1
|
Abstract
Membrane lateral heterogeneity, historically referred to as the lipid raft hypothesis, has been extensively investigated through physiochemical experiments on model membranes. Currently, the basic principles are well understood; however, the physiological relevance of these structures in living organisms is still not clear. Thus, studying membrane organization in vivo is extremely important and elucidates the role of such structures in various membrane-associated processes. This is particularly true when a whole single-celled organism can be studied rather than an isolated cell. The ordered and disordered membrane phases are characterized by the degree of acyl chain packing in the lipid bilayer. Polar water molecules can penetrate into the low-density lipid packing of the disordered phase, but are more excluded from the tightly packed ordered phase. Here, polarity-sensitive probes, embedded in the lipid bilayer, are used to report on membrane organization and to quantitate this parameter via 2-channel fluorescence microscopy. Coupling genetic approaches, which are easily accessible in yeast model organisms, with the imaging approach described here provides a great opportunity to investigate how membrane heterogeneity impacts physiology.
Collapse
Affiliation(s)
- Maria Makarova
- School of Biosciences, University of Birmingham, Birmingham, UK.
| | - Dylan M Owen
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, UK
- School of Mathematics, University of Birmingham, Birmingham, UK
| |
Collapse
|
2
|
Fan W, Tang S, Fan X, Fang Y, Xu X, Li L, Xu J, Li JL, Wang Z, Li X. SIRT1 regulates sphingolipid metabolism and neural differentiation of mouse embryonic stem cells through c-Myc-SMPDL3B. eLife 2021; 10:67452. [PMID: 34042046 PMCID: PMC8216717 DOI: 10.7554/elife.67452] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/26/2021] [Indexed: 12/16/2022] Open
Abstract
Sphingolipids are important structural components of cell membranes and prominent signaling molecules controlling cell growth, differentiation, and apoptosis. Sphingolipids are particularly abundant in the brain, and defects in sphingolipid degradation are associated with several human neurodegenerative diseases. However, molecular mechanisms governing sphingolipid metabolism remain unclear. Here, we report that sphingolipid degradation is under transcriptional control of SIRT1, a highly conserved mammalian NAD+-dependent protein deacetylase, in mouse embryonic stem cells (mESCs). Deletion of SIRT1 results in accumulation of sphingomyelin in mESCs, primarily due to reduction of SMPDL3B, a GPI-anchored plasma membrane bound sphingomyelin phosphodiesterase. Mechanistically, SIRT1 regulates transcription of Smpdl3b through c-Myc. Functionally, SIRT1 deficiency-induced accumulation of sphingomyelin increases membrane fluidity and impairs neural differentiation in vitro and in vivo. Our findings discover a key regulatory mechanism for sphingolipid homeostasis and neural differentiation, further imply that pharmacological manipulation of SIRT1-mediated sphingomyelin degradation might be beneficial for treatment of human neurological diseases. All cells in the brain start life as stem cells which are yet to have a defined role in the body. A wide range of molecules and chemical signals guide stem cells towards a neuronal fate, including a group of molecules called sphingolipids. These molecules sit in the membrane surrounding the cell and play a pivotal role in a number of processes which help keep the neuronal cell healthy. Various enzymes work together to break down sphingolipids and remove them from the membrane. Defects in these enzymes can result in excess levels of sphingolipids, which can lead to neurodegenerative diseases, such as Alzheimer’s, Parkinson’s and Huntington’s disease. But how these enzymes are used and controlled during neuronal development is still somewhat of a mystery. To help answer this question, Fan et al. studied an enzyme called SIRT1 which has been shown to alleviate symptoms in animal models of neurodegenerative diseases. Stem cells were extracted from a mouse embryo lacking the gene for SIRT1 and cultured in the laboratory. These faulty cells were found to have superfluous amounts of sphingolipids, which made their membranes more fluid and reduced their ability to develop into neuronal cells. Further investigation revealed that SIRT1 regulates the degradation of sphingolipids by promoting the production of another enzyme called SMPDL3B. Fan et al. also found that when female mice were fed a high-fat diet, this caused sphingolipids to accumulate in their embryos which lacked the gene for SIRT1; this, in turn, impaired the neural development of their offspring. These findings suggest that targeting SIRT1 may offer new strategies for treating neurological diseases. The discovery that embryos deficient in SIRT1 are sensitive to high-fat diets implies that activating this enzyme might attenuate some of the neonatal complications associated with maternal obesity.
Collapse
Affiliation(s)
- Wei Fan
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States
| | - Shuang Tang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States
| | - Xiaojuan Fan
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Yi Fang
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States
| | - Xiaojiang Xu
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States
| | - Leping Li
- Biostatistics & Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States
| | - Jian Xu
- Children's Medical Center Research Institute, Department of Pediatrics, Harold C. Simmons Comprehensive Cancer Center, and Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jian-Liang Li
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Xiaoling Li
- Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Triangle Park, United States
| |
Collapse
|
3
|
High-speed super-resolution imaging of rotationally symmetric structures using SPEED microscopy and 2D-to-3D transformation. Nat Protoc 2020; 16:532-560. [PMID: 33318694 DOI: 10.1038/s41596-020-00440-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/09/2020] [Indexed: 02/05/2023]
Abstract
Various super-resolution imaging techniques have been developed to break the diffraction-limited resolution of light microscopy. However, it still remains challenging to obtain three-dimensional (3D) super-resolution information of structures and dynamic processes in live cells at high speed. We recently developed high-speed single-point edge-excitation sub-diffraction (SPEED) microscopy and its two-dimensional (2D)-to-3D transformation algorithm to provide an effective approach to achieving 3D sub-diffraction-limit information in subcellular structures and organelles that have rotational symmetry. In contrast to most other 3D super-resolution microscopy or 3D particle-tracking microscopy approaches, SPEED microscopy does not depend on complex optical components and can be implemented onto a standard inverted epifluorescence microscope. SPEED microscopy is specifically designed to obtain 2D spatial locations of individual immobile or moving fluorescent molecules inside sub-micrometer biological channels or cavities at high spatiotemporal resolution. After data collection, post-localization 2D-to-3D transformation is applied to obtain 3D super-resolution structural and dynamic information. The complete protocol, including cell culture and sample preparation (6-7 d), SPEED imaging (4-5 h), data analysis and validation through simulation (5-13 h), takes ~9 d to complete.
Collapse
|
4
|
Membrane Dynamics in Health and Disease: Impact on Cellular Signalling. J Membr Biol 2019; 252:213-226. [PMID: 31435696 DOI: 10.1007/s00232-019-00087-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 08/07/2019] [Indexed: 12/16/2022]
Abstract
Biological membranes display a staggering complexity of lipids and proteins orchestrating cellular functions. Superior analytical tools coupled with numerous functional cellular screens have enabled us to query their role in cellular signalling, trafficking, guiding protein structure and function-all of which rely on the dynamic membrane lipid properties indispensable for proper cellular functions. Alteration of these has led to emergence of various pathological conditions, thus opening an area of lipid-centric therapeutic approaches. This perspective is a short summary of the dynamic properties of membranes essential for proper cellular functions, dictating both protein and lipid functions, and mis-regulated in diseases. Towards the end, we focus on some challenges lying ahead and potential means to tackle the same, mainly underscored by multi-disciplinary approaches.
Collapse
|
5
|
Zhang S, Reinhard BM. Characterizing Large-Scale Receptor Clustering on the Single Cell Level: A Comparative Plasmon Coupling and Fluorescence Superresolution Microscopy Study. J Phys Chem B 2019; 123:5494-5505. [PMID: 31244098 DOI: 10.1021/acs.jpcb.9b05176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Spatial clustering of cell membrane receptors has been indicated to play a regulatory role in signal initiation, and the distribution of receptors on the cell surface may represent a potential biomarker. To realize its potential for diagnostic purposes, scalable assays capable of mapping spatial receptor heterogeneity with high throughput are needed. In this work, we use gold nanoparticle (NP) labels with an average diameter of 72.17 ± 2.16 nm as bright markers for large-scale epidermal growth factor receptor (EGFR) clustering in hyperspectral plasmon coupling microscopy and compare the obtained clustering maps with those obtained through fluorescence superresolution microscopy (direct stochastic optical reconstruction microscopy, dSTORM). Our dSTORM experiments reveal average EGFR cluster sizes of 172 ± 99 and 150 ± 90 nm for MDA-MB-468 and HeLa, respectively. The cluster sizes decrease after EGFR activation. Hyperspectral imaging of the NP labels shows that differences in the EGFR cluster sizes are accompanied by differences in the average separations between electromagnetically coupled NPs. Because of the distance dependence of plasmon coupling, changes in the average interparticle separation result in significant spectral shifts. For the experimental conditions investigated in this work, hyperspectral plasmon coupling microscopy of NP labels identified the same trends in large-scale EGFR clustering as dSTORM, but the NP imaging approach provided the information in a fraction of the time. Both dSTORM and hyperspectral plasmon coupling microscopy confirm the cortical actin network as one structural component that determines the average size of EGFR clusters.
Collapse
Affiliation(s)
- Sandy Zhang
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Björn M Reinhard
- Department of Chemistry and The Photonics Center , Boston University , Boston , Massachusetts 02215 , United States
| |
Collapse
|
6
|
Heller JP, Rusakov DA. The Nanoworld of the Tripartite Synapse: Insights from Super-Resolution Microscopy. Front Cell Neurosci 2017; 11:374. [PMID: 29225567 PMCID: PMC5705901 DOI: 10.3389/fncel.2017.00374] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/10/2017] [Indexed: 12/17/2022] Open
Abstract
Synaptic connections between individual nerve cells are fundamental to the process of information transfer and storage in the brain. Over the past decades a third key partner of the synaptic machinery has been unveiled: ultrathin processes of electrically passive astroglia which often surround pre- and postsynaptic structures. The recent advent of super-resolution (SR) microscopy has begun to uncover the dynamic nanoworld of synapses and their astroglial environment. Here we overview and discuss the current progress in our understanding of the synaptic nanoenvironment, as gleaned from the imaging methods that go beyond the diffraction limit of conventional light microscopy. We argue that such methods are essential to achieve a new level of comprehension pertinent to the principles of signal integration in the brain.
Collapse
Affiliation(s)
- Janosch P Heller
- UCL Institute of Neurology, University College London, London, United Kingdom
| | - Dmitri A Rusakov
- UCL Institute of Neurology, University College London, London, United Kingdom.,Institute of Neuroscience, University of Nizhny Novgorod, Nizhny Novgorod, Russia
| |
Collapse
|
7
|
Uddin SZ, Talukder MA. Imaging of cell membrane topography using Tamm plasmon coupled emission. Biomed Phys Eng Express 2017. [DOI: 10.1088/2057-1976/aa881a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
8
|
Localisation Microscopy of Breast Epithelial ErbB-2 Receptors and Gap Junctions: Trafficking after γ-Irradiation, Neuregulin-1β, and Trastuzumab Application. Int J Mol Sci 2017; 18:ijms18020362. [PMID: 28208769 PMCID: PMC5343897 DOI: 10.3390/ijms18020362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/28/2017] [Accepted: 01/30/2017] [Indexed: 12/28/2022] Open
Abstract
In cancer, vulnerable breast epithelium malignance tendency correlates with number and activation of ErbB receptor tyrosine kinases. In the presented work, we observe ErbB receptors activated by irradiation-induced DNA injury or neuregulin-1β application, or alternatively, attenuated by a therapeutic antibody using high resolution fluorescence localization microscopy. The gap junction turnover coinciding with ErbB receptor activation and co-transport is simultaneously recorded. DNA injury caused by 4 Gray of 6 MeV photon γ-irradiation or alternatively neuregulin-1β application mobilized ErbB receptors in a nucleograde fashion—a process attenuated by trastuzumab antibody application. This was accompanied by increased receptor density, indicating packing into transport units. Factors mobilizing ErbB receptors also mobilized plasma membrane resident gap junction channels. The time course of ErbB receptor activation and gap junction mobilization recapitulates the time course of non-homologous end-joining DNA repair. We explain our findings under terms of DNA injury-induced membrane receptor tyrosine kinase activation and retrograde trafficking. In addition, we interpret the phenomenon of retrograde co-trafficking of gap junction connexons stimulated by ErbB receptor activation.
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Matamales M, Götz J, Bertran-Gonzalez J. Quantitative Imaging of Cholinergic Interneurons Reveals a Distinctive Spatial Organization and a Functional Gradient across the Mouse Striatum. PLoS One 2016; 11:e0157682. [PMID: 27314496 PMCID: PMC4912095 DOI: 10.1371/journal.pone.0157682] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/02/2016] [Indexed: 11/19/2022] Open
Abstract
Information processing in the striatum requires the postsynaptic integration of glutamatergic and dopaminergic signals, which are then relayed to the output nuclei of the basal ganglia to influence behavior. Although cellularly homogeneous in appearance, the striatum contains several rare interneuron populations which tightly modulate striatal function. Of these, cholinergic interneurons (CINs) have been recently shown to play a critical role in the control of reward-related learning; however how the striatal cholinergic network is functionally organized at the mesoscopic level and the way this organization influences striatal function remains poorly understood. Here, we systematically mapped and digitally reconstructed the entire ensemble of CINs in the mouse striatum and quantitatively assessed differences in densities, spatial arrangement and neuropil content across striatal functional territories. This approach demonstrated that the rostral portion of the striatum contained a higher concentration of CINs than the caudal striatum and that the cholinergic content in the core of the ventral striatum was significantly lower than in the rest of the regions. Additionally, statistical comparison of spatial point patterns in the striatal cholinergic ensemble revealed that only a minor portion of CINs (17%) aggregated into cluster and that they were predominantly organized in a random fashion. Furthermore, we used a fluorescence reporter to estimate the activity of over two thousand CINs in naïve mice and found that there was a decreasing gradient of CIN overall function along the dorsomedial-to-ventrolateral axis, which appeared to be independent of their propensity to aggregate within the striatum. Altogether this work suggests that the regulation of striatal function by acetylcholine across the striatum is highly heterogeneous, and that signals originating in external afferent systems may be principally determining the function of CINs in the striatum.
Collapse
Affiliation(s)
- Miriam Matamales
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (MM); (JBG)
| | - Jürgen Götz
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Jesus Bertran-Gonzalez
- Clem Jones Centre for Ageing Dementia Research, Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail: (MM); (JBG)
| |
Collapse
|
12
|
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.
Collapse
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:
| |
Collapse
|
13
|
Abu-Siniyeh A, Owen DM, Benzing C, Rinkwitz S, Becker TS, Majumdar A, Gaus K. The aPKC/Par3/Par6 Polarity Complex and Membrane Order Are Functionally Interdependent in Epithelia During Vertebrate Organogenesis. Traffic 2015; 17:66-79. [PMID: 26456025 DOI: 10.1111/tra.12339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 10/06/2015] [Accepted: 10/06/2015] [Indexed: 12/17/2022]
Abstract
The differential distribution of lipids between apical and basolateral membranes is necessary for many epithelial cell functions, but how this characteristic membrane organization is integrated within the polarity network during ductal organ development is poorly understood. Here we quantified membrane order in the gut, kidney and liver ductal epithelia in zebrafish larvae at 3-11 days post fertilization (dpf) with Laurdan 2-photon microscopy. We then applied a combination of Laurdan imaging, antisense knock-down and analysis of polarity markers to understand the relationship between membrane order and apical-basal polarity. We found a reciprocal relationship between membrane order and the cell polarity network. Reducing membrane condensation by exogenously added oxysterol or depletion of cholesterol reduced apical targeting of the polarity protein, aPKC. Conversely, using morpholino knock down in zebrafish, we found that membrane order was dependent upon the Crb3 and Par3 polarity protein expression in ductal epithelia. Hence our data suggest that the biophysical property of membrane lipid packing is a regulatory element in apical basal polarity.
Collapse
Affiliation(s)
- Ahmed Abu-Siniyeh
- School of Medical Sciences, ARC Centre for Advanced Molecular Imaging and Australian Centre for NanoMedicine, The University of New South Wales, Australia.,Present address: Department of Chemistry and Medical Analysis, Faculty of Science, Al-Balqa' Applied University, Al-Salt, 19117, Jordan
| | - Dylan M Owen
- Department of Physics and Randall Division of Cell and Molecular Biophysics, King's College London, UK
| | - Carola Benzing
- School of Medical Sciences, ARC Centre for Advanced Molecular Imaging and Australian Centre for NanoMedicine, The University of New South Wales, Australia
| | - Silke Rinkwitz
- Brain and Mind Research Institute, Sydney Medical School and Department of Health Sciences, University of Sydney, Australia
| | - Thomas S Becker
- Brain and Mind Research Institute, Sydney Medical School and Department of Health Sciences, University of Sydney, Australia
| | - Arindam Majumdar
- Department of Immunology, Genetics, and Pathology, Uppsala University, Sweden
| | - Katharina Gaus
- School of Medical Sciences, ARC Centre for Advanced Molecular Imaging and Australian Centre for NanoMedicine, The University of New South Wales, Australia
| |
Collapse
|
14
|
Ziomkiewicz I, Sporring J, Pomorski TG, Schulz A. Novel approach to measure the size of plasma-membrane nanodomains in single molecule localization microscopy. Cytometry A 2015; 87:868-77. [PMID: 26109552 DOI: 10.1002/cyto.a.22708] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 05/14/2015] [Accepted: 05/26/2015] [Indexed: 01/20/2023]
Abstract
Many membrane proteins are not evenly distributed over the plasma membrane, but gathered in domains assumed to have a particular lipid composition. Using single molecule localization microscopy (SMLM) we have immunolocalized a glycosylphosphatidylinositol (GPI)-anchor protein that labels nanodomains in a specialized plant cell type, and compared the suitability of three methods to estimate their size. As conventional methods full width at half maximum (FWHM) and the full diameter (FWMin) of domains were used. A boundary detection method of the domain area (DA) was performed in order to take irregular shapes into account. In order to compare the influence of the chosen measurement methods, we have developed a MatLab program that allows for automated analysis of domain sizes from multiple SMLM images and provides the statistics of three key features of domains: FWHM and FWMin along their long and short axes as well as the DA, derived from the molecular density. Domains formed by the GPI-anchor protein are approximating elliptical shapes. Direct and indirect immunolabeling resulted in a statistically significant difference in apparent domain size, reflecting the fact that the secondary antibody molecules extend the uncertainty along the nanodomain border. FWMin values along the long and short axis give good estimates of regular, geometrically centred domain shapes, while the DA value matches regular as well as irregular shapes best, as derived from computer-generated, irregular point clusters.
Collapse
Affiliation(s)
- Iwona Ziomkiewicz
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| | - Jon Sporring
- Department of Computer Science, University of Copenhagen, Denmark
| | | | - Alexander Schulz
- Department of Plant and Environmental Sciences, University of Copenhagen, Denmark
| |
Collapse
|
15
|
Healey EG, Bishop B, Elegheert J, Bell CH, Padilla-Parra S, Siebold C. Repulsive guidance molecule is a structural bridge between neogenin and bone morphogenetic protein. Nat Struct Mol Biol 2015; 22:458-65. [PMID: 25938661 PMCID: PMC4456160 DOI: 10.1038/nsmb.3016] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/31/2015] [Indexed: 02/07/2023]
Abstract
Repulsive guidance molecules (RGMs) control crucial processes including cell motility, adhesion, immune-cell regulation and systemic iron metabolism. RGMs signal via the neogenin (NEO1) and the bone morphogenetic protein (BMP) pathways. Here, we report crystal structures of the N-terminal domains of all human RGM family members in complex with the BMP ligand BMP2, revealing a new protein fold and a conserved BMP-binding mode. Our structural and functional data suggest a pH-linked mechanism for RGM-activated BMP signaling and offer a rationale for RGM mutations causing juvenile hemochromatosis. We also determined the crystal structure of the ternary BMP2-RGM-NEO1 complex, which, along with solution scattering and live-cell super-resolution fluorescence microscopy, indicates BMP-induced clustering of the RGM-NEO1 complex. Our results show how RGM acts as the central hub that links BMP and NEO1 and physically connects these fundamental signaling pathways.
Collapse
Affiliation(s)
- Eleanor G Healey
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benjamin Bishop
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jonathan Elegheert
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian H Bell
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sergi Padilla-Parra
- 1] Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. [2] Cellular Imaging Core, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christian Siebold
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| |
Collapse
|
16
|
Paladino S, Lebreton S, Zurzolo C. Trafficking and Membrane Organization of GPI-Anchored Proteins in Health and Diseases. CURRENT TOPICS IN MEMBRANES 2015; 75:269-303. [PMID: 26015286 DOI: 10.1016/bs.ctm.2015.03.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Glycosylphosphatidylinositol (GPI)-anchored proteins (GPI-APs) are a class of lipid-anchored proteins attached to the membranes by a glycolipid anchor that is added, as posttranslation modification, in the endoplasmic reticulum. GPI-APs are expressed at the cell surface of eukaryotes where they play diverse vital functions. Like all plasma membrane proteins, GPI-APs must be correctly sorted along the different steps of the secretory pathway to their final destination. The presence of both a glycolipid anchor and a protein portion confers special trafficking features to GPI-APs. Here, we discuss the recent advances in the field of GPI-AP trafficking, focusing on the mechanisms regulating their biosynthetic pathway and plasma membrane organization. We also discuss how alterations of these mechanisms can result in different diseases. Finally, we will examine the strict relationship between the trafficking and function of GPI-APs in epithelial cells.
Collapse
Affiliation(s)
- Simona Paladino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy; CEINGE Biotecnologie Avanzate, Napoli, Italy
| | - Stéphanie Lebreton
- Unité de Trafic Membranaire et Pathogénèse, Institut Pasteur, Paris, France
| | - Chiara Zurzolo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università Federico II, Napoli, Italy; Unité de Trafic Membranaire et Pathogénèse, Institut Pasteur, Paris, France
| |
Collapse
|
17
|
Gerbeau-Pissot P, Der C, Thomas D, Anca IA, Grosjean K, Roche Y, Perrier-Cornet JM, Mongrand S, Simon-Plas F. Modification of plasma membrane organization in tobacco cells elicited by cryptogein. PLANT PHYSIOLOGY 2014; 164:273-86. [PMID: 24235133 PMCID: PMC3875808 DOI: 10.1104/pp.113.225755] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 11/05/2013] [Indexed: 05/07/2023]
Abstract
Lipid mixtures within artificial membranes undergo a separation into liquid-disordered and liquid-ordered phases. However, the existence of this segregation into microscopic liquid-ordered phases has been difficult to prove in living cells, and the precise organization of the plasma membrane into such phases has not been elucidated in plant cells. We developed a multispectral confocal microscopy approach to generate ratiometric images of the plasma membrane surface of Bright Yellow 2 tobacco (Nicotiana tabacum) suspension cells labeled with an environment sensitive fluorescent probe. This allowed the in vivo characterization of the global level of order of this membrane, by which we could demonstrate that an increase in its proportion of ordered phases transiently occurred in the early steps of the signaling triggered by cryptogein and flagellin, two elicitors of plant defense reactions. The use of fluorescence recovery after photobleaching revealed an increase in plasma membrane fluidity induced by cryptogein, but not by flagellin. Moreover, we characterized the spatial distribution of liquid-ordered phases on the membrane of living plant cells and monitored their variations induced by cryptogein elicitation. We analyze these results in the context of plant defense signaling, discuss their meaning within the framework of the "membrane raft" hypothesis, and propose a new mechanism of signaling platform formation in response to elicitor treatment.
Collapse
Affiliation(s)
| | - Christophe Der
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| | - Dominique Thomas
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| | - Iulia-Andra Anca
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| | - Kevin Grosjean
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| | - Yann Roche
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| | - Jean-Marie Perrier-Cornet
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| | - Sébastien Mongrand
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| | - Françoise Simon-Plas
- Université de Bourgogne (P.G.-P., C.D., D.T., K.G.), and Institut National de la Recherche Agronomique (I.-A.A., Y.R., F.S.-P.), Unité Mixte de Recherche 1347 Agroécologie, Equipe de Recherche Labelisée 6300 Centre National de la Recherche Scientifique, BP 86510, F–21000 Dijon, France
- AgroSup Dijon, Laboratoire Procédés Alimentaires et Microbiologiques, F–21000 Dijon, France (J.-M.P.-C.); and
- Centre National de la Recherche Scientifique, Laboratoire de Biogenèse Membranaire, Unité Mixte de Recherche 5200, Université Victor Segalen, Institut National de la Recherche Agronomique Bordeaux Aquitaine, BP 81, F–33883 Villenave d’Ornon, France (S.M.)
| |
Collapse
|
18
|
Pageon SV, Cordoba SP, Owen DM, Rothery SM, Oszmiana A, Davis DM. Superresolution microscopy reveals nanometer-scale reorganization of inhibitory natural killer cell receptors upon activation of NKG2D. Sci Signal 2013; 6:ra62. [PMID: 23882121 DOI: 10.1126/scisignal.2003947] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Natural killer (NK) cell responses are regulated by a dynamic equilibrium between activating and inhibitory receptor signals at the immune synapse (or interface) with target cells. Although the organization of receptors at the immune synapse is important for appropriate integration of these signals, there is little understanding of this in detail, because research has been hampered by the limited resolution of light microscopy. Through the use of superresolution single-molecule fluorescence microscopy to reveal the organization of the NK cell surface at the single-protein level, we report that the inhibitory receptor KIR2DL1 is organized in nanometer-scale clusters at the surface of human resting NK cells. Nanoclusters of KIR2DL1 became smaller and denser upon engagement of the activating receptor NKG2D, establishing an unexpected crosstalk between activating receptor signals and the positioning of inhibitory receptors. These rearrangements in the nanoscale organization of surface NK cell receptors were dependent on the actin cytoskeleton. Together, these data establish that NK cell activation involves a nanometer-scale reorganization of surface receptors, which in turn affects models for signal integration and thresholds that control NK cell effector functions and NK cell development.
Collapse
Affiliation(s)
- Sophie V Pageon
- Division of Cell and Molecular Biology, Sir Alexander Fleming Building, Imperial College London, London SW7 2AZ, UK
| | | | | | | | | | | |
Collapse
|