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Svobodová B, Št'astný D, Blom H, Mikhalyov I, Gretskaya N, Balleková A, Sezgin E, Hof M, Šachl R. Revised Diffusion Law Permits Quantitative Nanoscale Characterization of Membrane Organization. Anal Chem 2025; 97:11478-11485. [PMID: 40437882 DOI: 10.1021/acs.analchem.5c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2025]
Abstract
The formation of functional nanoscopic domains is an inherent property of plasma membranes. Stimulated emission depletion combined with fluorescence correlation spectroscopy (STED-FCS) has been previously used to identify such domains; however, the information obtained by STED-FCS has been limited to the presence of such domains while crucial parameters have not been accessible, such as size (Rd), the fraction of occupied membrane surface (f), in-membrane lipid diffusion inside (Din) and outside (Dout) the nanodomains as well as their self-diffusion (Dd). Here, we introduce a quantitative approach based on a revised interpretation of the diffusion law. By analyzing experimentally recorded STED-FCS diffusion law plots using a comprehensive library of simulated diffusion law plots, we extract these five parameters from STED-FCS data. That approach is verified on ganglioside nanodomains in giant unilamellar vesicles, validating the Saffman-Delbrück assumption for Dd. STED-FCS data in both plasma membranes of living PtK2 cells and giant plasma membrane vesicles are examined, and a quantitative framework for molecular diffusion modes in biological membranes is presented.
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Affiliation(s)
- Barbora Svobodová
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, Prague 182 23, Czech Republic
- Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, Prague 121 16, Czech Republic
| | - David Št'astný
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, Prague 182 23, Czech Republic
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, Hlavova 8, Prague 128 40, Czech Republic
| | - Hans Blom
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Solna 17165, Sweden
| | - Ilya Mikhalyov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Rusian Academy of Science, Moscow 117997, Russia
| | - Natalia Gretskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Rusian Academy of Science, Moscow 117997, Russia
| | - Alena Balleková
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, Prague 182 23, Czech Republic
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Tomtebodavägen 23, Solna 17165, Sweden
| | - Martin Hof
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, Prague 182 23, Czech Republic
| | - Radek Šachl
- J. Heyrovský Institute of Physical Chemistry of the Czech Academy of Sciences, Dolejškova 3, Prague 182 23, Czech Republic
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Mazloom-Farsibaf H, Kanagy WK, Lidke DS, Lidke KA. Fast Single-Particle Tracking of Membrane Proteins Combined with Super-Resolution Imaging of Actin Nanodomains. Sci Data 2025; 12:562. [PMID: 40181024 PMCID: PMC11968936 DOI: 10.1038/s41597-025-04782-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 03/07/2025] [Indexed: 04/05/2025] Open
Abstract
Membrane protein dynamics regulates cell functions by initiating downstream signaling cascades. The cell membrane is compartmentalized into nanodomains by actin structures, restricting lateral protein diffusion. Single-particle tracking offers high spatiotemporal resolution for studying protein dynamics in living cells. However, directly observing actin filaments that form barriers of nanodomains for fast protein diffusion is challenging due to their size being below the diffraction limit. Single-molecule localization microscopy resolves these structures but requires imaging in fixed cells. We integrated fast single-particle tracking with single-molecule localization microscopy to generate a dataset of membrane protein dynamics and actin filaments within the same cells at the nanoscales. Optimizing the fixation protocol enabled transition from live-cell tracking to fixed-cell super-resolution imaging. Data for the high-affinity IgE receptor, a transmembrane protein, and the GPI-anchored protein, an outer leaflet protein, was collected at 490 Hz. After fixation, actin filaments were imaged using dSTORM. The treatment of actin structures with phalloidin and PMA generated a dataset of distinct actin architectures for studying their potential influence on membrane protein dynamics.
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Affiliation(s)
- Hanieh Mazloom-Farsibaf
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, USA.
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - William K Kanagy
- Department of Pathology, University of New Mexico, Albuquerque, New Mexico, USA
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Diane S Lidke
- Department of Pathology, University of New Mexico, Albuquerque, New Mexico, USA
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, USA
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, USA.
- University of New Mexico Comprehensive Cancer Center, Albuquerque, New Mexico, USA.
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3
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Fritz C, Reimann TM, Adler J, Knab J, Schulmeister S, Kriechbaum C, Müller S, Parmryd I, Kost B. Plasma membrane and cytoplasmic compartmentalization: A dynamic structural framework required for pollen tube tip growth. PLANT PHYSIOLOGY 2024; 197:kiae558. [PMID: 39446406 DOI: 10.1093/plphys/kiae558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 09/28/2024] [Indexed: 12/24/2024]
Abstract
Rapid, unidirectional pollen tube tip growth is essential for fertilization and widely employed as a model of polar cell expansion, a process crucial for plant morphogenesis. Different proteins and lipids with key functions in the control of polar cell expansion are associated with distinct domains of the plasma membrane (PM) at the pollen tube tip. These domains need to be dynamically maintained during tip growth, which depends on massive secretory and endocytic membrane trafficking. Very little is currently known about the molecular and cellular mechanisms responsible for the compartmentalization of the pollen tube PM. To provide a reliable structural framework for the further characterization of these mechanisms, an integrated quantitative map was compiled of the relative positions in normally growing Nicotiana tabacum (tobacco) pollen tubes of PM domains (i) enriched in key signaling proteins or lipids, (ii) displaying high membrane order, or (iii) in contact with cytoplasmic structures playing important roles in apical membrane trafficking. Previously identified secretory and endocytic PM domains were also included in this map. Internalization of regulatory proteins or lipids associated with PM regions overlapping with the lateral endocytic domain was assessed based on brefeldin A treatment. These analyses revealed remarkable aspects of the structural organization of tobacco pollen tube tips, which (i) enhance our understanding of cellular and regulatory processes underlying tip growth and (ii) highlight important areas of future research.
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Affiliation(s)
- Carolin Fritz
- Division of Cell Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Theresa Maria Reimann
- Division of Cell Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Jeremy Adler
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Johanna Knab
- Division of Cell Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Sylwia Schulmeister
- Division of Cell Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Choy Kriechbaum
- Division of Cell Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Sabine Müller
- Division of Cell Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
| | - Ingela Parmryd
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Benedikt Kost
- Division of Cell Biology, Department of Biology, Friedrich-Alexander-University of Erlangen-Nürnberg, Erlangen, Germany
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4
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Pandey S, Wohland T. EGFR does not directly interact with cortical actin: A SRRF'n'TIRF study. Biophys J 2024; 123:3736-3749. [PMID: 39340155 PMCID: PMC11560307 DOI: 10.1016/j.bpj.2024.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/13/2024] [Accepted: 09/23/2024] [Indexed: 09/30/2024] Open
Abstract
The epidermal growth factor receptor (EGFR) governs pivotal signaling pathways in cell proliferation and survival, with mutations implicated in numerous cancers. The organization of EGFR on the plasma membrane (PM) is influenced by the lipids and the cortical actin (CA) cytoskeleton. Despite the presence of a putative actin-binding domain (ABD) spanning 13 residues, a direct interaction between EGFR and CA has not been definitively established. While disrupting the cytoskeleton can impact EGFR behavior, suggesting a connection, the influence of the static actin cytoskeleton has been found to be indirect. Here, we investigate the potential interaction between EGFR and CA, as well as the extent to which CA regulates EGFR's distribution on the PM using SRRF'n'TIRF, a spatiotemporal super-resolution microscopy technique that provides sub-100 nm resolution and ms-scale dynamics from the same data set. To label CA, we constructed PMT-mEGFP-F-tractin, which combines an inner leaflet targeting domain PMT, fluorescent probe mEGFP, and the actin-binding protein F-tractin. In addition to EGFR-mEGFP, we included two control constructs: 1) an ABD deletion mutant, EGFRΔABD-mEGFP serving as a negative control and 2) EGFR-mApple-F-tractin, where F-tractin is fused to the C-terminus of EGFR-mApple, serving as the positive control. We find that EGFR-mEGFP and EGFRΔABD-mEGFP show similar membrane dynamics, implying that EGFR-mEGFP dynamics and organization are independent of CA. EGFR dynamics show CA dependence when F-tractin is anchored to the cytoplasmic tail. Together, our results demonstrate that EGFR does not directly interact with the CA in its resting and activated state.
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Affiliation(s)
- Shambhavi Pandey
- Centre for Bio-Imaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Thorsten Wohland
- Centre for Bio-Imaging Sciences, Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Biological Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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5
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Shubhrasmita Sahu S, Sarkar P, Chattopadhyay A. Quantitation of F-actin in cytoskeletal reorganization: Context, methodology and implications. Methods 2024; 230:44-58. [PMID: 39074540 DOI: 10.1016/j.ymeth.2024.07.009] [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] [Received: 04/05/2024] [Revised: 07/08/2024] [Accepted: 07/17/2024] [Indexed: 07/31/2024] Open
Abstract
The actin cytoskeleton is involved in a large number of cellular signaling events in addition to providing structural integrity to the cell. Actin polymerization is a key event during cellular signaling. Although the role of actin cytoskeleton in cellular processes such as trafficking and motility has been extensively studied, the reorganization of the actin cytoskeleton upon signaling has been rarely explored due to lack of suitable assays. Keeping in mind this lacuna, we developed a confocal microscopy based approach that relies on high magnification imaging of cellular F-actin, followed by image reconstruction using commercially available software. In this review, we discuss the context and relevance of actin quantitation, followed by a detailed hands-on approach of the methodology involved with specific points on troubleshooting and useful precautions. In the latter part of the review, we elucidate the method by discussing applications of actin quantitation from our work in several important problems in contemporary membrane biology ranging from pathogen entry into host cells, to GPCR signaling and membrane-cytoskeleton interaction. We envision that future discovery of cell-permeable novel fluorescent probes, in combination with genetically encoded actin-binding reporters, would allow real-time visualization of actin cytoskeleton dynamics to gain deeper insights into active cellular processes in health and disease.
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Affiliation(s)
- Subhashree Shubhrasmita Sahu
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India; Department of Biochemistry, Stanford University, School of Medicine, Stanford, CA 94305, USA
| | - Amitabha Chattopadhyay
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.
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6
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Winkelmann H, Richter CP, Eising J, Piehler J, Kurre R. Correlative single-molecule and structured illumination microscopy of fast dynamics at the plasma membrane. Nat Commun 2024; 15:5813. [PMID: 38987559 PMCID: PMC11236984 DOI: 10.1038/s41467-024-49876-9] [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: 09/25/2023] [Accepted: 06/21/2024] [Indexed: 07/12/2024] Open
Abstract
Total internal reflection fluorescence (TIRF) microscopy offers powerful means to uncover the functional organization of proteins in the plasma membrane with very high spatial and temporal resolution. Traditional TIRF illumination, however, shows a Gaussian intensity profile, which is typically deteriorated by overlaying interference fringes hampering precise quantification of intensities-an important requisite for quantitative analyses in single-molecule localization microscopy (SMLM). Here, we combine flat-field illumination by using a standard πShaper with multi-angular TIR illumination by incorporating a spatial light modulator compatible with fast super-resolution structured illumination microscopy (SIM). This distinct combination enables quantitative multi-color SMLM with a highly homogenous illumination. By using a dual camera setup with optimized image splitting optics, we achieve a versatile combination of SMLM and SIM with up to three channels. We deploy this setup for establishing robust detection of receptor stoichiometries based on single-molecule intensity analysis and single-molecule Förster resonance energy transfer (smFRET). Homogeneous illumination furthermore enables long-term tracking and localization microscopy (TALM) of cell surface receptors identifying spatial heterogeneity of mobility and accessibility in the plasma membrane. By combination of TALM and SIM, spatially and molecularly heterogenous diffusion properties can be correlated with nanoscale cytoskeletal organization and dynamics.
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Affiliation(s)
- Hauke Winkelmann
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Christian P Richter
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jasper Eising
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany
| | - Jacob Piehler
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
| | - Rainer Kurre
- Division of Biophysics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Center for Cellular Nanoanalytics, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
- Integrated Bioimaging Facility iBiOs, Department of Biology/Chemistry, Osnabrück University, Barbarastraße 11, D-49076, Osnabrück, Germany.
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7
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Voce N, Stevenson P. Experimentally Probing the Effect of Confinement Geometry on Lipid Diffusion. J Phys Chem B 2024; 128:4404-4413. [PMID: 38574293 PMCID: PMC11089508 DOI: 10.1021/acs.jpcb.3c07388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 04/06/2024]
Abstract
The lateral mobility of molecules within the cell membrane is ultimately governed by the local environment of the membrane. Confined regions induced by membrane structures, such as protein aggregates or the actin meshwork, occur over a wide range of length scales and can impede or steer the diffusion of membrane components. However, a detailed picture of the origins and nature of these confinement effects remains elusive. Here, we prepare model lipid systems on substrates patterned with confined domains of varying geometries constructed with different materials to explore the influences of physical boundary conditions and specific molecular interactions on diffusion. We demonstrate a platform that is capable of significantly altering and steering the long-range diffusion of lipids by using simple oxide deposition approaches, enabling us to systematically explore how confinement size and shape impact diffusion over multiple length scales. While we find that a "boundary condition" description of the system captures underlying trends in some cases, we are also able to directly compare our systems to analytical models, revealing the unexpected breakdown of several approximate solutions. Our results highlight the importance of considering the length scale dependence when discussing properties such as diffusion.
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Affiliation(s)
- Nicole Voce
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
| | - Paul Stevenson
- Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States
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8
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Rentsch J, Bandstra S, Sezen B, Sigrist P, Bottanelli F, Schmerl B, Shoichet S, Noé F, Sadeghi M, Ewers H. Sub-membrane actin rings compartmentalize the plasma membrane. J Cell Biol 2024; 223:e202310138. [PMID: 38252080 PMCID: PMC10807028 DOI: 10.1083/jcb.202310138] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024] Open
Abstract
The compartmentalization of the plasma membrane (PM) is a fundamental feature of cells. The diffusivity of membrane proteins is significantly lower in biological than in artificial membranes. This is likely due to actin filaments, but assays to prove a direct dependence remain elusive. We recently showed that periodic actin rings in the neuronal axon initial segment (AIS) confine membrane protein motion between them. Still, the local enrichment of ion channels offers an alternative explanation. Here we show, using computational modeling, that in contrast to actin rings, ion channels in the AIS cannot mediate confinement. Furthermore, we show, employing a combinatorial approach of single particle tracking and super-resolution microscopy, that actin rings are close to the PM and that they confine membrane proteins in several neuronal cell types. Finally, we show that actin disruption leads to loss of compartmentalization. Taken together, we here develop a system for the investigation of membrane compartmentalization and show that actin rings compartmentalize the PM.
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Affiliation(s)
- Jakob Rentsch
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Selle Bandstra
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Batuhan Sezen
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Philipp Sigrist
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Francesca Bottanelli
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Bettina Schmerl
- Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Frank Noé
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Mohsen Sadeghi
- Department of Mathematics and Computer Science, Freie Universität Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
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Wüstner D, Egebjerg JM, Lauritsen L. Dynamic Mode Decomposition of Multiphoton and Stimulated Emission Depletion Microscopy Data for Analysis of Fluorescent Probes in Cellular Membranes. SENSORS (BASEL, SWITZERLAND) 2024; 24:2096. [PMID: 38610307 PMCID: PMC11013970 DOI: 10.3390/s24072096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
An analysis of the membrane organization and intracellular trafficking of lipids often relies on multiphoton (MP) and super-resolution microscopy of fluorescent lipid probes. A disadvantage of particularly intrinsically fluorescent lipid probes, such as the cholesterol and ergosterol analogue, dehydroergosterol (DHE), is their low MP absorption cross-section, resulting in a low signal-to-noise ratio (SNR) in live-cell imaging. Stimulated emission depletion (STED) microscopy of membrane probes like Nile Red enables one to resolve membrane features beyond the diffraction limit but exposes the sample to a lot of excitation light and suffers from a low SNR and photobleaching. Here, dynamic mode decomposition (DMD) and its variant, higher-order DMD (HoDMD), are applied to efficiently reconstruct and denoise the MP and STED microscopy data of lipid probes, allowing for an improved visualization of the membranes in cells. HoDMD also allows us to decompose and reconstruct two-photon polarimetry images of TopFluor-cholesterol in model and cellular membranes. Finally, DMD is shown to not only reconstruct and denoise 3D-STED image stacks of Nile Red-labeled cells but also to predict unseen image frames, thereby allowing for interpolation images along the optical axis. This important feature of DMD can be used to reduce the number of image acquisitions, thereby minimizing the light exposure of biological samples without compromising image quality. Thus, DMD as a computational tool enables gentler live-cell imaging of fluorescent probes in cellular membranes by MP and STED microscopy.
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Affiliation(s)
- Daniel Wüstner
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark; (J.M.E.); (L.L.)
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Dibsy R, Bremaud E, Mak J, Favard C, Muriaux D. HIV-1 diverts cortical actin for particle assembly and release. Nat Commun 2023; 14:6945. [PMID: 37907528 PMCID: PMC10618566 DOI: 10.1038/s41467-023-41940-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 09/25/2023] [Indexed: 11/02/2023] Open
Abstract
Enveloped viruses assemble and bud from the host cell membranes. Any role of cortical actin in these processes have often been a source of debate. Here, we assessed if cortical actin was involved in HIV-1 assembly in infected CD4 T lymphocytes. Our results show that preventing actin branching not only increases HIV-1 particle release but also the number of individual HIV-1 Gag assembly clusters at the T cell plasma membrane. Indeed, in infected T lymphocytes and in in vitro quantitative model systems, we show that HIV-1 Gag protein prefers areas deficient in F-actin for assembling. Finally, we found that the host factor Arpin, an inhibitor of Arp2/3 branched actin, is recruited at the membrane of infected T cells and it can associate with the viral Gag protein. Altogether, our data show that, for virus assembly and particle release, HIV-1 prefers low density of cortical actin and may favor local actin debranching by subverting Arpin.
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Affiliation(s)
- Rayane Dibsy
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Erwan Bremaud
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Johnson Mak
- Institute for Glycomics, Griffith University, Brisbane, Australia
| | - Cyril Favard
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France
| | - Delphine Muriaux
- Institute of Research in Infectious disease of Montpellier (IRIM), University of Montpellier, UMR9004 CNRS, Montpellier, France.
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Mayor S, Bhat A, Kusumi A. A Survey of Models of Cell Membranes: Toward a New Understanding of Membrane Organization. Cold Spring Harb Perspect Biol 2023; 15:a041394. [PMID: 37643877 PMCID: PMC10547391 DOI: 10.1101/cshperspect.a041394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
The cell membrane, the boundary that separates living cells from their environment, has been the subject of study for over a century. The fluid-mosaic model of Singer and Nicolson in 1972 proposed the plasma membrane as a two-dimensional fluid composed of lipids and proteins. Fifty years hence, advances in biophysical and biochemical tools, particularly optical imaging techniques, have allowed for a better understanding of the physical nature, organization, and composition of cell membranes. This has been made possible by visualizing membrane heterogeneities and their dynamics and appreciating the asymmetrical arrangement of lipids in living cell membranes. Despite these advances, mechanisms underlying the local spatiotemporal organization of membrane components remain unclear. This review surveys various models of membrane organization, culminating in a new model that incorporates nonequilibrium processes and forces exerted by interactions with extramembrane elements such as the actin cytoskeleton. The proposed model provides a comprehensive understanding of membrane organization, taking into account the dynamic nature of the cell membrane and its interactions with its immediate environment.
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Affiliation(s)
- Satyajit Mayor
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Abrar Bhat
- National Centre for Biological Science, TIFR, Bangalore 560065, India
| | - Akihiro Kusumi
- Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904-0495, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
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12
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Henning P, Köster T, Haack F, Burrage K, Uhrmacher AM. Implications of different membrane compartmentalization models in particle-based in silico studies. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221177. [PMID: 37416823 PMCID: PMC10320350 DOI: 10.1098/rsos.221177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 06/12/2023] [Indexed: 07/08/2023]
Abstract
Studying membrane dynamics is important to understand the cellular response to environmental stimuli. A decisive spatial characteristic of the plasma membrane is its compartmental structure created by the actin-based membrane-skeleton (fences) and anchored transmembrane proteins (pickets). Particle-based reaction-diffusion simulation of the membrane offers a suitable temporal and spatial resolution to analyse its spatially heterogeneous and stochastic dynamics. Fences have been modelled via hop probabilities, potentials or explicit picket fences. Our study analyses the different approaches' constraints and their impact on simulation results and performance. Each of the methods comes with its own constraints; the picket fences require small timesteps, potential fences might induce a bias in diffusion in crowded systems, and probabilistic fences, in addition to carefully scaling the probability with the timesteps, induce higher computational costs for each propagation step.
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Affiliation(s)
- Philipp Henning
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
| | - Till Köster
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
| | - Fiete Haack
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
| | - Kevin Burrage
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- Visiting Professor, Department of Computer Science, University of Oxford, Oxford, UK
| | - Adelinde M. Uhrmacher
- Institute for Visual and Analytic Computing, University of Rostock, Rostock, Germany
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13
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Kusumi A, Tsunoyama TA, Tang B, Hirosawa KM, Morone N, Fujiwara TK, Suzuki KGN. Cholesterol- and actin-centered view of the plasma membrane: updating the Singer-Nicolson fluid mosaic model to commemorate its 50th anniversary †. Mol Biol Cell 2023; 34:pl1. [PMID: 37039596 PMCID: PMC10162409 DOI: 10.1091/mbc.e20-12-0809] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/07/2022] [Accepted: 02/07/2023] [Indexed: 04/12/2023] Open
Abstract
Two very polarized views exist for understanding the cellular plasma membrane (PM). For some, it is the simple fluid described by the original Singer-Nicolson fluid mosaic model. For others, due to the presence of thousands of molecular species that extensively interact with each other, the PM forms various clusters and domains that are constantly changing and therefore, no simple rules exist that can explain the structure and molecular dynamics of the PM. In this article, we propose that viewing the PM from its two predominant components, cholesterol and actin filaments, provides an excellent and transparent perspective of PM organization, dynamics, and mechanisms for its functions. We focus on the actin-induced membrane compartmentalization and lipid raft domains coexisting in the PM and how they interact with each other to perform PM functions. This view provides an important update of the fluid mosaic model.
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Affiliation(s)
- Akihiro Kusumi
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa 904-0495, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Taka A. Tsunoyama
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa 904-0495, Japan
| | - Bo Tang
- Membrane Cooperativity Unit, Okinawa Institute of Science and Technology Graduate University (OIST), Okinawa 904-0495, Japan
| | - Koichiro M. Hirosawa
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
| | - Nobuhiro Morone
- MRC Toxicology Unit, University of Cambridge, Cambridge CB2 1QR, UK
| | - Takahiro K. Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Kenichi G. N. Suzuki
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan
- Institute for Glyco-Core Research (iGCORE), Gifu University, Gifu 501-1193, Japan
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14
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Pacheco J, Cassidy AC, Zewe JP, Wills RC, Hammond GR. PI(4,5)P2 diffuses freely in the plasma membrane even within high-density effector protein complexes. J Cell Biol 2023; 222:e202204099. [PMID: 36416724 PMCID: PMC9698391 DOI: 10.1083/jcb.202204099] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/11/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
The lipid phosphatidyl-D-myo-inositol-4,5-bisphosphate [PI(4,5)P2] is a master regulator of plasma membrane (PM) function. Its effector proteins regulate transport, signaling, and cytoskeletal processes that define PM structure and function. How a single type of lipid regulates so many parallel processes is unclear. We tested the hypothesis that spatially separate PI(4,5)P2 pools associate with different PM complexes. The mobility of PI(4,5)P2 was measured using biosensors by single-particle tracking. We found that PM lipids including PI(4,5)P2 diffuse rapidly (∼0.3 µm2/s) with Brownian motion, although they spend one third of their time diffusing more slowly. Surprisingly, areas of the PM occupied by PI(4,5)P2-dependent complexes did not slow PI(4,5)P2 lateral mobility. Only the spectrin and septin cytoskeletons showed reduced PI(4,5)P2 diffusion. We conclude that even structures with high densities of PI(4,5)P2 effector proteins, such as clathrin-coated pits and focal adhesions, do not corral unbound PI(4,5)P2, questioning a role for spatially segregated PI(4,5)P2 pools in organizing and regulating PM functions.
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Affiliation(s)
- Jonathan Pacheco
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Anna C. Cassidy
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - James P. Zewe
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Rachel C. Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Gerald R.V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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15
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Wills RC, Hammond GRV. PI(4,5)P2: signaling the plasma membrane. Biochem J 2022; 479:2311-2325. [PMID: 36367756 PMCID: PMC9704524 DOI: 10.1042/bcj20220445] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/13/2022]
Abstract
In the almost 70 years since the first hints of its existence, the phosphoinositide, phosphatidyl-D-myo-inositol 4,5-bisphosphate has been found to be central in the biological regulation of plasma membrane (PM) function. Here, we provide an overview of the signaling, transport and structural roles the lipid plays at the cell surface in animal cells. These include being substrate for second messenger generation, direct modulation of receptors, control of membrane traffic, regulation of ion channels and transporters, and modulation of the cytoskeleton and cell polarity. We conclude by re-evaluating PI(4,5)P2's designation as a signaling molecule, instead proposing a cofactor role, enabling PM-selective function for many proteins.
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Affiliation(s)
- Rachel C. Wills
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Gerald R. V. Hammond
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
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16
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Chai YJ, Cheng CY, Liao YH, Lin CH, Hsieh CL. Heterogeneous nanoscopic lipid diffusion in the live cell membrane and its dependency on cholesterol. Biophys J 2022; 121:3146-3161. [PMID: 35841144 PMCID: PMC9463655 DOI: 10.1016/j.bpj.2022.07.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/08/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022] Open
Abstract
Cholesterol plays a unique role in the regulation of membrane organization and dynamics by modulating the membrane phase transition at the nanoscale. Unfortunately, due to their small sizes and dynamic nature, the effects of cholesterol-mediated membrane nanodomains on membrane dynamics remain elusive. Here, using ultrahigh-speed single-molecule tracking with advanced optical microscope techniques, we investigate the diffusive motion of single phospholipids in the live cell plasma membrane at the nanoscale and its dependency on the cholesterol concentration. We find that both saturated and unsaturated phospholipids undergo anomalous subdiffusion on the length scale of 10-100 nm. The diffusion characteristics exhibit considerable variations in space and in time, indicating that the nanoscopic lipid diffusion is highly heterogeneous. Importantly, through the statistical analysis, apparent dual-mobility subdiffusion is observed from the mixed diffusion behaviors. The measured subdiffusion agrees well with the hop diffusion model that represents a diffuser moving in a compartmentalized membrane created by the cytoskeleton meshwork. Cholesterol depletion diminishes the lipid mobility with an apparently smaller compartment size and a stronger confinement strength. Similar results are measured with temperature reduction, suggesting that the more heterogeneous and restricted diffusion is connected to the nanoscopic membrane phase transition. Our conclusion supports the model that cholesterol depletion induces the formation of gel-phase, solid-like membrane nanodomains. These nanodomains undergo restricted diffusion and act as diffusion obstacles to the membrane molecules that are excluded from the nanodomains. This work provides the experimental evidence that the nanoscopic lipid diffusion in the cell plasma membrane is heterogeneous and sensitive to the cholesterol concentration and temperature, shedding new light on the regulation mechanisms of nanoscopic membrane dynamics.
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Affiliation(s)
- Yu-Jo Chai
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Ching-Ya Cheng
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Yi-Hung Liao
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Chih-Hsiang Lin
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences (IAMS), Academia Sinica, Taipei, Taiwan.
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17
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Sarkar P, Chattopadhyay A. Statin-induced Increase in Actin Polymerization Modulates GPCR Dynamics and Compartmentalization. Biophys J 2022:S0006-3495(22)00708-1. [DOI: 10.1016/j.bpj.2022.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/16/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
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18
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Abstract
Lipid-protein interactions in cells are involved in various biological processes, including metabolism, trafficking, signaling, host-pathogen interactions, and transmembrane transport. At the plasma membrane, lipid-protein interactions play major roles in membrane organization and function. Several membrane proteins have motifs for specific lipid binding, which modulate protein conformation and consequent function. In addition to such specific lipid-protein interactions, protein function can be regulated by the dynamic, collective behavior of lipids in membranes. Emerging analytical, biochemical, and computational technologies allow us to study the influence of specific lipid-protein interactions, as well as the collective behavior of membranes on protein function. In this article, we review the recent literature on lipid-protein interactions with a specific focus on the current state-of-the-art technologies that enable novel insights into these interactions.
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Affiliation(s)
- Taras Sych
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden; ,
| | - Kandice R Levental
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia, USA;
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Solna, Sweden; ,
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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19
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Platelet Membrane: An Outstanding Factor in Cancer Metastasis. MEMBRANES 2022; 12:membranes12020182. [PMID: 35207103 PMCID: PMC8875259 DOI: 10.3390/membranes12020182] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 12/02/2022]
Abstract
In addition to being biological barriers where the internalization or release of biomolecules is decided, cell membranes are contact structures between the interior and exterior of the cell. Here, the processes of cell signaling mediated by receptors, ions, hormones, cytokines, enzymes, growth factors, extracellular matrix (ECM), and vesicles begin. They triggering several responses from the cell membrane that include rearranging its components according to the immediate needs of the cell, for example, in the membrane of platelets, the formation of filopodia and lamellipodia as a tissue repair response. In cancer, the cancer cells must adapt to the new tumor microenvironment (TME) and acquire capacities in the cell membrane to transform their shape, such as in the case of epithelial−mesenchymal transition (EMT) in the metastatic process. The cancer cells must also attract allies in this challenging process, such as platelets, fibroblasts associated with cancer (CAF), stromal cells, adipocytes, and the extracellular matrix itself, which limits tumor growth. The platelets are enucleated cells with fairly interesting growth factors, proangiogenic factors, cytokines, mRNA, and proteins, which support the development of a tumor microenvironment and support the metastatic process. This review will discuss the different actions that platelet membranes and cancer cell membranes carry out during their relationship in the tumor microenvironment and metastasis.
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20
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Vallés AS, Barrantes FJ. Nanoscale Sub-Compartmentalization of the Dendritic Spine Compartment. Biomolecules 2021; 11:1697. [PMID: 34827695 PMCID: PMC8615865 DOI: 10.3390/biom11111697] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 01/04/2023] Open
Abstract
Compartmentalization of the membrane is essential for cells to perform highly specific tasks and spatially constrained biochemical functions in topographically defined areas. These membrane lateral heterogeneities range from nanoscopic dimensions, often involving only a few molecular constituents, to micron-sized mesoscopic domains resulting from the coalescence of nanodomains. Short-lived domains lasting for a few milliseconds coexist with more stable platforms lasting from minutes to days. This panoply of lateral domains subserves the great variety of demands of cell physiology, particularly high for those implicated in signaling. The dendritic spine, a subcellular structure of neurons at the receiving (postsynaptic) end of central nervous system excitatory synapses, exploits this compartmentalization principle. In its most frequent adult morphology, the mushroom-shaped spine harbors neurotransmitter receptors, enzymes, and scaffolding proteins tightly packed in a volume of a few femtoliters. In addition to constituting a mesoscopic lateral heterogeneity of the dendritic arborization, the dendritic spine postsynaptic membrane is further compartmentalized into spatially delimited nanodomains that execute separate functions in the synapse. This review discusses the functional relevance of compartmentalization and nanodomain organization in synaptic transmission and plasticity and exemplifies the importance of this parcelization in various neurotransmitter signaling systems operating at dendritic spines, using two fast ligand-gated ionotropic receptors, the nicotinic acetylcholine receptor and the glutamatergic receptor, and a second-messenger G-protein coupled receptor, the cannabinoid receptor, as paradigmatic examples.
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Affiliation(s)
- Ana Sofía Vallés
- Instituto de Investigaciones Bioquímicas de Bahía Blanca (UNS-CONICET), Bahía Blanca 8000, Argentina;
| | - Francisco J. Barrantes
- Laboratory of Molecular Neurobiology, Institute of Biomedical Research (BIOMED), UCA-CONICET, Av. Alicia Moreau de Justo 1600, Buenos Aires C1107AFF, Argentina
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21
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Reina F, Wigg JM, Dmitrieva M, Vogler B, Lefebvre J, Rittscher J, Eggeling C. TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data. F1000Res 2021; 10:838. [PMID: 35186271 PMCID: PMC8829092 DOI: 10.12688/f1000research.54788.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/25/2022] [Indexed: 11/20/2022] Open
Abstract
Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox - 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
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Affiliation(s)
- Francesco Reina
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
| | - John M.A. Wigg
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Mariia Dmitrieva
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Bela Vogler
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Joël Lefebvre
- Département d'informatique, University of Quebec at Montreal, Montreal, Canada
| | - Jens Rittscher
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Christian Eggeling
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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22
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Reina F, Wigg JM, Dmitrieva M, Vogler B, Lefebvre J, Rittscher J, Eggeling C. TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data. F1000Res 2021; 10:838. [PMID: 35186271 PMCID: PMC8829092 DOI: 10.12688/f1000research.54788.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 02/15/2024] Open
Abstract
Single particle tracking (SPT) is one of the most widely used tools in optical microscopy to evaluate particle mobility in a variety of situations, including cellular and model membrane dynamics. Recent technological developments, such as Interferometric Scattering microscopy, have allowed recording of long, uninterrupted single particle trajectories at kilohertz framerates. The resulting data, where particles are continuously detected and do not displace much between observations, thereby do not require complex linking algorithms. Moreover, while these measurements offer more details into the short-term diffusion behaviour of the tracked particles, they are also subject to the influence of localisation uncertainties, which are often underestimated by conventional analysis pipelines. we thus developed a Python library, under the name of TRAIT2D (Tracking Analysis Toolbox - 2D version), in order to track particle diffusion at high sampling rates, and analyse the resulting trajectories with an innovative approach. The data analysis pipeline introduced is more localisation-uncertainty aware, and also selects the most appropriate diffusion model for the data provided on a statistical basis. A trajectory simulation platform also allows the user to handily generate trajectories and even synthetic time-lapses to test alternative tracking algorithms and data analysis approaches. A high degree of customisation for the analysis pipeline, for example with the introduction of different diffusion modes, is possible from the source code. Finally, the presence of graphical user interfaces lowers the access barrier for users with little to no programming experience.
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Affiliation(s)
- Francesco Reina
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
| | - John M.A. Wigg
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Mariia Dmitrieva
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Bela Vogler
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
| | - Joël Lefebvre
- Département d'informatique, University of Quebec at Montreal, Montreal, Canada
| | - Jens Rittscher
- Department of Engineering Science, University of Oxford, Oxford, UK
| | - Christian Eggeling
- Leibniz-Institut für Photonische Technologien e.V, Jena, Germany
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-Universität, Jena, Germany
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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23
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Advanced Static and Dynamic Fluorescence Microscopy Techniques to Investigate Drug Delivery Systems. Pharmaceutics 2021; 13:pharmaceutics13060861. [PMID: 34208080 PMCID: PMC8230741 DOI: 10.3390/pharmaceutics13060861] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 01/01/2023] Open
Abstract
In the past decade(s), fluorescence microscopy and laser scanning confocal microscopy (LSCM) have been widely employed to investigate biological and biomimetic systems for pharmaceutical applications, to determine the localization of drugs in tissues or entire organisms or the extent of their cellular uptake (in vitro). However, the diffraction limit of light, which limits the resolution to hundreds of nanometers, has for long time restricted the extent and quality of information and insight achievable through these techniques. The advent of super-resolution microscopic techniques, recognized with the 2014 Nobel prize in Chemistry, revolutionized the field thanks to the possibility to achieve nanometric resolution, i.e., the typical scale length of chemical and biological phenomena. Since then, fluorescence microscopy-related techniques have acquired renewed interest for the scientific community, both from the perspective of instrument/techniques development and from the perspective of the advanced scientific applications. In this contribution we will review the application of these techniques to the field of drug delivery, discussing how the latest advancements of static and dynamic methodologies have tremendously expanded the experimental opportunities for the characterization of drug delivery systems and for the understanding of their behaviour in biologically relevant environments.
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24
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Sarkar P, Chattopadhyay A. Insights into cellular signaling from membrane dynamics. Arch Biochem Biophys 2021; 701:108794. [PMID: 33571482 DOI: 10.1016/j.abb.2021.108794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/20/2021] [Accepted: 02/03/2021] [Indexed: 12/16/2022]
Abstract
Biological membranes allow morphological compartmentalization of cells and represent complex micro-heterogeneous fluids exhibiting a range of dynamics. The plasma membrane occupies a central place in cellular signaling which allows the cell to perform a variety of functions. In this review, we analyze cellular signaling in a dynamic biophysical framework guided by the "mobile receptor hypothesis". We describe a variety of examples from literature in which lateral diffusion of signaling membrane proteins acts as an important determinant in the efficiency of signaling. A major focus in our review is on membrane-embedded G protein-coupled receptors (GPCRs) which act as cellular signaling hubs for diverse cellular functions. Taken together, we describe a dynamics-based signaling paradigm with chosen examples from literature to elucidate how such a paradigm helps us understand signaling by GPCRs, maintenance of cellular polarity in yeast and infection by pathogens. We envision that with further technological advancement, it would be possible to explore cellular signaling more holistically as cells undergo development, differentiation and aging, thereby providing us a robust window into the dynamics of the cellular interior and its functional correlates.
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Affiliation(s)
- Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007, India
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25
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Schneider F, Colin-York H, Fritzsche M. Quantitative Bio-Imaging Tools to Dissect the Interplay of Membrane and Cytoskeletal Actin Dynamics in Immune Cells. Front Immunol 2021; 11:612542. [PMID: 33505401 PMCID: PMC7829180 DOI: 10.3389/fimmu.2020.612542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/23/2020] [Indexed: 12/13/2022] Open
Abstract
Cellular function is reliant on the dynamic interplay between the plasma membrane and the actin cytoskeleton. This critical relationship is of particular importance in immune cells, where both the cytoskeleton and the plasma membrane work in concert to organize and potentiate immune signaling events. Despite their importance, there remains a critical gap in understanding how these respective dynamics are coupled, and how this coupling in turn may influence immune cell function from the bottom up. In this review, we highlight recent optical technologies that could provide strategies to investigate the simultaneous dynamics of both the cytoskeleton and membrane as well as their interplay, focusing on current and future applications in immune cells. We provide a guide of the spatio-temporal scale of each technique as well as highlighting novel probes and labels that have the potential to provide insights into membrane and cytoskeletal dynamics. The quantitative biophysical tools presented here provide a new and exciting route to uncover the relationship between plasma membrane and cytoskeletal dynamics that underlies immune cell function.
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Affiliation(s)
- Falk Schneider
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Huw Colin-York
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Marco Fritzsche
- Medical Research Council (MRC) Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, Oxford, United Kingdom
- Rosalind Franklin Institute, Harwell Campus, Didcot, United Kingdom
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26
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Borges-Araújo L, Fernandes F. Structure and Lateral Organization of Phosphatidylinositol 4,5-bisphosphate. Molecules 2020; 25:molecules25173885. [PMID: 32858905 PMCID: PMC7503891 DOI: 10.3390/molecules25173885] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 08/22/2020] [Accepted: 08/23/2020] [Indexed: 02/07/2023] Open
Abstract
Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is a minor but ubiquitous component of the inner leaflet of the plasma membrane of eukaryotic cells. However, due to its particular complex biophysical properties, it stands out from its neighboring lipids as one of the most important regulators of membrane-associated signaling events. Despite its very low steady-state concentration, PI(4,5)P2 is able to engage in a multitude of simultaneous cellular functions that are temporally and spatially regulated through the presence of localized transient pools of PI(4,5)P2 in the membrane. These pools are crucial for the recruitment, activation, and organization of signaling proteins and consequent regulation of downstream signaling. The present review showcases some of the most important PI(4,5)P2 molecular and biophysical properties as well as their impact on its membrane dynamics, lateral organization, and interactions with other biochemical partners.
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Affiliation(s)
- Luís Borges-Araújo
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal;
- Correspondence:
| | - Fabio Fernandes
- iBB—Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal;
- Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
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27
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Céspedes PF, Beckers D, Dustin ML, Sezgin E. Model membrane systems to reconstitute immune cell signaling. FEBS J 2020; 288:1070-1090. [DOI: 10.1111/febs.15488] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/26/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Pablo F. Céspedes
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences University of Oxford UK
| | - Daniel Beckers
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular Medicine University of Oxford UK
| | - Michael L. Dustin
- Kennedy Institute of Rheumatology Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences University of Oxford UK
| | - Erdinc Sezgin
- MRC Human Immunology Unit MRC Weatherall Institute of Molecular Medicine University of Oxford UK
- Science for Life Laboratory Department of Women's and Children's Health Karolinska Institutet Stockholm Sweden
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28
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Kalappurakkal JM, Sil P, Mayor S. Toward a new picture of the living plasma membrane. Protein Sci 2020; 29:1355-1365. [PMID: 32297381 DOI: 10.1002/pro.3874] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 01/08/2023]
Abstract
Our understanding of the plasma membrane structure has undergone a major change since the proposal of the fluid mosaic model of Singer and Nicholson in the 1970s. In this model, the membrane, composed of over thousand lipid and protein species, is organized as a well-equilibrated two-dimensional fluid. Here, the distribution of lipids is largely expected to reflect a multicomponent system, and proteins are expected to be surrounded by an annulus of specialized lipid species. With the recognition that a multicomponent lipid membrane is capable of phase segregation, the membrane is expected to appear as patchwork quilt pattern of membrane domains. However, the constituents of a living membrane are far from being well equilibrated. The living cell membrane actively maintains a trans-bilayer asymmetry of composition, and its constituents are subject to a number of dynamic processes due to synthesis, lipid transfer as well as membrane traffic and turnover. Moreover, membrane constituents engage with the dynamic cytoskeleton of a living cell, and are both passively as well as actively manipulated by this engagement. The extracellular matrix and associated elements also interact with membrane proteins contributing to another layer of interaction. At the nano- and mesoscale, the organization of lipids and proteins emerge from these encounters, as well as from protein-protein, protein-lipid, and lipid-lipid interactions in the membrane. New methods to study the organization of membrane components at these scales have also been developed, and provide an opportunity to synthesize a new picture of the living cell surface as an active membrane composite.
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Affiliation(s)
- Joseph Mathew Kalappurakkal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Parijat Sil
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
| | - Satyajit Mayor
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, Karnataka, India
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29
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Gupta A, Phang IY, Wohland T. To Hop or not to Hop: Exceptions in the FCS Diffusion Law. Biophys J 2020; 118:2434-2447. [PMID: 32333863 PMCID: PMC7231916 DOI: 10.1016/j.bpj.2020.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/31/2020] [Accepted: 04/06/2020] [Indexed: 12/13/2022] Open
Abstract
Diffusion obstacles in membranes have not been directly visualized because of fast membrane dynamics and the occurrence of subresolution molecular complexes. To understand the obstacle characteristics, mobility-based methods are often used as an indirect way of assessing the membrane structure. Molecular movement in biological plasma membranes is often characterized by anomalous diffusion, but the exact underlying mechanisms are still elusive. Imaging total internal reflection fluorescence correlation spectroscopy (ITIR-FCS) is a well-established mobility-based method that provides spatially resolved diffusion coefficient maps and is combined with FCS diffusion law analysis to examine subresolution membrane organization. In recent years, although FCS diffusion law analysis has been instrumental in providing new insights into the membrane structure below the optical diffraction limit, there are certain exceptions and anomalies that require further clarification. To this end, we correlate the membrane structural features imaged by atomic force microscopy (AFM) with the dynamics measured using ITIR-FCS. We perform ITIR-FCS measurements on supported lipid bilayers (SLBs) of various lipid compositions to characterize the anomalous diffusion of lipid molecules in distinct obstacle configurations, along with the high-resolution imaging of the membrane structures with AFM. Furthermore, we validate our experimental results by performing simulations on image grids with experimentally determined obstacle configurations. This study demonstrates that FCS diffusion law analysis is a powerful tool to determine membrane heterogeneities implied from dynamics measurements. Our results corroborate the commonly accepted interpretations of imaging FCS diffusion law analysis, and we show that exceptions happen when domains reach the percolation threshold in a biphasic membrane and a network of domains behaves rather like a meshwork, resulting in hop diffusion.
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Affiliation(s)
- Anjali Gupta
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore
| | - Inn Yee Phang
- Institute of Materials Research and Engineering, Singapore, Singapore
| | - Thorsten Wohland
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, Singapore, Singapore; Department of Chemistry, National University of Singapore, Singapore, Singapore.
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30
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Garcia E, Ismail S. Spatiotemporal Regulation of Signaling: Focus on T Cell Activation and the Immunological Synapse. Int J Mol Sci 2020; 21:E3283. [PMID: 32384769 PMCID: PMC7247333 DOI: 10.3390/ijms21093283] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 01/22/2023] Open
Abstract
In a signaling network, not only the functions of molecules are important but when (temporal) and where (spatial) those functions are exerted and orchestrated is what defines the signaling output. To temporally and spatially modulate signaling events, cells generate specialized functional domains with variable lifetime and size that concentrate signaling molecules, enhancing their transduction potential. The plasma membrane is a key in this regulation, as it constitutes a primary signaling hub that integrates signals within and across the membrane. Here, we examine some of the mechanisms that cells exhibit to spatiotemporally regulate signal transduction, focusing on the early events of T cell activation from triggering of T cell receptor to formation and maturation of the immunological synapse.
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Affiliation(s)
- Esther Garcia
- CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Shehab Ismail
- CR-UK Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
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31
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Jacobson K, Liu P, Lagerholm BC. The Lateral Organization and Mobility of Plasma Membrane Components. Cell 2020; 177:806-819. [PMID: 31051105 DOI: 10.1016/j.cell.2019.04.018] [Citation(s) in RCA: 165] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 02/01/2019] [Accepted: 04/09/2019] [Indexed: 01/22/2023]
Abstract
Over the last several decades, an impressive array of advanced microscopic and analytical tools, such as single-particle tracking and nanoscopic fluorescence correlation spectroscopy, has been applied to characterize the lateral organization and mobility of components in the plasma membrane. Such analysis can tell researchers about the local dynamic composition and structure of membranes and is important for predicting the outcome of membrane-based reactions. However, owing to the unresolved complexity of the membrane and the structures peripheral to it, identification of the detailed molecular origin of the interactions that regulate the organization and mobility of the membrane has not proceeded quickly. This Perspective presents an overview of how cell-surface structure may give rise to the types of lateral mobility that are observed and some potentially fruitful future directions to elucidate the architecture of these structures in more molecular detail.
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Affiliation(s)
- Ken Jacobson
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Ping Liu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074 Hubei, China
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
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32
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Stanly TA, Fritzsche M, Banerji S, Shrestha D, Schneider F, Eggeling C, Jackson DG. The cortical actin network regulates avidity-dependent binding of hyaluronan by the lymphatic vessel endothelial receptor LYVE-1. J Biol Chem 2020; 295:5036-5050. [PMID: 32034091 PMCID: PMC7152780 DOI: 10.1074/jbc.ra119.011992] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/29/2020] [Indexed: 12/16/2022] Open
Abstract
Lymphatic vessel endothelial hyaluronan receptor 1 (LYVE-1) mediates the docking and entry of dendritic cells to lymphatic vessels through selective adhesion to its ligand hyaluronan in the leukocyte surface glycocalyx. To bind hyaluronan efficiently, LYVE-1 must undergo surface clustering, a process that is induced efficiently by the large cross-linked assemblages of glycosaminoglycan present within leukocyte pericellular matrices but is induced poorly by the shorter polymer alone. These properties suggested that LYVE-1 may have limited mobility in the endothelial plasma membrane, but no biophysical investigation of these parameters has been carried out to date. Here, using super-resolution fluorescence microscopy and spectroscopy combined with biochemical analyses of the receptor in primary lymphatic endothelial cells, we provide the first evidence that LYVE-1 dynamics are indeed restricted by the submembranous actin network. We show that actin disruption not only increases LYVE-1 lateral diffusion but also enhances hyaluronan-binding activity. However, unlike the related leukocyte HA receptor CD44, which uses ERM and ankyrin motifs within its cytoplasmic tail to bind actin, LYVE-1 displays little if any direct interaction with actin, as determined by co-immunoprecipitation. Instead, as shown by super-resolution stimulated emission depletion microscopy in combination with fluorescence correlation spectroscopy, LYVE-1 diffusion is restricted by transient entrapment within submembranous actin corrals. These results point to an actin-mediated constraint on LYVE-1 clustering in lymphatic endothelium that tunes the receptor for selective engagement with hyaluronan assemblages in the glycocalyx that are large enough to cross-bridge the corral-bound LYVE-1 molecules and thereby facilitate leukocyte adhesion and transmigration.
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Affiliation(s)
- Tess A Stanly
- Medical Research Council Human Immunology Unit, University of Oxford, Oxford OX3 9DS, United Kingdom.,York Biomedical Research Institute, Department of Biology, University of York, York YO10 5DD, United Kingdom
| | - Marco Fritzsche
- Medical Research Council Human Immunology Unit, University of Oxford, Oxford OX3 9DS, United Kingdom.,Kennedy Institute for Rheumatology, University of Oxford, Oxford OX3 7FY, United Kingdom
| | - Suneale Banerji
- Medical Research Council Human Immunology Unit, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Dilip Shrestha
- Medical Research Council Human Immunology Unit, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Falk Schneider
- Medical Research Council Human Immunology Unit, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- Medical Research Council Human Immunology Unit, University of Oxford, Oxford OX3 9DS, United Kingdom .,Wolfson Imaging Centre, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Strasse 9, 07745 Jena, Germany.,Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
| | - David G Jackson
- Medical Research Council Human Immunology Unit, University of Oxford, Oxford OX3 9DS, United Kingdom
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33
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Bag N, Holowka DA, Baird BA. Imaging FCS delineates subtle heterogeneity in plasma membranes of resting mast cells. Mol Biol Cell 2020; 31:709-723. [PMID: 31895009 PMCID: PMC7202073 DOI: 10.1091/mbc.e19-10-0559] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
A myriad of transient, nanoscopic lipid- and protein-based interactions confer a steady-state organization of the plasma membrane in resting cells that is poised to orchestrate assembly of key signaling components upon reception of an extracellular stimulus. Although difficult to observe directly in live cells, these subtle interactions can be discerned by their impact on the diffusion of membrane constituents. Here, we quantified the diffusion properties of a panel of structurally distinct lipid, lipid-anchored, and transmembrane (TM) probes in RBL mast cells by imaging fluorescence correlation spectroscopy (ImFCS). We developed a statistical analysis of data combined from many pixels over multiple cells to characterize differences in diffusion coefficients as small as 10%, which reflect differences in underlying interactions. We found that the distinctive diffusion properties of lipid probes can be explained by their dynamic partitioning into Lo-like proteolipid nanodomains, which encompass a major fraction of the membrane and whose physical properties are influenced by actin polymerization. Effects on diffusion of functional protein modules in both lipid-anchored and TM probes reflect additional complexity in steady state membrane organization. The contrast we observe between different probes diffusing through the same membrane milieu represents the dynamic resting steady state, which serves as a baseline for monitoring plasma membrane remodeling that occurs upon stimulation.
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Affiliation(s)
- Nirmalya Bag
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - David A Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853
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34
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Bedard M, Shrestha D, Priestman DA, Wang Y, Schneider F, Matute JD, Iyer SS, Gileadi U, Prota G, Kandasamy M, Veerapen N, Besra G, Fritzsche M, Zeissig S, Shevchenko A, Christianson JC, Platt FM, Eggeling C, Blumberg RS, Salio M, Cerundolo V. Sterile activation of invariant natural killer T cells by ER-stressed antigen-presenting cells. Proc Natl Acad Sci U S A 2019; 116:23671-23681. [PMID: 31690657 PMCID: PMC6876220 DOI: 10.1073/pnas.1910097116] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Invariant NKT (iNKT) cells have the unique ability to shape immunity during antitumor immune responses and other forms of sterile and nonsterile inflammation. Recent studies have highlighted a variety of classes of endogenous and pathogen-derived lipid antigens that can trigger iNKT cell activation under sterile and nonsterile conditions. However, the context and mechanisms that drive the presentation of self-lipid antigens in sterile inflammation remain unclear. Here we report that endoplasmic reticulum (ER)-stressed myeloid cells, via signaling events modulated by the protein kinase RNA-like ER kinase (PERK) pathway, increase CD1d-mediated presentation of immunogenic endogenous lipid species, which results in enhanced iNKT cell activation both in vitro and in vivo. In addition, we demonstrate that actin cytoskeletal reorganization during ER stress results in an altered distribution of CD1d on the cell surface, which contributes to enhanced iNKT cell activation. These results define a previously unidentified mechanism that controls iNKT cell activation during sterile inflammation.
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Affiliation(s)
- Melissa Bedard
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Dilip Shrestha
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - David A Priestman
- Department of Pharmacology, University of Oxford, OX1 3QT Oxford, United Kingdom
| | - Yuting Wang
- Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Falk Schneider
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Juan D Matute
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Boston, MA 02115
- Division of Neonatology, Department of Pediatrics, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114
| | - Shankar S Iyer
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Boston, MA 02115
| | - Uzi Gileadi
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Gennaro Prota
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Matheswaran Kandasamy
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Natacha Veerapen
- School of Biosciences, University of Birmingham, B15 2TT Egdbaston, United Kingdom
| | - Gurdyal Besra
- School of Biosciences, University of Birmingham, B15 2TT Egdbaston, United Kingdom
| | - Marco Fritzsche
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
- Kennedy Institute for Rheumatology, University of Oxford, OX3 7LF Oxford, United Kingdom
| | - Sebastian Zeissig
- Center for Regenerative Therapies, Technische Universität Dresden, 01307 Dresden, Germany
- Department of Medicine I, University Medical Center Dresden, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - John C Christianson
- Botnar Research Centre, Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Science, University of Oxford, OX3 7LD Oxford, United Kingdom
| | - Frances M Platt
- Department of Pharmacology, University of Oxford, OX1 3QT Oxford, United Kingdom
| | - Christian Eggeling
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
- Institute of Applied Optics and Biophysics, 07743 Jena, Germany
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technologies e.V., 07745 Jena, Germany
| | - Richard S Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women's Hospital Harvard Medical School, Boston, MA 02115
| | - Mariolina Salio
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom
| | - Vincenzo Cerundolo
- Medical Research Council Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS Oxford, United Kingdom;
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35
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Marolf DM, Jones MR. Measurement Challenges in Dynamic and Nonequilibrium Nanoscale Systems. Anal Chem 2019; 91:13324-13336. [DOI: 10.1021/acs.analchem.9b02702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- David M. Marolf
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
| | - Matthew R. Jones
- Department of Chemistry, Rice University, Houston, Texas 77005, United States
- Department of Materials Science and Nanoengineering, Rice University, Houston, Texas 77005, United States
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36
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Yu Y, Li M, Yu Y. Tracking Single Molecules in Biomembranes: Is Seeing Always Believing? ACS NANO 2019; 13:10860-10868. [PMID: 31589406 PMCID: PMC7179047 DOI: 10.1021/acsnano.9b07445] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The spatial organization of molecules in cell membranes and their dynamic interactions play a central role in regulating cell functions. Single-particle tracking (SPT), a technique in which single molecules are imaged and tracked in real time, has led to breakthrough discoveries regarding these spatiotemporal complexities of cell membranes. There are, however, emerging concerns about factors that might produce misleading interpretations of SPT results. Here, we briefly review the application of SPT to understanding the nanoscale heterogeneities of plasma membranes, with a focus on the unique challenges, pitfalls, and limitations that confront the use of nanoparticles as imaging probes for tracking the dynamics of single molecules in cell membranes.
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37
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Matrix promote mesenchymal stromal cell migration with improved deformation via nuclear stiffness decrease. Biomaterials 2019; 217:119300. [DOI: 10.1016/j.biomaterials.2019.119300] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/16/2019] [Accepted: 06/22/2019] [Indexed: 12/13/2022]
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38
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Bajur AT, Iyer KV, Knust E. Cytocortex-dependent dynamics of Drosophila Crumbs controls junctional stability and tension during germ band retraction. J Cell Sci 2019; 132:jcs.228338. [PMID: 31300472 DOI: 10.1242/jcs.228338] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 07/05/2019] [Indexed: 12/21/2022] Open
Abstract
During morphogenesis, epithelia undergo dynamic rearrangements, which requires continuous remodelling of junctions and cell shape, but at the same time mechanisms preserving cell polarity and tissue integrity. Apico-basal polarity is key for the localisation of the machinery that enables cell shape changes. The evolutionarily conserved Drosophila Crumbs protein is critical for maintaining apico-basal polarity and epithelial integrity. How Crumbs is maintained in a dynamically developing embryo remains largely unknown. Here, we applied quantitative fluorescence techniques to show that, during germ band retraction, Crumbs dynamics correlates with the morphogenetic activity of the epithelium. Genetic and pharmacological perturbations revealed that the mobile pool of Crumbs is fine-tuned by the actomyosin cortex in a stage-dependent manner. Stabilisation of Crumbs at the plasma membrane depends on a proper link to the actomyosin cortex via an intact FERM-domain-binding site in its intracellular domain, loss of which leads to increased junctional tension and higher DE-cadherin (also known as Shotgun) turnover, resulting in impaired junctional rearrangements. These data define Crumbs as a mediator between polarity and junctional regulation to orchestrate epithelial remodelling in response to changes in actomyosin activity.This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Anna T Bajur
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - K Venkatesan Iyer
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Elisabeth Knust
- Max-Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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39
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Pinkwart K, Schneider F, Lukoseviciute M, Sauka-Spengler T, Lyman E, Eggeling C, Sezgin E. Nanoscale dynamics of cholesterol in the cell membrane. J Biol Chem 2019; 294:12599-12609. [PMID: 31270209 PMCID: PMC6709632 DOI: 10.1074/jbc.ra119.009683] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/26/2019] [Indexed: 12/22/2022] Open
Abstract
Cholesterol constitutes ∼30-40% of the mammalian plasma membrane, a larger fraction than of any other single component. It is a major player in numerous signaling processes as well as in shaping molecular membrane architecture. However, our knowledge of the dynamics of cholesterol in the plasma membrane is limited, restricting our understanding of the mechanisms regulating its involvement in cell signaling. Here, we applied advanced fluorescence imaging and spectroscopy approaches on in vitro (model membranes) and in vivo (live cells and embryos) membranes as well as in silico analysis to systematically study the nanoscale dynamics of cholesterol in biological membranes. Our results indicate that cholesterol diffuses faster than phospholipids in live membranes, but not in model membranes. Interestingly, a detailed statistical diffusion analysis suggested two-component diffusion for cholesterol in the plasma membrane of live cells. One of these components was similar to a freely diffusing phospholipid analogue, whereas the other one was significantly faster. When a cholesterol analogue was localized to the outer leaflet only, the fast diffusion of cholesterol disappeared, and it diffused similarly to phospholipids. Overall, our results suggest that cholesterol diffusion in the cell membrane is heterogeneous and that this diffusional heterogeneity is due to cholesterol's nanoscale interactions and localization in the membrane.
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Affiliation(s)
- Kerstin Pinkwart
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Martyna Lukoseviciute
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Tatjana Sauka-Spengler
- Radcliffe Department of Medicine, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
| | - Edward Lyman
- Departments of Physics and Astronomy and Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom.,Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany.,Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, United Kingdom
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40
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Sezgin E, Schneider F, Galiani S, Urbančič I, Waithe D, Lagerholm BC, Eggeling C. Measuring nanoscale diffusion dynamics in cellular membranes with super-resolution STED-FCS. Nat Protoc 2019; 14:1054-1083. [PMID: 30842616 DOI: 10.1038/s41596-019-0127-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/04/2019] [Indexed: 11/08/2022]
Abstract
Super-resolution microscopy techniques enable optical imaging in live cells with unprecedented spatial resolution. They unfortunately lack the temporal resolution required to directly investigate cellular dynamics at scales sufficient to measure molecular diffusion. These fast time scales are, on the other hand, routinely accessible by spectroscopic techniques such as fluorescence correlation spectroscopy (FCS). To enable the direct investigation of fast dynamics at the relevant spatial scales, FCS has been combined with super-resolution stimulated emission depletion (STED) microscopy. STED-FCS has been applied in point or scanning mode to reveal nanoscale diffusion behavior of molecules in live cells. In this protocol, we describe the technical details of performing point STED-FCS (pSTED-FCS) and scanning STED-FCS (sSTED-FCS) measurements, from calibration and sample preparation to data acquisition and analysis. We give particular emphasis to 2D diffusion dynamics in cellular membranes, using molecules tagged with organic fluorophores. These measurements can be accomplished within 4-6 h by those proficient in fluorescence imaging.
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Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Silvia Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Solid State Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Dominic Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Institute of Applied Optics, Friedrich-Schiller-University Jena, Jena, Germany.
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technology e.V., Jena, Germany.
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41
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Adler J, Sintorn IM, Strand R, Parmryd I. Conventional analysis of movement on non-flat surfaces like the plasma membrane makes Brownian motion appear anomalous. Commun Biol 2019; 2:12. [PMID: 30652124 PMCID: PMC6325064 DOI: 10.1038/s42003-018-0240-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 11/26/2018] [Indexed: 01/09/2023] Open
Abstract
Cells are neither flat nor smooth, which has serious implications for prevailing plasma membrane models and cellular processes like cell signalling, adhesion and molecular clustering. Using probability distributions from diffusion simulations, we demonstrate that 2D and 3D Euclidean distance measurements substantially underestimate diffusion on non-flat surfaces. Intuitively, the shortest within surface distance (SWSD), the geodesic distance, should reduce this problem. The SWSD is accurate for foldable surfaces but, although it outperforms 2D and 3D Euclidean measurements, it still underestimates movement on deformed surfaces. We demonstrate that the reason behind the underestimation is that topographical features themselves can produce both super- and subdiffusion, i.e. the appearance of anomalous diffusion. Differentiating between topography-induced and genuine anomalous diffusion requires characterising the surface by simulating Brownian motion on high-resolution cell surface images and a comparison with the experimental data.
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Affiliation(s)
- Jeremy Adler
- Science for Life Laboratory, Medical Cell Biology, Uppsala University, Uppsala University, Box 571, 751 21 Uppsala, Sweden
| | - Ida-Maria Sintorn
- Department of Information Technology, Uppsala University, Box 331, 751 05 Uppsala, Sweden
| | - Robin Strand
- Department of Information Technology, Uppsala University, Box 331, 751 05 Uppsala, Sweden
| | - Ingela Parmryd
- Science for Life Laboratory, Medical Cell Biology, Uppsala University, Uppsala University, Box 571, 751 21 Uppsala, Sweden
- Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden
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42
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Abstract
Advances in microfluidic techniques have prompted researchers to study the inherent heterogeneity of single cells in cell populations.
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Affiliation(s)
- Qiushi Huang
- Department of Chemistry
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
| | - Sifeng Mao
- Department of Chemistry
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
| | - Mashooq Khan
- Department of Chemistry
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
| | - Jin-Ming Lin
- Department of Chemistry
- Beijing Key Laboratory of Microanalytical Methods and Instrumentation
- MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology
- Tsinghua University
- Beijing 100084
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43
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Sarkar P, Chattopadhyay A. Exploring membrane organization at varying spatiotemporal resolutions utilizing fluorescence-based approaches: implications in membrane biology. Phys Chem Chem Phys 2019; 21:11554-11563. [DOI: 10.1039/c9cp02087j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Representative experimental approaches based on dynamic fluorescence microscopy to analyze organization and dynamics of membrane lipids and proteins.
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Affiliation(s)
- Parijat Sarkar
- CSIR-Centre for Cellular and Molecular Biology
- Hyderabad 500 007
- India
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44
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Favard C. Numerical Simulation and FRAP Experiments Show That the Plasma Membrane Binding Protein PH-EFA6 Does Not Exhibit Anomalous Subdiffusion in Cells. Biomolecules 2018; 8:biom8030090. [PMID: 30189682 PMCID: PMC6164371 DOI: 10.3390/biom8030090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 02/07/2023] Open
Abstract
The fluorescence recovery after photobleaching (FRAP) technique has been used for decades to measure movements of molecules in two-dimension (2D). Data obtained by FRAP experiments in cell plasma membranes are assumed to be described through a means of two parameters, a diffusion coefficient, D (as defined in a pure Brownian model) and a mobile fraction, M. Nevertheless, it has also been shown that recoveries can be nicely fit using anomalous subdiffusion. Fluorescence recovery after photobleaching (FRAP) at variable radii has been developed using the Brownian diffusion model to access geometrical characteristics of the surrounding landscape of the molecule. Here, we performed numerical simulations of continuous time random walk (CTRW) anomalous subdiffusion and interpreted them in the context of variable radii FRAP. These simulations were compared to experimental data obtained at variable radii on living cells using the pleckstrin homology (PH) domain of the membrane binding protein EFA6 (exchange factor for ARF6, a small G protein). This protein domain is an excellent candidate to explore the structure of the interface between cytosol and plasma membrane in cells. By direct comparison of our numerical simulations to the experiments, we show that this protein does not exhibit anomalous diffusion in baby hamster kidney (BHK) cells. The non Brownian PH-EFA6 dynamics observed here are more related to spatial heterogeneities such as cytoskeleton fence effects.
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Affiliation(s)
- Cyril Favard
- Membrane Domains and Viral Assembly, IRIM, UMR 9004 CNRS-Université Montpellier, 1919, Route de Mende, 34 000 Montpellier, France.
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45
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Schneider F, Waithe D, Lagerholm BC, Shrestha D, Sezgin E, Eggeling C, Fritzsche M. Statistical Analysis of Scanning Fluorescence Correlation Spectroscopy Data Differentiates Free from Hindered Diffusion. ACS NANO 2018; 12:8540-8546. [PMID: 30028588 PMCID: PMC6117752 DOI: 10.1021/acsnano.8b04080] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/20/2018] [Indexed: 05/28/2023]
Abstract
Cells rely on versatile diffusion dynamics in their plasma membrane. Quantification of this often heterogeneous diffusion is essential to the understanding of cell regulation and function. Yet such measurements remain a major challenge in cell biology, usually due to low sampling throughput, a necessity for dedicated equipment, sophisticated fluorescent label strategies, and limited sensitivity. Here, we introduce a robust, broadly applicable statistical analysis pipeline for large scanning fluorescence correlation spectroscopy data sets, which uncovers the nanoscale heterogeneity of the plasma membrane in living cells by differentiating free from hindered diffusion modes of fluorescent lipid and protein analogues.
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Affiliation(s)
- Falk Schneider
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Dominic Waithe
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - B. Christoffer Lagerholm
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Dilip Shrestha
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Erdinc Sezgin
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
| | - Christian Eggeling
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
- Institute of Applied
Optics, Friedrich-Schiller-University and
Leibniz Institute of Photonic Technology, Helmholtzweg 4, 07743 Jena, Germany
| | - Marco Fritzsche
- MRC
Human Immunology Unit, Wolfson Imaging Centre Oxford, and MRC Centre for Computational Biology, Weatherall Institute of Molecular Medicine, University
of Oxford, Headley Way, Oxford OX3 9DS, United Kingdom
- Kennedy
Institute for Rheumatology, University of
Oxford, Roosevelt Drive, Oxford OX3 7LF, United Kingdom
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46
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Lyman E, Hsieh CL, Eggeling C. From Dynamics to Membrane Organization: Experimental Breakthroughs Occasion a "Modeling Manifesto". Biophys J 2018; 115:595-604. [PMID: 30075850 PMCID: PMC6103736 DOI: 10.1016/j.bpj.2018.07.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 06/29/2018] [Accepted: 07/16/2018] [Indexed: 11/19/2022] Open
Abstract
New experimental techniques, especially in the context of observing molecular dynamics, reveal the plasma membrane to be heterogeneous and "scale rich," from nanometers to microns and from microseconds to seconds. This is critical information, which shows that scale-dependent transport governs the molecular encounters that underlie cellular signaling. The data are rich and reaffirm the importance of the cortical cytoskeleton, protein aggregates, and lipidomic complexity on the statistics of molecular encounters. Moreover, the data demand simulation approaches with a particular set of features, hence the "manifesto." Together with the experimental data, simulations that satisfy these requirements hold the promise of a deeper understanding of membrane spatiotemporal organization. Several experimental breakthroughs in measuring molecular membrane dynamics are reviewed, the constraints that they place on simulations are discussed, and the status of simulation approaches that aim to meet them are detailed.
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Affiliation(s)
- Edward Lyman
- Department of Physics and Astrophysics, University of Delaware, Newark, Delaware; Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware.
| | - Chia-Lung Hsieh
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taiwan
| | - Christian Eggeling
- MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom; Institute of Applied Optics, Friedrich-Schiller-University Jena, Jena, Germany; Leibniz Institute of Photonic Technology, Jena, Germany
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47
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Barabás K, Godó S, Lengyel F, Ernszt D, Pál J, Ábrahám IM. Rapid non-classical effects of steroids on the membrane receptor dynamics and downstream signaling in neurons. Horm Behav 2018; 104:183-191. [PMID: 29775570 DOI: 10.1016/j.yhbeh.2018.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/08/2018] [Accepted: 05/09/2018] [Indexed: 12/26/2022]
Abstract
Contribution to Special Issue on Fast effects of steroids. Although rapid effects of steroid hormones on membrane receptors and intracellular signaling molecules have been extensively studied in neurons, we are only beginning to understand the molecular mechanisms behind these non-classical steroid actions. Single molecule tracking (SMT) studies on live cells demonstrated that surface trafficking of membrane receptors determines their ligand binding properties and downstream signaling events. Recent findings suggest that one of the underlying mechanisms of non-classical steroid actions is the alteration of receptor movements on the membrane surface. In order to highlight this novel aspect of steroid effects, we first address the types of receptor movements in the plasma membrane and the role of cortical actin dynamics in receptor movement. We then discuss how single molecules and the surface movements of receptors can be detected in live cells. Next, we review the fundamental processes, which determine the effect of steroids on the plasma membrane: steroid movement through the lipid bilayer and the role of steroid membrane receptors. Using glutamate and neurotrophin receptors (NTRs) as examples, we demonstrate the features of receptor dynamics in the membrane. In addition, we survey the available data of rapid steroid actions on membrane receptor trafficking: we discuss how glucocorticoids act on the surface diffusion of glutamate receptor molecules and how estradiol acts on NTRs and gamma-aminobutyric acid type A receptors (GABAARs) and their related signaling events as well as on cortical actin. Finally, we address the physiological relevance of rapid steroid action on membrane receptors dynamics.
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Affiliation(s)
- Klaudia Barabás
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - Soma Godó
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - Ferenc Lengyel
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - Dávid Ernszt
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - József Pál
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary
| | - István M Ábrahám
- MTA NAP-B Molecular Neuroendocrinology Research Group, Institute of Physiology, Medical School, Centre for Neuroscience, Szentágothai Research Institute, University of Pécs, Pécs, Hungary.
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48
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abLIM1 constructs non-erythroid cortical actin networks to prevent mechanical tension-induced blebbing. Cell Discov 2018; 4:42. [PMID: 30062045 PMCID: PMC6056535 DOI: 10.1038/s41421-018-0040-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/04/2018] [Accepted: 05/08/2018] [Indexed: 12/11/2022] Open
Abstract
The cell cortex is a layer of cytoskeletal networks underneath the plasma membrane, formed by filamentous actin (F-actin) and cortex proteins including spectrin, adducin, and myosin. It provides cells with proper stiffness, elasticity, and surface tension to allow morphogenesis, division, and migration. Although its architecture and formation have been widely studied in red blood cells, they are poorly understood in non-erythrocytes due to structural complexity and versatile functions. In this study, we identify the actin-binding protein abLIM1 as a novel non-erythroid cell-specific cortex organizer. Endogenous abLIM1 colocalized with cortical βII spectrin but upon overexpression redistributed to thick cortical actin bundles. abLIM1 associated with major cortex proteins such as spectrins and adducin in vivo. Depletion of abLIM1 by RNAi induced prominent blebbing during membrane protrusions of spreading or migrating RPE1 cells and impaired migration efficiency. Reducing cortical tensions by culturing the cells to confluency or inhibiting myosin activity repressed the blebbing phenotype. abLIM1-depleted RPE1 or U2OS cells lacked the dense interwoven cortical actin meshwork observed in control cells but were abundant in long cortical actin bundles along the long axis of the cells. In-vitro assays indicated that abLIM1 was able to crosslink and bundle F-actin to induce dense F-actin network formation. Therefore, abLIM1 governs the formation of dense interconnected cortical actin meshwork in non-erythroid cells to prevent mechanical tension-induced blebbing during cellular activities such as spreading and migration.
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49
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Unsain N, Stefani FD, Cáceres A. The Actin/Spectrin Membrane-Associated Periodic Skeleton in Neurons. Front Synaptic Neurosci 2018; 10:10. [PMID: 29875650 PMCID: PMC5974029 DOI: 10.3389/fnsyn.2018.00010] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/04/2018] [Indexed: 11/28/2022] Open
Abstract
Neurons are the most asymmetric cell types, with their axons commonly extending over lengths that are thousand times longer than the diameter of the cell soma. Fluorescence nanoscopy has recently unveiled that actin, spectrin and accompanying proteins form a membrane-associated periodic skeleton (MPS) that is ubiquitously present in mature axons from all neuronal types evaluated so far. The MPS is a regular supramolecular protein structure consisting of actin “rings” separated by spectrin tetramer “spacers”. Although the MPS is best organized in axons, it is also present in dendrites, dendritic spine necks and thin cellular extensions of non-neuronal cells such as oligodendrocytes and microglia. The unique organization of the actin/spectrin skeleton has raised the hypothesis that it might serve to support the extreme physical and structural conditions that axons must resist during the lifespan of an organism. Another plausible function of the MPS consists of membrane compartmentalization and subsequent organization of protein domains. This review focuses on what we know so far about the structure of the MPS in different neuronal subdomains, its dynamics and the emerging evidence of its impact in axonal biology.
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Affiliation(s)
- Nicolas Unsain
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.,Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto Universitario Ciencias Biomédicas de Córdoba (IUCBC), Córdoba, Argentina
| | - Fernando D Stefani
- Centro de Investigaciones en Bionanociencias (CIBION), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina.,Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alfredo Cáceres
- Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Córdoba, Argentina.,Universidad Nacional de Córdoba, Córdoba, Argentina.,Instituto Universitario Ciencias Biomédicas de Córdoba (IUCBC), Córdoba, Argentina
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50
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Sarangi NK, Roobala C, Basu JK. Unraveling complex nanoscale lipid dynamics in simple model biomembranes: Insights from fluorescence correlation spectroscopy in super-resolution stimulated emission depletion mode. Methods 2018; 140-141:198-211. [DOI: 10.1016/j.ymeth.2017.11.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 11/18/2017] [Accepted: 11/19/2017] [Indexed: 12/24/2022] Open
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