1
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Jimah JR, Kundu N, Stanton AE, Sochacki KA, Canagarajah B, Chan L, Strub MP, Wang H, Taraska JW, Hinshaw JE. Cryo-EM structures of membrane-bound dynamin in a post-hydrolysis state primed for membrane fission. Dev Cell 2024; 59:1783-1793.e5. [PMID: 38663399 PMCID: PMC11265984 DOI: 10.1016/j.devcel.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/29/2023] [Accepted: 04/04/2024] [Indexed: 07/25/2024]
Abstract
Dynamin assembles as a helical polymer at the neck of budding endocytic vesicles, constricting the underlying membrane as it progresses through the GTPase cycle to sever vesicles from the plasma membrane. Although atomic models of the dynamin helical polymer bound to guanosine triphosphate (GTP) analogs define earlier stages of membrane constriction, there are no atomic models of the assembled state post-GTP hydrolysis. Here, we used cryo-EM methods to determine atomic structures of the dynamin helical polymer assembled on lipid tubules, akin to necks of budding endocytic vesicles, in a guanosine diphosphate (GDP)-bound, super-constricted state. In this state, dynamin is assembled as a 2-start helix with an inner lumen of 3.4 nm, primed for spontaneous fission. Additionally, by cryo-electron tomography, we trapped dynamin helical assemblies within HeLa cells using the GTPase-defective dynamin K44A mutant and observed diverse dynamin helices, demonstrating that dynamin can accommodate a range of assembled complexes in cells that likely precede membrane fission.
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Affiliation(s)
- John R Jimah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Nidhi Kundu
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abigail E Stanton
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kem A Sochacki
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bertram Canagarajah
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lieza Chan
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marie-Paule Strub
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaibin Wang
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Justin W Taraska
- Biochemistry and Biophysics Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jenny E Hinshaw
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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2
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Harders RH, Morthorst TH, Landgrebe LE, Lande AD, Fuglsang MS, Mortensen SB, Feteira-Montero V, Jensen HH, Wesseltoft JB, Olsen A. CED-6/GULP and components of the clathrin-mediated endocytosis machinery act redundantly to correctly display CED-1 on the cell membrane in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2024; 14:jkae088. [PMID: 38696649 PMCID: PMC11228867 DOI: 10.1093/g3journal/jkae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/03/2024] [Accepted: 04/16/2024] [Indexed: 05/04/2024]
Abstract
CED-1 (cell death abnormal) is a transmembrane receptor involved in the recognition of "eat-me" signals displayed on the surface of apoptotic cells and thus central for the subsequent engulfment of the cell corpse in Caenorhabditis elegans. The roles of CED-1 in engulfment are well established, as are its downstream effectors. The latter include the adapter protein CED-6/GULP and the ATP-binding cassette family homolog CED-7. However, how CED-1 is maintained on the plasma membrane in the absence of engulfment is currently unknown. Here, we show that CED-6 and CED-7 have a novel role in maintaining CED-1 correctly on the plasma membrane. We propose that the underlying mechanism is via endocytosis as CED-6 and CED-7 act redundantly with clathrin and its adaptor, the Adaptor protein 2 complex, in ensuring correct CED-1 localization. In conclusion, CED-6 and CED-7 impact other cellular processes than engulfment of apoptotic cells.
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Affiliation(s)
- Rikke Hindsgaul Harders
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark
| | - Tine H Morthorst
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Line E Landgrebe
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Anna D Lande
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Marie Sikjær Fuglsang
- Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10C, Aarhus, DK-8000, Denmark
| | - Stine Bothilde Mortensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark
| | - Verónica Feteira-Montero
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark
| | - Helene Halkjær Jensen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark
| | - Jonas Bruhn Wesseltoft
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark
| | - Anders Olsen
- Department of Chemistry and Bioscience, Aalborg University, Fredrik Bajers Vej 7H, Aalborg, DK-9220, Denmark
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3
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Bussoletti M, Gallo M, Bottacchiari M, Abbondanza D, Casciola CM. Mesoscopic elasticity controls dynamin-driven fission of lipid tubules. Sci Rep 2024; 14:14003. [PMID: 38890460 PMCID: PMC11189461 DOI: 10.1038/s41598-024-64685-2] [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: 03/09/2024] [Accepted: 06/12/2024] [Indexed: 06/20/2024] Open
Abstract
Mesoscale physics bridges the gap between the microscopic degrees of freedom of a system and its large-scale continuous behavior and highlights the role of a few key quantities in complex and multiscale phenomena, like dynamin-driven fission of lipid membranes. The dynamin protein wraps the neck formed during clathrin-mediated endocytosis, for instance, and constricts it until severing occurs. Although ubiquitous and fundamental for life, the cooperation between the GTP-consuming conformational changes within the protein and the full-scale response of the underlying lipid substrate is yet to be unraveled. In this work, we build an effective mesoscopic model from constriction to fission of lipid tubules based on continuum membrane elasticity and implicitly accounting for ratchet-like power strokes of dynamins. Localization of the fission event, the overall geometry, and the energy expenditure we predict comply with the major experimental findings. This bolsters the idea that a continuous picture emerges soon enough to relate dynamin polymerization length and membrane rigidity and tension with the optimal pathway to fission. We therefore suggest that dynamins found in in vivo processes may optimize their structure accordingly. Ultimately, we shed light on real-time conductance measurements available in literature and predict the fission time dependency on elastic parameters.
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Affiliation(s)
- Marco Bussoletti
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Mirko Gallo
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Matteo Bottacchiari
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
- Department of Basic and Applied Sciences for Engineering, Sapienza University of Rome, Rome, Italy
| | - Dario Abbondanza
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy
| | - Carlo Massimo Casciola
- Department of Mechanical and Aerospace Engineering, Sapienza University of Rome, Rome, Italy.
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4
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Jiang A, Kudo K, Gormal RS, Ellis S, Guo S, Wallis TP, Longfield SF, Robinson PJ, Johnson ME, Joensuu M, Meunier FA. Dynamin1 long- and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters. Nat Commun 2024; 15:4060. [PMID: 38744819 PMCID: PMC11094030 DOI: 10.1038/s41467-024-47677-8] [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: 03/11/2023] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
Endocytosis requires a coordinated framework of molecular interactions that ultimately lead to the fission of nascent endocytic structures. How cytosolic proteins such as dynamin concentrate at discrete sites that are sparsely distributed across the plasma membrane remains poorly understood. Two dynamin-1 major splice variants differ by the length of their C-terminal proline-rich region (short-tail and long-tail). Using sptPALM in PC12 cells, neurons and MEF cells, we demonstrate that short-tail dynamin-1 isoforms ab and bb display an activity-dependent recruitment to the membrane, promptly followed by their concentration into nanoclusters. These nanoclusters are sensitive to both Calcineurin and dynamin GTPase inhibitors, and are larger, denser, and more numerous than that of long-tail isoform aa. Spatiotemporal modelling confirms that dynamin-1 isoforms perform distinct search patterns and undergo dimensional reduction to generate endocytic nanoclusters, with short-tail isoforms more robustly exploiting lateral trapping in the generation of nanoclusters compared to the long-tail isoform.
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Affiliation(s)
- Anmin Jiang
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kye Kudo
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Rachel S Gormal
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sevannah Ellis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Sikao Guo
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Tristan P Wallis
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Shanley F Longfield
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Phillip J Robinson
- Cell Signalling Unit, Children's Medical Research Institute, The University of Sydney, Sydney, NSW, 2145, Australia
| | - Margaret E Johnson
- Department of Biophysics, Johns Hopkins University, 3400 N Charles St, Baltimore, MD, 21218, USA
| | - Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia.
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5
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Peng R, Rochon K, Stagg SM, Mears JA. The Structure of the Drp1 Lattice on Membrane. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588123. [PMID: 38617273 PMCID: PMC11014616 DOI: 10.1101/2024.04.04.588123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Mitochondrial health relies on the membrane fission mediated by dynamin-related protein 1 (Drp1). Previous structural studies of Drp1 on remodeled membranes were hampered by heterogeneity, leaving a critical gap in the understanding of the mitochondrial fission mechanism. Here we present a cryo-electron microscopy structure of full-length human Drp1 decorated on membrane tubules. Using the reconstruction of average subtracted tubular regions (RASTR) technique, we report that Drp1 forms a locally ordered lattice along the tubule without global helical symmetry. The filaments in the lattice are similar to dynamin rungs with conserved stalk interactions. Adjacent filaments are connected by GTPase domain interactions in a novel stacked conformation. Additionally, we observed contact between Drp1 and membrane that can be assigned to variable domain sequence. We identified two states of the Drp1 lattice representing conformational changes related to membrane curvature differences. Together these structures revealed a putative mechanism by which Drp1 constricts mitochondria membranes in a stepwise, "ratchet" manner.
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Affiliation(s)
- Ruizhi Peng
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
| | - Kristy Rochon
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
| | - Scott M Stagg
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
- Department of Biological Sciences, Florida State University, Tallahassee, Florida, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
- Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH 44106 USA
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6
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Kim GW, Ha JW. Direct Observation of In-Focus Plasmonic Cargos via Breaking Angular Degeneracy in Differential Interference Contrast Microscopy. JACS AU 2023; 3:3436-3445. [PMID: 38155657 PMCID: PMC10751767 DOI: 10.1021/jacsau.3c00594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/30/2023]
Abstract
Breaking the angular degeneracy arising from the 2-fold optical symmetry of plasmonic anisotropic nanoprobes is critical in biological studies. In this study, we propose differential interference contrast (DIC) microscopy-based focused orientation and position imaging (dFOPI) to break the angular degeneracy of single gold nanorods (AuNRs). Single in-focus AuNRs (39 nm × 123 nm) within a spherical mesoporous silica shell were characterized with high throughput and produced distinct doughnut-shaped DIC image patterns featuring two lobes in the peripheral region, attributed to the scattering contribution of the AuNRs with large scattering cross sections. Interestingly, rotation of the lobes was observed in the focal plane for a large AuNR (>100 nm) tilted by more than ∼20° from the horizontal plane as the rotational stage was moved by 10° in a rotational study. From the rotation-dependent characteristic patterns, we directly visualized counterclockwise/clockwise rotations without the angular degeneracy at the localized surface plasmon resonance wavelength. Therefore, our dFOPI method can be applied for in vivo studies of important biological systems. To validate this claim, we tracked the three-dimensional rotational behavior of transferrin-modified in-focus AuNRs during clathrin-mediated endocytosis in real time without sacrificing the temporal and spatial resolution. In the invagination and scission stage, one or two directed twist motions of the AuNR cargos detached the AuNR-containing vesicles from the cell membrane. Furthermore, the dFOPI method directly visualized and revealed the right-handed twisting action along the dynamin helix in dynamin-catalyzed fission in live cells.
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Affiliation(s)
- Geun Wan Kim
- Department
of Chemistry, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, South Korea
| | - Ji Won Ha
- Department
of Chemistry, University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, South Korea
- Energy
Harvest-Storage Research Center (EHSRC), University of Ulsan, 93 Daehak-ro, Nam-gu, Ulsan 44610, South Korea
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7
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Wang X, Espadas J, Wu Y, Cai S, Ge J, Shao L, Roux A, De Camilli P. Membrane remodeling properties of the Parkinson's disease protein LRRK2. Proc Natl Acad Sci U S A 2023; 120:e2309698120. [PMID: 37844218 PMCID: PMC10614619 DOI: 10.1073/pnas.2309698120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023] Open
Abstract
Mutations in Leucine-rich repeat kinase 2 (LRRK2) are responsible for late-onset autosomal dominant Parkinson's disease. LRRK2 has been implicated in a wide range of physiological processes including membrane repair in the endolysosomal system. Here, using cell-free systems, we report that purified LRRK2 directly binds acidic lipid bilayers with a preference for highly curved bilayers. While this binding is nucleotide independent, LRRK2 can also deform low-curvature liposomes into narrow tubules in a guanylnucleotide-dependent but Adenosine 5'-triphosphate-independent way. Moreover, assembly of LRRK2 into scaffolds at the surface of lipid tubules can constrict them. We suggest that an interplay between the membrane remodeling and signaling properties of LRRK2 may be key to its physiological function. LRRK2, via its kinase activity, may achieve its signaling role at sites where membrane remodeling occurs.
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Affiliation(s)
- Xinbo Wang
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- HHMI, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Javier Espadas
- Department of Biochemistry, University of Geneva, GenevaCH-1211, Switzerland
| | - Yumei Wu
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- HHMI, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Shujun Cai
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- HHMI, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Jinghua Ge
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06510
| | - Lin Shao
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT06510
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, GenevaCH-1211, Switzerland
| | - Pietro De Camilli
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT06510
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT06510
- HHMI, Yale University School of Medicine, New Haven, CT06510
- Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT06510
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Kavli Institute for Neuroscience, Yale University School of Medicine, New Haven, CT06510
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8
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Gallen AF, Romero-Arias JR, Barrio RA, Hernandez-Machado A. Vesicle formation induced by thermal fluctuations. SOFT MATTER 2023; 19:2908-2918. [PMID: 37006200 DOI: 10.1039/d2sm01167k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The process of fission and vesicle formation depends on the geometry of the membrane that will split. For instance, a flat surface finds it difficult to form vesicles because of the lack of curved regions where to start the process. Here we show that vesicle formation can be promoted by temperature, by using a membrane phase field model with Gaussian curvature. We find a phase transition between fluctuating and vesiculation phases that depends on temperature, spontaneous curvature, and the ratio between bending and Gaussian moduli. We analysed the energy dynamical behaviour of these processes and found that the main driving ingredient is the Gaussian energy term, although the curvature energy term usually helps with the process as well. We also found that the chemical potential can be used to investigate the temperature of the system. Finally we address how temperature changes the condition for spontaneous vesiculation for all geometries, making it happen in a wider range of values of the Gaussian modulus.
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Affiliation(s)
- Andreu F Gallen
- Departament Fisica de la Materia Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.
| | - J Roberto Romero-Arias
- Instituto de Investigaciones en Matematicas Aplicadas y en Sistemas, Universidad Nacional Autonoma de Mexico, 01000 Ciudad de Mexico, Mexico
| | - Rafael A Barrio
- Instituto de Fisica, U.N.A.M., 01000, Ap. Postal 101000, Mexico D.F, Mexico
| | - Aurora Hernandez-Machado
- Departament Fisica de la Materia Condensada, Universitat de Barcelona, E-08028 Barcelona, Spain.
- Institute of Nanoscience and Nanotechnology (IN2UB), 08028 Barcelona, Spain
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9
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Lemaigre C, Ceuppens A, Valades-Cruz CA, Ledoux B, Vanbeneden B, Hassan M, Zetterberg FR, Nilsson UJ, Johannes L, Wunder C, Renard HF, Morsomme P. N-BAR and F-BAR proteins-endophilin-A3 and PSTPIP1-control clathrin-independent endocytosis of L1CAM. Traffic 2023; 24:190-212. [PMID: 36843549 DOI: 10.1111/tra.12883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 02/07/2023] [Accepted: 02/18/2023] [Indexed: 02/28/2023]
Abstract
Recent advances in the field demonstrate the high diversity and complexity of endocytic pathways. In the current study, we focus on the endocytosis of L1CAM. This glycoprotein plays a major role in the development of the nervous system, and is involved in cancer development and is associated with metastases and poor prognosis. Two L1CAM isoforms are subject to endocytosis: isoform 1, described as a clathrin-mediated cargo; isoform 2, whose endocytosis has never been studied. Deciphering the molecular machinery of isoform 2 internalisation should contribute to a better understanding of its pathophysiological role. First, we demonstrated in our cellular context that both isoforms of L1CAM are mainly a clathrin-independent cargo, which was not expected for isoform 1. Second, the mechanism of L1CAM endocytosis is specifically mediated by the N-BAR domain protein endophilin-A3. Third, we discovered PSTPIP1, an F-BAR domain protein, as a novel actor in this endocytic process. Finally, we identified galectins as endocytic partners and negative regulators of L1CAM endocytosis. In summary, the interplay of the BAR proteins endophilin-A3 and PSTPIP1, and galectins fine tune the clathrin-independent endocytosis of L1CAM.
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Affiliation(s)
- Camille Lemaigre
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Louvain-la-Neuve, Belgium
| | - Apolline Ceuppens
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Louvain-la-Neuve, Belgium
| | - Cesar Augusto Valades-Cruz
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, Paris, France.,SERPICO Project Team, UMR144 CNRS Institut Curie, PSL Research University, Paris, France.,SERPICO Project Team, Inria Centre Rennes-Bretagne Atlantique, Campus Universitaire de Beaulieu, Rennes, France
| | - Benjamin Ledoux
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Louvain-la-Neuve, Belgium
| | - Bastien Vanbeneden
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Louvain-la-Neuve, Belgium
| | | | | | - Ulf J Nilsson
- Department of Chemistry, Lund University, Lund, Sweden
| | - Ludger Johannes
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, Paris, France
| | - Christian Wunder
- Institut Curie, Université PSL, U1143 INSERM, UMR3666 CNRS, Cellular and Chemical Biology unit, Paris, France
| | - Henri-François Renard
- UNamur, NARILIS, Unité de recherche en biologie cellulaire animale (URBC), Namur, Belgium
| | - Pierre Morsomme
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Louvain-la-Neuve, Belgium
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10
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Friebel J, Schinnerling K, Weigt K, Heldt C, Fromm A, Bojarski C, Siegmund B, Epple HJ, Kikhney J, Moter A, Schneider T, Schulzke JD, Moos V, Schumann M. Uptake of Tropheryma whipplei by Intestinal Epithelia. Int J Mol Sci 2023; 24:ijms24076197. [PMID: 37047170 PMCID: PMC10094206 DOI: 10.3390/ijms24076197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/18/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Background: Tropheryma whipplei (TW) can cause different pathologies, e.g., Whipple’s disease and transient gastroenteritis. The mechanism by which the bacteria pass the intestinal epithelial barrier, and the mechanism of TW-induced gastroenteritis are currently unknown. Methods: Using ex vivo disease models comprising human duodenal mucosa exposed to TW in Ussing chambers, various intestinal epithelial cell (IEC) cultures exposed to TW and a macrophage/IEC coculture model served to characterize endocytic uptake mechanisms and barrier function. Results: TW exposed ex vivo to human small intestinal mucosae is capable of autonomously entering IECs, thereby invading the mucosa. Using dominant-negative mutants, TW uptake was shown to be dynamin- and caveolin-dependent but independent of clathrin-mediated endocytosis. Complementary inhibitor experiments suggested a role for the activation of the Ras/Rac1 pathway and actin polymerization. TW-invaded IECs underwent apoptosis, thereby causing an epithelial barrier defect, and were subsequently subject to phagocytosis by macrophages. Conclusions: TW enters epithelia via an actin-, dynamin-, caveolin-, and Ras-Rac1-dependent endocytosis mechanism and consecutively causes IEC apoptosis primarily in IECs invaded by multiple TW bacteria. This results in a barrier leak. Moreover, we propose that TW-packed IECs can be subject to phagocytic uptake by macrophages, thereby opening a potential entry point of TW into intestinal macrophages.
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Affiliation(s)
- Julian Friebel
- Department of Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum der Charité, 12203 Berlin, Germany
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Katina Schinnerling
- Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago 8370146, Chile
| | - Kathleen Weigt
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Claudia Heldt
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Anja Fromm
- Institute of Clinical Physiology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Christian Bojarski
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Britta Siegmund
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Hans-Jörg Epple
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Judith Kikhney
- Institute for Microbiology, Infectious Diseases, and Immunology, Biofilmcenter, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
- MoKi Analytics GmbH, 12207 Berlin, Germany
| | - Annette Moter
- Institute for Microbiology, Infectious Diseases, and Immunology, Biofilmcenter, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
- German Konsiliarlabor for Tropheryma whipplei, 10117 Berlin, Germany
- Moter Diagnostics, 12207 Berlin, Germany
| | - Thomas Schneider
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Jörg D. Schulzke
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
- Institute of Clinical Physiology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Verena Moos
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
| | - Michael Schumann
- Department of Gastroenterology, Infectiology and Rheumatology, Campus Benjamin Franklin, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 12203 Berlin, Germany
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany
- Correspondence: ; Tel.: +49-30-450-513536
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11
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Cheppali SK, Dharan R, Sorkin R. Forces of Change: Optical Tweezers in Membrane Remodeling Studies. J Membr Biol 2022; 255:677-690. [PMID: 35616705 DOI: 10.1007/s00232-022-00241-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/22/2022] [Indexed: 12/24/2022]
Abstract
Optical tweezers allow precise measurement of forces and distances with piconewton and nanometer precision, and have thus been instrumental in elucidating the mechanistic details of various biological processes. Some examples include the characterization of motor protein activity, studies of protein-DNA interactions, and characterizing protein folding trajectories. The use of optical tweezers (OT) to study membranes is, however, much less abundant. Here, we review biophysical studies of membranes that utilize optical tweezers, with emphasis on various assays that have been developed and their benefits and limitations. First, we discuss assays that employ membrane-coated beads, and overview protein-membrane interactions studies based on manipulation of such beads. We further overview a body of studies that make use of a very powerful experimental tool, the combination of OT, micropipette aspiration, and fluorescence microscopy, that allow detailed studies of membrane curvature generation and sensitivity. Finally, we describe studies focused on membrane fusion and fission. We then summarize the overall progress in the field and outline future directions.
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Affiliation(s)
- Sudheer K Cheppali
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel.,Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.,Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv, Israel
| | - Raviv Dharan
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel.,Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel.,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel.,Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv, Israel
| | - Raya Sorkin
- Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv, Israel. .,Center for Physics and Chemistry of Living Systems, Tel Aviv University, Tel Aviv, Israel. .,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel. .,Center for Light-Matter Interaction, Tel Aviv University, Tel Aviv, Israel.
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12
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Abstract
Atlastin (ATL) GTPases undergo trans dimerization and a power strokelike crossover conformational rearrangement to drive endoplasmic reticulum membrane fusion. Fusion depends on GTP, but the role of nucleotide hydrolysis has remained controversial. For instance, nonhydrolyzable GTP analogs block fusion altogether, suggesting a requirement for GTP hydrolysis in ATL dimerization and crossover, but this leaves unanswered the question of how the ATL dimer is disassembled after fusion. We recently used the truncated cytoplasmic domain of wild-type Drosophila ATL (DATL) and a novel hydrolysis-deficient D127N variant in single turnover assays to reveal that dimerization and crossover consistently precede GTP hydrolysis, with hydrolysis coinciding more closely with dimer disassembly. Moreover, while nonhydrolyzable analogs can bind the DATL G domain, they fail to fully recapitulate the GTP-bound state. This predicted that nucleotide hydrolysis would be dispensable for fusion. Here we report that the D127N variant of full-length DATL drives both outer and inner leaflet membrane fusion with little to no detectable hydrolysis of GTP. However, the trans dimer fails to disassemble and subsequent rounds of fusion fail to occur. Our findings confirm that ATL mediated fusion is driven in the GTP-bound state, with nucleotide hydrolysis serving to reset the fusion machinery for recycling.
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Affiliation(s)
- Daniel Crosby
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Tina H. Lee
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213,*Address correspondence to: Tina H. Lee ()
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13
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Liu L, Xiong Q, Xie C, Pincet F, Lin C. Actuating tension-loaded DNA clamps drives membrane tubulation. SCIENCE ADVANCES 2022; 8:eadd1830. [PMID: 36223466 PMCID: PMC9555772 DOI: 10.1126/sciadv.add1830] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Membrane dynamics in living organisms can arise from proteins adhering to, assembling on, and exerting force on cell membranes. Programmable synthetic materials, such as self-assembled DNA nanostructures, offer the capability to drive membrane-remodeling events that resemble protein-mediated dynamics but with user-defined outcomes. An illustrative example is the tubular deformation of liposomes by DNA nanostructures with purposely designed shapes, surface modifications, and self-assembling properties. However, stimulus-responsive membrane tubulation mediated by DNA reconfiguration remains challenging. Here, we present the triggered formation of membrane tubes in response to specific DNA signals that actuate membrane-bound DNA clamps from an open state to various predefined closed states, releasing prestored energy to activate membrane deformation. We show that the timing and efficiency of vesicle tubulation, as well as the membrane tube widths, are modulated by the conformational change of DNA clamps, marking a solid step toward spatiotemporal control of membrane dynamics in an artificial system.
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Affiliation(s)
- Longfei Liu
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Qiancheng Xiong
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Chun Xie
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Frederic Pincet
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Laboratoire de Physique de l’Ecole Normale Supérieure, Ecole Normale Supérieure (ENS), Université Paris Sciences et Lettres (PSL), CNRS, Sorbonne Université, Université Paris Cité, Paris, France
| | - Chenxiang Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
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14
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Menon D, Hummel D, Kaksonen M. Regulation of membrane scission in yeast endocytosisDepartment of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland. Mol Biol Cell 2022; 33:ar114. [PMID: 35976707 DOI: 10.1091/mbc.e21-07-0346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
During clathrin-mediated endocytosis, a flat plasma membrane is shaped into an invagination that undergoes scission to form a vesicle. In mammalian cells, the force that drives the transition from invagination to vesicle is primarily provided by the GTPase dynamin that acts in concert with crescent-shaped BAR domain proteins. In yeast cells, the mechanism of endocytic scission is unclear. The yeast BAR domain protein complex Rvs161/167 (Rvs) nevertheless plays an important role in this process: deletion of Rvs dramatically reduces scission efficiency. A mechanistic understanding of the influence of Rvs on scission however, remains incomplete. We used quantitative live-cell imaging and genetic manipulation to understand the recruitment and function of Rvs and other late-stage proteins at yeast endocytic sites. We found that arrival of Rvs at endocytic sites is timed by interaction of its BAR domain with specific membrane curvature. A second domain of Rvs167 - the SH3 domain - affects localization efficiency of Rvs. We show that Myo3, one of the two type-I myosins in Saccharomyces cerevisiae, has a role in recruiting Rvs167 via the SH3 domain. Removal of the SH3 domain also affects assembly and disassembly of actin and impedes membrane invagination. Our results indicate that both BAR and SH3 domains are important for the role of Rvs as a regulator of scission. We tested other proteins implicated in vesicle formation in Saccharomyces cerevisiae, and found that neither synaptojanins nor dynamin contribute directly to membrane scission. We propose that recruitment of Rvs BAR domains delays scission and allows invaginations to grow by stabilizing them. We also propose that vesicle formation is dependent on the force exerted by the actin network.
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Affiliation(s)
- Deepikaa Menon
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Daniel Hummel
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
| | - Marko Kaksonen
- Department of Biochemistry and National Centre of Competence in Research, Chemical Biology, University of Geneva, Geneva, Switzerland
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15
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Fujise K, Noguchi S, Takeda T. Centronuclear Myopathy Caused by Defective Membrane Remodelling of Dynamin 2 and BIN1 Variants. Int J Mol Sci 2022; 23:ijms23116274. [PMID: 35682949 PMCID: PMC9181712 DOI: 10.3390/ijms23116274] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 05/31/2022] [Accepted: 06/01/2022] [Indexed: 02/01/2023] Open
Abstract
Centronuclear myopathy (CNM) is a congenital myopathy characterised by centralised nuclei in skeletal myofibers. T-tubules, sarcolemmal invaginations required for excitation-contraction coupling, are disorganised in the skeletal muscles of CNM patients. Previous studies showed that various endocytic proteins are involved in T-tubule biogenesis and their dysfunction is tightly associated with CNM pathogenesis. DNM2 and BIN1 are two causative genes for CNM that encode essential membrane remodelling proteins in endocytosis, dynamin 2 and BIN1, respectively. In this review, we overview the functions of dynamin 2 and BIN1 in T-tubule biogenesis and discuss how their dysfunction in membrane remodelling leads to CNM pathogenesis.
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Affiliation(s)
- Kenshiro Fujise
- Departments of Neuroscience and Cell Biology, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06520-8001, USA;
| | - Satoru Noguchi
- National Institute of Neuroscience, National Center of Neurology and Psychiatry (NCNP), Tokyo 187-8502, Japan;
| | - Tetsuya Takeda
- Department of Biochemistry, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Shikata-cho 2-5-1, Kita-ku, Okayama 700-8558, Japan
- Correspondence: ; Tel.: +81-86-235-7125; Fax: +81-86-235-7126
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16
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Synthesis and Effect of Conformationally Locked Carbocyclic Guanine Nucleotides on Dynamin. Biomolecules 2022; 12:biom12040584. [PMID: 35454173 PMCID: PMC9031165 DOI: 10.3390/biom12040584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/14/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
Guanine nucleotides can flip between a North and South conformation in the ribose moiety. To test the enzymatic activity of GTPases bound to nucleotides in the two conformations, we generated methanocarba guanine nucleotides in the North or South envelope conformations, i.e., (N)-GTP and (S)-GTP, respectively. With dynamin as a model system, we examined the effects of (N)-GTP and (S)-GTP on dynamin-mediated membrane constriction, an activity essential for endocytosis. Dynamin membrane constriction and fission activity are dependent on GTP binding and hydrolysis, but the effect of the conformational state of the GTP nucleotide on dynamin activity is not known. After reconstituting dynamin-mediated lipid tubulation and membrane constriction in vitro, we observed via cryo-electron microscopy (cryo-EM) that (N)-GTP, but not (S)-GTP, enables the constriction of dynamin-decorated lipid tubules. These findings suggest that the activity of dynamin is dependent on the conformational state of the GTP nucleotide. However, a survey of nucleotide ribose conformations associated with dynamin structures in nature shows almost exclusively the (S)-conformation. The explanation for this mismatch of (N) vs. (S) required for GTP analogues in a dynamin-mediated process will be addressed in future studies.
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17
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Abstract
The mechanoenzyme dynamin 2 (DNM2) is crucial for intracellular organization and trafficking. DNM2 is mutated in dominant centronuclear myopathy (DNM2-CNM), a muscle disease characterized by defects in organelle positioning in myofibers. It remains unclear how the in vivo functions of DNM2 are regulated in muscle. Moreover, there is no therapy for DNM2-CNM to date. Here, we overexpressed human amphiphysin 2 (BIN1), a membrane remodeling protein mutated in other CNM forms, in Dnm2 RW/+ and Dnm2 RW/RW mice modeling mild and severe DNM2-CNM, through transgenesis or with adeno-associated virus (AAV). Increasing BIN1 improved muscle atrophy and main histopathological features of Dnm2 RW/+ mice and rescued the perinatal lethality and survival of Dnm2 RW/RW mice. In vitro experiments showed that BIN1 binds and recruits DNM2 to membrane tubules, and that the BIN1-DNM2 complex regulates tubules fission. Overall, BIN1 is a potential therapeutic target for dominant centronuclear myopathy linked to DNM2 mutations.
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18
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Kim WD, Wilson-Smillie MLDM, Thanabalasingam A, Lefrancois S, Cotman SL, Huber RJ. Autophagy in the Neuronal Ceroid Lipofuscinoses (Batten Disease). Front Cell Dev Biol 2022; 10:812728. [PMID: 35252181 PMCID: PMC8888908 DOI: 10.3389/fcell.2022.812728] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/24/2022] [Indexed: 12/22/2022] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs), also referred to as Batten disease, are a family of neurodegenerative diseases that affect all age groups and ethnicities around the globe. At least a dozen NCL subtypes have been identified that are each linked to a mutation in a distinct ceroid lipofuscinosis neuronal (CLN) gene. Mutations in CLN genes cause the accumulation of autofluorescent lipoprotein aggregates, called ceroid lipofuscin, in neurons and other cell types outside the central nervous system. The mechanisms regulating the accumulation of this material are not entirely known. The CLN genes encode cytosolic, lysosomal, and integral membrane proteins that are associated with a variety of cellular processes, and accumulated evidence suggests they participate in shared or convergent biological pathways. Research across a variety of non-mammalian and mammalian model systems clearly supports an effect of CLN gene mutations on autophagy, suggesting that autophagy plays an essential role in the development and progression of the NCLs. In this review, we summarize research linking the autophagy pathway to the NCLs to guide future work that further elucidates the contribution of altered autophagy to NCL pathology.
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Affiliation(s)
- William D. Kim
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | | | - Aruban Thanabalasingam
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON, Canada
| | - Stephane Lefrancois
- Centre Armand-Frappier Santé Biotechnologie, Institut National de La Recherche Scientifique, Laval, QC, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada
- Centre D'Excellence en Recherche sur Les Maladies Orphelines–Fondation Courtois (CERMO-FC), Université Du Québec à Montréal (UQAM), Montréal, QC, Canada
| | - Susan L. Cotman
- Department of Neurology, Center for Genomic Medicine, Massachusetts General Hospital Research Institute, Harvard Medical School, Boston, MA, United States
| | - Robert J. Huber
- Department of Biology, Trent University, Peterborough, ON, Canada
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19
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Nadeem A, Berg A, Pace H, Alam A, Toh E, Ådén J, Zlatkov N, Myint SL, Persson K, Gröbner G, Sjöstedt A, Bally M, Barandun J, Uhlin BE, Wai SN. Protein-lipid interaction at low pH induces oligomerization of the MakA cytotoxin from Vibrio cholerae. eLife 2022; 11:73439. [PMID: 35131030 PMCID: PMC8824476 DOI: 10.7554/elife.73439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 01/19/2022] [Indexed: 12/29/2022] Open
Abstract
The α-pore-forming toxins (α-PFTs) from pathogenic bacteria damage host cell membranes by pore formation. We demonstrate a remarkable, hitherto unknown mechanism by an α-PFT protein from Vibrio cholerae. As part of the MakA/B/E tripartite toxin, MakA is involved in membrane pore formation similar to other α-PFTs. In contrast, MakA in isolation induces tube-like structures in acidic endosomal compartments of epithelial cells in vitro. The present study unravels the dynamics of tubular growth, which occurs in a pH-, lipid-, and concentration-dependent manner. Within acidified organelle lumens or when incubated with cells in acidic media, MakA forms oligomers and remodels membranes into high-curvature tubes leading to loss of membrane integrity. A 3.7 Å cryo-electron microscopy structure of MakA filaments reveals a unique protein-lipid superstructure. MakA forms a pinecone-like spiral with a central cavity and a thin annular lipid bilayer embedded between the MakA transmembrane helices in its active α-PFT conformation. Our study provides insights into a novel tubulation mechanism of an α-PFT protein and a new mode of action by a secreted bacterial toxin.
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Affiliation(s)
- Aftab Nadeem
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Science for Life Laboratory (SciLifeLab), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Hudson Pace
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Athar Alam
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Eric Toh
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Jörgen Ådén
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Nikola Zlatkov
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Si Lhyam Myint
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Karina Persson
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Gerhard Gröbner
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Chemistry, Umeå University, Umeå, Sweden
| | - Anders Sjöstedt
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Marta Bally
- Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,Department of Clinical Microbiology, Umeå University, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Jonas Barandun
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Bernt Eric Uhlin
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
| | - Sun Nyunt Wai
- Department of Molecular Biology, Umeå University, Umeå, Sweden.,Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden
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20
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Prichard KL, O'Brien NS, Murcia SR, Baker JR, McCluskey A. Role of Clathrin and Dynamin in Clathrin Mediated Endocytosis/Synaptic Vesicle Recycling and Implications in Neurological Diseases. Front Cell Neurosci 2022; 15:754110. [PMID: 35115907 PMCID: PMC8805674 DOI: 10.3389/fncel.2021.754110] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 12/10/2021] [Indexed: 12/17/2022] Open
Abstract
Endocytosis is a process essential to the health and well-being of cell. It is required for the internalisation and sorting of “cargo”—the macromolecules, proteins, receptors and lipids of cell signalling. Clathrin mediated endocytosis (CME) is one of the key processes required for cellular well-being and signalling pathway activation. CME is key role to the recycling of synaptic vesicles [synaptic vesicle recycling (SVR)] in the brain, it is pivotal to signalling across synapses enabling intracellular communication in the sensory and nervous systems. In this review we provide an overview of the general process of CME with a particular focus on two key proteins: clathrin and dynamin that have a central role to play in ensuing successful completion of CME. We examine these two proteins as they are the two endocytotic proteins for which small molecule inhibitors, often of known mechanism of action, have been identified. Inhibition of CME offers the potential to develop therapeutic interventions into conditions involving defects in CME. This review will discuss the roles and the current scope of inhibitors of clathrin and dynamin, providing an insight into how further developments could affect neurological disease treatments.
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21
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Monnery BD. Polycation-Mediated Transfection: Mechanisms of Internalization and Intracellular Trafficking. Biomacromolecules 2021; 22:4060-4083. [PMID: 34498457 DOI: 10.1021/acs.biomac.1c00697] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Polyplex-mediated gene transfection is now in its' fourth decade of serious research, but the promise of polyplex-mediated gene therapy has yet to fully materialize. Only approximately one in a million applied plasmids actually expresses. A large part of this is due to an incomplete understanding of the mechanism of polyplex transfection. There is an assumption that internalization must follow a canonical mechanism of receptor mediated endocytosis. Herein, we present arguments that untargeted (and most targeted) polyplexes do not utilize these routes. By incorporating knowledge of syndecan-polyplex interactions, we can show that syndecans are the "target" for polyplexes. Further, it is known that free polycations (which disrupt cell-membranes by acid-catalyzed hydrolysis of phospholipid esters) are necessary for (untargeted) endocytosis. This can be incorporated into the model to produce a novel mechanism of endocytosis, which fits the observed phenomenology. After membrane translocation, polyplex containing vesicles reach the endosome after diffusing through the actin mesh below the cell membrane. From there, they are acidified and trafficked toward the lysosome. Some polyplexes are capable of escaping the endosome and unpacking, while others are not. Herein, it is argued that for some polycations, as acidification proceeds the polyplexes excluding free polycations, which disrupt the endosomal membrane by acid-catalyzed hydrolysis, allowing the polyplex to escape. The polyplex's internal charge ratio is now insufficient for stability and it releases plasmids which diffuse to the nucleus. A small proportion of these plasmids diffuse through the nuclear pore complex (NPC), with aggregation being the major cause of loss. Those plasmids that have diffused through the NPC will also aggregate, and this appears to be the reason such a small proportion of nuclear plasmids express mRNA. Thus, the structural features which promote unpacking in the endosome and allow for endosomal escape can be determined, and better polycations can be designed.
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Affiliation(s)
- Bryn D Monnery
- Department of Organic and (Bio)Polymer Chemistry, Hasselt University, Building F, Agoralaan 1, B-3590 Diepenbeek, Belgium
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22
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Sauvola CW, Littleton JT. SNARE Regulatory Proteins in Synaptic Vesicle Fusion and Recycling. Front Mol Neurosci 2021; 14:733138. [PMID: 34421538 PMCID: PMC8377282 DOI: 10.3389/fnmol.2021.733138] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/20/2021] [Indexed: 01/01/2023] Open
Abstract
Membrane fusion is a universal feature of eukaryotic protein trafficking and is mediated by the soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) family. SNARE proteins embedded in opposing membranes spontaneously assemble to drive membrane fusion and cargo exchange in vitro. Evolution has generated a diverse complement of SNARE regulatory proteins (SRPs) that ensure membrane fusion occurs at the right time and place in vivo. While a core set of SNAREs and SRPs are common to all eukaryotic cells, a specialized set of SRPs within neurons confer additional regulation to synaptic vesicle (SV) fusion. Neuronal communication is characterized by precise spatial and temporal control of SNARE dynamics within presynaptic subdomains specialized for neurotransmitter release. Action potential-elicited Ca2+ influx at these release sites triggers zippering of SNAREs embedded in the SV and plasma membrane to drive bilayer fusion and release of neurotransmitters that activate downstream targets. Here we discuss current models for how SRPs regulate SNARE dynamics and presynaptic output, emphasizing invertebrate genetic findings that advanced our understanding of SRP regulation of SV cycling.
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Affiliation(s)
- Chad W Sauvola
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - J Troy Littleton
- The Picower Institute for Learning and Memory, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA, United States.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, United States
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23
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Djakbarova U, Madraki Y, Chan ET, Kural C. Dynamic interplay between cell membrane tension and clathrin-mediated endocytosis. Biol Cell 2021; 113:344-373. [PMID: 33788963 PMCID: PMC8898183 DOI: 10.1111/boc.202000110] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 03/08/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
Deformability of the plasma membrane, the outermost surface of metazoan cells, allows cells to be dynamic, mobile and flexible. Factors that affect this deformability, such as tension on the membrane, can regulate a myriad of cellular functions, including membrane resealing, cell motility, polarisation, shape maintenance, membrane area control and endocytic vesicle trafficking. This review focuses on mechanoregulation of clathrin-mediated endocytosis (CME). We first delineate the origins of cell membrane tension and the factors that yield to its spatial and temporal fluctuations within cells. We then review the recent literature demonstrating that tension on the membrane is a fast-acting and reversible regulator of CME. Finally, we discuss tension-based regulation of endocytic clathrin coat formation during physiological processes.
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Affiliation(s)
| | - Yasaman Madraki
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
| | - Emily T. Chan
- Interdiscipiinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
- Molecular Biophysics Training Program, The Ohio State University, Columbus, OH 43210, USA
| | - Comert Kural
- Department of Physics, The Ohio State University, Columbus, OH 43210, USA
- Interdiscipiinary Biophysics Graduate Program, The Ohio State University, Columbus, OH 43210, USA
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24
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Cheng X, Chen K, Dong B, Yang M, Filbrun SL, Myoung Y, Huang TX, Gu Y, Wang G, Fang N. Dynamin-dependent vesicle twist at the final stage of clathrin-mediated endocytosis. Nat Cell Biol 2021; 23:859-869. [PMID: 34253896 PMCID: PMC8355216 DOI: 10.1038/s41556-021-00713-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/09/2021] [Indexed: 12/11/2022]
Abstract
Dynamin plays an important role in clathrin-mediated endocytosis (CME) by cutting the neck of nascent vesicles from the cell membrane. Here through using gold nanorods as cargos to image dynamin action during live CME, we show that near the peak of dynamin accumulation, the cargo-containing vesicles always exhibit abrupt, right-handed rotations that finish in a short time (~0.28 s). The large and quick twist, herein named the super twist, is the result of the coordinated dynamin helix action upon GTP hydrolysis. After the super twist, the rotational freedom of the vesicle drastically increases, accompanied with simultaneous or delayed translational movement, indicating that it detaches from the cell membrane. These observations suggest that dynamin-mediated scission involves a large torque generated by coordinated actions of multiple dynamins in the helix, which is the main driving force for vesicle scission.
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Affiliation(s)
- Xiaodong Cheng
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.,State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Kuangcai Chen
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Bin Dong
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Meek Yang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Seth L Filbrun
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Yong Myoung
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Teng-Xiang Huang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Yan Gu
- The Bristol-Myers Squibb Company, Devens, MA, USA
| | - Gufeng Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA.
| | - Ning Fang
- Department of Chemistry, Georgia State University, Atlanta, GA, USA. .,State Key Laboratory of Physical Chemistry of Solid Surfaces, Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China.
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25
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Baxter AM, Jordan LR, Kullappan M, Wittenberg NJ. Tubulation of Supported Lipid Bilayer Membranes Induced by Photosensitized Lipid Oxidation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:5753-5762. [PMID: 33939441 DOI: 10.1021/acs.langmuir.0c03363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We show that photosensitized phospholipid oxidation, initiated by the lipid-conjugated fluorophore TopFluor-PC, causes defects, namely, membrane tubes and vesicle-like structures, in supported lipid bilayers (SLBs). Lipid oxidation is detrimental to the integrity of the lipid molecules; when oxidized, they undergo a conformational expansion, which causes membrane tubes to protrude from the SLB. Lipid oxidation is verified by FT-IR spectroscopy, and area expansion is observed in Langmuir trough experiments. Upon growing to a critical length, the membrane tubes arising from SLBs rapidly undergo transition to vesicle-like structures. We find a correlation between the maximum tube length and the diameter of the resulting vesicle, suggesting the conservation of the surface area between these features. We use geometric modeling and the measured tube length and vesicle radius to calculate the tube radius; our calculated mean tube diameter of 243 nm is comparable to other groups' experimental findings. In the presence of fluid flow, membrane tubes can be extended to tens to hundreds of microns in length. SLBs composed of saturated lipids resist light-induced tubulation, and the inclusion of the lipophilic antioxidant α-tocopherol attenuates the tubulation process and increases the light intensity threshold for tubulation.
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Affiliation(s)
- Ashley M Baxter
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Luke R Jordan
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Monicka Kullappan
- Department of Chemical & Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Nathan J Wittenberg
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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26
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Abstract
We propose a three-dimensional mathematical model to describe dynamical processes of membrane fission. The model is based on a phase field equation that includes the Gaussian curvature contribution to the bending energy. With the addition of the Gaussian curvature energy term numerical simulations agree with the predictions that tubular shapes can break down into multiple vesicles. A dispersion relation obtained with linear analysis predicts the wavelength of the instability and the number of formed vesicles. Finally, a membrane shape diagram is obtained for the different Gaussian and bending modulus, showing different shape regimes.
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27
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O'Donnell JP, Kelly CM, Sondermann H. Nucleotide-Dependent Dimerization and Conformational Switching of Atlastin. Methods Mol Biol 2021; 2159:93-113. [PMID: 32529366 DOI: 10.1007/978-1-0716-0676-6_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A common feature of dynamin-related proteins (DRPs) is their use of guanosine triphosphate (GTP) to control protein dynamics. In the case of the endoplasmic- reticulum- (ER)-resident membrane protein atlastin (ATL), GTP binding and hydrolysis result in membrane fusion of ER tubules and the generation of a branched ER network. In this chapter, we describe two independent methods for dissecting the mechanism underlying nucleotide-dependent quaternary structure and conformational changes of ATL, focusing on size-exclusion chromatography coupled with multi-angle light scattering (SEC-MALS) and Förster resonance energy transfer (FRET), respectively. The high temporal resolution of the FRET-based assays enables the ordering of the molecular events identified in structural and equilibrium-based SEC-MALS studies. In combination, these complementary methods report on the oligomeric states of a system at equilibrium and timing of key steps along the enzyme's catalytic cycle. These methods are broadly applicable to proteins that undergo ligand-induced dimerization and/or conformational changes.
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Affiliation(s)
- John P O'Donnell
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Carolyn M Kelly
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Holger Sondermann
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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28
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Di Nottia M, Verrigni D, Torraco A, Rizza T, Bertini E, Carrozzo R. Mitochondrial Dynamics: Molecular Mechanisms, Related Primary Mitochondrial Disorders and Therapeutic Approaches. Genes (Basel) 2021; 12:247. [PMID: 33578638 PMCID: PMC7916359 DOI: 10.3390/genes12020247] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria do not exist as individual entities in the cell-conversely, they constitute an interconnected community governed by the constant and opposite process of fission and fusion. The mitochondrial fission leads to the formation of smaller mitochondria, promoting the biogenesis of new organelles. On the other hand, following the fusion process, mitochondria appear as longer and interconnected tubules, which enhance the communication with other organelles. Both fission and fusion are carried out by a small number of highly conserved guanosine triphosphatase proteins and their interactors. Disruption of this equilibrium has been associated with several pathological conditions, ranging from cancer to neurodegeneration, and mutations in genes involved in mitochondrial fission and fusion have been reported to be the cause of a subset of neurogenetic disorders.
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Affiliation(s)
| | | | | | | | | | - Rosalba Carrozzo
- Laboratory of Molecular Medicine, Unit of Muscular and Neurodegenerative Disorders, Bambino Gesù Children’s Hospital, IRCCS, 00146 Rome, Italy; (M.D.N.); (D.V.); (A.T.); (T.R.); (E.B.)
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29
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Hinostroza F, Neely A, Araya-Duran I, Marabolí V, Canan J, Rojas M, Aguayo D, Latorre R, González-Nilo FD, Cárdenas AM. Dynamin-2 R465W mutation induces long range perturbation in highly ordered oligomeric structures. Sci Rep 2020; 10:18151. [PMID: 33097808 PMCID: PMC7584598 DOI: 10.1038/s41598-020-75216-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 10/13/2020] [Indexed: 11/09/2022] Open
Abstract
High order oligomers are crucial for normal cell physiology, and protein function perturbed by missense mutations underlies several autosomal dominant diseases. Dynamin-2 is one of such protein forming helical oligomers that catalyze membrane fission. Mutations in this protein, where R465W is the most frequent, cause dominant centronuclear myopathy, but the molecular mechanisms underpinning the functional modifications remain to be investigated. To unveil the structural impact of this mutation in dynamin-2, we used full-atom molecular dynamics simulations and coarse-grained models and built dimers and helices of wild-type (WT) monomers, mutant monomers, or both WT and mutant monomers combined. Our results show that the mutation R465W causes changes in the interactions with neighbor amino acids that propagate through the oligomer. These new interactions perturb the contact between monomers and favor an extended conformation of the bundle signaling element (BSE), a dynamin region that transmits the conformational changes from the GTPase domain to the rest of the protein. This extended configuration of the BSE that is only relevant in the helices illustrates how a small change in the microenvironment surrounding a single residue can propagate through the oligomer structures of dynamin explaining how dominance emerges in large protein complexes.
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Affiliation(s)
- Fernando Hinostroza
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile.,Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectoría de Investigación y Postgrado, Universidad Católica del Maule, Av. San Miguel 3605, Talca, Chile
| | - Alan Neely
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile
| | - Ingrid Araya-Duran
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Vanessa Marabolí
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Jonathan Canan
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Maximiliano Rojas
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Daniel Aguayo
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile
| | - Ramón Latorre
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile
| | - Fernando D González-Nilo
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile. .,Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Nacional Andrés Bello, Av. República 330, Santiago, Chile.
| | - Ana M Cárdenas
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso, Gran Bretaña 1111, Valparaiso, Chile.
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30
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Bonnycastle K, Davenport EC, Cousin MA. Presynaptic dysfunction in neurodevelopmental disorders: Insights from the synaptic vesicle life cycle. J Neurochem 2020; 157:179-207. [PMID: 32378740 DOI: 10.1111/jnc.15035] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/14/2020] [Accepted: 04/22/2020] [Indexed: 12/11/2022]
Abstract
The activity-dependent fusion, retrieval and recycling of synaptic vesicles is essential for the maintenance of neurotransmission. Until relatively recently it was believed that most mutations in genes that were essential for this process would be incompatible with life, because of this fundamental role. However, an ever-expanding number of mutations in this very cohort of genes are being identified in individuals with neurodevelopmental disorders, including autism, intellectual disability and epilepsy. This article will summarize the current state of knowledge linking mutations in presynaptic genes to neurodevelopmental disorders by sequentially covering the various stages of the synaptic vesicle life cycle. It will also discuss how perturbations of specific stages within this recycling process could translate into human disease. Finally, it will also provide perspectives on the potential for future therapy that are targeted to presynaptic function.
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Affiliation(s)
- Katherine Bonnycastle
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Elizabeth C Davenport
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
| | - Michael A Cousin
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, UK.,Muir Maxwell Epilepsy Centre, University of Edinburgh, Edinburgh, UK.,Simons Initiative for the Developing Brain, University of Edinburgh, Edinburgh, UK
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31
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Kalia R, Frost A. Open and cut: allosteric motion and membrane fission by dynamin superfamily proteins. Mol Biol Cell 2020; 30:2097-2104. [PMID: 31365329 PMCID: PMC6743466 DOI: 10.1091/mbc.e16-10-0709] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cells have evolved diverse protein-based machinery to reshape, cut, or fuse their membrane-delimited compartments. Dynamin superfamily proteins are principal components of this machinery and use their ability to hydrolyze GTP and to polymerize into helices and rings to achieve these goals. Nucleotide-binding, hydrolysis, and exchange reactions drive significant conformational changes across the dynamin family, and these changes alter the shape and stability of supramolecular dynamin oligomers, as well as the ability of dynamins to bind receptors and membranes. Mutations that interfere with the conformational repertoire of these enzymes, and hence with membrane fission, exist in several inherited human diseases. Here, we discuss insights from new x-ray crystal structures and cryo-EM reconstructions that have enabled us to infer some of the allosteric dynamics for these proteins. Together, these studies help us to understand how dynamins perform mechanical work, as well as how specific mutants of dynamin family proteins exhibit pathogenic properties.
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Affiliation(s)
- Raghav Kalia
- Department of Physiology, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132
| | - Adam Frost
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84132.,Chan-Zuckerberg Biohub, San Francisco, CA 94158
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32
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Galkina SI, Fedorova NV, Golenkina EA, Stadnichuk VI, Sud’ina GF. Cytonemes Versus Neutrophil Extracellular Traps in the Fight of Neutrophils with Microbes. Int J Mol Sci 2020; 21:ijms21020586. [PMID: 31963289 PMCID: PMC7014225 DOI: 10.3390/ijms21020586] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 12/11/2022] Open
Abstract
Neutrophils can phagocytose microorganisms and destroy them intracellularly using special bactericides located in intracellular granules. Recent evidence suggests that neutrophils can catch and kill pathogens extracellularly using the same bactericidal agents. For this, live neutrophils create a cytoneme network, and dead neutrophils provide chromatin and proteins to form neutrophil extracellular traps (NETs). Cytonemes are filamentous tubulovesicular secretory protrusions of living neutrophils with intact nuclei. Granular bactericides are localized in membrane vesicles and tubules of which cytonemes are composed. NETs are strands of decondensed DNA associated with histones released by died neutrophils. In NETs, bactericidal neutrophilic agents are adsorbed onto DNA strands and are not covered with a membrane. Cytonemes and NETs occupy different places in protecting the body against infections. Cytonemes can develop within a few minutes at the site of infection through the action of nitric oxide or actin-depolymerizing alkaloids of invading microbes. The formation of NET in vitro occurs due to chromatin decondensation resulting from prolonged activation of neutrophils with PMA (phorbol 12-myristate 13-acetate) or other stimuli, or in vivo due to citrullination of histones with peptidylarginine deiminase 4. In addition to antibacterial activity, cytonemes are involved in cell adhesion and communications. NETs play a role in autoimmunity and thrombosis.
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Affiliation(s)
- Svetlana I. Galkina
- Lomonosov Moscow State University, A. N. Belozersky Institute of Physico-Chemical Biology, 119991 Moscow, Russia; (N.V.F.); (E.A.G.)
- Correspondence: (S.I.G.); (G.F.S.); Tel.: +7-495-939-5408 (S.I.G.)
| | - Natalia V. Fedorova
- Lomonosov Moscow State University, A. N. Belozersky Institute of Physico-Chemical Biology, 119991 Moscow, Russia; (N.V.F.); (E.A.G.)
| | - Ekaterina A. Golenkina
- Lomonosov Moscow State University, A. N. Belozersky Institute of Physico-Chemical Biology, 119991 Moscow, Russia; (N.V.F.); (E.A.G.)
| | | | - Galina F. Sud’ina
- Lomonosov Moscow State University, A. N. Belozersky Institute of Physico-Chemical Biology, 119991 Moscow, Russia; (N.V.F.); (E.A.G.)
- Correspondence: (S.I.G.); (G.F.S.); Tel.: +7-495-939-5408 (S.I.G.)
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33
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Varga K, Jiang ZJ, Gong LW. Phosphatidylserine is critical for vesicle fission during clathrin-mediated endocytosis. J Neurochem 2019; 152:48-60. [PMID: 31587282 DOI: 10.1111/jnc.14886] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/25/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022]
Abstract
Phosphatidylserine (PS), a negatively charged phospholipid present predominantly at the inner leaflet of the plasma membrane, has been widely implicated in many cellular processes including membrane trafficking. Along this line, PS has been demonstrated to be important for endocytosis, however, the involved mechanisms remain uncertain. By monitoring clathrin-mediated endocytosis (CME) of single vesicles in mouse chromaffin cells using cell-attached capacitance measurements that offer millisecond time resolution, we demonstrate in the present study that the fission-pore duration is reduced by PS addition, indicating a stimulatory role of PS in regulating the dynamics of vesicle fission during CME. Furthermore, our results show that the PS-mediated effect on the fission-pore duration is Ca2+ -dependent and abolished in the absence of synaptotagmin 1 (Syt1), implying that Syt1 is necessary for the stimulatory role of PS in vesicle fission during CME. Consistently, a Syt1 mutant with a defective PS-Syt1 interaction increases the fission-pore duration. Taken together, our study suggests that PS-Syt1 interaction may be critical in regulating fission dynamics during CME.
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Affiliation(s)
- Kelly Varga
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA.,Department of Biological Sciences, University of North Texas at Dallas, Dallas, Texas, USA
| | - Zhong-Jiao Jiang
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Liang-Wei Gong
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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34
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Polymer-like Model to Study the Dynamics of Dynamin Filaments on Deformable Membrane Tubes. Biophys J 2019; 117:1870-1891. [PMID: 31672269 DOI: 10.1016/j.bpj.2019.09.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/08/2019] [Accepted: 09/24/2019] [Indexed: 01/30/2023] Open
Abstract
Peripheral membrane proteins with intrinsic curvature can act both as sensors of membrane curvature and shape modulators of the underlying membranes. A well-studied example of such proteins is the mechanochemical GTPase dynamin, which assembles into helical filaments around membrane tubes and catalyzes their scission in a GTPase-dependent manner. It is known that the dynamin coat alone, without GTP, can constrict membrane tubes to radii of ∼10 nm, indicating that the intrinsic shape and elasticity of dynamin filaments should play an important role in membrane remodeling. However, molecular and dynamic understanding of the process is lacking. Here, we develop a dynamical polymer-chain model for a helical elastic filament bound on a deformable membrane tube of conserved mass, accounting for thermal fluctuations in the filament and lipid flows in the membrane. The model is based on the locally cylindrical helix approximation for dynamin. We obtain the elastic parameters of the dynamin filament by molecular dynamics simulations of its tetrameric building block and also from coarse-grained structure-based simulations of a 17-dimer filament. The results show that the stiffness of dynamin is comparable to that of the membrane. We determine equilibrium shapes of the filament and the membrane and find that mostly the pitch of the filament, not its radius, is sensitive to variations in membrane tension and stiffness. The close correspondence between experimental estimates of the inner tube radius and those predicted by the model suggests that dynamin's "stalk" region is responsible for its GTP-independent membrane-shaping ability. The model paves the way for future mesoscopic modeling of dynamin with explicit motor function.
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35
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De Vecchis D, Brandner A, Baaden M, Cohen MM, Taly A. A Molecular Perspective on Mitochondrial Membrane Fusion: From the Key Players to Oligomerization and Tethering of Mitofusin. J Membr Biol 2019; 252:293-306. [PMID: 31485701 DOI: 10.1007/s00232-019-00089-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 08/14/2019] [Indexed: 12/29/2022]
Abstract
Mitochondria are dynamic organelles characterized by an ultrastructural organization which is essential in maintaining their quality control and ensuring functional efficiency. The complex mitochondrial network is the result of the two ongoing forces of fusion and fission of inner and outer membranes. Understanding the functional details of mitochondrial dynamics is physiologically relevant as perturbations of this delicate equilibrium have critical consequences and involved in several neurological disorders. Molecular actors involved in this process are large GTPases from the dynamin-related protein family. They catalyze nucleotide-dependent membrane remodeling and are widely conserved from bacteria to higher eukaryotes. Although structural characterization of different family members has contributed in understanding molecular mechanisms of mitochondrial dynamics in more detail, the complete structure of some members as well as the precise assembly of functional oligomers remains largely unknown. As increasing structural data become available, the domain modularity across the dynamin superfamily emerged as a foundation for transfering the knowledge towards less characterized members. In this review, we will first provide an overview of the main actors involved in mitochondrial dynamics. We then discuss recent example of computational methodologies for the study of mitofusin oligomers, and present how the usage of integrative modeling in conjunction with biochemical data can be an asset in progressing the still challenging field of membrane dynamics.
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Affiliation(s)
- Dario De Vecchis
- School of Medicine, Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, LIGHT Building, Leeds, LS2 9JT, UK.
| | - Astrid Brandner
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005, Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Marc Baaden
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005, Paris, France.,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France
| | - Mickael M Cohen
- Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France.,Laboratoire de Biologie Cellulaire et Moléculaire des Eucaryotes, Sorbonne Université, CNRS, UMR 8226, Paris, France
| | - Antoine Taly
- CNRS, Université de Paris, UPR 9080, Laboratoire de Biochimie Théorique, 13 Rue Pierre et Marie Curie, 75005, Paris, France. .,Institut de Biologie Physico-Chimique - Fondation Edmond de Rothschild, PSL Research University, Paris, France.
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36
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Ford MGJ, Chappie JS. The structural biology of the dynamin-related proteins: New insights into a diverse, multitalented family. Traffic 2019; 20:717-740. [PMID: 31298797 DOI: 10.1111/tra.12676] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/10/2019] [Accepted: 07/10/2019] [Indexed: 12/13/2022]
Abstract
Dynamin-related proteins are multidomain, mechanochemical GTPases that self-assemble and orchestrate a wide array of cellular processes. Over the past decade, structural insights from X-ray crystallography and cryo-electron microscopy have reshaped our mechanistic understanding of these proteins. Here, we provide a historical perspective on these advances that highlights the structural attributes of different dynamin family members and explores how these characteristics affect GTP hydrolysis, conformational coupling and oligomerization. We also discuss a number of lingering challenges remaining in the field that suggest future directions of study.
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Affiliation(s)
- Marijn G J Ford
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, New York
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37
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Yoshida Y, Mogi Y. How do plastids and mitochondria divide? Microscopy (Oxf) 2019; 68:45-56. [PMID: 30476140 DOI: 10.1093/jmicro/dfy132] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/16/2018] [Indexed: 12/30/2022] Open
Abstract
Plastids and mitochondria are thought to have originated from free-living cyanobacterial and alpha-proteobacterial ancestors, respectively, via endosymbiosis. Their evolutionary origins dictate that these organelles do not multiply de novo but through the division of pre-existing plastids and mitochondria. Over the past three decades, studies have shown that plastid and mitochondrial division are performed by contractile ring-shaped structures, broadly termed the plastid and mitochondrial-division machineries. Interestingly, the division machineries are hybrid forms of the bacterial cell division system and eukaryotic membrane fission system. The structure and function of the plastid and mitochondrial-division machineries are similar to each other, implying that the division machineries evolved in parallel since their establishment in primitive eukaryotes. Compared with our knowledge of their structures, our understanding of the mechanical details of how these division machineries function is still quite limited. Here, we review and compare the structural frameworks of the plastid and mitochondrial-division machineries in both lower and higher eukaryotes. Then, we highlight fundamental issues that need to be resolved to reveal the underlying mechanisms of plastid and mitochondrial division. Finally, we highlight related studies that point to an exciting future for the field.
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Affiliation(s)
- Yamato Yoshida
- Department of Science, College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki, Japan
| | - Yuko Mogi
- Department of Science, College of Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki, Japan
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38
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The late stage of COPI vesicle fission requires shorter forms of phosphatidic acid and diacylglycerol. Nat Commun 2019; 10:3409. [PMID: 31363100 PMCID: PMC6667475 DOI: 10.1038/s41467-019-11324-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/21/2019] [Indexed: 12/19/2022] Open
Abstract
Studies on vesicle formation by the Coat Protein I (COPI) complex have contributed to a basic understanding of how vesicular transport is initiated. Phosphatidic acid (PA) and diacylglycerol (DAG) have been found previously to be required for the fission stage of COPI vesicle formation. Here, we find that PA with varying lipid geometry can all promote early fission, but only PA with shortened acyl chains promotes late fission. Moreover, diacylglycerol (DAG) acts after PA in late fission, with this role of DAG also requiring shorter acyl chains. Further highlighting the importance of the short-chain lipid geometry for late fission, we find that shorter forms of PA and DAG promote the vesiculation ability of COPI fission factors. These findings advance a general understanding of how lipid geometry contributes to membrane deformation for vesicle fission, and also how proteins and lipids coordinate their actions in driving this process.
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39
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Farkas Z, Petric M, Liu X, Herit F, Rajnavölgyi É, Szondy Z, Budai Z, Orbán TI, Sándor S, Mehta A, Bajtay Z, Kovács T, Jung SY, Afaq Shakir M, Qin J, Zhou Z, Niedergang F, Boissan M, Takács-Vellai K. The nucleoside diphosphate kinase NDK-1/NME1 promotes phagocytosis in concert with DYN-1/Dynamin. FASEB J 2019; 33:11606-11614. [PMID: 31242766 PMCID: PMC6819981 DOI: 10.1096/fj.201900220r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phagocytosis of various targets, such as apoptotic cells or opsonized pathogens, by macrophages is coordinated by a complex signaling network initiated by distinct phagocytic receptors. Despite the different initial signaling pathways, each pathway ends up regulating the actin cytoskeletal network, phagosome formation and closure, and phagosome maturation leading to degradation of the engulfed particle. Herein, we describe a new phagocytic function for the nucleoside diphosphate kinase 1 (NDK-1), the nematode counterpart of the first identified metastasis inhibitor NM23-H1 (nonmetastatic clone number 23) nonmetastatic clone number 23 or nonmetastatic isoform 1 (NME1). We reveal by coimmunoprecipitation, Duolink proximity ligation assay, and mass spectrometry that NDK-1/NME1 works in a complex with DYN-1/Dynamin (Caenorhabditis elegans/human homolog proteins), which is essential for engulfment and phagosome maturation. Time-lapse microscopy shows that NDK-1 is expressed on phagosomal surfaces during cell corpse clearance in the same time window as DYN-1. Silencing of NM23-M1 in mouse bone marrow–derived macrophages resulted in decreased phagocytosis of apoptotic thymocytes. In human macrophages, NM23-H1 and Dynamin are corecruited at sites of phagosome formation in F-actin–rich cups. In addition, NM23-H1 was required for efficient phagocytosis. Together, our data demonstrate that NDK-1/NME1 is an evolutionarily conserved element of successful phagocytosis.—Farkas, Z., Petric, M., Liu, X., Herit, F., Rajnavölgyi, É., Szondy, Z., Budai, Z., Orbán, T. I., Sándor, S., Mehta, A., Bajtay, Z., Kovács, T., Jung, S. Y., Afaq Shakir, M., Qin, J., Zhou, Z., Niedergang, F., Boissan, M., Takács-Vellai, K. The nucleoside diphosphate kinase NDK-1/NME1 promotes phagocytosis in concert with DYN-1/dynamin.
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Affiliation(s)
- Zsolt Farkas
- Department of Biological Anthropology, Eötvös Loránd University, Budapest, Hungary
| | - Metka Petric
- INSERM, Unité 1016, Institut Cochin, Paris, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Xianghua Liu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Floriane Herit
- INSERM, Unité 1016, Institut Cochin, Paris, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Éva Rajnavölgyi
- Department of Immunology, University of Debrecen, Debrecen, Hungary
| | - Zsuzsa Szondy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Zsófia Budai
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
| | - Tamás I Orbán
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Sára Sándor
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anil Mehta
- Division of Medical Sciences, Ninewells Hospital Medical School, Dundee, United Kingdom
| | - Zsuzsa Bajtay
- Department of Immunology and MTA-ELTE Immunology Research Group, Eötvös Loránd University, Budapest, Hungary
| | - Tibor Kovács
- Department of Genetics, Eötvös Loránd University, Budapest, Hungary
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.,Verna and Marrs McLean Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Muhammed Afaq Shakir
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Jun Qin
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.,Verna and Marrs McLean Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, USA
| | - Zheng Zhou
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
| | - Florence Niedergang
- INSERM, Unité 1016, Institut Cochin, Paris, France.,Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 8104, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Mathieu Boissan
- Sorbonne Université, University Pierre and Marie Curie (UPMC) Paris 06, INSERM, Unité Mixte de Recherche (UMR) S938, Saint-Antoine Research Center, Paris, France; and.,Assistance Publique-Hôpitaux de Paris (AP-HP), Hospital Tenon, Service de Biochimie et Hormonologie, Paris, France
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40
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Romanov V, McCullough J, Gale BK, Frost A. A Tunable Microfluidic Device Enables Cargo Encapsulation by Cell- or Organelle-Sized Lipid Vesicles Comprising Asymmetric Lipid Bilayers. ADVANCED BIOSYSTEMS 2019; 3:1900010. [PMID: 31428671 PMCID: PMC6699779 DOI: 10.1002/adbi.201900010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 01/14/2023]
Abstract
Cellular membranes play host to a wide variety of morphologically and chemically complex processes. Although model membranes, like liposomes, are already widely used to reconstitute and study these processes, better tools are needed for making model bilayers that faithfully mimic cellular membranes. Existing methods for fabricating cell-sized (μm) or organelle-sized (tens to hundreds of nanometers) lipid vesicles have distinctly different requirements. Of particular note for biology, it remains challenging for any technique to efficiently encapsulate fragile cargo molecules or to generate liposomes with stable, asymmetric lipid leaflets within the bilayer. Here a tunable microfluidic device and protocol for fabricating liposomes with desired diameters ranging from ≈10 μm to ≈100 nm are described. Lipid vesicle size is templated by the simple inclusion of a polycarbonate filter within the microfluidic system and tuned with flow rate. It is shown that the vesicles made with this device are stable, unilamellar, lipid asymmetric, and capable of supporting transmembrane protein assembly, peripheral membrane protein binding, as well as soluble cargo encapsulation (including designer nanocages for biotechnology applications). These fabricated vesicles provide a new platform for studying the biophysically rich processes found within lipid-lipid and lipid-protein systems typically associated with cellular membranes.
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Affiliation(s)
- Valentin Romanov
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - John McCullough
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Bruce K Gale
- Department of Mechanical Engineering, University of Utah, Salt Lake City, UT 84112, USA
| | - Adam Frost
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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41
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Jimah JR, Hinshaw JE. Structural Insights into the Mechanism of Dynamin Superfamily Proteins. Trends Cell Biol 2019; 29:257-273. [DOI: 10.1016/j.tcb.2018.11.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/30/2018] [Accepted: 11/02/2018] [Indexed: 12/28/2022]
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42
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Ayloo S, Gu C. Transcytosis at the blood-brain barrier. Curr Opin Neurobiol 2019; 57:32-38. [PMID: 30708291 DOI: 10.1016/j.conb.2018.12.014] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 12/28/2018] [Indexed: 12/11/2022]
Abstract
The blood-brain barrier (BBB) is a functional interface separating the brain from the circulatory system and is essential for homeostasis of the central nervous system (CNS). The BBB regulates molecular flux to maintain an optimal environment for neuronal function and protects the brain from toxins and pathogens. Endothelial cells forming the walls of CNS blood vessels constitute the BBB. CNS endothelial cells exhibit two features that underlie the restrictive properties of the BBB: specialized tight junctions that prevent paracellular passage between the blood and the brain, and unusually low levels of vesicle trafficking that limit transcellular transport or transcytosis. While the prevailing view in the field was that specialized tight junctions contributed to CNS barrier properties, recent findings have revealed the importance of maintaining low rates of transcytosis at the BBB. It is now clear that suppression of transcytosis at the BBB is an active process and CNS-specific genetic programs inhibit this pathway to maintain a functional barrier.
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Affiliation(s)
- Swathi Ayloo
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115, USA
| | - Chenghua Gu
- Department of Neurobiology, Harvard Medical School, 220 Longwood Ave., Boston, MA 02115, USA.
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43
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Erickson JL, Schattat MH. Shaping plastid stromules-principles of in vitro membrane tubulation applied in planta. CURRENT OPINION IN PLANT BIOLOGY 2018; 46:48-54. [PMID: 30041102 DOI: 10.1016/j.pbi.2018.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 07/01/2018] [Accepted: 07/06/2018] [Indexed: 05/10/2023]
Abstract
Plastids undergo drastic shape changes under stress, including the formation of stroma-filled tubules, or `stromules'. Stromules are dynamic, and may extend, branch and retract within minutes. There are two prerequisites for stromule extension: excess plastid membrane and a force(s) that shapes the membrane into a tubule. In vitro studies provide insight into the basic molecular machinery for tubulation, and are often cited when discussing stromule formation. In this review, we evaluate in vitro modes of tubulation in the context of stromule dynamics, and find that most mechanisms fail to explain stromule morphology and behavior observed in planta. Current data support a model of stromule formation relying on pulling motors (myosins and kinesins) and cytoskeleton (actin and microtubules).
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Affiliation(s)
- Jessica Lee Erickson
- Department of Plant Physiology, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06099 Halle, Germany
| | - Martin Hartmut Schattat
- Department of Plant Physiology, Institute for Biology, Martin Luther University Halle-Wittenberg, D-06099 Halle, Germany.
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44
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De Paoli SH, Tegegn TZ, Elhelu OK, Strader MB, Patel M, Diduch LL, Tarandovskiy ID, Wu Y, Zheng J, Ovanesov MV, Alayash A, Simak J. Dissecting the biochemical architecture and morphological release pathways of the human platelet extracellular vesiculome. Cell Mol Life Sci 2018; 75:3781-3801. [PMID: 29427073 PMCID: PMC11105464 DOI: 10.1007/s00018-018-2771-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/11/2018] [Accepted: 02/01/2018] [Indexed: 01/08/2023]
Abstract
Platelet extracellular vesicles (PEVs) have emerged as potential mediators in intercellular communication. PEVs exhibit several activities with pathophysiological importance and may serve as diagnostic biomarkers. Here, imaging and analytical techniques were employed to unveil morphological pathways of the release, structure, composition, and surface properties of PEVs derived from human platelets (PLTs) activated with the thrombin receptor activating peptide (TRAP). Based on extensive electron microscopy analysis, we propose four morphological pathways for PEVs release from TRAP-activated PLTs: (1) plasma membrane budding, (2) extrusion of multivesicular α-granules and cytoplasmic vacuoles, (3) plasma membrane blistering and (4) "pearling" of PLT pseudopodia. The PLT extracellular vesiculome encompasses ectosomes, exosomes, free mitochondria, mitochondria-containing vesicles, "podiasomes" and PLT "ghosts". Interestingly, a flow cytometry showed a population of TOM20+LC3+ PEVs, likely products of platelet mitophagy. We found that lipidomic and proteomic profiles were different between the small PEV (S-PEVs; mean diameter 103 nm) and the large vesicle (L-PEVs; mean diameter 350 nm) fractions separated by differential centrifugation. In addition, the majority of PEVs released by activated PLTs was composed of S-PEVs which have markedly higher thrombin generation activity per unit of PEV surface area compared to L-PEVs, and contribute approximately 60% of the PLT vesiculome procoagulant potency.
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Affiliation(s)
- Silvia H De Paoli
- Laboratory of Cellular Hematology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Room 4210, Silver Spring, MD, USA
| | - Tseday Z Tegegn
- Laboratory of Cellular Hematology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Room 4210, Silver Spring, MD, USA
| | - Oumsalama K Elhelu
- Laboratory of Cellular Hematology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Room 4210, Silver Spring, MD, USA
| | - Michael B Strader
- Laboratory of Biochemistry and Vascular Biology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Silver Spring, MD, 20993-0002, USA
| | - Mehulkumar Patel
- Laboratory of Cellular Hematology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Room 4210, Silver Spring, MD, USA
| | - Lukas L Diduch
- Dakota Consulting, Inc., 1110 Bonifant St., Silver Spring, MD, USA
| | - Ivan D Tarandovskiy
- Laboratory of Cellular Hematology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Room 4210, Silver Spring, MD, USA
| | - Yong Wu
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Jiwen Zheng
- Division of Biology, Chemistry and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Mikhail V Ovanesov
- Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD, USA
| | - Abdu Alayash
- Laboratory of Biochemistry and Vascular Biology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Silver Spring, MD, 20993-0002, USA
| | - Jan Simak
- Laboratory of Cellular Hematology, Office of Blood Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Avenue, WO Bldg. 52/72, Room 4210, Silver Spring, MD, USA.
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45
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Bassereau P, Jin R, Baumgart T, Deserno M, Dimova R, Frolov VA, Bashkirov PV, Grubmüller H, Jahn R, Risselada HJ, Johannes L, Kozlov MM, Lipowsky R, Pucadyil TJ, Zeno WF, Stachowiak JC, Stamou D, Breuer A, Lauritsen L, Simon C, Sykes C, Voth GA, Weikl TR. The 2018 biomembrane curvature and remodeling roadmap. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2018; 51:343001. [PMID: 30655651 PMCID: PMC6333427 DOI: 10.1088/1361-6463/aacb98] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
The importance of curvature as a structural feature of biological membranes has been recognized for many years and has fascinated scientists from a wide range of different backgrounds. On the one hand, changes in membrane morphology are involved in a plethora of phenomena involving the plasma membrane of eukaryotic cells, including endo- and exocytosis, phagocytosis and filopodia formation. On the other hand, a multitude of intracellular processes at the level of organelles rely on generation, modulation, and maintenance of membrane curvature to maintain the organelle shape and functionality. The contribution of biophysicists and biologists is essential for shedding light on the mechanistic understanding and quantification of these processes. Given the vast complexity of phenomena and mechanisms involved in the coupling between membrane shape and function, it is not always clear in what direction to advance to eventually arrive at an exhaustive understanding of this important research area. The 2018 Biomembrane Curvature and Remodeling Roadmap of Journal of Physics D: Applied Physics addresses this need for clarity and is intended to provide guidance both for students who have just entered the field as well as established scientists who would like to improve their orientation within this fascinating area.
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Affiliation(s)
- Patricia Bassereau
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Rui Jin
- Chemistry Department, University of Pennsylvania, Philadelphia, PA 19104-6323, United States of America
| | - Tobias Baumgart
- Chemistry Department, University of Pennsylvania, Philadelphia, PA 19104-6323, United States of America
| | - Markus Deserno
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, United States of America
| | - Rumiana Dimova
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | - Vadim A Frolov
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country, Leioa 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Pavel V Bashkirov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow 119435, Russia
- A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow 119071, Russia
| | - Helmut Grubmüller
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Reinhard Jahn
- Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - H Jelger Risselada
- Department of Theoretical Physics, Georg-August University, Göttingen, Germany
| | - Ludger Johannes
- Cellular and Chemical Biology Unit, Institut Curie, PSL Research University, U1143 INSERM, UMR3666 CNRS, 26 rue d'Ulm, 75248 Paris Cedex 05, France
| | - Michael M Kozlov
- Sackler Faculty of Medicine, Department of Physiology and Pharmacology, Tel Aviv University
| | - Reinhard Lipowsky
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
| | | | - Wade F Zeno
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States of America
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, United States of America
- University of Texas at Austin, Institute for Cellular and Molecular Biology, Austin, TX, United States of America
| | - Dimitrios Stamou
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Artú Breuer
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Line Lauritsen
- Bionanotechnology and Nanomedicine Laboratory, Department of Chemistry, Nano-Science Center, University of Copenhagen, Denmark
| | - Camille Simon
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Cécile Sykes
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, 75005 Paris, France
- Sorbonne Université, 75005 Paris, France
| | - Gregory A Voth
- Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, United States of America
| | - Thomas R Weikl
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Science Park Golm, 14424 Potsdam, Germany
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46
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Ramakrishnan N, Bradley RP, Tourdot RW, Radhakrishnan R. Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:273001. [PMID: 29786613 PMCID: PMC6066392 DOI: 10.1088/1361-648x/aac702] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.
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Affiliation(s)
- N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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Zhang G, Müller M. Rupturing the hemi-fission intermediate in membrane fission under tension: Reaction coordinates, kinetic pathways, and free-energy barriers. J Chem Phys 2018; 147:064906. [PMID: 28810752 DOI: 10.1063/1.4997575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Membrane fission is a fundamental process in cells, involved inter alia in endocytosis, intracellular trafficking, and virus infection. Its underlying molecular mechanism, however, is only incompletely understood. Recently, experiments and computer simulation studies have revealed that dynamin-mediated membrane fission is a two-step process that proceeds via a metastable hemi-fission intermediate (or wormlike micelle) formed by dynamin's constriction. Importantly, this hemi-fission intermediate is remarkably metastable, i.e., its subsequent rupture that completes the fission process does not occur spontaneously but requires additional, external effects, e.g., dynamin's (unknown) conformational changes or membrane tension. Using simulations of a coarse-grained, implicit-solvent model of lipid membranes, we investigate the molecular mechanism of rupturing the hemi-fission intermediate, such as its pathway, the concomitant transition states, and barriers, as well as the role of membrane tension. The membrane tension is controlled by the chemical potential of the lipids, and the free-energy landscape as a function of two reaction coordinates is obtained by grand canonical Wang-Landau sampling. Our results show that, in the course of rupturing, the hemi-fission intermediate undergoes a "thinning → local pinching → rupture/fission" pathway, with a bottle-neck-shaped cylindrical micelle as a transition state. Although an increase of membrane tension facilitates the fission process by reducing the corresponding free-energy barrier, for biologically relevant tensions, the free-energy barriers still significantly exceed the thermal energy scale kBT.
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Affiliation(s)
- Guojie Zhang
- Institute for Theoretical Physics, University of Goettingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Marcus Müller
- Institute for Theoretical Physics, University of Goettingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
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Takatori S, Tomita T. AP180 N-Terminal Homology (ANTH) and Epsin N-Terminal Homology (ENTH) Domains: Physiological Functions and Involvement in Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1111:55-76. [DOI: 10.1007/5584_2018_218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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49
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Miao Y, Tipakornsaowapak T, Zheng L, Mu Y, Lewellyn E. Phospho-regulation of intrinsically disordered proteins for actin assembly and endocytosis. FEBS J 2018; 285:2762-2784. [PMID: 29722136 DOI: 10.1111/febs.14493] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/04/2018] [Accepted: 04/26/2018] [Indexed: 12/13/2022]
Abstract
Actin filament assembly contributes to the endocytic pathway pleiotropically, with active roles in clathrin-dependent and clathrin-independent endocytosis as well as subsequent endosomal trafficking. Endocytosis comprises a series of dynamic events, including the initiation of membrane curvature, bud invagination, vesicle abscission and subsequent vesicular transport. The ultimate success of endocytosis requires the coordinated activities of proteins that trigger actin polymerization, recruit actin-binding proteins (ABPs) and organize endocytic proteins (EPs) that promote membrane curvature through molecular crowding or scaffolding mechanisms. A particularly interesting phenomenon is that multiple EPs and ABPs contain a substantial percentage of intrinsically disordered regions (IDRs), which can contribute to protein coacervation and phase separation. In addition, intrinsically disordered proteins (IDPs) frequently contain sites for post-translational modifications (PTMs) such as phosphorylation, and these modifications exhibit a high preference for IDR residues [Groban ES et al. (2006) PLoS Comput Biol 2, e32]. PTMs are implicated in regulating protein function by modulating the protein conformation, protein-protein interactions and the transition between order and disorder states of IDPs. The molecular mechanisms by which IDRs of ABPs and EPs fine-tune actin assembly and endocytosis remain mostly unexplored and elusive. In this review, we analyze protein sequences of budding yeast EPs and ABPs, and discuss the potential underlying mechanisms for regulating endocytosis and actin assembly through the emerging concept of IDR-mediated protein multivalency, coacervation, and phase transition, with an emphasis on the phospho-regulation of IDRs. Finally, we summarize the current understanding of how these mechanisms coordinate actin cytoskeleton assembly and membrane curvature formation during endocytosis in budding yeast.
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Affiliation(s)
- Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.,School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore, Singapore
| | | | - Liangzhen Zheng
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Eric Lewellyn
- Department of Biology, Division of Natural Sciences, St Norbert College, De Pere, WI, USA
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50
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Abstract
The coat protein complex I (COPI) allows the precise sorting of lipids and proteins between Golgi cisternae and retrieval from the Golgi to the ER. This essential role maintains the identity of the early secretory pathway and impinges on key cellular processes, such as protein quality control. In this Cell Science at a Glance and accompanying poster, we illustrate the different stages of COPI-coated vesicle formation and revisit decades of research in the context of recent advances in the elucidation of COPI coat structure. By calling attention to an array of questions that have remained unresolved, this review attempts to refocus the perspectives of the field.
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Affiliation(s)
- Eric C Arakel
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany
| | - Blanche Schwappach
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, 37073 Göttingen, Germany .,Max-Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
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