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Ledoux B, Zanin N, Yang J, Mercier V, Coster C, Dupont-Gillain C, Alsteens D, Morsomme P, Renard HF. Plasma membrane nanodeformations promote actin polymerization through CIP4/CDC42 recruitment and regulate type II IFN signaling. SCIENCE ADVANCES 2023; 9:eade1660. [PMID: 38091386 PMCID: PMC10848735 DOI: 10.1126/sciadv.ade1660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/10/2023] [Indexed: 12/18/2023]
Abstract
In their environment, cells must cope with mechanical stresses constantly. Among these, nanoscale deformations of plasma membrane induced by substrate nanotopography are now largely accepted as a biophysical stimulus influencing cell behavior and function. However, the mechanotransduction cascades involved and their precise molecular effects on cellular physiology are still poorly understood. Here, using homemade fluorescent nanostructured cell culture surfaces, we explored the role of Bin/Amphiphysin/Rvs (BAR) domain proteins as mechanosensors of plasma membrane geometry. Our data reveal that distinct subsets of BAR proteins bind to plasma membrane deformations in a membrane curvature radius-dependent manner. Furthermore, we show that membrane curvature promotes the formation of dynamic actin structures mediated by the Rho GTPase CDC42, the F-BAR protein CIP4, and the presence of PI(4,5)P2. In addition, these actin-enriched nanodomains can serve as platforms to regulate receptor signaling as they appear to contain interferon-γ receptor (IFNγ-R) and to lead to the partial inhibition of IFNγ-induced JAK/STAT signaling.
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Affiliation(s)
- Benjamin Ledoux
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Croix du Sud 4-5 bte L7.07.14, Louvain-la-Neuve 1348, Belgium
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Croix du Sud 4-5 bte L7.07.07, Louvain-la-Neuve 1348, Belgium
- UNamur, Morph-Im platform, Rue de Bruxelles 61, Namur 5000, Belgium
| | - Natacha Zanin
- UNamur, NAmur Research Institute for LIfe Sciences, Unité de Recherche en Biologie Cellulaire animale, Rue de Bruxelles 61, Namur 5000, Belgium
| | - Jinsung Yang
- Gyeongsang National University, Department of Biochemistry, College of Medicine, Department of Convergence Medical Sciences, Institute of Medical Science, Jinju 52727, South Korea
| | - Vincent Mercier
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Charlotte Coster
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Croix du Sud 4-5 bte L7.07.14, Louvain-la-Neuve 1348, Belgium
| | - Christine Dupont-Gillain
- UCLouvain, Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Place Louis Pasteur 1 bte L4.01.10, Louvain-la-Neuve 1348, Belgium
| | - David Alsteens
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, NanoBiophysics lab, Croix du Sud 4-5 bte L7.07.07, Louvain-la-Neuve 1348, Belgium
| | - Pierre Morsomme
- UCLouvain, Louvain Institute of Biomolecular Science and Technology, Group of Molecular Physiology, Croix du Sud 4-5 bte L7.07.14, Louvain-la-Neuve 1348, Belgium
| | - Henri-François Renard
- UNamur, Morph-Im platform, Rue de Bruxelles 61, Namur 5000, Belgium
- UNamur, NAmur Research Institute for LIfe Sciences, Unité de Recherche en Biologie Cellulaire animale, Rue de Bruxelles 61, Namur 5000, Belgium
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2
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Gnidovec A, Božič A, Jelerčič U, Čopar S. Measure of overlap between two arbitrary ellipses on a sphere. Proc Math Phys Eng Sci 2022; 478:20210807. [PMID: 35601962 PMCID: PMC9066605 DOI: 10.1098/rspa.2021.0807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/30/2022] [Indexed: 11/14/2022] Open
Abstract
Various packing problems and simulations of hard and soft interacting particles, such as microscopic models of nematic liquid crystals, reduce to calculations of intersections and pair interactions between ellipsoids. When constrained to a spherical surface, curvature and compactness lead to non-trivial behaviour that finds uses in physics, computer science and geometry. A well-known idealized isotropic example is the Tammes problem of finding optimal non-intersecting packings of equal hard disks. The anisotropic case of elliptic particles remains, on the other hand, comparatively unexplored. We develop an algorithm to detect collisions between ellipses constrained to the two-dimensional surface of a sphere based on a solution of an eigenvalue problem. We investigate and discuss topologically distinct ways two ellipses may touch or intersect on a sphere, and define a contact function that can be used for construction of short- and long-range pair potentials.
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Affiliation(s)
- Andraž Gnidovec
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
| | - Anže Božič
- Department of Theoretical Physics, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Urška Jelerčič
- Department of Chemical Engineering, Ilse Kats Institute for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer-Sheva, Israel
| | - Simon Čopar
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
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3
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Gasilina A, Yoon HY, Jian X, Luo R, Randazzo PA. A lysine-rich cluster in the N-BAR domain of ARF GTPase-activating protein ASAP1 is necessary for binding and bundling actin filaments. J Biol Chem 2022; 298:101700. [PMID: 35143843 PMCID: PMC8902617 DOI: 10.1016/j.jbc.2022.101700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/05/2022] Open
Abstract
Actin filament maintenance is critical for both normal cell homeostasis and events associated with malignant transformation. The ADP-ribosylation factor GTPase-activating protein ASAP1 regulates the dynamics of filamentous actin-based structures, including stress fibers, focal adhesions, and circular dorsal ruffles. Here, we have examined the molecular basis for ASAP1 association with actin. Using a combination of structural modeling, mutagenesis, and in vitro and cell-based assays, we identify a putative-binding interface between the N-Bin-Amphiphysin-Rvs (BAR) domain of ASAP1 and actin filaments. We found that neutralization of charges and charge reversal at positions 75, 76, and 79 of ASAP1 reduced the binding of ASAP1 BAR-pleckstrin homology tandem to actin filaments and abrogated actin bundle formation in vitro. In addition, overexpression of actin-binding defective ASAP1 BAR-pleckstrin homology [K75, K76, K79] mutants prevented cellular actin remodeling in U2OS cells. Exogenous expression of [K75E, K76E, K79E] mutant of full-length ASAP1 did not rescue the reduction of cellular actin fibers consequent to knockdown of endogenous ASAP1. Taken together, our results support the hypothesis that the lysine-rich cluster in the N-BAR domain of ASAP1 is important for regulating actin filament organization.
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Affiliation(s)
- Anjelika Gasilina
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Hye-Young Yoon
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Xiaoying Jian
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ruibai Luo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Paul A Randazzo
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
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4
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Phillips DA, Zacharoff LA, Hampton CM, Chong GW, Malanoski AP, Metskas LA, Xu S, Bird LJ, Eddie BJ, Miklos AE, Jensen GJ, Drummy LF, El-Naggar MY, Glaven SM. A bacterial membrane sculpting protein with BAR domain-like activity. eLife 2021; 10:60049. [PMID: 34643180 PMCID: PMC8687657 DOI: 10.7554/elife.60049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 10/12/2021] [Indexed: 11/13/2022] Open
Abstract
Bin/Amphiphysin/RVS (BAR) domain proteins belong to a superfamily of coiled-coil proteins influencing membrane curvature in eukaryotes and are associated with vesicle biogenesis, vesicle-mediated protein trafficking, and intracellular signaling. Here, we report a bacterial protein with BAR domain-like activity, BdpA, from Shewanella oneidensis MR-1, known to produce redox-active membrane vesicles and micrometer-scale outer membrane extensions (OMEs). BdpA is required for uniform size distribution of membrane vesicles and influences scaffolding of OMEs into a consistent diameter and curvature. Cryo-TEM reveals that a strain lacking BdpA produces lobed, disordered OMEs rather than membrane tubules or narrow chains produced by the wild-type strain. Overexpression of BdpA promotes OME formation during planktonic growth of S. oneidensis where they are not typically observed. Heterologous expression results in OME production in Marinobacter atlanticus and Escherichia coli. Based on the ability of BdpA to alter membrane architecture in vivo, we propose that BdpA and its homologs comprise a newly identified class of bacterial BAR domain-like proteins.
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Affiliation(s)
- Daniel A Phillips
- Oak Ridge Institute for Science and Education / US Army DEVCOM Chemical Biological Center, Aberdeen Proving Grounds, United States
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Cheri M Hampton
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Grace W Chong
- Department of Biological Sciences, University of Southern California, Los Angeles, United States
| | - Anthony P Malanoski
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Lauren Ann Metskas
- Biological Sciences, Chemistry, California Institute of Technology, Pasadena, United States
| | - Shuai Xu
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Lina J Bird
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Brian J Eddie
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
| | - Aleksandr E Miklos
- BioSciences Division, BioChemistry Branch, US Army DEVCOM Chemical Biological Center, Aberdeen Proving Ground, United States
| | - Grant J Jensen
- Biology and Bioengineering, California Institute of Technology, Pasadena, United States
| | - Lawrence F Drummy
- Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Dayton, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Sarah M Glaven
- Center for Bio/Molecular Science and Engineering, US Naval Research Laboratory, Washington, United States
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5
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The state of F-BAR domains as membrane-bound oligomeric platforms. Trends Cell Biol 2021; 31:644-655. [PMID: 33888395 DOI: 10.1016/j.tcb.2021.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/16/2022]
Abstract
Fes/Cip4 homology Bin/amphiphysin/Rvs (F-BAR) domains, like all BAR domains, are dimeric units that oligomerize and bind membranes. F-BAR domains are generally coupled to additional domains that function in protein binding or have enzymatic activity. Because of their crescent shape and ability to oligomerize, F-BAR domains have been traditionally viewed as membrane-deformation modules. However, multiple independent studies have provided no evidence that certain F-BAR domains are able to tubulate membrane. Instead, a growing body of literature featuring structural, biochemical, biophysical, and microscopy-based studies supports the idea that the F-BAR domain family can be unified only by their ability to form oligomeric assemblies on membranes to provide platforms for molecular assembly.
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6
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Leite DM, Matias D, Battaglia G. The Role of BAR Proteins and the Glycocalyx in Brain Endothelium Transcytosis. Cells 2020; 9:E2685. [PMID: 33327645 PMCID: PMC7765129 DOI: 10.3390/cells9122685] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 12/27/2022] Open
Abstract
Within the brain, endothelial cells lining the blood vessels meticulously coordinate the transport of nutrients, energy metabolites and other macromolecules essential in maintaining an appropriate activity of the brain. While small molecules are pumped across specialised molecular transporters, large macromolecular cargos are shuttled from one side to the other through membrane-bound carriers formed by endocytosis on one side, trafficked to the other side and released by exocytosis. Such a process is collectively known as transcytosis. The brain endothelium is recognised to possess an intricate vesicular endosomal network that mediates the transcellular transport of cargos from blood-to-brain and brain-to-blood. However, mounting evidence suggests that brain endothelial cells (BECs) employ a more direct route via tubular carriers for a fast and efficient transport from the blood to the brain. Here, we compile the mechanism of transcytosis in BECs, in which we highlight intracellular trafficking mediated by tubulation, and emphasise the possible role in transcytosis of the Bin/Amphiphysin/Rvs (BAR) proteins and glycocalyx (GC)-a layer of sugars covering BECs, in transcytosis. Both BAR proteins and the GC are intrinsically associated with cell membranes and involved in the modulation and shaping of these membranes. Hence, we aim to summarise the machinery involved in transcytosis in BECs and highlight an uncovered role of BAR proteins and the GC at the brain endothelium.
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Affiliation(s)
- Diana M. Leite
- Department of Chemistry, University College London, London WC1H 0AJ, UK; (D.M.L.); (D.M.)
- Institute of the Physics and Living Systems, University College London, London WC1H 0AJ, UK
| | - Diana Matias
- Department of Chemistry, University College London, London WC1H 0AJ, UK; (D.M.L.); (D.M.)
- Institute of the Physics and Living Systems, University College London, London WC1H 0AJ, UK
- Samantha Dickson Brain Cancer Unit, Cancer Institute, University College London, London WC1E 06DD, UK
- Cancer Research UK, City of London Centre, London WC1E 06DD, UK
| | - Giuseppe Battaglia
- Department of Chemistry, University College London, London WC1H 0AJ, UK; (D.M.L.); (D.M.)
- Institute of the Physics and Living Systems, University College London, London WC1H 0AJ, UK
- Cancer Research UK, City of London Centre, London WC1E 06DD, UK
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), 08028 Barcelona, Spain
- Catalan Institute for Research and Advanced Studies, 08010 Barcelona, Spain
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7
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Le Roux AL, Quiroga X, Walani N, Arroyo M, Roca-Cusachs P. The plasma membrane as a mechanochemical transducer. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180221. [PMID: 31431176 PMCID: PMC6627014 DOI: 10.1098/rstb.2018.0221] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
Cells are constantly submitted to external mechanical stresses, which they must withstand and respond to. By forming a physical boundary between cells and their environment that is also a biochemical platform, the plasma membrane (PM) is a key interface mediating both cellular response to mechanical stimuli, and subsequent biochemical responses. Here, we review the role of the PM as a mechanosensing structure. We first analyse how the PM responds to mechanical stresses, and then discuss how this mechanical response triggers downstream biochemical responses. The molecular players involved in PM mechanochemical transduction include sensors of membrane unfolding, membrane tension, membrane curvature or membrane domain rearrangement. These sensors trigger signalling cascades fundamental both in healthy scenarios and in diseases such as cancer, which cells harness to maintain integrity, keep or restore homeostasis and adapt to their external environment. This article is part of a discussion meeting issue 'Forces in cancer: interdisciplinary approaches in tumour mechanobiology'.
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Affiliation(s)
- Anabel-Lise Le Roux
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
| | - Xarxa Quiroga
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
| | - Nikhil Walani
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Spain
| | - Marino Arroyo
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
- LaCàN, Universitat Politècnica de Catalunya-BarcelonaTech, Spain
| | - Pere Roca-Cusachs
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona 08028, Spain
- Department of Biomedical Sciences, Universitat de Barcelona, Barcelona 08036, Spain
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8
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Postema MM, Grega-Larson NE, Meenderink LM, Tyska MJ. PACSIN2-dependent apical endocytosis regulates the morphology of epithelial microvilli. Mol Biol Cell 2019; 30:2515-2526. [PMID: 31390291 PMCID: PMC6743356 DOI: 10.1091/mbc.e19-06-0352] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Apical microvilli are critical for the homeostasis of transporting epithelia, yet mechanisms that control the assembly and morphology of these protrusions remain poorly understood. Previous studies in intestinal epithelial cell lines suggested a role for the F-BAR domain protein PACSIN2 in normal microvillar assembly. Here we report the phenotype of PACSIN2 KO mice and provide evidence that through its role in promoting apical endocytosis, this molecule plays a role in controlling microvillar morphology. PACSIN2 KO enterocytes exhibit reduced numbers of microvilli and defects in the microvillar ultrastructure, with membranes lifting away from rootlets of core bundles. Dynamin2, a PACSIN2 binding partner, and other endocytic factors were also lost from their normal localization near microvillar rootlets. To determine whether loss of endocytic machinery could explain defects in microvillar morphology, we examined the impact of PACSIN2 KD and endocytosis inhibition on live intestinal epithelial cells. These assays revealed that when endocytic vesicle scission fails, tubules are pulled into the cytoplasm and this, in turn, leads to a membrane-lifting phenomenon reminiscent of that observed at PACSIN2 KO brush borders. These findings lead to a new model where inward forces generated by endocytic machinery on the plasma membrane control the membrane wrapping of cell surface protrusions.
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Affiliation(s)
- Meagan M Postema
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, University Medical Center, Nashville, TN 37232
| | - Nathan E Grega-Larson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, University Medical Center, Nashville, TN 37232
| | - Leslie M Meenderink
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Matthew J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, University Medical Center, Nashville, TN 37232
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9
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Osawa T, Alam JM, Noda NN. Membrane-binding domains in autophagy. Chem Phys Lipids 2019; 218:1-9. [DOI: 10.1016/j.chemphyslip.2018.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023]
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10
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BAR domain proteins-a linkage between cellular membranes, signaling pathways, and the actin cytoskeleton. Biophys Rev 2018; 10:1587-1604. [PMID: 30456600 DOI: 10.1007/s12551-018-0467-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 10/17/2018] [Indexed: 12/23/2022] Open
Abstract
Actin filament assembly typically occurs in association with cellular membranes. A large number of proteins sit at the interface between actin networks and membranes, playing diverse roles such as initiation of actin polymerization, modulation of membrane curvature, and signaling. Bin/Amphiphysin/Rvs (BAR) domain proteins have been implicated in all of these functions. The BAR domain family of proteins comprises a diverse group of multi-functional effectors, characterized by their modular architecture. In addition to the membrane-curvature sensing/inducing BAR domain module, which also mediates antiparallel dimerization, most contain auxiliary domains implicated in protein-protein and/or protein-membrane interactions, including SH3, PX, PH, RhoGEF, and RhoGAP domains. The shape of the BAR domain itself varies, resulting in three major subfamilies: the classical crescent-shaped BAR, the more extended and less curved F-BAR, and the inverse curvature I-BAR subfamilies. Most members of this family have been implicated in cellular functions that require dynamic remodeling of the actin cytoskeleton, such as endocytosis, organelle trafficking, cell motility, and T-tubule biogenesis in muscle cells. Here, we review the structure and function of mammalian BAR domain proteins and the many ways in which they are interconnected with the actin cytoskeleton.
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11
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Ramakrishnan N, Bradley RP, Tourdot RW, Radhakrishnan R. Biophysics of membrane curvature remodeling at molecular and mesoscopic lengthscales. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:273001. [PMID: 29786613 PMCID: PMC6066392 DOI: 10.1088/1361-648x/aac702] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
At the micron scale, where cell organelles display an amazing complexity in their shape and organization, the physical properties of a biological membrane can be better-understood using continuum models subject to thermal (stochastic) undulations. Yet, the chief orchestrators of these complex and intriguing shapes are a specialized class of membrane associating often peripheral proteins called curvature remodeling proteins (CRPs) that operate at the molecular level through specific protein-lipid interactions. We review multiscale methodologies to model these systems at the molecular as well as at the mesoscopic and cellular scales, and also present a free energy perspective of membrane remodeling through the organization and assembly of CRPs. We discuss the morphological space of nearly planar to highly curved membranes, methods to include thermal fluctuations, and review studies that model such proteins as curvature fields to describe the emergent curved morphologies. We also discuss several mesoscale models applied to a variety of cellular processes, where the phenomenological parameters (such as curvature field strength) are often mapped to models of real systems based on molecular simulations. Much insight can be gained from the calculation of free energies of membranes states with protein fields, which enable accurate mapping of the state and parameter values at which the membrane undergoes morphological transformations such as vesiculation or tubulation. By tuning the strength, anisotropy, and spatial organization of the curvature-field, one can generate a rich array of membrane morphologies that are highly relevant to shapes of several cellular organelles. We review applications of these models to budding of vesicles commonly seen in cellular signaling and trafficking processes such as clathrin mediated endocytosis, sorting by the ESCRT protein complexes, and cellular exocytosis regulated by the exocyst complex. We discuss future prospects where such models can be combined with other models for cytoskeletal assembly, and discuss their role in understanding the effects of cell membrane tension and the mechanics of the extracellular microenvironment on cellular processes.
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Affiliation(s)
- N Ramakrishnan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, United States of America
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12
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Davtyan A, Simunovic M, Voth GA. The mesoscopic membrane with proteins (MesM-P) model. J Chem Phys 2017; 147:044101. [PMID: 28764362 PMCID: PMC5552407 DOI: 10.1063/1.4993514] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/26/2017] [Indexed: 12/30/2022] Open
Abstract
We present the Mesoscopic Membrane with Proteins (MesM-P) model, an extension of a previously developed elastic membrane model for mesoscale simulations of lipid membranes. MesM-P employs a discrete mesoscopic quasi-particle approach to model protein-facilitated shape and topology changes of the lipid membrane on length and time scales inaccessible to all-atom and quasimolecular coarse-grained molecular dynamics simulations. We investigate the ability of MesM-P to model the behavior of large lipid vesicles as a function of bound protein density. We find four distinct mechanisms for protein aggregation on the surface of the membrane, depending on membrane stiffness and protein spontaneous curvature. We also establish a connection between MesM-P and the results of higher resolution coarse-grained molecular dynamics simulations.
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Affiliation(s)
- Aram Davtyan
- Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Mijo Simunovic
- Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
| | - Gregory A Voth
- Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA
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13
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Multiscale simulations of protein-facilitated membrane remodeling. J Struct Biol 2016; 196:57-63. [PMID: 27327264 DOI: 10.1016/j.jsb.2016.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/14/2016] [Accepted: 06/15/2016] [Indexed: 12/19/2022]
Abstract
Protein-facilitated shape and topology changes of cell membranes are crucial for many biological processes, such as cell division, protein trafficking, and cell signaling. However, the inherently multiscale nature of membrane remodeling presents a considerable challenge for understanding the mechanisms and physics that drive this process. To address this problem, a multiscale approach that makes use of a diverse set of computational and experimental techniques is required. The atomistic simulations provide high-resolution information on protein-membrane interactions. Experimental techniques, like electron microscopy, on the other hand, resolve high-order organization of proteins on the membrane. Coarse-grained (CG) and mesoscale computational techniques provide the intermediate link between the two scales and can give new insights into the underlying mechanisms. In this Review, we present the recent advances in multiscale computational approaches established in our group. We discuss various CG and mesoscale approaches in studying the protein-mediated large-scale membrane remodeling.
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14
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Ramakrishnan N, Sunil Kumar PB, Radhakrishnan R. Mesoscale computational studies of membrane bilayer remodeling by curvature-inducing proteins. PHYSICS REPORTS 2014; 543:1-60. [PMID: 25484487 PMCID: PMC4251917 DOI: 10.1016/j.physrep.2014.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Biological membranes constitute boundaries of cells and cell organelles. These membranes are soft fluid interfaces whose thermodynamic states are dictated by bending moduli, induced curvature fields, and thermal fluctuations. Recently, there has been a flood of experimental evidence highlighting active roles for these structures in many cellular processes ranging from trafficking of cargo to cell motility. It is believed that the local membrane curvature, which is continuously altered due to its interactions with myriad proteins and other macromolecules attached to its surface, holds the key to the emergent functionality in these cellular processes. Mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the protein, shape and amino acid composition of the protein, and its amino acid contents. The specificity of molecular interactions together with the cooperativity of multiple proteins induce and stabilize complex membrane shapes at the mesoscale. These shapes span a wide spectrum ranging from the spherical plasma membrane to the complex cisternae of the Golgi apparatus. Mapping the relation between the protein-induced deformations at the molecular scale and the resulting mesoscale morphologies is key to bridging cellular experiments across the various length scales. In this review, we focus on the theoretical and computational methods used to understand the phenomenology underlying protein-driven membrane remodeling. Interactions at the molecular scale can be computationally probed by all atom and coarse grained molecular dynamics (MD, CGMD), as well as dissipative particle dynamics (DPD) simulations, which we only describe in passing. We choose to focus on several continuum approaches extending the Canham - Helfrich elastic energy model for membranes to include the effect of curvature-inducing proteins and explore the conformational phase space of such systems. In this description, the protein is expressed in the form of a spontaneous curvature field. The approaches include field theoretical methods limited to the small deformation regime, triangulated surfaces and particle-based computational models to investigate the large-deformation regimes observed in the natural state of many biological membranes. Applications of these methods to understand the properties of biological membranes in homogeneous and inhomogeneous environments of proteins, whose underlying curvature fields are either isotropic or anisotropic, are discussed. The diversity in the curvature fields elicits a rich variety of morphological states, including tubes, discs, branched tubes, and caveola. Mapping the thermodynamic stability of these states as a function of tuning parameters such as concentration and strength of curvature induction of the proteins is discussed. The relative stabilities of these self-organized shapes are examined through free-energy calculations. The suite of methods discussed here can be tailored to applications in specific cellular settings such as endocytosis during cargo trafficking and tubulation of filopodial structures in migrating cells, which makes these methods a powerful complement to experimental studies.
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Affiliation(s)
- N. Ramakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
| | - P. B. Sunil Kumar
- Department of Physics, Indian Institute of Technology Madras, Chennai, India - 600036
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular Engineering, Department of Bioengineering, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA-19104
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15
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Edwards M, Zwolak A, Schafer DA, Sept D, Dominguez R, Cooper JA. Capping protein regulators fine-tune actin assembly dynamics. Nat Rev Mol Cell Biol 2014; 15:677-89. [PMID: 25207437 DOI: 10.1038/nrm3869] [Citation(s) in RCA: 191] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Capping protein (CP) binds the fast growing barbed end of the actin filament and regulates actin assembly by blocking the addition and loss of actin subunits. Recent studies provide new insights into how CP and barbed-end capping are regulated. Filament elongation factors, such as formins and ENA/VASP (enabled/vasodilator-stimulated phosphoprotein), indirectly regulate CP by competing with CP for binding to the barbed end, whereas other molecules, including V-1 and phospholipids, directly bind to CP and sterically block its interaction with the filament. In addition, a diverse and unrelated group of proteins interact with CP through a conserved 'capping protein interaction' (CPI) motif. These proteins, including CARMIL (capping protein, ARP2/3 and myosin I linker), CD2AP (CD2-associated protein) and the WASH (WASP and SCAR homologue) complex subunit FAM21, recruit CP to specific subcellular locations and modulate its actin-capping activity via allosteric effects.
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Affiliation(s)
- Marc Edwards
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63110, USA
| | - Adam Zwolak
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Dorothy A Schafer
- Departments of Biology and Cell Biology, University of Virginia, Charlottesville, Virginia 22904, USA
| | - David Sept
- Department of Biomedical Engineering and Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Roberto Dominguez
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - John A Cooper
- Department of Cell Biology and Physiology, Washington University, St. Louis, Missouri 63110, USA
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16
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Roujeinikova A. Phospholipid binding residues of eukaryotic membrane-remodelling F-BAR domain proteins are conserved in Helicobacter pylori CagA. BMC Res Notes 2014; 7:525. [PMID: 25115379 PMCID: PMC4141123 DOI: 10.1186/1756-0500-7-525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Accepted: 08/04/2014] [Indexed: 12/22/2022] Open
Abstract
Background Cytotoxin associated gene product A (CagA) is an oncogenic protein secreted by the gastric bacterium Helicobacter pylori. Internalization of CagA by human epithelial cells occurs by an unknown mechanism that requires interaction with the host membrane lipid phosphatidylserine. Findings Local homology at the level of amino acid sequence and secondary structure has been identified between the membrane-tethering region of CagA and the lipid-binding Fes-CIP4 homology-Bin/Amphiphysin/Rvs (F-BAR) domains of eukaryotic proteins. The F-BAR proteins are major components of the endocytic machinery. In addition to the membrane-binding F-BAR domains, they contain other domains that interact with actin-regulatory networks and mediate interplay between membrane dynamics and cytoskeleton re-arrangements. Positively charged residues found on the lipid binding face of the F-BAR domains are conserved in CagA and represent residues involved in CagA binding to lipids. Conclusions The homologies with F-BAR proteins extend to lipid binding specificities and involvement in reorganization of the actin cytoskeleton. CagA and F-BAR domains share binding specificity for phosphatidylserine and phosphoinositides. Similar to the F-BAR proteins, CagA has a membrane-binding module and a module that shares structural homology with actin-binding proteins, and, like eukaryotic F-BAR domain proteins, CagA function is linked to actin dynamics. The uncovered similarities between the bacterial effector protein and eukaryotic F-BAR proteins suggest convergent evolution of CagA towards a similar function. Electronic supplementary material The online version of this article (doi:10.1186/1756-0500-7-525) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Roujeinikova
- Department of Microbiology, Monash University, Building 76, Monash University, Clayton, Victoria 3800, Australia.
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17
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Kozlov MM, Campelo F, Liska N, Chernomordik LV, Marrink SJ, McMahon HT. Mechanisms shaping cell membranes. Curr Opin Cell Biol 2014; 29:53-60. [PMID: 24747171 DOI: 10.1016/j.ceb.2014.03.006] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Revised: 03/18/2014] [Accepted: 03/19/2014] [Indexed: 01/08/2023]
Abstract
Membranes of intracellular organelles are characterized by large curvatures with radii of the order of 10-30nm. While, generally, membrane curvature can be a consequence of any asymmetry between the membrane monolayers, generation of large curvatures requires the action of mechanisms based on specialized proteins. Here we discuss the three most relevant classes of such mechanisms with emphasis on the physical requirements for proteins to be effective in generation of membrane curvature. We provide new quantitative estimates of membrane bending by shallow hydrophobic insertions and compare the efficiency of the insertion mechanism with those of the protein scaffolding and crowding mechanisms.
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Affiliation(s)
- Michael M Kozlov
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel.
| | - Felix Campelo
- Cell and Developmental Biology Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Nicole Liska
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Leonid V Chernomordik
- Section on Membrane Biology, Program of Physical Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, United States
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Harvey T McMahon
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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18
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Futó K, Bódis E, Machesky LM, Nyitrai M, Visegrády B. Membrane binding properties of IRSp53-missing in metastasis domain (IMD) protein. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1831:1651-5. [PMID: 23872532 DOI: 10.1016/j.bbalip.2013.07.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/05/2013] [Accepted: 07/10/2013] [Indexed: 12/31/2022]
Abstract
The 53-kDa insulin receptor substrate protein (IRSp53) organizes the actin cytoskeleton in response to stimulation of small GTPases, promoting the formation of cell protrusions such as filopodia and lamellipodia. IMD is the N-terminal 250 amino acid domain (IRSp53/MIM Homology Domain) of IRSp53 (also called I-BAR), which can bind to negatively charged lipid molecules. Overexpression of IMD induces filopodia formation in cells and purified IMD assembles finger-like protrusions in reconstituted lipid membranes. IMD was shown by several groups to bundle actin filaments, but other groups showed that it also binds to membranes. IMD binds to negatively charged lipid molecules with preference to clusters of PI(4,5)P2. Here, we performed a range of different in vitro fluorescence experiments to determine the binding properties of the IMD to phospholipids. We used different constructs of large unilamellar vesicles (LUVETs), containing neutral or negatively charged phospholipids. We found that IMD has a stronger binding interaction with negatively charged PI(4,5)P2 or PS lipids than PS/PC or neutral PC lipids. The equilibrium dissociation constant for the IMD-lipid interaction falls into the 78-170μM range for all the lipids tested. The solvent accessibility of the fluorescence labels on the IMD during its binding to lipids is also reduced as the lipids become more negatively charged. Actin affects the IMD-lipid interaction, depending on its polymerization state. Monomeric actin partially disrupts the binding, while filamentous actin can further stabilize the IMD-lipid interaction.
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Affiliation(s)
- Kinga Futó
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Emőke Bódis
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary
| | - Laura M Machesky
- Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Miklós Nyitrai
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary; Szentágothai Research Center, Pécs, Ifjúság str. 34, H-7624, Hungary; Hungarian Academy of Sciences, Office for Subsidized Research Units, Budapest, Nádor str. 7, H-1051, Hungary
| | - Balázs Visegrády
- Department of Biophysics, Medical School, University of Pécs, Szigeti str. 12, Pécs H-7624, Hungary.
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19
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Yu H, Schulten K. Membrane sculpting by F-BAR domains studied by molecular dynamics simulations. PLoS Comput Biol 2013; 9:e1002892. [PMID: 23382665 PMCID: PMC3561051 DOI: 10.1371/journal.pcbi.1002892] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Accepted: 12/02/2012] [Indexed: 12/11/2022] Open
Abstract
Interplay between cellular membranes and their peripheral proteins drives many processes in eukaryotic cells. Proteins of the Bin/Amphiphysin/Rvs (BAR) domain family, in particular, play a role in cellular morphogenesis, for example curving planar membranes into tubular membranes. However, it is still unclear how F-BAR domain proteins act on membranes. Electron microscopy revealed that, in vitro, F-BAR proteins form regular lattices on cylindrically deformed membrane surfaces. Using all-atom and coarse-grained (CG) molecular dynamics simulations, we show that such lattices, indeed, induce tubes of observed radii. A 250 ns all-atom simulation reveals that F-BAR domain curves membranes via the so-called scaffolding mechanism. Plasticity of the F-BAR domain permits conformational change in response to membrane interaction, via partial unwinding of the domains 3-helix bundle structure. A CG simulation covering more than 350 µs provides a dynamic picture of membrane tubulation by lattices of F-BAR domains. A series of CG simulations identified the optimal lattice type for membrane sculpting, which matches closely the lattices seen through cryo-electron microscopy. To generate organelles, eukaryotic cells sculpt their membranes into compartments, often employing proteins as chaperones, for example, F-BAR domains. The latter induce formation of tubular and vesicular membranes. Functional and structural studies suggest that F-BAR domains sculpt membranes through electrostatic interactions, driving the membrane to match the concave surface of the protein's banana-like shape. Cryo-electron microscopy (cryo-EM) studies provide an average static picture of how F-BAR domains form lattices on the surface of membranes to induce tube formation. Complementing the cryo-EM images, molecular dynamics simulations reported here offer a detailed, dynamic picture of membrane tubulation by a lattice of F-BAR domains and identified lattice types optimally attuned to producing high membrane curvature. The simulations reproduced also a process lasting 350 µs in which lattices of F-BAR domains form a complete tube out of an initially flat membrane. The molecular dynamics study offers, thereby, both a large-scale picture of membrane sculpting by F-BAR domain lattices as well as atomic-level dynamic information about the involvement of the individual F-BAR domain and its interactions with partner F-BAR domains and membrane in the sculpting process.
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Affiliation(s)
- Hang Yu
- Beckman Institute, University of Illinois, Urbana, Illinois, United States of America
- Center of Biophysics and Computational Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Klaus Schulten
- Beckman Institute, University of Illinois, Urbana, Illinois, United States of America
- Center of Biophysics and Computational Biology, University of Illinois, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois, Urbana, Illinois, United States of America
- * E-mail:
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20
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Coutinho-Budd J, Ghukasyan V, Zylka MJ, Polleux F. The F-BAR domains from srGAP1, srGAP2 and srGAP3 regulate membrane deformation differently. J Cell Sci 2012; 125:3390-401. [PMID: 22467852 DOI: 10.1242/jcs.098962] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Coordination of membrane deformation and cytoskeletal dynamics lies at the heart of many biological processes critical for cell polarity, motility and morphogenesis. We have recently shown that Slit-Robo GTPase-activating protein 2 (srGAP2) regulates neuronal morphogenesis through the ability of its F-BAR domain to regulate membrane deformation and induce filopodia formation. Here, we demonstrate that the F-BAR domains of two closely related family members, srGAP1 and srGAP3 [designated F-BAR(1) and F-BAR(3), respectively] display significantly different membrane deformation properties in non-neuronal COS7 cells and in cortical neurons. F-BAR(3) induces filopodia in both cell types, though less potently than F-BAR(2), whereas F-BAR(1) prevents filopodia formation in cortical neurons and reduces plasma membrane dynamics. These three F-BAR domains can heterodimerize, and they act synergistically towards filopodia induction in COS7 cells. As measured by fluorescence recovery after photobleaching, F-BAR(2) displays faster molecular dynamics than F-BAR(3) and F-BAR(1) at the plasma membrane, which correlates well with its increased potency to induce filopodia. We also show that the molecular dynamic properties of F-BAR(2) at the membrane are partially dependent on F-Actin. Interestingly, acute phosphatidylinositol 4,5-bisphosphate [PtdIns(4,5)P(2)] depletion in cells does not interfere with plasma membrane localization of F-BAR(2), which is compatible with our result showing that F-BAR(2) binds to a broad range of negatively-charged phospholipids present at the plasma membrane, including phosphatidylserine (PtdSer). Overall, our results provide novel insights into the functional diversity of the membrane deformation properties of this subclass of F-BAR-domains required for cell morphogenesis.
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Affiliation(s)
- Jaeda Coutinho-Budd
- Neurobiology Curriculum University of North Carolina, Chapel Hill, NC 27599-7250, USA
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21
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The F-BAR protein CIP4 inhibits neurite formation by producing lamellipodial protrusions. Curr Biol 2012; 22:494-501. [PMID: 22361215 DOI: 10.1016/j.cub.2012.01.038] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/22/2011] [Accepted: 01/19/2012] [Indexed: 02/01/2023]
Abstract
Neurite formation is a seminal event in the early development of neurons. However, little is known about the mechanisms by which neurons form neurites. F-BAR proteins function in sensing and inducing membrane curvature. Cdc42-interacting protein 4 (CIP4), a member of the F-BAR family, regulates endocytosis in a variety of cell types. However, there is little data on how CIP4 functions in neurons. Here we show that CIP4 plays a novel role in neuronal development by inhibiting neurite formation. Remarkably, CIP4 exerts this effect not through endocytosis, but by producing lamellipodial protrusions. In primary cortical neurons CIP4 is concentrated specifically at the tips of extending lamellipodia and filopodia, instead of endosomes as in other cell types. Overexpression of CIP4 results in lamellipodial protrusions around the cell body, subsequently delaying neurite formation and enlarging growth cones. These effects depend on the F-BAR and SH3 domains of CIP4 and on its ability to multimerize. Conversely, cortical neurons from CIP4-null mice initiate neurites twice as fast as controls. This is the first study to demonstrate that an F-BAR protein functions differently in neuronal versus nonneuronal cells and induces lamellipodial protrusions instead of invaginations or filopodia-like structures.
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22
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Quiñones GA, Oro AE. BAR domain competition during directional cellular migration. Cell Cycle 2011; 9:2522-8. [PMID: 20581461 DOI: 10.4161/cc.9.13.12123] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
While directed cellular migration facilitates the coordinated movement of cells during development and tissue repair, the precise mechanisms regulating the interplay between the extracellular environment, the actin cytoskeleton, and the overlying plasma membrane remain inadequately understood. The BAR domain family of lipid binding, actin cytoskeletal regulators are gaining greater appreciation for their role in these critical processes. BAR domain proteins are involved as both positive and negative regulators of endocytosis, membrane plasticity, and directional cell migration. This review focuses on the functional relationship between different classes of BAR domain proteins and their role in guiding cell migration through regulation of the endocytic machinery. Competition for key signaling substrates by positive and negative BAR domain endocytic regulators appears to mediate control of directional cell migration, and may have wider applicability to other trafficking functions associated with development and carcinogenesis.
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Affiliation(s)
- Gabriel A Quiñones
- Program in Epithelial Biology and Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA, USA
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23
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Lyman E, Cui H, Voth GA. Reconstructing protein remodeled membranes in molecular detail from mesoscopic models. Phys Chem Chem Phys 2011; 13:10430-6. [PMID: 21503332 DOI: 10.1039/c0cp02978e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a method for "inverse coarse graining," rebuilding a higher resolution model from a lower resolution one, in order to rebuild protein coats for remodeled membranes of complex topology. The specific case of membrane remodeling by N-BAR domain containing proteins is considered here, although the overall method is general and thus applicable to other membrane remodeling phenomena. Our approach begins with a previously developed, discretized mesoscopic continuum membrane model (EM2) which has been shown to capture the reticulated membrane topologies often observed for N-BAR/liposome systems by electron microscopy (EM). The information in the EM2 model-directions of the local curvatures and a low resolution sample of the membrane surface-is then used to construct a coarse-grained (CG) system with one site per lipid and 26 sites per protein. We demonstrate the approach on pieces of EM2 structures with three different topologies that have been observed by EM: A tubule, a "Y" junction, and a torus. We show that the approach leads to structures that are stable under subsequent constant temperature CG simulation, and end by considering the future application of the methodology as a hybrid approach that combines experimental information with computer modeling.
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Affiliation(s)
- Edward Lyman
- Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, 5735 S Ellis Ave., Chicago, IL 60637, USA
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24
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Guo S, Bao S. srGAP2 arginine methylation regulates cell migration and cell spreading through promoting dimerization. J Biol Chem 2010; 285:35133-41. [PMID: 20810653 DOI: 10.1074/jbc.m110.153429] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Slit-Robo GTPase-activating proteins (srGAPs) are critical for neuronal migration through inactivation of Rho GTPases Cdc42, Rac1, and RhoA. Here we report that srGAP2 physically interacts with protein arginine methyltransferase 5 (PRMT5). srGAP2 localizes to the cytoplasm and plasma membrane protrusion. srGAP2 knockdown reduces cell adhesion spreading and increases cell migration, but has no effect on cell proliferation. PRMT5 binds to the N terminus of srGAP2 (225-538 aa) and methylates its C-terminal arginine residue Arg-927. The methylation mutant srGAP2-R927A fails to rescue the cell spreading rate, is unable to localize to the plasma membrane leading edge, and perturbs srGAP2 homodimer formation mediated by the F-BAR domain. These results suggest that srGAP2 arginine methylation plays important roles in cell spreading and cell migration through influencing membrane protrusion.
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Affiliation(s)
- Shaoshi Guo
- Key Laboratory of Molecular and Developmental Biology, Center for Molecular and Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
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25
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Mizuno N, Jao CC, Langen R, Steven AC. Multiple modes of endophilin-mediated conversion of lipid vesicles into coated tubes: implications for synaptic endocytosis. J Biol Chem 2010; 285:23351-8. [PMID: 20484046 DOI: 10.1074/jbc.m110.143776] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Endophilin A1 is a BAR (Bin/amphiphysin/Rvs) protein abundant in neural synapses that senses and induces membrane curvature, contributing to neck formation in presynaptic endocytic vesicles. To investigate its role in membrane remodeling, we used cryoelectron microscopy to characterize structural changes induced in lipid vesicles by exposure to endophilin. The vesicles convert rapidly to coated tubules whose morphology reflects the local concentration of endophilin. Their diameters and curvature resemble those of synaptic vesicles in situ. Three-dimensional reconstructions of quasicylindrical tubes revealed arrays of BAR dimers, flanked by densities that we equate with amphipathic helices whose folding and membrane insertion were attested by EPR. We also observed the compression of bulbous coated tubes into 70-A-wide cylindrical micelles, which appear to mimic the penultimate (hemi-fission) stage of endocytosis. Our findings suggest that the adaptability of endophilin-lipid interactions underlies dynamic changes of endocytic membranes.
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Affiliation(s)
- Naoko Mizuno
- Laboratory of Structural Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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26
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Jao CC, Hegde BG, Gallop JL, Hegde PB, McMahon HT, Haworth IS, Langen R. Roles of amphipathic helices and the bin/amphiphysin/rvs (BAR) domain of endophilin in membrane curvature generation. J Biol Chem 2010; 285:20164-70. [PMID: 20418375 DOI: 10.1074/jbc.m110.127811] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Control of membrane curvature is required in many important cellular processes, including endocytosis and vesicular trafficking. Endophilin is a bin/amphiphysin/rvs (BAR) domain protein that induces vesicle formation by promotion of membrane curvature through membrane binding as a dimer. Using site-directed spin labeling and EPR spectroscopy, we show that the overall BAR domain structure of the rat endophilin A1 dimer determined crystallographically is maintained under predominantly vesiculating conditions. Spin-labeled side chains on the concave surface of the BAR domain do not penetrate into the acyl chain interior, indicating that the BAR domain interacts only peripherally with the surface of a curved bilayer. Using a combination of EPR data and computational refinement, we determined the structure of residues 63-86, a region that is disordered in the crystal structure of rat endophilin A1. Upon membrane binding, residues 63-75 in each subunit of the endophilin dimer form a slightly tilted, amphipathic alpha-helix that directly interacts with the membrane. In their predominant conformation, these helices are located orthogonal to the long axis of the BAR domain. In this conformation, the amphipathic helices are positioned to act as molecular wedges that induce membrane curvature along the concave surface of the BAR domain.
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Affiliation(s)
- Christine C Jao
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California 90033, USA
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27
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Quinones GA, Jin J, Oro AE. I-BAR protein antagonism of endocytosis mediates directional sensing during guided cell migration. ACTA ACUST UNITED AC 2010; 189:353-67. [PMID: 20385776 PMCID: PMC2856902 DOI: 10.1083/jcb.200910136] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The I-BAR domain–containing protein, missing-in-metastasis, directs cell motility by opposing the endocytic activity of the endophilin–CD2AP–cortactin complex. Although directed cellular migration facilitates the coordinated movement of cells during development and repair, the mechanisms regulating such migration remain poorly understood. Missing-in-metastasis (MIM) is a defining member of the inverse Bin/Amphiphysin/Rvs domain (I-BAR) subfamily of lipid binding, cytoskeletal regulators whose levels are altered in a number of cancers. Here, we provide the first genetic evidence that an I-BAR protein regulates directed cell migration in vivo. Drosophila MIM (dmim) is involved in Drosophila border cell migration, with loss of dmim function resulting in a lack of directional movement by the border cell cluster. In vivo endocytosis assays combined with genetic analyses demonstrate that the dmim product regulates directed cell movement by inhibiting endocytosis and antagonizing the activities of the CD2-associated protein/cortactin complex in these cells. These studies demonstrate that DMIM antagonizes pro-endocytic components to facilitate polarity and localized guidance cue sensing during directional cell migration.
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Affiliation(s)
- Gabriel A Quinones
- Program in Epithelial Biology and Cancer Biology Graduate Program, Stanford University School of Medicine, Stanford, CA 94305, USA
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28
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Abstract
The dynamic remolding of the actin cytoskeleton is a critical part of most cellular activities, and malfunction of cytoskeletal proteins results in various human diseases. The transition between two forms of actin, monomeric or G-actin and filamentous or F-actin, is tightly regulated in time and space by a large number of signaling, scaffolding and actin-binding proteins (ABPs). New ABPs are constantly being discovered in the post-genomic era. Most of these proteins are modular, integrating actin binding, protein-protein interaction, membrane-binding, and signaling domains. In response to extracellular signals, often mediated by Rho family GTPases, ABPs control different steps of actin cytoskeleton assembly, including filament nucleation, elongation, severing, capping, and depolymerization. This review summarizes structure-function relationships among ABPs in the regulation of actin cytoskeleton assembly.
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Affiliation(s)
- Sung Haeng Lee
- Chosun University School of Medicine, Department of Cellular and Molecular Medicine, Gwangju 501-759, Korea.
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Madsen KL, Bhatia VK, Gether U, Stamou D. BAR domains, amphipathic helices and membrane-anchored proteins use the same mechanism to sense membrane curvature. FEBS Lett 2010; 584:1848-55. [PMID: 20122931 DOI: 10.1016/j.febslet.2010.01.053] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 01/26/2010] [Indexed: 12/24/2022]
Abstract
The internal membranes of eukaryotic cells are all twists and bends characterized by high curvature. During recent years it has become clear that specific proteins sustain these curvatures while others simply recognize membrane shape and use it as "molecular information" to organize cellular processes in space and time. Here we discuss this new important recognition process termed membrane curvature sensing (MCS). First, we review a new fluorescence-based experimental method that allows characterization of MCS using measurements on single vesicles and compare it to sensing assays that use bulk/ensemble liposome samples of different mean diameter. Next, we describe two different MCS protein motifs (amphipathic helices and BAR domains) and suggest that in both cases curvature sensitive membrane binding results from asymmetric insertion of hydrophobic amino acids in the lipid membrane. This mechanism can be extended to include the insertion of alkyl chain in the lipid membrane and consequently palmitoylated and myristoylated proteins are predicted to display similar curvature sensitive binding. Surprisingly, in all the aforementioned cases, MCS is predominantly mediated by a higher density of binding sites on curved membranes instead of higher affinity as assumed so far. Finally, we integrate these new insights into the debate about which motifs are involved in sensing versus induction of membrane curvature and what role MCS proteins may play in biology.
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Affiliation(s)
- K L Madsen
- Molecular Neuropharmacology Group, Department of Neuroscience and Pharmacology, The Panum Institute, University of Copenhagen, Copenhagen, Denmark.
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Requirements for F-BAR proteins TOCA-1 and TOCA-2 in actin dynamics and membrane trafficking during Caenorhabditis elegans oocyte growth and embryonic epidermal morphogenesis. PLoS Genet 2009; 5:e1000675. [PMID: 19798448 PMCID: PMC2744924 DOI: 10.1371/journal.pgen.1000675] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 09/02/2009] [Indexed: 01/03/2023] Open
Abstract
The TOCA family of F-BAR–containing proteins bind to and remodel lipid bilayers via their conserved F-BAR domains, and regulate actin dynamics via their N-Wasp binding SH3 domains. Thus, these proteins are predicted to play a pivotal role in coordinating membrane traffic with actin dynamics during cell migration and tissue morphogenesis. By combining genetic analysis in Caenorhabditis elegans with cellular biochemical experiments in mammalian cells, we showed that: i) loss of CeTOCA proteins reduced the efficiency of Clathrin-mediated endocytosis (CME) in oocytes. Genetic interference with CeTOCAs interacting proteins WSP-1 and WVE-1, and other components of the WVE-1 complex, produced a similar effect. Oocyte endocytosis defects correlated well with reduced egg production in these mutants. ii) CeTOCA proteins localize to cell–cell junctions and are required for proper embryonic morphogenesis, to position hypodermal cells and to organize junctional actin and the junction-associated protein AJM-1. iii) Double mutant analysis indicated that the toca genes act in the same pathway as the nematode homologue of N-WASP/WASP, wsp-1. Furthermore, mammalian TOCA-1 and C. elegans CeTOCAs physically associated with N-WASP and WSP-1 directly, or WAVE2 indirectly via ABI-1. Thus, we propose that TOCA proteins control tissues morphogenesis by coordinating Clathrin-dependent membrane trafficking with WAVE and N-WASP–dependent actin-dynamics. Cells continuously remodel their shape especially during cell migration, differentiation, and tissues morphogenesis. This occurs through the dynamic reorganization of their plasma membrane and actin cytoskeleton: two processes that must therefore be intimately linked and coordinated. Molecules that sit at the crossroads of membrane remodeling and actin dynamics are predicted to play a pivotal role in coordinating these processes. The TOCA family of proteins represents a case in point. These proteins bind to and deform membranes during processes such as membrane trafficking. They also control actin dynamics through their interactions with actin remodeling factors, such as WASP and WAVEs. Here, we characterize the functional role of TOCA proteins in a model organism, the nematode Caenorhabditis elegans. We established that toca genes regulate Clathrin-mediated membrane trafficking during oocyte growth. We further discovered that these proteins play an important role in epithelial morphogenesis in developing embryos, and in egg production in adult nematodes. Moreover, the TOCA interacting proteins WASP/WSP-1 and WAVE/WVE-1, as well as other components of the WVE-1 complex, appear to be involved in TOCA-dependent processes. Thus, we propose that TOCA proteins control tissue morphogenesis by coordinating Clathrin-dependent membrane trafficking with WAVE and N-WASP–dependent actin-dynamics.
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fps/fes knockout mice display a lactation defect and the fps/fes tyrosine kinase is a component of E-cadherin-based adherens junctions in breast epithelial cells during lactation. Exp Cell Res 2009; 315:2929-40. [PMID: 19732771 DOI: 10.1016/j.yexcr.2009.08.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 08/21/2009] [Accepted: 08/25/2009] [Indexed: 12/18/2022]
Abstract
The fps/fes proto-oncogene encodes a cytoplasmic protein-tyrosine kinase implicated in vesicular trafficking and cytokine and growth factor signaling in hematopoietic, neuronal, vascular endothelial and epithelial lineages. Genetic evidence has suggested a tumor suppressor role for Fps/Fes in breast and colon. Here we used fps/fes knockout mice to investigate potential roles for this kinase in development and function of the mammary gland. Fps/Fes expression was induced during pregnancy and lactation, and its kinase activity was dramatically enhanced. Milk protein and fat composition from nursing fps/fes-null mothers was normal; however, pups reared by them gained weight more slowly than pups reared by wild-type mothers. Fps/Fes displayed a predominantly dispersed punctate intracellular distribution which was consistent with vesicles within the luminal epithelial cells of lactating breast, while a small fraction co-localized with beta-catenin and E-cadherin on their basolateral surfaces. Fps/Fes was found to be a component of the E-cadherin adherens junction (AJ) complex; however, the phosphotyrosine status of beta-catenin and core AJ components in fps/fes-null breast tissue was unaltered, and epithelial cell AJs and gland morphology were intact. We conclude that Fps/Fes is not essential for the maintenance of epithelial cell AJs in the lactating breast but may instead play important roles in vesicular trafficking and milk secretion.
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Waite AL, Schaner P, Richards N, Balci-Peynircioglu B, Masters SL, Brydges SD, Fox M, Hong A, Yilmaz E, Kastner DL, Reinherz EL, Gumucio DL. Pyrin Modulates the Intracellular Distribution of PSTPIP1. PLoS One 2009; 4:e6147. [PMID: 19584923 PMCID: PMC2702820 DOI: 10.1371/journal.pone.0006147] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 06/03/2009] [Indexed: 01/23/2023] Open
Abstract
PSTPIP1 is a cytoskeleton-associated adaptor protein that links PEST-type phosphatases to their substrates. Mutations in PSTPIP1 cause PAPA syndrome (Pyogenic sterile Arthritis, Pyoderma gangrenosum, and Acne), an autoinflammatory disease. PSTPIP1 binds to pyrin and mutations in pyrin result in familial Mediterranean fever (FMF), a related autoinflammatory disorder. Since disease-associated mutations in PSTPIP1 enhance pyrin binding, PAPA syndrome and FMF are thought to share a common pathoetiology. The studies outlined here describe several new aspects of PSTPIP1 and pyrin biology. We document that PSTPIP1, which has homology to membrane-deforming BAR proteins, forms homodimers and generates membrane-associated filaments in native and transfected cells. An extended FCH (Fes-Cip4 homology) domain in PSTPIP1 is necessary and sufficient for its self-aggregation. We further show that the PSTPIP1 filament network is dependent upon an intact tubulin cytoskeleton and that the distribution of this network can be modulated by pyrin, indicating that this is a dynamic structure. Finally, we demonstrate that pyrin can recruit PSTPIP1 into aggregations (specks) of ASC, another pyrin binding protein. ASC specks are associated with inflammasome activity. PSTPIP1 molecules with PAPA-associated mutations are recruited by pyrin to ASC specks with particularly high efficiency, suggesting a unique mechanism underlying the robust inflammatory phenotype of PAPA syndrome.
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Affiliation(s)
- Andrea L. Waite
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Philip Schaner
- Division of Radiology/Oncology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Neil Richards
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | | | - Seth L. Masters
- School of Biochemistry and Immunology, Trinity College, Dublin, Ireland
| | - Susannah D. Brydges
- Genetics and Genomics Branch, National Institute of Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Michelle Fox
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Arthur Hong
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Engin Yilmaz
- Department of Medical Biology, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Daniel L. Kastner
- Genetics and Genomics Branch, National Institute of Arthritis and Musculoskeletal and Skin Disease, National Institutes of Health (NIH), Bethesda, Maryland, United States of America
| | - Ellis L. Reinherz
- Harvard Medical School, Laboratory of Immunology, Dana Farber Cancer Institute, Boston, Massachusetts, United States of America
| | - Deborah L. Gumucio
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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Modeling morphological instabilities in lipid membranes with anchored amphiphilic polymers. J Chem Biol 2009; 2:65-80. [PMID: 19568784 PMCID: PMC2701491 DOI: 10.1007/s12154-009-0020-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2009] [Accepted: 04/29/2009] [Indexed: 12/13/2022] Open
Abstract
Anchoring molecules, like amphiphilic polymers, are able to dynamically regulate membrane morphology. Such molecules insert their hydrophobic groups into the bilayer, generating a local membrane curvature. In order to minimize the elastic energy penalty, a dynamic shape instability may occur, as in the case of the curvature-driven pearling instability or the polymer-induced tubulation of lipid vesicles. We review recent works on modeling of such instabilities by means of a mesoscopic dynamic model of the phase-field kind, which take into account the bending energy of lipid bilayers.
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Abstract
Membrane-shaping proteins of the BAR domain superfamily are determinants of organelle biogenesis, membrane trafficking, cell division, and cell migration. An upsurge of research now reveals new principles of BAR domain-mediated membrane remodeling, enhancing our understanding of membrane curvature-mediated information processing.
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Heath RJW, Insall RH. F-BAR domains: multifunctional regulators of membrane curvature. J Cell Sci 2009; 121:1951-4. [PMID: 18525024 DOI: 10.1242/jcs.023895] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Saarikangas J, Zhao H, Pykäläinen A, Laurinmäki P, Mattila PK, Kinnunen PKJ, Butcher SJ, Lappalainen P. Molecular mechanisms of membrane deformation by I-BAR domain proteins. Curr Biol 2009; 19:95-107. [PMID: 19150238 DOI: 10.1016/j.cub.2008.12.029] [Citation(s) in RCA: 232] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 11/26/2008] [Accepted: 12/08/2008] [Indexed: 02/06/2023]
Abstract
BACKGROUND Generation of membrane curvature is critical for the formation of plasma membrane protrusions and invaginations and for shaping intracellular organelles. Among the central regulators of membrane dynamics are the BAR superfamily domains, which deform membranes into tubular structures. In contrast to the relatively well characterized BAR and F-BAR domains that promote the formation of plasma membrane invaginations, I-BAR domains induce plasma membrane protrusions through a poorly understood mechanism. RESULTS We show that I-BAR domains induce strong PI(4,5)P(2) clustering upon membrane binding, bend the membrane through electrostatic interactions, and remain dynamically associated with the inner leaflet of membrane tubules. Thus, I-BAR domains induce the formation of dynamic membrane protrusions to the opposite direction than do BAR and F-BAR domains. Strikingly, comparison of different I-BAR domains revealed that they deform PI(4,5)P(2)-rich membranes through distinct mechanisms. IRSp53 and IRTKS I-BARs bind membranes mainly through electrostatic interactions, whereas MIM and ABBA I-BARs additionally insert an amphipathic helix into the membrane bilayer, resulting in larger tubule diameter in vitro and more efficient filopodia formation in vivo. Furthermore, FRAP analysis revealed that whereas the mammalian I-BAR domains display dynamic association with filopodia, the C. elegans I-BAR domain forms relatively stable structures inside the plasma membrane protrusions. CONCLUSIONS These data define I-BAR domain as a functional member of the BAR domain superfamily and unravel the mechanisms by which I-BAR domains deform membranes to induce filopodia in cells. Furthermore, our work reveals unexpected divergence in the mechanisms by which evolutionarily distinct groups of I-BAR domains interact with PI(4,5)P(2)-rich membranes.
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Affiliation(s)
- Juha Saarikangas
- Program in Cell and Molecular Biology, Institute of Biotechnology, P.O. Box 56, University of Helsinki, FIN-00014 Helsinki, Finland
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Abstract
The BAR (Bin/amphiphysin/Rvs) domain defines an emerging superfamily of proteins implicated in fundamental biological processes by sensing and inducing membrane curvature. We identified a novel autoregulatory function for the BAR domain of two related GAPs' (GTPase-activating proteins) of the GRAF (GTPase regulator associated with focal adhesion kinase) subfamily. We demonstrate that the N-terminal fragment of these GAPs including the BAR domain interacts directly with the GAP domain and inhibits its activity. Analysis of various BAR and GAP domains revealed that the BAR domain-mediated inhibition of these GAPs' function is highly specific. These GAPs, in their autoinhibited state, are able to bind and tubulate liposomes in vitro, and to generate lipid tubules in cells. Taken together, we identified BAR domains as cis-acting inhibitory elements that very likely mask the active sites of the GAP domains and thus prevent down-regulation of Rho proteins. Most remarkably, these BAR proteins represent a dual-site system with separate membrane-tubulation and GAP-inhibitory functions that operate simultaneously.
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Abstract
A wide spectrum of intracellular processes is dependent on the ability of cells to dynamically regulate membrane shape. Membrane bending by proteins is necessary for the generation of intracellular transport carriers and for the maintenance of otherwise intrinsically unstable regions of high membrane curvature in cell organelles. Understanding the mechanisms by which proteins curve membranes is therefore of primary importance. Here we suggest, for the first time to our knowledge, a quantitative mechanism of lipid membrane bending by hydrophobic or amphipathic rodlike inclusions which simulate amphipathic alpha-helices-structures shown to sculpt membranes. Considering the lipid monolayer matrix as an anisotropic elastic material, we compute the intramembrane stresses and strains generated by the embedded inclusions, determine the resulting membrane shapes, and the accumulated elastic energy. We characterize the ability of an inclusion to bend membranes by an effective spontaneous curvature, and show that shallow rodlike inclusions are more effective in membrane shaping than are lipids having a high propensity for curvature. Our computations provide experimentally testable predictions on the protein amounts needed to generate intracellular membrane shapes for various insertion depths and membrane thicknesses. We also predict that the ability of N-BAR domains to produce membrane tubules in vivo can be ascribed solely to insertion of their amphipathic helices.
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Heath RJW, Insall RH. Dictyostelium MEGAPs: F-BAR domain proteins that regulate motility and membrane tubulation in contractile vacuoles. J Cell Sci 2008; 121:1054-64. [DOI: 10.1242/jcs.021113] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
PCH family proteins are fundamentally important proteins, linking membrane curvature events with cytoskeletal reorganisation. One group, the MEGAPs (also called srGAPs and WRPs) contain RhoGAP domains in addition to the F-BAR domain. We disrupted MEGAP1 and MEGAP2 in Dictyostelium both singly and in combination. We found a strong cytoskeletal phenotype in MEGAP1– cells and a subtle phototaxis defect in MEGAP2– slugs. MEGAP1–/2– cells have an overabundance of filopodia and slug motility and function are affected. The most dramatic changes, however, are on contractile vacuoles. MEGAP1–/2– cells empty their contractile vacuoles less efficiently than normal and consequently have three times the usual number. GFP-tagged MEGAP1 localises to tubules of the contractile vacuole network and when vacuoles start to empty they recruit cytosolic GFP-MEGAP1. Mutants in the Saccharomyces homologues RGD1 and RGD2 also show abnormal vacuoles, implying that this role is conserved. Thus, MEGAP is an important regulator of the contractile vacuole network, and we propose that tubulation of the contractile vacuole by MEGAP1 represents a novel mechanism for driving vacuole emptying.
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Affiliation(s)
- Robert J. W. Heath
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Robert H. Insall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- The Beatson Institute for Cancer Research, Glasgow, G61 1BD, UK
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Hu J, Shibata Y, Voss C, Shemesh T, Li Z, Coughlin M, Kozlov MM, Rapoport TA, Prinz WA. Membrane proteins of the endoplasmic reticulum induce high-curvature tubules. Science 2008; 319:1247-50. [PMID: 18309084 DOI: 10.1126/science.1153634] [Citation(s) in RCA: 346] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The tubular structure of the endoplasmic reticulum (ER) appears to be generated by integral membrane proteins, the reticulons and a protein family consisting of DP1 in mammals and Yop1p in yeast. Here, individual members of these families were found to be sufficient to generate membrane tubules. When we purified yeast Yop1p and incorporated it into proteoliposomes, narrow tubules (approximately 15 to 17 nanometers in diameter) were generated. Tubule formation occurred with different lipids; required essentially only the central portion of the protein, including its two long hydrophobic segments; and was prevented by mutations that affected tubule formation in vivo. Tubules were also formed by reconstituted purified yeast Rtn1p. Tubules made in vitro were narrower than normal ER tubules, due to a higher concentration of tubule-inducing proteins. The shape and oligomerization of the "morphogenic" proteins could explain the formation of the tubular ER.
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Affiliation(s)
- Junjie Hu
- Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Scita G, Confalonieri S, Lappalainen P, Suetsugu S. IRSp53: crossing the road of membrane and actin dynamics in the formation of membrane protrusions. Trends Cell Biol 2008; 18:52-60. [DOI: 10.1016/j.tcb.2007.12.002] [Citation(s) in RCA: 208] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2007] [Revised: 12/04/2007] [Accepted: 12/04/2007] [Indexed: 11/16/2022]
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