51
|
Mookherjee D, Majumder P, Mukherjee R, Chatterjee D, Kaul Z, Das S, Sougrat R, Chakrabarti S, Chakrabarti O. Cytosolic aggregates in presence of non‐translocated proteins perturb endoplasmic reticulum structure and dynamics. Traffic 2019; 20:943-960. [DOI: 10.1111/tra.12694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 08/21/2019] [Accepted: 08/29/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Debdatto Mookherjee
- Biophysics & Structural Genomics DivisionSaha Institute of Nuclear Physics Kolkata India
| | - Priyanka Majumder
- Biophysics & Structural Genomics DivisionSaha Institute of Nuclear Physics Kolkata India
- Department of Life Sciences, School of Natural SciencesShiv Nadar University Dadri UP India
| | - Rukmini Mukherjee
- Biophysics & Structural Genomics DivisionSaha Institute of Nuclear Physics Kolkata India
- Buchmann Institute for Molecular Life Sciences Frankfurt Am Main Germany
| | - Debmita Chatterjee
- Biophysics & Structural Genomics DivisionSaha Institute of Nuclear Physics Kolkata India
| | - Zenia Kaul
- Biophysics & Structural Genomics DivisionSaha Institute of Nuclear Physics Kolkata India
- Department of Microbiology, Immunology, and Cancer BiologyUniversity of Virginia School of Medicine Charlottesville Virginia
| | - Subhrangshu Das
- Structural Biology and Bioinformatics DivisionCSIR‐Indian Institute of Chemical Biology Kolkata India
| | - Rachid Sougrat
- Imaging and Characterization Lab4700 King Abdullah University of Science and Technology Thuwal Kingdom of Saudi Arabia
| | - Saikat Chakrabarti
- Structural Biology and Bioinformatics DivisionCSIR‐Indian Institute of Chemical Biology Kolkata India
| | - Oishee Chakrabarti
- Biophysics & Structural Genomics DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
| |
Collapse
|
52
|
Chabanon M, Rangamani P. Geometric coupling of helicoidal ramps and curvature-inducing proteins in organelle membranes. J R Soc Interface 2019; 16:20190354. [PMID: 31480932 DOI: 10.1098/rsif.2019.0354] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Cellular membranes display an incredibly diverse range of shapes, both in the plasma membrane and at membrane bound organelles. These morphologies are intricately related to cellular functions, enabling and regulating fundamental membrane processes. However, the biophysical mechanisms at the origin of these complex geometries are not fully understood from the standpoint of membrane-protein coupling. In this study, we focused on a minimal model of helicoidal ramps representative of specialized endoplasmic reticulum compartments. Given a helicoidal membrane geometry, we asked what is the distribution of spontaneous curvature required to maintain this shape at mechanical equilibrium? Based on the Helfrich energy of elastic membranes with spontaneous curvature, we derived the shape equation for minimal surfaces, and applied it to helicoids. We showed the existence of switches in the sign of the spontaneous curvature associated with geometric variations of the membrane structures. Furthermore, for a prescribed gradient of spontaneous curvature along the exterior boundaries, we identified configurations of the helicoidal ramps that are confined between two infinitely large energy barriers. Overall our results suggest possible mechanisms for geometric control of helicoidal ramps in membrane organelles based on curvature-inducing proteins.
Collapse
Affiliation(s)
- Morgan Chabanon
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA, USA
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla CA, USA
| |
Collapse
|
53
|
Ulloa G, Hamati F, Dick A, Fitzgerald J, Mantell J, Verkade P, Collinson L, Arkill K, Larijani B, Poccia D. Lipid species affect morphology of endoplasmic reticulum: a sea urchin oocyte model of reversible manipulation. J Lipid Res 2019; 60:1880-1891. [PMID: 31548365 PMCID: PMC6824487 DOI: 10.1194/jlr.ra119000210] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/11/2019] [Indexed: 12/22/2022] Open
Abstract
The ER is a large multifunctional organelle of eukaryotic cells. Malfunction of the ER in various disease states, such as atherosclerosis, diabetes, cancer, Alzheimer’s and Parkinson’s and amyotrophic lateral sclerosis, often correlates with alterations in its morphology. The ER exhibits regionally variable membrane morphology that includes, at the extremes, large relatively flat surfaces and interconnected tubular structures highly curved in cross-section. ER morphology is controlled by shaping proteins that associate with membrane lipids. To investigate the role of these lipids, we developed a sea urchin oocyte model, a relatively quiescent cell in which the ER consists mostly of tubules. We altered levels of endogenous diacylglycerol (DAG), phosphatidylethanolamine (PtdEth), and phosphatidylcholine by microinjection of enzymes or lipid delivery by liposomes and evaluated shape changes with 2D and 3D confocal imaging and 3D electron microscopy. Decreases and increases in the levels of lipids such as DAG or PtdEth characterized by negative spontaneous curvature correlated with conversion to sheet structures or tubules, respectively. The effects of endogenous alterations of DAG were reversible upon exogenous delivery of lipids of negative spontaneous curvature. These data suggest that proteins require threshold amounts of such lipids and that localized deficiencies of the lipids could contribute to alterations of ER morphology. The oocyte modeling system should be beneficial to studies directed at understanding requirements of lipid species in interactions leading to alterations of organelle shaping.
Collapse
Affiliation(s)
| | - Fadi Hamati
- Department of Biology, Amherst College, Amherst, MA
| | | | | | - Judith Mantell
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | - Paul Verkade
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| | | | - Kenton Arkill
- School of Medicine, Faculty of Medicine and Health Sciences, University of Nottingham Medical School, Nottingham, United Kingdom
| | - Banafshe Larijani
- Centre for Therapeutic Innovation, Cell Biophysics Laboratory, Department of Pharmacy and Pharmacology and Department of Physics, University of Bath, Claverton Down, Bath, United Kingdom, and Cell Biophysics Laboratory, Ikerbasque, Basque Foundation for Science, Research Centre for Experimental Marine Biology and Biotechnology (PiE) and Biophysics Institute (UPV/EHU, CSIC), University of the Basque Country, Leioa, Spain
| | | |
Collapse
|
54
|
CAND1 regulates lunapark for the proper tubular network of the endoplasmic reticulum. Sci Rep 2019; 9:13152. [PMID: 31511573 PMCID: PMC6739345 DOI: 10.1038/s41598-019-49542-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 08/27/2019] [Indexed: 12/31/2022] Open
Abstract
Endoplasmic reticulum (ER) tubules connect each other by three-way junctions, resulting in a tubular ER network. Oligomerization of three-way junction protein lunapark (Lnp) is important for its localization and the three-way junction stability. On the other hand, Lnp has an N-terminal ubiquitin ligase activity domain, which is also important for the three-way junction localization. To understand the mode of action of Lnp, we isolated Cullin-associated and neddylation-dissociated 1 (CAND1), a regulator of Skp1-Cul1-F-box (SCF) ubiquitin ligase, as a Lnp-binding protein by affinity chromatography. CAND1 and Lnp form a higher-molecular-weight complex in vitro, while they do not co-localize at the three-way junctions. CAND1 reduces the auto-ubiquitination activity of Lnp. CAND1 knockdown enhances proteasomal degradation of Lnp and reduces the tubular ER network in mammalian cells. These results suggest that CAND1 has the potency to promote the formation of the higher-molecular-weight complex with Lnp and reduce the auto-ubiquitination activity of Lnp, thereby regulating the three-way junction stability of the tubular ER network.
Collapse
|
55
|
De Leonibus C, Cinque L, Settembre C. Emerging lysosomal pathways for quality control at the endoplasmic reticulum. FEBS Lett 2019; 593:2319-2329. [PMID: 31388984 DOI: 10.1002/1873-3468.13571] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 01/01/2023]
Abstract
Protein misfolding occurring in the endoplasmic reticulum (ER) might eventually lead to aggregation and cellular distress, and is a primary pathogenic mechanism in multiple human disorders. Mammals have developed evolutionary-conserved quality control mechanisms at the level of the ER. The best characterized is the ER-associated degradation (ERAD) pathway, through which misfolded proteins translocate from the ER to the cytosol and are subsequently proteasomally degraded. However, increasing evidence indicates that additional quality control mechanisms apply for misfolded ER clients that are not eligible for ERAD. This review focuses on the alternative, ERAD-independent, mechanisms of clearance of misfolded polypeptides from the ER. These processes, collectively referred to as ER-to-lysosome-associated degradation, involve ER-phagy, microautophagy or vesicular transport. The identification of the underlying molecular mechanisms is particularly important for developing new therapeutic approaches for human diseases associated with protein aggregate formation.
Collapse
Affiliation(s)
| | - Laura Cinque
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.,Department of Medical and Translational Science, University of Naples "Federico II", Italy
| |
Collapse
|
56
|
Bilir Ş, Kojidani T, Mori C, Osakada H, Kobayashi S, Koujin T, Hiraoka Y, Haraguchi T. Roles of Nup133, Nup153 and membrane fenestrations in assembly of the nuclear pore complex at the end of mitosis. Genes Cells 2019; 24:338-353. [PMID: 30821042 DOI: 10.1111/gtc.12677] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/15/2019] [Accepted: 02/24/2019] [Indexed: 12/25/2022]
Abstract
Reassembly of the nuclear pore complex (NPC) at the end of mitosis is an important event for eukaryotic nuclear function. In this study, we examined the dynamic behaviors of the endoplasmic reticulum (ER) by "Live CLEM" imaging. In metaphase, numerous fenestrations on the ER membrane were observed around chromosomes. In telophase, these fenestrations became filled at the region attached to chromosomes, whereas they remained open at the region unattached to chromosomes, suggesting that NPC assembly takes place at fenestrations on the membrane. To determine the roles of nucleoporins in postmitotic NPC formation, we used artificial beads conjugated with anti-GFP antibody, which captures GFP-fused proteins on the beads when incorporated into cells. Live CLEM imaging of telophase cells containing Nup133-coated beads or Nup153-coated beads showed that Nup133 and Nup153, as the sole effector molecules, assembled the NPC-like structure on the membrane fenestrations. Indirect immunofluorescence staining of the Nup133-coated beads showed that Nup133 effectively assembled Nup107 and ELYS, whereas minimal assembly of Nup98 and Nup62 was observed; the Nup153-coated bead effectively assembled Nup98, Nup62 and Pom121, but assembled neither Nup107 nor ELYS. Our results suggest that Nup133 and Nup153 play different roles in assembling the NPC on membrane fenestrations.
Collapse
Affiliation(s)
- Şükriye Bilir
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Tomoko Kojidani
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan.,Japan Women's University, Tokyo, Japan
| | - Chie Mori
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Hiroko Osakada
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Shouhei Kobayashi
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Takako Koujin
- Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan.,Advanced ICT Research Institute Kobe, National Institute of Information and Communications Technology (NICT), Kobe, Japan
| |
Collapse
|
57
|
Pain C, Kriechbaumer V, Kittelmann M, Hawes C, Fricker M. Quantitative analysis of plant ER architecture and dynamics. Nat Commun 2019; 10:984. [PMID: 30816109 PMCID: PMC6395764 DOI: 10.1038/s41467-019-08893-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 02/05/2019] [Indexed: 02/06/2023] Open
Abstract
The endoplasmic reticulum (ER) is a highly dynamic polygonal membrane network composed of interconnected tubules and sheets (cisternae) that forms the first compartment in the secretory pathway involved in protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signalling, and metabolon formation. Despite its central role in this plethora of biosynthetic, metabolic and physiological processes, there is little quantitative information on ER structure, morphology or dynamics. Here we describe a software package (AnalyzER) to automatically extract ER tubules and cisternae from multi-dimensional fluorescence images of plant ER. The structure, topology, protein-localisation patterns, and dynamics are automatically quantified using spatial, intensity and graph-theoretic metrics. We validate the method against manually-traced ground-truth networks, and calibrate the sub-resolution width estimates against ER profiles identified in serial block-face SEM images. We apply the approach to quantify the effects on ER morphology of drug treatments, abiotic stress and over-expression of ER tubule-shaping and cisternal-modifying proteins.
Collapse
Affiliation(s)
- Charlotte Pain
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Verena Kriechbaumer
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Maike Kittelmann
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Chris Hawes
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Mark Fricker
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK.
| |
Collapse
|
58
|
Krols M, Asselbergh B, De Rycke R, De Winter V, Seyer A, Müller FJ, Kurth I, Bultynck G, Timmerman V, Janssens S. Sensory neuropathy-causing mutations in ATL3 affect ER-mitochondria contact sites and impair axonal mitochondrial distribution. Hum Mol Genet 2019; 28:615-627. [PMID: 30339187 PMCID: PMC6360276 DOI: 10.1093/hmg/ddy352] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/22/2018] [Accepted: 09/28/2018] [Indexed: 11/25/2022] Open
Abstract
Axonopathies are neurodegenerative disorders caused by axonal degeneration, affecting predominantly the longest neurons. Several of these axonopathies are caused by genetic defects in proteins involved in the shaping and dynamics of the endoplasmic reticulum (ER); however, it is unclear how these defects impinge on neuronal survival. Given its central and widespread position within a cell, the ER is a pivotal player in inter-organelle communication. Here, we demonstrate that defects in the ER fusion protein ATL3, which were identified in patients suffering from hereditary sensory and autonomic neuropathy, result in an increased number of ER-mitochondria contact sites both in HeLa cells and in patient-derived fibroblasts. This increased contact is reflected in higher phospholipid metabolism, upregulated autophagy and augmented Ca2+ crosstalk between both organelles. Moreover, the mitochondria in these cells display lowered motility, and the number of axonal mitochondria in neurons expressing disease-causing mutations in ATL3 is strongly decreased. These results underscore the functional interdependence of subcellular organelles in health and disease and show that disorders caused by ER-shaping defects are more complex than previously assumed.
Collapse
Affiliation(s)
- Michiel Krols
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute Born Bunge, Antwerp, Belgium
| | - Bob Asselbergh
- VIB Center for Molecular Neurology, University of Antwerp, Antwerpen, Belgium
| | - Riet De Rycke
- VIB BioImaging Core, VIB, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- VIB Center for Inflammation Research, Ghent, Belgium
| | - Vicky De Winter
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute Born Bunge, Antwerp, Belgium
| | - Alexandre Seyer
- Profilomic SA, Boulogne-Billancourt, and MedDay Pharmaceuticals, Paris, France
| | - Franz-Josef Müller
- Zentrum für Integrative Psychiatrie, University Hospital Schleswig-Holstein, Kiel, Germany
- Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Geert Bultynck
- Laboratory of Molecular and Cellular Signaling, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Vincent Timmerman
- Peripheral Neuropathy Research Group, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Institute Born Bunge, Antwerp, Belgium
| | - Sophie Janssens
- Laboratory of ER Stress and Inflammation, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Internal Medicine, Ghent University, Ghent, Belgium
| |
Collapse
|
59
|
Wang N, Rapoport TA. Reconstituting the reticular ER network - mechanistic implications and open questions. J Cell Sci 2019; 132:132/4/jcs227611. [PMID: 30670475 DOI: 10.1242/jcs.227611] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The endoplasmic reticulum (ER) is a major membrane-bound organelle in all eukaryotic cells. This organelle comprises morphologically distinct domains, including the nuclear envelope and peripheral sheets and tubules. The tubules are connected by three-way junctions into a network. Several membrane proteins have been implicated in network formation; curvature-stabilizing proteins generate the tubules themselves, and membrane-anchored GTPases fuse tubules into a network. Recent experiments have shown that a tubular network can be formed with reconstituted proteoliposomes containing the yeast membrane-fusing GTPase Sey1 and a curvature-stabilizing protein of either the reticulon or REEP protein families. The network forms in the presence of GTP and is rapidly disassembled when GTP hydrolysis of Sey1 is inhibited, indicating that continuous membrane fusion is required for its maintenance. Atlastin, the ortholog of Sey1 in metazoans, forms a network on its own, serving both as a fusion and curvature-stabilizing protein. These results show that the reticular ER can be generated by a surprisingly small set of proteins, and represents an energy-dependent steady state between formation and disassembly. Models for the molecular mechanism by which curvature-stabilizing proteins cooperate with fusion GTPases to form a reticular network have been proposed, but many aspects remain speculative, including the function of additional proteins, such as the lunapark protein, and the mechanism by which the ER interacts with the cytoskeleton. How the nuclear envelope and peripheral ER sheets are formed remain major unresolved questions in the field. Here, we review reconstitution experiments with purified curvature-stabilizing proteins and fusion GTPases, discuss mechanistic implications and point out open questions.
Collapse
Affiliation(s)
- Ning Wang
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA
| |
Collapse
|
60
|
Agudo-Canalejo J, Knorr RL. Formation of Autophagosomes Coincides with Relaxation of Membrane Curvature. Methods Mol Biol 2019; 1880:173-188. [PMID: 30610696 DOI: 10.1007/978-1-4939-8873-0_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Autophagy is an intracellular degradation process that employs complex membrane dynamics to isolate and break down cellular components. However, many unanswered questions remain concerning remodeling of autophagic membranes. Here, we focus on the advantages of theoretical modeling to study the formation of autophagosomes and to understand the origin of autophagosomal membranes. Starting from the well-defined geometry of final autophagosomes, we ask the question of how these organelles can be formed by combining various pre-autophagosomal membranes such as vesicles, membrane tubules, or sheets. We analyze the geometric constraints of autophagosome formation by taking the area of the precursor membranes and their internal volume into account. Our results suggest that vesicle fusion contributes little to the formation of autophagosomes. In the second part, we quantify the curvature of the precursors and report that the formation of autophagosomes is associated with a strong relaxation of membrane curvature energy. This effect we find for a wide range of membrane asymmetries. It is especially strong for small distances between both autophagosomal membranes, as observed in vivo. We quantify the membrane bending energies of all precursors by considering membrane asymmetries. We propose that the generation and supply of pre-autophagosomal membranes is one limiting step for autophagosome formation.
Collapse
Affiliation(s)
- Jaime Agudo-Canalejo
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, UK.,Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
| | - Roland L Knorr
- Department of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany. .,Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Tokyo, Japan.
| |
Collapse
|
61
|
Reciprocal regulation between lunapark and atlastin facilitates ER three-way junction formation. Protein Cell 2018; 10:510-525. [PMID: 30498943 PMCID: PMC6588657 DOI: 10.1007/s13238-018-0595-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 10/23/2018] [Indexed: 11/12/2022] Open
Abstract
Three-way junctions are characteristic structures of the tubular endoplasmic reticulum (ER) network. Junctions are formed through atlastin (ATL)-mediated membrane fusion and stabilized by lunapark (Lnp). However, how Lnp is preferentially enriched at three-way junctions remains elusive. Here, we showed that Lnp loses its junction localization when ATLs are deleted. Reintroduction of ATL1 R77A and ATL3, which have been shown to cluster at the junctions, but not wild-type ATL1, relocates Lnp to the junctions. Mutations in the N-myristoylation site or hydrophobic residues in the coiled coil (CC1) of Lnp N-terminus (NT) cause mis-targeting of Lnp. Conversely, deletion of the lunapark motif in the C-terminal zinc finger domain, which affects the homo-oligomerization of Lnp, does not alter its localization. Purified Lnp-NT attaches to the membrane in a myristoylation-dependent manner. The mutation of hydrophobic residues in CC1 does not affect membrane association, but compromises ATL interactions. In addition, Lnp-NT inhibits ATL-mediated vesicle fusion in vitro. These results suggest that CC1 in Lnp-NT contacts junction-enriched ATLs for proper localization; subsequently, further ATL activity is limited by Lnp after the junction is formed. The proposed mechanism ensures coordinated actions of ATL and Lnp in generating and maintaining three-way junctions.
Collapse
|
62
|
Directed Supramolecular Organization of N-BAR Proteins through Regulation of H0 Membrane Immersion Depth. Sci Rep 2018; 8:16383. [PMID: 30401832 PMCID: PMC6219572 DOI: 10.1038/s41598-018-34273-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/11/2018] [Indexed: 11/12/2022] Open
Abstract
Many membrane remodeling events rely on the ability of curvature-generating N-BAR membrane proteins to organize into distinctive supramolecular configurations. Experiments have revealed a conformational switch in N-BAR proteins resulting in vesicular or tubular membrane shapes, with shallow membrane immersion of the H0 amphipathic helices of N-BAR proteins on vesicles but deep H0 immersion on tubes. We develop here a minimal elastic model of the local thinning of the lipid bilayer resulting from H0 immersion. Our model predicts that the observed conformational switch in N-BAR proteins produces a corresponding switch in the bilayer-mediated N-BAR interactions due to the H0 helices. In agreement with experiments, we find that bilayer-mediated H0 interactions oppose N-BAR multimerization for the shallow H0 membrane immersion depths measured on vesicles, but promote self-assembly of supramolecular N-BAR chains for the increased H0 membrane immersion depths measured on tubes. Finally, we consider the possibility that bilayer-mediated H0 interactions might contribute to the concerted structural reorganization of N-BAR proteins suggested by experiments. Our results indicate that the membrane immersion depth of amphipathic protein helices may provide a general molecular control parameter for membrane organization.
Collapse
|
63
|
Betancourt-Solis MA, Desai T, McNew JA. The atlastin membrane anchor forms an intramembrane hairpin that does not span the phospholipid bilayer. J Biol Chem 2018; 293:18514-18524. [PMID: 30287684 DOI: 10.1074/jbc.ra118.003812] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 09/27/2018] [Indexed: 12/27/2022] Open
Abstract
The endoplasmic reticulum (ER) is composed of flattened sheets and interconnected tubules that extend throughout the cytosol and makes physical contact with all other cytoplasmic organelles. This cytoplasmic distribution requires continuous remodeling. These discrete ER morphologies require specialized proteins that drive and maintain membrane curvature. The GTPase atlastin is required for homotypic fusion of ER tubules. All atlastin homologs possess a conserved domain architecture consisting of a GTPase domain, a three-helix bundle middle domain, a hydrophobic membrane anchor, and a C-terminal cytosolic tail. Here, we examined several Drosophila-human atlastin chimeras to identify functional domains of human atlastin-1 in vitro Although all chimeras could hydrolyze GTP, only chimeras containing the human C-terminal tail, hydrophobic segments, or both could fuse membranes in vitro We also determined that co-reconstitution of atlastin with reticulon does not influence GTPase activity or membrane fusion. Finally, we found that both human and Drosophila atlastin hydrophobic membrane anchors do not span the membrane, but rather form two intramembrane hairpin loops. The topology of these hairpins remains static during membrane fusion and does not appear to play an active role in lipid mixing.
Collapse
Affiliation(s)
| | - Tanvi Desai
- From the Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005
| | - James A McNew
- From the Department of Biochemistry and Cell Biology, Rice University, Houston, Texas 77005
| |
Collapse
|
64
|
Breuss MW, Nguyen A, Song Q, Nguyen T, Stanley V, James KN, Musaev D, Chai G, Wirth SA, Anzenberg P, George RD, Johansen A, Ali S, Zia-Ur-Rehman M, Sultan T, Zaki MS, Gleeson JG. Mutations in LNPK, Encoding the Endoplasmic Reticulum Junction Stabilizer Lunapark, Cause a Recessive Neurodevelopmental Syndrome. Am J Hum Genet 2018; 103:296-304. [PMID: 30032983 PMCID: PMC6080764 DOI: 10.1016/j.ajhg.2018.06.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/27/2018] [Indexed: 11/16/2022] Open
Abstract
The dynamic shape of the endoplasmic reticulum (ER) is a reflection of its wide variety of critical cell biological functions. Consequently, perturbation of ER-shaping proteins can cause a range of human phenotypes. Here, we describe three affected children (from two consanguineous families) who carry homozygous loss-of-function mutations in LNPK (previously known as KIAA1715); this gene encodes lunapark, which is proposed to serve as a curvature-stabilizing protein within tubular three-way junctions of the ER. All individuals presented with severe psychomotor delay, intellectual disability, hypotonia, epilepsy, and corpus callosum hypoplasia, and two of three showed mild cerebellar hypoplasia and atrophy. Consistent with a proposed role in neurodevelopmental disease, LNPK was expressed during brain development in humans and mice and was present in neurite-like processes in differentiating human neural progenitor cells. Affected cells showed the absence of full-length lunapark, aberrant ER structures, and increased luminal mass density. Together, our results implicate the ER junction stabilizer lunapark in establishing the corpus callosum.
Collapse
Affiliation(s)
- Martin W Breuss
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - An Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Qiong Song
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Thai Nguyen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Valentina Stanley
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Kiely N James
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Damir Musaev
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Guoliang Chai
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Sara A Wirth
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Paula Anzenberg
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Renee D George
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Anide Johansen
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA
| | - Shaila Ali
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Muhammad Zia-Ur-Rehman
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Tipu Sultan
- Department of Pediatric Neurology, Children's Hospital and Institute of Child Health, Lahore 54000, Pakistan
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Joseph G Gleeson
- Department of Neurosciences, Howard Hughes Medical Institute, University of California, San Diego, La Jolla, CA 92093, USA; Rady Children's Institute for Genomic Medicine, San Diego, CA 92025, USA.
| |
Collapse
|
65
|
Kriechbaumer V, Breeze E, Pain C, Tolmie F, Frigerio L, Hawes C. Arabidopsis Lunapark proteins are involved in ER cisternae formation. THE NEW PHYTOLOGIST 2018; 219:990-1004. [PMID: 29797722 PMCID: PMC6055799 DOI: 10.1111/nph.15228] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 04/17/2018] [Indexed: 05/04/2023]
Abstract
The plant endoplasmic reticulum (ER) is crucial to the maintenance of cellular homeostasis. The ER consists of a dynamic and continuously remodelling network of tubules and cisternae. Several conserved membrane proteins have been implicated in formation and maintenance of the ER network in plants, such as RHD3 and the reticulon proteins. Despite the recent work in mammalian and yeast cells, the detailed molecular mechanisms of ER network organization in plants remain largely unknown. Recently, novel ER network-shaping proteins called Lunapark (LNP) have been identified in yeast and mammalian cells. Here we identify two Arabidopsis LNP homologues and investigate their subcellular localization via confocal microscopy and potential function in shaping the ER network using protein-protein interaction assays and mutant analysis. We show that AtLNP1 overexpression in tobacco leaf epidermal cells mainly labels cisternae in the ER network, whereas AtLNP2 labels the whole ER. Overexpression of LNP proteins results in an increased abundance of ER cisternae and lnp1 and lnp1lnp2 amiRNA lines display a reduction in cisternae and larger polygonal areas. Thus, we hypothesize that AtLNP1 and AtLNP2 are involved in determining the network morphology of the plant ER, possibly by regulating the formation of ER cisternae.
Collapse
Affiliation(s)
- Verena Kriechbaumer
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Emily Breeze
- School of Life SciencesUniversity of WarwickGibbet HillCoventryCV4 7ALUK
| | - Charlotte Pain
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Frances Tolmie
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| | - Lorenzo Frigerio
- School of Life SciencesUniversity of WarwickGibbet HillCoventryCV4 7ALUK
| | - Chris Hawes
- Plant Cell Biology, Biological and Medical SciencesOxford Brookes UniversityOxfordOX3 0BPUK
| |
Collapse
|
66
|
DNA damage triggers tubular endoplasmic reticulum extension to promote apoptosis by facilitating ER-mitochondria signaling. Cell Res 2018; 28:833-854. [PMID: 30030520 PMCID: PMC6063967 DOI: 10.1038/s41422-018-0065-z] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Revised: 05/23/2018] [Accepted: 06/13/2018] [Indexed: 12/11/2022] Open
Abstract
The endoplasmic reticulum (ER) is composed of the nuclear envelope, perinuclear sheets and a peripheral tubular network. The peripheral ER and mitochondria form tight contacts at specific subdomains, which coordinate the functions of the two organelles and are required for multiple cellular processes such as Ca2+ transfer and apoptosis. However, it is largely unknown how ER morphology and ER-mitochondria signaling are dynamically regulated under different physiological or pathological conditions such as DNA damage. Here we show that the peripheral, tubular ER undergoes significant extension in response to DNA damage, and that this process is dependent on p53-mediated transcriptional activation of the ER-shaping proteins REEP1, REEP2 and EI24 (alias PIG8). This promotes the formation of ER-mitochondria contacts through EI24 and the mitochondrial outer membrane protein VDAC2, facilitates Ca2+ transfer from ER to mitochondria and promotes DNA damage-induced apoptosis. Thus, we identify a unique DNA damage response pathway involving alterations in ER morphology, ER-mitochondria signaling, and apoptosis.
Collapse
|
67
|
Abstract
Cui reflects on new coarse-grained simulations demonstrating that mitochondrial ATP synthase dimers spontaneously self-associate.
Collapse
Affiliation(s)
- Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, Boston, MA
| |
Collapse
|
68
|
Wang S, Powers RE, Gold VA, Rapoport TA. The ER morphology-regulating lunapark protein induces the formation of stacked bilayer discs. Life Sci Alliance 2018; 1:e201700014. [PMID: 30456344 PMCID: PMC6238531 DOI: 10.26508/lsa.201700014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 12/21/2017] [Accepted: 12/21/2017] [Indexed: 12/12/2022] Open
Abstract
Lunapark, an ER protein implicated in stabilizing junctions of the tubular network and regulating morphology changes during mitosis, forms stacked bilayer discs upon reconstitution with phospholipids. Lunapark (Lnp) is a conserved membrane protein that localizes to and stabilizes three-way junctions of the tubular ER network. In higher eukaryotes, phosphorylation of Lnp may contribute to the conversion of the ER from tubules to sheets during mitosis. Here, we report on the reconstitution of purified Lnp with phospholipids. Surprisingly, Lnp induces the formation of stacked membrane discs. Each disc is a bicelle, with Lnp sitting in the bilayer facing both directions. The interaction between bicelles is mediated by the cytosolic domains of Lnp, resulting in a constant distance between the discs. A phosphomimetic Lnp mutant shows reduced bicelle stacking. Based on these results, we propose that Lnp tethers ER membranes in vivo in a cell cycle–dependent manner. Lnp appears to be the first membrane protein that induces the formation of stacked bicelles.
Collapse
Affiliation(s)
- Songyu Wang
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Robert E Powers
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Vicki Am Gold
- Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Living Systems Institute, University of Exeter, Exeter, UK.,College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - Tom A Rapoport
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| |
Collapse
|
69
|
Georgiades P, Allan VJ, Wright GD, Woodman PG, Udommai P, Chung MA, Waigh TA. The flexibility and dynamics of the tubules in the endoplasmic reticulum. Sci Rep 2017; 7:16474. [PMID: 29184084 PMCID: PMC5705721 DOI: 10.1038/s41598-017-16570-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/10/2017] [Indexed: 12/27/2022] Open
Abstract
The endoplasmic reticulum (ER) is a single organelle in eukaryotic cells that extends throughout the cell and is involved in a large number of cellular functions. Using a combination of fixed and live cells (human MRC5 lung cells) in diffraction limited and super-resolved fluorescence microscopy (STORM) experiments, we determined that the average persistence length of the ER tubules was 3.03 ± 0.24 μm. Removing the branched network junctions from the analysis caused a slight increase in the average persistence length to 4.71 ± 0.14 μm, and provides the tubule's persistence length with a moderate length scale dependence. The average radius of the tubules was 44.1 ± 3.2 nm. The bending rigidity of the ER tubule membranes was found to be 10.9 ± 1.2 kT (17.0 ± 1.3 kT without branch points). We investigated the dynamic behaviour of ER tubules in live cells, and found that the ER tubules behaved like semi-flexible fibres under tension. The majority of the ER tubules experienced equilibrium transverse fluctuations under tension, whereas a minority number of them had active super-diffusive motions driven by motor proteins. Cells thus actively modulate the dynamics of the ER in a well-defined manner, which is expected in turn to impact on its many functions.
Collapse
Affiliation(s)
- Pantelis Georgiades
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK
| | - Victoria J Allan
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
| | - Graham D Wright
- IMB Microscopy Unit, Institute of Medical Biology, A*STAR, 8A Biomedical Grove, #06-06 Immunos, Singapore, 138648, Republic of Singapore
| | - Philip G Woodman
- Faculty of Biology, Medicine and Health, Michael Smith Building, The University of Manchester, Manchester, M13 9PT, UK
| | - Parinya Udommai
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Manloeng A Chung
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK
| | - Thomas A Waigh
- Biological Physics, School of Physics and Astronomy, The University of Manchester, Manchester, M13 9PL, UK.
- Photon Science Institute, Alan Turing Building, The University of Manchester, Oxford Rd., Manchester, M13 9PL, UK.
| |
Collapse
|
70
|
Abstract
Lipid membrane nanotubes are abundant in living cells, even though tubules are energetically less stable than sheet-like structures. According to membrane elastic theory, the tubular endoplasmic reticulum (ER), with its high area-to-volume ratio, appears to be particularly unstable. We explore how tubular membrane structures can nevertheless be induced and why they persist. In Monte Carlo simulations of a fluid-elastic membrane model subject to thermal fluctuations and without constraints on symmetry, we find that a steady increase in the area-to-volume ratio readily induces tubular structures. In simulations mimicking the ER wrapped around the cell nucleus, tubules emerge naturally as the membrane area increases. Once formed, a high energy barrier separates tubules from the thermodynamically favored sheet-like membrane structures. Remarkably, this barrier persists even at large area-to-volume ratios, protecting tubules against shape transformations despite enormous driving forces toward sheet-like structures. Molecular dynamics simulations of a molecular membrane model confirm the metastability of tubular structures. Volume reduction by osmotic regulation and membrane area growth by lipid production and by fusion of small vesicles emerge as powerful factors in the induction and stabilization of tubular membrane structures.
Collapse
Affiliation(s)
- Amir Houshang Bahrami
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics , Max-von-Laue Str. 3, 60438 Frankfurt am Main, Germany
- Institute for Biophysics, Goethe University Frankfurt , 60438 Frankfurt am Main, Germany
| |
Collapse
|
71
|
Lin C, White RR, Sparkes I, Ashwin P. Modeling Endoplasmic Reticulum Network Maintenance in a Plant Cell. Biophys J 2017; 113:214-222. [PMID: 28700920 PMCID: PMC5510808 DOI: 10.1016/j.bpj.2017.05.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 05/09/2017] [Accepted: 05/31/2017] [Indexed: 10/19/2022] Open
Abstract
The endoplasmic reticulum (ER) in plant cells forms a highly dynamic network of complex geometry. ER network morphology and dynamics are influenced by a number of biophysical processes, including filament/tubule tension, viscous forces, Brownian diffusion, and interactions with many other organelles and cytoskeletal elements. Previous studies have indicated that ER networks can be thought of as constrained minimal-length networks acted on by a variety of forces that perturb and/or remodel the network. Here, we study two specific biophysical processes involved in remodeling. One is the dynamic relaxation process involving a combination of tubule tension and viscous forces. The other is the rapid creation of cross-connection tubules by direct or indirect interactions with cytoskeletal elements. These processes are able to remodel the ER network: the first reduces network length and complexity whereas the second increases both. Using live cell imaging of ER network dynamics in tobacco leaf epidermal cells, we examine these processes on ER network dynamics. Away from regions of cytoplasmic streaming, we suggest that the dynamic network structure is a balance between the two processes, and we build an integrative model of the two processes for network remodeling. This model produces quantitatively similar ER networks to those observed in experiments. We use the model to explore the effect of parameter variation on statistical properties of the ER network.
Collapse
Affiliation(s)
- Congping Lin
- Center for Mathematical Sciences, Huazhong University of Science and Technology, Wuhan, China; Hubei Key Lab of Engineering Modeling and Scientific Computing, Huazhong University of Science and Technology, Wuhan, China; Department of Mathematics, University of Exeter, Exeter, United Kingdom.
| | - Rhiannon R White
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - Imogen Sparkes
- Department of Biosciences, University of Exeter, Exeter, United Kingdom; School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Peter Ashwin
- Department of Mathematics, University of Exeter, Exeter, United Kingdom
| |
Collapse
|
72
|
Fedorov EG, Shemesh T. Physical Model for Stabilization and Repair of Trans-endothelial Apertures. Biophys J 2017; 112:388-397. [PMID: 28122224 DOI: 10.1016/j.bpj.2016.11.3207] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 11/16/2016] [Accepted: 11/28/2016] [Indexed: 01/13/2023] Open
Abstract
Bacterial toxins that disrupt the stability of contractile structures in endothelial cells promote the opening of large-scale apertures, thereby breaching the endothelium barrier. These apertures are formed by fusion of the basal and apical membranes into a tunnel that spans the height of the cell. Subsequent to the aperture formation, an active repair process, driven by a stimulated polymerization of actin, results in asymmetrical membrane protrusions and, ultimately, the closure of the aperture. Here, we propose a physics-based model for the generation, stabilization and repair of trans-endothelial apertures. Our model is based on the mechanical interplay between tension in the plasma membrane and stresses that develop within different actin structures at the aperture's periphery. We suggest that accumulation of cytoskeletal fragments around the aperture's rim during the expansion phase results in parallel bundles of actin filaments and myosin motors, generating progressively greater contraction forces that resist further expansion of the aperture. Our results indicate that closure of the tunnel is driven by mechanical stresses that develop within a cross-linked actin gel that forms at localized regions of the aperture periphery. We show that stresses within the gel are due to continuous polymerization of actin filaments against the membrane surfaces of the aperture's edges. Based on our mechanical model, we construct a dynamic simulation of the aperture repair process. Our model fully accounts for the phenomenology of the trans-endothelial aperture formation and stabilization, and recaptures the experimentally observed asymmetry of the intermediate aperture shapes during closure. We make experimentally testable predictions for localization of myosin motors to the tunnel periphery and of adhesion complexes to the edges of apertures undergoing closure, and we estimate the minimal nucleation size of cross-linked actin gel that can lead to a successful repair of the aperture.
Collapse
Affiliation(s)
- Eduard G Fedorov
- Department of Biology, Israel Institute of Technology, Haifa, Israel
| | - Tom Shemesh
- Department of Biology, Israel Institute of Technology, Haifa, Israel.
| |
Collapse
|
73
|
Tarasenko D, Barbot M, Jans DC, Kroppen B, Sadowski B, Heim G, Möbius W, Jakobs S, Meinecke M. The MICOS component Mic60 displays a conserved membrane-bending activity that is necessary for normal cristae morphology. J Cell Biol 2017; 216:889-899. [PMID: 28254827 PMCID: PMC5379949 DOI: 10.1083/jcb.201609046] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 01/04/2017] [Accepted: 01/13/2017] [Indexed: 12/16/2022] Open
Abstract
The multisubunit mitochondrial contact site and cristae organizing system (MICOS) plays an important role in cristae junction formation. Tarasenko et al. show that the MICOS component Mic60 actively bends membranes and that this activity is evolutionarily conserved and necessary for cristae structure. The inner membrane (IM) of mitochondria displays an intricate, highly folded architecture and can be divided into two domains: the inner boundary membrane adjacent to the outer membrane and invaginations toward the matrix, called cristae. Both domains are connected by narrow, tubular membrane segments called cristae junctions (CJs). The formation and maintenance of CJs is of vital importance for the organization of the mitochondrial IM and for mitochondrial and cellular physiology. The multisubunit mitochondrial contact site and cristae organizing system (MICOS) was found to be a major factor in CJ formation. In this study, we show that the MICOS core component Mic60 actively bends membranes and, when inserted into prokaryotic membranes, induces the formation of cristae-like plasma membrane invaginations. The intermembrane space domain of Mic60 has a lipid-binding capacity and induces membrane curvature even in the absence of the transmembrane helix. Mic60 homologues from α-proteobacteria display the same membrane deforming activity and are able to partially overcome the deletion of Mic60 in eukaryotic cells. Our results show that membrane bending by Mic60 is an ancient mechanism, important for cristae formation, and had already evolved before α-proteobacteria developed into mitochondria.
Collapse
Affiliation(s)
- Daryna Tarasenko
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Mariam Barbot
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Daniel C Jans
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany.,Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Benjamin Kroppen
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany
| | - Boguslawa Sadowski
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Gudrun Heim
- Electron Microscopy Facility, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Wiebke Möbius
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany.,Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), 37073 Göttingen, Germany
| | - Stefan Jakobs
- Department of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany.,Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Michael Meinecke
- Department of Cellular Biochemistry, University Medical Center Göttingen, 37073 Göttingen, Germany .,European Neuroscience Institute Göttingen, 37077 Göttingen, Germany.,Göttinger Zentrum für Molekulare Biowissenschaften, 37077 Göttingen, Germany
| |
Collapse
|
74
|
Reconstitution of the tubular endoplasmic reticulum network with purified components. Nature 2017; 543:257-260. [PMID: 28225760 PMCID: PMC5853125 DOI: 10.1038/nature21387] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 01/10/2017] [Indexed: 12/22/2022]
Abstract
Organelles display characteristic morphologies that are intimately tied to their cellular function, but how organelles are shaped is poorly understood. The endoplasmic reticulum (ER) is particularly intriguing, as it is comprised of morphologically distinct domains, including a dynamic network of interconnected membrane tubules. Several membrane proteins have been implicated in network formation1–5, but how exactly they mediate network formation and whether they are all required is unclear. Here, we have reconstituted a dynamic tubular membrane network with purified ER proteins. Proteoliposomes containing the membrane-fusing GTPase Sey1p6,7 and the curvature-stabilizing protein Yop1p8,9 from Saccharomyces cerevisiae form a tubular network upon GTP addition. The tubules rapidly fragment when GTP hydrolysis of Sey1p is inhibited, indicating that network maintenance requires continuous membrane fusion and that Yop1p favors the generation of highly curved membrane structures. Sey1p also forms networks with other curvature-stabilizing proteins, including reticulon8 and REEP10 proteins from different species. Atlastin, the vertebrate ortholog of Sey1p6,11, forms a GTP-hydrolysis dependent network on its own, serving as both a fusion and curvature-stabilizing protein. Our results show that organelle shape can be generated by a surprisingly small set of proteins and represents an energy-dependent steady state between formation and disassembly.
Collapse
|
75
|
Griffing LR, Lin C, Perico C, White RR, Sparkes I. Plant ER geometry and dynamics: biophysical and cytoskeletal control during growth and biotic response. PROTOPLASMA 2017; 254:43-56. [PMID: 26862751 PMCID: PMC5216105 DOI: 10.1007/s00709-016-0945-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 01/13/2016] [Indexed: 05/20/2023]
Abstract
The endoplasmic reticulum (ER) is an intricate and dynamic network of membrane tubules and cisternae. In plant cells, the ER 'web' pervades the cortex and endoplasm and is continuous with adjacent cells as it passes through plasmodesmata. It is therefore the largest membranous organelle in plant cells. It performs essential functions including protein and lipid synthesis, and its morphology and movement are linked to cellular function. An emerging trend is that organelles can no longer be seen as discrete membrane-bound compartments, since they can physically interact and 'communicate' with one another. The ER may form a connecting central role in this process. This review tackles our current understanding and quantification of ER dynamics and how these change under a variety of biotic and developmental cues.
Collapse
Affiliation(s)
- Lawrence R Griffing
- Biology Department, Texas A&M University, 3258 TAMU, College Station, TX, 77843, USA
| | - Congping Lin
- Mathematics Research Institute, Harrison Building, University of Exeter, Exeter, EX4 4QF, UK
| | - Chiara Perico
- Biosciences, CLES, Exeter University, Geoffrey Pope Building, Stocker Rd, Exeter, EX4 4QD, UK
| | - Rhiannon R White
- Biosciences, CLES, Exeter University, Geoffrey Pope Building, Stocker Rd, Exeter, EX4 4QD, UK
| | - Imogen Sparkes
- Biosciences, CLES, Exeter University, Geoffrey Pope Building, Stocker Rd, Exeter, EX4 4QD, UK.
| |
Collapse
|
76
|
Biwer LA, Isakson BE. Endoplasmic reticulum-mediated signalling in cellular microdomains. Acta Physiol (Oxf) 2017; 219:162-175. [PMID: 26973141 DOI: 10.1111/apha.12675] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/01/2015] [Accepted: 03/01/2016] [Indexed: 12/17/2022]
Abstract
The endoplasmic reticulum (ER) is a prime mediator of cellular signalling due to its functions as an internal cellular store for calcium, as well as a site for synthesis of proteins and lipids. Its peripheral network of sheets and tubules facilitates calcium and lipid signalling, especially in areas of the cell that are more distant to the main cytoplasmic network. Specific membrane proteins shape the peripheral ER architecture and influence the network stability to project into restricted spaces. The signalling microdomains are anatomically separate from the cytoplasm as a whole and exhibit localized protein, ion channel and cytoskeletal element expression. Signalling can also occur between the ER and other organelles, such as the Golgi or mitochondria. Lipids made in the ER membrane can be sent to the Golgi via specialized transfer proteins and specific phospholipid synthases are enriched at ER-mitochondria junctions to more efficiently expedite phospholipid transfer. As a hub for protein and lipid synthesis, a store for intracellular calcium [Ca2+ ]i and a mediator of cellular stress, the ER is an important cellular organelle. Its ability to organize into tubules and project into restricted spaces allows for discrete and temporal signalling, which is important for cellular physiology and organism homoeostasis.
Collapse
Affiliation(s)
- L. A. Biwer
- Department of Molecular Physiology and Biophysics; University of Virginia; Charlottesville VA USA
- Robert M. Berne Cardiovascular Research Center; University of Virginia School of Medicine; Charlottesville VA USA
| | - B. E. Isakson
- Department of Molecular Physiology and Biophysics; University of Virginia; Charlottesville VA USA
- Robert M. Berne Cardiovascular Research Center; University of Virginia School of Medicine; Charlottesville VA USA
| |
Collapse
|
77
|
Joshi AS, Huang X, Choudhary V, Levine TP, Hu J, Prinz WA. A family of membrane-shaping proteins at ER subdomains regulates pre-peroxisomal vesicle biogenesis. J Cell Biol 2016; 215:515-529. [PMID: 27872254 PMCID: PMC5119935 DOI: 10.1083/jcb.201602064] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/29/2016] [Accepted: 10/21/2016] [Indexed: 11/22/2022] Open
Abstract
Saccharomyces cerevisiae contains three conserved reticulon and reticulon-like proteins that help maintain ER structure by stabilizing high membrane curvature in ER tubules and the edges of ER sheets. A mutant lacking all three proteins has dramatically altered ER morphology. We found that ER shape is restored in this mutant when Pex30p or its homologue Pex31p is overexpressed. Pex30p can tubulate membranes both in cells and when reconstituted into proteoliposomes, indicating that Pex30p is a novel ER-shaping protein. In contrast to the reticulons, Pex30p is low abundance, and we found that it localizes to subdomains in the ER. We show that these ER subdomains are the sites where most preperoxisomal vesicles (PPVs) are generated. In addition, overproduction or deletion of Pex30p or Pex31p alters the size, shape, and number of PPVs. Our findings suggest that Pex30p and Pex31p help shape and generate regions of the ER where PPV biogenesis occurs.
Collapse
Affiliation(s)
- Amit S Joshi
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Xiaofang Huang
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.,Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China
| | - Vineet Choudhary
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Tim P Levine
- University College London Institute of Ophthalmology, London EC1V 9EL, England, UK
| | - Junjie Hu
- Department of Genetics and Cell Biology, College of Life Sciences, Nankai University, Tianjin 300071, China.,Tianjin Key Laboratory of Protein Science, Nankai University, Tianjin 300071, China.,National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - William A Prinz
- Laboratory of Cell and Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
78
|
Nixon-Abell J, Obara CJ, Weigel AV, Li D, Legant WR, Xu CS, Pasolli HA, Harvey K, Hess HF, Betzig E, Blackstone C, Lippincott-Schwartz J. Increased spatiotemporal resolution reveals highly dynamic dense tubular matrices in the peripheral ER. Science 2016; 354:aaf3928. [PMID: 27789813 PMCID: PMC6528812 DOI: 10.1126/science.aaf3928] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 09/16/2016] [Indexed: 12/12/2022]
Abstract
The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle that plays crucial roles in numerous cellular functions. We used emerging superresolution imaging technologies to clarify the morphology and dynamics of the peripheral ER, which contacts and modulates most other intracellular organelles. Peripheral components of the ER have classically been described as comprising both tubules and flat sheets. We show that this system consists almost exclusively of tubules at varying densities, including structures that we term ER matrices. Conventional optical imaging technologies had led to misidentification of these structures as sheets because of the dense clustering of tubular junctions and a previously uncharacterized rapid form of ER motion. The existence of ER matrices explains previous confounding evidence that had indicated the occurrence of ER "sheet" proliferation after overexpression of tubular junction-forming proteins.
Collapse
Affiliation(s)
- Jonathon Nixon-Abell
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA. Department of Pharmacology, UCL School of Pharmacy, University College London, London, UK
| | - Christopher J Obara
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA. Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Aubrey V Weigel
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA. Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Dong Li
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA. National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Wesley R Legant
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - C Shan Xu
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - H Amalia Pasolli
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Kirsten Harvey
- Department of Pharmacology, UCL School of Pharmacy, University College London, London, UK
| | - Harald F Hess
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Craig Blackstone
- Cell Biology Section, Neurogenetics Branch, National Institute of Neurological Disorders and Stroke (NINDS), Bethesda, MD, USA.
| | - Jennifer Lippincott-Schwartz
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), Bethesda, MD, USA. Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA.
| |
Collapse
|
79
|
Barbot M, Meinecke M. Reconstitutions of mitochondrial inner membrane remodeling. J Struct Biol 2016; 196:20-28. [DOI: 10.1016/j.jsb.2016.07.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 07/20/2016] [Accepted: 07/21/2016] [Indexed: 02/03/2023]
|
80
|
Abstract
Three proteins work together to control the shape of the endoplasmic reticulum in animal cells.
Collapse
Affiliation(s)
- Craig Blackstone
- National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States
| | - William A Prinz
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, United States
| |
Collapse
|
81
|
Wang S, Tukachinsky H, Romano FB, Rapoport TA. Cooperation of the ER-shaping proteins atlastin, lunapark, and reticulons to generate a tubular membrane network. eLife 2016; 5. [PMID: 27619977 PMCID: PMC5021524 DOI: 10.7554/elife.18605] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 07/28/2016] [Indexed: 12/29/2022] Open
Abstract
In higher eukaryotes, the endoplasmic reticulum (ER) contains a network of membrane tubules, which transitions into sheets during mitosis. Network formation involves curvature-stabilizing proteins, including the reticulons (Rtns), as well as the membrane-fusing GTPase atlastin (ATL) and the lunapark protein (Lnp). Here, we have analyzed how these proteins cooperate. ATL is needed to not only form, but also maintain, the ER network. Maintenance requires a balance between ATL and Rtn, as too little ATL activity or too high Rtn4a concentrations cause ER fragmentation. Lnp only affects the abundance of three-way junctions and tubules. We suggest a model in which ATL-mediated fusion counteracts the instability of free tubule ends. ATL tethers and fuses tubules stabilized by the Rtns, and transiently sits in newly formed three-way junctions. Lnp subsequently moves into the junctional sheets and forms oligomers. Lnp is inactivated by mitotic phosphorylation, which contributes to the tubule-to-sheet conversion of the ER.
Collapse
Affiliation(s)
- Songyu Wang
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Hanna Tukachinsky
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Fabian B Romano
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| | - Tom A Rapoport
- Howard Hughes Medical Institute, Harvard Medical School, Boston, United States.,Department of Cell Biology, Harvard Medical School, Boston, United States
| |
Collapse
|
82
|
Zhao Y, Zhang T, Huo H, Ye Y, Liu Y. Lunapark Is a Component of a Ubiquitin Ligase Complex Localized to the Endoplasmic Reticulum Three-way Junctions. J Biol Chem 2016; 291:18252-62. [PMID: 27387505 DOI: 10.1074/jbc.m116.737783] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Indexed: 11/06/2022] Open
Abstract
The endoplasmic reticulum (ER) network comprises sheets and tubules that are connected by dynamic three-way junctions. Lunapark (Lnp) localizes to and stabilizes ER three-way junctions by antagonizing the small GTPase Atlastin, but how Lnp shapes the ER network is unclear. Here, we used an affinity purification approach and mass spectrometry to identify Lnp as an interacting partner of the ER protein quality control ubiquitin ligase gp78. Accordingly, Lnp purified from mammalian cells has a ubiquitin ligase activity in vitro Intriguingly, biochemical analyses show that this activity can be attributed not only to associated ubiquitin ligase, but also to an intrinsic ubiquitin ligase activity borne by Lnp itself. This activity is contained in the N-terminal 45 amino acids of Lnp although this segment does not share homology to any known ubiquitin ligase motifs. Despite its interaction with gp78, Lnp does not seem to have a broad function in degradation of misfolded ER proteins. On the other hand, the N-terminal ubiquitin ligase-bearing motif is required for the ER three-way junction localization of Lnp. Our study identifies a new type of ubiquitin ligase and reveals a potential link between ubiquitin and ER morphology regulation.
Collapse
Affiliation(s)
- Yupeng Zhao
- From the School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Shanghai 201210, China and
| | - Ting Zhang
- the Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Huanhuan Huo
- From the School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Shanghai 201210, China and
| | - Yihong Ye
- the Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892
| | - Yanfen Liu
- From the School of Life Science and Technology, ShanghaiTech University, 100 Haike Rd., Shanghai 201210, China and
| |
Collapse
|
83
|
Zhang H, Hu J. Shaping the Endoplasmic Reticulum into a Social Network. Trends Cell Biol 2016; 26:934-943. [PMID: 27339937 DOI: 10.1016/j.tcb.2016.06.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/25/2016] [Accepted: 06/02/2016] [Indexed: 10/21/2022]
Abstract
In eukaryotic cells, the endoplasmic reticulum (ER) is constructed as a network of tubules and sheets that exist in one continuous membrane system. Several classes of integral membrane protein have been shown to shape ER membranes. Functional studies using mutant proteins have begun to reveal the significance of ER morphology and membrane dynamics. In this review, we discuss the common protein modules and mechanisms that generate the characteristic shape of the ER. We also describe the cellular functions closely related to ER morphology, particularly contacts with other membrane systems, and their potential roles in the development of multicellular organisms.
Collapse
Affiliation(s)
- Hong Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Junjie Hu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| |
Collapse
|
84
|
Shaping the endoplasmic reticulum in vitro. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:2035-2040. [PMID: 27287725 DOI: 10.1016/j.bbamem.2016.06.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 06/02/2016] [Accepted: 06/05/2016] [Indexed: 11/22/2022]
Abstract
Organelles in eukaryotic cells often have complex shapes that deviate significantly from simple spheres. A prime example is the endoplasmic reticulum (ER) that forms an extensive network of membrane tubules in many mammalian cell types and in reconstitution assays in vitro. Despite the successful hunt for molecular determinants of ER shape we are still far from having a comprehensive understanding of ER network morphogenesis. Here, we have studied the hitherto neglected influence of the host substrate when reconstituting ER networks in vitro as compared to ER networks in vivo. In culture cells we observed cytoplasm-spanning ER networks with tubules being connected almost exclusively by three-way junctions and segment lengths being narrowly distributed around a mean length of about 1μm. In contrast, networks reconstituted from purified ER microsomes on flat glass or gel substrates of varying stiffness showed significantly broader length distributions with an up to fourfold larger mean length. Self-assembly of ER microsomes on small oil droplets, however, yielded networks that resembled more closely the native ER network of mammalian cells. We conclude from these observations that the ER microsomes' inherent self-assembly capacity is sufficient to support network formation with a native geometry if the influence of the host substrate's surface chemistry becomes negligible. We hypothesize that under these conditions the networks' preference for three-way junctions follows from creating 'starfish-shaped' vesicles when ER microsomes with a protein-induced spontaneous curvature undergo fusion.
Collapse
|
85
|
Fusion of the endoplasmic reticulum by membrane-bound GTPases. Semin Cell Dev Biol 2016; 60:105-111. [PMID: 27269373 DOI: 10.1016/j.semcdb.2016.06.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum (ER) membrane forms an elaborate network of tubules and sheets that is continuously remodeled. This dynamic behavior requires membrane fusion that is mediated by dynamin-like GTPases: the atlastins in metazoans and Sey1p and related proteins in yeast and plants. Crystal structures of the cytosolic domains of these membrane proteins and biochemical experiments can now be integrated into a model that explains many aspects of the molecular mechanism by which these membrane-bound GTPases mediate membrane fusion.
Collapse
|
86
|
Schweitzer Y, Shemesh T, Kozlov MM. A Model for Shaping Membrane Sheets by Protein Scaffolds. Biophys J 2016; 109:564-73. [PMID: 26244738 DOI: 10.1016/j.bpj.2015.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 05/31/2015] [Accepted: 06/02/2015] [Indexed: 01/16/2023] Open
Abstract
Membranes of peripheral endoplasmic reticulum form intricate morphologies consisting of tubules and sheets as basic elements. The physical mechanism of endoplasmic-reticulum shaping has been suggested to originate from the elastic behavior of the sheet edges formed by linear arrays of oligomeric protein scaffolds. The heart of this mechanism, lying in the relationships between the structure of the protein scaffolds and the effective intrinsic shapes and elastic properties of the sheets' edges, has remained hypothetical. Here we provide a detailed computational analysis of these issues. By minimizing the elastic energy of membrane bending, we determine the effects of a rowlike array of semicircular arclike membrane scaffolds on generation of a membrane fold, which shapes the entire membrane surface into a flat double-membrane sheet. We show, quantitatively, that the sheet's edge line tends to adopt a positive or negative curvature depending on the scaffold's geometrical parameters. We compute the effective elastic properties of the sheet edge and analyze the dependence of the equilibrium distance between the scaffolds along the edge line on the scaffold geometry.
Collapse
Affiliation(s)
- Yonatan Schweitzer
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel; Nuclear Physics Division, Soreq Nuclear Research Center, Yavne, Israel
| | - Tom Shemesh
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa, Israel
| | - Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
| |
Collapse
|
87
|
APEX Fingerprinting Reveals the Subcellular Localization of Proteins of Interest. Cell Rep 2016; 15:1837-47. [DOI: 10.1016/j.celrep.2016.04.064] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/01/2016] [Accepted: 04/17/2016] [Indexed: 12/13/2022] Open
|
88
|
Piña FJ, Fleming T, Pogliano K, Niwa M. Reticulons Regulate the ER Inheritance Block during ER Stress. Dev Cell 2016; 37:279-88. [PMID: 27117666 DOI: 10.1016/j.devcel.2016.03.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 03/07/2016] [Accepted: 03/28/2016] [Indexed: 01/05/2023]
Abstract
Segregation of functional organelles during the cell cycle is crucial to generate healthy daughter cells. In Saccharomyces cerevisiae, ER stress causes an ER inheritance block to ensure cells inherit a functional ER. Here, we report that formation of tubular ER in the mother cell, the first step in ER inheritance, depends on functional symmetry between the cortical ER (cER) and perinuclear ER (pnER). ER stress induces functional asymmetry, blocking tubular ER formation and ER inheritance. Using fluorescence recovery after photobleaching, we show that the ER chaperone Kar2/BiP fused to GFP and an ER membrane reporter, Hmg1-GFP, behave differently in the cER and pnER. The functional asymmetry and tubular ER formation depend on Reticulons/Yop1, which maintain ER structure. LUNAPARK1 deletion in rtn1Δrtn2Δyop1Δ cells restores the pnER/cER functional asymmetry, tubular ER generation, and ER inheritance blocks. Thus, Reticulon/Yop1-dependent changes in ER structure are linked to ER inheritance during the yeast cell cycle.
Collapse
Affiliation(s)
- Francisco Javier Piña
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 5328, La Jolla, CA 92093-0377, USA
| | - Tinya Fleming
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 4113, La Jolla, CA 92093-0377, USA
| | - Kit Pogliano
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 4113, La Jolla, CA 92093-0377, USA
| | - Maho Niwa
- Section of Molecular Biology, Division of Biological Sciences, University of California, San Diego, NSB#1, Room 5328, La Jolla, CA 92093-0377, USA.
| |
Collapse
|
89
|
Closing a gap in the nuclear envelope. Curr Opin Cell Biol 2016; 40:90-97. [PMID: 27016712 DOI: 10.1016/j.ceb.2016.03.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/13/2016] [Accepted: 03/05/2016] [Indexed: 11/22/2022]
Abstract
The nuclear envelope (NE) ensures nucleo-cytoplasmic compartmentalization, with trafficking of macromolecules across this double membrane controlled by embedded nuclear pore complexes (NPCs). The NE and associated proteins are dismantled during open mitosis and reestablishment of this barrier during mitotic exit requires dynamic remodeling of endoplasmic reticulum (ER) membranes and coordination with NPC reformation, with NPC deposition continuing during subsequent interphase. In this review, we discuss recent progress in our understanding of NE reformation and nuclear pore complex generation, with special focus on work implicating the endosomal sorting complex required for transport (ESCRT) membrane remodeling machinery in these events.
Collapse
|
90
|
ER sheet–tubule balance is regulated by an array of actin filaments and microtubules. Exp Cell Res 2015; 337:170-8. [DOI: 10.1016/j.yexcr.2015.04.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/13/2015] [Indexed: 12/28/2022]
|
91
|
Schweitzer Y, Kozlov MM. Membrane-mediated interaction between strongly anisotropic protein scaffolds. PLoS Comput Biol 2015; 11:e1004054. [PMID: 25710602 PMCID: PMC4339200 DOI: 10.1371/journal.pcbi.1004054] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 11/21/2014] [Indexed: 12/29/2022] Open
Abstract
Specialized proteins serve as scaffolds sculpting strongly curved membranes of intracellular organelles. Effective membrane shaping requires segregation of these proteins into domains and is, therefore, critically dependent on the protein-protein interaction. Interactions mediated by membrane elastic deformations have been extensively analyzed within approximations of large inter-protein distances, small extents of the protein-mediated membrane bending and small deviations of the protein shapes from isotropic spherical segments. At the same time, important classes of the realistic membrane-shaping proteins have strongly elongated shapes with large and highly anisotropic curvature. Here we investigated, computationally, the membrane mediated interaction between proteins or protein oligomers representing membrane scaffolds with strongly anisotropic curvature, and addressed, quantitatively, a specific case of the scaffold geometrical parameters characterizing BAR domains, which are crucial for membrane shaping in endocytosis. In addition to the previously analyzed contributions to the interaction, we considered a repulsive force stemming from the entropy of the scaffold orientation. We computed this interaction to be of the same order of magnitude as the well-known attractive force related to the entropy of membrane undulations. We demonstrated the scaffold shape anisotropy to cause a mutual aligning of the scaffolds and to generate a strong attractive interaction bringing the scaffolds close to each other to equilibrium distances much smaller than the scaffold size. We computed the energy of interaction between scaffolds of a realistic geometry to constitute tens of kBT, which guarantees a robust segregation of the scaffolds into domains.
Collapse
Affiliation(s)
- Yonatan Schweitzer
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michael M. Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
| |
Collapse
|