151
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State-of-the-Art Fluorescence Fluctuation-Based Spectroscopic Techniques for the Study of Protein Aggregation. Int J Mol Sci 2018; 19:ijms19040964. [PMID: 29570669 PMCID: PMC5979297 DOI: 10.3390/ijms19040964] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 03/17/2018] [Accepted: 03/21/2018] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), Alzheimer’s disease, Parkinson’s disease, and Huntington’s disease, are devastating proteinopathies with misfolded protein aggregates accumulating in neuronal cells. Inclusion bodies of protein aggregates are frequently observed in the neuronal cells of patients. Investigation of the underlying causes of neurodegeneration requires the establishment and selection of appropriate methodologies for detailed investigation of the state and conformation of protein aggregates. In the current review, we present an overview of the principles and application of several methodologies used for the elucidation of protein aggregation, specifically ones based on determination of fluctuations of fluorescence. The discussed methods include fluorescence correlation spectroscopy (FCS), imaging FCS, image correlation spectroscopy (ICS), photobleaching ICS (pbICS), number and brightness (N&B) analysis, super-resolution optical fluctuation imaging (SOFI), and transient state (TRAST) monitoring spectroscopy. Some of these methodologies are classical protein aggregation analyses, while others are not yet widely used. Collectively, the methods presented here should help the future development of research not only into protein aggregation but also neurodegenerative diseases.
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152
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Fukushima R, Yamamoto J, Ishikawa H, Kinjo M. Two-detector number and brightness analysis reveals spatio-temporal oligomerization of proteins in living cells. Methods 2018; 140-141:161-171. [PMID: 29572069 DOI: 10.1016/j.ymeth.2018.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 01/10/2023] Open
Abstract
Number and brightness analysis (N&B) is a useful tool for the simultaneous visualization of protein oligomers and their localization, with single-molecule sensitivity. N&B determines particle brightness (fluorescence intensity per particle) and maps the spatial distribution of fluorescently labeled proteins by performing statistical analyses of the image series obtained using laser scanning microscopy. The brightness map reveals presence of the oligomers of the targeted protein and their distribution in living cells. However, even when corrections are applied, conventional N&B is affected by afterpulsing, shot noise, thermal noise, dead time, and overestimation of particle brightness when the concentration of the fluorescent particles changes during measurement. The drawbacks of conventional N&B can be circumvented by using two detectors, a novel approach that we henceforth call two-detector number and brightness analysis (TD-N&B), and introducing a linear regression of fluorescence intensity. This statistically eliminates the effect of noise from the detectors, and ensures that the correct particle brightness is obtained. Our method was theoretically assessed by numerical simulations and experimentally validated using a dilution series of purified enhanced green fluorescent protein (EGFP), EGFP tandem oligomers in cell lysate, and EGFP tandem oligomers in living cells. Furthermore, this method was used to characterize the complex process of ligand-induced glucocorticoid receptor dimerization and their translocation to the cell nucleus in live cells. Our method can be applied to other oligomer-forming proteins in cell signaling, or to aggregations of proteins such as those that cause neurodegenerative diseases.
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Affiliation(s)
- Ryosuke Fukushima
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Johtaro Yamamoto
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Hideto Ishikawa
- Laboratory of Molecular Cell Dynamics, Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan
| | - Masataka Kinjo
- Laboratory of Molecular Cell Dynamics, Faculty of Advanced Life Science, Hokkaido University, Sapporo 001-0021, Japan.
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153
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Sagnella SM, Trieu J, Brahmbhatt H, MacDiarmid JA, MacMillan A, Whan RM, Fife CM, McCarroll JA, Gifford AJ, Ziegler DS, Kavallaris M. Targeted Doxorubicin-Loaded Bacterially Derived Nano-Cells for the Treatment of Neuroblastoma. Mol Cancer Ther 2018; 17:1012-1023. [PMID: 29491149 DOI: 10.1158/1535-7163.mct-17-0738] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 12/12/2017] [Accepted: 02/09/2018] [Indexed: 11/16/2022]
Abstract
Advanced stage neuroblastoma is an aggressive disease with limited treatment options for patients with drug-resistant tumors. Targeted delivery of chemotherapy for pediatric cancers offers promise to improve treatment efficacy and reduce toxicity associated with systemic chemotherapy. The EnGeneIC Dream Vector (EDVTM) is a nanocell, which can package chemotherapeutic drugs and target tumors via attachment of bispecific proteins to the surface of the nanocell. Phase I trials in adults with refractory tumors have shown an acceptable safety profile. Herein we investigated the activity of EGFR-targeted and doxorubicin-loaded EDVTM (EGFREDVTMDox) for the treatment of neuroblastoma. Two independent neuroblastoma cell lines with variable expression of EGFR protein [SK-N-BE(2), high; SH-SY-5Y, low] were used. EGFREDVTMDox induced apoptosis in these cells compared to control, doxorubicin, or non-doxorubicin loaded EGFREDVTM In three-dimensional tumor spheroids, imaging and fluorescence life-time microscopy revealed that EGFREDVTMDox had a marked enhancement of doxorubicin penetration compared to doxorubicin alone, and improved penetration compared to non-EGFR-targeted EDVTMDox, with enhanced spheroid penetration leading to increased apoptosis. In two independent orthotopic human neuroblastoma xenograft models, short-term studies (28 days) of tumor-bearing mice led to a significant decrease in tumor size in EGFREDVTMDox-treated animals compared to control, doxorubicin, or non-EGFR EDVTMDox There was increased TUNEL staining of tumors at day 28 compared to control, doxorubicin, or non-EGFR EDVTMDox Moreover, overall survival was increased in neuroblastoma mice treated with EGFREDVTMDox (P < 0007) compared to control. Drug-loaded bispecific-antibody targeted EDVsTM offer a highly promising approach for the treatment of aggressive pediatric malignancies such as neuroblastoma. Mol Cancer Ther; 17(5); 1012-23. ©2018 AACR.
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Affiliation(s)
- Sharon M Sagnella
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Centre for NanoMedicine, University of New South Wales Sydney, New South Wales, Australia.,EnGeneIC Ltd., Sydney, New South Wales, Australia
| | - Jennifer Trieu
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Centre for NanoMedicine, University of New South Wales Sydney, New South Wales, Australia
| | | | | | - Alex MacMillan
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Renee M Whan
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney, Australia
| | - Christopher M Fife
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Centre for NanoMedicine, University of New South Wales Sydney, New South Wales, Australia
| | - Joshua A McCarroll
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Centre for NanoMedicine, University of New South Wales Sydney, New South Wales, Australia
| | - Andrew J Gifford
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia.,Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - David S Ziegler
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia.,Kids Cancer Centre, Sydney Children's Hospital, Randwick, New South Wales, Australia
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, New South Wales, Australia. .,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology and Australian Centre for NanoMedicine, University of New South Wales Sydney, New South Wales, Australia
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154
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Papini C, Royer CA. Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks. Biophys Rev 2018; 10:87-96. [PMID: 29383593 DOI: 10.1007/s12551-017-0394-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/29/2017] [Indexed: 12/27/2022] Open
Abstract
Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.
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Affiliation(s)
- Christina Papini
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Catherine A Royer
- Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA.
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155
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Viral highway to nucleus exposed by image correlation analyses. Sci Rep 2018; 8:1152. [PMID: 29348472 PMCID: PMC5773500 DOI: 10.1038/s41598-018-19582-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/04/2018] [Indexed: 01/26/2023] Open
Abstract
Parvoviral genome translocation from the plasma membrane into the nucleus is a coordinated multistep process mediated by capsid proteins. We used fast confocal microscopy line scan imaging combined with image correlation methods including auto-, pair- and cross-correlation, and number and brightness analysis, to study the parvovirus entry pathway at the single-particle level in living cells. Our results show that the endosome-associated movement of virus particles fluctuates from fast to slow. Fast transit of single cytoplasmic capsids to the nuclear envelope is followed by slow movement of capsids and fast diffusion of capsid fragments in the nucleoplasm. The unique combination of image analyses allowed us to follow the fate of intracellular single virus particles and their interactions with importin β revealing previously unknown dynamics of the entry pathway.
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156
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Hortigüela V, Larrañaga E, Cutrale F, Seriola A, García-Díaz M, Lagunas A, Andilla J, Loza-Alvarez P, Samitier J, Ojosnegros S, Martínez E. Nanopatterns of Surface-Bound EphrinB1 Produce Multivalent Ligand-Receptor Interactions That Tune EphB2 Receptor Clustering. NANO LETTERS 2018; 18:629-637. [PMID: 29243484 DOI: 10.1021/acs.nanolett.7b04904] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Here we present a nanostructured surface able to produce multivalent interactions between surface-bound ephrinB1 ligands and membrane EphB2 receptors. We created ephrinB1 nanopatterns of regular size (<30 nm in diameter) by using self-assembled diblock copolymers. Next, we used a statistically enhanced version of the Number and Brightness technique, which can discriminate-with molecular sensitivity-the oligomeric states of diffusive species to quantitatively track the EphB2 receptor oligomerization process in real time. The results indicate that a stimulation using randomly distributed surface-bound ligands was not sufficient to fully induce receptor aggregation. Conversely, when nanopatterned onto our substrates, the ligands effectively induced a strong receptor oligomerization. This presentation of ligands improved the clustering efficiency of conventional ligand delivery systems, as it required a 9-fold lower ligand surface coverage and included faster receptor clustering kinetics compared to traditional cross-linked ligands. In conclusion, nanostructured diblock copolymers constitute a novel strategy to induce multivalent ligand-receptor interactions leading to a stronger, faster, and more efficient receptor activation, thus providing a useful strategy to precisely tune and potentiate receptor responses. The efficiency of these materials at inducing cell responses can benefit applications such as the design of new bioactive materials and drug-delivery systems.
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Affiliation(s)
- Verónica Hortigüela
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08028, Spain
| | - Enara Larrañaga
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08028, Spain
| | - Francesco Cutrale
- Translational Imaging Center, Molecular and Computational Biology, University of Southern California , Los Angeles, California 90089, United States
| | - Anna Seriola
- Center of Regenerative Medicine in Barcelona (CMRB) , Hospital Duran i Reynals, Hospitalet de Llobregat 08908, Spain
| | - María García-Díaz
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08028, Spain
| | - Anna Lagunas
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08028, Spain
- Centro de Investigación Biomédica en Red (CIBER) , Madrid 28029, Spain
| | - Jordi Andilla
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology , Castelldefels, Barcelona 08860, Spain
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology , Castelldefels, Barcelona 08860, Spain
| | - Josep Samitier
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08028, Spain
- Centro de Investigación Biomédica en Red (CIBER) , Madrid 28029, Spain
- Department of Engineering: Electronics, University of Barcelona (UB) , Barcelona 08028, Spain
| | - Samuel Ojosnegros
- Center of Regenerative Medicine in Barcelona (CMRB) , Hospital Duran i Reynals, Hospitalet de Llobregat 08908, Spain
| | - Elena Martínez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST) , Barcelona 08028, Spain
- Centro de Investigación Biomédica en Red (CIBER) , Madrid 28029, Spain
- Department of Engineering: Electronics, University of Barcelona (UB) , Barcelona 08028, Spain
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157
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Bibeau JP, Kingsley JL, Furt F, Tüzel E, Vidali L. F-Actin Mediated Focusing of Vesicles at the Cell Tip Is Essential for Polarized Growth. PLANT PHYSIOLOGY 2018; 176:352-363. [PMID: 28972078 PMCID: PMC5761772 DOI: 10.1104/pp.17.00753] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 09/26/2017] [Indexed: 05/18/2023]
Abstract
F-actin has been shown to be essential for tip growth in an array of plant models, including Physcomitrella patens One hypothesis is that diffusion can transport secretory vesicles, while actin plays a regulatory role during secretion. Alternatively, it is possible that actin-based transport is necessary to overcome vesicle transport limitations to sustain secretion. Therefore, a quantitative analysis of diffusion, secretion kinetics, and cell geometry is necessary to clarify the role of actin in polarized growth. Using fluorescence recovery after photobleaching analysis, we first show that secretory vesicles move toward and accumulate at the tip in an actin-dependent manner. We then depolymerized F-actin to decouple vesicle diffusion from actin-mediated transport and measured the diffusion coefficient and concentration of vesicles. Using these values, we constructed a theoretical diffusion-based model for growth, demonstrating that with fast-enough vesicle fusion kinetics, diffusion could support normal cell growth rates. We further refined our model to explore how experimentally extrapolated vesicle fusion kinetics and the size of the secretion zone limit diffusion-based growth. This model predicts that diffusion-mediated growth is dependent on the size of the region of exocytosis at the tip and that diffusion-based growth would be significantly slower than normal cell growth. To further explore the size of the secretion zone, we used a cell wall degradation enzyme cocktail and determined that the secretion zone is smaller than 6 μm in diameter at the tip. Taken together, our results highlight the requirement for active transport in polarized growth and provide important insight into vesicle secretion during tip growth.
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Affiliation(s)
- Jeffrey P Bibeau
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - James L Kingsley
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Fabienne Furt
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Erkan Tüzel
- Department of Physics, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Luis Vidali
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
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158
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Gambin Y, Giles N, O'Carroll A, Polinkovsky M, Hunter D, Sierecki E. Single-Molecule Fluorescence Reveals the Oligomerization and Folding Steps Driving the Prion-like Behavior of ASC. J Mol Biol 2017; 430:491-508. [PMID: 29288634 DOI: 10.1016/j.jmb.2017.12.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/01/2017] [Accepted: 12/17/2017] [Indexed: 10/24/2022]
Abstract
Single-molecule fluorescence has the unique ability to quantify small oligomers and track conformational changes at a single-protein level. Here we tackled one of the most extreme protein behaviors, found recently in an inflammation pathway. Upon danger recognition in the cytosol, NLRP3 recruits its signaling adaptor, ASC. ASC start polymerizing in a prion-like manner and the system goes in "overdrive" by producing a single micron-sized "speck." By precisely controlling protein expression levels in an in vitro translation system, we could trigger the polymerization of ASC and mimic formation of specks in the absence of inflammasome nucleators. We utilized single-molecule spectroscopy to fully characterize prion-like behaviors and self-propagation of ASC fibrils. We next used our controlled system to monitor the conformational changes of ASC upon fibrillation. Indeed, ASC consists of a PYD and CARD domains, separated by a flexible linker. Individually, both domains have been found to form fibrils, but the structure of the polymers formed by the full-length ASC proteins remains elusive. For the first time, using single-molecule Förster resonance energy transfer, we studied the relative positions of the CARD and PYD domains of full-length ASC. An unexpectedly large conformational change occurred upon ASC fibrillation, suggesting that the CARD domain folds back onto the PYD domain. However, contradicting current models, the "prion-like" conformer was not initiated by binding of ASC to the NLRP3 platform. Rather, using a new method, hybrid between Photon Counting Histogram and Number and Brightness analysis, we showed that NLRP3 forms hexamers with self-binding affinities around 300nM. Overall our data suggest a new mechanism, where NLRP3 can initiate ASC polymerization simply by increasing the local concentration of ASC above a supercritical level.
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Affiliation(s)
- Yann Gambin
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW 2052, Australia; The Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, 4072, Australia.
| | - Nichole Giles
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW 2052, Australia; The Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Ailís O'Carroll
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW 2052, Australia; The Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Mark Polinkovsky
- The Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Dominic Hunter
- The Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Kensington, NSW 2052, Australia; The Institute for Molecular Bioscience, University of Queensland, St Lucia, QLD, 4072, Australia.
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159
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Briddon SJ, Kilpatrick LE, Hill SJ. Studying GPCR Pharmacology in Membrane Microdomains: Fluorescence Correlation Spectroscopy Comes of Age. Trends Pharmacol Sci 2017; 39:158-174. [PMID: 29277246 DOI: 10.1016/j.tips.2017.11.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are organised within the cell membrane into highly ordered macromolecular complexes along with other receptors and signalling proteins. Understanding how heterogeneity in these complexes affects the pharmacology and functional response of these receptors is crucial for developing new and more selective ligands. Fluorescence correlation spectroscopy (FCS) and related techniques such as photon counting histogram (PCH) analysis and image-based FCS can be used to interrogate the properties of GPCRs in these membrane microdomains, as well as their interaction with fluorescent ligands. FCS analyses fluorescence fluctuations within a small-defined excitation volume to yield information about their movement, concentration and molecular brightness (aggregation). These techniques can be used on live cells with single-molecule sensitivity and high spatial resolution. Once the preserve of specialist equipment, FCS techniques can now be applied using standard confocal microscopes. This review describes how FCS and related techniques have revealed novel insights into GPCR biology.
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Affiliation(s)
- Stephen J Briddon
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK
| | - Laura E Kilpatrick
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK; Centre for Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, The Midlands, UK.
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160
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Nolan R, Iliopoulou M, Alvarez L, Padilla-Parra S. Detecting protein aggregation and interaction in live cells: A guide to number and brightness. Methods 2017; 140-141:172-177. [PMID: 29221925 DOI: 10.1016/j.ymeth.2017.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/01/2017] [Accepted: 12/03/2017] [Indexed: 12/31/2022] Open
Abstract
The possibility to detect and quantify protein-protein interactions with good spatial and temporal resolutions in live cells is crucial in biology. Number and brightness is a powerful approach to detect both protein aggregation/desegregation dynamics and stoichiometry in live cells. Importantly, this technique can be applied in commercial set ups: both camera based and laser scanning microscopes. It provides pixel-by-pixel information on protein oligomeric states. If performed with two colours, the technique can retrieve the stoichiometry of the reaction under study. In this review, we discuss the strengths and weaknesses of the technique, stressing which are the correct acquisition parameters for a given microscope, the main challenges in analysis, and the limitations of the technique.
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Affiliation(s)
- Rory Nolan
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Maro Iliopoulou
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Luis Alvarez
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Sergi Padilla-Parra
- Wellcome Centre Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford OX3 7BN, UK.
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161
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Eph-ephrin signaling modulated by polymerization and condensation of receptors. Proc Natl Acad Sci U S A 2017; 114:13188-13193. [PMID: 29192024 DOI: 10.1073/pnas.1713564114] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eph receptor signaling plays key roles in vertebrate tissue boundary formation, axonal pathfinding, and stem cell regeneration by steering cells to positions defined by its ligand ephrin. Some of the key events in Eph-ephrin signaling are understood: ephrin binding triggers the clustering of the Eph receptor, fostering transphosphorylation and signal transduction into the cell. However, a quantitative and mechanistic understanding of how the signal is processed by the recipient cell into precise and proportional responses is largely lacking. Studying Eph activation kinetics requires spatiotemporal data on the number and distribution of receptor oligomers, which is beyond the quantitative power offered by prevalent imaging methods. Here we describe an enhanced fluorescence fluctuation imaging analysis, which employs statistical resampling to measure the Eph receptor aggregation distribution within each pixel of an image. By performing this analysis over time courses extending tens of minutes, the information-rich 4D space (x, y, oligomerization, time) results were coupled to straightforward biophysical models of protein aggregation. This analysis reveals that Eph clustering can be explained by the combined contribution of polymerization of receptors into clusters, followed by their condensation into far larger aggregates. The modeling reveals that these two competing oligomerization mechanisms play distinct roles: polymerization mediates the activation of the receptor by assembling monomers into 6- to 8-mer oligomers; condensation of the preassembled oligomers into large clusters containing hundreds of monomers dampens the signaling. We propose that the polymerization-condensation dynamics creates mechanistic explanation for how cells properly respond to variable ligand concentrations and gradients.
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162
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Elson EL. Introduction to fluorescence correlation Spectroscopy-Brief and simple. Methods 2017; 140-141:3-9. [PMID: 29155128 DOI: 10.1016/j.ymeth.2017.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 11/13/2017] [Indexed: 02/04/2023] Open
Affiliation(s)
- Elliot L Elson
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 South Euclid Avenue, St. Louis, MO 63110, USA.
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163
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Nolan R, Alvarez LAJ, Elegheert J, Iliopoulou M, Jakobsdottir GM, Rodriguez-Muñoz M, Aricescu AR, Padilla-Parra S. nandb-number and brightness in R with a novel automatic detrending algorithm. Bioinformatics 2017; 33:3508-3510. [PMID: 29036562 PMCID: PMC5860167 DOI: 10.1093/bioinformatics/btx434] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/31/2017] [Accepted: 07/04/2017] [Indexed: 12/02/2022] Open
Abstract
SUMMARY An R package for performing number and brightness image analysis, with the implementation of a novel automatic detrending algorithm. AVAILABILITY AND IMPLEMENTATION Available at https://github.com/rorynolan/nandb for all platforms. CONTACT rnolan@well.ox.ac.uk or spadilla@well.ox.ac.uk. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Rory Nolan
- Wellcome Trust Centre for Human Genetics
| | | | - Jonathan Elegheert
- Department of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
| | | | | | | | - A Radu Aricescu
- Department of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
| | - Sergi Padilla-Parra
- Wellcome Trust Centre for Human Genetics
- Department of Structural Biology, University of Oxford, Oxford OX3 7BN, UK
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164
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Dunsing V, Mayer M, Liebsch F, Multhaup G, Chiantia S. Direct evidence of amyloid precursor-like protein 1 trans interactions in cell-cell adhesion platforms investigated via fluorescence fluctuation spectroscopy. Mol Biol Cell 2017; 28:3609-3620. [PMID: 29021345 PMCID: PMC5706989 DOI: 10.1091/mbc.e17-07-0459] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/13/2017] [Accepted: 10/04/2017] [Indexed: 01/25/2023] Open
Abstract
The amyloid precursor–like protein 1 (APLP1) plays a role in synaptic adhesion and synaptogenesis. In this work, we use quantitative fluorescence microscopy to demonstrate the existence of APLP1–APLP1 trans interaction across cell–cell junctions and propose a model explaining the molecular mechanism driving APLP1 multimerization. The amyloid precursor–like protein 1 (APLP1) is a type I transmembrane protein that plays a role in synaptic adhesion and synaptogenesis. Past investigations indicated that APLP1 is involved in the formation of protein–protein complexes that bridge the junctions between neighboring cells. Nevertheless, APLP1–APLP1 trans interactions have never been directly observed in higher eukaryotic cells. Here, we investigated APLP1 interactions and dynamics directly in living human embryonic kidney cells using fluorescence fluctuation spectroscopy techniques, namely cross-correlation scanning fluorescence correlation spectroscopy and number and brightness analysis. Our results show that APLP1 forms homotypic trans complexes at cell–cell contacts. In the presence of zinc ions, the protein forms macroscopic clusters, exhibiting an even higher degree of trans binding and strongly reduced dynamics. Further evidence from giant plasma membrane vesicles suggests that the presence of an intact cortical cytoskeleton is required for zinc-induced cis multimerization. Subsequently, large adhesion platforms bridging interacting cells are formed through APLP1–APLP1 trans interactions. Taken together, our results provide direct evidence that APLP1 functions as a neuronal zinc-dependent adhesion protein and allow a more detailed understanding of the molecular mechanisms driving the formation of APLP1 adhesion platforms.
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Affiliation(s)
- Valentin Dunsing
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
| | - Magnus Mayer
- Institute of Chemistry and Biochemistry, Free University of Berlin, 14195 Berlin, Germany
| | - Filip Liebsch
- Department of Pharmacology and Therapeutics/Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y63, Canada
| | - Gerhard Multhaup
- Department of Pharmacology and Therapeutics/Integrated Program in Neuroscience, McGill University, Montreal, QC H3G 1Y63, Canada
| | - Salvatore Chiantia
- Institute of Biochemistry and Biology, University of Potsdam, 14476 Potsdam, Germany
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165
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Sarkar-Banerjee S, Sayyed-Ahmad A, Prakash P, Cho KJ, Waxham MN, Hancock JF, Gorfe AA. Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes. J Am Chem Soc 2017; 139:13466-13475. [PMID: 28863262 PMCID: PMC5663506 DOI: 10.1021/jacs.7b06292] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Self-assembly of plasma membrane-associated Ras GTPases has major implications to the regulation of cell signaling. However, the structural basis of homo-oligomerization and the fractional distribution of oligomeric states remained undetermined. We have addressed these issues by deciphering the distribution of dimers and higher-order oligomers of K-Ras4B, the most frequently mutated Ras isoform in human cancers. We focused on the constitutively active G12V K-Ras and two of its variants, K101E and K101C/E107C, which respectively destabilize and stabilize oligomers. Using raster image correlation spectroscopy and number and brightness analysis combined with fluorescence recovery after photobleaching, fluorescence correlation spectroscopy and electron microscopy in live cells, we show that G12V K-Ras exists as a mixture of monomers, dimers and larger oligomers, while the K101E mutant is predominantly monomeric and K101C/E107C is dominated by oligomers. This observation demonstrates the ability of K-Ras to exist in multiple oligomeric states whose population can be altered by interfacial mutations. Using molecular modeling and simulations we further show that K-Ras uses two partially overlapping interfaces to form compositionally and topologically diverse oligomers. Our results thus provide the first detailed insight into the multiplicity, structure, and membrane organization of K-Ras homomers.
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Affiliation(s)
- Suparna Sarkar-Banerjee
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | | | - Priyanka Prakash
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, Ohio 45435, United States
| | - M. Neal Waxham
- Department of Neurobiology and Anatomy, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center at Houston, Houston, Texas 77030, United States
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166
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Bourges AC, Torres Montaguth OE, Ghosh A, Tadesse WM, Declerck N, Aertsen A, Royer CA. High pressure activation of the Mrr restriction endonuclease in Escherichia coli involves tetramer dissociation. Nucleic Acids Res 2017; 45:5323-5332. [PMID: 28369499 PMCID: PMC5435990 DOI: 10.1093/nar/gkx192] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/14/2017] [Indexed: 01/07/2023] Open
Abstract
A sub-lethal hydrostatic pressure (HP) shock of ∼100 MPa elicits a RecA-dependent DNA damage (SOS) response in Escherichia coli K-12, despite the fact that pressure cannot compromise the covalent integrity of DNA. Prior screens for HP resistance identified Mrr (Methylated adenine Recognition and Restriction), a Type IV restriction endonuclease (REase), as instigator for this enigmatic HP-induced SOS response. Type IV REases tend to target modified DNA sites, and E. coli Mrr activity was previously shown to be elicited by expression of the foreign M.HhaII Type II methytransferase (MTase), as well. Here we measured the concentration and stoichiometry of a functional GFP-Mrr fusion protein using in vivo fluorescence fluctuation microscopy. Our results demonstrate that Mrr is a tetramer in unstressed cells, but shifts to a dimer after HP shock or co-expression with M.HhaII. Based on the differences in reversibility of tetramer dissociation observed for wild-type GFP-Mrr and a catalytic mutant upon HP shock compared to M.HhaII expression, we propose a model by which (i) HP triggers Mrr activity by directly pushing inactive Mrr tetramers to dissociate into active Mrr dimers, while (ii) M.HhaII triggers Mrr activity by creating high affinity target sites on the chromosome, which pull the equilibrium from inactive tetrameric Mrr toward active dimer.
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Affiliation(s)
- Anaïs C Bourges
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.,Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université Montpellier, 34000 Montpellier, France
| | - Oscar E Torres Montaguth
- Department of Microbial and Molecular Systems, Laboratory of Food Microbiology, KU Leuven, B-3001 Leuven, Belgium
| | - Anirban Ghosh
- Department of Microbial and Molecular Systems, Laboratory of Food Microbiology, KU Leuven, B-3001 Leuven, Belgium
| | - Wubishet M Tadesse
- Department of Microbial and Molecular Systems, Laboratory of Food Microbiology, KU Leuven, B-3001 Leuven, Belgium
| | - Nathalie Declerck
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université Montpellier, 34000 Montpellier, France
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Laboratory of Food Microbiology, KU Leuven, B-3001 Leuven, Belgium
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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167
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Strom AR, Emelyanov AV, Mir M, Fyodorov DV, Darzacq X, Karpen GH. Phase separation drives heterochromatin domain formation. Nature 2017; 547:241-245. [PMID: 28636597 PMCID: PMC6022742 DOI: 10.1038/nature22989] [Citation(s) in RCA: 1181] [Impact Index Per Article: 168.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 05/31/2017] [Indexed: 12/13/2022]
Abstract
Constitutive heterochromatin is an important component of eukaryotic genomes that has essential roles in nuclear architecture, DNA repair and genome stability, and silencing of transposon and gene expression. Heterochromatin is highly enriched for repetitive sequences, and is defined epigenetically by methylation of histone H3 at lysine 9 and recruitment of its binding partner heterochromatin protein 1 (HP1). A prevalent view of heterochromatic silencing is that these and associated factors lead to chromatin compaction, resulting in steric exclusion of regulatory proteins such as RNA polymerase from the underlying DNA. However, compaction alone does not account for the formation of distinct, multi-chromosomal, membrane-less heterochromatin domains within the nucleus, fast diffusion of proteins inside the domain, and other dynamic features of heterochromatin. Here we present data that support an alternative hypothesis: that the formation of heterochromatin domains is mediated by phase separation, a phenomenon that gives rise to diverse non-membrane-bound nuclear, cytoplasmic and extracellular compartments. We show that Drosophila HP1a protein undergoes liquid-liquid demixing in vitro, and nucleates into foci that display liquid properties during the first stages of heterochromatin domain formation in early Drosophila embryos. Furthermore, in both Drosophila and mammalian cells, heterochromatin domains exhibit dynamics that are characteristic of liquid phase-separation, including sensitivity to the disruption of weak hydrophobic interactions, and reduced diffusion, increased coordinated movement and inert probe exclusion at the domain boundary. We conclude that heterochromatic domains form via phase separation, and mature into a structure that includes liquid and stable compartments. We propose that emergent biophysical properties associated with phase-separated systems are critical to understanding the unusual behaviours of heterochromatin, and how chromatin domains in general regulate essential nuclear functions.
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Affiliation(s)
- Amy R Strom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Alexander V Emelyanov
- Albert Einstein College of Medicine, Department of Cell Biology, New York, New York, USA
| | - Mustafa Mir
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Dmitry V Fyodorov
- Albert Einstein College of Medicine, Department of Cell Biology, New York, New York, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
| | - Gary H Karpen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, California, USA
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168
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Sanchez SR, Bachilo SM, Kadria-Vili Y, Weisman RB. Skewness Analysis in Variance Spectroscopy Measures Nanoparticle Individualization. J Phys Chem Lett 2017; 8:2924-2929. [PMID: 28604010 DOI: 10.1021/acs.jpclett.7b01184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An important enabling step in nanoparticle studies is the sorting of heterogeneous mixtures to prepare structurally homogeneous samples. It is also necessary to detect and monitor aggregation of the individual nanoparticles. Although variance spectroscopy provides a simple optical method for finding low concentrations of heteroaggregates in samples such as single-walled carbon nanotube dispersions, it cannot detect the homoaggregates that are relevant for well-sorted samples. Here we demonstrate that variance spectral data can be further analyzed to find third moments of intensity distributions (skewness), which reveal the presence of emissive homoaggregates. Using experimental measurements on variously processed nanotube dispersions, we deduce a simple numerical standard for recognizing aggregation in the highly sorted samples that are increasingly available to nanoscience researchers.
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Affiliation(s)
- Stephen R Sanchez
- Department of Chemistry and the Smalley-Curl Institute, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Sergei M Bachilo
- Department of Chemistry and the Smalley-Curl Institute, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - Yara Kadria-Vili
- Department of Chemistry and the Smalley-Curl Institute, Rice University , 6100 Main Street, Houston, Texas 77005, United States
| | - R Bruce Weisman
- Department of Chemistry and the Smalley-Curl Institute, Rice University , 6100 Main Street, Houston, Texas 77005, United States
- Department of Materials Science and NanoEngineering, Rice University , 6100 Main Street, Houston, Texas 77005, United States
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169
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Hendrix J, Dekens T, Schrimpf W, Lamb DC. Arbitrary-Region Raster Image Correlation Spectroscopy. Biophys J 2017; 111:1785-1796. [PMID: 27760364 PMCID: PMC5073057 DOI: 10.1016/j.bpj.2016.09.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 09/04/2016] [Accepted: 09/12/2016] [Indexed: 11/23/2022] Open
Abstract
Combining imaging with correlation spectroscopy, as in raster image correlation spectroscopy (RICS), makes it possible to extract molecular translational diffusion constants and absolute concentrations, and determine intermolecular interactions from single-channel or multicolor confocal laser-scanning microscopy (CLSM) images. Region-specific RICS analysis remains very challenging because correlations are always calculated in a square region-of-interest (ROI). In this study, we describe a generalized image correlation spectroscopy algorithm that accepts arbitrarily shaped ROIs. We show that an image series can be cleaned up before arbitrary-region RICS (ARICS) analysis. We demonstrate the power of ARICS by simultaneously measuring molecular mobility in the cell membrane and the cytosol. Mobility near dynamic subcellular structures can be investigated with ARICS by generating a dynamic ROI. Finally, we derive diffusion and concentration pseudo-maps using the ARICS method. ARICS is a powerful expansion of image correlation spectroscopy with the potential of becoming the new standard for extracting biophysical parameters from confocal fluorescence images.
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Affiliation(s)
- Jelle Hendrix
- Laboratory for Photochemistry and Spectroscopy, Division of Molecular Imaging and Photonics, KU Leuven, Leuven, Belgium.
| | - Tomas Dekens
- Department of ETRO, Vrije Universiteit Brussel, Brussels, Belgium; iMinds vzw, Zwijnaarde, Belgium
| | - Waldemar Schrimpf
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Don C Lamb
- Department of Chemistry, Ludwig-Maximilians-Universität München, München, Germany
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170
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Gallagher J, Delon A, Moreau P, Wang I. Optimizing the metric in sensorless adaptive optical microscopy with fluorescence fluctuations. OPTICS EXPRESS 2017; 25:15558-15571. [PMID: 28788978 DOI: 10.1364/oe.25.015558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Adaptive optics (AO) strategies using optimization-based, sensorless approaches are widely used, especially for microscopy applications. To converge rapidly to the best correction, such approaches require that a quality metric and a set of modes be chosen optimally. Fluorescence fluctuations microscopy, a family of methods that provides quantitative measurements of molecular concentration and mobility in living specimen, is in particular need of adaptive optics, since its results can be strongly biased by optical aberrations. We examined two possible metrics for sensorless AO, measured in a solution of fluorophores diffusing in 3D: the fluorescence count rate and the molecular brightness (or number of photons detected per molecule in the observation volume). We studied their respective measurement noise and sensitivity to aberrations. Then, AO correction accuracy was experimentally assessed by measuring the residual aberration after correcting a known wavefront. We proposed a theoretical framework to predict the correction accuracy, knowing the metric measurement noise and sensitivity. In the small aberration range, the brightness allows more accurate corrections when fluorophores are few but bright, whereas the count rate performs better in more concentrated solutions. When correcting large aberrations, the count rate is expected to be a more reliable metric.
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171
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Stone MB, Shelby SA, Veatch SL. Super-Resolution Microscopy: Shedding Light on the Cellular Plasma Membrane. Chem Rev 2017; 117:7457-7477. [PMID: 28211677 PMCID: PMC5471115 DOI: 10.1021/acs.chemrev.6b00716] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Lipids and the membranes they form are fundamental building blocks of cellular life, and their geometry and chemical properties distinguish membranes from other cellular environments. Collective processes occurring within membranes strongly impact cellular behavior and biochemistry, and understanding these processes presents unique challenges due to the often complex and myriad interactions between membrane components. Super-resolution microscopy offers a significant gain in resolution over traditional optical microscopy, enabling the localization of individual molecules even in densely labeled samples and in cellular and tissue environments. These microscopy techniques have been used to examine the organization and dynamics of plasma membrane components, providing insight into the fundamental interactions that determine membrane functions. Here, we broadly introduce the structure and organization of the mammalian plasma membrane and review recent applications of super-resolution microscopy to the study of membranes. We then highlight some inherent challenges faced when using super-resolution microscopy to study membranes, and we discuss recent technical advancements that promise further improvements to super-resolution microscopy and its application to the plasma membrane.
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Affiliation(s)
- Matthew B Stone
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah A Shelby
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
| | - Sarah L Veatch
- Biophysics, University of Michigan, Chemistry 930 N University Ave, Ann Arbor 48109
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172
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Fenz SF, Smith AS, Monzel C. Measuring the Invisible: Determining the Size of Growing Nanodomains Using the "Inverse FCS". Biophys J 2017; 112:2245-2246. [PMID: 28591596 DOI: 10.1016/j.bpj.2017.04.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/03/2017] [Accepted: 04/05/2017] [Indexed: 11/25/2022] Open
Affiliation(s)
- Susanne F Fenz
- Department of Cell and Developmental Biology, Biocenter, University of Würzburg, Würzburg, Germany.
| | - Ana-Sunčana Smith
- PULS Group, Institut für Theoretische Physik and the Excellence Cluster: Engineering of Advanced Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany; Institute Ruđer Bošković, Division of Physical Chemistry, Zagreb, Croatia
| | - Cornelia Monzel
- Laboratoire Physico-Chimie, Institut Curie, CNRS UMR168, Paris-Science Lettres, Université Pierre et Marie Curie-Paris 6, Paris, France
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173
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Song K, Xue Y, Wang X, Wan Y, Deng X, Lin J. A modified GFP facilitates counting membrane protein subunits by step-wise photobleaching in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2017; 213:129-133. [PMID: 28380405 DOI: 10.1016/j.jplph.2017.03.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 03/21/2017] [Accepted: 03/21/2017] [Indexed: 06/07/2023]
Abstract
Membrane proteins exert functions by forming oligomers or molecular complexes. Currently, step-wise photobleaching has been applied to count the fluorescently labelled subunits in plant cells, for which an accurate and reliable control is required to distinguish individual subunits and define the basal fluorescence. However, the common procedure using immobilized GFP molecules is obviously not applicable for analysis in living plant cells. Using the spatial intensity distribution analysis (SpIDA), we found that the A206K mutation reduced the dimerization of GFP molecules. Further ectopic expression of Myristoyl-GFPA206K driven by the endogenous AtCLC2 promoter allowed imaging of individual molecules at a low expression level. As a result, the percentage of dimers in the transgenic pCLC2::Myristoyl-mGFPA206K line was significantly reduced in comparison to that of the pCLC2::Myristoyl-GFP line, confirming its application in defining the basal fluorescence intensity of GFP. Taken together, our results demonstrated that pCLC2::Myristoyl-mGFPA206K can be used as a standard control for monomer GFP, facilitating the analysis of the step-wise photobleaching of membrane proteins in Arabidopsis thaliana.
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Affiliation(s)
- Kai Song
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiqun Xue
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohua Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yinglang Wan
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China
| | - Xin Deng
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jinxing Lin
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, China.
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174
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Walta S, Pergushov DV, Oppermann A, Steinschulte AA, Geisel K, Sigolaeva LV, Plamper FA, Wöll D, Richtering W. Microgels enable capacious uptake and controlled release of architecturally complex macromolecular species. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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175
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Phosphatidylserine Lateral Organization Influences the Interaction of Influenza Virus Matrix Protein 1 with Lipid Membranes. J Virol 2017; 91:JVI.00267-17. [PMID: 28356535 DOI: 10.1128/jvi.00267-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/21/2017] [Indexed: 01/21/2023] Open
Abstract
Influenza A virus matrix protein 1 (M1) is an essential component involved in the structural stability of the virus and in the budding of new virions from infected cells. A deeper understanding of the molecular basis of virion formation and the budding process is required in order to devise new therapeutic approaches. We performed a detailed investigation of the interaction between M1 and phosphatidylserine (PS) (i.e., its main binding target at the plasma membrane [PM]), as well as the distribution of PS itself, both in model membranes and in living cells. To this end, we used a combination of techniques, including Förster resonance energy transfer (FRET), confocal microscopy imaging, raster image correlation spectroscopy, and number and brightness (N&B) analysis. Our results show that PS can cluster in segregated regions in the plane of the lipid bilayer, both in model bilayers constituted of PS and phosphatidylcholine and in living cells. The viral protein M1 interacts specifically with PS-enriched domains, and such interaction in turn affects its oligomerization process. Furthermore, M1 can stabilize PS domains, as observed in model membranes. For living cells, the presence of PS clusters is suggested by N&B experiments monitoring the clustering of the PS sensor lactadherin. Also, colocalization between M1 and a fluorescent PS probe suggest that, in infected cells, the matrix protein can specifically bind to the regions of PM in which PS is clustered. Taken together, our observations provide novel evidence regarding the role of PS-rich domains in tuning M1-lipid and M1-M1 interactions at the PM of infected cells.IMPORTANCE Influenza virus particles assemble at the plasma membranes (PM) of infected cells. This process is orchestrated by the matrix protein M1, which interacts with membrane lipids while binding to the other proteins and genetic material of the virus. Despite its importance, the initial step in virus assembly (i.e., M1-lipid interaction) is still not well understood. In this work, we show that phosphatidylserine can form lipid domains in physical models of the inner leaflet of the PM. Furthermore, the spatial organization of PS in the plane of the bilayer modulates M1-M1 interactions. Finally, we show that PS domains appear to be present in the PM of living cells and that M1 seems to display a high affinity for them.
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176
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Zaldo C, Serrano MD, Han X, Cascales C, Cantero M, Montoliu L, Arza E, Caiolfa VR, Zamai M. Efficient up-conversion in Yb:Er:NaT(XO4)2 thermal nanoprobes. Imaging of their distribution in a perfused mouse. PLoS One 2017; 12:e0177596. [PMID: 28542327 PMCID: PMC5436681 DOI: 10.1371/journal.pone.0177596] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 04/28/2017] [Indexed: 11/19/2022] Open
Abstract
Yb and Er codoped NaT(XO4)2 (T = Y, La, Gd, Lu and X = Mo, W) disordered oxides show a green (Er3+ related) up-conversion (UC) efficiency comparable to that of Yb:Er:β-NaYF4 compound and unless 3 times larger UC ratiometric thermal sensitivity. The similar UC efficiency of Yb:Er doped NaT(XO4)2 and β-NaYF4 compounds allowed testing equal subcutaneous depths of ex-vivo chicken tissue in both cases. This extraordinary behavior for NaT(XO4)2 oxides with large cutoff phonon energy (ħω≈ 920 cm-1) is ascribed to 4F9/2 electron population recycling to higher energy 4G11/2 level by a phonon assisted transition. Crystalline nanoparticles of Yb:Er:NaLu(MoO4)2 have been synthesized by sol-gel with sizes most commonly in the 50-80 nm range, showing a relatively small reduction of the UC efficiency with regards to bulk materials. Fluorescence lifetime and multiphoton imaging microscopies show that these nanoparticles can be efficiently distributed to all body organs of a perfused mouse.
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Affiliation(s)
- Carlos Zaldo
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (ICMM-CSIC), Madrid, Spain
| | - María Dolores Serrano
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (ICMM-CSIC), Madrid, Spain
| | - Xiumei Han
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (ICMM-CSIC), Madrid, Spain
| | - Concepción Cascales
- Instituto de Ciencia de Materiales de Madrid, Consejo Superior de Investigaciones Científicas (ICMM-CSIC), Madrid, Spain
| | - Marta Cantero
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- CIBERER, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Lluís Montoliu
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid, Spain
- CIBERER, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Elvira Arza
- Unidad de Microscopía e Imagen Dinámica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Valeria R. Caiolfa
- Unidad de Microscopía e Imagen Dinámica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
- Centro di Imaging Sperimentale, Ospedale San Raffaele, Milano, Italy
| | - Moreno Zamai
- Unidad de Microscopía e Imagen Dinámica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
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177
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Liang EI, Mah EJ, Yee AF, Digman MA. Correlation of focal adhesion assembly and disassembly with cell migration on nanotopography. Integr Biol (Camb) 2017; 9:145-155. [PMID: 28092391 PMCID: PMC5399776 DOI: 10.1039/c6ib00193a] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Selective cell adhesion is desirable to control cell growth and migration on biomedical implants. Mesenchymal cell migration is regulated through focal adhesions (FAs) and can be modulated by their microenvironment, including changes in surface topography. We use the Number and Molecular Brightness (N&B) imaging analysis to provide a unique perspective on FA assembly and disassembly. This imaging analysis generates a map of real-time fluctuations of protein monomers, dimers, and higher order aggregates of FA proteins, such as paxillin during assembly and disassembly. We show a dynamic view of how nanostructured surfaces (nanoline gratings or nanopillars) regulate single molecular dynamics. In particular, we report that the smallest nanopillars (100 nm spacing) gave rise to a low population of disassembling adhesion clusters of ∼2 paxillin proteins whereas the larger nanopillars (380 nm spacing) gave rise to a much larger population of larger disassembling clusters of ∼3-5 paxillin proteins. Cells were more motile on the smaller nanopillars (spaced 100-130 nm apart) compared to all other surfaces studied. Thus, physical nanotopography influences cell motility, adhesion size, and adhesion assembly and disassembly. We report for the first time, with single molecular detection, how nanotopography influences cell motility and protein reorganization in adhesions.
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Affiliation(s)
- Elena I Liang
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697, USA.
| | - Emma J Mah
- Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 92697, USA
| | - Albert F Yee
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697, USA. and Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 92697, USA
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California, Irvine, Irvine, California 92697, USA. and Department of Chemical Engineering and Materials Science, University of California, Irvine, Irvine, California 92697, USA
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178
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Clark NM, Sozzani R. Measuring Protein Movement, Oligomerization State, and Protein-Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (Scanning FCS). Methods Mol Biol 2017; 1610:251-266. [PMID: 28439868 DOI: 10.1007/978-1-4939-7003-2_16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Scanning fluorescence correlation spectroscopy (scanning FCS) can be used to determine protein movement, oligomerization state, and protein-protein interaction. Here, we describe how to use the scanning FCS techniques of raster image correlation spectroscopy (RICS) and pair correlation function (pCF) to determine the rate and direction of protein movement. In addition, we detail how number and brightness (N&B) and cross-correlation analyses can be used to determine oligomerization state and binding ratios of protein complexes. We specifically describe how to acquire suitable images for scanning FCS analysis using the model plant Arabidopsis and how to perform the various analyses using the SimFCS software.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA.,Biomathematics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA. .,Biomathematics Graduate Program, North Carolina State University, Raleigh, NC, 27695, USA.
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179
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Zhao ZW, White MD, Bissiere S, Levi V, Plachta N. Quantitative imaging of mammalian transcriptional dynamics: from single cells to whole embryos. BMC Biol 2016; 14:115. [PMID: 28010727 PMCID: PMC5180410 DOI: 10.1186/s12915-016-0331-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Probing dynamic processes occurring within the cell nucleus at the quantitative level has long been a challenge in mammalian biology. Advances in bio-imaging techniques over the past decade have enabled us to directly visualize nuclear processes in situ with unprecedented spatial and temporal resolution and single-molecule sensitivity. Here, using transcription as our primary focus, we survey recent imaging studies that specifically emphasize the quantitative understanding of nuclear dynamics in both time and space. These analyses not only inform on previously hidden physical parameters and mechanistic details, but also reveal a hierarchical organizational landscape for coordinating a wide range of transcriptional processes shared by mammalian systems of varying complexity, from single cells to whole embryos.
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Affiliation(s)
- Ziqing W Zhao
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Melanie D White
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Stephanie Bissiere
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Valeria Levi
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Conicet, Buenos Aires, C1428EHA, Argentina
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore, 138673, Singapore.
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180
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Abstract
Glucocorticoid hormones (GC) regulate essential physiological functions including energy homeostasis, embryonic and postembryonic development, and the stress response. From the biomedical perspective, GC have garnered a tremendous amount of attention as highly potent anti-inflammatory and immunosuppressive medications indispensable in the clinic. GC signal through the GC receptor (GR), a ligand-dependent transcription factor whose structure, DNA binding, and the molecular partners that it employs to regulate transcription have been under intense investigation for decades. In particular, next-generation sequencing-based approaches have revolutionized the field by introducing a unified platform for a simultaneous genome-wide analysis of cellular activities at the level of RNA production, binding of transcription factors to DNA and RNA, and chromatin landscape and topology. Here we describe fundamental concepts of GC/GR function as established through traditional molecular and in vivo approaches and focus on the novel insights of GC biology that have emerged over the last 10 years from the rapidly expanding arsenal of system-wide genomic methodologies.
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Affiliation(s)
- Maria A Sacta
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
| | - Yurii Chinenov
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021;
| | - Inez Rogatsky
- Hospital for Special Surgery, The David Rosensweig Genomics Center, New York, NY 10021; .,Weill Cornell/Rockefeller/Sloan Kettering MD/PhD program, New York, NY 10021
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181
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Hur KH, Chen Y, Mueller JD. Characterization of Ternary Protein Systems In Vivo with Tricolor Heterospecies Partition Analysis. Biophys J 2016; 110:1158-67. [PMID: 26958892 DOI: 10.1016/j.bpj.2016.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 12/24/2015] [Accepted: 01/04/2016] [Indexed: 11/16/2022] Open
Abstract
Tools and assays that characterize protein-protein interactions are of fundamental importance to biology, because protein assemblies play a critical role in the control and regulation of nearly every cellular process. The availability of fluorescent proteins has facilitated the direct and real-time observation of protein-protein interactions inside living cells, but existing methods are mostly limited to binary interactions between two proteins. Because of the scarcity of techniques capable of identifying ternary interactions, we developed tricolor heterospecies partition analysis. The technique is based on brightness analysis of fluorescence fluctuations from three fluorescent proteins that serve as protein labels. We identified three fluorescent proteins suitable for tricolor brightness experiments. In addition, we developed the theory of identifying interactions in a ternary protein system using tricolor heterospecies partition analysis. The theory was verified by experiments on well-characterized protein systems. A graphical representation of the heterospecies partition data was introduced to visualize interactions in ternary protein systems. Lastly, we performed fluorescence fluctuation experiments on cells expressing a coactivator and two nuclear receptors and applied heterospecies partition analysis to explore the interactions of this ternary protein system.
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Affiliation(s)
- Kwang-Ho Hur
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota
| | - Yan Chen
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota
| | - Joachim D Mueller
- School of Physics and Astronomy, University of Minnesota, Minneapolis, Minnesota; Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota; Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota.
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182
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Sierecki E, Giles N, Bowden Q, Polinkovsky ME, Steinbeck J, Arrioti N, Rahman D, Bhumkar A, Nicovich PR, Ross I, Parton RG, Böcking T, Gambin Y. Nanomolar oligomerization and selective co-aggregation of α-synuclein pathogenic mutants revealed by single-molecule fluorescence. Sci Rep 2016; 6:37630. [PMID: 27892477 PMCID: PMC5385372 DOI: 10.1038/srep37630] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/28/2016] [Indexed: 02/08/2023] Open
Abstract
Protein aggregation is a hallmark of many neurodegenerative diseases, notably Alzheimer's and Parkinson's disease. Parkinson's disease is characterized by the presence of Lewy bodies, abnormal aggregates mainly composed of α-synuclein. Moreover, cases of familial Parkinson's disease have been linked to mutations in α-synuclein. In this study, we compared the behavior of wild-type (WT) α-synuclein and five of its pathological mutants (A30P, E46K, H50Q, G51D and A53T). To this end, single-molecule fluorescence detection was coupled to cell-free protein expression to measure precisely the oligomerization of proteins without purification, denaturation or labelling steps. In these conditions, we could detect the formation of oligomeric and pre-fibrillar species at very short time scale and low micromolar concentrations. The pathogenic mutants surprisingly segregated into two classes: one group forming large aggregates and fibrils while the other tending to form mostly oligomers. Strikingly, co-expression experiments reveal that members from the different groups do not generally interact with each other, both at the fibril and monomer levels. Together, this data paints a completely different picture of α-synuclein aggregation, with two possible pathways leading to the development of fibrils.
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Affiliation(s)
- Emma Sierecki
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
| | - Nichole Giles
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
| | - Quill Bowden
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
| | - Mark E. Polinkovsky
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
| | - Janina Steinbeck
- Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
| | - Nicholas Arrioti
- Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
| | - Diya Rahman
- Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
| | - Akshay Bhumkar
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
| | - Philip R. Nicovich
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
| | - Ian Ross
- Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
| | - Robert G. Parton
- Institute for Molecular Bioscience, The University of Queensland, St Lucia QLD 4072, Australia
| | - Till Böcking
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
| | - Yann Gambin
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Sydney NSW 2032 Australia
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183
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González Bardeci N, Angiolini JF, De Rossi MC, Bruno L, Levi V. Dynamics of intracellular processes in live-cell systems unveiled by fluorescence correlation microscopy. IUBMB Life 2016; 69:8-15. [PMID: 27896901 DOI: 10.1002/iub.1589] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/07/2016] [Indexed: 11/12/2022]
Abstract
Fluorescence fluctuation-based methods are non-invasive microscopy tools especially suited for the study of dynamical aspects of biological processes. These methods examine spontaneous intensity fluctuations produced by fluorescent molecules moving through the small, femtoliter-sized observation volume defined in confocal and multiphoton microscopes. The quantitative analysis of the intensity trace provides information on the processes producing the fluctuations that include diffusion, binding interactions, chemical reactions and photophysical phenomena. In this review, we present the basic principles of the most widespread fluctuation-based methods, discuss their implementation in standard confocal microscopes and briefly revise some examples of their applications to address relevant questions in living cells. The ultimate goal of these methods in the Cell Biology field is to observe biomolecules as they move, interact with targets and perform their biological action in the natural context. © 2016 IUBMB Life, 69(1):8-15, 2017.
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Affiliation(s)
- Nicolás González Bardeci
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
| | - Juan Francisco Angiolini
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
| | - María Cecilia De Rossi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
| | | | - Valeria Levi
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Argentina, IQUIBICEN, UBA-CONICET
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184
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The Dipole Potential Modifies the Clustering and Ligand Binding Affinity of ErbB Proteins and Their Signaling Efficiency. Sci Rep 2016; 6:35850. [PMID: 27775011 PMCID: PMC5075772 DOI: 10.1038/srep35850] [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: 07/01/2016] [Accepted: 10/06/2016] [Indexed: 01/22/2023] Open
Abstract
Although activation of the ErbB family of receptor tyrosine kinases (ErbB1-4) is driven by oligomerization mediated by intermolecular interactions between the extracellular, the kinase and the transmembrane domains, the transmembrane domain has been largely neglected in this regard. The largest contributor to the intramembrane electric field, the dipole potential, alters the conformation of transmembrane peptides, but its effect on ErbB proteins is unknown. Here, we show by Förster resonance energy transfer (FRET) and number and brightness (N&B) experiments that the epidermal growth factor (EGF)-induced increase in the homoassociation of ErbB1 and ErbB2 and their heteroassociation are augmented by increasing the dipole potential. These effects were even more pronounced for ErbB2 harboring an activating Val → Glu mutation in the transmembrane domain (NeuT). The signaling capacity of ErbB1 and ErbB2 was also correlated with the dipole potential. Since the dipole potential decreased the affinity of EGF to ErbB1, the augmented growth factor-induced effects at an elevated dipole potential were actually induced at lower receptor occupancy. We conclude that the dipole potential plays a permissive role in the clustering of ErbB receptors and that the effects of lipid rafts on ligand binding and receptor signaling can be partially attributed to the dipole potential.
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185
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Presman DM, Hager GL. More than meets the dimer: What is the quaternary structure of the glucocorticoid receptor? Transcription 2016; 8:32-39. [PMID: 27764575 PMCID: PMC5279712 DOI: 10.1080/21541264.2016.1249045] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
It is widely accepted that the glucocorticoid receptor (GR), a ligand-regulated transcription factor that triggers anti-inflammatory responses, binds specific response elements as a homodimer. Here, we will discuss the original primary data that established this model and contrast it with a recent report characterizing the GR-DNA complex as a tetramer.
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Affiliation(s)
- Diego M Presman
- a Laboratory of Receptor Biology and Gene Expression , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
| | - Gordon L Hager
- a Laboratory of Receptor Biology and Gene Expression , National Cancer Institute, National Institutes of Health , Bethesda , MD , USA
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186
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Kim YE, Hosp F, Frottin F, Ge H, Mann M, Hayer-Hartl M, Hartl FU. Soluble Oligomers of PolyQ-Expanded Huntingtin Target a Multiplicity of Key Cellular Factors. Mol Cell 2016; 63:951-64. [PMID: 27570076 DOI: 10.1016/j.molcel.2016.07.022] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 06/17/2016] [Accepted: 07/21/2016] [Indexed: 11/17/2022]
Abstract
Huntington's disease is one of several neurodegenerative disorders characterized by the aggregation of polyglutamine (polyQ)-expanded mutant protein. How polyQ aggregation leads to cellular dysfunction is not well understood. Here, we analyzed aberrant protein interactions of soluble oligomers and insoluble inclusions of mutant huntingtin using in-cell single molecule fluorescence spectroscopy and quantitative proteomics. We find that the interactome of soluble oligomers is highly complex, with an enrichment of RNA-binding proteins as well as proteins functioning in ribosome biogenesis, translation, transcription, and vesicle transport. The oligomers frequently target proteins containing extended low-complexity sequences, potentially interfering with key cellular pathways. In contrast, the insoluble inclusions are less interactive and associate strongly with protein quality control components, such as Hsp40 chaperones and factors of the ubiquitin-proteasome system. Our results suggest a "multiple hit" model for the pathogenic effects of mutant huntingtin, with soluble forms engaging more extensively in detrimental interactions than insoluble aggregates.
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Affiliation(s)
- Yujin E Kim
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Fabian Hosp
- Department of Proteomics & Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Frédéric Frottin
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Hui Ge
- Novartis Institutes for Biomedical Research, No. 2 BoYun Road, Pudong, Shanghai 201203, China
| | - Matthias Mann
- Department of Proteomics & Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany
| | - Manajit Hayer-Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany.
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82159 Martinsried, Germany; Munich Cluster for Systems Neurology, Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Schillerstrasse 44, 80336 München, Germany.
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187
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Paparelli L, Corthout N, Pavie B, Wakefield DL, Sannerud R, Jovanovic-Talisman T, Annaert W, Munck S. Inhomogeneity Based Characterization of Distribution Patterns on the Plasma Membrane. PLoS Comput Biol 2016; 12:e1005095. [PMID: 27603951 PMCID: PMC5014321 DOI: 10.1371/journal.pcbi.1005095] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 08/02/2016] [Indexed: 12/04/2022] Open
Abstract
Cell surface protein and lipid molecules are organized in various patterns: randomly, along gradients, or clustered when segregated into discrete micro- and nano-domains. Their distribution is tightly coupled to events such as polarization, endocytosis, and intracellular signaling, but challenging to quantify using traditional techniques. Here we present a novel approach to quantify the distribution of plasma membrane proteins and lipids. This approach describes spatial patterns in degrees of inhomogeneity and incorporates an intensity-based correction to analyze images with a wide range of resolutions; we have termed it Quantitative Analysis of the Spatial distributions in Images using Mosaic segmentation and Dual parameter Optimization in Histograms (QuASIMoDOH). We tested its applicability using simulated microscopy images and images acquired by widefield microscopy, total internal reflection microscopy, structured illumination microscopy, and photoactivated localization microscopy. We validated QuASIMoDOH, successfully quantifying the distribution of protein and lipid molecules detected with several labeling techniques, in different cell model systems. We also used this method to characterize the reorganization of cell surface lipids in response to disrupted endosomal trafficking and to detect dynamic changes in the global and local organization of epidermal growth factor receptors across the cell surface. Our findings demonstrate that QuASIMoDOH can be used to assess protein and lipid patterns, quantifying distribution changes and spatial reorganization at the cell surface. An ImageJ/Fiji plugin of this analysis tool is provided. Plasma membrane organization is fundamental to cellular signaling, transport of molecules, and cell adhesion. To achieve this, plasma membrane proteins and lipids are spatially organized: they form clusters, aggregate in signaling platforms, distribute into gradients on polarized cells, or randomly distribute across the membrane. It is also clear that these organizations can be affected in various contexts. For example, in aging or neurodegenerative diseases, the composition of the plasma membrane is altered and, consequently, the protein and lipid distributions in the membrane fluctuate. In addition, cancer progression is characterized by changes in cellular polarity, lipid content, and the redistribution of cell surface receptors and adhesion molecules. Here we have developed a method to quantify such alterations that, unlike current tools, is compatible with diverse types of cellular organization, including polarity. Our tool can be employed to screen for changes in a straightforward manner and to elucidate distributions of cell surface components in different disciplines, ranging from neurobiology to cancer research.
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Affiliation(s)
- Laura Paparelli
- VIB Bio Imaging Core, Herestraat, Leuven, Belgium
- Laboratory of Membrane Trafficking, Department of Human Genetics, KU Leuven, Herestraat, Leuven, Belgium
- VIB Center for the Biology of Disease, KU Leuven, Herestraat, Leuven, Belgium
| | - Nikky Corthout
- VIB Bio Imaging Core, Herestraat, Leuven, Belgium
- VIB Center for the Biology of Disease, KU Leuven, Herestraat, Leuven, Belgium
- VIB, LiMoNe, Herestraat, Leuven, Belgium
| | - Benjamin Pavie
- VIB Bio Imaging Core, Herestraat, Leuven, Belgium
- VIB Center for the Biology of Disease, KU Leuven, Herestraat, Leuven, Belgium
| | - Devin L. Wakefield
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Ragna Sannerud
- Laboratory of Membrane Trafficking, Department of Human Genetics, KU Leuven, Herestraat, Leuven, Belgium
- VIB Center for the Biology of Disease, KU Leuven, Herestraat, Leuven, Belgium
| | - Tijana Jovanovic-Talisman
- Department of Molecular Medicine, Beckman Research Institute of the City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Wim Annaert
- Laboratory of Membrane Trafficking, Department of Human Genetics, KU Leuven, Herestraat, Leuven, Belgium
- VIB Center for the Biology of Disease, KU Leuven, Herestraat, Leuven, Belgium
- * E-mail: (WA); Sebastian@ (SM)
| | - Sebastian Munck
- VIB Bio Imaging Core, Herestraat, Leuven, Belgium
- VIB Center for the Biology of Disease, KU Leuven, Herestraat, Leuven, Belgium
- VIB, LiMoNe, Herestraat, Leuven, Belgium
- * E-mail: (WA); Sebastian@ (SM)
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188
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Ozgen H, Baron W, Hoekstra D, Kahya N. Oligodendroglial membrane dynamics in relation to myelin biogenesis. Cell Mol Life Sci 2016; 73:3291-310. [PMID: 27141942 PMCID: PMC4967101 DOI: 10.1007/s00018-016-2228-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/14/2016] [Indexed: 12/12/2022]
Abstract
In the central nervous system, oligodendrocytes synthesize a specialized membrane, the myelin membrane, which enwraps the axons in a multilamellar fashion to provide fast action potential conduction and to ensure axonal integrity. When compared to other membranes, the composition of myelin membranes is unique with its relatively high lipid to protein ratio. Their biogenesis is quite complex and requires a tight regulation of sequential events, which are deregulated in demyelinating diseases such as multiple sclerosis. To devise strategies for remedying such defects, it is crucial to understand molecular mechanisms that underlie myelin assembly and dynamics, including the ability of specific lipids to organize proteins and/or mediate protein-protein interactions in healthy versus diseased myelin membranes. The tight regulation of myelin membrane formation has been widely investigated with classical biochemical and cell biological techniques, both in vitro and in vivo. However, our knowledge about myelin membrane dynamics, such as membrane fluidity in conjunction with the movement/diffusion of proteins and lipids in the membrane and the specificity and role of distinct lipid-protein and protein-protein interactions, is limited. Here, we provide an overview of recent findings about the myelin structure in terms of myelin lipids, proteins and membrane microdomains. To give insight into myelin membrane dynamics, we will particularly highlight the application of model membranes and advanced biophysical techniques, i.e., approaches which clearly provide an added value to insight obtained by classical biochemical techniques.
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Affiliation(s)
- Hande Ozgen
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Wia Baron
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
| | - Dick Hoekstra
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nicoletta Kahya
- Department of Cell Biology, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
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189
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Serebryannyy LA, Parilla M, Annibale P, Cruz CM, Laster K, Gratton E, Kudryashov D, Kosak ST, Gottardi CJ, de Lanerolle P. Persistent nuclear actin filaments inhibit transcription by RNA polymerase II. J Cell Sci 2016; 129:3412-25. [PMID: 27505898 DOI: 10.1242/jcs.195867] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 07/27/2016] [Indexed: 12/26/2022] Open
Abstract
Actin is abundant in the nucleus and it is clear that nuclear actin has important functions. However, mystery surrounds the absence of classical actin filaments in the nucleus. To address this question, we investigated how polymerizing nuclear actin into persistent nuclear actin filaments affected transcription by RNA polymerase II. Nuclear filaments impaired nuclear actin dynamics by polymerizing and sequestering nuclear actin. Polymerizing actin into stable nuclear filaments disrupted the interaction of actin with RNA polymerase II and correlated with impaired RNA polymerase II localization, dynamics, gene recruitment, and reduced global transcription and cell proliferation. Polymerizing and crosslinking nuclear actin in vitro similarly disrupted the actin-RNA-polymerase-II interaction and inhibited transcription. These data rationalize the general absence of stable actin filaments in mammalian somatic nuclei. They also suggest a dynamic pool of nuclear actin is required for the proper localization and activity of RNA polymerase II.
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Affiliation(s)
- Leonid A Serebryannyy
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Megan Parilla
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Paolo Annibale
- Laboratory of Fluorescence Dynamics, University of California Irvine, Irvine, CA 92697, USA
| | - Christina M Cruz
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Kyle Laster
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Enrico Gratton
- Laboratory of Fluorescence Dynamics, University of California Irvine, Irvine, CA 92697, USA
| | - Dmitri Kudryashov
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Steven T Kosak
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Cara J Gottardi
- Department of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Primal de Lanerolle
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
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190
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DNA binding triggers tetramerization of the glucocorticoid receptor in live cells. Proc Natl Acad Sci U S A 2016; 113:8236-41. [PMID: 27382178 DOI: 10.1073/pnas.1606774113] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factors dynamically bind to chromatin and are essential for the regulation of genes. Although a large percentage of these proteins appear to self-associate to form dimers or higher order oligomers, the stoichiometry of DNA-bound transcription factors has been poorly characterized in vivo. The glucocorticoid receptor (GR) is a ligand-regulated transcription factor widely believed to act as a dimer or a monomer. Using a unique set of imaging techniques coupled with a cell line containing an array of DNA binding elements, we show that GR is predominantly a tetramer when bound to its target DNA. We find that DNA binding triggers an interdomain allosteric regulation within the GR, leading to tetramerization. We therefore propose that dynamic changes in GR stoichiometry represent a previously unidentified level of regulation in steroid receptor activation. Quaternary structure analysis of other members of the steroid receptor family (estrogen, androgen, and progesterone receptors) reveals variation in oligomerization states among this family of transcription factors. Because GR's oligomerization state has been implicated in therapy outcome, our findings open new doors to the rational design of novel GR ligands and redefine the quaternary structure of steroid receptors.
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191
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Clark NM, Hinde E, Winter CM, Fisher AP, Crosti G, Blilou I, Gratton E, Benfey PN, Sozzani R. Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy. eLife 2016; 5. [PMID: 27288545 PMCID: PMC4946880 DOI: 10.7554/elife.14770] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/10/2016] [Indexed: 01/17/2023] Open
Abstract
To understand complex regulatory processes in multicellular organisms, it is critical to be able to quantitatively analyze protein movement and protein-protein interactions in time and space. During Arabidopsis development, the intercellular movement of SHORTROOT (SHR) and subsequent interaction with its downstream target SCARECROW (SCR) control root patterning and cell fate specification. However, quantitative information about the spatio-temporal dynamics of SHR movement and SHR-SCR interaction is currently unavailable. Here, we quantify parameters including SHR mobility, oligomeric state, and association with SCR using a combination of Fluorescent Correlation Spectroscopy (FCS) techniques. We then incorporate these parameters into a mathematical model of SHR and SCR, which shows that SHR reaches a steady state in minutes, while SCR and the SHR-SCR complex reach a steady-state between 18 and 24 hr. Our model reveals the timing of SHR and SCR dynamics and allows us to understand how protein movement and protein-protein stoichiometry contribute to development.
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Affiliation(s)
- Natalie M Clark
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States.,Biomathematics Graduate Program, North Carolina State University, Raleigh, United States
| | - Elizabeth Hinde
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Cara M Winter
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Adam P Fisher
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
| | - Giuseppe Crosti
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University, Wageningen, Netherlands
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California, Irvine, Irvine, United States
| | - Philip N Benfey
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, United States
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, United States
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192
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Ferrer M, Clerté C, Chamontin C, Basyuk E, Lainé S, Hottin J, Bertrand E, Margeat E, Mougel M. Imaging HIV-1 RNA dimerization in cells by multicolor super-resolution and fluctuation microscopies. Nucleic Acids Res 2016; 44:7922-34. [PMID: 27280976 PMCID: PMC5027490 DOI: 10.1093/nar/gkw511] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/27/2016] [Indexed: 11/15/2022] Open
Abstract
Dimerization is a unique and vital characteristic of retroviral genomes. It is commonly accepted that genomic RNA (gRNA) must be dimeric at the plasma membrane of the infected cells to be packaged during virus assembly. However, where, when and how HIV-1 gRNA find each other and dimerize in the cell are long-standing questions that cannot be answered using conventional approaches. Here, we combine two state-of-the-art, multicolor RNA labeling strategies with two single-molecule microscopy technologies to address these questions. We used 3D-super-resolution structured illumination microscopy to analyze and quantify the spatial gRNA association throughout the cell and monitored the dynamics of RNA-RNA complexes in living-cells by cross-correlation fluctuation analysis. These sensitive and complementary approaches, combined with trans-complementation experiments, reveal for the first time the presence of interacting gRNA in the cytosol, a challenging observation due to the low frequency of these events and their dilution among the bulk of other RNAs, and allow the determination of the subcellular orchestration of the HIV-1 dimerization process.
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Affiliation(s)
- Mireia Ferrer
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Caroline Clerté
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, France
| | - Célia Chamontin
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Eugenia Basyuk
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Sébastien Lainé
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Jérome Hottin
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, France
| | - Edouard Bertrand
- Institut de Génétique Moléculaire de Montpellier, University of Montpellier, CNRS UMR 5535, 1919 route de Mende, 34293, Montpellier Cedex 5, France
| | - Emmanuel Margeat
- CNRS UMR5048, Centre de Biochimie Structurale, 29 rue de Navacelles, 34090 Montpellier, France INSERM U1054, 34090 Montpellier, France Université de Montpellier, 34090 Montpellier, France
| | - Marylène Mougel
- Centre d'études d'agents pathogènes et biotechnologies pour la santé, CPBS-CNRS, Université de Montpellier, 1919 Route de Mende, 34293 Montpellier, France
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193
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Gambin Y, Polinkovsky M, Francois B, Giles N, Bhumkar A, Sierecki E. Confocal Spectroscopy to Study Dimerization, Oligomerization and Aggregation of Proteins: A Practical Guide. Int J Mol Sci 2016; 17:ijms17050655. [PMID: 27144560 PMCID: PMC4881481 DOI: 10.3390/ijms17050655] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/15/2016] [Accepted: 04/20/2016] [Indexed: 12/25/2022] Open
Abstract
Protein self-association is a key feature that can modulate the physiological role of proteins or lead to deleterious effects when uncontrolled. Protein oligomerization is a simple way to modify the activity of a protein, as the modulation of binding interfaces allows for self-activation or inhibition, or variation in the selectivity of binding partners. As such, dimerization and higher order oligomerization is a common feature in signaling proteins, for example, and more than 70% of enzymes have the potential to self-associate. On the other hand, protein aggregation can overcome the regulatory mechanisms of the cell and can have disastrous physiological effects. This is the case in a number of neurodegenerative diseases, where proteins, due to mutation or dysregulation later in life, start polymerizing and often fibrillate, leading to the creation of protein inclusion bodies in cells. Dimerization, well-defined oligomerization and random aggregation are often difficult to differentiate and characterize experimentally. Single molecule “counting” methods are particularly well suited to the study of self-oligomerization as they allow observation and quantification of behaviors in heterogeneous conditions. However, the extreme dilution of samples often causes weak complexes to dissociate, and rare events can be overlooked. Here, we discuss a straightforward alternative where the principles of single molecule detection are used at higher protein concentrations to quantify oligomers and aggregates in a background of monomers. We propose a practical guide for the use of confocal spectroscopy to quantify protein oligomerization status and also discuss about its use in monitoring changes in protein aggregation in drug screening assays.
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Affiliation(s)
- Yann Gambin
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Mark Polinkovsky
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Bill Francois
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Nichole Giles
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Akshay Bhumkar
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
| | - Emma Sierecki
- EMBL Australia Node in Single Molecule Sciences, School of Medical Science, the University of New South Wales, Sydney, NSW 2052, Australia.
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194
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Quantifying the dynamics of the oligomeric transcription factor STAT3 by pair correlation of molecular brightness. Nat Commun 2016; 7:11047. [PMID: 27009358 PMCID: PMC4820838 DOI: 10.1038/ncomms11047] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 02/16/2016] [Indexed: 12/21/2022] Open
Abstract
Oligomerization of transcription factors controls their translocation into the nucleus and DNA-binding activity. Here we present a fluorescence microscopy analysis termed pCOMB (pair correlation of molecular brightness) that tracks the mobility of different oligomeric species within live cell nuclear architecture. pCOMB amplifies the signal from the brightest species present and filters the dynamics of the extracted oligomeric population based on arrival time between two locations. We use this method to demonstrate a dependence of signal transducer and activator of transcription 3 (STAT3) mobility on oligomeric state. We find that on entering the nucleus STAT3 dimers must first bind DNA to form STAT3 tetramers, which are also DNA-bound but exhibit a different mobility signature. Examining the dimer-to-tetramer transition by a cross-pair correlation analysis (cpCOMB) reveals that chromatin accessibility modulates STAT3 tetramer formation. Thus, the pCOMB approach is suitable for mapping the impact oligomerization on transcription factor dynamics.
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195
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Imaging approaches for analysis of cholesterol distribution and dynamics in the plasma membrane. Chem Phys Lipids 2016; 199:106-135. [PMID: 27016337 DOI: 10.1016/j.chemphyslip.2016.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 03/04/2016] [Indexed: 11/21/2022]
Abstract
Cholesterol is an important lipid component of the plasma membrane (PM) of mammalian cells, where it is involved in control of many physiological processes, such as endocytosis, cell migration, cell signalling and surface ruffling. In an attempt to explain these functions of cholesterol, several models have been put forward about cholesterol's lateral and transbilayer organization in the PM. In this article, we review imaging techniques developed over the last two decades for assessing the distribution and dynamics of cholesterol in the PM of mammalian cells. Particular focus is on fluorescence techniques to study the lateral and inter-leaflet distribution of suitable cholesterol analogues in the PM of living cells. We describe also several methods for determining lateral cholesterol dynamics in the PM including fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS), single particle tracking (SPT) and spot variation FCS coupled to stimulated emission depletion (STED) microscopy. For proper interpretation of such measurements, we provide some background in probe photophysics and diffusion phenomena occurring in cell membranes. In particular, we show the equivalence of the reaction-diffusion approach, as used in FRAP and FCS, and continuous time random walk (CTRW) models, as often invoked in SPT studies. We also discuss mass spectrometry (MS) based imaging of cholesterol in the PM of fixed cells and compare this method with fluorescence imaging of sterols. We conclude that evidence from many experimental techniques converges towards a model of a homogeneous distribution of cholesterol with largely free and unhindered diffusion in both leaflets of the PM.
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196
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Mayer MC, Schauenburg L, Thompson-Steckel G, Dunsing V, Kaden D, Voigt P, Schaefer M, Chiantia S, Kennedy TE, Multhaup G. Amyloid precursor-like protein 1 (APLP1) exhibits stronger zinc-dependent neuronal adhesion than amyloid precursor protein and APLP2. J Neurochem 2016; 137:266-76. [PMID: 26801522 DOI: 10.1111/jnc.13540] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Revised: 12/09/2015] [Accepted: 01/06/2016] [Indexed: 01/24/2023]
Abstract
The amyloid precursor protein (APP) and its paralogs, amyloid precursor-like protein 1 (APLP1) and APLP2, are metalloproteins with a putative role both in synaptogenesis and in maintaining synapse structure. Here, we studied the effect of zinc on membrane localization, adhesion, and secretase cleavage of APP, APLP1, and APLP2 in cell culture and rat neurons. For this, we employed live-cell microscopy techniques, a microcontact printing adhesion assay and ELISA for protein detection in cell culture supernatants. We report that zinc induces the multimerization of proteins of the amyloid precursor protein family and enriches them at cellular adhesion sites. Thus, zinc facilitates the formation of de novo APP and APLP1 containing adhesion complexes, whereas it does not have such influence on APLP2. Furthermore, zinc-binding prevented cleavage of APP and APLPs by extracellular secretases. In conclusion, the complexation of zinc modulates neuronal functions of APP and APLPs by (i) regulating formation of adhesion complexes, most prominently for APLP1, and (ii) by reducing the concentrations of neurotrophic soluble APP/APLP ectodomains. Earlier studies suggest a function of the amyloid precursor protein (APP) family proteins in neuronal adhesion. We report here that adhesive function of these proteins is tightly regulated by zinc, most prominently for amyloid precursor-like protein 1 (APLP1). Zinc-mediated APLP1 multimerization, which induced formation of new neuronal contacts and decreased APLP1 shedding. This suggests that APLP1 could function as a zinc receptor processing zinc signals to stabilized or new neuronal contacts.
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Affiliation(s)
- Magnus C Mayer
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Linda Schauenburg
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Greta Thompson-Steckel
- McGill Program in Neuroengineering, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Valentin Dunsing
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Daniela Kaden
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany
| | - Philipp Voigt
- Molekulare Pharmakologie und Zellbiologie, Neurowissenschaftliches Forschungszentrum, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Michael Schaefer
- Medizinische Fakultät der Universität Leipzig, Rudolf-Boehm-Institut für Pharmakologie und Toxikologie, Leipzig, Germany
| | - Salvatore Chiantia
- Institut für Biochemie und Biologie, Universität Potsdam, Potsdam, Germany
| | - Timothy E Kennedy
- McGill Program in Neuroengineering, Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | - Gerhard Multhaup
- Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany.,Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
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197
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Taylor AMW, Castonguay A, Ghogha A, Vayssiere P, Pradhan AAA, Xue L, Mehrabani S, Wu J, Levitt P, Olmstead MC, De Koninck Y, Evans CJ, Cahill CM. Neuroimmune Regulation of GABAergic Neurons Within the Ventral Tegmental Area During Withdrawal from Chronic Morphine. Neuropsychopharmacology 2016; 41:949-59. [PMID: 26202104 PMCID: PMC4748420 DOI: 10.1038/npp.2015.221] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 07/10/2015] [Accepted: 07/11/2015] [Indexed: 12/13/2022]
Abstract
Opioid dependence is accompanied by neuroplastic changes in reward circuitry leading to a negative affective state contributing to addictive behaviors and risk of relapse. The current study presents a neuroimmune mechanism through which chronic opioids disrupt the ventral tegmental area (VTA) dopaminergic circuitry that contributes to impaired reward behavior. Opioid dependence was induced in rodents by treatment with escalating doses of morphine. Microglial activation was observed in the VTA following spontaneous withdrawal from chronic morphine treatment. Opioid-induced microglial activation resulted in an increase in brain-derived neurotrophic factor (BDNF) expression and a reduction in the expression and function of the K(+)Cl(-) co-transporter KCC2 within VTA GABAergic neurons. Inhibition of microglial activation or interfering with BDNF signaling prevented the loss of Cl(-) extrusion capacity and restored the rewarding effects of cocaine in opioid-dependent animals. Consistent with a microglial-derived BDNF-induced disruption of reward, intra-VTA injection of BDNF or a KCC2 inhibitor resulted in a loss of cocaine-induced place preference in opioid-naïve animals. The loss of the extracellular Cl(-) gradient undermines GABAA-mediated inhibition, and represents a mechanism by which chronic opioid treatments can result in blunted reward circuitry. This study directly implicates microglial-derived BDNF as a negative regulator of reward in opioid-dependent states, identifying new therapeutic targets for opiate addictive behaviors.
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Affiliation(s)
- Anna M W Taylor
- Department of Anesthesiology and Perioperative Care, University of California, Irvine, CA, USA
- Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Annie Castonguay
- Institut Universitaire en Santé Mentale de Québec, Québec, QC, Canada
- Department of Psychiatry and Neuroscience, Université Laval, Québec, QC, Canada
| | - Atefeh Ghogha
- Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Pia Vayssiere
- Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Amynah A A Pradhan
- Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Lihua Xue
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
| | - Sadaf Mehrabani
- Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Juli Wu
- Children's Hospital Los Angeles and the Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Pat Levitt
- Children's Hospital Los Angeles and the Keck School of Medicine of the University of Southern California, Los Angeles, CA, USA
| | - Mary C Olmstead
- Department of Psychology, Queen's University, Kingston, ON, Canada
| | - Yves De Koninck
- Institut Universitaire en Santé Mentale de Québec, Québec, QC, Canada
- Department of Psychiatry and Neuroscience, Université Laval, Québec, QC, Canada
| | - Christopher J Evans
- Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, USA
| | - Catherine M Cahill
- Department of Anesthesiology and Perioperative Care, University of California, Irvine, CA, USA
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, Canada
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198
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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199
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Apollo-NADP(+): a spectrally tunable family of genetically encoded sensors for NADP(+). Nat Methods 2016; 13:352-8. [PMID: 26878383 DOI: 10.1038/nmeth.3764] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/08/2016] [Indexed: 02/03/2023]
Abstract
NADPH-dependent antioxidant pathways have a critical role in scavenging hydrogen peroxide (H2O2) produced by oxidative phosphorylation. Inadequate scavenging results in H2O2 accumulation and can cause disease. To measure NADPH/NADP(+) redox states, we explored genetically encoded sensors based on steady-state fluorescence anisotropy due to FRET (fluorescence resonance energy transfer) between homologous fluorescent proteins (homoFRET); we refer to these sensors as Apollo sensors. We created an Apollo sensor for NADP(+) (Apollo-NADP(+)) that exploits NADP(+)-dependent homodimerization of enzymatically inactive glucose-6-phosphate dehydrogenase (G6PD). This sensor is reversible, responsive to glucose-stimulated metabolism and spectrally tunable for compatibility with many other sensors. We used Apollo-NADP(+) to study beta cells responding to oxidative stress and demonstrated that NADPH is significantly depleted before H2O2 accumulation by imaging a Cerulean-tagged version of Apollo-NADP(+) with the H2O2 sensor HyPer.
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200
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The Ebola Virus matrix protein, VP40, requires phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) for extensive oligomerization at the plasma membrane and viral egress. Sci Rep 2016; 6:19125. [PMID: 26753796 PMCID: PMC4709572 DOI: 10.1038/srep19125] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 12/07/2015] [Indexed: 12/25/2022] Open
Abstract
VP40 is one of eight proteins encoded by the Ebola Virus (EBOV) and serves as the primary matrix protein, forming virus like particles (VLPs) from mammalian cells without the need for other EBOV proteins. While VP40 is required for viral assembly and budding from host cells during infection, the mechanisms that target VP40 to the plasma membrane are not well understood. Phosphatidylserine is required for VP40 plasma membrane binding, VP40 hexamer formation, and VLP egress, However, PS also becomes exposed on the outer membrane leaflet at sites of VP40 budding, raising the question of how VP40 maintains an interaction with the plasma membrane inner leaflet when PS is flipped to the opposite side. To address this question, cellular and in vitro assays were employed to determine if phosphoinositides are important for efficient VP40 localization to the plasma membrane. Cellular studies demonstrated that PI(4,5)P2 was an important component of VP40 assembly at the plasma membrane and subsequent virus like particle formation. Additionally, PI(4,5)P2 was required for formation of extensive oligomers of VP40, suggesting PS and PI(4,5)P2 have different roles in VP40 assembly where PS regulates formation of hexamers from VP40 dimers and PI(4,5)P2 stabilizes and/or induces extensive VP40 oligomerization at the plasma membrane.
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