1
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Huang WYC, Boxer SG, Ferrell JE. Membrane localization accelerates association under conditions relevant to cellular signaling. Proc Natl Acad Sci U S A 2024; 121:e2319491121. [PMID: 38427601 PMCID: PMC10927583 DOI: 10.1073/pnas.2319491121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 01/16/2024] [Indexed: 03/03/2024] Open
Abstract
Translocation of cytoplasmic molecules to the plasma membrane is commonplace in cell signaling. Membrane localization has been hypothesized to increase intermolecular association rates; however, it has also been argued that association should be faster in the cytosol because membrane diffusion is slow. Here, we directly compare an identical association reaction, the binding of complementary DNA strands, in solution and on supported membranes. The measured rate constants show that for a 10-µm-radius spherical cell, association is 22- to 33-fold faster at the membrane than in the cytoplasm. The kinetic advantage depends on cell size and is essentially negligible for typical ~1 µm prokaryotic cells. The rate enhancement is attributable to a combination of higher encounter rates in two dimensions and a higher reaction probability per encounter.
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Affiliation(s)
- William Y. C. Huang
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA94305
| | - Steven G. Boxer
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - James E. Ferrell
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
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2
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Pezeshkian W, Ipsen JH. Mesoscale simulation of biomembranes with FreeDTS. Nat Commun 2024; 15:548. [PMID: 38228588 PMCID: PMC10792169 DOI: 10.1038/s41467-024-44819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 01/05/2024] [Indexed: 01/18/2024] Open
Abstract
We present FreeDTS software for performing computational research on biomembranes at the mesoscale. In this software, a membrane is represented by a dynamically triangulated surface equipped with vertex-based inclusions to integrate the effects of integral and peripheral membrane proteins. Several algorithms are included in the software to simulate complex membranes at different conditions such as framed membranes with constant tension, vesicles and high-genus membranes with various fixed volumes or constant pressure differences and applying external forces to membrane regions. Furthermore, the software allows the user to turn off the shape evolution of the membrane and focus solely on the organization of proteins. As a result, we can take realistic membrane shapes obtained from, for example, cryo-electron tomography and backmap them into a finer simulation model. In addition to many biomembrane applications, this software brings us a step closer to simulating realistic biomembranes with molecular resolution. Here we provide several interesting showcases of the power of the software but leave a wide range of potential applications for interested users.
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Affiliation(s)
- Weria Pezeshkian
- Niels Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100, Copenhagen, Denmark.
| | - John H Ipsen
- MEMPHYS/PhyLife, Department of Physics, Chemistry and Pharmacy (FKF), University of Southern Denmark, Campusvej 55, 5230, Odense M, Denmark
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3
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Aramesh M, Persson C. Induced Formation of Plasma Membrane Protrusions with Porous Materials as Instructive Surfaces. Methods Mol Biol 2024; 2800:27-34. [PMID: 38709475 DOI: 10.1007/978-1-0716-3834-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
The plasma membrane is a vital component in cellular processes, and its structure has a significant impact on cellular behavior. The physical characteristics of the extracellular environment, along with the presence of surface pores, can influence the formation of membrane protrusions. Nanoporous surfaces have demonstrated their capacity to induce membrane protrusions in both adherent and non-adherent cells. This chapter presents a methodology that utilizes a nanoporous substrate with nanotopographical constraints to effectively stimulate the formation of membrane protrusions in cells.
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Affiliation(s)
- Morteza Aramesh
- Division of Biomedical Engineering, Department of Materials Science and Engineering, Uppsala University, Uppsala, Sweden.
- AM4Life Competence Centre in Additive Manufacturing for the Life Sciences, Uppsala University, Uppsala, Sweden.
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland.
| | - Cecilia Persson
- Division of Biomedical Engineering, Department of Materials Science and Engineering, Uppsala University, Uppsala, Sweden.
- AM4Life Competence Centre in Additive Manufacturing for the Life Sciences, Uppsala University, Uppsala, Sweden.
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4
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Measuring three-dimensional organization on cell surfaces with cellular harmonics. NATURE COMPUTATIONAL SCIENCE 2023; 3:825-826. [PMID: 38177752 DOI: 10.1038/s43588-023-00517-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
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5
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Mazloom-Farsibaf H, Zou Q, Hsieh R, Danuser G, Driscoll MK. Cellular harmonics for the morphology-invariant analysis of molecular organization at the cell surface. NATURE COMPUTATIONAL SCIENCE 2023; 3:777-788. [PMID: 38177778 PMCID: PMC10840993 DOI: 10.1038/s43588-023-00512-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/08/2023] [Indexed: 01/06/2024]
Abstract
The spatiotemporal organization of membrane-associated molecules is central to the regulation of cellular signals. Powerful new microscopy techniques enable the three-dimensional visualization of localization and activation of these molecules; however, the quantitative interpretation and comparison of molecular organization on the three-dimensional cell surface remains challenging because cells themselves vary greatly in morphology. Here we introduce u-signal3D, a framework to assess the spatial scales of molecular organization at the cell surface in a cell-morphology-invariant manner. We validated the framework by analyzing synthetic signaling patterns painted onto observed cell morphologies, as well as measured distributions of cytoskeletal and signaling molecules. To demonstrate the framework's versatility, we further compared the spatial organization of cell surface signals both within, and between, cell populations, and powered an upstream machine-learning-based analysis of signaling motifs.
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Affiliation(s)
- Hanieh Mazloom-Farsibaf
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qiongjing Zou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rebecca Hsieh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Meghan K Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA.
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6
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Erazo-Oliveras A, Muñoz-Vega M, Mlih M, Thiriveedi V, Salinas ML, Rivera-Rodríguez JM, Kim E, Wright RC, Wang X, Landrock KK, Goldsby JS, Mullens DA, Roper J, Karpac J, Chapkin RS. Mutant APC reshapes Wnt signaling plasma membrane nanodomains by altering cholesterol levels via oncogenic β-catenin. Nat Commun 2023; 14:4342. [PMID: 37468468 PMCID: PMC10356786 DOI: 10.1038/s41467-023-39640-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
Although the role of the Wnt pathway in colon carcinogenesis has been described previously, it has been recently demonstrated that Wnt signaling originates from highly dynamic nano-assemblies at the plasma membrane. However, little is known regarding the role of oncogenic APC in reshaping Wnt nanodomains. This is noteworthy, because oncogenic APC does not act autonomously and requires activation of Wnt effectors upstream of APC to drive aberrant Wnt signaling. Here, we demonstrate the role of oncogenic APC in increasing plasma membrane free cholesterol and rigidity, thereby modulating Wnt signaling hubs. This results in an overactivation of Wnt signaling in the colon. Finally, using the Drosophila sterol auxotroph model, we demonstrate the unique ability of exogenous free cholesterol to disrupt plasma membrane homeostasis and drive Wnt signaling in a wildtype APC background. Collectively, these findings provide a link between oncogenic APC, loss of plasma membrane homeostasis and CRC development.
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Affiliation(s)
- Alfredo Erazo-Oliveras
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Mónica Muñoz-Vega
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Mohamed Mlih
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, Bryan, TX, 77807, USA
| | - Venkataramana Thiriveedi
- Department of Medicine, Division of Gastroenterology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Michael L Salinas
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Jaileen M Rivera-Rodríguez
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Eunjoo Kim
- Division of Pulmonary Sciences and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Denver, CO, 80045, USA
| | - Rachel C Wright
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - Xiaoli Wang
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - Kerstin K Landrock
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
| | - Jennifer S Goldsby
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Destiny A Mullens
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA
| | - Jatin Roper
- Department of Medicine, Division of Gastroenterology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Department of Cell Biology, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Jason Karpac
- Department of Cell Biology and Genetics, Texas A&M University, School of Medicine, Bryan, TX, 77807, USA
| | - Robert S Chapkin
- Program in Integrative Nutrition and Complex Diseases, Texas A&M University, College Station, TX, 77843, USA.
- Department of Nutrition, Texas A&M University, College Station, TX, 77843, USA.
- CPRIT Regional Center of Excellence in Cancer Research, Texas A&M University, College Station, TX, 77843, USA.
- Center for Environmental Health Research, Texas A&M University, College Station, TX, 77843, USA.
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7
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Zhou FY, Weems A, Gihana GM, Chen B, Chang BJ, Driscoll M, Danuser G. Surface-guided computing to analyze subcellular morphology and membrane-associated signals in 3D. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536640. [PMID: 37131779 PMCID: PMC10153113 DOI: 10.1101/2023.04.12.536640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Signal transduction and cell function are governed by the spatiotemporal organization of membrane-associated molecules. Despite significant advances in visualizing molecular distributions by 3D light microscopy, cell biologists still have limited quantitative understanding of the processes implicated in the regulation of molecular signals at the whole cell scale. In particular, complex and transient cell surface morphologies challenge the complete sampling of cell geometry, membrane-associated molecular concentration and activity and the computing of meaningful parameters such as the cofluctuation between morphology and signals. Here, we introduce u-Unwrap3D, a framework to remap arbitrarily complex 3D cell surfaces and membrane-associated signals into equivalent lower dimensional representations. The mappings are bidirectional, allowing the application of image processing operations in the data representation best suited for the task and to subsequently present the results in any of the other representations, including the original 3D cell surface. Leveraging this surface-guided computing paradigm, we track segmented surface motifs in 2D to quantify the recruitment of Septin polymers by blebbing events; we quantify actin enrichment in peripheral ruffles; and we measure the speed of ruffle movement along topographically complex cell surfaces. Thus, u-Unwrap3D provides access to spatiotemporal analyses of cell biological parameters on unconstrained 3D surface geometries and signals.
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Affiliation(s)
- Felix Y. Zhou
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew Weems
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gabriel M. Gihana
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bingying Chen
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bo-Jui Chang
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Meghan Driscoll
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Current address: Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Cecil H. & Ida Green Center for System Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
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8
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Kumar S, Karmacharya M, Cho YK. Bridging the Gap between Nonliving Matter and Cellular Life. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202962. [PMID: 35988151 DOI: 10.1002/smll.202202962] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/28/2022] [Indexed: 06/15/2023]
Abstract
A cell, the fundamental unit of life, contains the requisite blueprint information necessary to survive and to build tissues, organs, and systems, eventually forming a fully functional living creature. A slight structural alteration can result in data misprinting, throwing the entire life process off balance. Advances in synthetic biology and cell engineering enable the predictable redesign of biological systems to perform novel functions. Individual functions and fundamental processes at the core of the biology of cells can be investigated by employing a synthetically constrained micro or nanoreactor. However, constructing a life-like structure from nonliving building blocks remains a considerable challenge. Chemical compartments, cascade signaling, energy generation, growth, replication, and adaptation within micro or nanoreactors must be comparable with their biological counterparts. Although these reactors currently lack the power and behavioral sophistication of their biological equivalents, their interface with biological systems enables the development of hybrid solutions for real-world applications, such as therapeutic agents, biosensors, innovative materials, and biochemical microreactors. This review discusses the latest advances in cell membrane-engineered micro or nanoreactors, as well as the limitations associated with high-throughput preparation methods and biological applications for the real-time modulation of complex pathological states.
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Affiliation(s)
- Sumit Kumar
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Mamata Karmacharya
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
| | - Yoon-Kyoung Cho
- Center for Soft and Living Matter, Institute for Basic Science (IBS), UNIST-gil 50, Ulsan, 44919, Republic of Korea
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan, 44919, Republic of Korea
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9
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Fanani ML, Ambroggio EE. Phospholipases and Membrane Curvature: What Is Happening at the Surface? MEMBRANES 2023; 13:190. [PMID: 36837693 PMCID: PMC9965983 DOI: 10.3390/membranes13020190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
In this revision work, we emphasize the close relationship between the action of phospholipases and the modulation of membrane curvature and curvature stress resulting from this activity. The alteration of the tridimensional structure of membranes upon the action of phospholipases is analyzed based on studies on model lipid membranes. The transient unbalance of both compositional and physical membrane properties between the hemilayers upon phospholipase activity lead to curvature tension and the catalysis of several membrane-related processes. Several proteins' membrane-bound and soluble forms are susceptible to regulation by the curvature stress induced by phospholipase action, which has important consequences in cell signaling. Additionally, the modulation of membrane fusion by phospholipase products regulates membrane dynamics in several cellular scenarios. We commented on vesicle fusion in the Golgi-endoplasmic system, synaptic vesicle fusion to the plasma membrane, viral membrane fusion to host cell plasma membrane and gametes membrane fusion upon acrosomal reaction. Furthermore, we explored the modulation of membrane fusion by the asymmetric adsorption of amphiphilic drugs. A deep understanding of the relevance of lipid membrane structure, particularly membrane curvature and curvature stress, on different cellular events leads to the challenge of its regulation, which may become a powerful tool for pharmacological therapy.
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Affiliation(s)
- María Laura Fanani
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba X5000HUA, Argentina
| | - Ernesto Esteban Ambroggio
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba X5000HUA, Argentina
- Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Haya de la Torre y Medina Allende, Ciudad Universitaria, Córdoba X5000HUA, Argentina
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10
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Way JC, Burrill DR, Silver PA. Bioinspired Design of Artificial Signaling Systems. Biochemistry 2023; 62:178-186. [PMID: 35984429 PMCID: PMC9851155 DOI: 10.1021/acs.biochem.2c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Indexed: 02/02/2023]
Abstract
Natural systems use weak interactions and avidity effects to give biological systems high specificity and signal-to-noise ratios. Here we describe design principles for engineering fusion proteins that target therapeutic fusion proteins to membrane-bound signaling receptors by first binding to designer-chosen co-receptors on the same cell surface. The key design elements are separate protein modules, one that has no signaling activity and binds to a cell surface receptor with high affinity and a second that binds to a receptor with low or moderate affinity and carries out a desired signaling or inhibitory activity. These principles are inspired by natural cytokines such as CNTF, IL-2, and IL-4 that bind strongly to nonsignaling receptors and then signal through low-affinity receptors. Such designs take advantage of the fact that when a protein is anchored to a cell membrane, its local concentration is extremely high with respect to those of other membrane proteins, so a second-step, low-affinity binding event is favored. Protein engineers have used these principles to design treatments for cancer, anemia, hypoxia, and HIV infection.
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Affiliation(s)
- Jeffrey C. Way
- General
Biologics, Inc., 108
Fayerweather Street, Unit 2, Cambridge, Massachusetts 02138, United States
| | - Devin R. Burrill
- Department
of Systems Biology, Harvard Medical School, 210 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Pamela A. Silver
- Department
of Systems Biology, Harvard Medical School, 210 Longwood Avenue, Boston, Massachusetts 02115, United States
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11
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Yan P, Ke B, Fang X. Ion channels as a therapeutic target for renal fibrosis. Front Physiol 2022; 13:1019028. [PMID: 36277193 PMCID: PMC9581181 DOI: 10.3389/fphys.2022.1019028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022] Open
Abstract
Renal ion channel transport and electrolyte disturbances play an important role in the process of functional impairment and fibrosis in the kidney. It is well known that there are limited effective drugs for the treatment of renal fibrosis, and since a large number of ion channels are involved in the renal fibrosis process, understanding the mechanisms of ion channel transport and the complex network of signaling cascades between them is essential to identify potential therapeutic approaches to slow down renal fibrosis. This review summarizes the current work of ion channels in renal fibrosis. We pay close attention to the effect of cystic fibrosis transmembrane conductance regulator (CFTR), transmembrane Member 16A (TMEM16A) and other Cl− channel mediated signaling pathways and ion concentrations on fibrosis, as well as the various complex mechanisms for the action of Ca2+ handling channels including Ca2+-release-activated Ca2+ channel (CRAC), purinergic receptor, and transient receptor potential (TRP) channels. Furthermore, we also focus on the contribution of Na+ transport such as epithelial sodium channel (ENaC), Na+, K+-ATPase, Na+-H+ exchangers, and K+ channels like Ca2+-activated K+ channels, voltage-dependent K+ channel, ATP-sensitive K+ channels on renal fibrosis. Proposed potential therapeutic approaches through further dissection of these mechanisms may provide new therapeutic opportunities to reduce the burden of chronic kidney disease.
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12
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Sun D, LuValle-Burke I, Pombo-García K, Honigmann A. Biomolecular condensates in epithelial junctions. Curr Opin Cell Biol 2022; 77:102089. [PMID: 35696872 DOI: 10.1016/j.ceb.2022.102089] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/05/2022] [Accepted: 04/15/2022] [Indexed: 11/03/2022]
Abstract
Epithelial junctions are transmembrane protein complexes that regulate cell adhesion, cell polarity, tissue permeability, and tissue mechanics. Most junctional complexes contain membrane attached cytoplasmic plaques that regulate junction assembly and are composed of multivalent scaffold proteins. In this review, we discuss phase separation of multivalent proteins as a general process that drives assembly of many membrane-less cellular compartments. And we summarise recent evidence that phase separation of junctional scaffold proteins is involved in the assembly of tight junctions and focal adhesions.
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Affiliation(s)
- Daxiao Sun
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Karina Pombo-García
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Alf Honigmann
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany; Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität, Dresden, Germany.
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13
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14
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Jepson TA, Hall SC, Chung JK. Single-molecule phospholipase A2 becomes processive on melittin-induced membrane deformations. Biophys J 2022; 121:1417-1423. [PMID: 35314142 PMCID: PMC9072580 DOI: 10.1016/j.bpj.2022.03.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/13/2022] [Accepted: 03/15/2022] [Indexed: 11/30/2022] Open
Abstract
While it is established that the topology of lipid membranes plays an important role in biochemical processes, few direct observations exist regarding how the membranes are actively restructured and its consequences on subsequent reactions. In this work, we investigated how the two major components of bee venom, melittin and phospholipase A2 (PLA2), achieve activation by such membrane remodeling. Their membrane-disrupting functions have been reported to increase when both are present, but the mechanism of this synergism had not been established. Using membrane reconstitution, we found that melittin can form large-scale membrane deformities upon which PLA2 activity is 25-fold higher. Tracking of single-molecule PLA2 revealed that its processive behavior on these deformities underlies the enhanced activity. These results show how melittin and PLA2 work synergistically to enhance the lytic effects of the bee venom. More broadly, they also demonstrate how the membrane topology may be actively altered to modulate cellular membrane-bound reactions.
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Affiliation(s)
| | - Sarah C Hall
- Colorado State University, Fort Collins, Colorado
| | - Jean K Chung
- Colorado State University, Fort Collins, Colorado.
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15
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Parchekani J, Allahverdi A, Taghdir M, Naderi-Manesh H. Design and simulation of the liposomal model by using a coarse-grained molecular dynamics approach towards drug delivery goals. Sci Rep 2022; 12:2371. [PMID: 35149771 PMCID: PMC8837752 DOI: 10.1038/s41598-022-06380-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/27/2022] [Indexed: 12/19/2022] Open
Abstract
The simulated liposome models provide events in molecular biological science and cellular biology. These models may help to understand the cell membrane mechanisms, biological cell interactions, and drug delivery systems. In addition, the liposomes model may resolve specific issues such as membrane transports, ion channels, drug penetration in the membrane, vesicle formation, membrane fusion, and membrane protein function mechanism. One of the approaches to investigate the lipid membranes and the mechanism of their formation is by molecular dynamics (MD) simulations. In this study, we used the coarse-grained MD simulation approach and designed a liposome model system. To simulate the liposome model, we used phospholipids that are present in the structure of natural cell membranes (1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) and 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)). Simulation conditions such as temperature, ions, water, lipid concentration were performed based on experimental conditions. Our results showed a liposome model (ellipse vesicle structure) during the 2100 ns was formed. Moreover, the analysis confirmed that the stretched and ellipse structure is the best structure that could be formed. The eukaryotic and even the bacterial cells have elliptical and flexible structures. Usually, an elliptical structure is more stable than other assembled structures. The results indicated the assembly of the lipids is directed through short-range interactions (electrostatic interactions and, van der Waals interactions). Total energy (Van der Waals and electrostatic interaction energy) confirmed the designed elliptical liposome structure has suitable stability at the end of the simulation process. Our findings confirmed that phospholipids DOPC and DOPE have a good tendency to form bilayer membranes (liposomal structure) based on their geometric shapes and chemical-physical properties. Finally, we expected the simulated liposomal structure as a simple model to be useful in understanding the function and structure of biological cell membranes. Furthermore, it is useful to design optimal, suitable, and biocompatible liposomes as potential drug carriers.
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Affiliation(s)
- Jalil Parchekani
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Abdollah Allahverdi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran
| | - Majid Taghdir
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran.
| | - Hossein Naderi-Manesh
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran. .,Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, 14115-154, Iran.
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16
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Huebinger J, Grecco H, Masip ME, Christmann J, Fuhr GR, Bastiaens PIH. Ultrarapid cryo-arrest of living cells on a microscope enables multiscale imaging of out-of-equilibrium molecular patterns. SCIENCE ADVANCES 2021; 7:eabk0882. [PMID: 34890224 PMCID: PMC8664253 DOI: 10.1126/sciadv.abk0882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
Imaging molecular patterns in cells by fluorescence micro- or nanoscopy has the potential to relate collective molecular behavior to cellular function. However, spatial and spectroscopic resolution is fundamentally limited by motional blur caused by finite photon fluxes and photobleaching. At physiological temperatures, photochemical reactivity does not only limit imaging at multiple scales but is also toxic to biochemical reactions that maintain cellular organization. Here, we present cryoprotectant-free ultrarapid cryo-arrest directly on a multimodal fluorescence microscope that preserves the out-of-equilibrium molecular organization of living cells. This allows the imaging of dynamic processes before cryo-arrest in combination with precise molecular pattern determination at multiple scales within the same cells under cryo-arrest. We both experimentally and theoretically show that ultrarapid cryo-arrest overcomes the fundamental resolution barrier imposed by motional blur and photochemical reactivity, enabling observation of native molecular distributions and reaction patterns that are not resolvable at physiological temperatures.
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Affiliation(s)
- Jan Huebinger
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Hernan Grecco
- Department of Physics, FCEN, University of Buenos Aires and IFIBA, CONICET, Buenos Aires, Argentina
| | - Martín E. Masip
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Jens Christmann
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
| | - Günter R. Fuhr
- Fraunhofer Institute for Biomedical Engineering, Joseph-von-Fraunhofer-Weg 1, 66280 Sulzbach, Germany
| | - Philippe I. H. Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str.11, 44227 Dortmund, Germany
- Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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17
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Stochasticity and positive feedback enable enzyme kinetics at the membrane to sense reaction size. Proc Natl Acad Sci U S A 2021; 118:2103626118. [PMID: 34789575 PMCID: PMC8617498 DOI: 10.1073/pnas.2103626118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/10/2021] [Indexed: 12/27/2022] Open
Abstract
Cellular membranes span a wide range of spatial dimensions, from the plasma membrane with a scale of microns to vesicles on the nanometer scale. The work presented here identifies a molecular mechanism, based on common features of cellular signaling enzymes, that causes the average enzymatic catalytic rate to exhibit reaction size dependency. This effect stems from stochastic variation, but the final results can be essentially deterministic. In competitive enzymatic reaction cycles, the final product can depend on the size of the reaction system. The simplicity of the mechanism suggests that size-dependent reaction rates may be widespread among signaling enzymes and thus enable reaction size to be an important factor in signal regulation at the membrane. Here, we present detailed kinetic analyses of a panel of soluble lipid kinases and phosphatases, as well as Ras activating proteins, acting on their respective membrane surface substrates. The results reveal that the mean catalytic rate of such interfacial enzymes can exhibit a strong dependence on the size of the reaction system—in this case membrane area. Experimental measurements and kinetic modeling reveal how stochastic effects stemming from low molecular copy numbers of the enzymes alter reaction kinetics based on mechanistic characteristics of the enzyme, such as positive feedback. For the competitive enzymatic cycles studied here, the final product—consisting of a specific lipid composition or Ras activity state—depends on the size of the reaction system. Furthermore, we demonstrate how these reaction size dependencies can be controlled by engineering feedback mechanisms into the enzymes.
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18
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Ang MJY, Chan SY, Goh YY, Luo Z, Lau JW, Liu X. Emerging strategies in developing multifunctional nanomaterials for cancer nanotheranostics. Adv Drug Deliv Rev 2021; 178:113907. [PMID: 34371084 DOI: 10.1016/j.addr.2021.113907] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 12/11/2022]
Abstract
Cancer involves a collection of diseases with a common trait - dysregulation in cell proliferation. At present, traditional therapeutic strategies against cancer have limitations in tackling various tumors in clinical settings. These include chemotherapeutic resistance and the inability to overcome intrinsic physiological barriers to drug delivery. Nanomaterials have presented promising strategies for tumor treatment in recent years. Nanotheranostics combine therapeutic and bioimaging functionalities at the single nanoparticle level and have experienced tremendous growth over the past few years. This review highlights recent developments of advanced nanomaterials and nanotheranostics in three main directions: stimulus-responsive nanomaterials, nanocarriers targeting the tumor microenvironment, and emerging nanomaterials that integrate with phototherapies and immunotherapies. We also discuss the cytotoxicity and outlook of next-generation nanomaterials towards clinical implementation.
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Affiliation(s)
- Melgious Jin Yan Ang
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; NUS Graduate School (ISEP), National University of Singapore, Singapore 119077, Singapore
| | - Siew Yin Chan
- Institute of Materials Research and Engineering, Agency for Science, Technology, and Research, Singapore 138634, Singapore
| | - Yi-Yiing Goh
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; NUS Graduate School (ISEP), National University of Singapore, Singapore 119077, Singapore
| | - Zichao Luo
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Jun Wei Lau
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Xiaogang Liu
- Department of Chemistry, National University of Singapore, Singapore 117543, Singapore; NUS Graduate School (ISEP), National University of Singapore, Singapore 119077, Singapore.
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19
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Eroumé KS, Cavill R, Staňková K, de Boer J, Carlier A. Exploring the influence of cytosolic and membrane FAK activation on YAP/TAZ nuclear translocation. Biophys J 2021; 120:4360-4377. [PMID: 34509508 PMCID: PMC8553670 DOI: 10.1016/j.bpj.2021.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/16/2021] [Accepted: 09/07/2021] [Indexed: 11/12/2022] Open
Abstract
Membrane binding and unbinding dynamics play a crucial role in the biological activity of several nonintegral membrane proteins, which have to be recruited to the membrane to perform their functions. By localizing to the membrane, these proteins are able to induce downstream signal amplification in their respective signaling pathways. Here, we present a 3D computational approach using reaction-diffusion equations to investigate the relation between membrane localization of focal adhesion kinase (FAK), Ras homolog family member A (RhoA), and signal amplification of the YAP/TAZ signaling pathway. Our results show that the theoretical scenarios in which FAK is membrane bound yield robust and amplified YAP/TAZ nuclear translocation signals. Moreover, we predict that the amount of YAP/TAZ nuclear translocation increases with cell spreading, confirming the experimental findings in the literature. In summary, our in silico predictions show that when the cell membrane interaction area with the underlying substrate increases, for example, through cell spreading, this leads to more encounters between membrane-bound signaling partners and downstream signal amplification. Because membrane activation is a motif common to many signaling pathways, this study has important implications for understanding the design principles of signaling networks.
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Affiliation(s)
- Kerbaï Saïd Eroumé
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, the Netherlands
| | - Rachel Cavill
- Department of Data Science and Knowledge Engineering, Faculty of Science and Engineering, Maastricht University, Maastricht, the Netherlands
| | - Katerina Staňková
- Department of Data Science and Knowledge Engineering, Faculty of Science and Engineering, Maastricht University, Maastricht, the Netherlands
| | - Jan de Boer
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands
| | - Aurélie Carlier
- MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Maastricht, the Netherlands.
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20
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Abstract
Morphological transitions are typically attributed to the actions of proteins and lipids. Largely overlooked in membrane shape regulation is the glycocalyx, a pericellular membrane coat that resides on all cells in the human body. Comprised of complex sugar polymers known as glycans as well as glycosylated lipids and proteins, the glycocalyx is ideally positioned to impart forces on the plasma membrane. Large, unstructured polysaccharides and glycoproteins in the glycocalyx can generate crowding pressures strong enough to induce membrane curvature. Stress may also originate from glycan chains that convey curvature preference on asymmetrically distributed lipids, which are exploited by binding factors and infectious agents to induce morphological changes. Through such forces, the glycocalyx can have profound effects on the biogenesis of functional cell surface structures as well as the secretion of extracellular vesicles. In this review, we discuss recent evidence and examples of these mechanisms in normal health and disease.
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Affiliation(s)
- Joe Chin-Hun Kuo
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA; ,
| | - Matthew J Paszek
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA; , .,Field of Biomedical Engineering and Field of Biophysics, Cornell University, Ithaca, New York 14853, USA.,Kavli Institute at Cornell for Nanoscale Science, Ithaca, New York 14853, USA
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21
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Lee HJ, Donati A, Feliers D, Sun Y, Ding Y, Madesh M, Salmon AB, Ikeno Y, Ross C, O'Connor CL, Ju W, Bitzer M, Chen Y, Choudhury GG, Singh BB, Sharma K, Kasinath BS. Chloride channel accessory 1 integrates chloride channel activity and mTORC1 in aging-related kidney injury. Aging Cell 2021; 20:e13407. [PMID: 34118180 PMCID: PMC8282273 DOI: 10.1111/acel.13407] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/30/2021] [Accepted: 05/08/2021] [Indexed: 12/19/2022] Open
Abstract
The mechanism of kidney injury in aging are not well understood. In order to identify hitherto unknown pathways of aging‐related kidney injury, we performed RNA‐Seq on kidney extracts of young and aged mice. Expression of chloride (Cl) channel accessory 1 (CLCA1) mRNA and protein was increased in the kidneys of aged mice. Immunostaining showed a marked increase in CLCLA1 expression in the proximal tubules of the kidney from aged mice. Increased kidney CLCA1 gene expression also correlated with aging in marmosets and in a human cohort. In aging mice, increased renal cortical CLCA1 content was associated with hydrogen sulfide (H2S) deficiency, which was ameliorated by administering sodium hydrosulfide (NaHS), a source of H2S. In order to study whether increased CLCA1 expression leads to injury phenotype and the mechanisms involved, stable transfection of proximal tubule epithelial cells overexpressing human CLCA1 (hCLCA1) was performed. Overexpression of hCLCA1 augmented Cl− current via the Ca++‐dependent Cl− channel TMEM16A (anoctamin‐1) by patch‐clamp studies. hCLCA1 overexpression also increased the expression of fibronectin, a matrix protein, and induced the senescence‐associated secretory phenotype (SASP). Mechanistic studies underlying these changes showed that hCLCA1 overexpression leads to inhibition of AMPK activity and stimulation of mTORC1 as cellular signaling determinants of injury. Both TMEM16A inhibitor and NaHS reversed these signaling events and prevented changes in fibronectin and SASP. We conclude that CLCA1‐TMEM16A‐Cl− current pathway is a novel mediator of kidney injury in aging that is regulated by endogenous H2S.
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Affiliation(s)
- Hak Joo Lee
- Department of Medicine Center for Renal Precision Medicine University of Texas Health San Antonio TX USA
| | - Andrew Donati
- Department of Medicine Center for Renal Precision Medicine University of Texas Health San Antonio TX USA
| | - Denis Feliers
- Department of Medicine Center for Renal Precision Medicine University of Texas Health San Antonio TX USA
| | - Yuyang Sun
- Department of Periodontics University of Texas Health San Antonio TX USA
| | - Yanli Ding
- Department of Pathology University of Texas Health San Antonio TX USA
| | - Muniswamy Madesh
- Department of Medicine Center for Renal Precision Medicine University of Texas Health San Antonio TX USA
| | - Adam B. Salmon
- Department of Molecular Medicine University of Texas Health San Antonio TX USA
- Barshop Institute for Longevity and Aging Studies University of Texas Health San Antonio TX USA
- South Texas Veterans Health Care System San Antonio TX USA
- Geriatric Research Education & Clinical Center South Texas Veterans Health Care System San Antonio TX USA
| | - Yuji Ikeno
- Department of Pathology University of Texas Health San Antonio TX USA
- Department of Molecular Medicine University of Texas Health San Antonio TX USA
- South Texas Veterans Health Care System San Antonio TX USA
| | - Corinna Ross
- Texas Biomedical Research Institute Southwest National Primate Research Center San Antonio TX USA
- Department of Science and Mathematics Texas A&M University San Antonio San Antonio TX USA
| | | | - Wenjun Ju
- Department of Internal Medicine University of Michigan Ann Arbor MI USA
| | - Markus Bitzer
- Department of Internal Medicine University of Michigan Ann Arbor MI USA
| | - Yidong Chen
- Department of Population Health Sciences University of Texas Health San Antonio TX USA
- Greehey Children's Cancer Research Institute University of Texas Health San Antonio TX USA
| | - Goutam Ghosh Choudhury
- Department of Medicine Center for Renal Precision Medicine University of Texas Health San Antonio TX USA
- South Texas Veterans Health Care System San Antonio TX USA
- Geriatric Research Education & Clinical Center South Texas Veterans Health Care System San Antonio TX USA
| | - Brij B. Singh
- Department of Periodontics University of Texas Health San Antonio TX USA
| | - Kumar Sharma
- Department of Medicine Center for Renal Precision Medicine University of Texas Health San Antonio TX USA
- South Texas Veterans Health Care System San Antonio TX USA
| | - Balakuntalam S. Kasinath
- Department of Medicine Center for Renal Precision Medicine University of Texas Health San Antonio TX USA
- Barshop Institute for Longevity and Aging Studies University of Texas Health San Antonio TX USA
- South Texas Veterans Health Care System San Antonio TX USA
- Geriatric Research Education & Clinical Center South Texas Veterans Health Care System San Antonio TX USA
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22
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Junyent S, Reeves JC, Szczerkowski JLA, Garcin CL, Trieu TJ, Wilson M, Lundie-Brown J, Habib SJ. Wnt- and glutamate-receptors orchestrate stem cell dynamics and asymmetric cell division. eLife 2021; 10:59791. [PMID: 34028355 PMCID: PMC8177892 DOI: 10.7554/elife.59791] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 05/21/2021] [Indexed: 12/16/2022] Open
Abstract
The Wnt-pathway is part of a signalling network that regulates many aspects of cell biology. Recently, we discovered crosstalk between AMPA/Kainate-type ionotropic glutamate receptors (iGluRs) and the Wnt-pathway during the initial Wnt3a-interaction at the cytonemes of mouse embryonic stem cells (ESCs). Here, we demonstrate that this crosstalk persists throughout the Wnt3a-response in ESCs. Both AMPA and Kainate receptors regulate early Wnt3a-recruitment, dynamics on the cell membrane, and orientation of the spindle towards a Wnt3a-source at mitosis. AMPA receptors specifically are required for segregating cell fate components during Wnt3a-mediated asymmetric cell division (ACD). Using Wnt-pathway component knockout lines, we determine that Wnt co-receptor Lrp6 has particular functionality over Lrp5 in cytoneme formation, and in facilitating ACD. Both Lrp5 and 6, alongside pathway effector β-catenin act in concert to mediate the positioning of the dynamic interaction with, and spindle orientation to, a localised Wnt3a-source. Wnt-iGluR crosstalk may prove pervasive throughout embryonic and adult stem cell signalling.
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Affiliation(s)
- Sergi Junyent
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Joshua C Reeves
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - James LA Szczerkowski
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Clare L Garcin
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Tung-Jui Trieu
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Matthew Wilson
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Jethro Lundie-Brown
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
| | - Shukry J Habib
- Centre for Stem Cells and Regenerative Medicine, King's College LondonLondonUnited Kingdom
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23
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Rosado A, Bayer EM. Geometry and cellular function of organelle membrane interfaces. PLANT PHYSIOLOGY 2021; 185:650-662. [PMID: 33793898 PMCID: PMC8133572 DOI: 10.1093/plphys/kiaa079] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/17/2020] [Indexed: 05/09/2023]
Abstract
A vast majority of cellular processes take root at the surface of biological membranes. By providing a two-dimensional platform with limited diffusion, membranes are, by nature, perfect devices to concentrate signaling and metabolic components. As such, membranes often act as "key processors" of cellular information. Biological membranes are highly dynamic and deformable and can be shaped into curved, tubular, or flat conformations, resulting in differentiated biophysical properties. At membrane contact sites, membranes from adjacent organelles come together into a unique 3D configuration, forming functionally distinct microdomains, which facilitate spatially regulated functions, such as organelle communication. Here, we describe the diversity of geometries of contact site-forming membranes in different eukaryotic organisms and explore the emerging notion that their shape, 3D architecture, and remodeling jointly define their cellular activity. The review also provides selected examples highlighting changes in membrane contact site architecture acting as rapid and local responses to cellular perturbations, and summarizes our current understanding of how those structural changes confer functional specificity to those cellular territories.
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Affiliation(s)
- Abel Rosado
- Department of Botany, University of British Columbia, Vancouver, BC, Canada
| | - Emmanuelle M Bayer
- Univ. Bordeaux, CNRS, Laboratoire de Biogenèse Membranaire, UMR 5200, F-33140 Villenave d’Ornon, France
- Author for communication:
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24
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Zakirov B, Charalambous G, Thuret R, Aspalter IM, Van-Vuuren K, Mead T, Harrington K, Regan ER, Herbert SP, Bentley K. Active perception during angiogenesis: filopodia speed up Notch selection of tip cells in silico and in vivo. Philos Trans R Soc Lond B Biol Sci 2021; 376:20190753. [PMID: 33550953 PMCID: PMC7934951 DOI: 10.1098/rstb.2019.0753] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 12/19/2022] Open
Abstract
How do cells make efficient collective decisions during tissue morphogenesis? Humans and other organisms use feedback between movement and sensing known as 'sensorimotor coordination' or 'active perception' to inform behaviour, but active perception has not before been investigated at a cellular level within organs. Here we provide the first proof of concept in silico/in vivo study demonstrating that filopodia (actin-rich, dynamic, finger-like cell membrane protrusions) play an unexpected role in speeding up collective endothelial decisions during the time-constrained process of 'tip cell' selection during blood vessel formation (angiogenesis). We first validate simulation predictions in vivo with live imaging of zebrafish intersegmental vessel growth. Further simulation studies then indicate the effect is due to the coupled positive feedback between movement and sensing on filopodia conferring a bistable switch-like property to Notch lateral inhibition, ensuring tip selection is a rapid and robust process. We then employ measures from computational neuroscience to assess whether filopodia function as a primitive (basal) form of active perception and find evidence in support. By viewing cell behaviour through the 'basal cognitive lens' we acquire a fresh perspective on the tip cell selection process, revealing a hidden, yet vital time-keeping role for filopodia. Finally, we discuss a myriad of new and exciting research directions stemming from our conceptual approach to interpreting cell behaviour. This article is part of the theme issue 'Basal cognition: multicellularity, neurons and the cognitive lens'.
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Affiliation(s)
- Bahti Zakirov
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
| | - Georgios Charalambous
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Raphael Thuret
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Irene M. Aspalter
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
| | - Kelvin Van-Vuuren
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
| | - Thomas Mead
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
| | - Kyle Harrington
- Virtual Technology and Design, University of Idaho, Moscow, ID, USA
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Erzsébet Ravasz Regan
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
- Department of Biology, The College of Wooster, Wooster, OH, USA
| | - Shane Paul Herbert
- Division of Developmental Biology and Medicine, University of Manchester, Manchester, UK
| | - Katie Bentley
- Cellular Adaptive Behaviour Lab, Francis Crick Institute, London, NW1 1AT, UK
- Department of Informatics, King's College London, London, UK
- Center for Vascular Biology Research, Beth Israel Deaconess Medical Center, Department of Pathology, Harvard Medical School, Boston, MA, USA
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25
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Abstract
Structural DNA nanotechnology is a pioneering biotechnology that presents the opportunity to engineer DNA-based hardware that will mediate a profound interface to the nanoscale. To date, an enormous library of shaped 3D DNA nanostructures have been designed and assembled. Moreover, recent research has demonstrated DNA nanostructures that are not only static but can exhibit specific dynamic motion. DNA nanostructures have thus garnered significant research interest as a template for pursuing shape and motion-dependent nanoscale phenomena. Potential applications have been explored in many interdisciplinary areas spanning medicine, biosensing, nanofabrication, plasmonics, single-molecule chemistry, and facilitating biophysical studies. In this review, we begin with a brief overview of general and versatile design techniques for 3D DNA nanostructures as well as some techniques and studies that have focused on improving the stability of DNA nanostructures in diverse environments, which is pivotal for its reliable utilization in downstream applications. Our main focus will be to compile a wide body of existing research on applications of 3D DNA nanostructures that demonstrably rely on the versatility of their mechanical design. Furthermore, we frame reviewed applications into three primary categories, namely encapsulation, surface templating, and nanomechanics, that we propose to be archetypal shape- or motion-related functions of DNA nanostructures found in nanoscience applications. Our intent is to identify core concepts that may define and motivate specific directions of progress in this field as we conclude the review with some perspectives on the future.
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26
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Gavriljuk K, Scocozza B, Ghasemalizadeh F, Seidel H, Nandan AP, Campos-Medina M, Schmick M, Koseska A, Bastiaens PIH. A self-organized synthetic morphogenic liposome responds with shape changes to local light cues. Nat Commun 2021; 12:1548. [PMID: 33750780 PMCID: PMC7943604 DOI: 10.1038/s41467-021-21679-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/29/2021] [Indexed: 12/02/2022] Open
Abstract
Reconstituting artificial proto-cells capable of transducing extracellular signals into cytoskeletal changes can reveal fundamental principles of how non-equilibrium phenomena in cellular signal transduction affect morphogenesis. Here, we generated a Synthetic Morphogenic Membrane System (SynMMS) by encapsulating a dynamic microtubule (MT) aster and a light-inducible signaling system driven by GTP/ATP chemical potential into cell-sized liposomes. Responding to light cues in analogy to morphogens, this biomimetic design embodies basic principles of localized Rho-GTPase signal transduction that generate an intracellular MT-regulator signaling gradient. Light-induced signaling promotes membrane-deforming growth of MT-filaments by dynamically elevating the membrane-proximal tubulin concentration. The resulting membrane deformations enable recursive coupling of the MT-aster with the signaling system, which generates global self-organized morphologies that reorganize towards local external cues in dependence on prior shape. SynMMS thereby signifies a step towards bio-inspired engineering of self-organized cellular morphogenesis. The authors generated a Synthetic Morphogenic Membrane System by encapsulating a dynamic microtubule aster and a light-inducible signaling system driven by GTP/ATP chemical potential into cell-sized liposomes. This reconstitution of artificial proto-cells reveals how non-equilibrium phenomena affect cellular information processing in morphogenesis.
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Affiliation(s)
- Konstantin Gavriljuk
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Bruno Scocozza
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Farid Ghasemalizadeh
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Hans Seidel
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Akhilesh P Nandan
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany.,Cellular Computations and Learning, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - Manuel Campos-Medina
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Malte Schmick
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany
| | - Aneta Koseska
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany.,Cellular Computations and Learning, Center of Advanced European Studies and Research (caesar), Bonn, Germany
| | - Philippe I H Bastiaens
- Department of Systemic Cell Biology, Max Planck Institute for Molecular Physiology, Dortmund, Germany. .,Faculty of Chemistry and Chemical Biology, TU Dortmund, Dortmund, Germany.
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27
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Batta G, Hajdu T, Nagy P. Characterization of the Effect of Sphingolipid Accumulation on Membrane Compactness, Dipole Potential, and Mobility of Membrane Components. Methods Mol Biol 2021; 2187:283-301. [PMID: 32770513 DOI: 10.1007/978-1-0716-0814-2_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Communication between cells and their environment is carried out through the plasma membrane including the action of most pharmaceutical drugs. Although such a communication typically involves specific binding of a messenger to a membrane receptor, the biophysical state of the lipid bilayer strongly influences the outcome of this interaction. Sphingolipids constitute an important part of the lipid membrane, and their mole fraction modifies the biophysical characteristics of the membrane. Here, we describe methods that can be used for measuring how sphingolipid accumulation alters the compactness, microviscosity, and dipole potential of the lipid bilayer and the mobility of membrane components.
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Affiliation(s)
- Gyula Batta
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Department of Genetics and Applied Microbiology, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Tímea Hajdu
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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28
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Cooper-Knock J, Zhang S, Kenna KP, Moll T, Franklin JP, Allen S, Nezhad HG, Iacoangeli A, Yacovzada NY, Eitan C, Hornstein E, Elhaik E, Celadova P, Bose D, Farhan S, Fishilevich S, Lancet D, Morrison KE, Shaw CE, Al-Chalabi A, Veldink JH, Kirby J, Snyder MP, Shaw PJ. Rare Variant Burden Analysis within Enhancers Identifies CAV1 as an ALS Risk Gene. Cell Rep 2020; 33:108456. [PMID: 33264630 PMCID: PMC7710676 DOI: 10.1016/j.celrep.2020.108456] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/15/2020] [Accepted: 11/09/2020] [Indexed: 02/01/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is an incurable neurodegenerative disease. CAV1 and CAV2 organize membrane lipid rafts (MLRs) important for cell signaling and neuronal survival, and overexpression of CAV1 ameliorates ALS phenotypes in vivo. Genome-wide association studies localize a large proportion of ALS risk variants within the non-coding genome, but further characterization has been limited by lack of appropriate tools. By designing and applying a pipeline to identify pathogenic genetic variation within enhancer elements responsible for regulating gene expression, we identify disease-associated variation within CAV1/CAV2 enhancers, which replicate in an independent cohort. Discovered enhancer mutations reduce CAV1/CAV2 expression and disrupt MLRs in patient-derived cells, and CRISPR-Cas9 perturbation proximate to a patient mutation is sufficient to reduce CAV1/CAV2 expression in neurons. Additional enrichment of ALS-associated mutations within CAV1 exons positions CAV1 as an ALS risk gene. We propose CAV1/CAV2 overexpression as a personalized medicine target for ALS.
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Affiliation(s)
- Johnathan Cooper-Knock
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK.
| | - Sai Zhang
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kevin P Kenna
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tobias Moll
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - John P Franklin
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Samantha Allen
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Helia Ghahremani Nezhad
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Nancy Y Yacovzada
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Chen Eitan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Hornstein
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
| | - Petra Celadova
- Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | - Daniel Bose
- Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | - Sali Farhan
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Simon Fishilevich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Christopher E Shaw
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jan H Veldink
- Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Michael P Snyder
- Stanford Center for Genomics and Personalized Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK.
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29
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps**. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
- Living Matter AMOLF P.O. Box 41883-1009 DB Amsterdam The Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Thomas Litschel
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Frank Siedler
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics Max Planck Institute of Biochemistry Am Klopferspitz 18 82152 Martinsried Germany
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Ganzinger KA, Merino‐Salomón A, García‐Soriano DA, Butterfield AN, Litschel T, Siedler F, Schwille P. FtsZ Reorganization Facilitates Deformation of Giant Vesicles in Microfluidic Traps*. Angew Chem Int Ed Engl 2020; 59:21372-21376. [PMID: 32735732 PMCID: PMC7756778 DOI: 10.1002/anie.202001928] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 07/27/2020] [Indexed: 12/23/2022]
Abstract
The geometry of reaction compartments can affect the local outcome of interface-restricted reactions. Giant unilamellar vesicles (GUVs) are commonly used to generate cell-sized, membrane-bound reaction compartments, which are, however, always spherical. Herein, we report the development of a microfluidic chip to trap and reversibly deform GUVs into cigar-like shapes. When trapping and elongating GUVs that contain the primary protein of the bacterial Z ring, FtsZ, we find that membrane-bound FtsZ filaments align preferentially with the short GUV axis. When GUVs are released from this confinement and membrane tension is relaxed, FtsZ reorganizes reversibly from filaments into dynamic rings that stabilize membrane protrusions; a process that allows reversible GUV deformation. We conclude that microfluidic traps are useful for manipulating both geometry and tension of GUVs, and for investigating how both affect the outcome of spatially-sensitive reactions inside them, such as that of protein self-organization.
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Affiliation(s)
- Kristina A. Ganzinger
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
- Living MatterAMOLFP.O. Box 41883-1009 DBAmsterdamThe Netherlands
| | - Adrián Merino‐Salomón
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Daniela A. García‐Soriano
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - A. Nelson Butterfield
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Thomas Litschel
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Frank Siedler
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
| | - Petra Schwille
- Department of Cellular and Molecular BiophysicsMax Planck Institute of BiochemistryAm Klopferspitz 1882152MartinsriedGermany
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31
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Membrane Curvature Revisited-the Archetype of Rhodopsin Studied by Time-Resolved Electronic Spectroscopy. Biophys J 2020; 120:440-452. [PMID: 33217383 DOI: 10.1016/j.bpj.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/01/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) comprise the largest and most pharmacologically targeted membrane protein family. Here, we used the visual receptor rhodopsin as an archetype for understanding membrane lipid influences on conformational changes involved in GPCR activation. Visual rhodopsin was recombined with lipids varying in their degree of acyl chain unsaturation and polar headgroup size using 1-palmitoyl-2-oleoyl-sn-glycero- and 1,2-dioleoyl-sn-glycerophospholipids with phosphocholine (PC) or phosphoethanolamine (PE) substituents. The receptor activation profile after light excitation was measured using time-resolved ultraviolet-visible spectroscopy. We discovered that more saturated POPC lipids back shifted the equilibrium to the inactive state, whereas the small-headgroup, highly unsaturated DOPE lipids favored the active state. Increasing unsaturation and decreasing headgroup size have similar effects that combine to yield control of rhodopsin activation, and necessitate factors beyond proteolipid solvation energy and bilayer surface electrostatics. Hence, we consider a balance of curvature free energy with hydrophobic matching and demonstrate how our data support a flexible surface model (FSM) for the coupling between proteins and lipids. The FSM is based on the Helfrich formulation of membrane bending energy as we previously first applied to lipid-protein interactions. Membrane elasticity and curvature strain are induced by lateral pressure imbalances between the constituent lipids and drive key physiological processes at the membrane level. Spontaneous negative monolayer curvature toward water is mediated by unsaturated, small-headgroup lipids and couples directly to GPCR activation upon light absorption by rhodopsin. For the first time to our knowledge, we demonstrate this modulation in both the equilibrium and pre-equilibrium evolving states using a time-resolved approach.
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32
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Chataigner LMP, Leloup N, Janssen BJC. Structural Perspectives on Extracellular Recognition and Conformational Changes of Several Type-I Transmembrane Receptors. Front Mol Biosci 2020; 7:129. [PMID: 32850948 PMCID: PMC7427315 DOI: 10.3389/fmolb.2020.00129] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/02/2020] [Indexed: 12/19/2022] Open
Abstract
Type-I transmembrane proteins represent a large group of 1,412 proteins in humans with a multitude of functions in cells and tissues. They are characterized by an extracellular, or luminal, N-terminus followed by a single transmembrane helix and a cytosolic C-terminus. The domain composition and structures of the extracellular and intercellular segments differ substantially amongst its members. Most of the type-I transmembrane proteins have roles in cell signaling processes, as ligands or receptors, and in cellular adhesion. The extracellular segment often determines specificity and can control signaling and adhesion. Here we focus on recent structural understanding on how the extracellular segments of several diverse type-I transmembrane proteins engage in interactions and can undergo conformational changes for their function. Interactions at the extracellular side by proteins on the same cell or between cells are enhanced by the transmembrane setting. Extracellular conformational domain rearrangement and structural changes within domains alter the properties of the proteins and are used to regulate signaling events. The combination of structural properties and interactions can support the formation of larger-order assemblies on the membrane surface that are important for cellular adhesion and intercellular signaling.
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Affiliation(s)
- Lucas M. P. Chataigner
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Nadia Leloup
- Structural Biology and Protein Biochemistry, Morphic Therapeutic, Waltham, MA, United States
| | - Bert J. C. Janssen
- Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Utrecht, Netherlands
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33
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Bozelli JC, Epand RM. Membrane Shape and the Regulation of Biological Processes. J Mol Biol 2020; 432:5124-5136. [DOI: 10.1016/j.jmb.2020.03.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023]
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34
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Xulu K, Duarte R, Augustine T. Combined Anastrozole and Antiplatelet Therapy Treatment Differentially Promotes Breast Cancer Cell Survival. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2020; 26:497-508. [PMID: 32241309 DOI: 10.1017/s1431927620001324] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Thromboembolic disorders are the second leading cause of death in breast cancer. Antiplatelet therapy combined with cancer therapy is a potential treatment strategy against cancer-associated thromboembolic disorders; however, the efficacy of such dual treatment has not been established. This study reports novel findings on the response of hormone-dependent breast cancer cell lines (MCF7/T47D) following 24 h treatment with Anastrozole, combined with Aspirin and Clopidogrel cocktail; and Atopaxar. Neutral red and lactate dehydrogenase assays were conducted to assess viability and cytotoxicity respectively. Flow cytometric Annexin-V/PI assay was used to assess the mode of cell death. Morphological alterations were studied using scanning electron microscopy. Statistical analysis was conducted using Statistica V13. Definitive outcomes were established with flow cytometric detection of phosphatidylserine exposure and propidium iodide staining, complemented with ultrastructural analysis. Results showed that a few cells were undergoing death mainly through secondary necrosis. Morphological features suggesting induced cell motility (pseudopodia/ruffled membranes) were observed in both cell lines; notably, T47D cells presented pronounced features than MCF7 cells. Overall, these findings suggest that such combined treatment may differentially promote cell survival, inducing a more aggressive breast cancer phenotype.
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Affiliation(s)
- Kutlwano Xulu
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193Johannesburg, South Africa
| | - Raquel Duarte
- Department of Internal Medicine, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193Johannesburg, South Africa
| | - Tanya Augustine
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, 7 York Road, Parktown, 2193Johannesburg, South Africa
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35
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Jones T, Liu A, Cui B. Light-Inducible Generation of Membrane Curvature in Live Cells with Engineered BAR Domain Proteins. ACS Synth Biol 2020; 9:893-901. [PMID: 32212723 DOI: 10.1021/acssynbio.9b00516] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nanoscale membrane curvature is now understood to play an active role in essential cellular processes such as endocytosis, exocytosis, and actin dynamics. Previous studies have shown that membrane curvature can directly affect protein function and intracellular signaling. However, few methods are able to precisely manipulate membrane curvature in live cells. Here, we report the development of a new method of generating nanoscale membrane curvature in live cells that is controllable, reversible, and capable of precise spatial and temporal manipulation. For this purpose, we make use of Bin/Amphiphysin/Rvs (BAR) domain proteins, a family of well-studied membrane-remodeling and membrane-sculpting proteins. Specifically, we engineered two optogenetic systems, opto-FBAR and opto-IBAR, that allow light-inducible formation of positive and negative membrane curvature, respectively. Using opto-FBAR, blue light activation results in the formation of tubular membrane invaginations (positive curvature), controllable down to the subcellular level. Using opto-IBAR, blue light illumination results in the formation of membrane protrusions or filopodia (negative curvature). These systems present a novel approach for light-inducible manipulation of nanoscale membrane curvature in live cells.
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Affiliation(s)
- Taylor Jones
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Aofei Liu
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Bianxiao Cui
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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36
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Mechanistic models of PLC/PKC signaling implicate phosphatidic acid as a key amplifier of chemotactic gradient sensing. PLoS Comput Biol 2020; 16:e1007708. [PMID: 32255775 PMCID: PMC7164671 DOI: 10.1371/journal.pcbi.1007708] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 04/17/2020] [Accepted: 02/03/2020] [Indexed: 01/05/2023] Open
Abstract
Chemotaxis of fibroblasts and other mesenchymal cells is critical for embryonic development and wound healing. Fibroblast chemotaxis directed by a gradient of platelet-derived growth factor (PDGF) requires signaling through the phospholipase C (PLC)/protein kinase C (PKC) pathway. Diacylglycerol (DAG), the lipid product of PLC that activates conventional PKCs, is focally enriched at the up-gradient leading edge of fibroblasts responding to a shallow gradient of PDGF, signifying polarization. To explain the underlying mechanisms, we formulated reaction-diffusion models including as many as three putative feedback loops based on known biochemistry. These include the previously analyzed mechanism of substrate-buffering by myristoylated alanine-rich C kinase substrate (MARCKS) and two newly considered feedback loops involving the lipid, phosphatidic acid (PA). DAG kinases and phospholipase D, the enzymes that produce PA, are identified as key regulators in the models. Paradoxically, increasing DAG kinase activity can enhance the robustness of DAG/active PKC polarization with respect to chemoattractant concentration while decreasing their whole-cell levels. Finally, in simulations of wound invasion, efficient collective migration is achieved with thresholds for chemotaxis matching those of polarization in the reaction-diffusion models. This multi-scale modeling framework offers testable predictions to guide further study of signal transduction and cell behavior that affect mesenchymal chemotaxis. Cell movement directed by external gradients of chemical composition is critical for immune responses, wound healing, and development. Although theoretical concepts explaining how shallow external gradients might definitively polarize a cell’s motility have been offered over the past two decades, mathematical models cast in terms of defined molecules and mechanisms are uncommon in this context. Based on both recent and older insights from the literature, we offer mechanistic models that are able to explain experimentally observed polarization of signal transduction elicited by shallow attractant gradients. A novel insight of our models is the implicated role of phosphatidic acid, a membrane lipid produced by at least two enzymatic pathways, in two positive feedback loops that amplify signal transduction locally. In separate simulations, we explored the implications of polarization for efficient cell invasion during wound healing. We expected that the ability to polarize in response to shallow gradients would enhance the speed of wound invasion, but an unexpected finding is that this property can promote intermittent polarization throughout the wound.
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37
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Cell shape determines gene expression: cardiomyocyte morphotypic transcriptomes. Basic Res Cardiol 2019; 115:7. [PMID: 31872302 PMCID: PMC6928094 DOI: 10.1007/s00395-019-0765-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 12/03/2019] [Indexed: 12/19/2022]
Abstract
Cardiomyocytes undergo considerable changes in cell shape. These can be due to hemodynamic constraints, including changes in preload and afterload conditions, or to mutations in genes important for cardiac function. These changes instigate significant changes in cellular architecture and lead to the addition of sarcomeres, at the same time or at a later stage. However, it is currently unknown whether changes in cell shape on their own affect gene expression and the aim of this study was to fill that gap in our knowledge. We developed a single-cell morphotyping strategy, followed by single-cell RNA sequencing, to determine the effects of altered cell shape in gene expression. This enabled us to profile the transcriptomes of individual cardiomyocytes of defined geometrical morphotypes and characterize them as either normal or pathological conditions. We observed that deviations from normal cell shapes were associated with significant downregulation of gene expression and deactivation of specific pathways, like oxidative phosphorylation, protein kinase A, and cardiac beta-adrenergic signaling pathways. In addition, we observed that genes involved in apoptosis of cardiomyocytes and necrosis were upregulated in square-like pathological shapes. Mechano-sensory pathways, including integrin and Src kinase mediated signaling, appear to be involved in the regulation of shape-dependent gene expression. Our study demonstrates that cell shape per se affects the regulation of the transcriptome in cardiac myocytes, an effect with possible implications for cardiovascular disease.
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Abstract
The notion that graded distributions of signals underlie the spatial organization of biological systems has long been a central pillar in the fields of cell and developmental biology. During morphogenesis, morphogens spread across tissues to guide development of the embryo. Similarly, a variety of dynamic gradients and pattern-forming networks have been discovered that shape subcellular organization. Here we discuss the principles of intracellular pattern formation by these intracellular morphogens and relate them to conceptually similar processes operating at the tissue scale. We will specifically review mechanisms for generating cellular asymmetry and consider how intracellular patterning networks are controlled and adapt to cellular geometry. Finally, we assess the general concept of intracellular gradients as a mechanism for positional control in light of current data, highlighting how the simple readout of fixed concentration thresholds fails to fully capture the complexity of spatial patterning processes occurring inside cells.
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Affiliation(s)
- Lars Hubatsch
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Nathan W Goehring
- The Francis Crick Institute, London, United Kingdom; Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.
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Vaidžiulytė K, Coppey M, Schauer K. Intracellular organization in cell polarity - placing organelles into the polarity loop. J Cell Sci 2019; 132:132/24/jcs230995. [PMID: 31836687 DOI: 10.1242/jcs.230995] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Many studies have investigated the processes that support polarity establishment and maintenance in cells. On the one hand, polarity complexes at the cell cortex and their downstream signaling pathways have been assigned as major regulators of polarity. On the other hand, intracellular organelles and their polarized trafficking routes have emerged as important components of polarity. In this Review, we argue that rather than trying to identify the prime 'culprit', now it is time to consider all these players as a collective. We highlight that understanding the intimate coordination between the polarized cell cortex and the intracellular compass that is defined by organelle positioning is essential to capture the concept of polarity. After briefly reviewing how polarity emerges from a dynamic maintenance of cellular asymmetries, we highlight how intracellular organelles and their associated trafficking routes provide diverse feedback for dynamic cell polarity maintenance. We argue that the asymmetric organelle compass is an indispensable element of the polarity network.
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Affiliation(s)
- Kotryna Vaidžiulytė
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, Sorbonne Université, CNRS, Paris 75005, France.,Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS, Paris 75005, France.,Faculty of Science and Engineering, Sorbonne Université, Paris 75005, France
| | - Mathieu Coppey
- Laboratoire Physico Chimie Curie, Institut Curie, PSL Research University, Sorbonne Université, CNRS, Paris 75005, France
| | - Kristine Schauer
- Cell Biology and Cancer Unit, Institut Curie, PSL Research University, Sorbonne Université, CNRS, Paris 75005, France
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40
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Li S, Yan Z, Huang F, Zhang X, Yue T. How a lipid bilayer membrane responds to an oscillating nanoparticle: Promoted membrane undulation and directional wave propagation. Colloids Surf B Biointerfaces 2019; 187:110651. [PMID: 31784121 DOI: 10.1016/j.colsurfb.2019.110651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 01/14/2023]
Abstract
Mechanical forces acting on a plasma membrane are of essential importance to cellular functioning via inducing delicate change of the membrane shape with the underlying mechanism yet to be elucidated. Here, we introduce an oscillating nanoparticle (NP) interaction with a lipid bilayer membrane, using the coarse-grained simulation to investigate the dynamic membrane response to constrained mechanical stimulation, which is ubiquitous in biology. Our results demonstrate that, the membrane responds to an oscillating NP by generating nanoscale undulation waves, which immediately propagate through the membrane. In dynamics, propagation of the generated membrane undulation waves always starts from flattening of the region where the NP locates, thus producing a lateral force to propel the waves away from the point of stimulation. The speed of membrane undulation wave propagation is proportional to that of NP oscillation and accelerated by increasing the integral membrane surface tension, suggesting that both the membrane bending and stretching contribute to the energy driving the unique response of membrane undulation wave propagation.
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Affiliation(s)
- Shixin Li
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Zengshuai Yan
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China
| | - Xianren Zhang
- State Key Laboratory of Organic-Inorganic Composites, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Tongtao Yue
- State Key Laboratory of Heavy Oil Processing, Center for Bioengineering and Biotechnology, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, China.
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41
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Lee Y, Phelps C, Huang T, Mostofian B, Wu L, Zhang Y, Tao K, Chang YH, Stork PJ, Gray JW, Zuckerman DM, Nan X. High-throughput, single-particle tracking reveals nested membrane domains that dictate KRas G12D diffusion and trafficking. eLife 2019; 8:46393. [PMID: 31674905 PMCID: PMC7060040 DOI: 10.7554/elife.46393] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 10/30/2019] [Indexed: 12/13/2022] Open
Abstract
Membrane nanodomains have been implicated in Ras signaling, but what these domains are and how they interact with Ras remain obscure. Here, using single particle tracking with photoactivated localization microscopy (spt-PALM) and detailed trajectory analysis, we show that distinct membrane domains dictate KRasG12D (an active KRas mutant) diffusion and trafficking in U2OS cells. KRasG12D exhibits an immobile state in ~70 nm domains, each embedded in a larger domain (~200 nm) that confers intermediate mobility, while the rest of the membrane supports fast diffusion. Moreover, KRasG12D is continuously removed from the membrane via the immobile state and replenished to the fast state, reminiscent of Ras internalization and recycling. Importantly, both the diffusion and trafficking properties of KRasG12D remain invariant over a broad range of protein expression levels. Our results reveal how membrane organization dictates membrane diffusion and trafficking of Ras and offer new insight into the spatial regulation of Ras signaling. The Ras family of proteins play an important role in relaying signals from the outside to the inside of the cell. Ras proteins are attached by a fatty tail to the inner surface of the cell membrane. When activated they transmit a burst of signal that controls critical behaviors like growth, survival and movement. It has been suggested that to prevent these signals from being accidently activated, Ras molecules must group together at specialized sites within the membrane before passing on their message. However, visualizing how Ras molecules cluster together at these domains has thus far been challenging. As a result, little is known about where these sites are located and how Ras molecules come to a stop at these domains. Now, Lee et al. have combined two microscopy techniques called ‘single-particle tracking’ and ‘photoactivated localization microscopy' to track how individual molecules of activated Ras move in human cells grown in the lab. This revealed that Ras molecules quickly diffuse along the inside of the membrane until they arrive at certain locations that cause them to halt. However, computer models consisting of just the ‘fast’ and ‘immobile’ state could not correctly re-capture the way Ras molecules moved along the membrane. Lee et al. found that for these models to mimic the movement of Ras, a third ‘intermediate’ state of Ras mobility needed to be included. To investigate this further, Lee et al. created a fluorescent map that overlaid all the individual paths taken by each Ras molecule. The map showed regions in the membrane where the Ras molecules had stopped and possibly clustered together. Each of these ‘immobilization domains’ were then surrounded by an ‘intermediate domain’ where Ras molecules had begun to slow down their movement. Although the intermediate domains did not last long, they seemed to guide Ras molecules into the immobilization domains where they could cluster together with other molecules. From there, the cell constantly removed Ras molecules from these membrane domains and returned them back to their ‘fast’ diffusing state. Mutations in Ras proteins occur in around a third of all cancers, so a better understanding of their dynamics could help with future drug discovery. The methods used here could also be used to investigate the movement of other signaling molecules.
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Affiliation(s)
- Yerim Lee
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Carey Phelps
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Tao Huang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Barmak Mostofian
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Lei Wu
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Department of Oral Maxillofacial-Head Neck Oncology, School and Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Ying Zhang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Kai Tao
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Young Hwan Chang
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Philip Js Stork
- Vollum Institute, Oregon Health and Science University, Portland, United States
| | - Joe W Gray
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Daniel M Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States
| | - Xiaolin Nan
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,OHSU Center for Spatial Systems Biomedicine (OCSSB), Oregon Health and Science University, Portland, United States.,Knight Cancer Early Detection Advanced Research (CEDAR) Center, Oregon Health and Science University, Portland, United States
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42
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Bouvier B. Curvature as a Collective Coordinate in Enhanced Sampling Membrane Simulations. J Chem Theory Comput 2019; 15:6551-6561. [DOI: 10.1021/acs.jctc.9b00716] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Benjamin Bouvier
- Laboratoire de Glycochimie, des Antimicrobiens et des Agroressources, CNRS UMR7378/Université de Picardie Jules Verne, 10, rue Baudelocque, 80039 Amiens Cedex, France
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43
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Kandy SK, Radhakrishnan R. Emergent membrane morphologies in relaxed and tense membranes in presence of reversible adhesive pinning interactions. Phys Biol 2019; 16:066011. [PMID: 31561242 PMCID: PMC6830734 DOI: 10.1088/1478-3975/ab48d5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The morphologies of cell membranes, and specifically the local curvature distributions are determined either by its intrinsic components such as lipids and membrane-associated proteins or by the adhesion forces due to membrane interactions with the cytoskeleton, extracellular matrix (ECM) and other cells in the tissue, as well as physical variables such as membrane and frame tensions. We present a computational analysis for a model of pinned membranes based on the dynamically triangulated Monte Carlo (MC) model for membranes. We show that membrane adhesion to ECM or a substrate promotes curvature generation on cell membranes, and this process depends on the excess area, or equivalently membrane tension, and the density of adhesion sites. This biophysics based model predicts adhesion induced biogenesis of microvesicles in cell membranes. For a moderate density of adhesion sites and high excess membrane area, an increase in membrane tension can result in the formation of microvesicles and tubules on the membrane. We also demonstrate the significance of intrinsically curved proteins in promoting vesiculation on pinned membranes. The results presented here are relevant to the understanding of microvesicle biogenesis and curved membrane topographies due to physical factors such as substrate stiffness and ECM interactions.
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Affiliation(s)
- Sreeja Kutti Kandy
- Department of Chemical and Biomolecular engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ravi Radhakrishnan
- Department of Chemical and Biomolecular engineering, University of Pennsylvania, Philadelphia, PA, 19104, USA
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44
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Váradi T, Schneider M, Sevcsik E, Kiesenhofer D, Baumgart F, Batta G, Kovács T, Platzer R, Huppa JB, Szöllősi J, Schütz GJ, Brameshuber M, Nagy P. Homo- and Heteroassociations Drive Activation of ErbB3. Biophys J 2019; 117:1935-1947. [PMID: 31653451 PMCID: PMC7018998 DOI: 10.1016/j.bpj.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 10/01/2019] [Accepted: 10/03/2019] [Indexed: 01/19/2023] Open
Abstract
Dimerization or the formation of higher-order oligomers is required for the activation of ErbB receptor tyrosine kinases. The heregulin (HRG) receptor, ErbB3, must heterodimerize with other members of the family, preferentially ErbB2, to form a functional signal transducing complex. Here, we applied single molecule imaging capable of detecting long-lived and mobile associations to measure their stoichiometry and mobility and analyzed data from experiments globally, taking the different lateral mobility of monomeric and dimeric molecular species into account. Although ErbB3 was largely monomeric in the absence of stimulation and ErbB2 co-expression, a small fraction was present as constitutive homodimers exhibiting a ∼40% lower mobility than monomers. HRG stimulation increased the homodimeric fraction of ErbB3 significantly and reduced the mobility of homodimers fourfold compared to constitutive homodimers. Expression of ErbB2 elevated the homodimeric fraction of ErbB3 even in unstimulated cells and induced a ∼2-fold reduction in the lateral mobility of ErbB3 homodimers. The mobility of ErbB2 was significantly lower than that of ErbB3, and HRG induced a less pronounced decrease in the diffusion coefficient of all ErbB2 molecules and ErbB3/ErbB2 heterodimers than in the mobility of ErbB3. The slower diffusion of ErbB2 compared to ErbB3 was abolished by depolymerizing actin filaments, whereas ErbB2 expression induced a substantial rearrangement of microfilaments, implying a bidirectional interaction between ErbB2 and actin. HRG stimulation of cells co-expressing ErbB3 and ErbB2 led to the formation of ErbB3 homodimers and ErbB3/ErbB2 heterodimers in a competitive fashion. Although pertuzumab, an antibody binding to the dimerization arm of ErbB2, completely abolished the formation of constitutive and HRG-induced ErbB3/ErbB2 heterodimers, it only slightly blocked ErbB3 homodimerization. The results imply that a dynamic equilibrium exists between constitutive and ligand-induced homo- and heterodimers capable of shaping transmembrane signaling.
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Affiliation(s)
- Tímea Váradi
- Institute of Applied Physics, TU Wien, Vienna, Austria; Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | | | - Eva Sevcsik
- Institute of Applied Physics, TU Wien, Vienna, Austria
| | | | | | - Gyula Batta
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; Department of Genetics and Applied Microbiology, Faculty of Science of Technology, University of Debrecen, Debrecen, Hungary
| | - Tamás Kovács
- Institute of Applied Physics, TU Wien, Vienna, Austria
| | - René Platzer
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - Johannes B Huppa
- Institute for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Vienna, Austria
| | - János Szöllősi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary; MTA-DE Cell Biology and Signaling Research Group, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | | | | | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary.
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45
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Robust and automated detection of subcellular morphological motifs in 3D microscopy images. Nat Methods 2019; 16:1037-1044. [PMID: 31501548 PMCID: PMC7238333 DOI: 10.1038/s41592-019-0539-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 07/23/2019] [Indexed: 12/21/2022]
Abstract
Rapid developments in live-cell 3D microscopy enable imaging of cell morphology and signaling with unprecedented detail. However, tools to systematically measure and visualize the intricate relationships between intracellular signaling, cytoskeletal organization, and downstream cell morphological outputs do not exist. Here we introduce u-shape3D, a computer graphics and machine-learning pipeline to probe molecular mechanisms underlying 3D cell morphogenesis and to test the intriguing possibility that morphogenesis itself affects intracellular signaling. We demonstrate a generic morphological motif detector that automatically finds lamellipodia, filopodia, blebs, and other motifs. Combining motif detection with molecular localization, we measure the differential association of PIP2 and KrasV12 with blebs. Both signals associate with bleb edges, as expected for membrane-localized proteins, but only PIP2 is enhanced on blebs. This indicates that sub-cellular signaling processes are differentially modulated by local morphological motifs. Overall, our computational workflow enables the objective, 3D analysis of the coupling of cell shape and signaling.
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46
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Ebrahimkutty MP, Galic M. Receptor‐Free Signaling at Curved Cellular Membranes. Bioessays 2019; 41:e1900068. [DOI: 10.1002/bies.201900068] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/09/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Mirsana P. Ebrahimkutty
- DFG Cluster of Excellence “Cells in Motion”University of Muenster Muenster 48149 Germany
- Institute of Medical Physics and BiophysicsUniversity of Muenster Muenster 48149 Germany
- CIM‐IMRPS Graduate School Muenster 48149 Germany
| | - Milos Galic
- DFG Cluster of Excellence “Cells in Motion”University of Muenster Muenster 48149 Germany
- Institute of Medical Physics and BiophysicsUniversity of Muenster Muenster 48149 Germany
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47
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Marx S, Dal Maso T, Chen JW, Bury M, Wouters J, Michiels C, Le Calvé B. Transmembrane (TMEM) protein family members: Poorly characterized even if essential for the metastatic process. Semin Cancer Biol 2019; 60:96-106. [PMID: 31454669 DOI: 10.1016/j.semcancer.2019.08.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 08/13/2019] [Accepted: 08/14/2019] [Indexed: 01/02/2023]
Abstract
The majority of cancer-associated deaths are related to secondary tumor formation. This multistep process involves the migration of cancer cells to anatomically distant organs. Metastasis formation relies on cancer cell dissemination and survival in the circulatory system, as well as adaptation to the new tissue notably through genetic and/or epigenetic alterations. A large number of proteins are clearly identified to play a role in the metastatic process but the structures and modes of action of these proteins are essentially unknown or poorly described. In this review, we detail the involvement of members of the transmembrane (TMEM) protein family in the formation of metastases or in the mechanisms leading to cancer cell dissemination such as migration and extra-cellular matrix remodelling. While the phenotype associated with TMEM over or down-expression is clear, the mechanisms by which these proteins allow cancer cell spreading remain, for most of them, unclear. In parallel, the 3D structures of these proteins are presented. Moreover, we proposed that TMEM proteins could be used as prognostic markers in different types of cancers and could represent potential targets for cancer treatment. A better understanding of this heterogeneous family of poorly characterized proteins thus opens perspectives for better cancer patient care.
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Affiliation(s)
- Sébastien Marx
- Department of Chemistry, NAmur MEdicine & Drug Innovation Center (NAMEDIC-NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Thomas Dal Maso
- Department of Chemistry, NAmur MEdicine & Drug Innovation Center (NAMEDIC-NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Jia-Wei Chen
- URBC - NARILIS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Marina Bury
- de Duve Institute, 75 Avenue Hippocrate, 1200 Bruxelles, Belgium
| | - Johan Wouters
- Department of Chemistry, NAmur MEdicine & Drug Innovation Center (NAMEDIC-NARILIS), University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Carine Michiels
- URBC - NARILIS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium
| | - Benjamin Le Calvé
- URBC - NARILIS, University of Namur, 61 rue de Bruxelles, 5000 Namur, Belgium.
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48
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Hansen SD, Huang WYC, Lee YK, Bieling P, Christensen SM, Groves JT. Stochastic geometry sensing and polarization in a lipid kinase-phosphatase competitive reaction. Proc Natl Acad Sci U S A 2019; 116:15013-15022. [PMID: 31278151 PMCID: PMC6660746 DOI: 10.1073/pnas.1901744116] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Phosphorylation reactions, driven by competing kinases and phosphatases, are central elements of cellular signal transduction. We reconstituted a native eukaryotic lipid kinase-phosphatase reaction that drives the interconversion of phosphatidylinositol-4-phosphate [PI(4)P] and phosphatidylinositol-4,5-phosphate [PI(4,5)P2] on membrane surfaces. This system exhibited bistability and formed spatial composition patterns on supported membranes. In smaller confined regions of membrane, rapid diffusion ensures the system remains spatially homogeneous, but the final outcome-a predominantly PI(4)P or PI(4,5)P2 membrane composition-was governed by the size of the reaction environment. In larger confined regions, interplay between the reactions, diffusion, and confinement created a variety of differentially patterned states, including polarization. Experiments and kinetic modeling reveal how these geometric confinement effects arise from a mechanism based on stochastic fluctuations in the copy number of membrane-bound kinases and phosphatases. The underlying requirements for such behavior are unexpectedly simple and likely to occur in natural biological signaling systems.
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Affiliation(s)
- Scott D Hansen
- Department of Chemistry, University of California, Berkeley, CA 94720;
- California Institute for Quantitative Biosciences, Berkeley, CA 94720
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, OR 97403
| | - William Y C Huang
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Young Kwang Lee
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Peter Bieling
- California Institute for Quantitative Biosciences, Berkeley, CA 94720
| | | | - Jay T Groves
- Department of Chemistry, University of California, Berkeley, CA 94720;
- California Institute for Quantitative Biosciences, Berkeley, CA 94720
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49
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Machado R, Bendesky J, Brown M, Spendier K, Hagen GM. Imaging Membrane Curvature inside a FcεRI-Centric Synapse in RBL-2H3 Cells Using TIRF Microscopy with Polarized Excitation. J Imaging 2019; 5:63. [PMID: 31360699 PMCID: PMC6663088 DOI: 10.3390/jimaging5070063] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 06/28/2019] [Indexed: 01/06/2023] Open
Abstract
Total internal reflection fluorescence microscopy with polarized excitation (P-TIRF) can be used to image nanoscale curvature phenomena in live cells. We used P-TIRF to visualize rat basophilic leukemia cells (RBL-2H3 cells) primed with fluorescent anti-dinitrophenyl (anti-DNP) immunoglobulin E (IgE) coming into contact with a supported lipid bilayer containing mobile, monovalent DNP, modeling an immunological synapse. The spatial relationship of the IgE-bound high affinity IgE receptor (FcεRI) to the ratio image of P-polarized excitation and S-polarized excitation was analyzed. These studies help correlate the dynamics of cell surface molecules with the mechanical properties of the plasma membrane during synapse formation.
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Affiliation(s)
- Rosa Machado
- UCCS Center for the Biofrontiers Institute, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
| | - Justin Bendesky
- UCCS Center for the Biofrontiers Institute, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
| | - Madison Brown
- UCCS Center for the Biofrontiers Institute, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
- Department of Physics and Energy Science, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
| | - Kathrin Spendier
- UCCS Center for the Biofrontiers Institute, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
- Department of Physics and Energy Science, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
| | - Guy M. Hagen
- UCCS Center for the Biofrontiers Institute, University of Colorado at Colorado Springs, Colorado Springs, CO 80918, USA
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50
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Complex Membrane Remodeling during Virion Assembly of the 30,000-Year-Old Mollivirus Sibericum. J Virol 2019; 93:JVI.00388-19. [PMID: 30996095 DOI: 10.1128/jvi.00388-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 04/11/2019] [Indexed: 01/14/2023] Open
Abstract
Cellular membranes ensure functional compartmentalization by dynamic fusion-fission remodeling and are often targeted by viruses during entry, replication, assembly, and egress. Nucleocytoplasmic large DNA viruses (NCLDVs) can recruit host-derived open membrane precursors to form their inner viral membrane. Using complementary three-dimensional (3D)-electron microscopy techniques, including focused-ion beam scanning electron microscopy and electron tomography, we show that the giant Mollivirus sibericum utilizes the same strategy but also displays unique features. Indeed, assembly is specifically triggered by an open cisterna with a flat pole in its center and open curling ends that grow by recruitment of vesicles never reported for NCLDVs. These vesicles, abundant in the viral factory (VF), are initially closed but open once in close proximity to the open curling ends of the growing viral membrane. The flat pole appears to play a central role during the entire virus assembly process. While additional capsid layers are assembled from it, it also shapes the growing cisterna into immature crescent-like virions and is located opposite to the membrane elongation and closure sites, thereby providing virions with a polarity. In the VF, DNA-associated filaments are abundant, and DNA is packed within virions prior to particle closure. Altogether, our results highlight the complexity of the interaction between giant viruses and their host. Mollivirus assembly relies on the general strategy of vesicle recruitment, opening, and shaping by capsid layers similar to all NCLDVs studied until now. However, the specific features of its assembly suggest that the molecular mechanisms for cellular membrane remodeling and persistence are unique.IMPORTANCE Since the first giant virus Mimivirus was identified, other giant representatives are isolated regularly around the world and appear to be unique in several aspects. They belong to at least four viral families, and the ways they interact with their hosts remain poorly understood. We focused on Mollivirus sibericum, the sole representative of "Molliviridae," which was isolated from a 30,000-year-old permafrost sample and exhibits spherical virions of complex composition. In particular, we show that (i) assembly is initiated by a unique structure containing a flat pole positioned at the center of an open cisterna, (ii) core packing involves another cisterna-like element seemingly pushing core proteins into particles being assembled, and (iii) specific filamentous structures contain the viral genome before packaging. Altogether, our findings increase our understanding of how complex giant viruses interact with their host and provide the foundation for future studies to elucidate the molecular mechanisms of Mollivirus assembly.
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