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Abstract
The plasma membrane is a complex medium where transmembrane proteins diffuse and interact to facilitate cell function. Membrane protein mobility is affected by multiple mechanisms, including crowding, trapping, medium elasticity and structure, thus limiting our ability to distinguish them in intact cells. Here we characterize the mobility and organization of a short transmembrane protein at the plasma membrane of live T cells, using single particle tracking and photoactivated-localization microscopy. Protein mobility is highly heterogeneous, subdiffusive and ergodic-like. Using mobility characteristics, we segment individual trajectories into subpopulations with distinct Gaussian step-size distributions. Particles of low-to-medium mobility consist of clusters, diffusing in a viscoelastic and fractal-like medium and are enriched at the centre of the cell footprint. Particles of high mobility undergo weak confinement and are more evenly distributed. This study presents a methodological approach to resolve simultaneous mixed subdiffusion mechanisms acting on polydispersed samples and complex media such as cell membranes. Membrane protein diffusion is affected by distinct mechanisms such as molecular crowding and medium elasticity. Here the authors present an analytical approach to analyse single particle trajectories and distinguish mixed subdiffusive processes affecting membrane protein mobility in living cells.
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102
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Stone MB, Shelby SA, Veatch SL. Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane. Chem Rev 2017; 117:7457-7477. [PMID: 28211677 PMCID: PMC5471115 DOI: 10.1021/acs.chemrev.6b00716] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments. These microscopy techniques have been used to examine the organization and dynamics of plasma membrane components, providing insight into the fundamental interactions that determine membrane functions. Here, we broadly introduce the structure and organization of the mammalian plasma membrane and review recent applications of super-resolution microscopy to the study of membranes. We then highlight some inherent challenges faced when using super-resolution microscopy to study membranes, and we discuss recent technical advancements that promise further improvements to super-resolution microscopy and its application to the plasma membrane.
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Affiliation(s)
- Matthew B Stone
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah A Shelby
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah L Veatch
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
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103
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Peckys DB, Stoerger C, Latta L, Wissenbach U, Flockerzi V, de Jonge N. The stoichiometry of the TMEM16A ion channel determined in intact plasma membranes of COS-7 cells using liquid-phase electron microscopy. J Struct Biol 2017; 199:102-113. [PMID: 28559167 DOI: 10.1016/j.jsb.2017.05.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 11/29/2022]
Abstract
TMEM16A is a membrane protein forming a calcium-activated chloride channel. A homodimeric stoichiometry of the TMEM16 family of proteins has been reported but an important question is whether the protein resides always in a dimeric configuration in the plasma membrane or whether monomers of the protein are also present in its native state within in the intact plasma membrane. We have determined the stoichiometry of the human (h)TMEM16A within whole COS-7 cells in liquid. For the purpose of detecting TMEM16A subunits, single proteins were tagged by the streptavidin-binding peptide within extracellular loops accessible by streptavidin coated quantum dot (QD) nanoparticles. The labeled proteins were then imaged using correlative light microscopy and environmental scanning electron microscopy (ESEM) using scanning transmission electron microscopy (STEM) detection. The locations of 19,583 individual proteins were determined of which a statistical analysis using the pair correlation function revealed the presence of a dimeric conformation of the protein. The amounts of detected label pairs and single labels were compared between experiments in which the TMEM16A SBP-tag position was varied, and experiments in which tagged and non-tagged TMEM16A proteins were present. It followed that hTMEM16A resides in the plasma membrane as dimer only and is not present as monomer. This strategy may help to elucidate the stoichiometry of other membrane protein species within the context of the intact plasma membrane in future.
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Affiliation(s)
- Diana B Peckys
- Department of Biophysics, Saarland University, 66421 Homburg, Germany
| | - Christof Stoerger
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Lorenz Latta
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Ulrich Wissenbach
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Veit Flockerzi
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, Saarland University, 66123 Saarbrücken, Germany; Department of Physics, Saarland University, 66123 Saarbrücken, Germany.
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104
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Garza de Leon F, Sellars L, Stracy M, Busby SJW, Kapanidis AN. Tracking Low-Copy Transcription Factors in Living Bacteria: The Case of the lac Repressor. Biophys J 2017; 112:1316-1327. [PMID: 28402875 PMCID: PMC5390046 DOI: 10.1016/j.bpj.2017.02.028] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 01/20/2017] [Accepted: 02/16/2017] [Indexed: 11/30/2022] Open
Abstract
Transcription factors control the expression of genes by binding to specific sites in DNA and repressing or activating transcription in response to stimuli. The lac repressor (LacI) is a well characterized transcription factor that regulates the ability of bacterial cells to uptake and metabolize lactose. Here, we study the intracellular mobility and spatial distribution of LacI in live bacteria using photoactivated localization microscopy combined with single-particle tracking. Since we track single LacI molecules in live cells by stochastically photoactivating and observing fluorescent proteins individually, there are no limitations on the copy number of the protein under study; as a result, we were able to study the behavior of LacI in bacterial strains containing the natural copy numbers (∼40 monomers), as well as in strains with much higher copy numbers due to LacI overexpression. Our results allowed us to determine the relative abundance of specific, near-specific, and non-specific DNA binding modes of LacI in vivo, showing that all these modes are operational inside living cells. Further, we examined the spatial distribution of LacI in live cells, confirming its specific binding to lac operator regions on the chromosome; we also showed that mobile LacI molecules explore the bacterial nucleoid in a way similar to exploration by other DNA-binding proteins. Our work also provides an example of applying tracking photoactivated localization microscopy to studies of low-copy-number proteins in living bacteria.
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Affiliation(s)
- Federico Garza de Leon
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Laura Sellars
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Mathew Stracy
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
| | - Stephen J W Busby
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Achillefs N Kapanidis
- Gene Machines Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom.
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105
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Rowland DJ, Biteen JS. Measuring molecular motions inside single cells with improved analysis of single-particle trajectories. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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106
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Epilepsy and intellectual disability linked protein Shrm4 interaction with GABA BRs shapes inhibitory neurotransmission. Nat Commun 2017; 8:14536. [PMID: 28262662 PMCID: PMC5343488 DOI: 10.1038/ncomms14536] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 01/09/2017] [Indexed: 02/07/2023] Open
Abstract
Shrm4, a protein expressed only in polarized tissues, is encoded by the KIAA1202 gene, whose mutations have been linked to epilepsy and intellectual disability. However, a physiological role for Shrm4 in the brain is yet to be established. Here, we report that Shrm4 is localized to synapses where it regulates dendritic spine morphology and interacts with the C terminus of GABAB receptors (GABABRs) to control their cell surface expression and intracellular trafficking via a dynein-dependent mechanism. Knockdown of Shrm4 in rat severely impairs GABABR activity causing increased anxiety-like behaviour and susceptibility to seizures. Moreover, Shrm4 influences hippocampal excitability by modulating tonic inhibition in dentate gyrus granule cells, in a process involving crosstalk between GABABRs and extrasynaptic δ-subunit-containing GABAARs. Our data highlights a role for Shrm4 in synaptogenesis and in maintaining GABABR-mediated inhibition, perturbation of which may be responsible for the involvement of Shrm4 in cognitive disorders and epilepsy. Mutations in the gene encoding Shrm4 are associated with epilepsy and intellectual disability. The authors show that Shrm4 interacts with GABAB receptors and regulates tonic inhibition in the hippocampus, and knockdown of Shrm4 in rats leads to anxiety-like behaviour and seizures.
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107
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Irajizad E, Walani N, Veatch SL, Liu AP, Agrawal A. Clathrin polymerization exhibits high mechano-geometric sensitivity. SOFT MATTER 2017; 13:1455-1462. [PMID: 28124714 PMCID: PMC5452080 DOI: 10.1039/c6sm02623k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
How tension modulates cellular transport has become a topic of interest in the recent past. However, the effect of tension on clathrin assembly and vesicle growth remains less understood. Here, we use the classical Helfrich theory to predict the energetic cost that clathrin is required to pay to remodel the membrane at different stages of vesicle formation. Our study reveals that this energetic cost is highly sensitive to not only the tension in the membrane but also to the instantaneous geometry of the membrane during shape evolution. Our study predicts a sharp reduction in clathrin coat size in the intermediate tension regime (0.01-0.1 mN m-1). Remarkably, the natural propensity of the membrane to undergo bending beyond the Ω shape causes a significant decrease in the energy needed from clathrin to drive vesicle growth. Our studies in mammalian cells confirm a reduction in clathrin coat size in an increased tension environment. In addition, our findings suggest that the two apparently distinct clathrin assembly modes, namely coated pits and coated plaques, observed in experimental investigations might be a consequence of varied tensions in the plasma membrane. Overall, the mechano-geometric sensitivity revealed in this study might also be at play during the polymerization of other membrane remodeling proteins.
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Affiliation(s)
- Ehsan Irajizad
- Department of Mechanical Engineering, University of Houston, Houston, TX, USA
| | - Nikhil Walani
- Department of Mechanical Engineering, University of Houston, Houston, TX, USA
| | - Sarah L Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, USA
| | - Ashutosh Agrawal
- Department of Mechanical Engineering, University of Houston, Houston, TX, USA.
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108
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Nicovich PR, Owen DM, Gaus K. Turning single-molecule localization microscopy into a quantitative bioanalytical tool. Nat Protoc 2017; 12:453-460. [DOI: 10.1038/nprot.2016.166] [Citation(s) in RCA: 122] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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109
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Stone MB, Shelby SA, Núñez MF, Wisser K, Veatch SL. Protein sorting by lipid phase-like domains supports emergent signaling function in B lymphocyte plasma membranes. eLife 2017; 6. [PMID: 28145867 PMCID: PMC5373823 DOI: 10.7554/elife.19891] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/31/2017] [Indexed: 12/19/2022] Open
Abstract
Diverse cellular signaling events, including B cell receptor (BCR) activation, are hypothesized to be facilitated by domains enriched in specific plasma membrane lipids and proteins that resemble liquid-ordered phase-separated domains in model membranes. This concept remains controversial and lacks direct experimental support in intact cells. Here, we visualize ordered and disordered domains in mouse B lymphoma cell membranes using super-resolution fluorescence localization microscopy, demonstrate that clustered BCR resides within ordered phase-like domains capable of sorting key regulators of BCR activation, and present a minimal, predictive model where clustering receptors leads to their collective activation by stabilizing an extended ordered domain. These results provide evidence for the role of membrane domains in BCR signaling and a plausible mechanism of BCR activation via receptor clustering that could be generalized to other signaling pathways. Overall, these studies demonstrate that lipid mediated forces can bias biochemical networks in ways that broadly impact signal transduction. DOI:http://dx.doi.org/10.7554/eLife.19891.001 Membranes made of molecules called lipids surround every living cell to protect the cell's contents. Cells also communicate with the outside environment via their membranes. Proteins in the membrane receive information from the environment and trigger signaling pathways inside the cell to relay this information to the center of cell. The way in which proteins are organized on the membrane has a major influence on their signaling activity. Some areas of the membrane are more crowded with certain lipids and signaling proteins than others. Lipid and protein molecules of particular types can come together and form distinct areas called “ordered” and “disordered” domains. The lipids in ordered domains are more tightly packed than disordered domains and it is thought that this difference allows domains to selectively exclude or include certain proteins. Ordered domains are also known as "lipid rafts". Lipid rafts and disordered domains may help cells to control the activities of signaling pathways, however, technical limitations have made it difficult to study the roles of these domains. The membranes surrounding immune cells called B cells contain a protein called the B cell receptor, which engages with proteins from microbes and other foreign invaders. When the B cell receptor binds to a foreign protein it forms clusters with other B cell receptors and becomes active, triggering a signaling pathway that leads to immune responses. Stone, Shelby et al. examined lipid rafts and disordered domains in B cells from mice using a technique called super-resolution fluorescence microscopy. The results show that clusters of B cell receptors are present within lipid rafts. These clusters made the lipid rafts larger and more stable. A protein that is needed during the early stages of B cell receptor signaling was also found in the same lipid rafts. Another protein that terminates signaling was excluded because it prefers disordered domains. Together, this provides a local environment in certain areas of the membrane that favors receptor activity and supports the subsequent immune response. Future work is needed to understand how cells control the make-up of lipids and proteins within their membranes, and how defects in this regulation can alter signaling activity and lead to disease. DOI:http://dx.doi.org/10.7554/eLife.19891.002
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Affiliation(s)
- Matthew B Stone
- Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Sarah A Shelby
- Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Marcos F Núñez
- Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Kathleen Wisser
- Department of Biophysics, University of Michigan, Ann Arbor, United States
| | - Sarah L Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, United States
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110
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Target Cell Type-Dependent Differences in Ca 2+ Channel Function Underlie Distinct Release Probabilities at Hippocampal Glutamatergic Terminals. J Neurosci 2017; 37:1910-1924. [PMID: 28115484 DOI: 10.1523/jneurosci.2024-16.2017] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 12/24/2022] Open
Abstract
Target cell type-dependent differences in presynaptic release probability (Pr ) and short-term plasticity are intriguing features of cortical microcircuits that increase the computational power of neuronal networks. Here, we tested the hypothesis that different voltage-gated Ca2+ channel densities in presynaptic active zones (AZs) underlie different Pr values. Two-photon Ca2+ imaging, triple immunofluorescent labeling, and 3D electron microscopic (EM) reconstruction of rat CA3 pyramidal cell axon terminals revealed ∼1.7-1.9 times higher Ca2+ inflow per AZ area in high Pr boutons synapsing onto parvalbumin-positive interneurons (INs) than in low Pr boutons synapsing onto mGluR1α-positive INs. EM replica immunogold labeling, however, demonstrated only 1.15 times larger Cav2.1 and Cav2.2 subunit densities in high Pr AZs. Our results indicate target cell type-specific modulation of voltage-gated Ca2+ channel function or different subunit composition as possible mechanisms underlying the functional differences. In addition, high Pr synapses are also characterized by a higher density of docked vesicles, suggesting that a concerted action of these mechanisms underlies the functional differences.SIGNIFICANCE STATEMENT Target cell type-dependent variability in presynaptic properties is an intriguing feature of cortical synapses. When a single cortical pyramidal cell establishes a synapse onto a somatostatin-expressing interneuron (IN), the synapse releases glutamate with low probability, whereas the next bouton of the same axon has high release probability when its postsynaptic target is a parvalbumin-expressing IN. Here, we used combined molecular, imaging, and anatomical approaches to investigate the mechanisms underlying these differences. Our functional experiments implied an approximately twofold larger Ca2+ channel density in high release probability boutons, whereas freeze-fracture immunolocalization demonstrated only a 15% difference in Ca2+ channel subunit densities. Our results point toward a postsynaptic target cell type-dependent regulation of Ca2+ channel function or different subunit composition as the underlying mechanism.
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111
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Valley CC, Lewis AK, Sachs JN. Piecing it together: Unraveling the elusive structure-function relationship in single-pass membrane receptors. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1398-1416. [PMID: 28089689 DOI: 10.1016/j.bbamem.2017.01.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 01/06/2017] [Accepted: 01/09/2017] [Indexed: 12/17/2022]
Abstract
The challenge of crystallizing single-pass plasma membrane receptors has remained an obstacle to understanding the structural mechanisms that connect extracellular ligand binding to cytosolic activation. For example, the complex interplay between receptor oligomerization and conformational dynamics has been, historically, only inferred from static structures of isolated receptor domains. A fundamental challenge in the field of membrane receptor biology, then, has been to integrate experimentally observable dynamics of full-length receptors (e.g. diffusion and conformational flexibility) into static structural models of the disparate domains. In certain receptor families, e.g. the ErbB receptors, structures have led somewhat linearly to a putative model of activation. In other families, e.g. the tumor necrosis factor (TNF) receptors, structures have produced divergent hypothetical mechanisms of activation and transduction. Here, we discuss in detail these and other related receptors, with the goal of illuminating the current challenges and opportunities in building comprehensive models of single-pass receptor activation. The deepening understanding of these receptors has recently been accelerated by new experimental and computational tools that offer orthogonal perspectives on both structure and dynamics. As such, this review aims to contextualize those technological developments as we highlight the elegant and complex conformational communication between receptor domains. This article is part of a Special Issue entitled: Interactions between membrane receptors in cellular membranes edited by Kalina Hristova.
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Affiliation(s)
| | - Andrew K Lewis
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jonathan N Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
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112
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Bademosi AT, Lauwers E, Padmanabhan P, Odierna L, Chai YJ, Papadopulos A, Goodhill GJ, Verstreken P, van Swinderen B, Meunier FA. In vivo single-molecule imaging of syntaxin1A reveals polyphosphoinositide- and activity-dependent trapping in presynaptic nanoclusters. Nat Commun 2017; 8:13660. [PMID: 28045048 PMCID: PMC5171881 DOI: 10.1038/ncomms13660] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/21/2016] [Indexed: 01/03/2023] Open
Abstract
Syntaxin1A is organized in nanoclusters that are critical for the docking and priming of secretory vesicles from neurosecretory cells. Whether and how these nanoclusters are affected by neurotransmitter release in nerve terminals from a living organism is unknown. Here we imaged photoconvertible syntaxin1A-mEos2 in the motor nerve terminal of Drosophila larvae by single-particle tracking photoactivation localization microscopy. Opto- and thermo-genetic neuronal stimulation increased syntaxin1A-mEos2 mobility, and reduced the size and molecular density of nanoclusters, suggesting an activity-dependent release of syntaxin1A from the confinement of nanoclusters. Syntaxin1A mobility was increased by mutating its polyphosphoinositide-binding site or preventing SNARE complex assembly via co-expression of tetanus toxin light chain. In contrast, syntaxin1A mobility was reduced by preventing SNARE complex disassembly. Our data demonstrate that polyphosphoinositide favours syntaxin1A trapping, and show that SNARE complex disassembly leads to syntaxin1A dissociation from nanoclusters. Lateral diffusion and trapping of syntaxin1A in nanoclusters therefore dynamically regulate neurotransmitter release. Syntaxin1A (Sx1A) is organized in nanoclusters in neurosecretory cells but how these nanoclusters are affected by neurotransmitter release in a living organism is unknown. Here the authors perform single molecule imaging analysis in live fly larvae and show that the lateral diffusion and trapping of Sx1A in nanoclusters are altered by synaptic activity.
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Affiliation(s)
- Adekunle T Bademosi
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Elsa Lauwers
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium.,KU Leuven Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), 3000 Leuven, Belgium
| | - Pranesh Padmanabhan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Lorenzo Odierna
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ye Jin Chai
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Andreas Papadopulos
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Patrik Verstreken
- VIB Center for the Biology of Disease, 3000 Leuven, Belgium.,KU Leuven Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), 3000 Leuven, Belgium
| | - Bruno van Swinderen
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland 4072, Australia
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113
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Kinetic disruption of lipid rafts is a mechanosensor for phospholipase D. Nat Commun 2016; 7:13873. [PMID: 27976674 PMCID: PMC5171650 DOI: 10.1038/ncomms13873] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 11/04/2016] [Indexed: 12/24/2022] Open
Abstract
The sensing of physical force, mechanosensation, underlies two of five human senses—touch and hearing. How transduction of force in a membrane occurs remains unclear. We asked if a biological membrane could employ kinetic energy to transduce a signal absent tension. Here we show that lipid rafts are dynamic compartments that inactivate the signalling enzyme phospholipase D2 (PLD2) by sequestering the enzyme from its substrate. Mechanical disruption of the lipid rafts activates PLD2 by mixing the enzyme with its substrate to produce the signalling lipid phosphatidic acid (PA). We calculate a latency time of <650 μs for PLD activation by mixing. Our results establish a fast, non-tension mechanism for mechanotransduction where disruption of ordered lipids initiates a mechanosensitive signal for cell growth through mechanical mixing.
Mechanosensation by biological membranes can be relayed by mechanical tension to ion channels. Here the authors show that phospholipase D (PLD) is activated by mechanical disruption of lipid rafts which allows PLD to mix with its substrate in the lipid membrane, and propose a kinetic model of force transduction.
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114
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Lee J, Sengupta P, Brzostowski J, Lippincott-Schwartz J, Pierce SK. The nanoscale spatial organization of B-cell receptors on immunoglobulin M- and G-expressing human B-cells. Mol Biol Cell 2016; 28:511-523. [PMID: 27974642 PMCID: PMC5305258 DOI: 10.1091/mbc.e16-06-0452] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 12/01/2016] [Accepted: 12/08/2016] [Indexed: 12/12/2022] Open
Abstract
In resting and activated B-cells, IgM and IgG B-cell receptors (BCRs) reside in highly heterogeneous protein islands that vary in size and number of BCRs but intrinsically maintain a high frequency of BCR monomers. IgG BCRs are more clustered than IgM BCRs on resting cells and form larger protein islands after antigen activation. B-cell activation is initiated by the binding of antigen to the B-cell receptor (BCR). Here we used dSTORM superresolution imaging to characterize the nanoscale spatial organization of immunoglobulin M (IgM) and IgG BCRs on the surfaces of resting and antigen-activated human peripheral blood B-cells. We provide insights into both the fundamental process of antigen-driven BCR clustering and differences in the spatial organization of IgM and IgG BCRs that may contribute to the characteristic differences in the responses of naive and memory B-cells to antigen. We provide evidence that although both IgM and IgG BCRs reside in highly heterogeneous protein islands that vary in size and number of BCR single-molecule localizations, both resting and activated B-cells intrinsically maintain a high frequency of single isolated BCR localizations, which likely represent BCR monomers. IgG BCRs are more clustered than IgM BCRs on resting cells and form larger protein islands after antigen activation. Small, dense BCR clusters likely formed via protein–protein interactions are present on the surface of resting cells, and antigen activation induces these to come together to form less dense, larger islands, a process likely governed, at least in part, by protein–lipid interactions.
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Affiliation(s)
- Jinmin Lee
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Prabuddha Sengupta
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147.,Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Joseph Brzostowski
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Jennifer Lippincott-Schwartz
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147.,Cell Biology and Metabolism Program, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Susan K Pierce
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
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115
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You C, Marquez-Lago TT, Richter CP, Wilmes S, Moraga I, Garcia KC, Leier A, Piehler J. Receptor dimer stabilization by hierarchical plasma membrane microcompartments regulates cytokine signaling. SCIENCE ADVANCES 2016; 2:e1600452. [PMID: 27957535 PMCID: PMC5135388 DOI: 10.1126/sciadv.1600452] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 10/26/2016] [Indexed: 06/06/2023]
Abstract
The interaction dynamics of signaling complexes is emerging as a key determinant that regulates the specificity of cellular responses. We present a combined experimental and computational study that quantifies the consequences of plasma membrane microcompartmentalization for the dynamics of type I interferon receptor complexes. By using long-term dual-color quantum dot (QD) tracking, we found that the lifetime of individual ligand-induced receptor heterodimers depends on the integrity of the membrane skeleton (MSK), which also proved important for efficient downstream signaling. By pair correlation tracking and localization microscopy as well as by fast QD tracking, we identified a secondary confinement within ~300-nm-sized zones. A quantitative spatial stochastic diffusion-reaction model, entirely parameterized on the basis of experimental data, predicts that transient receptor confinement by the MSK meshwork allows for rapid reassociation of dissociated receptor dimers. Moreover, the experimentally observed apparent stabilization of receptor dimers in the plasma membrane was reproduced by simulations of a refined, hierarchical compartment model. Our simulations further revealed that the two-dimensional association rate constant is a key parameter for controlling the extent of MSK-mediated stabilization of protein complexes, thus ensuring the specificity of this effect. Together, experimental evidence and simulations support the hypothesis that passive receptor confinement by MSK-based microcompartmentalization promotes maintenance of signaling complexes in the plasma membrane.
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Affiliation(s)
- Changjiang You
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | | | | | - Stephan Wilmes
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
| | - Ignacio Moraga
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - K. Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - André Leier
- Isaac Newton Institute for Mathematical Sciences, University of Cambridge, Cambridge, U.K
- Okinawa Institute of Science and Technology, Onna-son, Kunigami-gun, Okinawa 904-0495, Japan
| | - Jacob Piehler
- Department of Biology, University of Osnabrück, Barbarastraße 11, 49076 Osnabrück, Germany
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116
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Deschamps J, Rowald A, Ries J. Efficient homogeneous illumination and optical sectioning for quantitative single-molecule localization microscopy. OPTICS EXPRESS 2016; 24:28080-28090. [PMID: 27906373 DOI: 10.1364/oe.24.028080] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule localization microscopy (SMLM) relies on the switching of fluorescent molecules between a fluorescent and a dark state to achieve super resolution. This process is inherently dependent on the intensity distribution of the laser light used for both activation from the dark state and excitation of the bright state. Typically, laser light is coupled directly or via a single-mode fiber into the microscope, which leads to a Gaussian intensity profile in total internal reflection (TIR) or epi illumination. As a result, switching dynamics and brightness of the fluorescent molecules vary strongly across the field of view, impacting their localization precision and impeding quantitative analysis. Here we present a simple illumination scheme based on the use of a multimode fiber and a laser speckle-reducer, which results in a flat, homogeneous and speckle-free illumination across the entire field of view. In addition, we combined homogeneous multimode excitation of the sample with single-mode based TIR activation to simultaneously obtain the advantages of both approaches: uniform brightness of single fluorophores and TIR-like optical sectioning.
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117
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Gao L, Chen J, Gao J, Wang H, Xiong W. Super-resolution microscopy reveals the insulin-resistance-regulated reorganization of GLUT4 on plasma membranes. J Cell Sci 2016; 130:396-405. [PMID: 27888215 DOI: 10.1242/jcs.192450] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 11/11/2016] [Indexed: 02/01/2023] Open
Abstract
GLUT4 (also known as SLC2A4) is essential for glucose uptake in skeletal muscles and adipocytes, which play central roles in whole-body glucose metabolism. Here, using direct stochastic optical reconstruction microscopy (dSTORM) to investigate the characteristics of plasma-membrane-fused GLUT4 at the single-molecule level, we have demonstrated that insulin and insulin resistance regulate the spatial organization of GLUT4 in adipocytes. Stimulation with insulin shifted the balance of GLUT4 on the plasma membrane toward a more dispersed configuration. In contrast, insulin resistance induced a more clustered distribution of GLUT4 and increased the mean number of molecules per cluster. Furthermore, our data demonstrate that the F5QQI motif and lipid rafts mediate the maintenance of GLUT4 clusters on the plasma membrane. Mutation of F5QQI (F5QQA-GLUT4) induced a more clustered distribution of GLUT4; moreover, destruction of lipid rafts in adipocytes expressing F5QQA-GLUT4 dramatically decreased the percentage of large clusters and the mean number of molecules per cluster. In conclusion, our data clarify the effects of insulin stimulation or insulin resistance on GLUT4 reorganization on the plasma membrane and reveal new pathogenic mechanisms of insulin resistance.
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Affiliation(s)
- Lan Gao
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China.,Graduate University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Junling Chen
- Graduate University of Chinese Academy of Sciences, Beijing 100049, P.R. China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilil 130022, P.R. China
| | - Jing Gao
- Graduate University of Chinese Academy of Sciences, Beijing 100049, P.R. China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilil 130022, P.R. China
| | - Hongda Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilil 130022, P.R. China
| | - Wenyong Xiong
- State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, P.R. China
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118
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Griffié J, Shannon M, Bromley CL, Boelen L, Burn GL, Williamson DJ, Heard NA, Cope AP, Owen DM, Rubin-Delanchy P. A Bayesian cluster analysis method for single-molecule localization microscopy data. Nat Protoc 2016; 11:2499-2514. [PMID: 27854362 DOI: 10.1038/nprot.2016.149] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Cell function is regulated by the spatiotemporal organization of the signaling machinery, and a key facet of this is molecular clustering. Here, we present a protocol for the analysis of clustering in data generated by 2D single-molecule localization microscopy (SMLM)-for example, photoactivated localization microscopy (PALM) or stochastic optical reconstruction microscopy (STORM). Three features of such data can cause standard cluster analysis approaches to be ineffective: (i) the data take the form of a list of points rather than a pixel array; (ii) there is a non-negligible unclustered background density of points that must be accounted for; and (iii) each localization has an associated uncertainty in regard to its position. These issues are overcome using a Bayesian, model-based approach. Many possible cluster configurations are proposed and scored against a generative model, which assumes Gaussian clusters overlaid on a completely spatially random (CSR) background, before every point is scrambled by its localization precision. We present the process of generating simulated and experimental data that are suitable to our algorithm, the analysis itself, and the extraction and interpretation of key cluster descriptors such as the number of clusters, cluster radii and the number of localizations per cluster. Variations in these descriptors can be interpreted as arising from changes in the organization of the cellular nanoarchitecture. The protocol requires no specific programming ability, and the processing time for one data set, typically containing 30 regions of interest, is ∼18 h; user input takes ∼1 h.
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Affiliation(s)
- Juliette Griffié
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Michael Shannon
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Claire L Bromley
- MRC Centre for Developmental Biology, King's College London, London, UK
| | - Lies Boelen
- Faculty of Medicine, Imperial College London, London, UK
| | - Garth L Burn
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - David J Williamson
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Nicholas A Heard
- Department of Mathematics, Imperial College London and Heilbronn Institute for Mathematical Research, University of Bristol, Bristol, UK
| | - Andrew P Cope
- Division of Immunology, Infection and Inflammatory Disease, Academic Department of Rheumatology, King's College London, London, UK
| | - Dylan M Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Patrick Rubin-Delanchy
- Department of Statistics, University of Oxford and Heilbronn Institute for Mathematical Research, University of Bristol, Bristol, UK
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119
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Zhang Z, Nishimura Y, Kanchanawong P. Extracting microtubule networks from superresolution single-molecule localization microscopy data. Mol Biol Cell 2016; 28:333-345. [PMID: 27852898 PMCID: PMC5231901 DOI: 10.1091/mbc.e16-06-0421] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/07/2016] [Accepted: 11/10/2016] [Indexed: 12/05/2022] Open
Abstract
Microtubule filaments form ubiquitous networks. However, quantitative analysis of this structure is difficult due to its complex architecture. A tool is given for the automated retrieval of microtubule filaments from superresolution microscopy images and used for a quantitative analysis of microtubule network architecture phenotypes in fibroblasts. Microtubule filaments form ubiquitous networks that specify spatial organization in cells. However, quantitative analysis of microtubule networks is hampered by their complex architecture, limiting insights into the interplay between their organization and cellular functions. Although superresolution microscopy has greatly facilitated high-resolution imaging of microtubule filaments, extraction of complete filament networks from such data sets is challenging. Here we describe a computational tool for automated retrieval of microtubule filaments from single-molecule-localization–based superresolution microscopy images. We present a user-friendly, graphically interfaced implementation and a quantitative analysis of microtubule network architecture phenotypes in fibroblasts.
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Affiliation(s)
- Zhen Zhang
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Yukako Nishimura
- Mechanobiology Institute, National University of Singapore, 117411 Singapore
| | - Pakorn Kanchanawong
- Mechanobiology Institute, National University of Singapore, 117411 Singapore .,Department of Biomedical Engineering, National University of Singapore, 117411 Singapore
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120
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Pageon SV, Nicovich PR, Mollazade M, Tabarin T, Gaus K. Clus-DoC: a combined cluster detection and colocalization analysis for single-molecule localization microscopy data. Mol Biol Cell 2016; 27:3627-3636. [PMID: 27582387 PMCID: PMC5221594 DOI: 10.1091/mbc.e16-07-0478] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 08/16/2016] [Accepted: 08/23/2016] [Indexed: 11/21/2022] Open
Abstract
Advances in fluorescence microscopy are providing increasing evidence that the spatial organization of proteins in cell membranes may facilitate signal initiation and integration for appropriate cellular responses. Our understanding of how changes in spatial organization are linked to function has been hampered by the inability to directly measure signaling activity or protein association at the level of individual proteins in intact cells. Here we solve this measurement challenge by developing Clus-DoC, an analysis strategy that quantifies both the spatial distribution of a protein and its colocalization status. We apply this approach to the triggering of the T-cell receptor during T-cell activation, as well as to the functionality of focal adhesions in fibroblasts, thereby demonstrating an experimental and analytical workflow that can be used to quantify signaling activity and protein colocalization at the level of individual proteins.
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Affiliation(s)
- Sophie V Pageon
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Philip R Nicovich
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mahdie Mollazade
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Thibault Tabarin
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences, and ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney, NSW 2052, Australia
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121
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Abstract
Ptdns(4,5)P2 is a minor structural lipid of the plasma membrane (PM), but a master regulator of PM function. Serving either as a substrate for the generation of second messengers, or more commonly as a ligand triggering protein recruitment or activation, it regulates most aspects of PM function. Understanding how this relatively simple biological macromolecule can regulate such a vast array of different functions in parallel, is the key to understanding the biology of the PM as a whole, in both health and disease. In this review, potential mechanisms are discussed that might explain how a lipid can separately regulate so many protein complexes. The focus is on the spatial distribution of the lipid molecules, their metabolism and their interactions. Open questions that still need to be resolved are highlighted, as are potential experimental approaches that might shed light on the mechanisms at play. Moreover, the broader question is raised as to whether PtdIns(4,5)P2 should be thought of as a bona fide signalling molecule or more of a simple lipid cofactor or perhaps both, depending on the context of the particular function in question.
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122
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Lu X, Nicovich PR, Gaus K, Gooding JJ. Towards single molecule biosensors using super-resolution fluorescence microscopy. Biosens Bioelectron 2016; 93:1-8. [PMID: 27829565 DOI: 10.1016/j.bios.2016.10.048] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/21/2016] [Accepted: 10/20/2016] [Indexed: 11/15/2022]
Abstract
Conventional immunosensors require many binding events to give a single transducer output which represents the concentration of the analyte in the sample. Because of the requirements to selectively detect species in complex samples, immunosensing interfaces must allow immobilisation of antibodies while repelling nonspecific adsorption of other species. These requirements lead to quite sophisticated interfacial design, often with molecular level control, but we have no tools to characterise how well these interfaces work at the molecular level. The work reported herein is an initial feasibility study to show that antibody-antigen binding events can be monitored at the single molecule level using single molecule localisation microscopy (SMLM). The steps to achieve this first requires showing that indium tin oxide surfaces can be used for SMLM, then that these surfaces can be modified with self-assembled monolayers using organophosphonic acid derivatives, that the amount of antigens and antibodies on the surface can be controlled and monitored at the single molecule level and finally antibody binding to antigen modified surfaces can be monitored. The results show the amount of antibody that binds to an antigen modified surface is dependent on both the concentration of antigen on the surface and the concentration of antibody in solution. This study demonstrates the potential of SMLM for characterising biosensing interfaces and as the transducer in a massively parallel, wide field, single molecule detection scheme for quantitative analysis.
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Affiliation(s)
- Xun Lu
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Philip R Nicovich
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, School of Medical Sciences and the ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine and the ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia.
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123
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Giliberti V, Baldassarre L, Rosa A, de Turris V, Ortolani M, Calvani P, Nucara A. Protein clustering in chemically stressed HeLa cells studied by infrared nanospectroscopy. NANOSCALE 2016; 8:17560-17567. [PMID: 27714081 DOI: 10.1039/c6nr05783g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Photo-Thermal Induced Resonance (PTIR) nanospectroscopy, tuned towards amide-I absorption, was used to study the distribution of proteic material in 34 different HeLa cells, of which 18 were chemically stressed by oxidative stress with Na3AsO3. The cell nucleus was found to provide a weaker amide-I signal than the surrounding cytoplasm, while the strongest PTIR signal comes from the perinuclear region. AFM topography shows that the cells exposed to oxidative stress undergo a volume reduction with respect to the control cells, through an accumulation of the proteic material around and above the nucleus. This is confirmed by the PTIR maps of the cytoplasm, where the pixels providing a high amide-I signal were identified with a space resolution of ∼300 × 300 nm. By analyzing their distribution with two different statistical procedures we found that the probability to find protein clusters smaller than 0.6 μm in the cytoplasm of stressed HeLa cells is higher by 35% than in the control cells. These results indicate that it is possible to study proteic clustering within single cells by label-free optical nanospectroscopy.
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Affiliation(s)
- V Giliberti
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161 Roma, Italy
| | - L Baldassarre
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161 Roma, Italy and Dipartimento di Fisica, Università di Roma La Sapienza, P.le Aldo Moro 5, 00185 Roma, Italy.
| | - A Rosa
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161 Roma, Italy and Dipartimento di Biologia e Biotecnologie Charles Darwin, Universita di Roma La Sapienza, P.le Aldo Moro 5, 00185 Roma, Italy
| | - V de Turris
- Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, V.le Regina Elena 291, 00161 Roma, Italy
| | - M Ortolani
- Dipartimento di Fisica, Università di Roma La Sapienza, P.le Aldo Moro 5, 00185 Roma, Italy.
| | - P Calvani
- Dipartimento di Fisica, Università di Roma La Sapienza, P.le Aldo Moro 5, 00185 Roma, Italy.
| | - A Nucara
- Dipartimento di Fisica, Università di Roma La Sapienza, P.le Aldo Moro 5, 00185 Roma, Italy.
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124
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Shelby SA, Veatch SL, Holowka DA, Baird BA. Functional nanoscale coupling of Lyn kinase with IgE-FcεRI is restricted by the actin cytoskeleton in early antigen-stimulated signaling. Mol Biol Cell 2016; 27:3645-3658. [PMID: 27682583 PMCID: PMC5221596 DOI: 10.1091/mbc.e16-06-0425] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/20/2016] [Indexed: 12/13/2022] Open
Abstract
Spatial targeting of signaling components to activated receptors on the plasma membrane is key for initiating signal transduction. The actin cytoskeleton restricts antigen-stimulated colocalization of IgE-FcεRI with membrane-anchored signaling partner Lyn kinase, and this regulation is mediated by organization of plasma membrane lipids. The allergic response is initiated on the plasma membrane of mast cells by phosphorylation of the receptor for immunoglobulin E (IgE), FcεRI, by Lyn kinase after IgE-FcεRI complexes are cross-linked by multivalent antigen. Signal transduction requires reorganization of receptors and membrane signaling proteins, but this spatial regulation is not well defined. We used fluorescence localization microscopy (FLM) and pair-correlation analysis to measure the codistribution of IgE-FcεRI and Lyn on the plasma membrane of fixed cells with 20- to 25-nm resolution. We directly visualized Lyn recruitment to IgE-FcεRI within 1 min of antigen stimulation. Parallel FLM experiments captured stimulation-induced FcεRI phosphorylation and colocalization of a saturated lipid-anchor probe derived from Lyn’s membrane anchorage. We used cytochalasin and latrunculin to investigate participation of the actin cytoskeleton in regulating functional interactions of FcεRI. Inhibition of actin polymerization by these agents enhanced colocalization of IgE-FcεRI with Lyn and its saturated lipid anchor at early stimulation times, accompanied by augmented phosphorylation within FcεRI clusters. Ising model simulations provide a simplified model consistent with our results. These findings extend previous evidence that IgE-FcεRI signaling is initiated by colocalization with Lyn in ordered lipid regions and that the actin cytoskeleton regulates this functional interaction by influencing the organization of membrane lipids.
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Affiliation(s)
- Sarah A Shelby
- Department of Chemistry and Chemical Biology and Field of Biophysics, Cornell University, Ithaca, NY 14853
| | - Sarah L Veatch
- Department of Biophysics, University of Michigan, Ann Arbor, MI 48109
| | - David A Holowka
- Department of Chemistry and Chemical Biology and Field of Biophysics, Cornell University, Ithaca, NY 14853
| | - Barbara A Baird
- Department of Chemistry and Chemical Biology and Field of Biophysics, Cornell University, Ithaca, NY 14853
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125
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Smith AJ, Verkman AS. Superresolution Imaging of Aquaporin-4 Cluster Size in Antibody-Stained Paraffin Brain Sections. Biophys J 2016; 109:2511-2522. [PMID: 26682810 DOI: 10.1016/j.bpj.2015.10.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 10/27/2015] [Accepted: 10/29/2015] [Indexed: 12/14/2022] Open
Abstract
The water channel aquaporin-4 (AQP4) forms supramolecular clusters whose size is determined by the ratio of M1- and M23-AQP4 isoforms. In cultured astrocytes, differences in the subcellular localization and macromolecular interactions of small and large AQP4 clusters results in distinct physiological roles for M1- and M23-AQP4. Here, we developed quantitative superresolution optical imaging methodology to measure AQP4 cluster size in antibody-stained paraffin sections of mouse cerebral cortex and spinal cord, human postmortem brain, and glioma biopsy specimens. This methodology was used to demonstrate that large AQP4 clusters are formed in AQP4(-/-) astrocytes transfected with only M23-AQP4, but not in those expressing only M1-AQP4, both in vitro and in vivo. Native AQP4 in mouse cortex, where both isoforms are expressed, was enriched in astrocyte foot-processes adjacent to microcapillaries; clusters in perivascular regions of the cortex were larger than in parenchymal regions, demonstrating size-dependent subcellular segregation of AQP4 clusters. Two-color superresolution imaging demonstrated colocalization of Kir4.1 with AQP4 clusters in perivascular areas but not in parenchyma. Surprisingly, the subcellular distribution of AQP4 clusters was different between gray and white matter astrocytes in spinal cord, demonstrating regional specificity in cluster polarization. Changes in AQP4 subcellular distribution are associated with several neurological diseases and we demonstrate that AQP4 clustering was preserved in a postmortem human cortical brain tissue specimen, but that AQP4 was not substantially clustered in a human glioblastoma specimen despite high-level expression. Our results demonstrate the utility of superresolution optical imaging for measuring the size of AQP4 supramolecular clusters in paraffin sections of brain tissue and support AQP4 cluster size as a primary determinant of its subcellular distribution.
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Affiliation(s)
- Alex J Smith
- Departments of Medicine and Physiology, University of California at San Francisco, San Francisco, California.
| | - Alan S Verkman
- Departments of Medicine and Physiology, University of California at San Francisco, San Francisco, California.
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126
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Kasula R, Chai YJ, Bademosi AT, Harper CB, Gormal RS, Morrow IC, Hosy E, Collins BM, Choquet D, Papadopulos A, Meunier FA. The Munc18-1 domain 3a hinge-loop controls syntaxin-1A nanodomain assembly and engagement with the SNARE complex during secretory vesicle priming. J Cell Biol 2016; 214:847-58. [PMID: 27646276 PMCID: PMC5037406 DOI: 10.1083/jcb.201508118] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 08/24/2016] [Indexed: 12/12/2022] Open
Abstract
Kasula et al. use single-molecule imaging to reveal the diffusional signature for the SNARE proteins Munc18-1 and syntaxin-1A during secretory vesicle priming. The authors show that a conformational change in the Munc18-1 domain 3a hinge-loop regulates engagement of syntaxin-1A in the SNARE complex. Munc18-1 and syntaxin-1A control SNARE-dependent neuroexocytosis and are organized in nanodomains on the plasma membrane of neurons and neurosecretory cells. Deciphering the intra- and intermolecular steps via which they prepare secretory vesicles (SVs) for fusion is key to understanding neuronal and hormonal communication. Here, we demonstrate that expression of a priming-deficient mutant lacking 17 residues of the domain 3a hinge-loop (Munc18-1Δ317-333) in PC12 cells engineered to knockdown Munc18-1/2 markedly prolonged SV docking. Single-molecule analysis revealed nonhomogeneous diffusion of Munc18-1 and syntaxin-1A in and out of partially overlapping nanodomains. Whereas Munc18-1WT mobility increased in response to stimulation, syntaxin-1A became less mobile. These Munc18-1 and syntaxin-1A diffusional switches were blocked by the expression of Munc18-1Δ317-333, suggesting that a conformational change in the Munc18-1 hinge-loop controls syntaxin-1A and subsequent SNARE complex assembly. Accordingly, syntaxin-1A confinement was prevented by expression of botulinum neurotoxin type E. The Munc18-1 domain 3a hinge-loop therefore controls syntaxin-1A engagement into SNARE complex formation during priming.
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Affiliation(s)
- Ravikiran Kasula
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ye Jin Chai
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Adekunle T Bademosi
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Callista B Harper
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rachel S Gormal
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Isabel C Morrow
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Eric Hosy
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, 33077 Bordeaux, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5297, 33077 Bordeaux, France
| | - Brett M Collins
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Daniel Choquet
- Interdisciplinary Institute for Neuroscience, University of Bordeaux, 33077 Bordeaux, France Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5297, 33077 Bordeaux, France Bordeaux Imaging Center, Unité Mixte de Service 3420, Centre National de la Recherche Scientifique, US4 Institut National de la Santé et de la Recherche Médicale, University of Bordeaux, 33077 Bordeaux, France
| | - Andreas Papadopulos
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Frédéric A Meunier
- Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland 4072, Australia
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127
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Mateos-Gil P, Letschert S, Doose S, Sauer M. Super-Resolution Imaging of Plasma Membrane Proteins with Click Chemistry. Front Cell Dev Biol 2016; 4:98. [PMID: 27668214 PMCID: PMC5016519 DOI: 10.3389/fcell.2016.00098] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/24/2016] [Indexed: 12/30/2022] Open
Abstract
Besides its function as a passive cell wall, the plasma membrane (PM) serves as a platform for different physiological processes such as signal transduction and cell adhesion, determining the ability of cells to communicate with the exterior, and form tissues. Therefore, the spatial distribution of PM components, and the molecular mechanisms underlying it, have important implications in various biological fields including cell development, neurobiology, and immunology. The existence of confined compartments in the plasma membrane that vary on many length scales from protein multimers to micrometer-size domains with different protein and lipid composition is today beyond all questions. As much as the physiology of cells is controlled by the spatial organization of PM components, the study of distribution, size, and composition remains challenging. Visualization of the molecular distribution of PM components has been impeded mainly due to two problems: the specific labeling of lipids and proteins without perturbing their native distribution and the diffraction-limit of fluorescence microscopy restricting the resolution to about half the wavelength of light. Here, we present a bioorthogonal chemical reporter strategy based on click chemistry and metabolic labeling for efficient and specific visualization of PM proteins and glycans with organic fluorophores in combination with super-resolution fluorescence imaging by direct stochastic optical reconstruction microscopy (dSTORM) with single-molecule sensitivity.
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Affiliation(s)
- Pablo Mateos-Gil
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Sebastian Letschert
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Sören Doose
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology and Biophysics, Julius Maximilian University of Würzburg Würzburg, Germany
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128
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Levental I, Veatch S. The Continuing Mystery of Lipid Rafts. J Mol Biol 2016; 428:4749-4764. [PMID: 27575334 DOI: 10.1016/j.jmb.2016.08.022] [Citation(s) in RCA: 192] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/16/2016] [Accepted: 08/19/2016] [Indexed: 12/12/2022]
Abstract
Since its initial formalization nearly 20 years ago, the concept of lipid rafts has generated a tremendous amount of attention and interest and nearly as much controversy. The controversy is perhaps surprising because the notion itself is intuitive: compartmentalization in time and space is a ubiquitous theme at all scales of biology, and therefore, the partitioning of cellular membranes into lateral subdivision should be expected. Nevertheless, the physicochemical principles responsible for compartmentalization and the molecular mechanisms by which they are functionalized remain nearly as mysterious today as they were two decades ago. Herein, we review recent literature on this topic with a specific focus on the major open questions in the field including: (1) what are the best tools to assay raft behavior in living membranes? (2) what is the function of the complex lipidome of mammalian cells with respect to membrane organization? (3) what are the mechanisms that drive raft formation and determine their properties? (4) how can rafts be modulated? (5) how is membrane compartmentalization integrated into cellular signaling? Despite decades of intensive research, this compelling field remains full of fundamental questions.
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Affiliation(s)
- Ilya Levental
- McGovern Medical School at the University of Texas Houston, Department of Integrative Biology and Pharmacology
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129
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Yin Y, Rothenberg E. Probing the Spatial Organization of Molecular Complexes Using Triple-Pair-Correlation. Sci Rep 2016; 6:30819. [PMID: 27545293 PMCID: PMC4992864 DOI: 10.1038/srep30819] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 07/08/2016] [Indexed: 11/25/2022] Open
Abstract
Super-resolution microscopy coupled with multiplexing techniques can resolve specific spatial arrangements of different components within molecular complexes. However, reliable quantification and analysis of such specific organization is extremely problematic because it is frequently obstructed by random co-localization incidents between crowded molecular species and the intrinsic heterogeneity of molecular complexes. To address this, we present a Triple-Pair-Correlation (TPC) analysis approach for unbiased interpretation of the spatial organization of molecular assemblies in crowded three-color super-resolution (SR) images. We validate this approach using simulated data, as well as SR images of DNA replication foci in human cells. This demonstrates the applicability of TPC in deciphering the specific spatial organization of molecular complexes hidden in dense multi-color super-resolution images.
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Affiliation(s)
- Yandong Yin
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 1st Avenue, New York, NY 10016, USA
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 550 1st Avenue, New York, NY 10016, USA
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130
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Tang AH, Chen H, Li TP, Metzbower SR, MacGillavry HD, Blanpied TA. A trans-synaptic nanocolumn aligns neurotransmitter release to receptors. Nature 2016; 536:210-4. [PMID: 27462810 PMCID: PMC5002394 DOI: 10.1038/nature19058] [Citation(s) in RCA: 425] [Impact Index Per Article: 53.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 06/27/2016] [Indexed: 12/29/2022]
Abstract
Synaptic transmission is maintained by a delicate, sub-synaptic molecular architecture, and even mild alterations in synapse structure drive functional changes during experience-dependent plasticity and pathological disorders. Key to this architecture is how the distribution of presynaptic vesicle fusion sites corresponds to the position of receptors in the postsynaptic density. However, while it has long been recognized that this spatial relationship modulates synaptic strength, it has not been precisely described, owing in part to the limited resolution of light microscopy. Using localization microscopy, here we show that key proteins mediating vesicle priming and fusion are mutually co-enriched within nanometre-scale subregions of the presynaptic active zone. Through development of a new method to map vesicle fusion positions within single synapses in cultured rat hippocampal neurons, we find that action-potential-evoked fusion is guided by this protein gradient and occurs preferentially in confined areas with higher local density of Rab3-interacting molecule (RIM) within the active zones. These presynaptic RIM nanoclusters closely align with concentrated postsynaptic receptors and scaffolding proteins, suggesting the existence of a trans-synaptic molecular 'nanocolumn'. Thus, we propose that the nanoarchitecture of the active zone directs action-potential-evoked vesicle fusion to occur preferentially at sites directly opposing postsynaptic receptor-scaffold ensembles. Remarkably, NMDA receptor activation triggered distinct phases of plasticity in which postsynaptic reorganization was followed by trans-synaptic nanoscale realignment. This architecture suggests a simple organizational principle of central nervous system synapses to maintain and modulate synaptic efficiency.
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131
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Shivanandan A, Unnikrishnan J, Radenovic A. On characterizing protein spatial clusters with correlation approaches. Sci Rep 2016; 6:31164. [PMID: 27507257 PMCID: PMC4979030 DOI: 10.1038/srep31164] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 07/15/2016] [Indexed: 12/31/2022] Open
Abstract
Spatial aggregation of proteins might have functional importance, e.g., in signaling, and nano-imaging can be used to study them. Such studies require accurate characterization of clusters based on noisy data. A set of spatial correlation approaches free of underlying cluster processes and input parameters have been widely used for this purpose. They include the radius of maximal aggregation ra obtained from Ripley’s L(r) − r function as an estimator of cluster size, and the estimation of various cluster parameters based on an exponential model of the Pair Correlation Function(PCF). While convenient, the accuracy of these methods is not clear: e.g., does it depend on how the molecules are distributed within the clusters, or on cluster parameters? We analyze these methods for a variety of cluster models. We find that ra relates to true cluster size by a factor that is nonlinearly dependent on parameters and that can be arbitrarily large. For the PCF method, for the models analyzed, we obtain linear relationships between the estimators and true parameters, and the estimators were found to be within ±100% of true parameters, depending on the model. Our results, based on an extendable general framework, point to the need for caution in applying these methods.
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Affiliation(s)
- Arun Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Jayakrishnan Unnikrishnan
- Audiovisual Communications Laboratory, School of Computer and Communication Sciences, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne 1015, Switzerland
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132
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Sherman E, Barr VA, Merrill RK, Regan CK, Sommers CL, Samelson LE. Hierarchical nanostructure and synergy of multimolecular signalling complexes. Nat Commun 2016; 7:12161. [PMID: 27396911 PMCID: PMC4942584 DOI: 10.1038/ncomms12161] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 06/07/2016] [Indexed: 01/15/2023] Open
Abstract
Signalling complexes are dynamic, multimolecular structures and sites for intracellular signal transduction. Although they play a crucial role in cellular activation, current research techniques fail to resolve their structure in intact cells. Here we present a multicolour, photoactivated localization microscopy approach for imaging multiple types of single molecules in fixed and live cells and statistical tools to determine the nanoscale organization, topology and synergy of molecular interactions in signalling complexes downstream of the T-cell antigen receptor. We observe that signalling complexes nucleated at the key adapter LAT show a hierarchical topology. The critical enzymes PLCγ1 and VAV1 localize to the centre of LAT-based complexes, and the adapter SLP-76 and actin molecules localize to the periphery. Conditional second-order statistics reveal a hierarchical network of synergic interactions between these molecules. Our results extend our understanding of the nanostructure of signalling complexes and are relevant to studying a wide range of multimolecular complexes.
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Affiliation(s)
- Eilon Sherman
- Racah Institute of Physics, The Hebrew University,
Jerusalem
91904, Israel
| | - Valarie A. Barr
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Robert K. Merrill
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Carole K. Regan
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Connie L. Sommers
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
| | - Lawrence E. Samelson
- Laboratory of Cellular and Molecular Biology, CCR, NCI,
NIH, Bethesda, Maryland
20892, USA
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133
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Kratochvil HT, Ha DG, Zanni MT. Counting tagged molecules one by one: Quantitative photoactivation and bleaching of photoactivatable fluorophores. J Chem Phys 2016; 143:104201. [PMID: 26374025 DOI: 10.1063/1.4929991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Determining the number of molecules in a given assembly, such as the number of proteins in a toxic aggregate, is often critical to understanding chemistry and function. Herein, we report a variation of a limitless method for counting photoactivatable fluorescent dyes in which single dye molecules are photoswitched to a fluorescent state, counted, and then irreversibly photobleached. We use this method to count the number of CAGE 552 covalently bound to the surface of 500 nm polystyrene beads. Activation of CAGE 552 was achieved with a 405 nm laser pulse. Once activated, the dye was excited with 532 nm light, and the fluorescence emission was collected with a CCD camera. The results from the fluorescence experiments were then compared to bulk fluorescence measurements to assess the error in counting. There are other ways of counting molecules, such as photobleaching and statistical analysis of reversible switchable chromophores. The method reported here provides a lower bound to the number of chromophores, with no upper limit to the number of molecules that can be quantified.
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Affiliation(s)
- Huong T Kratochvil
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Dong G Ha
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | - Martin T Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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134
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Beuzer P, La Clair JJ, Cang H. Color-Coded Super-Resolution Small-Molecule Imaging. Chembiochem 2016; 17:999-1003. [PMID: 26994590 PMCID: PMC5291120 DOI: 10.1002/cbic.201600013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Indexed: 12/15/2022]
Abstract
Although the development of super-resolution microscopy dates back to 1994, its applications have been primarily focused on visualizing cellular structures and targets, including proteins, DNA and sugars. We now report on a system that allows both monitoring of the localization of exogenous small molecules in live cells at low resolution and subsequent super-resolution imaging by using stochastic optical reconstruction microscopy (STORM) on fixed cells. This represents a powerful new tool to understand the dynamics of subcellular trafficking associated with the mode and mechanism of action of exogenous small molecules.
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Affiliation(s)
- Paolo Beuzer
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA
| | - James J La Clair
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
- Xenobe Research Institute, P. O. Box 3052, San Diego, CA, 92163-1052, USA.
| | - Hu Cang
- Waitt Advanced Biophotonics Center, The Salk Institute for Biological Sciences, 10010 N Torrey Pines Road, La Jolla, CA, 92037, USA.
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135
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da Silva RMP, van der Zwaag D, Albertazzi L, Lee SS, Meijer EW, Stupp SI. Super-resolution microscopy reveals structural diversity in molecular exchange among peptide amphiphile nanofibres. Nat Commun 2016; 7:11561. [PMID: 27194204 PMCID: PMC4874009 DOI: 10.1038/ncomms11561] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/08/2016] [Indexed: 12/22/2022] Open
Abstract
The dynamic behaviour of supramolecular systems is an important dimension of their potential functions. Here, we report on the use of stochastic optical reconstruction microscopy to study the molecular exchange of peptide amphiphile nanofibres, supramolecular systems known to have important biomedical functions. Solutions of nanofibres labelled with different dyes (Cy3 and Cy5) were mixed, and the distribution of dyes inserting into initially single-colour nanofibres was quantified using correlative image analysis. Our observations are consistent with an exchange mechanism involving monomers or small clusters of molecules inserting randomly into a fibre. Different exchange rates are observed within the same fibre, suggesting that local cohesive structures exist on the basis of β-sheet discontinuous domains. The results reported here show that peptide amphiphile supramolecular systems can be dynamic and that their intermolecular interactions affect exchange patterns. This information can be used to generate useful aggregate morphologies for improved biomedical function. Dynamic behaviour in supramolecular systems is an important aspect of their functionality. Here, the authors use stochastic optical reconstruction microscopy to unveil structural diversity in self-assembled peptide amphiphile nanofibres, with potential relevance to biomedical applications.
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Affiliation(s)
- Ricardo M P da Silva
- Simpson Querrey Institute for BioNanotechnology (SQI), Northwestern University, Chicago, Illinois 60611, USA.,Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven MB 5600, The Netherlands.,Craniofacial Development &Stem Cell Biology, King's College London, London, SE1 9RT, UK
| | - Daan van der Zwaag
- Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven MB 5600, The Netherlands
| | - Lorenzo Albertazzi
- Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven MB 5600, The Netherlands.,Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), Barcelona 08028, Spain
| | - Sungsoo S Lee
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - E W Meijer
- Laboratory of Macromolecular and Organic Chemistry and Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven MB 5600, The Netherlands
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology (SQI), Northwestern University, Chicago, Illinois 60611, USA.,Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA.,Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA.,Department of Medicine, Northwestern University, Chicago, Illinois 60611, USA.,Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, USA
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136
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Andronov L, Orlov I, Lutz Y, Vonesch JL, Klaholz BP. ClusterViSu, a method for clustering of protein complexes by Voronoi tessellation in super-resolution microscopy. Sci Rep 2016; 6:24084. [PMID: 27068792 PMCID: PMC4828638 DOI: 10.1038/srep24084] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 03/18/2016] [Indexed: 11/24/2022] Open
Abstract
Super-resolution microscopy (PALM, STORM etc.) provides a plethora of fluorescent signals in dense cellular environments which can be difficult to interpret. Here we describe ClusterViSu, a method for image reconstruction, visualization and quantification of labelled protein clusters, based on Voronoi tessellation of the individual fluorescence events. The general applicability of this clustering approach for the segmentation of super-resolution microscopy data, including for co-localization, is illustrated on a series of important biological objects such as chromatin complexes, RNA polymerase, nuclear pore complexes and microtubules.
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Affiliation(s)
- Leonid Andronov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Igor Orlov
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Yves Lutz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Jean-Luc Vonesch
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
| | - Bruno P Klaholz
- Centre for Integrative Biology (CBI), Department of Integrated Structural Biology, IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, Illkirch, France.,Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, Illkirch, France.,Université de Strasbourg, Strasbourg, France
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137
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Hartley JM, Zhang R, Gudheti M, Yang J, Kopeček J. Tracking and quantifying polymer therapeutic distribution on a cellular level using 3D dSTORM. J Control Release 2016; 231:50-9. [PMID: 26855050 DOI: 10.1016/j.jconrel.2016.02.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Revised: 01/27/2016] [Accepted: 02/03/2016] [Indexed: 12/30/2022]
Abstract
We used a single-molecule localization technique called direct stochastic optical reconstruction microscopy (dSTORM) to quantify both colocalization and spatial distribution on a cellular level for two conceptually different N-(2-hydroxypropyl)methacrylamide (HPMA) copolymer conjugates. Microscopy images were acquired of entire cells with resolutions as high as 25nm revealing the nanoscale distribution of the fluorescently labeled therapeutic components. Drug-free macromolecular therapeutics consisting of two self-assembling nanoconjugates showed slight increase in nanoclusters on the cell surface with time. Additionally, dSTORM provided high resolution images of the nanoscale organization of the self-assembling conjugates at the interface between two cells. A conjugate designed for treating ovarian cancer showed that the model drug (Cy3) and polymer bound to Cy5 were colocalized at an early time point before the model drug was enzymatically cleaved from the polymer. Using spatial descriptive statistics it was found that the drug was randomly distributed after 24h while the polymer bound dye remained in clusters. Four different fluorescent dyes were used and two different therapeutic systems were tested to demonstrate the versatility and possible general applicability of dSTORM for use in studying drug delivery systems.
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Affiliation(s)
- Jonathan M Hartley
- Department of Bioengineering, University of Utah, 20 S. 2030 E., Rm. 108, Salt Lake City, UT 84112, USA
| | - Rui Zhang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 20 S. 2030 E., Rm. 205, Salt Lake City, UT 84112, USA
| | - Manasa Gudheti
- Department of Biology, University of Utah, 257S 1400 E, Salt Lake City, UT 84112, USA; Bruker Nano Surfaces, 630 Komas Drive, Salt Lake City, UT 84108, USA
| | - Jiyuan Yang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 20 S. 2030 E., Rm. 205, Salt Lake City, UT 84112, USA
| | - Jindřich Kopeček
- Department of Bioengineering, University of Utah, 20 S. 2030 E., Rm. 108, Salt Lake City, UT 84112, USA; Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 20 S. 2030 E., Rm. 205, Salt Lake City, UT 84112, USA.
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138
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Abstract
Bacterial cytokinesis is accomplished by the essential 'divisome' machinery. The most widely conserved divisome component, FtsZ, is a tubulin homolog that polymerizes into the 'FtsZ-ring' ('Z-ring'). Previous in vitro studies suggest that Z-ring contraction serves as a major constrictive force generator to limit the progression of cytokinesis. Here, we applied quantitative superresolution imaging to examine whether and how Z-ring contraction limits the rate of septum closure during cytokinesis in Escherichia coli cells. Surprisingly, septum closure rate was robust to substantial changes in all Z-ring properties proposed to be coupled to force generation: FtsZ's GTPase activity, Z-ring density, and the timing of Z-ring assembly and disassembly. Instead, the rate was limited by the activity of an essential cell wall synthesis enzyme and further modulated by a physical divisome-chromosome coupling. These results challenge a Z-ring-centric view of bacterial cytokinesis and identify cell wall synthesis and chromosome segregation as limiting processes of cytokinesis.
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139
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Harper CB, Papadopulos A, Martin S, Matthews DR, Morgan GP, Nguyen TH, Wang T, Nair D, Choquet D, Meunier FA. Botulinum neurotoxin type-A enters a non-recycling pool of synaptic vesicles. Sci Rep 2016; 6:19654. [PMID: 26805017 PMCID: PMC4726273 DOI: 10.1038/srep19654] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 11/20/2015] [Indexed: 02/03/2023] Open
Abstract
Neuronal communication relies on synaptic vesicles undergoing regulated exocytosis and recycling for multiple rounds of fusion. Whether all synaptic vesicles have identical protein content has been challenged, suggesting that their recycling ability may differ greatly. Botulinum neurotoxin type-A (BoNT/A) is a highly potent neurotoxin that is internalized in synaptic vesicles at motor nerve terminals and induces flaccid paralysis. Recently, BoNT/A was also shown to undergo retrograde transport, suggesting it might enter a specific pool of synaptic vesicles with a retrograde trafficking fate. Using high-resolution microscopy techniques including electron microscopy and single molecule imaging, we found that the BoNT/A binding domain is internalized within a subset of vesicles that only partially co-localize with cholera toxin B-subunit and have markedly reduced VAMP2 immunoreactivity. Synaptic vesicles loaded with pHrodo-BoNT/A-Hc exhibited a significantly reduced ability to fuse with the plasma membrane in mouse hippocampal nerve terminals when compared with pHrodo-dextran-containing synaptic vesicles and pHrodo-labeled anti-GFP nanobodies bound to VAMP2-pHluorin or vGlut-pHluorin. Similar results were also obtained at the amphibian neuromuscular junction. These results reveal that BoNT/A is internalized in a subpopulation of synaptic vesicles that are not destined to recycle, highlighting the existence of significant molecular and functional heterogeneity between synaptic vesicles.
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Affiliation(s)
- Callista B Harper
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Queensland 4072, Australia
| | - Andreas Papadopulos
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Queensland 4072, Australia
| | - Sally Martin
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Queensland 4072, Australia
| | - Daniel R Matthews
- The University of Queensland, Queensland Brain Institute, Brisbane, Queensland 4072, Australia
| | - Garry P Morgan
- The University of Queensland, Centre for Microscopy and Microanalysis, Brisbane, Queensland 4072, Australia
| | - Tam H Nguyen
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Queensland 4072, Australia
| | - Tong Wang
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Queensland 4072, Australia
| | - Deepak Nair
- Interdisciplinary Institute for Neuroscience, The University of Bordeaux, Bordeaux, 33000, France.,Centre for Neuroscience, Indian Institute of Science, Bangalore, 560012, India
| | - Daniel Choquet
- Interdisciplinary Institute for Neuroscience, The University of Bordeaux, Bordeaux, 33000, France
| | - Frederic A Meunier
- The University of Queensland, Queensland Brain Institute, Clem Jones Centre for Ageing Dementia Research, Brisbane, Queensland 4072, Australia
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140
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Lin J, Wester MJ, Graus MS, Lidke KA, Neumann AK. Nanoscopic cell-wall architecture of an immunogenic ligand in Candida albicans during antifungal drug treatment. Mol Biol Cell 2016; 27:1002-14. [PMID: 26792838 PMCID: PMC4791122 DOI: 10.1091/mbc.e15-06-0355] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 01/12/2016] [Indexed: 12/25/2022] Open
Abstract
Candida albicans evades immunity by limiting cell-wall β-glucan exposure. dSTORM imaging reveals that “unmasking”of glucan by an antifungal drug occurs through nanoscale reorganization of glucan exposure geometry. Nanostructuring of glucan might play a role in innate immune activation and provides insights into the physical regulation of glucan exposure. The cell wall of Candida albicans is composed largely of polysaccharides. Here we focus on β-glucan, an immunogenic cell-wall polysaccharide whose surface exposure is often restricted, or “masked,” from immune recognition by Dectin-1 on dendritic cells (DCs) and other innate immune cells. Previous research suggested that the physical presentation geometry of β-glucan might determine whether it can be recognized by Dectin-1. We used direct stochastic optical reconstruction microscopy to explore the fine structure of β-glucan exposed on C. albicans cell walls before and after treatment with the antimycotic drug caspofungin, which alters glucan exposure. Most surface-accessible glucan on C. albicans yeast and hyphae is limited to isolated Dectin-1–binding sites. Caspofungin-induced unmasking caused approximately fourfold to sevenfold increase in total glucan exposure, accompanied by increased phagocytosis efficiency of DCs for unmasked yeasts. Nanoscopic imaging of caspofungin-unmasked C. albicans cell walls revealed that the increase in glucan exposure is due to increased density of glucan exposures and increased multiglucan exposure sizes. These findings reveal that glucan exhibits significant nanostructure, which is a previously unknown physical component of the host–Candida interaction that might change during antifungal chemotherapy and affect innate immune activation.
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Affiliation(s)
- Jia Lin
- Center for Spatiotemporal Modeling of Cell Signaling, University of New Mexico, Albuquerque, NM 87131 Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Michael J Wester
- Center for Spatiotemporal Modeling of Cell Signaling, University of New Mexico, Albuquerque, NM 87131 Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM 87131
| | - Matthew S Graus
- Center for Spatiotemporal Modeling of Cell Signaling, University of New Mexico, Albuquerque, NM 87131 Department of Pathology, University of New Mexico, Albuquerque, NM 87131
| | - Keith A Lidke
- Center for Spatiotemporal Modeling of Cell Signaling, University of New Mexico, Albuquerque, NM 87131 Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Aaron K Neumann
- Center for Spatiotemporal Modeling of Cell Signaling, University of New Mexico, Albuquerque, NM 87131 Department of Pathology, University of New Mexico, Albuquerque, NM 87131
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141
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Abstract
The ability to detect individual fluorescent molecules inside living cells has enabled a range of powerful microscopy techniques that resolve biological processes on the molecular scale. These methods have also transformed the study of bacterial cell biology, which was previously obstructed by the limited spatial resolution of conventional microscopy. In the case of DNA-binding proteins, super-resolution microscopy can visualize the detailed spatial organization of DNA replication, transcription, and repair processes by reconstructing a map of single-molecule localizations. Furthermore, DNA-binding activities can be observed directly by tracking protein movement in real time. This allows identifying subpopulations of DNA-bound and diffusing proteins, and can be used to measure DNA-binding times in vivo. This chapter provides a detailed protocol for super-resolution microscopy and tracking of DNA-binding proteins in Escherichia coli cells. The protocol covers the construction of cell strains and describes data acquisition and analysis procedures, such as super-resolution image reconstruction, mapping single-molecule tracks, computing diffusion coefficients to identify molecular subpopulations with different mobility, and analysis of DNA-binding kinetics. While the focus is on the study of bacterial chromosome biology, these approaches are generally applicable to other molecular processes and cell types.
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Affiliation(s)
- Stephan Uphoff
- Department of Biochemistry, University of Oxford, Parks Road, Oxford, OX1 3QU, UK.
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142
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Analyzing Protein Clusters on the Plasma Membrane: Application of Spatial Statistical Analysis Methods on Super-Resolution Microscopy Images. FOCUS ON BIO-IMAGE INFORMATICS 2016; 219:95-122. [DOI: 10.1007/978-3-319-28549-8_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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143
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Caetano FA, Dirk BS, Tam JHK, Cavanagh PC, Goiko M, Ferguson SSG, Pasternak SH, Dikeakos JD, de Bruyn JR, Heit B. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures. PLoS Comput Biol 2015; 11:e1004634. [PMID: 26657340 PMCID: PMC4676698 DOI: 10.1371/journal.pcbi.1004634] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 10/27/2015] [Indexed: 11/18/2022] Open
Abstract
Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell. In this paper we present the software package Molecular Interactions in Super Resolution (MIiSR), which provides a series of quantitative analytical tools for measuring molecular interactions and the formation of higher-order molecular complexes in super-resolution microscopy images.
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Affiliation(s)
- Fabiana A. Caetano
- The J. Allyn Taylor Centre for Cell Biology, Robarts Research Institute and the Department of Physiology and Pharmacology, The University of Western Ontario, London, Ontario, Canada
| | - Brennan S. Dirk
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Joshua H. K. Tam
- The J. Allyn Taylor Centre for Cell Biology, Robarts Research Institute and the Department of Physiology and Pharmacology, The University of Western Ontario, London, Ontario, Canada
| | - P. Craig Cavanagh
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
| | - Maria Goiko
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
- Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | | | - Stephen H. Pasternak
- The J. Allyn Taylor Centre for Cell Biology, Robarts Research Institute and the Department of Physiology and Pharmacology, The University of Western Ontario, London, Ontario, Canada
- Department of Clinical Neurological Sciences, Schulich School of Medicine, The University of Western Ontario, London, Ontario, Canada
| | - Jimmy D. Dikeakos
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
| | - John R. de Bruyn
- Department of Physics and Astronomy, The University of Western Ontario, London, Ontario, Canada
| | - Bryan Heit
- Department of Microbiology and Immunology, The University of Western Ontario, London, Ontario, Canada
- * E-mail:
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144
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Sydor AM, Czymmek KJ, Puchner EM, Mennella V. Super-Resolution Microscopy: From Single Molecules to Supramolecular Assemblies. Trends Cell Biol 2015; 25:730-748. [DOI: 10.1016/j.tcb.2015.10.004] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 10/03/2015] [Accepted: 10/05/2015] [Indexed: 11/25/2022]
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145
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Griffié J, Boelen L, Burn G, Cope AP, Owen DM. Topographic prominence as a method for cluster identification in single-molecule localisation data. JOURNAL OF BIOPHOTONICS 2015; 8:925-934. [PMID: 25663080 DOI: 10.1002/jbio.201400127] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/03/2014] [Accepted: 12/19/2014] [Indexed: 06/04/2023]
Abstract
Single-molecule localisation based super-resolution fluorescence imaging produces maps of the coordinates of fluorescent molecules in a region of interest. Cluster analysis algorithms provide information concerning the clustering characteristics of these molecules, often through the generation of cluster heat maps based on local molecular density. The goal of this study was to generate a new cluster analysis method based on a topographic approach. In particular, a topographic map of the level of clustering across a region is generated based on Getis' variant of Ripley's K-function. By using the relative heights (topographic prominence, TP) of the peaks in the map, cluster characteristics can be identified more accurately than by using previously demonstrated height thresholds. Analogous to geological TP, the concepts of wet and dry TP and topographic isolation are introduced to generate binary maps. The algorithm is validated using simulated and experimental data and found to significantly outperform previous cluster identification methods. Illustration of the topographic prominence based cluster analysis algorithm.
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Affiliation(s)
- Juliette Griffié
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Lies Boelen
- Section of Immunology, Division of Infectious Diseases, Faculty of Medicine, Imperial College London, Praed Street, St Mary's Campus, London, United Kingdom
| | - Garth Burn
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Andrew P Cope
- Academic Department of Rheumatology, Division of Immunology, Infection and Inflammatory Disease, Faculty of Life Sciences and Medicine, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Dylan M Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, Hodgkin Building, Guy's Campus, London, SE1 1UL, United Kingdom.
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146
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Rubin-Delanchy P, Burn GL, Griffié J, Williamson DJ, Heard NA, Cope AP, Owen DM. Bayesian cluster identification in single-molecule localization microscopy data. Nat Methods 2015; 12:1072-6. [PMID: 26436479 DOI: 10.1038/nmeth.3612] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 09/02/2015] [Indexed: 12/18/2022]
Abstract
Single-molecule localization-based super-resolution microscopy techniques such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) produce pointillist data sets of molecular coordinates. Although many algorithms exist for the identification and localization of molecules from raw image data, methods for analyzing the resulting point patterns for properties such as clustering have remained relatively under-studied. Here we present a model-based Bayesian approach to evaluate molecular cluster assignment proposals, generated in this study by analysis based on Ripley's K function. The method takes full account of the individual localization precisions calculated for each emitter. We validate the approach using simulated data, as well as experimental data on the clustering behavior of CD3ζ, a subunit of the CD3 T cell receptor complex, in resting and activated primary human T cells.
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Affiliation(s)
- Patrick Rubin-Delanchy
- School of Mathematics, Heilbronn Institute for Mathematical Research, University of Bristol, Bristol, UK
| | - Garth L Burn
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - Juliette Griffié
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
| | - David J Williamson
- Manchester Collaborative Centre for Inflammation Research, University of Manchester, Manchester, UK
| | | | - Andrew P Cope
- Division of Immunology, Infection and Inflammatory Disease, Academic Department of Rheumatology, King's College London, London, UK
| | - Dylan M Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, London, UK
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147
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Maity PC, Blount A, Jumaa H, Ronneberger O, Lillemeier BF, Reth M. B cell antigen receptors of the IgM and IgD classes are clustered in different protein islands that are altered during B cell activation. Sci Signal 2015; 8:ra93. [PMID: 26373673 DOI: 10.1126/scisignal.2005887] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The B cell antigen receptors (BCRs) play an important role in the clonal selection of B cells and their differentiation into antibody-secreting plasma cells. Mature B cells have both immunoglobulin M (IgM) and IgD types of BCRs, which have identical antigen-binding sites and are both associated with the signaling subunits Igα and Igβ, but differ in their membrane-bound heavy chain isoforms. By two-color direct stochastic optical reconstruction microscopy (dSTORM), we showed that IgM-BCRs and IgD-BCRs reside in the plasma membrane in different protein islands with average sizes of 150 and 240 nm, respectively. Upon B cell activation, the BCR protein islands became smaller and more dispersed such that the IgM-BCRs and IgD-BCRs were found in close proximity to each other. Moreover, specific stimulation of one class of BCR had minimal effects on the organization of the other. These conclusions were supported by the findings from two-marker transmission electron microscopy and proximity ligation assays. Together, these data provide evidence for a preformed multimeric organization of BCRs on the plasma membrane that is remodeled after B cell activation.
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Affiliation(s)
- Palash Chandra Maity
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany. Department of Molecular Immunology, Institute of Biology III at the Faculty of Biology of the University of Freiburg, D-79104, and at the Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany.
| | - Amy Blount
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Hassan Jumaa
- Department of Molecular Immunology, Institute of Biology III at the Faculty of Biology of the University of Freiburg, D-79104, and at the Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany. Institute of Immunology, Ulm University, D-89081 Ulm, Germany
| | - Olaf Ronneberger
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany. Institute of Computer Science, University of Freiburg, D-79110 Freiburg Germany
| | | | - Michael Reth
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, D-79104 Freiburg, Germany. Department of Molecular Immunology, Institute of Biology III at the Faculty of Biology of the University of Freiburg, D-79104, and at the Max Planck Institute of Immunobiology and Epigenetics, D-79108 Freiburg, Germany.
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148
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Fricke F, Beaudouin J, Eils R, Heilemann M. One, two or three? Probing the stoichiometry of membrane proteins by single-molecule localization microscopy. Sci Rep 2015; 5:14072. [PMID: 26358640 PMCID: PMC4642553 DOI: 10.1038/srep14072] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/18/2015] [Indexed: 12/18/2022] Open
Abstract
Probing the oligomeric state of abundant molecules, such as membrane proteins in intact cells, is essential, but has not been straightforward. We address this challenge with a simple counting strategy that is capable of reporting the oligomeric state of dense, membrane-bound protein complexes. It is based on single-molecule localization microscopy to super-resolve protein structures in intact cells and basic quantitative evaluation. We validate our method with membrane-bound monomeric CD86 and dimeric cytotoxic T-lymphocyte-associated protein as model proteins and confirm their oligomeric states. We further detect oligomerization of CD80 and vesicular stomatitis virus glycoprotein and propose coexistence of monomers and dimers for CD80 and trimeric assembly of the viral protein at the cell membrane. This approach should prove valuable for researchers striving for reliable molecular counting in cells.
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Affiliation(s)
- Franziska Fricke
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Joel Beaudouin
- Department for Bioinformatics and Functional Genomics, Bioquant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, and Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Roland Eils
- Department for Bioinformatics and Functional Genomics, Bioquant and Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, and Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 267, 69120 Heidelberg, Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
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149
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Valley CC, Arndt-Jovin DJ, Karedla N, Steinkamp MP, Chizhik AI, Hlavacek WS, Wilson BS, Lidke KA, Lidke DS. Enhanced dimerization drives ligand-independent activity of mutant epidermal growth factor receptor in lung cancer. Mol Biol Cell 2015; 26:4087-99. [PMID: 26337388 PMCID: PMC4710239 DOI: 10.1091/mbc.e15-05-0269] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/27/2015] [Indexed: 12/12/2022] Open
Abstract
Epidermal growth factor receptor kinase mutations drive oncogenesis, but the molecular mechanism of pathological signal initiation is poorly understood. Using high-resolution microscopy methods, the authors reveal that these kinase mutations induce structural changes in the receptor ectodomain that lead to enhanced, ligand-independent dimerization. Mutations within the epidermal growth factor receptor (EGFR/erbB1/Her1) are often associated with tumorigenesis. In particular, a number of EGFR mutants that demonstrate ligand-independent signaling are common in non–small cell lung cancer (NSCLC), including kinase domain mutations L858R (also called L834R) and exon 19 deletions (e.g., ΔL747-P753insS), which collectively make up nearly 90% of mutations in NSCLC. The molecular mechanisms by which these mutations confer constitutive activity remain unresolved. Using multiple subdiffraction-limit imaging modalities, we reveal the altered receptor structure and interaction kinetics of NSCLC-associated EGFR mutants. We applied two-color single quantum dot tracking to quantify receptor dimerization kinetics on living cells and show that, in contrast to wild-type EGFR, mutants are capable of forming stable, ligand-independent dimers. Two-color superresolution localization microscopy confirmed ligand-independent aggregation of EGFR mutants. Live-cell Förster resonance energy transfer measurements revealed that the L858R kinase mutation alters ectodomain structure such that unliganded mutant EGFR adopts an extended, dimerization-competent conformation. Finally, mutation of the putative dimerization arm confirmed a critical role for ectodomain engagement in ligand-independent signaling. These data support a model in which dysregulated activity of NSCLC-associated kinase mutants is driven by coordinated interactions involving both the kinase and extracellular domains that lead to enhanced dimerization.
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Affiliation(s)
- Christopher C Valley
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Donna J Arndt-Jovin
- Laboratory of Cellular Dynamics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Narain Karedla
- III. Institute of Physics, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Mara P Steinkamp
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Alexey I Chizhik
- III. Institute of Physics, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - William S Hlavacek
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Bridget S Wilson
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - Diane S Lidke
- Department of Pathology and Cancer Research and Treatment Center, University of New Mexico, Albuquerque, NM 87131
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150
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Hartley JM, Chu TW, Peterson EM, Zhang R, Yang J, Harris J, Kopeček J. Super-Resolution Imaging and Quantitative Analysis of Membrane Protein/Lipid Raft Clustering Mediated by Cell-Surface Self-Assembly of Hybrid Nanoconjugates. Chembiochem 2015; 16:1725-9. [PMID: 26097072 PMCID: PMC4551445 DOI: 10.1002/cbic.201500278] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Indexed: 11/12/2022]
Abstract
Super-resolution imaging was used to quantify organizational changes in the plasma membrane after treatment with hybrid nanoconjugates. The nanoconjugates crosslinked CD20 on the surface of malignant B cells, thereby inducing apoptosis. Super-resolution images were analyzed by using pair-correlation analysis to determine cluster size and to count the average number of molecules in the clusters. The role of lipid rafts was investigated by pre-treating cells with a cholesterol chelator and actin destabilizer to prevent lipid raft formation. Lipid raft cluster size correlated with apoptosis induction after treatment with the nanoconjugates. Lipid raft clusters had radii of ∼ 200 nm in cells treated with the hybrid nanoconjugates. Super-resolution images provided precise molecule location coordinates that could be used to determine density of bound conjugates, cluster size, and number of molecules per cluster.
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Affiliation(s)
- Jonathan M Hartley
- Department of Bioengineering, University of Utah, 20 S. 2030 E., Room 108, Salt Lake City, UT 84112 (USA)
| | - Te-Wei Chu
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 30 S. 2000 E Room 301, Salt Lake City, UT 84112 (USA)
| | - Eric M Peterson
- Department of Chemistry, University of Utah, 315 S. 1400 E, Room 2020, Salt Lake City, UT 84112 (USA)
| | - Rui Zhang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 30 S. 2000 E Room 301, Salt Lake City, UT 84112 (USA)
| | - Jiyuan Yang
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 30 S. 2000 E Room 301, Salt Lake City, UT 84112 (USA)
| | - Joel Harris
- Department of Chemistry, University of Utah, 315 S. 1400 E, Room 2020, Salt Lake City, UT 84112 (USA)
| | - Jindřich Kopeček
- Department of Bioengineering, University of Utah, 20 S. 2030 E., Room 108, Salt Lake City, UT 84112 (USA).
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, 30 S. 2000 E Room 301, Salt Lake City, UT 84112 (USA).
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