Membranes and Cellular Functions

Publications

Year of publication 2019

Mijo Simunovic, Emma Evergren, Andrew Callan-Jones*, Patricia Bassereau* (2019 Oct 7)

Curving Cells Inside and Out: Roles of BAR Domain Proteins in Membrane Shaping and Its Cellular Implications.

Annual Review of Cell and Developmental Biology : 35 : DOI : 10.1146/annurev-cellbio-100617-060558 Learn more
Summary

Many cellular processes rely on precise and timely deformation of the cell membrane. While many proteins participate in membrane reshaping and scission, usually in highly specialized ways, Bin/amphiphysin/Rvs (BAR) domain proteins play a pervasive role, as they not only participate in many aspects of cell trafficking but also are highly versatile membrane remodelers. Subtle changes in the shape and size of the BAR domain can greatly impact the way in which BAR domain proteins interact with the membrane. Furthermore, the activity of BAR domain proteins can be tuned by external physical parameters, and so they behave differently depending on protein surface density, membrane tension, or membrane shape. These proteins can form 3D structures that mold the membrane and alter its liquid properties, even promoting scission under various circumstances. As such, BAR domain proteins have numerous roles within the cell. Endocytosis is among the most highly studied processes in which BAR domain proteins take on important roles. Over the years, a more complete picture has emerged in which BAR domain proteins are tied to almost all intracellular compartments; examples include endosomal sorting and tubular networks in the endoplasmic reticulum and T-tubules. These proteins also have a role in autophagy, and their activity has been linked with cancer. Here, we briefly review the history of BAR domain protein discovery, discuss the mechanisms by which BAR domain proteins induce curvature, and attempt to settle important controversies in the field. Finally, we review BAR domain proteins in the context of a cell, highlighting their emerging roles in cell signaling and organelle shaping.

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Zack Jarin, Feng-Ching Tsai, Aram Davtyan, Alexander J.Pak, Patricia Bassereau, Gregory A.Voth (2019 Aug 6)

Unusual Organization of I-BAR Proteins on Tubular and Vesicular Membranes.

Biophysical Journal : 117 : 553-562 : DOI : 10.1016/j.bpj.2019.06.025 Learn more
Summary

Protein-mediated membrane remodeling is a ubiquitous and critical process for proper cellular function. Inverse Bin/Amphiphysin/Rvs (I-BAR) domains drive local membrane deformation as a precursor to large-scale membrane remodeling. We employ a multiscale approach to provide the molecular mechanism of unusual I-BAR domain-driven membrane remodeling at a low protein surface concentration with near-atomistic detail. We generate a bottom-up coarse-grained model that demonstrates similar membrane-bound I-BAR domain aggregation behavior as our recent Mesoscopic Membrane with Explicit Proteins model. Together, these models bridge several length scales and reveal an aggregation behavior of I-BAR domains. We find that at low surface coverage (i.e., low bound protein density), I-BAR domains form transient, tip-to-tip strings on periodic flat membrane sheets. Inside of lipid bilayer tubules, we find linear aggregates parallel to the axis of the tubule. Finally, we find that I-BAR domains form tip-to-tip aggregates around the edges of membrane domes. These results are supported by in vitro experiments showing low curvature bulges surrounded by I-BAR domains on giant unilamellar vesicles. Overall, our models reveal new I-BAR domain aggregation behavior in membrane tubules and on the surface of vesicles at low surface concentration that add insight into how I-BAR domain proteins may contribute to certain aspects of membrane remodeling in cells.

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Nicola de Franceschi, Maryam Alqabandi, Winfried Weissenhorn, Patricia Bassereau (2019 Jul 5)

Dynamic and Sequential Protein Reconstitution on Negatively Curved Membranes by Giant Vesicles Fusion.

Bio-Protocol : 9 : e3294 : DOI : 10.21769/BioProtoc.3294 Learn more
Summary

In vitro investigation of the interaction between proteins and positively curved membranes can be performed using a classic nanotube pulling method. However, characterizing protein interaction with negatively curved membranes still represents a formidable challenge. Here, we describe our recently developed approach based on laser-triggered Giant Unilamellar Vesicles (GUVs) fusion. Our protocol allows sequential addition of proteins to a negatively curved membrane, while at the same time controlling the buffer composition, lipid composition and membrane tension. Moreover, this method does not require a step of protein detachment, greatly simplifying the process of protein encapsulation over existing methods.

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Elena Beltrán-Heredia, Feng-Ching Tsai, Samuel Salinas-Almaguer, Francisco J. Cao*, Patricia Bassereau*, Francisco Monroy* (2019 Jun 20)

Membrane curvature induces cardiolipin sorting.

Communications Biology : 2 : 225 : DOI : 10.1038/s42003-019-0471-x Learn more
Summary

Cardiolipin is a cone-shaped lipid predominantly localized in curved membrane sites of bacteria and in the mitochondrial cristae. This specific localization has been argued to be geometry-driven, since the CL’s conical shape relaxes curvature frustration. Although previous evidence suggests a coupling between CL concentration and membrane shape in vivo, no precise experimental data are available for curvature-based CL sorting in vitro. Here, we test this hypothesis in experiments that isolate the effects of membrane curvature in lipid-bilayer nanotubes. CL sorting is observed with increasing tube curvature, reaching a maximum at optimal CL concentrations, a fact compatible with self-associative clustering. Observations are compatible with a model of membrane elasticity including van der Waals entropy, from which a negative intrinsic curvature of -1.1 nm-1 is predicted for CL. The results contribute to understanding the physicochemical interplay between membrane curvature and composition, providing key insights into mitochondrial and bacterial membrane organization and dynamics.

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Joanna Podkalicka, Patricia Bassereau (2019 Apr 1)

How membrane physics rules the HIV envelope.

Nature Cell Biology : 21 : 413–415 : DOI : 10.1038/s41556-019-0312-7 Learn more
Summary

HIV particles incorporate host membrane proteins into their envelope to evade the immune system and infect other cells. A study now shows that Gag assembly on the host cell membrane produces a raft-like nanodomain favourable for protein partitioning due to a transbilayer coupling mechanism assisted by long saturated chain lipids and cholesterol.

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Beber A, Taveneau C, Nania M, Tsai FC, Di Cicco A, Bassereau P, Lévy D, Cabral JT, Isambert H, Mangenot S*, Bertin A* (2019 Jan 24)

Membrane reshaping by micrometric curvature sensitive septin filaments

Nature communications : DOI : 10.1038/s41467-019-08344-5 Learn more
Summary

Septins are cytoskeletal filaments that assemble at the inner face of the plasma membrane.They are localized at constriction sites and impact membrane remodeling. We report in vitro tools to examine how yeast septins behave on curved and deformable membranes. Septins reshape the membranes of Giant Unilamellar Vesicles with the formation of periodic spikes, while flattening smaller vesicles. We show that membrane deformations are associated to preferential arrangement of Septin filaments on specific curvatures. When binding to bilayers supported on custom-designed periodic wavy patterns displaying positive and negative micrometric radii of curvatures, septin filaments remain straight and perpendicular to the curvature of the convex parts, while bending negatively to follow concave geometries. Based on these results, we propose a theoretical model that describes the deformations and micrometric curvature sensitivity observed in vitro. The model captures the reorganizations of septin filaments throughout cytokinesis in vivo, providing mechanistic insights into cell division.

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Year of publication 2018

Feng-Ching Tsai*, Aurelie Bertin*, Hugo Bousquet, John Manzi, Yosuke Senju, Meng-Chen Tsai, Laura Picas, Stephanie Miserey-Lenkei, Pekka Lappalainen, Emmanuel Lemichez, Evelyne Coudrier*, Patricia Bassereau* (2018 Sep 30)

Ezrin enrichment on curved membranes requires a specific conformation or interaction with a curvature-sensitive partner.

elife : 7 : e37262 : DOI : 10.7554/eLife.37262 Learn more
Summary

One challenge in cell biology is to decipher the biophysical mechanisms governing protein enrichment on curved membranes and the resulting membrane deformation. The ERM protein ezrin is abundant and associated with cellular membranes that are flat, positively or negatively curved. Using in vitro and cell biology approaches, we assess mechanisms of ezrin’s enrichment on curved membranes. We evidence that wild-type ezrin (ezrinWT) and its phosphomimetic mutant T567D (ezrinTD) do not deform membranes but self-assemble anti-parallelly, zipping adjacent membranes. EzrinTD’s specific conformation reduces intermolecular interactions, allows binding to actin filaments, which reduces membrane tethering, and promotes ezrin binding to positively-curved membranes. While neither ezrinTD nor ezrinWT senses negative curvature alone, we demonstrate that interacting with curvature-sensing I-BAR-domain proteins facilitates ezrin enrichment in negatively-curved membrane protrusions. Overall, our work demonstrates that ezrin can tether membranes, or be targeted to curved membranes, depending on conformations and interactions with actin and curvature-sensing binding partners.

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Arthur Charles-Orszag, Feng-Ching Tsai, Daria Bonazzi, Valeria Manriquez, Martin Sachse, Adeline Mallet, Audrey Salles, Keira Melican, Ralitza Staneva, Aurelie Bertin, Corinne Millien, Sylvie Goussard, Pierre Lafaye, Spencer Shorte, Matthieu Piel, Jacomine Krijnse-Locker, Francoise Brochard-Wyart, Patricia Bassereau, Guillaume Dumenil (2018 Aug 16)

Adhesion to nanofibers drives cell membrane remodeling through 1D wetting

Nature Communications : DOI : org/10.1101/393744 Learn more
Summary

The shape of cellular membranes is highly regulated by a set of conserved mechanisms. These mechanisms can be manipulated by bacterial pathogens to infect cells. Human endothelial cell plasma membrane remodeling by the bacterium Neisseria meningitidis is thought to be essential during the blood phase of meningococcal infection, but the underlying mechanisms are unknown. Here we show that plasma membrane remodeling occurs independently of Factin, along meningococcal type IV pili fibers, by a novel physical mechanism we term “one dimensional” membrane wetting. We provide a theoretical model that gives the physical basis of 1D wetting and show that this mechanism occurs in model membranes interacting with model nanofibers, and in human cells interacting with model extracellular matrices. It is thus a new general principle driving the interaction of cells with their environment at the nanoscale that is diverted by meningococcus during infection.

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Nicola De Franceschi, Maryam Alqabandi, Nolwenn Miguet, Christophe Caillat, Stephanie Mangenot, Winfried Weissenhorn*, Patricia Bassereau* (2018 Aug 3)

The ESCRT protein CHMP2B acts as a diffusion barrier on reconstituted membrane necks.

Journal of Cell Science : 132 : jcs217968 : DOI : 10.1242/jcs.217968 Learn more
Summary

Endosomal sorting complexes required for transport (ESCRT)-III family proteins catalyze membrane remodeling processes that stabilize and constrict membrane structures. It has been proposed that stable ESCRT-III complexes containing CHMP2B could establish diffusion barriers at the post-synaptic spine neck. In order to better understand this process, we developed a novel method based on fusion of giant unilamellar vesicles to reconstitute ESCRT-III proteins inside GUVs, from which membrane nanotubes are pulled. The new assay ensures that ESCRT-III proteins polymerize only when they become exposed to physiologically relevant membrane topology mimicking the complex geometry of post-synaptic spines. We establish that CHMP2B, both full-length and with a C-terminal deletion (ΔC), preferentially binds to membranes containing phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2]. Moreover, we show that CHMP2B preferentially accumulates at the neck of membrane nanotubes, and provide evidence that CHMP2B-ΔC prevents the diffusion of PI(4,5)P2 lipids and membrane-bound proteins across the tube neck. This indicates that CHMP2B polymers formed at a membrane neck may function as a diffusion barrier, highlighting a potential important function of CHMP2B in maintaining synaptic spine structures.

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Patricia Bassereau, Rui Jin, Tobias Baumgart, Markus Deserno, Rumiana Dimova, Vadim A. Frolov, Pavel V. Bashkirov, Helmut Grubmüller, Reinhard Jahn, H. Jelger Risselada, Ludger Johannes, Michael M. Kozlov, Reinhard Lipowsky, Thomas J. Pucadyil, Wade F. Zeno, Jeanne C. Stachowiak, Dimitrios Stamou, Artù Breuer, Line Lauritsen, Camille Simon, Cécile Sykes, Gregory A. Voth, Thomas R Weikl (2018 Jul 20)

The 2018 biomembrane curvature and remodeling roadmap.

Journal of Physics D: Applied Physics : 51 : 343001 : DOI : 10.1088/1361-6463/aacb98 Learn more
Summary

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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Alexandre Beber, Maryam Alqabandi, Coline Prevost, Fanny Viars, Daniel Levy, Patricia Bassereau, Aurélie Bertin*, Stéphanie Mangenot* (2018 Jul 16)

Septin-based readout of PI(4,5)P2 incorporation into membranes of giant unilamellar vesicles

Cytoskeleton : DOI : 10.1002/cm.21480 Learn more
Summary

Septins constitute a novel class of cytoskeletal proteins. Budding yeast septins self-assemble into non-polar filaments bound to the inner plasma membrane through specific interactions with L- α-phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2). Biomimetic in vitro assays using Giant Unilamellar Vesicles (GUVs) are relevant tools to dissect and reveal insights in proteins-lipids interactions, membrane mechanics and curvature sensitivity. GUVs doped with PI(4,5)P2 are challenging to prepare. This report is dedicated to optimize the incorporation of PI(4,5)P2 lipids into GUVs by probing the proteins-PI(4,5)P2 GUVs interactions. We show that the interaction between budding yeast septins and PI(4,5)P2 is more specific than using usual reporters (phospholipase  Cd1). Septins have thus been chosen as reporters to probe the proper incorporation of PI(4,5)P2 into giant vesicles. We have shown that electro-formation on platinum wires is the most appropriate method to achieve an optimal septin-lipid interaction resulting from an optimal PI(4,5)P2 incorporation for which, we have optimized the growth conditions. Finally, we have shown that PI(4,5)P2 GUVs have to be used within a few hours after their preparation. Indeed, over time, PI(4,5)P2 is expelled from he GUV membrane and the PI(4,5)P2 concentration in the bilayer decreases .

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Begoña Ugarte-Uribe, Coline Prévost, Kushal Kumar Das, Patricia Bassereau, Ana J. García-Sáez (2018 Apr 19)

Drp1 polymerization stabilizes curved tubular membranes similar to those of constricted mitochondria.

Journal of Cell Science : 132 : jcs208603 : DOI : 10.1242/jcs.208603 Learn more
Summary

Dynamin-related protein 1 (Drp1), an 80 kDa mechanochemical GTPase of the dynamin superfamily, is required for mitochondrial division in mammals. Despite the role of Drp1 dysfunction in human disease, its molecular mechanism remains poorly understood. Here, we examined the effect of Drp1 on membrane curvature using tubes pulled from giant unilamellar vesicles (GUVs). We found that GTP promoted rapid rearrangement of Drp1 from a uniform distribution to discrete foci, in line with the assembly of Drp1 scaffolds at multiple nucleation sites around the lipid tube. Polymerized Drp1 preserved the membrane tube below the protein coat, also in the absence of pulling forces, but did not induce spontaneous membrane fission. Strikingly, Drp1 polymers stabilized membrane curvatures similar to those of constricted mitochondria against pressure changes. Our findings support a new model for mitochondrial division whereby Drp1 mainly acts as a scaffold for membrane curvature stabilization, which sets it apart from other dynamin homologs.

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Guillaume Kulakowski, Hugo Bousquet Jean‐Baptiste Manneville, Patricia Bassereau, Bruno Goud, Lena K. Oesterlin (2018 Apr 6)

Lipid packing defects and membrane charge control RAB GTPase recruitment.

Traffic : 19 : 536-545 : DOI : 10.1111/tra.12568 Learn more
Summary

Specific intracellular localization of RAB GTPases has been reported to be dependent on protein factors, but the contribution of the membrane physicochemical properties to this process has been poorly described. Here, we show that three RAB proteins (RAB1/RAB5/RAB6) preferentially bind in vitro to disordered and curved membranes, and that this feature is uniquely dependent on their prenyl group. Our results imply that the addition of a prenyl group confers to RAB proteins, and most probably also to other prenylated proteins, the ability to sense lipid packing defects induced by unsaturated conical-shaped lipids and curvature. Consistently, RAB recruitment increases with the amount of lipid packing defects, further indicating that these defects drive RAB membrane targeting. Membrane binding of RAB35 is also modulated by lipid packing defects but primarily dependent on negatively charged lipids. Our results suggest that a balance between hydrophobic insertion of the prenyl group into lipid packing defects and electrostatic interactions of the RAB C-terminal region with charged membranes tunes the specific intracellular localization of RAB proteins.

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Mijo Simunovic, Patricia Bassereau, Gregory A. Voth (2018 Mar 30)

Organizing membrane-curving proteins: the emerging dynamical picture.

Current Opinion in Structural Biology : 51 : 99-105 : DOI : 10.1016/j.sbi.2018.03.018 Learn more
Summary

Lipid membranes play key roles in cells, such as in trafficking, division, infection, remodeling of organelles, among others. The key step in all these processes is creating membrane curvature, typically under the control of many anchored, adhered or included proteins. However, it has become clear that the membrane itself can mediate the interactions among proteins to produce highly ordered assemblies. Computer simulations are ideally suited to investigate protein organization and the dynamics of membrane remodeling at near-micron scales, something that is extremely challenging to tackle experimentally. We review recent computational efforts in modeling protein-caused membrane deformation mechanisms, specifically focusing on coarse-grained simulations. We highlight work that exposed the membrane-mediated ordering of proteins into lines, meshwork, spirals and other assemblies, in what seems to be a very generic mechanism driven by a combination of short and long-ranged forces. Modulating the mechanical properties of membranes is an underexplored signaling mechanism in various processes deserving of more attention in the near future.

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Eran Agmon, Jérôme Solon, Patricia Bassereau, Brent R. Stockwell (2018 Mar 26)

Modeling the effects of lipid peroxidation during ferroptosis on membrane properties.

Scientific Reports : 8 : 5155 : DOI : 10.1038/s41598-018-23408-0 Learn more
Summary

Ferroptosis is a form of regulated cell death characterized by the accumulation of lipid hydroperoxides. There has been significant research on the pathways leading to the accumulation of oxidized lipids, but the downstream effects and how lipid peroxides cause cell death during ferroptosis remain a major puzzle. We evaluated key features of ferroptosis in newly developed molecular dynamics models of lipid membranes to investigate the biophysical consequences of lipid peroxidation, and generated hypotheses about how lipid peroxides contribute to cell death during ferroptosis.

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