51
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Blom H, Bernhem K, Brismar H. Sodium pump organization in dendritic spines. NEUROPHOTONICS 2016; 3:041803. [PMID: 27175374 PMCID: PMC4855081 DOI: 10.1117/1.nph.3.4.041803] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 04/04/2016] [Indexed: 05/16/2023]
Affiliation(s)
- Hans Blom
- Royal Institute of Technology, Department of Applied Physics, Roslagstullsbacken 21, Stockholm 10691, SwedenbScience for Life Laboratory, Advanced Light Microscopy Facility, Tomtebodavägen 23A, Solna 17165, Sweden
| | - Kristoffer Bernhem
- Royal Institute of Technology, Department of Applied Physics, Roslagstullsbacken 21, Stockholm 10691, Sweden
| | - Hjalmar Brismar
- Royal Institute of Technology, Department of Applied Physics, Roslagstullsbacken 21, Stockholm 10691, SwedenbScience for Life Laboratory, Advanced Light Microscopy Facility, Tomtebodavägen 23A, Solna 17165, SwedencKarolinska Institutet, Department of Wome
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52
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Coumans JVF, Palanisamy SKA, McFarlane J, Moens PDJ. Proteomic and Microscopic Strategies towards the Analysis of the Cytoskeletal Networks in Major Neuropsychiatric Disorders. Int J Mol Sci 2016; 17:E581. [PMID: 27104521 PMCID: PMC4849037 DOI: 10.3390/ijms17040581] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 04/06/2016] [Accepted: 04/08/2016] [Indexed: 11/17/2022] Open
Abstract
Mental health disorders have become worldwide health priorities. It is estimated that in the next 20 years they will account for a 16 trillion United State dollars (US$) loss. Up to now, the underlying pathophysiology of psychiatric disorders remains elusive. Altered cytoskeleton proteins expression that may influence the assembly, organization and maintenance of cytoskeletal integrity has been reported in major depressive disorders, schizophrenia and to some extent bipolar disorders. The use of quantitative proteomics, dynamic microscopy and super-resolution microscopy to investigate disease-specific protein signatures holds great promise to improve our understanding of these disorders. In this review, we present the currently available quantitative proteomic approaches use in neurology, gel-based, stable isotope-labelling and label-free methodologies and evaluate their strengths and limitations. We also reported on enrichment/subfractionation methods that target the cytoskeleton associated proteins and discuss the need of alternative methods for further characterization of the neurocytoskeletal proteome. Finally, we present live cell imaging approaches and emerging dynamic microscopy technology that will provide the tools necessary to investigate protein interactions and their dynamics in the whole cells. While these areas of research are still in their infancy, they offer huge potential towards the understanding of the neuronal network stability and its modification across neuropsychiatric disorders.
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Affiliation(s)
- Joëlle V F Coumans
- School of Rural Medicine, University of New England, Armidale, NSW 2351, Australia.
| | - Suresh K A Palanisamy
- Center for Bioactive Discovery in Health and Aging, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
| | - Jim McFarlane
- Center for Bioactive Discovery in Health and Aging, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
| | - Pierre D J Moens
- Center for Bioactive Discovery in Health and Aging, School of Science and Technology, University of New England, Armidale, NSW 2351, Australia.
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53
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Granuphilin exclusively mediates functional granule docking to the plasma membrane. Sci Rep 2016; 6:23909. [PMID: 27032672 PMCID: PMC4817151 DOI: 10.1038/srep23909] [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: 11/10/2015] [Accepted: 03/16/2016] [Indexed: 11/08/2022] Open
Abstract
In regulated exocytosis, it is generally assumed that vesicles must stably “dock” at the plasma membrane before they are primed to become fusion-competent. However, recent biophysical analyses in living cells that visualize fluorescent secretory granules have revealed that exocytic behaviors are not necessarily uniform: some granules beneath the plasma membrane are resistant to Ca2+ -triggered release, while others are accelerated to fuse without a pause for stable docking. These findings suggest that stable docking is unnecessary, and can even be inhibitory or nonfunctional, for fusion. Consistently, pancreatic β cells deficient in the Rab27 effector, granuphilin, lack insulin granules directly attached to the plasma membrane in electron micrographs but nevertheless exhibit augmented exocytosis. Here we directly compare the exocytic behaviors between granuphilin-positive and -negative insulin granules. Although granuphilin makes granules immobile and fusion-reluctant beneath the plasma membrane, those granuphilin-positive, docked granules release a portion of granuphilin upon fusion, and fuse at a frequency and time course similar to those of granuphilin-negative undocked granules. Furthermore, granuphilin forms a 180-nm cluster at the site of each docked granule, along with granuphilin-interacting Rab27a and Munc18-1 clusters. These findings indicate that granuphilin is an exclusive component of the functional and fusion-inhibitory docking machinery of secretory granules.
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Abstract
Extensive research has yielded crucial insights into the mechanism of neurotransmitter release, and working models for the functions of key proteins involved in release. The SNAREs Syntaxin-1, Synaptobrevin, and SNAP-25 play a central role in membrane fusion, forming SNARE complexes that bridge the vesicle and plasma membranes and that are disassembled by NSF-SNAPs. Exocytosis likely starts with Syntaxin-1 folded into a self-inhibited closed conformation that binds to Munc18-1. Munc13s open Syntaxin-1, orchestrating SNARE complex assembly in an NSF-SNAP-resistant manner together with Munc18-1. In the resulting primed state, with partially assembled SNARE complexes, fusion is inhibited by Synaptotagmin-1 and Complexins, which also perform active functions in release. Upon influx of Ca(2+), Synaptotagmin-1 activates fast release, likely by relieving the inhibition caused by Complexins and cooperating with the SNAREs in bringing the membranes together. Although alternative models exist and fundamental questions remain unanswered, a definitive description of the basic release mechanism may be available soon.
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Affiliation(s)
- Josep Rizo
- Departments of Biophysics, Biochemistry, and Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas 75390;
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55
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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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56
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Ma L, Rebane AA, Yang G, Xi Z, Kang Y, Gao Y, Zhang Y. Munc18-1-regulated stage-wise SNARE assembly underlying synaptic exocytosis. eLife 2015; 4. [PMID: 26701912 PMCID: PMC4744192 DOI: 10.7554/elife.09580] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 12/22/2015] [Indexed: 12/20/2022] Open
Abstract
Synaptic-soluble N-ethylmaleimide-sensitive factor attachment receptor (SNARE) proteins couple their stage-wise folding/assembly to rapid exocytosis of neurotransmitters in a Munc18-1-dependent manner. The functions of the different assembly stages in exocytosis and the role of Munc18-1 in SNARE assembly are not well understood. Using optical tweezers, we observed four distinct stages of assembly in SNARE N-terminal, middle, C-terminal, and linker domains (or NTD, MD, CTD, and LD, respectively). We found that SNARE layer mutations differentially affect SNARE assembly. Comparison of their effects on SNARE assembly and on exocytosis reveals that NTD and CTD are responsible for vesicle docking and fusion, respectively, whereas MD regulates SNARE assembly and fusion. Munc18-1 initiates SNARE assembly and structures t-SNARE C-terminus independent of syntaxin N-terminal regulatory domain (NRD) and stabilizes the half-zippered SNARE complex dependent upon the NRD. Our observations demonstrate distinct functions of SNARE domains whose assembly is intimately chaperoned by Munc18-1. DOI:http://dx.doi.org/10.7554/eLife.09580.001 Plants, animals and other eukaryotes transport many large molecules within their cells inside membrane-bound packages called vesicles. These vesicles can fuse with the membrane of a target compartment in the cell to deliver their contents inside, or fuse with the cell’s membrane to release the contents outside of the cell. Membrane fusion is carried out by a group of proteins called SNAREs. These proteins are embedded on the membranes of both the vesicle and its target, and they bind to each other to form a tight complex. This complex docks the vesicle to the target and then acts like a “zipper” to pull the two membranes close enough to fuse. The best-studied SNARE proteins act in nerve cells and fuse vesicles to the cell’s membrane in order to release molecules called neurotransmitters. This process is essential for communication between nerve cells, and relies on a protein called Munc18-1. However, it is not well understood how SNARE proteins assemble into the complex and how Munc18-1 regulates this process. Ma et al. have now used a tool called “optical tweezers” to pull an assembled SNARE complex apart in the laboratory and then observe how it folds and assembles in a step-by-step process. These experiments showed that the complex assembled in four stages and not three as has been reported in previous work. SNARE proteins are made up of four parts called domains, and Ma et al. observed that the N-terminal domains were the first to bind to each other. Next, the binding progressed to the middle domain, then to the C-terminal domain and finally to the linker domain. An intermediate, half-zippered form was also observed. Ma et al. next analysed each domain in more detail and found that the N-terminal and C-terminal domains drive the docking of vesicles to the target membrane, the middle domain is crucial for assembling the SNARE complex correctly, and all three domains regulate the fusing of the membranes. Further experiments showed that Munc18-1 promoted the assembly of new SNARE complexes and stabilized the half-zippered form, rather than stabilizing the complex after it had fully assembled. This study will provide a new tool to examine many other proteins that regulate SNARE assembly, and a basis to understand the role of SNARE proteins in brain activity. DOI:http://dx.doi.org/10.7554/eLife.09580.002
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Affiliation(s)
- Lu Ma
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
| | - Aleksander A Rebane
- Department of Cell Biology, Yale School of Medicine, New Haven, United States.,Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, United States.,Department of Physics, Yale University, New Haven, United States
| | - Guangcan Yang
- Department of Cell Biology, Yale School of Medicine, New Haven, United States.,Department of Physics, Wenzhou University, Wenzhou, China
| | - Zhiqun Xi
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
| | - Yuhao Kang
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
| | - Ying Gao
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
| | - Yongli Zhang
- Department of Cell Biology, Yale School of Medicine, New Haven, United States
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57
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Quantification of protein copy number in single mitochondria: The Bcl-2 family proteins. Biosens Bioelectron 2015; 74:476-82. [DOI: 10.1016/j.bios.2015.06.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 01/06/2023]
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58
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Destainville N, Schmidt TH, Lang T. Where Biology Meets Physics--A Converging View on Membrane Microdomain Dynamics. CURRENT TOPICS IN MEMBRANES 2015; 77:27-65. [PMID: 26781829 DOI: 10.1016/bs.ctm.2015.10.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
For several decades, the phenomenon of membrane component segregation into microdomains has been a well-known and highly debated subject, and varying concepts including the raft hypothesis, the fence-and-picket model, hydrophobic-mismatch, and specific protein-protein interactions have been offered as explanations. Here, we review the level of insight into the molecular architecture of membrane domains one is capable of obtaining through biological experimentation. Using SNARE proteins as a paradigm, comprehensive data suggest that several dozens of molecules crowd together into almost circular spots smaller than 100 nm. Such clusters are highly dynamical as they constantly capture and lose molecules. The organization has a strong influence on the functional availability of proteins and likely provides a molecular scaffold for more complex protein networks. Despite this high level of insight, fundamental open questions remain, applying not only to SNARE protein domains but more generally to all types of membrane domains. In this context, we explain the view of physical models and how they are beneficial in advancing our concept of micropatterning. While biological models generally remain qualitative and descriptive, physics aims towards making them quantitative and providing reproducible numbers, in order to discriminate between different mechanisms which have been proposed to account for experimental observations. Despite the fundamental differences in biological and physical approaches as far as cell membrane microdomains are concerned, we are able to show that convergence on common points of views is in reach.
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Affiliation(s)
- Nicolas Destainville
- Laboratoire de Physique Theorique (IRSAMC), Universite Toulouse 3-Paul Sabatier, UPS/CNRS, Toulouse, France
| | - Thomas H Schmidt
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Thorsten Lang
- Department of Membrane Biochemistry, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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59
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von Diezmann A, Lee MY, Lew MD, Moerner WE. Correcting field-dependent aberrations with nanoscale accuracy in three-dimensional single-molecule localization microscopy. OPTICA 2015; 2:985-993. [PMID: 26973863 PMCID: PMC4782984 DOI: 10.1364/optica.2.000985] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The localization of single fluorescent molecules enables the imaging of molecular structure and dynamics with subdiffraction precision and can be extended to three dimensions using point spread function (PSF) engineering. However, the nanoscale accuracy of localization throughout a 3D single-molecule microscope's field of view has not yet been rigorously examined. By using regularly spaced subdiffraction apertures filled with fluorescent dyes, we reveal field-dependent aberrations as large as 50-100 nm and show that they can be corrected to less than 25 nm over an extended 3D focal volume. We demonstrate the applicability of this technique for two engineered PSFs, the double-helix PSF and the astigmatic PSF. We expect these results to be broadly applicable to 3D single-molecule tracking and superresolution methods demanding high accuracy.
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Affiliation(s)
- Alex von Diezmann
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Maurice Y. Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Biophysics Program, Stanford University, Stanford, California 94305, USA
| | - Matthew D. Lew
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
- Corresponding author:
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60
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Mazouchi A, Milstein JN. Fast Optimized Cluster Algorithm for Localizations (FOCAL): a spatial cluster analysis for super-resolved microscopy. Bioinformatics 2015; 32:747-54. [PMID: 26543172 DOI: 10.1093/bioinformatics/btv630] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/24/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Single-molecule localization microscopy (SMLM) microscopy provides images of cellular structure at a resolution an order of magnitude below what can be achieved by conventional diffraction limited techniques. The concomitantly larger data sets generated by SMLM require increasingly efficient image analysis software. Density based clustering algorithms, with the most ubiquitous being DBSCAN, are commonly used to quantitatively assess sub-cellular assemblies. DBSCAN, however, is slow, scaling with the number of localizations like O(n log (n)) at best, and it's performance is highly dependent upon a subjectively selected choice of parameters. RESULTS We have developed a grid-based clustering algorithm FOCAL, which explicitly accounts for several dominant artifacts arising in SMLM image reconstructions. FOCAL is fast and efficient, scaling like O(n), and only has one set parameter. We assess DBSCAN and FOCAL on experimental dSTORM data of clusters of eukaryotic RNAP II and PALM data of the bacterial protein H-NS, then provide a detailed comparison via simulation. FOCAL performs comparable and often superior to DBSCAN while yielding a significantly faster analysis. Additionally, FOCAL provides a novel method for filtering out of focus clusters from complex SMLM images. AVAILABILITY AND IMPLEMENTATION The data and code are available at: http://www.utm.utoronto.ca/milsteinlab/resources/Software/FOCAL/ CONTACT: josh.milstein@utoronto.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- A Mazouchi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada
| | - J N Milstein
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON L5L 1C6, Canada Department of Physics, University of Toronto, Toronto, ON M5S 1A7, Canada
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61
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Liu B, Xue Y, Zhao W, Chen Y, Fan C, Gu L, Zhang Y, Zhang X, Sun L, Huang X, Ding W, Sun F, Ji W, Xu T. Three-dimensional super-resolution protein localization correlated with vitrified cellular context. Sci Rep 2015; 5:13017. [PMID: 26462878 PMCID: PMC4604464 DOI: 10.1038/srep13017] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/14/2015] [Indexed: 11/17/2022] Open
Abstract
We demonstrate the use of cryogenic super-resolution correlative light and electron microscopy (csCLEM) to precisely determine the spatial relationship between proteins and their native cellular structures. Several fluorescent proteins (FPs) were found to be photoswitchable and emitted far more photons under our cryogenic imaging condition, resulting in higher localization precision which is comparable to ambient super-resolution imaging. Vitrified specimens were prepared by high pressure freezing and cryo-sectioning to maintain a near-native state with better fluorescence preservation. A 2-3-fold improvement of resolution over the recent reports was achieved due to the photon budget performance of screening out Dronpa and optimized imaging conditions, even with thin sections which is at a disadvantage when calculate the structure resolution from label density. We extended csCLEM to mammalian cells by introducing cryo-sectioning and observed good correlation of a mitochondrial protein with the mitochondrial outer membrane at nanometer resolution in three dimensions.
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Affiliation(s)
- Bei Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yanhong Xue
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Zhao
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Chen
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunyan Fan
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Lusheng Gu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Yongdeng Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Xiang Zhang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xiaojun Huang
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Ding
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fei Sun
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Ji
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tao Xu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China.,College of Life Sciences, University of the Chinese Academy of Sciences, Beijing, 100049, China.,Center for Biological Imaging, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
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62
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Ji C, Zhang Y, Xu P, Xu T, Lou X. Nanoscale Landscape of Phosphoinositides Revealed by Specific Pleckstrin Homology (PH) Domains Using Single-molecule Superresolution Imaging in the Plasma Membrane. J Biol Chem 2015; 290:26978-26993. [PMID: 26396197 DOI: 10.1074/jbc.m115.663013] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Indexed: 11/06/2022] Open
Abstract
Both phosphatidylinositol 4-phosphate (PI4P) and phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) are independent plasma membrane (PM) determinant lipids that are essential for multiple cellular functions. However, their nanoscale spatial organization in the PM remains elusive. Using single-molecule superresolution microscopy and new photoactivatable fluorescence probes on the basis of pleckstrin homology domains that specifically recognize phosphatidylinositides in insulin-secreting INS-1 cells, we report that the PI(4,5)P2 probes exhibited a remarkably uniform distribution in the major regions of the PM, with some sparse PI(4,5)P2-enriched membrane patches/domains of diverse sizes (383 ± 14 nm on average). Quantitative analysis revealed a modest concentration gradient that was much less steep than previously thought, and no densely packed PI(4,5)P2 nanodomains were observed. Live-cell superresolution imaging further demonstrated the dynamic structural changes of those domains in the flat PM and membrane protrusions. PI4P and phosphatidylinositol (3,4,5)-trisphosphate (PI(3,4,5)P3) showed similar spatial distributions as PI(4,5)P2. These data reveal the nanoscale landscape of key inositol phospholipids in the native PM and imply a framework for local cellular signaling and lipid-protein interactions at a nanometer scale.
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Affiliation(s)
- Chen Ji
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705 and
| | - Yongdeng Zhang
- the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Pingyong Xu
- the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Xu
- the National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuelin Lou
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705 and.
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63
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Ullrich A, Böhme MA, Schöneberg J, Depner H, Sigrist SJ, Noé F. Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone. PLoS Comput Biol 2015; 11:e1004407. [PMID: 26367029 PMCID: PMC4569342 DOI: 10.1371/journal.pcbi.1004407] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 06/15/2015] [Indexed: 01/10/2023] Open
Abstract
Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle (v-SNARE) and plasma membrane (t-SNARE), one of which is Syntaxin-1A. Although exocytosis mainly occurs at active zones, Syntaxin-1A appears to cover the entire neuronal membrane. By using STED super-resolution light microscopy and image analysis of Drosophila neuro-muscular junctions, we show that Syntaxin-1A clusters are more abundant and have an increased size at active zones. A computational particle-based model of syntaxin cluster formation and dynamics is developed. The model is parametrized to reproduce Syntaxin cluster-size distributions found by STED analysis, and successfully reproduces existing FRAP results. The model shows that the neuronal membrane is adjusted in a way to strike a balance between having most syntaxins stored in large clusters, while still keeping a mobile fraction of syntaxins free or in small clusters that can efficiently search the membrane or be traded between clusters. This balance is subtle and can be shifted toward almost no clustering and almost complete clustering by modifying the syntaxin interaction energy on the order of only 1 kBT. This capability appears to be exploited at active zones. The larger active-zone syntaxin clusters are more stable and provide regions of high docking and fusion capability, whereas the smaller clusters outside may serve as flexible reserve pool or sites of spontaneous ectopic release.
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Affiliation(s)
- Alexander Ullrich
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
| | - Mathias A. Böhme
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | | | - Harald Depner
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
| | - Stephan J. Sigrist
- Institute for Biology/Genetics, Freie Universität Berlin, Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Berlin, Berlin, Germany
| | - Frank Noé
- Department of Mathematics, Freie Universität Berlin, Berlin, Germany
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64
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Zhu Q, Yamakuchi M, Lowenstein CJ. SNAP23 Regulates Endothelial Exocytosis of von Willebrand Factor. PLoS One 2015; 10:e0118737. [PMID: 26266817 PMCID: PMC4534191 DOI: 10.1371/journal.pone.0118737] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 07/22/2015] [Indexed: 11/18/2022] Open
Abstract
Endothelial exocytosis regulates vascular thrombosis and inflammation. The trafficking and release of endothelial vesicles is mediated by SNARE (Soluble NSF Attachment protein REceptors) molecules, but the exact identity of endothelial SNAREs has been unclear. Three SNARE molecules form a ternary complex, including isoforms of the syntaxin (STX), vesicle-associated membrane protein (VAMP), and synaptosomal-associated protein (SNAP) families. We now identify SNAP23 as the predominant endothelial SNAP isoform that mediates endothelial exocytosis of von Willebrand Factor (VWF). SNAP23 was localized to the plasma membrane. Knockdown of SNAP23 decreased endothelial exocytosis, suggesting it is important for endothelial exocytosis. SNAP23 interacted with the endothelial exocytic machinery, and formed complexes with other known endothelial SNARE molecules. Taken together, these data suggest that SNAP23 is a key component of the endothelial SNARE machinery that mediates endothelial exocytosis.
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Affiliation(s)
- Qiuyu Zhu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Munekazu Yamakuchi
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
| | - Charles J. Lowenstein
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
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65
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Accounting for limited detection efficiency and localization precision in cluster analysis in single molecule localization microscopy. PLoS One 2015; 10:e0118767. [PMID: 25794150 PMCID: PMC4368834 DOI: 10.1371/journal.pone.0118767] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Accepted: 01/14/2015] [Indexed: 11/20/2022] Open
Abstract
Single Molecule Localization Microscopy techniques like PhotoActivated Localization Microscopy, with their sub-diffraction limit spatial resolution, have been popularly used to characterize the spatial organization of membrane proteins, by means of quantitative cluster analysis. However, such quantitative studies remain challenged by the techniques’ inherent sources of errors such as a limited detection efficiency of less than 60%, due to incomplete photo-conversion, and a limited localization precision in the range of 10 – 30nm, varying across the detected molecules, mainly depending on the number of photons collected from each. We provide analytical methods to estimate the effect of these errors in cluster analysis and to correct for them. These methods, based on the Ripley’s L(r) – r or Pair Correlation Function popularly used by the community, can facilitate potentially breakthrough results in quantitative biology by providing a more accurate and precise quantification of protein spatial organization.
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66
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Zhong H. Applying superresolution localization-based microscopy to neurons. Synapse 2015; 69:283-94. [PMID: 25648102 DOI: 10.1002/syn.21806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 01/19/2015] [Accepted: 01/26/2015] [Indexed: 01/15/2023]
Abstract
Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue.
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Affiliation(s)
- Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, Oregon, 97239; Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, 20147
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67
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Zhang Y, Diao J, Colbert KN, Lai Y, Pfuetzner RA, Padolina MS, Vivona S, Ressl S, Cipriano DJ, Choi UB, Shah N, Weis WI, Brunger AT. Munc18a does not alter fusion rates mediated by neuronal SNAREs, synaptotagmin, and complexin. J Biol Chem 2015; 290:10518-34. [PMID: 25716318 PMCID: PMC4400359 DOI: 10.1074/jbc.m114.630772] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Indexed: 01/25/2023] Open
Abstract
Sec1/Munc18 (SM) proteins are essential for membrane trafficking, but their molecular mechanism remains unclear. Using a single vesicle-vesicle content-mixing assay with reconstituted neuronal SNAREs, synaptotagmin-1, and complexin-1, we show that the neuronal SM protein Munc18a/nSec1 has no effect on the intrinsic kinetics of both spontaneous fusion and Ca2+-triggered fusion between vesicles that mimic synaptic vesicles and the plasma membrane. However, wild type Munc18a reduced vesicle association ∼50% when the vesicles bearing the t-SNAREs syntaxin-1A and SNAP-25 were preincubated with Munc18 for 30 min. Single molecule experiments with labeled SNAP-25 indicate that the reduction of vesicle association is a consequence of sequestration of syntaxin-1A by Munc18a and subsequent release of SNAP-25 (i.e. Munc18a captures syntaxin-1A via its high affinity interaction). Moreover, a phosphorylation mimic mutant of Munc18a with reduced affinity to syntaxin-1A results in less reduction of vesicle association. In summary, Munc18a does not directly affect fusion, although it has an effect on the t-SNARE complex, depending on the presence of other factors and experimental conditions. Our results suggest that Munc18a primarily acts at the prefusion stage.
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Affiliation(s)
- Yunxiang Zhang
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and
| | - Jiajie Diao
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Karen N Colbert
- From the Departments of Molecular and Cellular Physiology, Structural Biology, and
| | - Ying Lai
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and
| | - Richard A Pfuetzner
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Mark S Padolina
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Sandro Vivona
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and
| | - Susanne Ressl
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and
| | - Daniel J Cipriano
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | - Ucheor B Choi
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
| | | | - William I Weis
- From the Departments of Molecular and Cellular Physiology, Structural Biology, and Photon Science and
| | - Axel T Brunger
- From the Departments of Molecular and Cellular Physiology, Neurology and Neurological Sciences, Structural Biology, and Photon Science and the Howard Hughes Medical Institute, Stanford University, Stanford, California 94305
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68
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Wang Y, Cai E, Rosenkranz T, Ge P, Teng KW, Lim SJ, Smith AM, Chung HJ, Sachs F, Green WN, Gottlieb P, Selvin PR. Small quantum dots conjugated to nanobodies as immunofluorescence probes for nanometric microscopy. Bioconjug Chem 2014; 25:2205-11. [PMID: 25397889 PMCID: PMC4275168 DOI: 10.1021/bc5004179] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Immunofluorescence,
a powerful technique to detect specific targets
using fluorescently labeled antibodies, has been widely used in both
scientific research and clinical diagnostics. The probes should be
made with small antibodies and high brightness. We conjugated GFP
binding protein (GBP) nanobodies, small single-chain antibodies from
llamas, with new ∼7 nm quantum dots. These provide simple and
versatile immunofluorescence nanoprobes with nanometer accuracy and
resolution. Using the new probes we tracked the walking of individual
kinesin motors and measured their 8 nm step sizes; we tracked Piezo1
channels, which are eukaryotic mechanosensitive channels; we also
tracked AMPA receptors on living neurons. Finally, we used a new super-resolution
algorithm based on blinking of (small) quantum dots that allowed ∼2
nm precision.
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Affiliation(s)
- Yong Wang
- Department of Physics, ‡Center for the Physics of Living Cells, and §Center for Biophysics and Computational Biology, ∥Department of Bioengineering, and ⊥Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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69
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Weisenburger S, Jing B, Hänni D, Reymond L, Schuler B, Renn A, Sandoghdar V. Cryogenic colocalization microscopy for nanometer-distance measurements. Chemphyschem 2014; 15:763-70. [PMID: 24677759 DOI: 10.1002/cphc.201301080] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 01/18/2014] [Indexed: 01/13/2023]
Abstract
The main limiting factor in spatial resolution of localization microscopy is the number of detected photons. Recently we showed that cryogenic measurements improve the photostability of fluorophores, giving access to Angstrom precision in localization of single molecules. Here, we extend this method to colocalize two fluorophores attached to well-defined positions of a double-stranded DNA. By measuring the separations of the fluorophore pairs prepared at different design positions, we verify the feasibility of cryogenic distance measurement with sub-nanometer accuracy. We discuss the important challenges of our method as well as its potential for further improvement and various applications.
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70
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Martin TFJ. PI(4,5)P₂-binding effector proteins for vesicle exocytosis. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1851:785-93. [PMID: 25280637 DOI: 10.1016/j.bbalip.2014.09.017] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/20/2014] [Accepted: 09/23/2014] [Indexed: 12/27/2022]
Abstract
PI(4,5)P₂participates directly in priming and possibly in fusion steps of Ca²⁺-triggered vesicle exocytosis. High concentration nanodomains of PI(4,5)P₂reside on the plasma membrane of neuroendocrine cells. A subset of vesicles that co-localize with PI(4,5)P₂ domains appear to undergo preferential exocytosis in stimulated cells. PI(4,5)P₂directly regulates vesicle exocytosis by recruiting and activating PI(4,5)P₂-binding proteins that regulate SNARE protein function including CAPS, Munc13-1/2, synaptotagmin-1, and other C2 domain-containing proteins. These PI(4,5)P₂effector proteins are coincidence detectors that engage in multiple interactions at vesicle exocytic sites. The SNARE protein syntaxin-1 also binds to PI(4,5)P₂, which promotes clustering, but an activating role for PI(4,5)P₂in syntaxin-1 function remains to be fully characterized. Similar principles underlie polarized constitutive vesicle fusion mediated in part by the PI(4,5)P₂-binding subunits of the exocyst complex (Sec3, Exo70). Overall, focal vesicle exocytosis occurs at sites landmarked by PI(4,5)P2, which serves to recruit and/or activate multifunctional PI(4,5)P₂-binding proteins. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- Thomas F J Martin
- Biochemistry Department, University of Wisconsin, 433 Babcock Drive, Madison, WI 53706, USA.
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71
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Mivelle M, van Zanten TS, Garcia-Parajo MF. Hybrid photonic antennas for subnanometer multicolor localization and nanoimaging of single molecules. NANO LETTERS 2014; 14:4895-4900. [PMID: 25050445 DOI: 10.1021/nl502393b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Photonic antennas amplify and confine optical fields at the nanoscale offering excellent perspectives for nanoimaging and nanospectroscopy. Increased resolution beyond the diffraction limit has been demonstrated using a variety of antenna designs, but multicolor nanoscale imaging is precluded by their resonance behavior. Here we report on the design of a novel hybrid antenna probe based on a monopole nanoantenna engineered on a bowtie nanoaperture. The device combines broadband enhanced emission, extreme field confinement down to few nanometers, and zero-background illumination. We demonstrate simultaneous dual-color single molecule nanoimaging with 20 nm resolution and angstrom localization precision, corresponding to 10(3)-fold improvement compared to diffraction-limited optics. When interacting with individual molecules in the near-field, our innovative design enables the emission of 10(4) photon-counts per molecule in a 20 nm excitation region, allowing direct discrimination of spectrally distinct molecules separated by 2.1 ± 0.4 nm. We foresee that background-free nanolight sources will open new horizons in optical nanoscopy and fluorescence spectroscopy by providing multicolor detection of standard fluorescent molecules fully compatible with live cell research.
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Affiliation(s)
- Mathieu Mivelle
- ICFO-Institut de Ciencies Fotoniques , Mediterranean Technology Park, 08860 Castelldefels (Barcelona), Spain
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72
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Acuna C, Guo Q, Burré J, Sharma M, Sun J, Südhof TC. Microsecond dissection of neurotransmitter release: SNARE-complex assembly dictates speed and Ca²⁺ sensitivity. Neuron 2014; 82:1088-100. [PMID: 24908488 DOI: 10.1016/j.neuron.2014.04.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2014] [Indexed: 10/25/2022]
Abstract
SNARE-complex assembly mediates synaptic vesicle fusion during neurotransmitter release and requires that the target-SNARE protein syntaxin-1 switches from a closed to an open conformation. Although many SNARE proteins are available per vesicle, only one to three SNARE complexes are minimally needed for a fusion reaction. Here, we use high-resolution measurements of synaptic transmission in the calyx-of-Held synapse from mutant mice in which syntaxin-1 is rendered constitutively open and SNARE-complex assembly is enhanced to examine the relation between SNARE-complex assembly and neurotransmitter release. We show that enhancing SNARE-complex assembly dramatically increases the speed of evoked release, potentiates the Ca(2+)-affinity of release, and accelerates fusion-pore expansion during individual vesicle fusion events. Our data indicate that the number of assembled SNARE complexes per vesicle during fusion determines the presynaptic release probability and fusion kinetics and suggest a mechanism whereby proteins (Munc13 or RIM) may control presynaptic plasticity by regulating SNARE-complex assembly.
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Affiliation(s)
- Claudio Acuna
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, 265 Campus Drive, Stanford, CA 94305-5453, USA.
| | - Qingchen Guo
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Jacqueline Burré
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, 265 Campus Drive, Stanford, CA 94305-5453, USA
| | - Manu Sharma
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, 265 Campus Drive, Stanford, CA 94305-5453, USA
| | - Jianyuan Sun
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China; Center of Parkinson's Disease, Beijing Institute for Brain Disorders, 15 Datun Road, Chaoyang District, Beijing 100101, China
| | - Thomas C Südhof
- Department of Molecular and Cellular Physiology and Howard Hughes Medical Institute, Stanford University, 265 Campus Drive, Stanford, CA 94305-5453, USA.
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73
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Brinkmalm A, Brinkmalm G, Honer WG, Moreno JA, Jakobsson J, Mallucci GR, Zetterberg H, Blennow K, Öhrfelt A. Targeting synaptic pathology with a novel affinity mass spectrometry approach. Mol Cell Proteomics 2014; 13:2584-92. [PMID: 24973420 DOI: 10.1074/mcp.m114.040113] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We report a novel strategy for studying synaptic pathology by concurrently measuring levels of four SNARE complex proteins from individual brain tissue samples. This method combines affinity purification and mass spectrometry and can be applied directly for studies of SNARE complex proteins in multiple species or modified to target other key elements in neuronal function. We use the technique to demonstrate altered levels of presynaptic proteins in Alzheimer disease patients and prion-infected mice.
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Affiliation(s)
- Ann Brinkmalm
- From the ‡Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, S43180 Mölndal, Sweden;
| | - Gunnar Brinkmalm
- From the ‡Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, S43180 Mölndal, Sweden
| | - William G Honer
- ¶Department of Psychiatry, University of British Columbia, Vancouver V6H3Z6, British Columbia, Canada
| | - Julie A Moreno
- ‖MRC Toxicology Unit, Hodgkin Building, University of Leicester, LE19HN Leicester, UK
| | - Joel Jakobsson
- From the ‡Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, S43180 Mölndal, Sweden
| | - Giovanna R Mallucci
- ‖MRC Toxicology Unit, Hodgkin Building, University of Leicester, LE19HN Leicester, UK
| | - Henrik Zetterberg
- From the ‡Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, S43180 Mölndal, Sweden; **UCL Institute of Neurology, Queen Square WC1N3BG, London, UK
| | - Kaj Blennow
- From the ‡Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, S43180 Mölndal, Sweden
| | - Annika Öhrfelt
- From the ‡Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, S43180 Mölndal, Sweden
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74
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Shivanandan A, Deschout H, Scarselli M, Radenovic A. Challenges in quantitative single molecule localization microscopy. FEBS Lett 2014; 588:3595-602. [PMID: 24928440 DOI: 10.1016/j.febslet.2014.06.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/01/2014] [Accepted: 06/02/2014] [Indexed: 11/18/2022]
Abstract
Single molecule localization microscopy (SMLM), which can provide up to an order of magnitude improvement in spatial resolution over conventional fluorescence microscopy, has the potential to be a highly useful tool for quantitative biological experiments. It has already been used for this purpose in varied fields in biology, ranging from molecular biology to neuroscience. In this review article, we briefly review the applications of SMLM in quantitative biology, and also the challenges involved and some of the solutions that have been proposed. Due to its advantages in labeling specificity and the relatively low overcounting caused by photoblinking when photo-activable fluorescent proteins (PA-FPs) are used as labels, we focus specifically on Photo-Activated Localization Microscopy (PALM), even though the ideas presented might be applicable to SMLM in general. Also, we focus on the following three quantitative measurements: single molecule counting, analysis of protein spatial distribution heterogeneity and co-localization analysis.
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Affiliation(s)
- A Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - H Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - M Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland.
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75
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Raab M, Schmied JJ, Jusuk I, Forthmann C, Tinnefeld P. Fluorescence microscopy with 6 nm resolution on DNA origami. Chemphyschem 2014; 15:2431-5. [PMID: 24895173 DOI: 10.1002/cphc.201402179] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Indexed: 11/10/2022]
Abstract
Resolution of emerging superresolution microscopy is commonly characterized by the width of a point-spread-function or by the localization accuracy of single molecules. In contrast, resolution is defined as the ability to separate two objects. Recently, DNA origamis have been proven as valuable scaffold for self-assembled nanorulers in superresolution microscopy. Here, we use DNA origami nanorulers to overcome the discrepancy of localizing single objects and separating two objects by resolving two docking sites at distances of 18, 12, and 6 nm by using the superresolution technique DNA PAINT(point accumulation for imaging in nanoscale topography). For the smallest distances, we reveal the influence of localization noise on the yield of resolvable structures that we rationalize by Monte Carlo simulations.
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Affiliation(s)
- Mario Raab
- Institute for Physical and Theoretical Chemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig University of Technology, Hans-Sommer Str. 10, 38106 Braunschweig (Germany)
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76
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Gandasi NR, Barg S. Contact-induced clustering of syntaxin and munc18 docks secretory granules at the exocytosis site. Nat Commun 2014; 5:3914. [PMID: 24835618 DOI: 10.1038/ncomms4914] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/17/2014] [Indexed: 02/06/2023] Open
Abstract
Docking of secretory vesicles at the plasma membrane is a poorly understood prerequisite for exocytosis. Current models propose raft-like clusters containing syntaxin as docking receptor, but direct evidence for this is lacking. Here we provide quantitative measurements of several exocytosis proteins (syntaxin, SNAP25, munc18, munc13 and rab3) at the insulin granule release site and show that docking coincides with rapid de novo formation of syntaxin1/munc18 clusters at the nascent docking site. Formation of such clusters prevents undocking and is not observed during failed docking attempts. Overexpression of syntaxins' N-terminal Habc-domain competitively interferes with both cluster formation and successful docking. SNAP25 and munc13 are recruited to the docking site more than a minute later, consistent with munc13's reported role in granule priming rather than docking. We conclude that secretory vesicles dock by inducing syntaxin1/munc18 clustering in the target membrane, and find no evidence for preformed docking receptors.
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Affiliation(s)
- Nikhil R Gandasi
- Department of Medical Cell Biology, Uppsala University, BMC 571, 75123 Uppsala, Sweden
| | - Sebastian Barg
- Department of Medical Cell Biology, Uppsala University, BMC 571, 75123 Uppsala, Sweden
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77
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Sun M, Huang J, Bunyak F, Gumpper K, De G, Sermersheim M, Liu G, Lin PH, Palaniappan K, Ma J. Superresolution microscope image reconstruction by spatiotemporal object decomposition and association: application in resolving t-tubule structure in skeletal muscle. OPTICS EXPRESS 2014; 22:12160-12176. [PMID: 24921337 PMCID: PMC4162352 DOI: 10.1364/oe.22.012160] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 03/05/2014] [Accepted: 04/01/2014] [Indexed: 05/28/2023]
Abstract
One key factor that limits resolution of single-molecule superresolution microscopy relates to the localization accuracy of the activated emitters, which is usually deteriorated by two factors. One originates from the background noise due to out-of-focus signals, sample auto-fluorescence, and camera acquisition noise; and the other is due to the low photon count of emitters at a single frame. With fast acquisition rate, the activated emitters can last multiple frames before they transiently switch off or permanently bleach. Effectively incorporating the temporal information of these emitters is critical to improve the spatial resolution. However, majority of the existing reconstruction algorithms locate the emitters frame by frame, discarding or underusing the temporal information. Here we present a new image reconstruction algorithm based on tracklets, short trajectories of the same objects. We improve the localization accuracy by associating the same emitters from multiple frames to form tracklets and by aggregating signals to enhance the signal to noise ratio. We also introduce a weighted mean-shift algorithm (WMS) to automatically detect the number of modes (emitters) in overlapping regions of tracklets so that not only well-separated single emitters but also individual emitters within multi-emitter groups can be identified and tracked. In combination with a maximum likelihood estimator method (MLE), we are able to resolve low to medium density of overlapping emitters with improved localization accuracy. We evaluate the performance of our method with both synthetic and experimental data, and show that the tracklet-based reconstruction is superior in localization accuracy, particularly for weak signals embedded in a strong background. Using this method, for the first time, we resolve the transverse tubule structure of the mammalian skeletal muscle.
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Affiliation(s)
- Mingzhai Sun
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
- These authors contributed equally to this work
| | - Jiaqing Huang
- Department of Electrical and Computer Engineering, The Ohio State University, Columbus, OH, 43210,
USA
- These authors contributed equally to this work
| | - Filiz Bunyak
- Department of Computer Science, University of Missouri, Columbia, MO, 65211,
USA
- These authors contributed equally to this work
| | - Kristyn Gumpper
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
| | - Gejing De
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
| | - Matthew Sermersheim
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
| | - George Liu
- Department of Physics, Princeton University, Princeton, NJ, 08544,
USA
| | - Pei-Hui Lin
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
| | | | - Jianjie Ma
- Department of Surgery, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, 43210,
USA
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78
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Cijsouw T, Weber JP, Broeke JH, Broek JAC, Schut D, Kroon T, Saarloos I, Verhage M, Toonen RF. Munc18-1 redistributes in nerve terminals in an activity- and PKC-dependent manner. ACTA ACUST UNITED AC 2014; 204:759-75. [PMID: 24590174 PMCID: PMC3941046 DOI: 10.1083/jcb.201308026] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
PKC-dependent dynamic control of Munc18-1 levels enables individual synapses to tune their output during periods of activity. Munc18-1 is a soluble protein essential for synaptic transmission. To investigate the dynamics of endogenous Munc18-1 in neurons, we created a mouse model expressing fluorescently tagged Munc18-1 from the endogenous munc18-1 locus. We show using fluorescence recovery after photobleaching in hippocampal neurons that the majority of Munc18-1 trafficked through axons and targeted to synapses via lateral diffusion together with syntaxin-1. Munc18-1 was strongly expressed at presynaptic terminals, with individual synapses showing a large variation in expression. Axon–synapse exchange rates of Munc18-1 were high: during stimulation, Munc18-1 rapidly dispersed from synapses and reclustered within minutes. Munc18-1 reclustering was independent of syntaxin-1, but required calcium influx and protein kinase C (PKC) activity. Importantly, a PKC-insensitive Munc18-1 mutant did not recluster. We show that synaptic Munc18-1 levels correlate with synaptic strength, and that synapses that recruit more Munc18-1 after stimulation have a larger releasable vesicle pool. Hence, PKC-dependent dynamic control of Munc18-1 levels enables individual synapses to tune their output during periods of activity.
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Affiliation(s)
- Tony Cijsouw
- Department of Functional Genomics and Clinical Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam and VU Medical Center, 1081 HV Amsterdam, Netherlands
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79
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Bielopolski N, Lam AD, Bar-On D, Sauer M, Stuenkel EL, Ashery U. Differential interaction of tomosyn with syntaxin and SNAP25 depends on domains in the WD40 β-propeller core and determines its inhibitory activity. J Biol Chem 2014; 289:17087-99. [PMID: 24782308 DOI: 10.1074/jbc.m113.515296] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Neuronal exocytosis depends on efficient formation of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes and is regulated by tomosyn, a SNARE-binding protein. To gain new information about tomosyn's activity, we characterized its mobility and organization on the plasma membrane (PM) in relation to other SNARE proteins and inhibition of exocytosis. By using direct stochastic optical reconstruction microscopy (dSTORM), we found tomosyn to be organized in small clusters adjacent to syntaxin clusters. In addition, we show that tomosyn is present in both syntaxin-tomosyn complexes and syntaxin-SNAP25-tomosyn complexes. Tomosyn mutants that lack residues 537-578 or 897-917 from its β-propeller core diffused faster on the PM and exhibited reduced binding to SNAP25, suggesting that these mutants shift the equilibrium between tomosyn-syntaxin-SNAP25 complexes on the PM to tomosyn-syntaxin complexes. As these deletion mutants impose less inhibition on exocytosis, we suggest that tomosyn inhibition is mediated via tomosyn-syntaxin-SNAP25 complexes and not tomosyn-syntaxin complexes. These findings characterize, for the first time, tomosyn's dynamics at the PM and its relation to its inhibition of exocytosis.
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Affiliation(s)
- Noa Bielopolski
- From the Department of Neurobiology, Life Sciences Faculty, and
| | - Alice D Lam
- the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109, and
| | - Dana Bar-On
- From the Department of Neurobiology, Life Sciences Faculty, and Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Markus Sauer
- the Department of Biotechnology and Biophysics, Julius Maximilians University Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Edward L Stuenkel
- the Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan 48109, and
| | - Uri Ashery
- From the Department of Neurobiology, Life Sciences Faculty, and Sagol School of Neuroscience, Tel Aviv University, 69978 Tel Aviv, Israel,
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80
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Deschout H, Shivanandan A, Annibale P, Scarselli M, Radenovic A. Progress in quantitative single-molecule localization microscopy. Histochem Cell Biol 2014; 142:5-17. [PMID: 24748502 PMCID: PMC4072926 DOI: 10.1007/s00418-014-1217-y] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2014] [Indexed: 01/10/2023]
Abstract
With the advent of single-molecule localization microscopy (SMLM) techniques, intracellular proteins can be imaged at unprecedented resolution with high specificity and contrast. These techniques can lead to a better understanding of cell functioning, as they allow, among other applications, counting the number of molecules of a protein specie in a single cell, studying the heterogeneity in protein spatial organization, and probing the spatial interactions between different protein species. However, the use of these techniques for accurate quantitative measurements requires corrections for multiple inherent sources of error, including: overcounting due to multiple localizations of a single fluorophore (i.e., photoblinking), undercounting caused by incomplete photoconversion, uncertainty in the localization of single molecules, sample drift during the long imaging time, and inaccurate image registration in the case of dual-color imaging. In this paper, we review recent efforts that address some of these sources of error in quantitative SMLM and give examples in the context of photoactivated localization microscopy (PALM).
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Affiliation(s)
- H. Deschout
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - A. Shivanandan
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
| | - P. Annibale
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Biomedical Engineering Department, University of California, Irvine, CA USA
| | - M. Scarselli
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
- Present Address: Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - A. Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, School of Engineering, EPFL, Lausanne, Switzerland
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81
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Notelaers K, Rocha S, Paesen R, Swinnen N, Vangindertael J, Meier JC, Rigo JM, Ameloot M, Hofkens J. Membrane distribution of the glycine receptor α3 studied by optical super-resolution microscopy. Histochem Cell Biol 2014; 142:79-90. [PMID: 24553792 DOI: 10.1007/s00418-014-1197-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2014] [Indexed: 11/24/2022]
Abstract
In this study, the effect of glycine receptor (GlyR) α3 alternative RNA splicing on the distribution of receptors in the membrane of human embryonic kidney 293 cells is investigated using optical super-resolution microscopy. Direct stochastic optical reconstruction microscopy is used to image both α3K and α3L splice variants individually and together using single- and dual-color imaging. Pair correlation analysis is used to extract quantitative measures from the resulting images. Autocorrelation analysis of the individually expressed variants reveals clustering of both variants, yet with differing properties. The cluster size is increased for α3L compared to α3K (mean radius 92 ± 4 and 56 ± 3 nm, respectively), yet an even bigger difference is found in the cluster density (9,870 ± 1,433 and 1,747 ± 200 μm(-2), respectively). Furthermore, cross-correlation analysis revealed that upon co-expression, clusters colocalize on the same spatial scales as for individually expressed receptors (mean co-cluster radius 94 ± 6 nm). These results demonstrate that RNA splicing determines GlyR α3 membrane distribution, which has consequences for neuronal GlyR physiology and function.
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Affiliation(s)
- Kristof Notelaers
- Biomedical Research Institute, Hasselt University and School of Life Sciences, Transnational University Limburg, Agoralaan Gebouw C, 3590, Diepenbeek, Belgium
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82
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Petersen OH. Calcium signalling and secretory epithelia. Cell Calcium 2014; 55:282-9. [PMID: 24508392 DOI: 10.1016/j.ceca.2014.01.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 01/10/2014] [Indexed: 12/15/2022]
Abstract
Ca(2+) is now firmly established as the most important intracellular regulator of physiological and pathological events in a vast number of different cell types, including secretory epithelia. In these tissues, Ca(2+) signalling is crucially important for the control of both fluid secretion and electrolyte secretion as well as the regulation of macromolecule secretion. In this overview article, I shall attempt to give some general background to the concepts underlying our current thinking about Ca(2+) signalling in epithelia and its roles in regulating secretion. It is outside the scope of this review to provide a comprehensive account of Ca(2+) signalling and the many different processes in the many different secretory epithelia that are controlled by Ca(2+) signals. It is my aim to draw attention to some general features of Ca(2+) signalling processes in secretory epithelia, which are rather different from those in, for example, endocrine glands. The principal examples will be taken from studies of exocrine cells and, in particular, pancreatic acinar cells, as they are the pioneer cells with regard to investigations of Ca(2+) signalling due to primary intracellular Ca(2+) release. They also represent the cell type which has been characterized in most detail with regard to Ca(2+) transport events and mechanisms.
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Affiliation(s)
- O H Petersen
- MRC Secretory Control Research Group, Cardiff School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, Wales, UK.
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83
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Long BR, Robinson DC, Zhong H. Subdiffractive microscopy: techniques, applications, and challenges. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2014; 6:151-68. [PMID: 24443323 DOI: 10.1002/wsbm.1259] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Revised: 12/03/2013] [Accepted: 12/03/2013] [Indexed: 01/30/2023]
Abstract
Cellular processes rely on the precise orchestration of signaling and effector molecules in space and time, yet it remains challenging to gain a comprehensive picture of the molecular organization underlying most basic biological functions. This organization often takes place at length scales below the resolving power of conventional microscopy. In recent years, several 'superresolution' fluorescence microscopic techniques have emerged that can surpass the diffraction limit of conventional microscopy by a factor of 2-20. These methods have been used to reveal previously unknown organization of macromolecular complexes and cytoskeletal structures. The resulting high-resolution view of molecular organization and dynamics is already changing our understanding of cellular processes at the systems level. However, current subdiffractive microscopic techniques are not without limitations; challenges remain to be overcome before these techniques achieve their full potential. Here, we introduce three primary types of subdiffractive microscopic techniques, consider their current limitations and challenges, and discuss recent biological applications.
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Affiliation(s)
- Brian R Long
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
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Abstract
During an action potential, Ca(2+) entering a presynaptic terminal triggers synaptic vesicle exocytosis and neurotransmitter release in less than a millisecond. How does Ca(2+) stimulate release so rapidly and precisely? Work over the last decades revealed that Ca(2+) binding to synaptotagmin triggers release by stimulating synaptotagmin binding to a core fusion machinery composed of SNARE and SM proteins that mediates membrane fusion during exocytosis. Complexin adaptor proteins assist synaptotagmin by activating and clamping this core fusion machinery. Synaptic vesicles containing synaptotagmin are positioned at the active zone, the site of vesicle fusion, by a protein complex containing RIM proteins. RIM proteins activate docking and priming of synaptic vesicles and simultaneously recruit Ca(2+) channels to active zones, thereby connecting in a single complex primed synaptic vesicles to Ca(2+) channels. This architecture allows direct flow of Ca(2+) ions from Ca(2+) channels to synaptotagmin, which then triggers fusion, thus mediating tight millisecond coupling of an action potential to neurotransmitter release.
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Affiliation(s)
- Thomas C Südhof
- Department of Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Lorry Lokey SIM1 Building, 265 Campus Drive, Stanford University School of Medicine, Stanford, CA 94305, USA.
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85
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