain to be fully elucidated. Early models proposed that specificity was encoded entirely by SNARE proteins; more recent models include contributions from Rab proteins, Syntaxin-binding (SM) proteins and tethering factors. Most information on membrane trafficking derives from an evolutionarily narrow sampling of model organisms. However, considering factors from a wider diversity of eukaryotes can provide both functional information on core systems and insight into the evolutionary history of the trafficking machinery. For example, the major Qa/syntaxin SNARE families are present in most eukaryotic genomes and likely each evolved via gene duplication from a single ancestral syntaxin before the existing eukaryotic groups diversified. This pattern is also likely for Rabs and various other components of the membrane trafficking machinery. Results We performed comparative genomic and phylogenetic analyses, when relevant, on the SM proteins and components of the tethering complexes, both thought to contribute to vesicle fusion specificity. Despite evidence suggestive of secondary losses amongst many lineages, the tethering complexes are well represented across the eukaryotes, suggesting an origin predating the radiation of eukaryotic lineages. Further, whilst we detect distant sequence relations between GARP, COG, exocyst and DSL1 components, these similarities most likely reflect convergent evolution of similar secondary structural elements. No similarity is found between the TRAPP and HOPS complexes and the other tethering factors. Overall, our data favour independent origins for the various tethering complexes. The taxa examined possess at least one homologue of each of the four SM protein families; since the four monophyletic families each encompass a wide diversity of eukaryotes, the SM protein families very likely evolved before the last common eukaryotic ancestor (LCEA). Conclusion These data further support a highly complex LCEA and indicate that the basic architecture of the trafficking system is remarkably conserved and ancient, with the SM proteins and tethering factors having originated very early in eukaryotic evolution. However, the independent origin of the tethering complexes suggests a novel pattern for increasing complexity in the membrane trafficking system, in addition to the pattern of paralogous machinery elaboration seen thus far.
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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