151
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Steady-state cross-correlations for live two-colour super-resolution localization data sets. Nat Commun 2015; 6:7347. [PMID: 26066572 PMCID: PMC4467025 DOI: 10.1038/ncomms8347] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 04/28/2015] [Indexed: 01/12/2023] Open
Abstract
Cross-correlation of super-resolution images gathered from point localizations allows for robust quantification of protein co-distributions in chemically fixed cells. Here this is extended to dynamic systems through an analysis that quantifies the steady-state cross-correlation between spectrally distinguishable probes. This methodology is used to quantify the co-distribution of several mobile membrane proteins in both vesicles and live cells, including Lyn kinase and the B-cell receptor during antigen stimulation.
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152
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Nieuwenhuizen RPJ, Bates M, Szymborska A, Lidke KA, Rieger B, Stallinga S. Quantitative localization microscopy: effects of photophysics and labeling stoichiometry. PLoS One 2015; 10:e0127989. [PMID: 25992915 PMCID: PMC4439177 DOI: 10.1371/journal.pone.0127989] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 04/22/2015] [Indexed: 01/06/2023] Open
Abstract
Quantification in localization microscopy with reversibly switchable fluorophores is severely hampered by the unknown number of switching cycles a fluorophore undergoes and the unknown stoichiometry of fluorophores on a marker such as an antibody. We overcome this problem by measuring the average number of localizations per fluorophore, or generally per fluorescently labeled site from the build-up of spatial image correlation during acquisition. To this end we employ a model for the interplay between the statistics of activation, bleaching, and labeling stoichiometry. We validated our method using single fluorophore labeled DNA oligomers and multiple-labeled neutravidin tetramers where we find a counting error of less than 17% without any calibration of transition rates. Furthermore, we demonstrated our quantification method on nanobody- and antibody-labeled biological specimens.
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Affiliation(s)
| | - Mark Bates
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Anna Szymborska
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Keith A. Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico, USA
| | - Bernd Rieger
- Quantitative Imaging Group, Delft University of Technology, Delft, The Netherlands
- * E-mail: (BR); (SS)
| | - Sjoerd Stallinga
- Quantitative Imaging Group, Delft University of Technology, Delft, The Netherlands
- * E-mail: (BR); (SS)
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153
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Single-molecule tracking of inositol trisphosphate receptors reveals different motilities and distributions. Biophys J 2015; 107:834-45. [PMID: 25140418 DOI: 10.1016/j.bpj.2014.05.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 04/24/2014] [Accepted: 05/01/2014] [Indexed: 11/20/2022] Open
Abstract
Puffs are local Ca(2+) signals that arise by Ca(2+) liberation from the endoplasmic reticulum through the concerted opening of tightly clustered inositol trisphosphate receptors/channels (IP3Rs). The locations of puff sites observed by Ca(2+) imaging remain static over several minutes, whereas fluorescence recovery after photobleaching (FRAP) experiments employing overexpression of fluorescently tagged IP3Rs have shown that the majority of IP3Rs are freely motile. To address this discrepancy, we applied single-molecule imaging to locate and track type 1 IP3Rs tagged with a photoswitchable fluorescent protein and expressed in COS-7 cells. We found that ∼ 70% of the IP3R1 molecules were freely motile, undergoing random walk motility with an apparent diffusion coefficient of ∼ 0.095 μm s(-1), whereas the remaining molecules were essentially immotile. A fraction of the immotile IP3Rs were organized in clusters, with dimensions (a few hundred nanometers across) comparable to those previously estimated for the IP3R clusters underlying functional puff sites. No short-term (seconds) changes in overall motility or in clustering of immotile IP3Rs were apparent following activation of IP3/Ca(2+) signaling. We conclude that stable clusters of small numbers of immotile IP3Rs may underlie local Ca(2+) release sites, whereas the more numerous motile IP3Rs appear to be functionally silent.
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154
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Valley CC, Liu S, Lidke DS, Lidke KA. Sequential superresolution imaging of multiple targets using a single fluorophore. PLoS One 2015; 10:e0123941. [PMID: 25860558 PMCID: PMC4393115 DOI: 10.1371/journal.pone.0123941] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/09/2015] [Indexed: 12/11/2022] Open
Abstract
Fluorescence superresolution (SR) microscopy, or fluorescence nanoscopy, provides nanometer scale detail of cellular structures and allows for imaging of biological processes at the molecular level. Specific SR imaging methods, such as localization-based imaging, rely on stochastic transitions between on (fluorescent) and off (dark) states of fluorophores. Imaging multiple cellular structures using multi-color imaging is complicated and limited by the differing properties of various organic dyes including their fluorescent state duty cycle, photons per switching event, number of fluorescent cycles before irreversible photobleaching, and overall sensitivity to buffer conditions. In addition, multiple color imaging requires consideration of multiple optical paths or chromatic aberration that can lead to differential aberrations that are important at the nanometer scale. Here, we report a method for sequential labeling and imaging that allows for SR imaging of multiple targets using a single fluorophore with negligible cross-talk between images. Using brightfield image correlation to register and overlay multiple image acquisitions with ~10 nm overlay precision in the x-y imaging plane, we have exploited the optimal properties of AlexaFluor647 for dSTORM to image four distinct cellular proteins. We also visualize the changes in co-localization of the epidermal growth factor (EGF) receptor and clathrin upon EGF addition that are consistent with clathrin-mediated endocytosis. These results are the first to demonstrate sequential SR (s-SR) imaging using direct stochastic reconstruction microscopy (dSTORM), and this method for sequential imaging can be applied to any superresolution technique.
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Affiliation(s)
- Christopher C. Valley
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Sheng Liu
- Department of Physics & Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Diane S. Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Keith A. Lidke
- Department of Physics & Astronomy, University of New Mexico, Albuquerque, New Mexico, United States of America
- * E-mail:
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155
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A multi-layered protein network stabilizes the Escherichia coli FtsZ-ring and modulates constriction dynamics. PLoS Genet 2015; 11:e1005128. [PMID: 25848771 PMCID: PMC4388696 DOI: 10.1371/journal.pgen.1005128] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 03/04/2015] [Indexed: 11/19/2022] Open
Abstract
The prokaryotic tubulin homolog, FtsZ, forms a ring-like structure (FtsZ-ring) at midcell. The FtsZ-ring establishes the division plane and enables the assembly of the macromolecular division machinery (divisome). Although many molecular components of the divisome have been identified and their interactions extensively characterized, the spatial organization of these proteins within the divisome is unclear. Consequently, the physical mechanisms that drive divisome assembly, maintenance, and constriction remain elusive. Here we applied single-molecule based superresolution imaging, combined with genetic and biophysical investigations, to reveal the spatial organization of cellular structures formed by four important divisome proteins in E. coli: FtsZ, ZapA, ZapB and MatP. We show that these interacting proteins are arranged into a multi-layered protein network extending from the cell membrane to the chromosome, each with unique structural and dynamic properties. Further, we find that this protein network stabilizes the FtsZ-ring, and unexpectedly, slows down cell constriction, suggesting a new, unrecognized role for this network in bacterial cell division. Our results provide new insight into the structure and function of the divisome, and highlight the importance of coordinated cell constriction and chromosome segregation. Bacterial cell division is a highly regulated process that must be coordinated with other cellular processes (i.e. DNA replication and chromosome segregation) to promote faithful reproduction. In Escherichia coli, this regulation is most often mediated through the polymerization of the prokaryotic tubulin homolog, FtsZ, which forms a ring-like structure (FtsZ-ring) at midcell. The establishment of the FtsZ-ring marks the site of division and enables the assembly of the macromolecular division machinery (divisome). Here we applied single-molecule based superresolution imaging to reveal the three-dimensional structure of FtsZ in the context of its regulatory proteins: ZapA, ZapB and MatP. We found that these four proteins exist in a multi-layered network that extends from the cell membrane to the chromosome. This layered organization not only helps to stabilize the FtsZ-ring, but also serves to coordinate division with DNA status by influencing constriction rate. Our results not only provide a comprehensive view of the divisome, but also allow new insight to be garnered regarding the structure and function of the divisome.
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156
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Meerschaert RL, Kelly CV. Trace membrane additives affect lipid phases with distinct mechanisms: a modified Ising model. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:227-33. [PMID: 25820530 PMCID: PMC4412547 DOI: 10.1007/s00249-015-1017-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/25/2015] [Accepted: 03/05/2015] [Indexed: 12/13/2022]
Abstract
The addition of trace molecules into membranes can significantly alter the morphology of the co-existing liquid phases and lipid phase transition temperature. Membrane additives may affect lipid phase dynamics through preferentially partitioning to the boundary between lipid phases or preferentially mixing into one lipid phase. The characteristic differences between these mechanisms are demonstrated here in a minimalistic nearest neighbor model to provide a framework for how slight changes to membrane composition may affect lipid-phase-dependent processes, such as lipid-raft formation, immunological signaling, and molecular sorting preceding endocytosis with coexisting liquid phases. Within the low mole fractions explored here (≤3 mol%), increasing the additive concentration linearly changed the phase miscibility temperature. Rotationally asymmetric Janus particles reduced the miscibility transition temperature for all fractions and degree of phase polarization. Rotationally symmetric additives, however, either increased or decreased the phase miscibility temperature depending on the phase preference of the additive. While most experimental molecules may contain aspects of both of these idealized additives, this model provides a broad framework to quantify the effects of membrane additives in regard to lipid phase preference, lipid-raft association, and contribution to lipid phase-dependent molecular sorting.
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157
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Diffraction-unlimited imaging: from pretty pictures to hard numbers. Cell Tissue Res 2015; 360:151-78. [DOI: 10.1007/s00441-014-2109-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/22/2014] [Indexed: 10/23/2022]
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158
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Chen YH, Du W, Hagemeijer MC, Takvorian PM, Pau C, Cali A, Brantner CA, Stempinski ES, Connelly PS, Ma HC, Jiang P, Wimmer E, Altan-Bonnet G, Altan-Bonnet N. Phosphatidylserine vesicles enable efficient en bloc transmission of enteroviruses. Cell 2015; 160:619-630. [PMID: 25679758 PMCID: PMC6704014 DOI: 10.1016/j.cell.2015.01.032] [Citation(s) in RCA: 332] [Impact Index Per Article: 36.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/13/2014] [Accepted: 01/12/2015] [Indexed: 12/17/2022]
Abstract
A central paradigm within virology is that each viral particle largely behaves as an independent infectious unit. Here, we demonstrate that clusters of enteroviral particles are packaged within phosphatidylserine (PS) lipid-enriched vesicles that are non-lytically released from cells and provide greater infection efficiency than free single viral particles. We show that vesicular PS lipids are co-factors to the relevant enterovirus receptors in mediating subsequent infectivity and transmission, in particular to primary human macrophages. We demonstrate that clustered packaging of viral particles within vesicles enables multiple viral RNA genomes to be collectively transferred into single cells. This study reveals a novel mode of viral transmission, where enteroviral genomes are transmitted from cell-to-cell en bloc in membrane-bound PS vesicles instead of as single independent genomes. This has implications for facilitating genetic cooperativity among viral quasispecies as well as enhancing viral replication.
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Affiliation(s)
- Ying-Han Chen
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA; Federated Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - WenLi Du
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Marne C Hagemeijer
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Peter M Takvorian
- Federated Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Cyrilla Pau
- Federated Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Ann Cali
- Federated Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA
| | - Christine A Brantner
- Electron Microscopy Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Erin S Stempinski
- Electron Microscopy Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Patricia S Connelly
- Electron Microscopy Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA
| | - Hsin-Chieh Ma
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Ping Jiang
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Eckard Wimmer
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794, USA
| | - Grégoire Altan-Bonnet
- Program in Computational Biology and Immunology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nihal Altan-Bonnet
- Laboratory of Host-Pathogen Dynamics, National Heart Lung and Blood Institute, NIH, Bethesda, MD 20892, USA.
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159
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Abstract
Single-molecule localization-based super-resolution microscopy can be performed with regular, bright, and photostable organic fluorophores. We review a concept termed direct stochastic optical reconstruction microscopy (dSTORM), which operates conventional fluorophores as photoswitches and provides an optical resolution of ~20 nm. We introduce the principle of dSTORM, illustrate experimental schemes, and discuss approaches for data analysis.
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Affiliation(s)
- Ulrike Endesfelder
- Institute of Physical & Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue-Street 7, Frankfurt, 60438, Germany
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160
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Abstract
Our long-term efforts to elucidate receptor-mediated signalling in immune cells, particularly transmembrane signalling initiated by FcɛRI, the receptor for IgE in mast cells, led us unavoidably to contemplate the role of the heterogeneous plasma membrane. Our early investigations with fluorescence microscopy revealed co-redistribution of certain lipids and signalling components with antigen-cross-linked IgE-FcɛRI and pointed to participation of ordered membrane domains in the signalling process. With a focus on this function, we have worked along with others to develop diverse and increasingly sophisticated tools to analyse the complexity of membrane structure that facilitates regulation and targeting of signalling events. The present chapter describes how initial membrane interactions of clustered IgE-FcɛRI lead to downstream cellular responses and how biochemical information integrated with nanoscale resolution spectroscopy and imaging is providing mechanistic insights at the level of molecular complexes.
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Affiliation(s)
- David Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, U.S.A
| | - Barbara Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, U.S.A
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161
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Timmermans FJ, Otto C. Contributed review: Review of integrated correlative light and electron microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:011501. [PMID: 25638065 DOI: 10.1063/1.4905434] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
New developments in the field of microscopy enable to acquire increasing amounts of information from large sample areas and at an increased resolution. Depending on the nature of the technique, the information may reveal morphological, structural, chemical, and still other sample characteristics. In research fields, such as cell biology and materials science, there is an increasing demand to correlate these individual levels of information and in this way to obtain a better understanding of sample preparation and specific sample properties. To address this need, integrated systems were developed that combine nanometer resolution electron microscopes with optical microscopes, which produce chemically or label specific information through spectroscopy. The complementary information from electron microscopy and light microscopy presents an opportunity to investigate a broad range of sample properties in a correlated fashion. An important part of correlating the differences in information lies in bridging the different resolution and image contrast features. The trend to analyse samples using multiple correlated microscopes has resulted in a new research field. Current research is focused, for instance, on (a) the investigation of samples with nanometer scale distribution of inorganic and organic materials, (b) live cell analysis combined with electron microscopy, and (c) in situ spectroscopic and electron microscopy analysis of catalytic materials, but more areas will benefit from integrated correlative microscopy.
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Affiliation(s)
- F J Timmermans
- Medical Cell Biophysics Group, MIRA Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
| | - C Otto
- Medical Cell Biophysics Group, MIRA Institute, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands
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162
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Liu Z, Legant WR, Chen BC, Li L, Grimm JB, Lavis LD, Betzig E, Tjian R. 3D imaging of Sox2 enhancer clusters in embryonic stem cells. eLife 2014; 3:e04236. [PMID: 25537195 PMCID: PMC4381973 DOI: 10.7554/elife.04236] [Citation(s) in RCA: 163] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2014] [Accepted: 11/26/2014] [Indexed: 12/19/2022] Open
Abstract
Combinatorial cis-regulatory networks encoded in animal genomes represent the foundational gene expression mechanism for directing cell-fate commitment and maintenance of cell identity by transcription factors (TFs). However, the 3D spatial organization of cis-elements and how such sub-nuclear structures influence TF activity remain poorly understood. Here, we combine lattice light-sheet imaging, single-molecule tracking, numerical simulations, and ChIP-exo mapping to localize and functionally probe Sox2 enhancer-organization in living embryonic stem cells. Sox2 enhancers form 3D-clusters that are segregated from heterochromatin but overlap with a subset of Pol II enriched regions. Sox2 searches for specific binding targets via a 3D-diffusion dominant mode when shuttling long-distances between clusters while chromatin-bound states predominate within individual clusters. Thus, enhancer clustering may reduce global search efficiency but enables rapid local fine-tuning of TF search parameters. Our results suggest an integrated model linking cis-element 3D spatial distribution to local-versus-global target search modalities essential for regulating eukaryotic gene transcription.
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Affiliation(s)
- Zhe Liu
- Junior Fellow Program, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Wesley R Legant
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Bi-Chang Chen
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Li Li
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Jonathan B Grimm
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Luke D Lavis
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Eric Betzig
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
| | - Robert Tjian
- Transcription Imaging Consortium, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, United States
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163
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Cell-specific STORM super-resolution imaging reveals nanoscale organization of cannabinoid signaling. Nat Neurosci 2014; 18:75-86. [PMID: 25485758 PMCID: PMC4281300 DOI: 10.1038/nn.3892] [Citation(s) in RCA: 170] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 10/31/2014] [Indexed: 02/07/2023]
Abstract
A major challenge in neuroscience is to determine the nanoscale position and quantity of signaling molecules in a cell type- and subcellular compartment-specific manner. We developed a new approach to this problem by combining cell-specific physiological and anatomical characterization with super-resolution imaging and studied the molecular and structural parameters shaping the physiological properties of synaptic endocannabinoid signaling in the mouse hippocampus. We found that axon terminals of perisomatically projecting GABAergic interneurons possessed increased CB1 receptor number, active-zone complexity and receptor/effector ratio compared with dendritically projecting interneurons, consistent with higher efficiency of cannabinoid signaling at somatic versus dendritic synapses. Furthermore, chronic Δ(9)-tetrahydrocannabinol administration, which reduces cannabinoid efficacy on GABA release, evoked marked CB1 downregulation in a dose-dependent manner. Full receptor recovery required several weeks after the cessation of Δ(9)-tetrahydrocannabinol treatment. These findings indicate that cell type-specific nanoscale analysis of endogenous protein distribution is possible in brain circuits and identify previously unknown molecular properties controlling endocannabinoid signaling and cannabis-induced cognitive dysfunction.
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164
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Tuson HH, Biteen JS. Unveiling the inner workings of live bacteria using super-resolution microscopy. Anal Chem 2014; 87:42-63. [PMID: 25380480 DOI: 10.1021/ac5041346] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Hannah H Tuson
- Department of Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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165
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Maity PC, Yang J, Klaesener K, Reth M. The nanoscale organization of the B lymphocyte membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:830-40. [PMID: 25450974 PMCID: PMC4547082 DOI: 10.1016/j.bbamcr.2014.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 10/30/2014] [Accepted: 11/07/2014] [Indexed: 12/13/2022]
Abstract
The fluid mosaic model of Singer and Nicolson correctly predicted that the plasma membrane (PM) forms a lipid bi-layer containing many integral trans-membrane proteins. This model also suggested that most of these proteins were randomly dispersed and freely diffusing moieties. Initially, this view of a dynamic and rather unorganized membrane was supported by early observations of the cell surfaces using the light microscope. However, recent studies on the PM below the diffraction limit of visible light (~250nm) revealed that, at nanoscale dimensions, membranes are highly organized and compartmentalized structures. Lymphocytes are particularly useful to study this nanoscale membrane organization because they grow as single cells and are not permanently engaged in cell:cell contacts within a tissue that can influence membrane organization. In this review, we describe the methods that can be used to better study the protein:protein interaction and nanoscale organization of lymphocyte membrane proteins, with a focus on the B cell antigen receptor (BCR). Furthermore, we discuss the factors that may generate and maintain these membrane structures.
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Affiliation(s)
- Palash Chandra Maity
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany; Department of Molecular Immunology, Biology III, University of Freiburg, Germany; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Jianying Yang
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany; Department of Molecular Immunology, Biology III, University of Freiburg, Germany; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Kathrin Klaesener
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany; Department of Molecular Immunology, Biology III, University of Freiburg, Germany; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Michael Reth
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Germany; Department of Molecular Immunology, Biology III, University of Freiburg, Germany; Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
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166
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Abstract
Gut microbes play a key role in human health and nutrition by catabolizing a wide variety of glycans via enzymatic activities that are not encoded in the human genome. The ability to recognize and process carbohydrates strongly influences the structure of the gut microbial community. While the effects of diet on the microbiota are well documented, little is known about the molecular processes driving metabolism. To provide mechanistic insight into carbohydrate catabolism in gut symbionts, we studied starch processing in real time in the model Bacteroides thetaiotaomicron starch utilization system (Sus) by single-molecule fluorescence. Although previous studies have explored Sus protein structure and function, the transient interactions, assembly, and collaboration of these outer membrane proteins have not yet been elucidated in live cells. Our live-cell superresolution imaging reveals that the polymeric starch substrate dynamically recruits Sus proteins, serving as an external scaffold for bacterial membrane assembly of the Sus complex, which may promote efficient capturing and degradation of starch. Furthermore, by simultaneously localizing multiple Sus outer membrane proteins on the B. thetaiotaomicron cell surface, we have characterized the dynamics and stoichiometry of starch-induced Sus complex assembly on the molecular scale. Finally, based on Sus protein knockout strains, we have discerned the mechanism of starch-induced Sus complex assembly in live anaerobic cells with nanometer-scale resolution. Our insights into the starch-induced outer membrane protein assembly central to this conserved nutrient uptake mechanism pave the way for the development of dietary or pharmaceutical therapies to control Bacteroidetes in the intestinal tract to enhance human health and treat disease. In this study, we used nanometer-scale superresolution imaging to reveal dynamic interactions between the proteins involved in starch processing by the prominent human gut symbiont Bacteroides thetaiotaomicron in real time in live cells. These results represent the first working model of starch utilization system (Sus) complex assembly and function during glycan catabolism and are likely to describe aspects of how other Sus-like systems function in human gut Bacteroidetes. Our results provide unique mechanistic insights into a glycan catabolism strategy that is prevalent within the human gut microbial community. Proper understanding of this conserved nutrient uptake mechanism is essential for the development of dietary or pharmaceutical therapies to control intestinal tract microbial populations, to enhance human health, and to treat disease.
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167
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Pi J, Jin H, Yang F, Chen ZW, Cai J. In situ single molecule imaging of cell membranes: linking basic nanotechniques to cell biology, immunology and medicine. NANOSCALE 2014; 6:12229-12249. [PMID: 25227707 DOI: 10.1039/c4nr04195j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The cell membrane, which consists of a viscous phospholipid bilayer, different kinds of proteins and various nano/micrometer-sized domains, plays a very important role in ensuring the stability of the intracellular environment and the order of cellular signal transductions. Exploring the precise cell membrane structure and detailed functions of the biomolecules in a cell membrane would be helpful to understand the underlying mechanisms involved in cell membrane signal transductions, which could further benefit research into cell biology, immunology and medicine. The detection of membrane biomolecules at the single molecule level can provide some subtle information about the molecular structure and the functions of the cell membrane. In particular, information obtained about the molecular mechanisms and other information at the single molecule level are significantly different from that detected from a large amount of biomolecules at the large-scale through traditional techniques, and can thus provide a novel perspective for the study of cell membrane structures and functions. However, the precise investigations of membrane biomolecules prompts researchers to explore cell membranes at the single molecule level by the use of in situ imaging methods, as the exact conformation and functions of biomolecules are highly controlled by the native cellular environment. Recently, the in situ single molecule imaging of cell membranes has attracted increasing attention from cell biologists and immunologists. The size of biomolecules and their clusters on the cell surface are set at the nanoscale, which makes it mandatory to use high- and super-resolution imaging techniques to realize the in situ single molecule imaging of cell membranes. In the past few decades, some amazing imaging techniques and instruments with super resolution have been widely developed for molecule imaging, which can also be further employed for the in situ single molecule imaging of cell membranes. In this review, we attempt to summarize the characteristics of these advanced techniques for use in the in situ single molecule imaging of cell membranes. We believe that this work will help to promote the technological and methodological developments of super-resolution techniques for the single molecule imaging of cell membranes and help researchers better understand which technique is most suitable for their future exploring of membrane biomolecules; ultimately promoting further developments in cell biology, immunology and medicine.
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Affiliation(s)
- Jiang Pi
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technique, Macau, China.
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168
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Basic motifs target PSGL-1, CD43, and CD44 to plasma membrane sites where HIV-1 assembles. J Virol 2014; 89:454-67. [PMID: 25320329 DOI: 10.1128/jvi.02178-14] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED HIV-1 incorporates various host membrane proteins during particle assembly at the plasma membrane; however, the mechanisms mediating this incorporation process remain poorly understood. We previously showed that the HIV-1 structural protein Gag localizes to the uropod, a rear-end structure of polarized T cells, and that assembling Gag copatches with a subset, but not all, of the uropod-directed proteins, i.e., PSGL-1, CD43, and CD44, in nonpolarized T cells. The latter observation suggests the presence of a mechanism promoting virion incorporation of these cellular proteins. To address this possibility and identify molecular determinants, in the present study we examined coclustering between Gag and the transmembrane proteins in T and HeLa cells using quantitative two-color superresolution localization microscopy. Consistent with the findings of the T-cell copatching study, we found that basic residues within the matrix domain of Gag are required for Gag-PSGL-1 coclustering. Notably, the presence of a polybasic sequence in the PSGL-1 cytoplasmic domain significantly enhanced this coclustering. We also found that polybasic motifs present in the cytoplasmic tails of CD43 and CD44 also promote their coclustering with Gag. ICAM-1 and ICAM-3, uropod-directed proteins that do not copatch with Gag in T cells, and CD46, a non-uropod-directed protein, showed no or little coclustering with Gag. However, replacing their cytoplasmic tails with the cytoplasmic tail of PSGL-1 significantly enhanced their coclustering with Gag. Altogether, these results identify a novel mechanism for host membrane protein association with assembling HIV-1 Gag in which polybasic sequences present in the cytoplasmic tails of the membrane proteins and in Gag are the major determinants. IMPORTANCE Nascent HIV-1 particles incorporate many host plasma membrane proteins during assembly. However, it is largely unknown what mechanisms promote the association of these proteins with virus assembly sites within the plasma membrane. Notably, our previous study showed that HIV-1 structural protein Gag colocalizes with a group of uropod-directed transmembrane proteins, PSGL-1, CD43, and CD44, at the plasma membrane of T cells. The results obtained in the current study using superresolution localization microscopy suggest the presence of a novel molecular mechanism promoting the association of PSGL-1, CD43, and CD44 with assembling HIV-1 which relies on polybasic sequences in HIV-1 Gag and in cytoplasmic domains of the transmembrane proteins. This information advances our understanding of virion incorporation of host plasma membrane proteins, some of which modulate virus spread positively or negatively, and suggests a possible new strategy to enrich HIV-1-based lentiviral vectors with a desired transmembrane protein.
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169
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Baumgart F, Schütz GJ. Detecting protein association at the T cell plasma membrane. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1853:791-801. [PMID: 25300585 DOI: 10.1016/j.bbamcr.2014.09.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/18/2014] [Accepted: 09/29/2014] [Indexed: 10/24/2022]
Abstract
At the moment, many models on T cell signaling rely on results obtained via rather indirect methodologies, which makes direct comparison and conclusions to the in vivo situation difficult. Recently, a variety of new imaging methods were developed, which have the potential to directly shed light onto the mysteries of protein association at the T cell membrane. While the new modalities are extremely promising, for a broad readership it may be difficult to judge the results, since technological shortcomings are not always obvious. In this review article, we put key questions on the mechanism of protein interactions in the T cell plasma membrane into relation with techniques that allow to address such questions. We discuss applicability of the techniques, their strengths and weaknesses. This article is part of a Special Issue entitled: Nanoscale membrane organisation and signalling.
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Affiliation(s)
- Florian Baumgart
- Vienna University of Technology, Institute for Applied Physics, Wiedner Hauptstraße 8-10, 1040 Vienna, Austria
| | - Gerhard J Schütz
- Vienna University of Technology, Institute for Applied Physics, Wiedner Hauptstraße 8-10, 1040 Vienna, Austria.
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170
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Mabry JN, Skaug MJ, Schwartz DK. Single-molecule insights into retention at a reversed-phase chromatographic interface. Anal Chem 2014; 86:9451-8. [PMID: 25188676 DOI: 10.1021/ac5026418] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The efficiency of chromatographic separations decreases markedly when peaks exhibit asymmetry (e.g., "peak tailing"). Theoretically, these effects can arise from heterogeneous adsorption kinetics. To investigate the nature and consequences of such heterogeneity, we used a combination of single-molecule imaging and reversed-phase liquid chromatography (RPLC). In both single-molecule and macroscopic RPLC experiments, the stationary phase was hydrophobic end-capped (trimethylsilyl-functionalized) silica, which we exposed to different methanol/water solutions (50%-62% methanol), containing a fluorescent fatty acid analyte. Super-resolution maps based on single-molecule observations revealed rare, strong adsorption sites with activity that varied significantly with methanol concentration. The adsorption and desorption kinetics on the strong sites were heterogeneous and positively correlated, suggesting a broad underlying distribution of site binding energies. Adsorption equilibrium on the strong sites was more sensitive to solution conditions than overall retention measured in RPLC experiments, suggesting that the effect of strong sites on the overall adsorption kinetics should change with solution conditions. Interestingly, in RPLC experiments, peak tailing had a nonmonotonic dependence on methanol concentration within the range studied. Using the stochastic model of chromatography, we showed quantitatively that our single-molecule kinetic results were consistent with this macroscopic trend. This approach to identifying and quantifying adsorption sites should be useful for designing better chromatographic separations and for identifying the role of heterogeneous surface chemistry in molecular dynamics.
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Affiliation(s)
- Joshua N Mabry
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Colorado 80309-0596, United States
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171
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Coltharp C, Yang X, Xiao J. Quantitative analysis of single-molecule superresolution images. Curr Opin Struct Biol 2014; 28:112-21. [PMID: 25179006 DOI: 10.1016/j.sbi.2014.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/14/2014] [Accepted: 08/14/2014] [Indexed: 10/24/2022]
Abstract
This review highlights the quantitative capabilities of single-molecule localization-based superresolution imaging methods. In addition to revealing fine structural details, the molecule coordinate lists generated by these methods provide the critical ability to quantify the number, clustering, and colocalization of molecules with 10-50 nm resolution. Here we describe typical workflows and precautions for quantitative analysis of single-molecule superresolution images. These guidelines include potential pitfalls and essential control experiments, allowing critical assessment and interpretation of superresolution images.
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Affiliation(s)
- Carla Coltharp
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Xinxing Yang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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172
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You C, Richter CP, Löchte S, Wilmes S, Piehler J. Dynamic Submicroscopic Signaling Zones Revealed by Pair Correlation Tracking and Localization Microscopy. Anal Chem 2014; 86:8593-602. [DOI: 10.1021/ac501127r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Changjiang You
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Christian P. Richter
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Stephan Wilmes
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
| | - Jacob Piehler
- Department
of Biology, University of Osnabrück, Barbarastrasse 11, 49076 Osnabrück, Germany
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173
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Tracking single molecules at work in living cells. Nat Chem Biol 2014; 10:524-32. [PMID: 24937070 DOI: 10.1038/nchembio.1558] [Citation(s) in RCA: 218] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Accepted: 05/21/2014] [Indexed: 11/09/2022]
Abstract
Methods for imaging and tracking single molecules conjugated with fluorescent probes, called single-molecule tracking (SMT), are now providing researchers with the unprecedented ability to directly observe molecular behaviors and interactions in living cells. Current SMT methods are achieving almost the ultimate spatial precision and time resolution for tracking single molecules, determined by the currently available dyes. In cells, various molecular interactions and reactions occur as stochastic and probabilistic processes. SMT provides an ideal way to directly track these processes by observing individual molecules at work in living cells, leading to totally new views of the biochemical and molecular processes used by cells whether in signal transduction, gene regulation or formation and disintegration of macromolecular complexes. Here we review SMT methods, summarize the recent results obtained by SMT, including related superresolution microscopy data, and describe the special concerns when SMT applications are shifted from the in vitro paradigms to living cells.
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174
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Stone MB, Veatch SL. Far-red organic fluorophores contain a fluorescent impurity. Chemphyschem 2014; 15:2240-6. [PMID: 24782148 PMCID: PMC4180537 DOI: 10.1002/cphc.201402002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/06/2014] [Indexed: 11/06/2022]
Abstract
Far-red organic fluorophores commonly used in traditional and super-resolution localization microscopy are found to contain a fluorescent impurity with green excitation and near-red emission. This near-red fluorescent impurity can interfere with some multicolor stochastic optical reconstruction microscopy/photoactivated localization microscopy measurements in live cells and produce subtle artifacts in chemically fixed cells. We additionally describe alternatives to avoid artifacts in super-resolution localization microscopy.
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Affiliation(s)
- Matthew B. Stone
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor MI 48109
| | - Sarah L. Veatch
- Department of Biophysics, University of Michigan, 930 N University, Ann Arbor MI 48109
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175
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Itano MS, Graus MS, Pehlke C, Wester MJ, Liu P, Lidke KA, Thompson NL, Jacobson K, Neumann AK. Super-resolution imaging of C-type lectin spatial rearrangement within the dendritic cell plasma membrane at fungal microbe contact sites. FRONTIERS IN PHYSICS 2014; 2:46. [PMID: 25506589 PMCID: PMC4262399 DOI: 10.3389/fphy.2014.00046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Dendritic cells express DC-SIGN and CD206, C-type lectins (CTLs) that bind a variety of pathogens and may facilitate pathogen uptake for subsequent antigen presentation. Both proteins form punctate membrane nanodomains (∼80 nm) on naïve cells. We analyzed the spatiotemporal distribution of CTLs following host-fungal particle contact using confocal microscopy and three distinct methods of cluster identification and measurement of receptor clusters in super-resolution datasets: DBSCAN, Pair Correlation and a custom implementation of the Getis spatial statistic. Quantitative analysis of confocal and super-resolution images demonstrated that CTL nanodomains become concentrated in the contact site relative to non-contact membrane after the first hour of exposure and established that this recruitment is sustained out to 4 h. DC-SIGN nanodomains in fungal contact sites exhibit a 70% area increase and a 38% decrease in interdomain separation. Contact site CD206 nanodomains possess 90% greater area and 42% lower interdomain separation relative to non-contact regions. Contact site CTL clusters appear as disk-shaped domains of approximately 150-175 nm in diameter. The increase in length scale of CTL nanostructure in contact sites suggests that the smaller nanodomains on resting membranes may merge during fungal recognition, or that they become packed closely enough to achieve sub-resolution inter-domain edge separations of <30 nm. This study provides evidence of local receptor spatial rearrangements on the nanoscale that occur in the plasma membrane upon pathogen binding and may direct important signaling interactions required to recognize and respond to the presence of a relatively large pathogen.
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Affiliation(s)
- Michelle S. Itano
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew S. Graus
- Department of Pathology, Spatiotemporal Modeling Center, University of New Mexico, Albuquerque, NM, USA
| | - Carolyn Pehlke
- Spatiotemporal Modeling Center, University of New Mexico, Albuquerque, NM, USA
| | - Michael J. Wester
- Department of Mathematics and Statistics, Spatiotemporal Modeling Center, University of New Mexico, Albuquerque, NM, USA
| | - Ping Liu
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Keith A. Lidke
- Department of Physics, Spatiotemporal Modeling Center, University of New Mexico, Albuquerque, NM, USA
| | - Nancy L. Thompson
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ken Jacobson
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Aaron K. Neumann
- Department of Pathology, Spatiotemporal Modeling Center, University of New Mexico, Albuquerque, NM, USA
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176
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Kelly CV, Wakefield DL, Holowka DA, Craighead HG, Baird BA. Near-field fluorescence cross-correlation spectroscopy on planar membranes. ACS NANO 2014; 8:7392-404. [PMID: 25004429 PMCID: PMC4326781 DOI: 10.1021/nn502593k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/08/2014] [Indexed: 05/23/2023]
Abstract
The organization and dynamics of plasma membrane components at the nanometer scale are essential for biological functions such as transmembrane signaling and endocytosis. Planarized nanoscale apertures in a metallic film are demonstrated as a means of confining the excitation light for multicolor fluorescence spectroscopy to a 55 ± 10 nm beam waist. This technique provides simultaneous two-color, subdiffraction-limited fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy on planar membranes. The fabrication and implementation of this technique are demonstrated for both model membranes and live cells. Membrane-bound proteins were observed to cluster upon the addition of a multivalent cross-linker: On supported lipid bilayers, clusters of cholera toxin subunit B were formed upon cross-linking by an antibody specific for this protein; on living cells, immunoglobulin E bound to its receptor (FcεRI) on the plasma membranes of RBL mast cells was observed to form clusters upon exposure to a trivalent antigen. The formation of membrane clusters was quantified via fluorescence intensity vs time and changes in the temporal auto- and cross-correlations above a single nanoscale aperture. The illumination profile from a single aperture is analyzed experimentally and computationally with a rim-dominated illumination profile, yielding no change in the autocorrelation dwell time with changes in aperture diameter from 60 to 250 nm. This near-field fluorescence cross-correlation methodology provides access to nanoscale details of dynamic membrane interactions and motivates further development of near-field optical methods.
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Affiliation(s)
- Christopher V. Kelly
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
- Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
- Address correspondence to
| | - Devin L. Wakefield
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - David A. Holowka
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Harold G. Craighead
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
| | - Barbara A. Baird
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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177
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Shelby SA, Holowka D, Baird B, Veatch SL. Distinct stages of stimulated FcεRI receptor clustering and immobilization are identified through superresolution imaging. Biophys J 2014; 105:2343-54. [PMID: 24268146 DOI: 10.1016/j.bpj.2013.09.049] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/05/2013] [Accepted: 09/09/2013] [Indexed: 12/25/2022] Open
Abstract
Recent advances in fluorescence localization microscopy have made it possible to image chemically fixed and living cells at 20 nm lateral resolution. We apply this methodology to simultaneously record receptor organization and dynamics on the ventral surface of live RBL-2H3 mast cells undergoing antigen-mediated signaling. Cross-linking of IgE bound to FcεRI by multivalent antigen initiates mast cell activation, which leads to inflammatory responses physiologically. We quantify receptor organization and dynamics as cells are stimulated at room temperature (22°C). Within 2 min of antigen addition, receptor diffusion coefficients decrease by an order of magnitude, and single-particle trajectories are confined. Within 5 min of antigen addition, receptors organize into clusters containing ∼100 receptors with average radii of ∼70 nm. By comparing simultaneous measurements of clustering and mobility, we determine that there are two distinct stages of receptor clustering. In the first stage, which precedes stimulated Ca(2+) mobilization, receptors slow dramatically but are not tightly clustered. In the second stage, receptors are tightly packed and confined. We find that stimulation-dependent changes in both receptor clustering and mobility can be reversed by displacing multivalent antigen with monovalent ligands, and that these changes can be modulated through enrichment or reduction in cellular cholesterol levels.
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Affiliation(s)
- Sarah A Shelby
- Department of Chemistry and Chemical Biology, and Field of Biophysics, Cornell University, Ithaca, NY
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178
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Almarza G, Sánchez F, Barrantes FJ. Transient cholesterol effects on nicotinic acetylcholine receptor cell-surface mobility. PLoS One 2014; 9:e100346. [PMID: 24971757 PMCID: PMC4074099 DOI: 10.1371/journal.pone.0100346] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 05/24/2014] [Indexed: 11/23/2022] Open
Abstract
To what extent do cholesterol-rich lipid platforms modulate the supramolecular organization of the nicotinic acetylcholine receptor (AChR)? To address this question, the dynamics of AChR particles at high density and its cholesterol dependence at the surface of mammalian cells were studied by combining total internal reflection fluorescence microscopy and single-particle tracking. AChR particles tagged with a monovalent ligand, fluorescent α-bungarotoxin (αBTX), exhibited two mobile pools: i) a highly mobile one undergoing simple Brownian motion (16%) and ii) one with restricted motion (∼50%), the rest being relatively immobile (∼44%). Depletion of membrane cholesterol by methyl-α-cyclodextrin increased the fraction of the first pool to 22% and 33% after 15 and 40 min, respectively; the pool undergoing restricted motion diminished from 50% to 44% and 37%, respectively. Monoclonal antibody binding results in AChR crosslinking-internalization after 2 h; here, antibody binding immobilized within minutes ∼20% of the totally mobile AChR. This proportion dramatically increased upon cholesterol depletion, especially during the initial 10 min (83.3%). Thus, antibody crosslinking and cholesterol depletion exhibited a mutually synergistic effect, increasing the average lifetime of cell-surface AChRs∼10 s to ∼20 s. The instantaneous (microscopic) diffusion coefficient D2-4 of the AChR obtained from the MSD analysis diminished from ∼0.001 µm2 s(-1) to ∼0.0001-0.00033 µm2 s(-1) upon cholesterol depletion, ∼30% of all particles falling into the stationary mode. Thus, muscle-type AChR exhibits heterogeneous motional regimes at the cell surface, modulated by the combination of intrinsic (its supramolecular organization) and extrinsic (membrane cholesterol content) factors.
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Affiliation(s)
- Gonzalo Almarza
- Laboratory of Molecular Neurobiology, Biomedical Research Institute, Pontifical Catholic University of Argentina (UCA) and National Scientific and Technical Research Council of Argentina (CONICET), Buenos Aires, Argentina
| | - Francisco Sánchez
- Laboratory of Molecular Neurobiology, Biomedical Research Institute, Pontifical Catholic University of Argentina (UCA) and National Scientific and Technical Research Council of Argentina (CONICET), Buenos Aires, Argentina
| | - Francisco J. Barrantes
- Laboratory of Molecular Neurobiology, Biomedical Research Institute, Pontifical Catholic University of Argentina (UCA) and National Scientific and Technical Research Council of Argentina (CONICET), Buenos Aires, Argentina
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179
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Albertazzi L, van der Zwaag D, Leenders CMA, Fitzner R, van der Hofstad RW, Meijer EW. Probing exchange pathways in one-dimensional aggregates with super-resolution microscopy. Science 2014; 344:491-5. [PMID: 24786073 DOI: 10.1126/science.1250945] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Supramolecular fibers are prominent structures in biology and chemistry. A quantitative understanding of molecular exchange pathways in these one-dimensional aggregates was obtained by a combination of super-resolution stochastic optical reconstruction microscopy and stochastic simulation. The potential of this methodology is demonstrated with a set of well-defined synthetic building blocks that self-assemble into supramolecular fibrils. Previous ensemble measurements hid all molecular phenomena underpinning monomer exchange, but the molecular pathway determined from single-aggregate studies revealed unexpected homogeneous exchange along the polymer backbone. These results pave the way for experimental investigation of the structure and exchange pathways of synthetic and natural supramolecular fibers.
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Affiliation(s)
- Lorenzo Albertazzi
- Institute for Complex Molecular Systems, Eindhoven University of Technology, Post Office Box 513, 5600 MD Eindhoven, Netherlands
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180
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Sauer M. Localization microscopy coming of age: from concepts to biological impact. J Cell Sci 2014; 126:3505-13. [PMID: 23950110 DOI: 10.1242/jcs.123612] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Super-resolution fluorescence imaging by single-molecule photoactivation or photoswitching and position determination (localization microscopy) has the potential to fundamentally revolutionize our understanding of how cellular function is encoded at the molecular level. Among all powerful, high-resolution imaging techniques introduced in recent years, localization microscopy excels because it delivers single-molecule information about molecular distributions, even giving absolute numbers of proteins present in subcellular compartments. This provides insight into biological systems at a molecular level that can yield direct experimental feedback for modeling the complexity of biological interactions. In addition, efficient new labeling methods and strategies to improve localization are emerging that promise to achieve true molecular resolution. This raises localization microscopy as a powerful complementary method for correlative light and electron microscopy experiments.
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Affiliation(s)
- Markus Sauer
- Department of Biotechnology and Biophysics, Julius-Maximilians-University Würzburg, Am Hubland, 97074 Würzburg, Germany.
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181
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Habuchi S. Super-resolution molecular and functional imaging of nanoscale architectures in life and materials science. Front Bioeng Biotechnol 2014; 2:20. [PMID: 25152893 PMCID: PMC4126472 DOI: 10.3389/fbioe.2014.00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/30/2014] [Indexed: 11/13/2022] Open
Abstract
Super-resolution (SR) fluorescence microscopy has been revolutionizing the way in which we investigate the structures, dynamics, and functions of a wide range of nanoscale systems. In this review, I describe the current state of various SR fluorescence microscopy techniques along with the latest developments of fluorophores and labeling for the SR microscopy. I discuss the applications of SR microscopy in the fields of life science and materials science with a special emphasis on quantitative molecular imaging and nanoscale functional imaging. These studies open new opportunities for unraveling the physical, chemical, and optical properties of a wide range of nanoscale architectures together with their nanostructures and will enable the development of new (bio-)nanotechnology.
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Affiliation(s)
- Satoshi Habuchi
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Jeddah , Saudi Arabia
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182
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Durisic N, Cuervo LL, Lakadamyali M. Quantitative super-resolution microscopy: pitfalls and strategies for image analysis. Curr Opin Chem Biol 2014; 20:22-8. [PMID: 24793374 DOI: 10.1016/j.cbpa.2014.04.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 04/04/2014] [Accepted: 04/08/2014] [Indexed: 11/19/2022]
Abstract
Super-resolution microscopy is an enabling technology that allows biologists to visualize cellular structures at nanometer length scales using far-field optics. To break the diffraction barrier, it is necessary to leverage the distinct molecular states of fluorescent probes. At the same time, the existence of these different molecular states and the photophysical properties of the fluorescent probes can complicate data quantification and interpretation. Here, we review the pitfalls in super-resolution data analysis that must be avoided for proper interpretation of images.
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Affiliation(s)
- Nela Durisic
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels (Barcelona), Spain
| | - Lara Laparra Cuervo
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels (Barcelona), Spain
| | - Melike Lakadamyali
- ICFO-Institut de Ciencies Fotoniques, Mediterranean Technology Park, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels (Barcelona), Spain.
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183
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Deschout H, Shivanandan A, Annibale P, Scarselli M, Radenovic A. Progress in quantitative single-molecule localization microscopy. Histochem Cell Biol 2014; 142:5-17. [PMID: 24748502 PMCID: PMC4072926 DOI: 10.1007/s00418-014-1217-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 01/10/2023]
Abstract
With the advent of single-molecule localization microscopy (SMLM) techniques, intracellular proteins can be imaged at unprecedented resolution with high specificity and contrast. These techniques can lead to a better understanding of cell functioning, as they allow, among other applications, counting the number of molecules of a protein specie in a single cell, studying the heterogeneity in protein spatial organization, and probing the spatial interactions between different protein species. However, the use of these techniques for accurate quantitative measurements requires corrections for multiple inherent sources of error, including: overcounting due to multiple localizations of a single fluorophore (i.e., photoblinking), undercounting caused by incomplete photoconversion, uncertainty in the localization of single molecules, sample drift during the long imaging time, and inaccurate image registration in the case of dual-color imaging. In this paper, we review recent efforts that address some of these sources of error in quantitative SMLM and give examples in the context of photoactivated localization microscopy (PALM).
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Affiliation(s)
- H. Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A. Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - P. Annibale
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Biomedical Engineering Department, University of California, Irvine, CA USA
| | - M. Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A. Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
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184
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Rossy J, Cohen E, Gaus K, Owen DM. Method for co-cluster analysis in multichannel single-molecule localisation data. Histochem Cell Biol 2014; 141:605-12. [PMID: 24643361 DOI: 10.1007/s00418-014-1208-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2014] [Indexed: 01/05/2023]
Abstract
We demonstrate a combined univariate and bivariate Getis and Franklin's local point pattern analysis method to investigate the co-clustering of membrane proteins in two-dimensional single-molecule localisation data. This method assesses the degree of clustering of each molecule relative to its own species and relative to a second species. Using simulated data, we show that this approach can quantify the degree of cluster overlap in multichannel point patterns. The method is validated using photo-activated localisation microscopy and direct stochastic optical reconstruction microscopy data of the proteins Lck and CD45 at the T cell immunological synapse. Analysing co-clustering in this manner is generalizable to higher numbers of fluorescent species and to three-dimensional or live cell data sets.
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Affiliation(s)
- Jérémie Rossy
- Centre for Vascular Research and Australian Centre for NanoMedicine, University of New South Wales, Sydney, Australia
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185
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PSF decomposition of nanoscopy images via Bayesian analysis unravels distinct molecular organization of the cell membrane. Sci Rep 2014; 4:4354. [PMID: 24619088 PMCID: PMC3950809 DOI: 10.1038/srep04354] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 02/24/2014] [Indexed: 11/08/2022] Open
Abstract
The spatial organization of membrane receptors at the nanoscale has major implications in cellular function and signaling. The advent of super-resolution techniques has greatly contributed to our understanding of the cellular membrane. Yet, despite the increased resolution, unbiased quantification of highly dense features, such as molecular aggregates, remains challenging. Here we describe an algorithm based on Bayesian inference of the marker intensity distribution that improves the determination of molecular positions inside dense nanometer-scale molecular aggregates. We tested the performance of the method on synthetic images representing a broad range of experimental conditions, demonstrating its wide applicability. We further applied this approach to STED images of GPI-anchored and model transmembrane proteins expressed in mammalian cells. The analysis revealed subtle differences in the organization of these receptors, emphasizing the role of cortical actin in the compartmentalization of the cell membrane.
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186
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Termini CM, Cotter ML, Marjon KD, Buranda T, Lidke KA, Gillette JM. The membrane scaffold CD82 regulates cell adhesion by altering α4 integrin stability and molecular density. Mol Biol Cell 2014; 25:1560-73. [PMID: 24623721 PMCID: PMC4019488 DOI: 10.1091/mbc.e13-11-0660] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Hematopoietic stem/progenitor cell (HSPC) interactions with the bone marrow microenvironment are important for maintaining HSPC self-renewal and differentiation. In recent work, we identified the tetraspanin protein, CD82, as a regulator of HPSC adhesion and homing to the bone marrow, although the mechanism by which CD82 mediated adhesion was unclear. In the present study, we determine that CD82 expression alters cell-matrix adhesion, as well as integrin surface expression. By combining the superresolution microscopy imaging technique, direct stochastic optical reconstruction microscopy, with protein clustering algorithms, we identify a critical role for CD82 in regulating the membrane organization of α4 integrin subunits. Our data demonstrate that CD82 overexpression increases the molecular density of α4 within membrane clusters, thereby increasing cellular adhesion. Furthermore, we find that the tight packing of α4 into membrane clusters depend on CD82 palmitoylation and the presence of α4 integrin ligands. In combination, these results provide unique quantifiable evidence of CD82's contribution to the spatial arrangement of integrins within the plasma membrane and suggest that regulation of integrin density by tetraspanins is a critical component of cell adhesion.
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Affiliation(s)
- Christina M Termini
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
| | - Maura L Cotter
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
| | - Kristopher D Marjon
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
| | - Tione Buranda
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Jennifer M Gillette
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131
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187
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Namadurai S, Balasuriya D, Rajappa R, Wiemhöfer M, Stott K, Klingauf J, Edwardson JM, Chirgadze DY, Jackson AP. Crystal structure and molecular imaging of the Nav channel β3 subunit indicates a trimeric assembly. J Biol Chem 2014; 289:10797-10811. [PMID: 24567321 PMCID: PMC4036194 DOI: 10.1074/jbc.m113.527994] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The vertebrate sodium (Nav) channel is composed of an ion-conducting α subunit and associated β subunits. Here, we report the crystal structure of the human β3 subunit immunoglobulin (Ig) domain, a functionally important component of Nav channels in neurons and cardiomyocytes. Surprisingly, we found that the β3 subunit Ig domain assembles as a trimer in the crystal asymmetric unit. Analytical ultracentrifugation confirmed the presence of Ig domain monomers, dimers, and trimers in free solution, and atomic force microscopy imaging also detected full-length β3 subunit monomers, dimers, and trimers. Mutation of a cysteine residue critical for maintaining the trimer interface destabilized both dimers and trimers. Using fluorescence photoactivated localization microscopy, we detected full-length β3 subunit trimers on the plasma membrane of transfected HEK293 cells. We further show that β3 subunits can bind to more than one site on the Nav 1.5 α subunit and induce the formation of α subunit oligomers, including trimers. Our results suggest a new and unexpected role for the β3 subunits in Nav channel cross-linking and provide new structural insights into some pathological Nav channel mutations.
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Affiliation(s)
- Sivakumar Namadurai
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Dilshan Balasuriya
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Rajit Rajappa
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse, 31 48149 Münster, Germany
| | - Martin Wiemhöfer
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse, 31 48149 Münster, Germany
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom
| | - Jurgen Klingauf
- Institute of Medical Physics and Biophysics, University of Münster, Robert-Koch Strasse, 31 48149 Münster, Germany
| | - J Michael Edwardson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Dimitri Y Chirgadze
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom.
| | - Antony P Jackson
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QW, United Kingdom.
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188
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Notelaers K, Rocha S, Paesen R, Swinnen N, Vangindertael J, Meier JC, Rigo JM, Ameloot M, Hofkens J. Membrane distribution of the glycine receptor α3 studied by optical super-resolution microscopy. Histochem Cell Biol 2014; 142:79-90. [PMID: 24553792 DOI: 10.1007/s00418-014-1197-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2014] [Indexed: 11/24/2022]
Abstract
In this study, the effect of glycine receptor (GlyR) α3 alternative RNA splicing on the distribution of receptors in the membrane of human embryonic kidney 293 cells is investigated using optical super-resolution microscopy. Direct stochastic optical reconstruction microscopy is used to image both α3K and α3L splice variants individually and together using single- and dual-color imaging. Pair correlation analysis is used to extract quantitative measures from the resulting images. Autocorrelation analysis of the individually expressed variants reveals clustering of both variants, yet with differing properties. The cluster size is increased for α3L compared to α3K (mean radius 92 ± 4 and 56 ± 3 nm, respectively), yet an even bigger difference is found in the cluster density (9,870 ± 1,433 and 1,747 ± 200 μm(-2), respectively). Furthermore, cross-correlation analysis revealed that upon co-expression, clusters colocalize on the same spatial scales as for individually expressed receptors (mean co-cluster radius 94 ± 6 nm). These results demonstrate that RNA splicing determines GlyR α3 membrane distribution, which has consequences for neuronal GlyR physiology and function.
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Affiliation(s)
- Kristof Notelaers
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, Agoralaan Gebouw C, 3590, Diepenbeek, Belgium
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189
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Tabarin T, Pageon SV, Bach CTT, Lu Y, O'Neill GM, Gooding JJ, Gaus K. Insights into Adhesion Biology Using Single-Molecule Localization Microscopy. Chemphyschem 2014; 15:606-18. [DOI: 10.1002/cphc.201301041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Indexed: 01/07/2023]
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190
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Valley CC, Lidke KA, Lidke DS. The spatiotemporal organization of ErbB receptors: insights from microscopy. Cold Spring Harb Perspect Biol 2014; 6:cshperspect.a020735. [PMID: 24370847 DOI: 10.1101/cshperspect.a020735] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Signal transduction is regulated by protein-protein interactions. In the case of the ErbB family of receptor tyrosine kinases (RTKs), the precise nature of these interactions remains a topic of debate. In this review, we describe state-of-the-art imaging techniques that are providing new details into receptor dynamics, clustering, and interactions. We present the general principles of these techniques, their limitations, and the unique observations they provide about ErbB spatiotemporal organization.
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Affiliation(s)
- Christopher C Valley
- Department of Pathology and the Cancer Research and Treatment Center, University of New Mexico, Albuquerque, New Mexico 87131
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191
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Long BR, Robinson DC, Zhong H. Subdiffractive microscopy: techniques, applications, and challenges. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014; 6:151-68. [PMID: 24443323 DOI: 10.1002/wsbm.1259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 01/30/2023]
Abstract
Cellular processes rely on the precise orchestration of signaling and effector molecules in space and time, yet it remains challenging to gain a comprehensive picture of the molecular organization underlying most basic biological functions. This organization often takes place at length scales below the resolving power of conventional microscopy. In recent years, several 'superresolution' fluorescence microscopic techniques have emerged that can surpass the diffraction limit of conventional microscopy by a factor of 2-20. These methods have been used to reveal previously unknown organization of macromolecular complexes and cytoskeletal structures. The resulting high-resolution view of molecular organization and dynamics is already changing our understanding of cellular processes at the systems level. However, current subdiffractive microscopic techniques are not without limitations; challenges remain to be overcome before these techniques achieve their full potential. Here, we introduce three primary types of subdiffractive microscopic techniques, consider their current limitations and challenges, and discuss recent biological applications.
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Affiliation(s)
- Brian R Long
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
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192
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Sengupta P, van Engelenburg SB, Lippincott-Schwartz J. Superresolution imaging of biological systems using photoactivated localization microscopy. Chem Rev 2014; 114:3189-202. [PMID: 24417572 DOI: 10.1021/cr400614m] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Prabuddha Sengupta
- Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health , Bethesda, Maryland 20892, United States
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193
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Truong-Quang BA, Lenne PF. Membrane microdomains: from seeing to understanding. FRONTIERS IN PLANT SCIENCE 2014; 5:18. [PMID: 24600455 PMCID: PMC3927121 DOI: 10.3389/fpls.2014.00018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 01/15/2014] [Indexed: 05/08/2023]
Abstract
The plasma membrane is a composite material, which forms a semi-permeable barrier and an interface for communication between the intracellular and extracellular environments. While the existence of membrane microdomains with nanoscale organization has been proved by the application of numerous biochemical and physical methods, direct observation of these heterogeneities using optical microscopy has remained challenging for decades, partly due to the optical diffraction limit, which restricts the resolution to ~200 nm. During the past years, new optical methods which circumvent this fundamental limit have emerged. Not only do these techniques allow direct visualization, but also quantitative characterization of nanoscopic structures. We discuss how these emerging optical methods have refined our knowledge of membrane microdomains and how they may shed light on the basic principles of the mesoscopic membrane organization.
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Affiliation(s)
| | - Pierre-François Lenne
- *Correspondence: Pierre-François Lenne, Developmental Biology Institute of Marseilles, UMR 7288 CNRS, Aix-Marseille Université, 13288 Marseille Cedex 9, France e-mail:
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194
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Abstract
Conventional light and fluorescence microscopy techniques have offered tremendous insight into cellular processes and structures. Their resolution is however intrinsically limited by diffraction. Superresolution techniques achieve an order of magnitude higher resolution. Among these, localization microscopy relies on the position determination of single emitters with nanometer accuracy, which allows the subsequent reconstruction of an image of the target structure. In this chapter, we provide general guidelines for localization microscopy with a focus on Saccharomyces cerevisiae. Its different cellular architecture complicates efforts to directly transfer protocols established in mammalian cells to yeast. We compare different methodologies to label structures of interest and provide protocols for the respective sample preparation, which are not limited to yeast. Using these guidelines, nanoscopic subcellular structures in yeast can be investigated by localization microscopy, which perfectly complements live-cell fluorescence and electron microscopy.
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Affiliation(s)
- Markus Mund
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
| | | | - Jonas Ries
- European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Heidelberg, Germany
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195
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Ishitsuka Y, Nienhaus K, Nienhaus GU. Photoactivatable fluorescent proteins for super-resolution microscopy. Methods Mol Biol 2014; 1148:239-60. [PMID: 24718806 DOI: 10.1007/978-1-4939-0470-9_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Super-resolution fluorescence microscopy techniques such as simulated emission depletion (STED) microscopy and photoactivated localization microscopy (PALM) allow substructures, organelles or even proteins within a cell to be imaged with a resolution far below the diffraction limit of ~200 nm. The development of advanced fluorescent proteins, especially photoactivatable fluorescent proteins of the GFP family, has greatly contributed to the successful application of these techniques to live-cell imaging. Here, we will illustrate how two fluorescent proteins with different photoactivation mechanisms can be utilized in high resolution dual color PALM imaging to obtain insights into a cellular process that otherwise would not be accessible. We will explain how to set up and perform the experiment and how to use our latest software "a-livePALM" for fast and efficient data analysis.
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Affiliation(s)
- Yuji Ishitsuka
- Institute of Applied Physics and Center for Functional Nanostructures (CFN), Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, Karlsruhe, 76131, Germany
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196
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van de Linde S, Sauer M. How to switch a fluorophore: from undesired blinking to controlled photoswitching. Chem Soc Rev 2014; 43:1076-87. [DOI: 10.1039/c3cs60195a] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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197
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Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc Natl Acad Sci U S A 2013; 111:681-6. [PMID: 24379392 DOI: 10.1073/pnas.1318496111] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Superresolution microscopy based on single-molecule centroid determination has been widely applied to cellular imaging in recent years. However, quantitative imaging of the mammalian nucleus has been challenging due to the lack of 3D optical sectioning methods for normal-sized cells, as well as the inability to accurately count the absolute copy numbers of biomolecules in highly dense structures. Here we report a reflected light-sheet superresolution microscopy method capable of imaging inside the mammalian nucleus with superior signal-to-background ratio as well as molecular counting with single-copy accuracy. Using reflected light-sheet superresolution microscopy, we probed the spatial organization of transcription by RNA polymerase II (RNAP II) molecules and quantified their global extent of clustering inside the mammalian nucleus. Spatiotemporal clustering analysis that leverages on the blinking photophysics of specific organic dyes showed that the majority (>70%) of the transcription foci originate from single RNAP II molecules, and no significant clustering between RNAP II molecules was detected within the length scale of the reported diameter of "transcription factories." Colocalization measurements of RNAP II molecules equally labeled by two spectrally distinct dyes confirmed the primarily unclustered distribution, arguing against a prevalent existence of transcription factories in the mammalian nucleus as previously proposed. The methods developed in our study pave the way for quantitative mapping and stoichiometric characterization of key biomolecular species deep inside mammalian cells.
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198
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Gudheti MV, Curthoys NM, Gould TJ, Kim D, Gunewardene MS, Gabor KA, Gosse JA, Kim CH, Zimmerberg J, Hess ST. Actin mediates the nanoscale membrane organization of the clustered membrane protein influenza hemagglutinin. Biophys J 2013; 104:2182-92. [PMID: 23708358 DOI: 10.1016/j.bpj.2013.03.054] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Revised: 03/15/2013] [Accepted: 03/20/2013] [Indexed: 12/22/2022] Open
Abstract
The influenza viral membrane protein hemagglutinin (HA) is required at high concentrations on virion and host-cell membranes for infectivity. Because the role of actin in membrane organization is not completely understood, we quantified the relationship between HA and host-cell actin at the nanoscale. Results obtained using superresolution fluorescence photoactivation localization microscopy (FPALM) in nonpolarized cells show that HA clusters colocalize with actin-rich membrane regions (ARMRs). Individual molecular trajectories in live cells indicate restricted HA mobility in ARMRs, and actin disruption caused specific changes to HA clustering. Surprisingly, the actin-binding protein cofilin was excluded from some regions within several hundred nanometers of HA clusters, suggesting that HA clusters or adjacent proteins within the same clusters influence local actin structure. Thus, with the use of imaging, we demonstrate a dynamic relationship between glycoprotein membrane organization and the actin cytoskeleton at the nanoscale.
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Affiliation(s)
- Manasa V Gudheti
- Department of Physics and Astronomy, University of Maine, Orono, ME, USA
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199
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Pore D, Parameswaran N, Matsui K, Stone MB, Saotome I, McClatchey AI, Veatch SL, Gupta N. Ezrin tunes the magnitude of humoral immunity. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2013; 191:4048-58. [PMID: 24043890 PMCID: PMC3808844 DOI: 10.4049/jimmunol.1301315] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ezrin is a member of the ezrin-radixin-moesin family of membrane-actin cytoskeleton cross-linkers that participate in a variety of cellular processes. In B cells, phosphorylation of ezrin at different sites regulates multiple processes, such as lipid raft coalescence, BCR diffusion, microclustering, and endosomal JNK activation. In this study, we generated mice with conditional deletion of ezrin in the B cell lineage to investigate the physiological significance of ezrin's function in Ag receptor-mediated B cell activation and humoral immunity. B cell development, as well as the proportion and numbers of major B cell subsets in peripheral lymphoid organs, was unaffected by the loss of ezrin. Using superresolution imaging methods, we show that, in the absence of ezrin, BCRs respond to Ag binding by accumulating into larger and more stable signaling microclusters. Loss of ezrin led to delayed BCR capping and accelerated lipid raft coalescence. Although proximal signaling proteins showed stronger activation in the absence of ezrin, components of the distal BCR signaling pathways displayed distinct effects. Ezrin deficiency resulted in increased B cell proliferation and differentiation into Ab-secreting cells ex vivo and stronger T cell-independent and -dependent responses to Ag in vivo. Overall, our data demonstrate that ezrin regulates amplification of BCR signals and tunes the strength of B cell activation and humoral immunity.
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Affiliation(s)
- Debasis Pore
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
| | - Neetha Parameswaran
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
| | - Ken Matsui
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
| | - Matthew B. Stone
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109
| | - Ichiko Saotome
- Department of Pathology, Massachusetts General Hospital Cancer Center and Harvard Medical School, 13 Street, Charlestown, MA 02129
| | - Andrea I. McClatchey
- Department of Pathology, Massachusetts General Hospital Cancer Center and Harvard Medical School, 13 Street, Charlestown, MA 02129
| | - Sarah L. Veatch
- Department of Biophysics, University of Michigan, 930 N. University Avenue, Ann Arbor, MI 48109
| | - Neetu Gupta
- Department of Immunology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195
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200
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Counting molecules in single organelles with superresolution microscopy allows tracking of the endosome maturation trajectory. Proc Natl Acad Sci U S A 2013; 110:16015-20. [PMID: 24043832 DOI: 10.1073/pnas.1309676110] [Citation(s) in RCA: 149] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Cells tightly regulate trafficking of intracellular organelles, but a deeper understanding of this process is technically limited by our inability to track the molecular composition of individual organelles below the diffraction limit in size. Here we develop a technique for intracellularly calibrated superresolution microscopy that can measure the size of individual organelles as well as accurately count absolute numbers of molecules, by correcting for undercounting owing to immature fluorescent proteins and overcounting owing to fluorophore blinking. Using this technique, we characterized the size of individual vesicles in the yeast endocytic pathway and the number of accessible phosphatidylinositol 3-phosphate binding sites they contain. This analysis reveals a characteristic vesicle maturation trajectory of composition and size with both stochastic and regulated components. The trajectory displays some cell-to-cell variability, with smaller variation between organelles within the same cell. This approach also reveals mechanistic information on the order of events in this trajectory: Colocalization analysis with known markers of different vesicle maturation stages shows that phosphatidylinositol 3-phosphate production precedes fusion into larger endosomes. This single-organelle analysis can potentially be applied to a range of small organelles to shed light on their precise composition/structure relationships, the dynamics of their regulation, and the noise in these processes.
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