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Sherpa RT, Moshal KS, Agarwal SR, Ostrom RS, Harvey RD. Role of protein kinase A and A kinase anchoring proteins in buffering and compartmentation of cAMP signalling in human airway smooth muscle cells. Br J Pharmacol 2024; 181:2622-2635. [PMID: 38613158 PMCID: PMC11219259 DOI: 10.1111/bph.16357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND AND PURPOSE In human airway smooth muscle (hASM) cells, not all receptors stimulating cAMP production elicit the same effects. This can only be explained if cAMP movement throughout the cell is restricted, yet the mechanisms involved are not fully understood. Phosphodiesterases (PDEs) contribute to compartmentation of many cAMP responses, but PDE activity alone is predicted to be insufficient if cAMP is otherwise freely diffusible. We tested the hypothesis that buffering of cAMP by protein kinase A (PKA) associated with A kinase anchoring proteins (AKAPs) slows cAMP diffusion and that this contributes to receptor-mediated, compartmentalized responses. EXPERIMENTAL APPROACH Raster image correlation spectroscopy (RICS) was used to measure intracellular cAMP diffusion coefficients and evaluate the contribution of PKA-AKAP interactions. Western blotting and immunocytochemistry were used to identify the AKAPs involved. RNA interference was used to down-regulate AKAP expression and determine its effects on cAMP diffusion. Compartmentalized cAMP responses were measured using fluorescence resonance energy transfer (FRET) based biosensors. KEY RESULTS Cyclic AMP movement was significantly slower than that of free-diffusion in hASM cells, and disrupting PKA-AKAP interactions significantly increased the diffusion coefficient. PKA associated with the outer mitochondrial membrane appears to play a prominent role in this effect. Consistent with this idea, knocking down expression of D-AKAP2, the primary mitochondrial AKAP, increased cAMP diffusion and disrupted compartmentation of receptor-mediated responses. CONCLUSION AND IMPLICATIONS Our results confirm that AKAP-anchored PKA contributes to the buffering of cAMP and is consequential in the compartmentation of cAMP responses in hASM cells.
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Affiliation(s)
- Rinzhin T Sherpa
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Karni S Moshal
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Shailesh R Agarwal
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Rennolds S Ostrom
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California, USA
| | - Robert D Harvey
- Department of Pharmacology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA
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2
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Rani K, Pal A, Gurnani B, Agarwala P, Sasmal DK, Jain N. An Innate Host Defense Protein β 2-Microglobulin Keeps a Check on α-Synuclein amyloid Assembly: Implications in Parkinson's Disease. J Mol Biol 2023; 435:168285. [PMID: 37741548 DOI: 10.1016/j.jmb.2023.168285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/25/2023]
Abstract
Amyloid formation due to protein misfolding has gained significant attention due to its association with neurodegenerative diseases. α-Synuclein (α-syn) is one such protein that undergoes a profound conformational switch to form higher order cross-β-sheet structures, resulting in amyloid formation, which is linked to the pathophysiology of Parkinson's disease (PD). The present status of research on α-syn aggregation and PD reveals that the disease progression may be linked with many other diseases, such as kidney-related disorders. Unraveling the link between PD and non-neurological diseases may help in early detection and a better understanding of PD progression. Herein, we investigated the modulation of α-syn in the presence of β2-microglobulin (β2m), a structural protein associated with dialysis-related amyloidosis. We took a multi-disciplinary approach to establish that β2m mitigates amyloid formation by α-syn. Our fluorescence, microscopy and toxicity data demonstrated that sub-stoichiometric ratio of β2m drives α-syn into off-pathway non-toxic aggregates incompetent of transforming into amyloids. Using AlphaFold2 and all-atom MD simulation, we showed that the β-strand segments (β1 and β2) of α-synuclein, which frequently engage in interactions within amyloid fibrils, interact with the last β-strand at the C-terminal of β2m. The outcome of this study will unravel the yet unknown potential linkage of PD with kidney-related disorders. Insights from the cross-talk between two amyloidogenic proteins will lead to early diagnosis and new therapeutic approaches for treating Parkinson's disease. Finally, disruption of the nucleation process of α-syn amyloids by targeting the β1-β2 region will constitute a potential therapeutic approach for inhibiting amyloid formation.
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Affiliation(s)
- Khushboo Rani
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Nagaur Road, Karwar 342030, Rajasthan, India. https://twitter.com/khushboo251995
| | - Arumay Pal
- School of Bioengineering, Vellore Institute of Technology, Bhopal, India. https://twitter.com/Arumay_Pal
| | - Bharat Gurnani
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Nagaur Road, Karwar 342030, Rajasthan, India. https://twitter.com/bgurnani05
| | - Pratibha Agarwala
- Department of Chemistry, Indian Institute of Technology Jodhpur, NH 62, Nagaur Road, Karwar 342030, Rajasthan, India
| | - Dibyendu K Sasmal
- Department of Chemistry, Indian Institute of Technology Jodhpur, NH 62, Nagaur Road, Karwar 342030, Rajasthan, India
| | - Neha Jain
- Department of Bioscience and Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Nagaur Road, Karwar 342030, Rajasthan, India; Centre for Emerging Technologies for Sustainable Development (CETSD), Indian Institute of Technology Jodhpur, Nagaur Road, Karwar 342030, Rajasthan, India.
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3
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Fazel M, Grussmayer KS, Ferdman B, Radenovic A, Shechtman Y, Enderlein J, Pressé S. Fluorescence Microscopy: a statistics-optics perspective. ARXIV 2023:arXiv:2304.01456v3. [PMID: 37064525 PMCID: PMC10104198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Fundamental properties of light unavoidably impose features on images collected using fluorescence microscopes. Modeling these features is ever more important in quantitatively interpreting microscopy images collected at scales on par or smaller than light's wavelength. Here we review the optics responsible for generating fluorescent images, fluorophore properties, microscopy modalities leveraging properties of both light and fluorophores, in addition to the necessarily probabilistic modeling tools imposed by the stochastic nature of light and measurement.
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Affiliation(s)
- Mohamadreza Fazel
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
| | - Kristin S Grussmayer
- Department of Bionanoscience, Faculty of Applied Science and Kavli Institute for Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Boris Ferdman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Aleksandra Radenovic
- Laboratory of Nanoscale Biology, Institute of Bioengineering, Ecole Polytechnique Federale de Lausanne (EPFL), Lausanne, Switzerland
| | - Yoav Shechtman
- Russel Berrie Nanotechnology Institute and Department of Biomedical Engineering, Technion - Israel Institute of Technology, Haifa, Israel
| | - Jörg Enderlein
- III. Institute of Physics - Biophysics, Georg August University, Göttingen, Germany
| | - Steve Pressé
- Department of Physics, Arizona State University, Tempe, Arizona, USA
- Center for Biological Physics, Arizona State University, Tempe, Arizona, USA
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4
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Sankaran J, Wohland T. Current capabilities and future perspectives of FCS: super-resolution microscopy, machine learning, and in vivo applications. Commun Biol 2023; 6:699. [PMID: 37419967 PMCID: PMC10328937 DOI: 10.1038/s42003-023-05069-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023] Open
Abstract
Fluorescence correlation spectroscopy (FCS) is a single molecule sensitive tool for the quantitative measurement of biomolecular dynamics and interactions. Improvements in biology, computation, and detection technology enable real-time FCS experiments with multiplexed detection even in vivo. These new imaging modalities of FCS generate data at the rate of hundreds of MB/s requiring efficient data processing tools to extract information. Here, we briefly review FCS's capabilities and limitations before discussing recent directions that address these limitations with a focus on imaging modalities of FCS, their combinations with super-resolution microscopy, new evaluation strategies, especially machine learning, and applications in vivo.
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Affiliation(s)
- Jagadish Sankaran
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, 138632, Singapore.
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, Singapore, 117558, Singapore.
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5
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Manchanda Y, Bitsi S, Chen S, Broichhagen J, Bernardino de la Serna J, Jones B, Tomas A. Enhanced Endosomal Signaling and Desensitization of GLP-1R vs GIPR in Pancreatic Beta Cells. Endocrinology 2023; 164:7034684. [PMID: 36774542 PMCID: PMC10016038 DOI: 10.1210/endocr/bqad028] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 02/13/2023]
Abstract
The incretin receptors, glucagon-like peptide-1 receptor (GLP-1R) and glucose-dependent insulinotropic polypeptide receptor (GIPR), are prime therapeutic targets for the treatment of type 2 diabetes (T2D) and obesity. They are expressed in pancreatic beta cells where they potentiate insulin release in response to food intake. Despite GIP being the main incretin in healthy individuals, GLP-1R has been favored as a therapeutic target due to blunted GIPR responses in T2D patients and conflicting effects of GIPR agonists and antagonists in improving glucose tolerance and preventing weight gain. There is, however, a recently renewed interest in GIPR biology, following the realization that GIPR responses can be restored after an initial period of blood glucose normalization and the recent development of dual GLP-1R/GIPR agonists with superior capacity for controlling blood glucose levels and weight. The importance of GLP-1R trafficking and subcellular signaling in the control of receptor outputs is well established, but little is known about the pattern of spatiotemporal signaling from the GIPR in beta cells. Here, we have directly compared surface expression, trafficking, and signaling characteristics of both incretin receptors in pancreatic beta cells to identify potential differences that might underlie distinct pharmacological responses associated with each receptor. Our results indicate increased cell surface levels, internalization, degradation, and endosomal vs plasma membrane activity for the GLP-1R, while the GIPR is instead associated with increased plasma membrane recycling, reduced desensitization, and enhanced downstream signal amplification. These differences might have potential implications for the capacity of each incretin receptor to control beta cell function.
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Affiliation(s)
- Yusman Manchanda
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK
| | - Stavroula Bitsi
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK
| | - Shiqian Chen
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London W12 0NN, UK
| | - Johannes Broichhagen
- Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Berlin 13125, Germany
| | | | - Ben Jones
- Correspondence: Alejandra Tomas, PhD, Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK, ; or Ben Jones, MD, PhD, Section of Endocrinology and Investigative Medicine, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK,
| | - Alejandra Tomas
- Correspondence: Alejandra Tomas, PhD, Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK, ; or Ben Jones, MD, PhD, Section of Endocrinology and Investigative Medicine, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK,
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6
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Mørch AM, Schneider F. Investigating Diffusion Dynamics and Interactions with Scanning Fluorescence Correlation Spectroscopy (sFCS). Methods Mol Biol 2023; 2654:61-89. [PMID: 37106176 DOI: 10.1007/978-1-0716-3135-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Activation of immune cells and formation of immunological synapses (IS) rely critically on the reorganization of the plasma membrane. These highly orchestrated processes are driven by diffusion and oligomerization dynamics, as well as by single molecule interactions. While slow macro- and meso-scale changes in organization can be observed with conventional imaging, fast nano-scale dynamics are often missed with traditional approaches, but resolving them is, nonetheless, essential to understand the underlying biological mechanisms at play. Here, we describe the use of scanning fluorescence correlation spectroscopy (sFCS) and scanning fluorescence cross-correlation spectroscopy (sFCCS) to study reorganization and changes in molecular diffusion dynamics and interactions during IS formation and in other biological settings. We focus on the practical aspects of the measurements including calibration and alignment of the optical setup, present a comprehensive protocol to perform the measurements, and provide data analysis pipelines and strategies. Finally, we show an exemplary application of the technology to studying Lck diffusion during T-cell signaling.
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Affiliation(s)
| | - Falk Schneider
- Translational Imaging Center, University of Southern California, Los Angeles, California, USA.
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7
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Leong SK, Hsiao JC, Shie JJ. A Multiscale Molecular Dynamic Analysis Reveals the Effect of Sialylation on EGFR Clustering in a CRISPR/Cas9-Derived Model. Int J Mol Sci 2022; 23:ijms23158754. [PMID: 35955894 PMCID: PMC9368999 DOI: 10.3390/ijms23158754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial and viral pathogens can modulate the glycosylation of key host proteins to facilitate pathogenesis by using various glycosidases, particularly sialidases. Epidermal growth factor receptor (EGFR) signaling is activated by ligand-induced receptor dimerization and oligomerization. Ligand binding induces conformational changes in EGFR, leading to clusters and aggregation. However, information on the relevance of EGFR clustering in the pattern of glycosylation during bacterial and viral invasion remains unclear. In this study, (1) we established CRISPR/Cas9-mediated GFP knock-in (EGFP-KI) HeLa cells expressing fluorescently tagged EGFR at close to endogenous levels to study EGF-induced EGFR clustering and molecular dynamics; (2) We studied the effect of sialylation on EGF-induced EGFR clustering and localization in live cells using a high content analysis platform and raster image correlation spectroscopy (RICS) coupled with a number and brightness (N&B) analysis; (3) Our data reveal that the removal of cell surface sialic acids by sialidase treatment significantly decreases EGF receptor clustering with reduced fluorescence intensity, number, and area of EGFR-GFP clusters per cell upon EGF stimulation. Sialylation appears to mediate EGF-induced EGFR clustering as demonstrated by the change of EGFR-GFP clusters in the diffusion coefficient and molecular brightness, providing new insights into the role of sialylation in EGF-induced EGFR activation; and (4) We envision that the combination of CRISPR/Cas9-mediated fluorescent tagging of endogenous proteins and fluorescence imaging techniques can be the method of choice for studying the molecular dynamics and interactions of proteins in live cells.
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Affiliation(s)
- Shwee Khuan Leong
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Taiwan International Graduate Program (TIGP), Sustainable Chemical Science & Technology (SCST), Academia Sinica, Taipei 11529, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University (NYCU), Hsinchu 30050, Taiwan
| | - Jye-Chian Hsiao
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Jiun-Jie Shie
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Correspondence:
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8
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Ng WS, Sielaff H, Zhao ZW. Phase Separation-Mediated Chromatin Organization and Dynamics: From Imaging-Based Quantitative Characterizations to Functional Implications. Int J Mol Sci 2022; 23:8039. [PMID: 35887384 PMCID: PMC9316379 DOI: 10.3390/ijms23148039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/14/2022] Open
Abstract
As an effective and versatile strategy to compartmentalize cellular components without the need for lipid membranes, phase separation has been found to underpin a wide range of intranuclear processes, particularly those involving chromatin. Many of the unique physico-chemical properties of chromatin-based phase condensates are harnessed by the cell to accomplish complex regulatory functions in a spatially and temporally controlled manner. Here, we survey key recent findings on the mechanistic roles of phase separation in regulating the organization and dynamics of chromatin-based molecular processes across length scales, packing states and intranuclear functions, with a particular emphasis on quantitative characterizations of these condensates enabled by advanced imaging-based approaches. By illuminating the complex interplay between chromatin and various chromatin-interacting molecular species mediated by phase separation, this review sheds light on an emerging multi-scale, multi-modal and multi-faceted landscape that hierarchically regulates the genome within the highly crowded and dynamic nuclear space. Moreover, deficiencies in existing studies also highlight the need for mechanism-specific criteria and multi-parametric approaches for the characterization of chromatin-based phase separation using complementary techniques and call for greater efforts to correlate the quantitative features of these condensates with their functional consequences in close-to-native cellular contexts.
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Affiliation(s)
- Woei Shyuan Ng
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Hendrik Sielaff
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
| | - Ziqing Winston Zhao
- Department of Chemistry, Faculty of Science, National University of Singapore, Singapore 119543, Singapore; (W.S.N.); (H.S.)
- Centre for BioImaging Sciences (CBIS), Faculty of Science, National University of Singapore, Singapore 117557, Singapore
- Mechanobiology Institute (MBI), National University of Singapore, Singapore 117411, Singapore
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9
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Gardeta SR, García-Cuesta EM, D’Agostino G, Soler Palacios B, Quijada-Freire A, Lucas P, Bernardino de la Serna J, Gonzalez-Riano C, Barbas C, Rodríguez-Frade JM, Mellado M. Sphingomyelin Depletion Inhibits CXCR4 Dynamics and CXCL12-Mediated Directed Cell Migration in Human T Cells. Front Immunol 2022; 13:925559. [PMID: 35903108 PMCID: PMC9315926 DOI: 10.3389/fimmu.2022.925559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/17/2022] [Indexed: 11/29/2022] Open
Abstract
Sphingolipids, ceramides and cholesterol are integral components of cellular membranes, and they also play important roles in signal transduction by regulating the dynamics of membrane receptors through their effects on membrane fluidity. Here, we combined biochemical and functional assays with single-particle tracking analysis of diffusion in the plasma membrane to demonstrate that the local lipid environment regulates CXCR4 organization and function and modulates chemokine-triggered directed cell migration. Prolonged treatment of T cells with bacterial sphingomyelinase promoted the complete and sustained breakdown of sphingomyelins and the accumulation of the corresponding ceramides, which altered both membrane fluidity and CXCR4 nanoclustering and dynamics. Under these conditions CXCR4 retained some CXCL12-mediated signaling activity but failed to promote efficient directed cell migration. Our data underscore a critical role for the local lipid composition at the cell membrane in regulating the lateral mobility of chemokine receptors, and their ability to dynamically increase receptor density at the leading edge to promote efficient cell migration.
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Affiliation(s)
- Sofía R. Gardeta
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Eva M. García-Cuesta
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Gianluca D’Agostino
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Blanca Soler Palacios
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Adriana Quijada-Freire
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Pilar Lucas
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jorge Bernardino de la Serna
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Central Laser Facility, Rutherford Appleton Laboratory, Medical Research Council-Research Complex at Harwell, Science and Technology Facilities Council, Harwell, United Kingdom
- National Institute for Health and Care Research Imperial Biomedical Research Center, London, United Kingdom
| | - Carolina Gonzalez-Riano
- Metabolomic and Bioanalysis Center (CEMBIO), Pharmacy Faculty, Centro de Estudios Universitarios Universities, Madrid, Spain
| | - Coral Barbas
- Metabolomic and Bioanalysis Center (CEMBIO), Pharmacy Faculty, Centro de Estudios Universitarios Universities, Madrid, Spain
| | - José Miguel Rodríguez-Frade
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Mario Mellado
- Chemokine Signaling Group, Department of Immunology and Oncology, National Center for Biotechnology/Consejo Superior de Investigaciones Científicas, Madrid, Spain
- *Correspondence: Mario Mellado,
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10
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Morana O, Nieto‐Garai JA, Björkholm P, Bernardino de la Serna J, Terrones O, Arboleya A, Ciceri D, Rojo‐Bartolomé I, Blouin CM, Lamaze C, Lorizate M, Contreras F. Identification of a New Cholesterol-Binding Site within the IFN-γ Receptor that is Required for Signal Transduction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105170. [PMID: 35166455 PMCID: PMC9008429 DOI: 10.1002/advs.202105170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/26/2022] [Indexed: 05/05/2023]
Abstract
The cytokine interferon-gamma (IFN-γ) is a master regulator of innate and adaptive immunity involved in a broad array of human diseases that range from atherosclerosis to cancer. IFN-γ exerts it signaling action by binding to a specific cell surface receptor, the IFN-γ receptor (IFN-γR), whose activation critically depends on its partition into lipid nanodomains. However, little is known about the impact of specific lipids on IFN-γR signal transduction activity. Here, a new conserved cholesterol (chol) binding motif localized within its single transmembrane domain is identified. Through direct binding, chol drives the partition of IFN-γR2 chains into plasma membrane lipid nanodomains, orchestrating IFN-γR oligomerization and transmembrane signaling. Bioinformatics studies show that the signature sequence stands for a conserved chol-binding motif presented in many mammalian membrane proteins. The discovery of chol as the molecular switch governing IFN-γR transmembrane signaling represents a significant advance for understanding the mechanism of lipid selectivity by membrane proteins, but also for figuring out the role of lipids in modulating cell surface receptor function. Finally, this study suggests that inhibition of the chol-IFNγR2 interaction may represent a potential therapeutic strategy for various IFN-γ-dependent diseases.
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Affiliation(s)
- Ornella Morana
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Jon Ander Nieto‐Garai
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Patrik Björkholm
- Center for Biomembrane ResearchDepartment of Biochemistry and BiophysicsStockholm UniversityStockholmSE‐106 91Sweden
- Science for Life LaboratoryStockholm UniversitySolnaSE‐171 21Sweden
| | - Jorge Bernardino de la Serna
- National Heart and Lung InstituteFaculty of MedicineImperial College LondonSouth KensingtonSir Alexander Fleming BuildingLondonSW7 2AZUK
- Central Laser FacilityRutherford Appleton LaboratoryMRC‐Research Complex at HarwellScience and Technology Facilities CouncilHarwellOX11 0QXUK
- NIHR Imperial Biomedical Research CentreLondonSW7 2AZUK
| | - Oihana Terrones
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Aroa Arboleya
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Dalila Ciceri
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Iratxe Rojo‐Bartolomé
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Cédric M. Blouin
- Institut Curie ‐ Centre de RecherchePSL Research UniversityMembrane Mechanics and Dynamics of Intracellular Signaling LaboratoryParis75248France
- Institut National de la Santé et de la Recherche Médicale (INSERM)ParisU1143France
- Centre National de la Recherche Scientifique (CNRS)UMR 3666Paris75248France
| | - Christophe Lamaze
- Institut Curie ‐ Centre de RecherchePSL Research UniversityMembrane Mechanics and Dynamics of Intracellular Signaling LaboratoryParis75248France
- Institut National de la Santé et de la Recherche Médicale (INSERM)ParisU1143France
- Centre National de la Recherche Scientifique (CNRS)UMR 3666Paris75248France
| | - Maier Lorizate
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
| | - Francesc‐Xabier Contreras
- Instituto Biofisika (UPV/EHU, CSIC)University of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- Department of Biochemistry and Molecular BiologyFaculty of Science and TechnologyUniversity of the Basque Country (UPV/EHU)Barrio Sarriena s/nLeioaE‐48940Spain
- IKERBASQUEBasque Foundation for ScienceBilbao48011Spain
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11
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Owyong TC, Hong Y. Emerging fluorescence tools for the study of proteostasis in cells. Curr Opin Chem Biol 2022; 67:102116. [PMID: 35176555 DOI: 10.1016/j.cbpa.2022.102116] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/22/2021] [Accepted: 01/12/2022] [Indexed: 11/25/2022]
Abstract
Understanding how cells maintain the functional proteome and respond to stress conditions is critical for deciphering molecular pathogenesis and developing treatments for conditions such as neurodegenerative diseases. Efforts towards finer quantification of cellular proteostasis machinery efficiency, phase transitions and local environment changes remain a priority. Herein, we describe recent developments in fluorescence-based strategy and methodology, building on the experimental toolkit, for the study of proteostasis (protein homeostasis) in cells. We hope this review can assist in bridging gaps between a multitude of research disciplines and promote interdisciplinary collaboration to address the crucial topic of proteostasis.
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Affiliation(s)
- Tze Cin Owyong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia; ARC Centre of Excellence in Exciton Science, School of Chemistry, Bio21 Institute, The University of Melbourne, Victoria, 3010, Australia
| | - Yuning Hong
- Department of Biochemistry and Chemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia.
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12
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Makaremi S, Moran-Mirabal J. Measuring the Lateral Diffusion of Plasma Membrane Receptors Using Raster Image Correlation Spectroscopy. Methods Mol Biol 2022; 2440:289-303. [PMID: 35218546 DOI: 10.1007/978-1-0716-2051-9_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Raster image correlation spectroscopy (RICS) enables detecting and quantifying diffusion in live cells using standard commercial laser scanning confocal microscopes. Here, we describe a protocol based on RICS for measuring the lateral diffusion of two immunoreceptors within the plasma membrane of the macrophage cell line RAW 264.7. The sample images and measurements presented in this chapter were obtained from RICS analysis of Toll-like receptor 2 (TLR2) and cluster of differentiation 14 (CD14), which are transmembrane and membrane-anchored receptors, respectively. A step-by-step guideline is provided to acquire raster-scanned images and to extract the diffusion coefficients using RICS analysis.
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Affiliation(s)
- Sara Makaremi
- School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada
| | - Jose Moran-Mirabal
- School of Biomedical Engineering, McMaster University, Hamilton, ON, Canada.
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada.
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13
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Agarwal SR, Sherpa RT, Moshal KS, Harvey RD. Compartmentalized cAMP signaling in cardiac ventricular myocytes. Cell Signal 2022; 89:110172. [PMID: 34687901 PMCID: PMC8602782 DOI: 10.1016/j.cellsig.2021.110172] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 01/03/2023]
Abstract
Activation of different receptors that act by generating the common second messenger cyclic adenosine monophosphate (cAMP) can elicit distinct functional responses in cardiac myocytes. Selectively sequestering cAMP activity to discrete intracellular microdomains is considered essential for generating receptor-specific responses. The processes that control this aspect of compartmentalized cAMP signaling, however, are not completely clear. Over the years, technological innovations have provided critical breakthroughs in advancing our understanding of the mechanisms underlying cAMP compartmentation. Some of the factors identified include localized production of cAMP by differential distribution of receptors, localized breakdown of this second messenger by targeted distribution of phosphodiesterase enzymes, and limited diffusion of cAMP by protein kinase A (PKA)-dependent buffering or physically restricted barriers. The aim of this review is to provide a discussion of our current knowledge and highlight some of the gaps that still exist in the field of cAMP compartmentation in cardiac myocytes.
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14
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Van den Broeck L, Gobble M, Sozzani R. Quantifying Intercellular Movement and Protein Stoichiometry for Computational Modeling. Methods Mol Biol 2022; 2457:367-382. [PMID: 35349154 DOI: 10.1007/978-1-0716-2132-5_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Analyzing protein movement dynamics and their regulation has shown to be important in the study of cell fate decisions. Such analyses can be performed with scanning fluorescence correlation spectroscopy (scanning FCS), a versatile imaging methodology that has been applied in the animal kingdom and recently adapted to the plant kingdom. Specifically, scanning FCS allows for qualitatively capturing protein movement across barriers, such as the active transport through plasmodesmata, the analysis of protein movement rates, and the quantification of the stoichiometry of protein complexes, composed of one or more different proteins. Importantly, the quantifiable data generated with scanning FCS can be used to inform computational models, enhancing model simulations of in vivo events, such as cell fate decisions, during plant development.
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Affiliation(s)
- Lisa Van den Broeck
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA
| | - Mariah Gobble
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA
| | - Rosangela Sozzani
- Plant and Microbial Biology Department, North Carolina State University, Raleigh, NC, USA.
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15
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Pannek A, Houghton FJ, Verhagen AM, Dower SK, Hinde E, Gleeson PA. Dynamics of intracellular neonatal Fc receptor-ligand interactions in primary macrophages using biophysical fluorescence techniques. Mol Biol Cell 2021; 33:ar6. [PMID: 34731029 PMCID: PMC8886815 DOI: 10.1091/mbc.e21-02-0061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The neonatal Fc receptor (FcRn) is responsible for the recycling of endocytosed albumin and IgG, and contributes to their long plasma half-life. We recently identified an FcRn-dependent recycling pathway from macropinosomes in macrophages; however, little is known about the dynamics of intracellular FcRn–ligand interactions to promote recycling. Here we demonstrate a multiplexed biophysical fluorescent microscopy approach to resolve the spatiotemporal dynamics of albumin–FcRn interactions in living bone marrow–derived macrophages (BMDMs). We used the phasor approach to fluorescence lifetime imaging microscopy (FLIM) of Förster resonance energy transfer (FRET) to detect the interaction of a FcRn–mCherry fusion protein with endocytosed Alexa Fluor 488–labeled human serum albumin (HSA–AF488) in BMDMs, and raster image correlation spectroscopy (RICS) analysis of single fluorescent-labeled albumin molecules to monitor the diffusion kinetics of internalized albumin. Our data identified a major fraction of immobile HSA–AF488 molecules in endosomal structures of human FcRn-positive mouse macrophages and an increase in FLIM-FRET following endocytosis, including detection of FRET in tubular-like structures. A nonbinding mutant of albumin showed minimum FLIM-FRET and high mobility. These data reveal the kinetics of FcRn–ligand binding within endosomal structures for recruitment into transport carriers for recycling. These approaches have wide applicability for analyses of intracellular ligand–receptor interactions.
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Affiliation(s)
- Andreas Pannek
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010.,Institute of Experimental Immunology, University of Bonn, Venusberg Campus, D-53127, Germany
| | - Fiona J Houghton
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010
| | - Anne M Verhagen
- CSL Limited, Research, Bio21 Molecular Science and Biotechnology Institute, Victoria 3010, Australia
| | - Steven K Dower
- CSL Limited, Research, Bio21 Molecular Science and Biotechnology Institute, Victoria 3010, Australia
| | - Elizabeth Hinde
- School of Physics and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.,Department of Biochemistry and Pharmacology, The University of Melbourne, Victoria 3010, Australia
| | - Paul A Gleeson
- Department of Biochemistry and Pharmacology and Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010
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16
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Harvey RD, Clancy CE. Mechanisms of cAMP compartmentation in cardiac myocytes: experimental and computational approaches to understanding. J Physiol 2021; 599:4527-4544. [PMID: 34510451 DOI: 10.1113/jp280801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/07/2021] [Indexed: 01/04/2023] Open
Abstract
The small diffusible second messenger 3',5'-cyclic adenosine monophosphate (cAMP) is found in virtually every cell in our bodies, where it mediates responses to a variety of different G protein coupled receptors (GPCRs). In the heart, cAMP plays a critical role in regulating many different aspects of cardiac myocyte function, including gene transcription, cell metabolism, and excitation-contraction coupling. Yet, not all GPCRs that stimulate cAMP production elicit the same responses. Subcellular compartmentation of cAMP is essential to explain how different receptors can utilize the same diffusible second messenger to elicit unique functional responses. However, the mechanisms contributing to this behaviour and its significance in producing physiological and pathological responses are incompletely understood. Mathematical modelling has played an essential role in gaining insight into these questions. This review discusses what we currently know about cAMP compartmentation in cardiac myocytes and questions that are yet to be answered.
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Affiliation(s)
- Robert D Harvey
- Department of Pharmacology, University of Nevada, Reno, NV, 89557, USA
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California-Davis, Davis, CA, 95616, USA
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17
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Shi B, Li W, Song Y, Wang Z, Ju R, Ulman A, Hu J, Palomba F, Zhao Y, Le JP, Jarrard W, Dimoff D, Digman MA, Gratton E, Zang C, Jiang H. UTX condensation underlies its tumour-suppressive activity. Nature 2021; 597:726-731. [PMID: 34526716 PMCID: PMC9008583 DOI: 10.1038/s41586-021-03903-7] [Citation(s) in RCA: 101] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
UTX (also known as KDM6A) encodes a histone H3K27 demethylase and is an important tumour suppressor that is frequently mutated in human cancers1. However, as the demethylase activity of UTX is often dispensable for mediating tumour suppression and developmental regulation2-8, the underlying molecular activity of UTX remains unknown. Here we show that phase separation of UTX underlies its chromatin-regulatory activity in tumour suppression. A core intrinsically disordered region (cIDR) of UTX forms phase-separated liquid condensates, and cIDR loss caused by the most frequent cancer mutation of UTX is mainly responsible for abolishing tumour suppression. Deletion, mutagenesis and replacement assays of the intrinsically disordered region demonstrate a critical role of UTX condensation in tumour suppression and embryonic stem cell differentiation. As shown by reconstitution in vitro and engineered systems in cells, UTX recruits the histone methyltransferase MLL4 (also known as KMT2D) to the same condensates and enriches the H3K4 methylation activity of MLL4. Moreover, UTX regulates genome-wide histone modifications and high-order chromatin interactions in a condensation-dependent manner. We also found that UTY, the Y chromosome homologue of UTX with weaker tumour-suppressive activity, forms condensates with reduced molecular dynamics. These studies demonstrate a crucial biological function of liquid condensates with proper material states in enabling the tumour-suppressive activity of a chromatin regulator.
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Affiliation(s)
- Bi Shi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Wei Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Yansu Song
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Zhenjia Wang
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Rui Ju
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Aleksandra Ulman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jing Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Francesco Palomba
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Yanfang Zhao
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - John Philip Le
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - William Jarrard
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - David Dimoff
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Michelle A. Digman
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Chongzhi Zang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA,Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA,Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA,UVA Cancer Center, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA,Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA,UVA Cancer Center, University of Virginia School of Medicine, Charlottesville, VA, USA
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18
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Lorizate M, Terrones O, Nieto-Garai JA, Rojo-Bartolomé I, Ciceri D, Morana O, Olazar-Intxausti J, Arboleya A, Martin A, Szynkiewicz M, Calleja-Felipe M, Bernardino de la Serna J, Contreras FX. Super-Resolution Microscopy Using a Bioorthogonal-Based Cholesterol Probe Provides Unprecedented Capabilities for Imaging Nanoscale Lipid Heterogeneity in Living Cells. SMALL METHODS 2021; 5:e2100430. [PMID: 34928061 DOI: 10.1002/smtd.202100430] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/26/2021] [Indexed: 06/14/2023]
Abstract
Despite more than 20 years of work since the lipid raft concept was proposed, the existence of these nanostructures remains highly controversial due to the lack of noninvasive methods to investigate their native nanorganization in living unperturbed cells. There is an unmet need for probes for direct imaging of nanoscale membrane dynamics with high spatial and temporal resolution in living cells. In this paper, a bioorthogonal-based cholesterol probe (chol-N3 ) is developed that, combined with nanoscopy, becomes a new powerful method for direct visualization and characterization of lipid raft at unprecedented resolution in living cells. The chol-N3 probe mimics cholesterol in synthetic and cellular membranes without perturbation. When combined with live-cell super-resolution microscopy, chol-N3 demonstrates the existence of cholesterol-rich nanodomains of <50 nm at the plasma membrane of resting living cells. Using this tool, the lipid membrane structure of such subdiffraction limit domains is identified, and the nanoscale spatiotemporal organization of cholesterol in the plasma membrane of living cells reveals multiple cholesterol diffusion modes at different spatial localizations. Finally, imaging across thick organ samples outlines the potential of this new method to address essential biological questions that were previously beyond reach.
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Affiliation(s)
- Maier Lorizate
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Oihana Terrones
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Jon Ander Nieto-Garai
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Iratxe Rojo-Bartolomé
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Dalila Ciceri
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Ornella Morana
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - June Olazar-Intxausti
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Aroa Arboleya
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Alexia Martin
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
| | - Marta Szynkiewicz
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, OX11 0FA, UK
| | - Maria Calleja-Felipe
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
| | - Jorge Bernardino de la Serna
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
- Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Research Complex at Harwell, Oxford, OX11 0FA, UK
- NIHR Imperial Biomedical Research Centre, London, SW7 2AZ, UK
| | - F-Xabier Contreras
- Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU) and Instituto Biofisika (UPV/EHU, CSIC), Barrio Sarriena s/n, Leioa, 48940, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, 48011, Spain
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19
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Johnson KA, Bhattarai N, Budicini MR, LaBonia CM, Baker SCB, Gerstman BS, Chapagain PP, Stahelin RV. Cysteine Mutations in the Ebolavirus Matrix Protein VP40 Promote Phosphatidylserine Binding by Increasing the Flexibility of a Lipid-Binding Loop. Viruses 2021; 13:1375. [PMID: 34372582 PMCID: PMC8310056 DOI: 10.3390/v13071375] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/25/2022] Open
Abstract
Ebolavirus (EBOV) is a negative-sense RNA virus that causes severe hemorrhagic fever in humans. The matrix protein VP40 facilitates viral budding by binding to lipids in the host cell plasma membrane and driving the formation of filamentous, pleomorphic virus particles. The C-terminal domain of VP40 contains two highly-conserved cysteine residues at positions 311 and 314, but their role in the viral life cycle is unknown. We therefore investigated the properties of VP40 mutants in which the conserved cysteine residues were replaced with alanine. The C311A mutation significantly increased the affinity of VP40 for membranes containing phosphatidylserine (PS), resulting in the assembly of longer virus-like particles (VLPs) compared to wild-type VP40. The C314A mutation also increased the affinity of VP40 for membranes containing PS, albeit to a lesser degree than C311A. The double mutant behaved in a similar manner to the individual mutants. Computer modeling revealed that both cysteine residues restrain a loop segment containing lysine residues that interact with the plasma membrane, but Cys311 has the dominant role. Accordingly, the C311A mutation increases the flexibility of this membrane-binding loop, changes the profile of hydrogen bonding within VP40 and therefore binds to PS with greater affinity. This is the first evidence that mutations in VP40 can increase its affinity for biological membranes and modify the length of Ebola VLPs. The Cys311 and Cys314 residues therefore play an important role in dynamic interactions at the plasma membrane by modulating the ability of VP40 to bind PS.
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Affiliation(s)
- Kristen A. Johnson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Nisha Bhattarai
- Department of Physics, Florida International University, Miami, FL 33199, USA; (N.B.); (B.S.G.); (P.P.C.)
| | - Melissa R. Budicini
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Carolyn M. LaBonia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Sarah Catherine B. Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.A.J.); (M.R.B.); (C.M.L.); (S.C.B.B.)
| | - Bernard S. Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA; (N.B.); (B.S.G.); (P.P.C.)
- The Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem P. Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA; (N.B.); (B.S.G.); (P.P.C.)
- The Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology and the Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
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20
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Meng D, Yang Q, Melick CH, Park BC, Hsieh T, Curukovic A, Jeong M, Zhang J, James NG, Jewell JL. ArfGAP1 inhibits mTORC1 lysosomal localization and activation. EMBO J 2021; 40:e106412. [PMID: 33988249 PMCID: PMC8204869 DOI: 10.15252/embj.2020106412] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 03/14/2021] [Accepted: 03/24/2021] [Indexed: 12/11/2022] Open
Abstract
The mammalian target of rapamycin complex 1 (mTORC1) integrates nutrients, growth factors, stress, and energy status to regulate cell growth and metabolism. Amino acids promote mTORC1 lysosomal localization and subsequent activation. However, the subcellular location or interacting proteins of mTORC1 under amino acid-deficient conditions is not completely understood. Here, we identify ADP-ribosylation factor GTPase-activating protein 1 (ArfGAP1) as a crucial regulator of mTORC1. ArfGAP1 interacts with mTORC1 in the absence of amino acids and inhibits mTORC1 lysosomal localization and activation. Mechanistically, the membrane curvature-sensing amphipathic lipid packing sensor (ALPS) motifs that bind to vesicle membranes are crucial for ArfGAP1 to interact with and regulate mTORC1 activity. Importantly, ArfGAP1 represses cell growth through mTORC1 and is an independent prognostic factor for the overall survival of pancreatic cancer patients. Our study identifies ArfGAP1 as a critical regulator of mTORC1 that functions by preventing the lysosomal transport and activation of mTORC1, with potential for cancer therapeutics.
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Affiliation(s)
- Delong Meng
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Qianmei Yang
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Chase H Melick
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Brenden C Park
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Ting‐Sung Hsieh
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Adna Curukovic
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Mi‐Hyeon Jeong
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Junmei Zhang
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
| | - Nicholas G James
- Department of Cell and Molecular BiologyJohn A. Burns School of MedicineUniversity of HawaiiHonoluluHIUSA
| | - Jenna L Jewell
- Department of Molecular BiologyUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTXUSA
- Hamon Center for Regenerative Science and MedicineUniversity of Texas Southwestern Medical CenterDallasTXUSA
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21
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Bernabé-Rubio M, Bosch-Fortea M, Alonso MA, Bernardino de la Serna J. Multi-dimensional and spatiotemporal correlative imaging at the plasma membrane of live cells to determine the continuum nano-to-micro scale lipid adaptation and collective motion. Methods 2021; 193:136-147. [PMID: 34126167 DOI: 10.1016/j.ymeth.2021.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/25/2022] Open
Abstract
The primary cilium is a specialized plasma membrane protrusion with important receptors for signalling pathways. In polarized epithelial cells, the primary cilium assembles after the midbody remnant (MBR) encounters the centrosome at the apical surface. The membrane surrounding the MBR, namely remnant-associated membrane patch (RAMP), once situated next to the centrosome, releases some of its lipid components to form a centrosome-associated membrane patch (CAMP) from which the ciliary membrane stems. The RAMP undergoes a spatiotemporal membrane refinement during the formation of the CAMP, which becomes highly enriched in condensed membranes with low lateral mobility. To better understand this process, we have developed a correlative imaging approach that yields quantitative information about the lipid lateral packing, its mobility and collective assembly at the plasma membrane at different spatial scales over time. Our work paves the way towards a quantitative understanding of the spatiotemporal lipid collective assembly at the plasma membrane as a functional determinant in cell biology and its direct correlation with the membrane physicochemical state. These findings allowed us to gain a deeper insight into the mechanisms behind the biogenesis of the ciliary membrane of polarized epithelial cells.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London SE1 9RT, UK
| | - Minerva Bosch-Fortea
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain; Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary, University of London, Mile End Road, London E1 4NS, UK
| | - Miguel A Alonso
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell OX11 0QX, UK; National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London SW7 2AZ, UK; NIHR Imperial Biomedical Research Centre, London SW7 2AZ, UK.
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22
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Priest DG, Bernardini A, Lou J, Mantovani R, Hinde E. Live cell dynamics of the NF-Y transcription factor. Sci Rep 2021; 11:10992. [PMID: 34040015 PMCID: PMC8155045 DOI: 10.1038/s41598-021-90081-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 04/29/2021] [Indexed: 11/24/2022] Open
Abstract
Transcription factors (TFs) are core players in the control of gene expression, evolutionarily selected to recognise a subset of specific DNA sequences and nucleate the recruitment of the transcriptional machinery. How TFs assemble and move in the nucleus to locate and bind their DNA targets and cause a transcriptional response, remains mostly unclear. NF-Y is a highly conserved, heterotrimeric TF with important roles in both housekeeping and lineage-specific gene expression, functioning as a promoter organiser. Despite a large number of biochemical, structural and genomic studies of NF-Y, there is a lack of experiments in single living cells; therefore, basic assumptions of NF-Y biology remain unproven in vivo. Here we employ a series of dynamic fluorescence microscopy methods (FLIM-FRET, NB, RICS and FRAP) to study NF-Y dynamics and complex formation in live cells. Specifically, we provide quantitative measurement of NF-Y subunit association and diffusion kinetics in the nucleus that collectively suggest NF-Y to move and bind chromatin as a trimeric complex in vivo.
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Affiliation(s)
- David G Priest
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia
| | - Andrea Bernardini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Jieqiong Lou
- School of Physics, University of Melbourne, Melbourne, VIC, Australia
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milan, Italy.
| | - Elizabeth Hinde
- School of Physics, University of Melbourne, Melbourne, VIC, Australia.
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, VIC, Australia.
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23
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Fluorescence Fluctuation Spectroscopy enables quantification of potassium channel subunit dynamics and stoichiometry. Sci Rep 2021; 11:10719. [PMID: 34021177 PMCID: PMC8140153 DOI: 10.1038/s41598-021-90002-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 04/15/2021] [Indexed: 11/08/2022] Open
Abstract
Voltage-gated potassium (Kv) channels are a family of membrane proteins that facilitate K+ ion diffusion across the plasma membrane, regulating both resting and action potentials. Kv channels comprise four pore-forming α subunits, each with a voltage sensing domain, and they are regulated by interaction with β subunits such as those belonging to the KCNE family. Here we conducted a comprehensive biophysical characterization of stoichiometry and protein diffusion across the plasma membrane of the epithelial KCNQ1-KCNE2 complex, combining total internal reflection fluorescence (TIRF) microscopy and a series of complementary Fluorescence Fluctuation Spectroscopy (FFS) techniques. Using this approach, we found that KCNQ1-KCNE2 has a predominant 4:4 stoichiometry, while non-bound KCNE2 subunits are mostly present as dimers in the plasma membrane. At the same time, we identified unique spatio-temporal diffusion modalities and nano-environment organization for each channel subunit. These findings improve our understanding of KCNQ1-KCNE2 channel function and suggest strategies for elucidating the subunit stoichiometry and forces directing localization and diffusion of ion channel complexes in general.
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24
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Oligomerization and Cell Egress Controlled by Two Microdomains of Canine Distemper Virus Matrix Protein. mSphere 2021; 6:6/2/e01024-20. [PMID: 33853875 PMCID: PMC8546710 DOI: 10.1128/msphere.01024-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The multimeric matrix (M) protein of clinically relevant paramyxoviruses orchestrates assembly and budding activity of viral particles at the plasma membrane (PM). We identified within the canine distemper virus (CDV) M protein two microdomains, potentially assuming α-helix structures, which are essential for membrane budding activity. Remarkably, while two rationally designed microdomain M mutants (E89R, microdomain 1 and L239D, microdomain 2) preserved proper folding, dimerization, interaction with the nucleocapsid protein, localization at and deformation of the PM, the virus-like particle formation, as well as production of infectious virions (as monitored using a membrane budding-complementation system), were, in sharp contrast, strongly impaired. Of major importance, raster image correlation spectroscopy (RICS) revealed that both microdomains contributed to finely tune M protein mobility specifically at the PM. Collectively, our data highlighted the cornerstone membrane budding-priming activity of two spatially discrete M microdomains, potentially by coordinating the assembly of productive higher oligomers at the PM. IMPORTANCE Despite the availability of efficient vaccines, morbilliviruses (e.g., canine distemper virus [CDV] and measles virus [MeV]) still cause major health impairments. Although antivirals may support vaccination campaigns, approved inhibitors are to date still lacking. Targeting late stages of the viral life cycle (i.e., the cell exit system) represents a viable option to potentially counteract morbilliviral infections. The matrix (M) protein of morbillivirus is a major contributor to membrane budding activity and is assumed to assemble into dimers that further associate to form higher oligomers. Here, we rationally engineered M protein variants with modifications in two microdomains that potentially locate at dimer-dimer interfaces. Our results spotlight the cornerstone impact of both microdomains in membrane budding activity and further suggest a role of finely tuned high-order oligomer formation in regulating late stages of cell exit. Collectively, our findings highlight two microdomains in the morbilliviral M protein as novel attractive targets for drug design.
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25
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Wang W, Ma Y, Bonaccorsi S, Cong VT, Pandžić E, Yang Z, Goyette J, Lisi F, Tilley RD, Gaus K, Gooding JJ. Investigating Spatial Heterogeneity of Nanoparticles Movement in Live Cells with Pair-Correlation Microscopy and Phasor Analysis. Anal Chem 2021; 93:3803-3812. [PMID: 33590750 DOI: 10.1021/acs.analchem.0c04285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
How nanoparticles distribute in living cells and overcome cellular barriers are important criteria in the design of drug carriers. Pair-correlation microscopy is a correlation analysis of fluctuation in the fluorescence intensity obtained by a confocal line scan that can quantify the dynamic properties of nanoparticle diffusion including the number of mobile nanoparticles, diffusion coefficient, and transit time across a spatial distance. Due to the potential heterogeneities in nanoparticle properties and the complexity within the cellular environment, quantification of averaged auto- and pair-correlation profiles may obscure important insights into the ability of nanoparticles to deliver drugs. To overcome this issue, we used phasor analysis to develop a data standardizing method, which can segment the scanned line into several subregions according to diffusion and address the spatial heterogeneity of nanoparticles moving inside cells. The phasor analysis is a fit-free method that represents autocorrelation profiles for each pixel relative to free diffusion on the so-called phasor plots. Phasor plots can then be used to select subpopulations for which the auto- and pair-correlation analysis can be performed separately. We demonstrate the phasor analysis for pair-correlation microscopy for investigating 16 nm, Cy5-labeled silica nanoparticles diffusing across the plasma membrane and green fluorescent proteins (GFP) diffusing across nuclear envelope in MCF-7 cells.
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Affiliation(s)
- Wenqian Wang
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Yuanqing Ma
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Simone Bonaccorsi
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Vu Thanh Cong
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Elvis Pandžić
- Biomedical Imaging Facility, Mark Wainwright Analytical Centre, University of New South Wales, Sydney 2052, Australia
| | - Zhengmin Yang
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Jesse Goyette
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - Fabio Lisi
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
| | - Richard D Tilley
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,Electron Microscope Unit, Mark Wainwright Analytical Centre, University of New South Wales, Sydney 2052, Australia
| | - Katharina Gaus
- School of Medical Science, University of New South Wales, Sydney 2052, Australia.,EMBL Australia Node in Single Molecule Science, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Sydney 2052, Australia
| | - J Justin Gooding
- School of Chemistry, University of New South Wales, Sydney 2052, Australia.,Australian Centre for NanoMedicine, University of New South Wales, Sydney 2052, Australia.,ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, University of New South Wales, Sydney 2052, Australia
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26
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Van't Padje A, Oyarte Galvez L, Klein M, Hink MA, Postma M, Shimizu T, Kiers ET. Temporal tracking of quantum-dot apatite across in vitro mycorrhizal networks shows how host demand can influence fungal nutrient transfer strategies. THE ISME JOURNAL 2021; 15:435-449. [PMID: 32989245 PMCID: PMC8027207 DOI: 10.1038/s41396-020-00786-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/04/2020] [Accepted: 09/17/2020] [Indexed: 11/18/2022]
Abstract
Arbuscular mycorrhizal fungi function as conduits for underground nutrient transport. While the fungal partner is dependent on the plant host for its carbon (C) needs, the amount of nutrients that the fungus allocates to hosts can vary with context. Because fungal allocation patterns to hosts can change over time, they have historically been difficult to quantify accurately. We developed a technique to tag rock phosphorus (P) apatite with fluorescent quantum-dot (QD) nanoparticles of three different colors, allowing us to study nutrient transfer in an in vitro fungal network formed between two host roots of different ages and different P demands over a 3-week period. Using confocal microscopy and raster image correlation spectroscopy, we could distinguish between P transfer from the hyphae to the roots and P retention in the hyphae. By tracking QD-apatite from its point of origin, we found that the P demands of the younger root influenced both: (1) how the fungus distributed nutrients among different root hosts and (2) the storage patterns in the fungus itself. Our work highlights that fungal trade strategies are highly dynamic over time to local conditions, and stresses the need for precise measurements of symbiotic nutrient transfer across both space and time.
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Affiliation(s)
- Anouk Van't Padje
- Laboratory of Genetics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- Department of Ecological Sciences, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Loreto Oyarte Galvez
- Department of Ecological Sciences, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- AMOLF Institute, Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - Malin Klein
- Department of Ecological Sciences, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Mark A Hink
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Faculty of Science, University of Amsterdam, Science park 904, 1090 GE, Amsterdam, The Netherlands
| | - Marten Postma
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Faculty of Science, University of Amsterdam, Science park 904, 1090 GE, Amsterdam, The Netherlands
| | - Thomas Shimizu
- AMOLF Institute, Science Park 104, 1098 XG, Amsterdam, The Netherlands
| | - E Toby Kiers
- Department of Ecological Sciences, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, de Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
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27
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Bernabé-Rubio M, Bosch-Fortea M, García E, Bernardino de la Serna J, Alonso MA. Adaptive Lipid Immiscibility and Membrane Remodeling Are Active Functional Determinants of Primary Ciliogenesis. SMALL METHODS 2021; 5:e2000711. [PMID: 34927881 DOI: 10.1002/smtd.202000711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/11/2020] [Indexed: 06/14/2023]
Abstract
Lipid liquid-liquid immiscibility and its consequent lateral heterogeneity have been observed under thermodynamic equilibrium in model and native membranes. However, cholesterol-rich membrane domains, sometimes referred to as lipid rafts, are difficult to observe spatiotemporally in live cells. Despite their importance in many biological processes, robust evidence for their existence remains elusive. This is mainly due to the difficulty in simultaneously determining their chemical composition and physicochemical nature, whilst spatiotemporally resolving their nanodomain lifetime and molecular dynamics. In this study, a bespoke method based on super-resolution stimulated emission depletion (STED) microscopy and raster imaging correlation spectroscopy (RICS) is used to overcome this issue. This methodology, laser interleaved confocal RICS and STED-RICS (LICSR), enables simultaneous tracking of lipid lateral packing and dynamics at the nanoscale. Previous work indicated that, in polarized epithelial cells, the midbody remnant licenses primary cilium formation through an unidentified mechanism. LICSR shows that lipid immiscibility and its adaptive collective nanoscale self-assembly are crucial for the midbody remnant to supply condensed membranes to the centrosome for the biogenesis of the ciliary membrane. Hence, this work poses a breakthrough in the field of lipid biology by providing compelling evidence of a functional role for liquid ordered-like membranes in primary ciliogenesis.
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Affiliation(s)
- Miguel Bernabé-Rubio
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28049, Spain
- King's College London Centre for Stem Cells and Regenerative Medicine, 28th Floor, Tower Wing, Guy's Campus, Great Maze Pond, London, SE1 9RT, UK
| | - Minerva Bosch-Fortea
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28049, Spain
- Institute of Bioengineering and School of Engineering and Materials Science, Queen Mary, University of London, Mile End Road, London, E1 4NS, UK
| | - Esther García
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell, OX11 0QX, UK
- CR-UK Beatson Institute, Switchback Road, Glasgow, G61 1BD, UK
| | - Jorge Bernardino de la Serna
- Central Laser Facility, Rutherford Appleton Laboratory, MRC-Research Complex at Harwell, Science and Technology Facilities Council, Harwell, OX11 0QX, UK
- National Heart and Lung Institute, Imperial College London, Sir Alexander Fleming Building, London, SW7 2AZ, UK
- NIHR Imperial Biomedical Research Centre, London, SW7 2AZ, UK
| | - Miguel A Alonso
- Department of Cell Biology and Immunology, Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, 28049, Spain
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28
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Sachon E, Walrant A, Sagan S, Cribier S, Rodriguez N. Binding and crossing: Methods for the characterization of membrane-active peptides interactions with membranes at the molecular level. Arch Biochem Biophys 2021; 699:108751. [PMID: 33421380 DOI: 10.1016/j.abb.2021.108751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/29/2020] [Accepted: 01/01/2021] [Indexed: 11/16/2022]
Abstract
Antimicrobial and cell-penetrating peptides have been the object of extensive studies for more than 60 years. Initially these two families were studied separately, and more recently parallels have been drawn. These studies have given rise to numerous methodological developments both in terms of observation techniques and membrane models. This review presents some of the most recent original and innovative developments in this field, namely droplet interface bilayers (DIBs), new fluorescence approaches, force measurements, and photolabelling.
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Affiliation(s)
- Emmanuelle Sachon
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Astrid Walrant
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Sandrine Sagan
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
| | - Sophie Cribier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France.
| | - Nicolas Rodriguez
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
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29
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Lateral diffusion of CD14 and TLR2 in macrophage plasma membrane assessed by raster image correlation spectroscopy and single particle tracking. Sci Rep 2020; 10:19375. [PMID: 33168941 PMCID: PMC7652837 DOI: 10.1038/s41598-020-76272-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 10/23/2020] [Indexed: 01/02/2023] Open
Abstract
The diffusion of membrane receptors is central to many biological processes, such as signal transduction, molecule translocation, and ion transport, among others; consequently, several advanced fluorescence microscopy techniques have been developed to measure membrane receptor mobility within live cells. The membrane-anchored receptor cluster of differentiation 14 (CD14) and the transmembrane toll-like receptor 2 (TLR2) are important receptors in the plasma membrane of macrophages that activate the intracellular signaling cascade in response to pathogenic stimuli. The aim of the present work was to compare the diffusion coefficients of CD14 and TLR2 on the apical and basal membranes of macrophages using two fluorescence-based methods: raster image correlation spectroscopy (RICS) and single particle tracking (SPT). In the basal membrane, the diffusion coefficients obtained from SPT and RICS were found to be comparable and revealed significantly faster diffusion of CD14 compared with TLR2. In addition, RICS showed that the diffusion of both receptors was significantly faster in the apical membrane than in the basal membrane, suggesting diffusion hindrance by the adhesion of the cells to the substrate. This finding highlights the importance of selecting the appropriate membrane (i.e., basal or apical) and corresponding method when measuring receptor diffusion in live cells. Accurately knowing the diffusion coefficient of two macrophage receptors involved in the response to pathogen insults will facilitate the study of changes that occur in signaling in these cells as a result of aging and disease.
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30
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Thirukkumaran OM, Kluba M, Hofkens J, Mizuno H. Autophosphorylation of EGFR at Y954 Facilitated Homodimerization and Enhanced Downstream Signals. Biophys J 2020; 119:2127-2137. [PMID: 33096081 DOI: 10.1016/j.bpj.2020.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
Asymmetric dimer formation of epidermal growth factor receptor (EGFR) is crucial for EGF-induced receptor activation. Even though autophosphorylation is important for activation, its role remains elusive in the context of regulating dimers. In this study, employing overlapping time series analysis to raster image correlation spectroscopy (RICS), we observed time-dependent transient dynamics of EGFR dimerization and found EGFR kinase activity to be essential for dimerization. As a result of which, we hypothesized that phosphorylation could influence dimerization. Evaluating this point, we observed that one of the tyrosine residues (Y954) located in the C-terminal lobe of the activator kinase domain was important to potentiate dimerization. Functional imaging to monitor Ca2+ and ERK signals revealed a significant role of Y954 in influencing downstream signaling cascade. Crucial for stabilization of EGFR asymmetric dimer is a "latch" formed between kinase domains of the binding partners. Because Y954 is positioned adjacent to the latch binding region on the kinase domain, we propose that phosphorylation strengthened the latch interaction. On the contrary, we identified that threonine phosphorylation (T669) in the latch domain negatively regulated EGFR dimerization and the downstream signals. Overall, we have delineated the previously anonymous role of phosphorylation at the latch interface of kinase domains in regulating EGFR dimerization.
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Affiliation(s)
- Ovia M Thirukkumaran
- Laboratory of Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Malgorzata Kluba
- Laboratory of Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Johan Hofkens
- Chem&Tech-Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Hideaki Mizuno
- Laboratory of Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, Department of Chemistry, KU Leuven, Heverlee, Belgium.
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31
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Titlow J, Robertson F, Järvelin A, Ish-Horowicz D, Smith C, Gratton E, Davis I. Syncrip/hnRNP Q is required for activity-induced Msp300/Nesprin-1 expression and new synapse formation. J Cell Biol 2020; 219:133707. [PMID: 32040548 PMCID: PMC7055005 DOI: 10.1083/jcb.201903135] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/21/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
Memory and learning involve activity-driven expression of proteins and cytoskeletal reorganization at new synapses, requiring posttranscriptional regulation of localized mRNA a long distance from corresponding nuclei. A key factor expressed early in synapse formation is Msp300/Nesprin-1, which organizes actin filaments around the new synapse. How Msp300 expression is regulated during synaptic plasticity is poorly understood. Here, we show that activity-dependent accumulation of Msp300 in the postsynaptic compartment of the Drosophila larval neuromuscular junction is regulated by the conserved RNA binding protein Syncrip/hnRNP Q. Syncrip (Syp) binds to msp300 transcripts and is essential for plasticity. Single-molecule imaging shows that msp300 is associated with Syp in vivo and forms ribosome-rich granules that contain the translation factor eIF4E. Elevated neural activity alters the dynamics of Syp and the number of msp300:Syp:eIF4E RNP granules at the synapse, suggesting that these particles facilitate translation. These results introduce Syp as an important early acting activity-dependent regulator of a plasticity gene that is strongly associated with human ataxias.
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Affiliation(s)
- Joshua Titlow
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Aino Järvelin
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - David Ish-Horowicz
- Department of Biochemistry, University of Oxford, Oxford, UK.,Medical Research Council Lab for Molecular Cell Biology, University College London, London, UK
| | - Carlas Smith
- Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, University of California Irvine, Irvine, CA
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, UK
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32
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Ranjit S, Lanzanò L, Libby AE, Gratton E, Levi M. Advances in fluorescence microscopy techniques to study kidney function. Nat Rev Nephrol 2020; 17:128-144. [PMID: 32948857 DOI: 10.1038/s41581-020-00337-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2020] [Indexed: 02/07/2023]
Abstract
Fluorescence microscopy, in particular immunofluorescence microscopy, has been used extensively for the assessment of kidney function and pathology for both research and diagnostic purposes. The development of confocal microscopy in the 1950s enabled imaging of live cells and intravital imaging of the kidney; however, confocal microscopy is limited by its maximal spatial resolution and depth. More recent advances in fluorescence microscopy techniques have enabled increasingly detailed assessment of kidney structure and provided extraordinary insights into kidney function. For example, nanoscale precise imaging by rapid beam oscillation (nSPIRO) is a super-resolution microscopy technique that was originally developed for functional imaging of kidney microvilli and enables detection of dynamic physiological events in the kidney. A variety of techniques such as fluorescence recovery after photobleaching (FRAP), fluorescence correlation spectroscopy (FCS) and Förster resonance energy transfer (FRET) enable assessment of interaction between proteins. The emergence of other super-resolution techniques, including super-resolution stimulated emission depletion (STED), photoactivated localization microscopy (PALM), stochastic optical reconstruction microscopy (STORM) and structured illumination microscopy (SIM), has enabled functional imaging of cellular and subcellular organelles at ≤50 nm resolution. The deep imaging via emission recovery (DIVER) detector allows deep, label-free and high-sensitivity imaging of second harmonics, enabling assessment of processes such as fibrosis, whereas fluorescence lifetime imaging microscopy (FLIM) enables assessment of metabolic processes.
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Affiliation(s)
- Suman Ranjit
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA. .,Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Luca Lanzanò
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Genoa, Italy.,Department of Physics and Astronomy "Ettore Majorana", University of Catania, Catania, Italy
| | - Andrew E Libby
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA
| | - Enrico Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA, USA.
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, DC, USA.
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33
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Montecinos-Franjola F, Bauer BL, Mears JA, Ramachandran R. GFP fluorescence tagging alters dynamin-related protein 1 oligomerization dynamics and creates disassembly-refractory puncta to mediate mitochondrial fission. Sci Rep 2020; 10:14777. [PMID: 32901052 PMCID: PMC7479153 DOI: 10.1038/s41598-020-71655-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/19/2020] [Indexed: 01/22/2023] Open
Abstract
Green fluorescent protein (GFP)-tagging is the prevalent strategy to monitor protein dynamics in living cells. However, the consequences of appending the bulky GFP moiety to the protein of interest are rarely investigated. Here, using a powerful combination of quantitative fluorescence spectroscopic and imaging techniques, we have examined the oligomerization dynamics of the GFP-tagged mitochondrial fission GTPase dynamin-related protein 1 (Drp1) both in vitro and in vivo. We find that GFP-tagged Drp1 exhibits impaired oligomerization equilibria in solution that corresponds to a greatly diminished cooperative GTPase activity in comparison to native Drp1. Consequently, GFP-tagged Drp1 constitutes aberrantly stable, GTP-resistant supramolecular assemblies both in vitro and in vivo, neither of which reflects a more dynamic native Drp1 oligomerization state. Indeed, GFP-tagged Drp1 is detected more frequently per unit length over mitochondria in Drp1-null mouse embryonic fibroblasts (MEFs) compared to wild-type (wt) MEFs, indicating that the drastically reduced GTP turnover restricts oligomer disassembly from the mitochondrial surface relative to mixed oligomers comprising native and GFP-tagged Drp1. Yet, GFP-tagged Drp1 retains the capacity to mediate membrane constriction in vitro and mitochondrial division in vivo. These findings suggest that instead of robust assembly-disassembly dynamics, persistent Drp1 higher-order oligomerization over membranes is sufficient for mitochondrial fission.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Brianna L Bauer
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Jason A Mears
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.,Center for Mitochondrial Diseases, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Rajesh Ramachandran
- Department of Physiology and Biophysics, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA. .,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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34
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Kwapiszewska K, Szczepański K, Kalwarczyk T, Michalska B, Patalas-Krawczyk P, Szymański J, Andryszewski T, Iwan M, Duszyński J, Hołyst R. Nanoscale Viscosity of Cytoplasm Is Conserved in Human Cell Lines. J Phys Chem Lett 2020; 11:6914-6920. [PMID: 32787203 PMCID: PMC7450658 DOI: 10.1021/acs.jpclett.0c01748] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Metabolic reactions in living cells are limited by diffusion of reagents in the cytoplasm. Any attempt to quantify the kinetics of biochemical reactions in the cytosol should be preceded by careful measurements of the physical properties of the cellular interior. The cytoplasm is a complex, crowded fluid characterized by effective viscosity dependent on its structure at a nanoscopic length scale. In this work, we present and validate the model describing the cytoplasmic nanoviscosity, based on measurements in seven human cell lines, for nanoprobes ranging in diameters from 1 to 150 nm. Irrespective of cell line origin (epithelial-mesenchymal, cancerous-noncancerous, male-female, young-adult), we obtained a similar dependence of the viscosity on the size of the nanoprobes, with characteristic length-scales of 20 ± 11 nm (hydrodynamic radii of major crowders in the cytoplasm) and 4.6 ± 0.7 nm (radii of intercrowder gaps). Moreover, we revealed that the cytoplasm behaves as a liquid for length scales smaller than 100 nm and as a physical gel for larger length scales.
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Affiliation(s)
- Karina Kwapiszewska
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Krzysztof Szczepański
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Tomasz Kalwarczyk
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Bernadeta Michalska
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | | | - Jędrzej Szymański
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | - Tomasz Andryszewski
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Michalina Iwan
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Jerzy Duszyński
- Nencki
Institute of Experimental Biology, Pasteura 3, Warsaw, 02-093, Poland
| | - Robert Hołyst
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, Warsaw, 01-224, Poland
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35
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Li W, Hu J, Shi B, Palomba F, Digman MA, Gratton E, Jiang H. Biophysical properties of AKAP95 protein condensates regulate splicing and tumorigenesis. Nat Cell Biol 2020; 22:960-972. [PMID: 32719551 PMCID: PMC7425812 DOI: 10.1038/s41556-020-0550-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 06/24/2020] [Indexed: 12/14/2022]
Abstract
It remains unknown if biophysical or material properties of biomolecular condensates regulate cancer. Here we show that AKAP95, a nuclear protein that regulates transcription and RNA splicing, plays an important role in tumorigenesis by supporting cancer cell growth and suppressing oncogene-induced senescence. AKAP95 forms phase-separated and liquid-like condensates in vitro and in nucleus. Mutations of key residues to different amino acids perturb AKAP95 condensation in opposite directions. Importantly, the activity of AKAP95 in splice regulation is abolished by disruption of condensation, significantly impaired by hardening of condensates, and regained by substituting its condensation-mediating region with other condensation-mediating regions from irrelevant proteins. Moreover, the abilities of AKAP95 in regulating gene expression and supporting tumorigenesis require AKAP95 to form condensates with proper liquidity and dynamicity. These results link phase separation to tumorigenesis and uncover an important role of appropriate biophysical properties of protein condensates in gene regulation and cancer.
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Affiliation(s)
- Wei Li
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Jing Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Bi Shi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Francesco Palomba
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Michelle A Digman
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Enrico Gratton
- Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California, Irvine, CA, USA
| | - Hao Jiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA.
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Boutant E, Bonzi J, Anton H, Nasim MB, Cathagne R, Réal E, Dujardin D, Carl P, Didier P, Paillart JC, Marquet R, Mély Y, de Rocquigny H, Bernacchi S. Zinc Fingers in HIV-1 Gag Precursor Are Not Equivalent for gRNA Recruitment at the Plasma Membrane. Biophys J 2020; 119:419-433. [PMID: 32574557 PMCID: PMC7376094 DOI: 10.1016/j.bpj.2020.05.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 01/16/2023] Open
Abstract
The human immunodeficiency virus type 1 Gag precursor specifically selects the unspliced viral genomic RNA (gRNA) from the bulk of cellular and spliced viral RNAs via its nucleocapsid (NC) domain and drives gRNA encapsidation at the plasma membrane (PM). To further identify the determinants governing the intracellular trafficking of Gag-gRNA complexes and their accumulation at the PM, we compared, in living and fixed cells, the interactions between gRNA and wild-type Gag or Gag mutants carrying deletions in NC zinc fingers (ZFs) or a nonmyristoylated version of Gag. Our data showed that the deletion of both ZFs simultaneously or the complete NC domain completely abolished intracytoplasmic Gag-gRNA interactions. Deletion of either ZF delayed the delivery of gRNA to the PM but did not prevent Gag-gRNA interactions in the cytoplasm, indicating that the two ZFs display redundant roles in this respect. However, ZF2 played a more prominent role than ZF1 in the accumulation of the ribonucleoprotein complexes at the PM. Finally, the myristate group, which is mandatory for anchoring the complexes at the PM, was found to be dispensable for the association of Gag with the gRNA in the cytosol.
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Affiliation(s)
- Emmanuel Boutant
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France.
| | - Jeremy Bonzi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Halina Anton
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Maaz Bin Nasim
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Raphael Cathagne
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Eléonore Réal
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Denis Dujardin
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Philippe Carl
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Jean-Christophe Paillart
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Roland Marquet
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Hugues de Rocquigny
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm - U1259 MAVIVH, Tours, France.
| | - Serena Bernacchi
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR9002, Strasbourg, France.
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37
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Gabriel M, Navarro GSC, de Borba L, Rossi AH, Gamarnik AV, Estrada LC. Dengue Virus Capsid Protein Dynamics Reveals Spatially Heterogeneous Motion in Live-Infected-Cells. Sci Rep 2020; 10:8751. [PMID: 32472078 PMCID: PMC7260208 DOI: 10.1038/s41598-020-65625-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/05/2020] [Indexed: 11/15/2022] Open
Abstract
Dengue is the single most important human viral infection transmitted by insects. The function of the viral proteins andtheir interactions with the host cell is under exhaustive investigation with the aim of identifying antiviral strategies. Here,using recombinant full-length dengue virus genomes, carrying a fluorescent mCherry fused to capsid, we studied biophysicalproperties of the viral protein during one infectious cycle in living cells. Dengue virus capsid protein associates to differentcellular compartments but its function in these locations is largely unknown. We evaluated the diffusion of capsid inside the celland determined a higher effective diffusion coefficient in the cytoplasm than in the nucleus. Using advanced fluorescencecorrelation methods, including the recently developed two-dimensional pair correlation analysis, we constructed for the first timehigh resolution maps of capsid mobility in an infected cell. We observed that the motion of capsid in the nucleoplasm-nucleolusinterface was highly organized, indicating an obstacle in this interface. Although nucleoli are membraneless structures, theydisplayed liquid-liquid phase separation. Once inside nucleoli, the protein showed isotropic mobility, indicating free diffusion orimmobilized capsid inside these structures. This is the first study presenting spatial and temporal dynamics of the dengue viruscapsid protein during infection.
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Affiliation(s)
- Manuela Gabriel
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), Buenos Aires, 1428, Argentina
| | - Guadalupe S Costa Navarro
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Luana de Borba
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Andrés H Rossi
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Andrea V Gamarnik
- Fundación Instituto Leloir-National Research Council for Science and Technology (CONICET), Buenos Aires, 1405, Argentina
| | - Laura C Estrada
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and IFIBA-National Research Council for Science and Technology (CONICET), Buenos Aires, 1428, Argentina.
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38
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DE Mets R, Delon A, Balland M, Destaing O, Wang I. Dynamic range and background filtering in raster image correlation spectroscopy. J Microsc 2020; 279:123-138. [PMID: 32441342 DOI: 10.1111/jmi.12925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 11/28/2022]
Abstract
Raster-scan image correlation spectroscopy (RICS) enables researchers to measure molecular translational diffusion constants and concentrations from standard confocal laser scanning microscope images and is suitable for measuring a wide range of mobility, especially fast-diffusing molecules. However, as RICS analysis is based on the spatial autocorrelation function of fluorescence images, it is sensitive to the presence of fluorescent structures within the image. In this study, we investigate methods to filter out immobile or slow moving background structures and their impact on RICS results. Both the conventional moving-average subtraction-based method and cross-correlation subtraction-based method are rationalized and quantified. Simulated data and experimental measurements in living cells stress the importance of optimizing the temporal resolution of background filtering for reliable RICS measurements. Finally, the capacity of RICS analysis to separate two species is studied.
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Affiliation(s)
- R DE Mets
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France.,Mechanobiology Institute, National University of Singapore, Singapore
| | - A Delon
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - M Balland
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
| | - O Destaing
- Institute for Advanced Biosciences, Université Grenoble Alpes, Grenoble, France
| | - I Wang
- Université Grenoble Alpes, CNRS, LIPhy, Grenoble, France
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39
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A Conserved Tryptophan in the Ebola Virus Matrix Protein C-Terminal Domain Is Required for Efficient Virus-Like Particle Formation. Pathogens 2020; 9:pathogens9050402. [PMID: 32455873 PMCID: PMC7281420 DOI: 10.3390/pathogens9050402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/19/2020] [Accepted: 05/19/2020] [Indexed: 02/05/2023] Open
Abstract
The Ebola virus (EBOV) harbors seven genes, one of which is the matrix protein eVP40, a peripheral protein that is sufficient to induce the formation of virus-like particles from the host cell plasma membrane. eVP40 can form different structures to fulfil different functions during the viral life cycle, although the structural dynamics of eVP40 that warrant dimer, hexamer, and octamer formation are still poorly understood. eVP40 has two conserved Trp residues at positions 95 and 191. The role of Trp95 has been characterized in depth as it serves as an important residue in eVP40 oligomer formation. To gain insight into the functional role of Trp191 in eVP40, we prepared mutations of Trp191 (W191A or W191F) to determine the effects of mutation on eVP40 plasma membrane localization and budding as well as eVP40 oligomerization. These in vitro and cellular experiments were complemented by molecular dynamics simulations of the wild-type (WT) eVP40 structure versus that of W191A. Taken together, Trp is shown to be a critical amino acid at position 191 as mutation to Ala reduces the ability of VP40 to localize to the plasma membrane inner leaflet and form new virus-like particles. Further, mutation of Trp191 to Ala or Phe shifted the in vitro equilibrium to the octamer form by destabilizing Trp191 interactions with nearby residues. This study has shed new light on the importance of interdomain interactions in stability of the eVP40 structure and the critical nature of timing of eVP40 oligomerization for plasma membrane localization and viral budding.
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40
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Ward KE, Sengupta R, Ropa JP, Amiar S, Stahelin RV. The Cytosolic Phospholipase A 2α N-terminal C2 Domain Binds and Oligomerizes on Membranes with Positive Curvature. Biomolecules 2020; 10:biom10040647. [PMID: 32331436 PMCID: PMC7226022 DOI: 10.3390/biom10040647] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/16/2020] [Accepted: 04/19/2020] [Indexed: 01/04/2023] Open
Abstract
Group IV phospholipase A2α (cPLA2α) regulates the production of prostaglandins and leukotrienes via the formation of arachidonic acid from membrane phospholipids. The targeting and membrane binding of cPLA2α to the Golgi involves the N-terminal C2 domain, whereas the catalytic domain produces arachidonic acid. Although most studies of cPLA2α concern its catalytic activity, it is also linked to homeostatic processes involving the generation of vesicles that traffic material from the Golgi to the plasma membrane. Here we investigated how membrane curvature influences the homeostatic role of cPLA2α in vesicular trafficking. The cPLA2α C2 domain is known to induce changes in positive membrane curvature, a process which is dependent on cPLA2α membrane penetration. We showed that cPLA2α undergoes C2 domain-dependent oligomerization on membranes in vitro and in cells. We found that the association of the cPLA2α C2 domain with membranes is limited to membranes with positive curvature, and enhanced C2 domain oligomerization was observed on vesicles ~50 nm in diameter. We demonstrated that the cPLA2α C2 domain localizes to cholesterol enriched Golgi-derived vesicles independently of cPLA2α catalytic activity. Moreover, we demonstrate the C2 domain selectively localizes to lipid droplets whereas the full-length enzyme to a much lesser extent. Our results therefore provide novel insight into the molecular forces that mediate C2 domain-dependent membrane localization in vitro and in cells.
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Affiliation(s)
- Katherine E. Ward
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN 46556, USA; (K.E.W.); (J.P.R.)
| | - Ranjan Sengupta
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA; (R.S.); (S.A.)
| | - James P. Ropa
- Department of Chemistry and Biochemistry, University of Notre Dame, South Bend, IN 46556, USA; (K.E.W.); (J.P.R.)
| | - Souad Amiar
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA; (R.S.); (S.A.)
| | - Robert V. Stahelin
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47906, USA; (R.S.); (S.A.)
- Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +01-765-494-4152
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41
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Schneider F, Hernandez-Varas P, Christoffer Lagerholm B, Shrestha D, Sezgin E, Julia Roberti M, Ossato G, Hecht F, Eggeling C, Urbančič I. High photon count rates improve the quality of super-resolution fluorescence fluctuation spectroscopy. JOURNAL OF PHYSICS D: APPLIED PHYSICS 2020; 53:164003. [PMID: 33191951 PMCID: PMC7655148 DOI: 10.1088/1361-6463/ab6cca] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/19/2019] [Accepted: 01/16/2020] [Indexed: 05/15/2023]
Abstract
Probing the diffusion of molecules has become a routine measurement across the life sciences, chemistry and physics. It provides valuable insights into reaction dynamics, oligomerisation, molecular (re-)organisation or cellular heterogeneities. Fluorescence correlation spectroscopy (FCS) is one of the widely applied techniques to determine diffusion dynamics in two and three dimensions. This technique relies on the temporal autocorrelation of intensity fluctuations but recording these fluctuations has thus far been limited by the detection electronics, which could not efficiently and accurately time-tag photons at high count rates. This has until now restricted the range of measurable dye concentrations, as well as the data quality of the FCS recordings, especially in combination with super-resolution stimulated emission depletion (STED) nanoscopy. Here, we investigate the applicability and reliability of (STED-)FCS at high photon count rates (average intensities of more than 1 MHz) using novel detection equipment, namely hybrid detectors and real-time gigahertz sampling of the photon streams implemented on a commercial microscope. By measuring the diffusion of fluorophores in solution and cytoplasm of live cells, as well as in model and cellular membranes, we show that accurate diffusion and concentration measurements are possible in these previously inaccessible high photon count regimes. Specifically, it offers much greater flexibility of experiments with biological samples with highly variable intensity, e.g. due to a wide range of expression levels of fluorescent proteins. In this context, we highlight the independence of diffusion properties of cytosolic GFP in a concentration range of approx. 0.01-1 µm. We further show that higher photon count rates also allow for much shorter acquisition times, and improved data quality. Finally, this approach also pronouncedly increases the robustness of challenging live cell STED-FCS measurements of nanoscale diffusion dynamics, which we testify by confirming a free diffusion pattern for a fluorescent lipid analogue on the apical membrane of adherent cells.
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Affiliation(s)
- Falk Schneider
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Pablo Hernandez-Varas
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Core Facility for Integrated Microscopy, Panum Institute, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Dilip Shrestha
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
| | - Erdinc Sezgin
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - M Julia Roberti
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Giulia Ossato
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Frank Hecht
- Leica Microsystems CMS GmbH, Am Friedensplatz 3, 68163 Mannheim, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Institute of Applied Optics and Biophysics, Friedrich-Schiller-University Jena, Max-Wien Platz 4, 07743 Jena, Germany
- Leibniz Institute of Photonic Technology e.V., Albert-Einstein-Straße 9, 07745 Jena, Germany
| | - Iztok Urbančič
- MRC Human Immunology Unit and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford, OX3 9DS, United Kingdom
- Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia
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42
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Guthmann M, Burton A, Torres‐Padilla M. Expression and phase separation potential of heterochromatin proteins during early mouse development. EMBO Rep 2019; 20:e47952. [PMID: 31701657 PMCID: PMC6893284 DOI: 10.15252/embr.201947952] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/03/2019] [Accepted: 10/16/2019] [Indexed: 12/29/2022] Open
Abstract
In most eukaryotes, constitutive heterochromatin is associated with H3K9me3 and HP1α. The latter has been shown to play a role in heterochromatin formation through liquid-liquid phase separation. However, many other proteins are known to regulate and/or interact with constitutive heterochromatic regions in several species. We postulate that some of these heterochromatic proteins may play a role in the regulation of heterochromatin formation by liquid-liquid phase separation. Indeed, an analysis of the constitutive heterochromatin proteome shows that proteins associated with constitutive heterochromatin are significantly more disordered than a random set or a full nucleome set of proteins. Interestingly, their expression begins low and increases during preimplantation development. These observations suggest that the preimplantation embryo is a useful model to address the potential role for phase separation in heterochromatin formation, anticipating exciting research in the years to come.
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Affiliation(s)
- Manuel Guthmann
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Adam Burton
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Maria‐Elena Torres‐Padilla
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
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43
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Longfils M, Smisdom N, Ameloot M, Rudemo M, Lemmens V, Fernández GS, Röding M, Lorén N, Hendrix J, Särkkä A. Raster Image Correlation Spectroscopy Performance Evaluation. Biophys J 2019; 117:1900-1914. [PMID: 31668746 PMCID: PMC7018992 DOI: 10.1016/j.bpj.2019.09.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 08/28/2019] [Accepted: 09/30/2019] [Indexed: 01/02/2023] Open
Abstract
Raster image correlation spectroscopy (RICS) is a fluorescence image analysis method for extracting the mobility, concentration, and stoichiometry of diffusing fluorescent molecules from confocal image stacks. The method works by calculating a spatial correlation function for each image and analyzing the average of those by model fitting. Rules of thumb exist for RICS image acquisitioning, yet a rigorous theoretical approach to predict the accuracy and precision of the recovered parameters has been lacking. We outline explicit expressions to reveal the dependence of RICS results on experimental parameters. In terms of imaging settings, we observed that a twofold decrease of the pixel size, e.g., from 100 to 50 nm, decreases the error on the translational diffusion constant (D) between three- and fivefold. For D = 1 μm2 s-1, a typical value for intracellular measurements, ∼25-fold lower mean-squared relative error was obtained when the optimal scan speed was used, although more drastic improvements were observed for other values of D. We proposed a slightly modified RICS calculation that allows correcting for the significant bias of the autocorrelation function at small (≪50 × 50 pixels) sizes of the region of interest. In terms of sample properties, at molecular brightness E = 100 kHz and higher, RICS data quality was sufficient using as little as 20 images, whereas the optimal number of frames for lower E scaled pro rata. RICS data quality was constant over the nM-μM concentration range. We developed a bootstrap-based confidence interval of D that outperformed the classical least-squares approach in terms of coverage probability of the true value of D. We validated the theory via in vitro experiments of enhanced green fluorescent protein at different buffer viscosities. Finally, we outline robust practical guidelines and provide free software to simulate the parameter effects on recovery of the diffusion coefficient.
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Affiliation(s)
- Marco Longfils
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden.
| | - Nick Smisdom
- Stadius Centre for Dynamical Systems, Signal Processing and Data Analytics, KU Leuven, Leuven, Belgium; Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Marcel Ameloot
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Mats Rudemo
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Veerle Lemmens
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium; Dynamic Bioimaging Lab, Hasselt University, Diepenbeek, Belgium; Molecular Imaging and Photonics, Chemistry Department, KU Leuven, Heverlee, Belgium
| | | | | | - Niklas Lorén
- RISE Bioscience and Materials, Gothenburg, Sweden; Department of Physics, Chalmers University of Technology, Gothenburg, Sweden
| | - Jelle Hendrix
- Advanced Optical Microscopy Centre, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium; Dynamic Bioimaging Lab, Hasselt University, Diepenbeek, Belgium.
| | - Aila Särkkä
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
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44
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Cheruku S, D'Olieslaeger L, Smisdom N, Smits J, Vanderzande D, Maes W, Ameloot M, Ethirajan A. Fluorescent PCDTBT Nanoparticles with Tunable Size for Versatile Bioimaging. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2497. [PMID: 31390806 PMCID: PMC6695891 DOI: 10.3390/ma12152497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 07/30/2019] [Accepted: 08/06/2019] [Indexed: 01/03/2023]
Abstract
Conjugated polymer nanoparticles exhibit very interesting properties for use as bio-imaging agents. In this paper, we report the synthesis of PCDTBT (poly([9-(1'-octylnonyl)-9H-carbazole-2,7-diyl]-2,5-thiophenediyl-2,1,3-benzothiadiazole-4,7-diyl-2,5-thiophene-diyl)) nanoparticles of varying sizes using the mini-emulsion and emulsion/solvent evaporation approach. The effect of the size of the particles on the optical properties is investigated using UV-Vis absorption and fluorescence emission spectroscopy. It is shown that PCDTBT nanoparticles have a fluorescence emission maximum around 710 nm, within the biological near-infrared "optical window". The photoluminescence quantum yield shows a characteristic trend as a function of size. The particles are not cytotoxic and are taken up successfully by human lung cancer carcinoma A549 cells. Irrespective of the size, all particles show excellent fluorescent brightness for bioimaging. The fidelity of the particles as fluorescent probes to study particle dynamics in situ is shown as a proof of concept by performing raster image correlation spectroscopy. Combined, these results show that PCDTBT is an excellent candidate to serve as a fluorescent probe for near-infrared bio-imaging.
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Affiliation(s)
- Srujan Cheruku
- Nanobiophysics and Soft Matter Interfaces group (NSI), Institute for Materials Research (IMO-IMOMEC), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium
| | - Lien D'Olieslaeger
- Nanobiophysics and Soft Matter Interfaces group (NSI), Institute for Materials Research (IMO-IMOMEC), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium
| | - Nick Smisdom
- Biomedical Research Institute (BIOMED), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium
| | - Joeri Smits
- Nanobiophysics and Soft Matter Interfaces group (NSI), Institute for Materials Research (IMO-IMOMEC), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium
| | - Dirk Vanderzande
- Design & Synthesis of Organic Semiconductors (DSOS), Institute for Materials Research (IMO-IMOMEC), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium
- IMEC, Associated lab IMOMEC, 3590 Diepenbeek, Belgium
| | - Wouter Maes
- Design & Synthesis of Organic Semiconductors (DSOS), Institute for Materials Research (IMO-IMOMEC), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium
- IMEC, Associated lab IMOMEC, 3590 Diepenbeek, Belgium
| | - Marcel Ameloot
- Biomedical Research Institute (BIOMED), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium
| | - Anitha Ethirajan
- Nanobiophysics and Soft Matter Interfaces group (NSI), Institute for Materials Research (IMO-IMOMEC), UHasselt-Hasselt University, 3590 Diepenbeek, Belgium.
- IMEC, Associated lab IMOMEC, 3590 Diepenbeek, Belgium.
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45
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Whiteside MD, Werner GDA, Caldas VEA, Van't Padje A, Dupin SE, Elbers B, Bakker M, Wyatt GAK, Klein M, Hink MA, Postma M, Vaitla B, Noë R, Shimizu TS, West SA, Kiers ET. Mycorrhizal Fungi Respond to Resource Inequality by Moving Phosphorus from Rich to Poor Patches across Networks. Curr Biol 2019; 29:2043-2050.e8. [PMID: 31178314 PMCID: PMC6584331 DOI: 10.1016/j.cub.2019.04.061] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/04/2019] [Accepted: 04/23/2019] [Indexed: 01/01/2023]
Abstract
The world's ecosystems are characterized by an unequal distribution of resources [1]. Trade partnerships between organisms of different species-mutualisms-can help individuals cope with such resource inequality [2-4]. Trade allows individuals to exchange commodities they can provide at low cost for resources that are otherwise impossible or more difficult to access [5, 6]. However, as resources become increasingly patchy in time or space, it is unknown how organisms alter their trading strategies [7, 8]. Here, we show how a symbiotic fungus mediates trade with a host root in response to different levels of resource inequality across its network. We developed a quantum-dot-tracking technique to quantify phosphorus-trading strategies of arbuscular mycorrhizal fungi simultaneously exposed to rich and poor resource patches. By following fluorescent nanoparticles of different colors across fungal networks, we determined where phosphorus was hoarded, relocated, and transferred to plant hosts. We found that increasing exposure to inequality stimulated trade. Fungi responded to high resource variation by (1) increasing the total amount of phosphorus distributed to host roots, (2) decreasing allocation to storage, and (3) differentially moving resources within the network from rich to poor patches. Using single-particle tracking and high-resolution video, we show how dynamic resource movement may help the fungus capitalize on value differences across the trade network, physically moving resources to areas of high demand to gain better returns. Such translocation strategies can help symbiotic organisms cope with exposure to resource inequality.
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Affiliation(s)
- Matthew D Whiteside
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Gijsbert D A Werner
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Balliol College, University of Oxford, Oxford OX1 3BJ, UK
| | - Victor E A Caldas
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands; AMOLF Institute, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Anouk Van't Padje
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Simon E Dupin
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Bram Elbers
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Milenka Bakker
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Gregory A K Wyatt
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Malin Klein
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands
| | - Mark A Hink
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Marten Postma
- Section of Molecular Cytology and van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 XH Amsterdam, the Netherlands
| | - Bapu Vaitla
- Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA
| | - Ronald Noë
- Faculté Psychologie, Université de Strasbourg, 12 Rue Goethe, 67000 Strasbourg, France
| | - Thomas S Shimizu
- AMOLF Institute, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Stuart A West
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - E Toby Kiers
- Department of Ecological Science, Vrije Universiteit, De Boelelaan 108, 1081 HV Amsterdam, the Netherlands.
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46
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Nguyen H, Ward WS, James NG. Spatial and temporal resolution of mORC4 fluorescent variants reveals structural requirements for achieving higher order self-association and pronuclei entry. Methods Appl Fluoresc 2019; 7:035002. [PMID: 30865939 PMCID: PMC6636821 DOI: 10.1088/2050-6120/ab0f57] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The Origin Replication Complex (ORC), which is a multi-subunit protein complex composed of six proteins ORC1-6, is essential for initiating licensing at DNA replication origins. We have previously reported that ORC4 has an alternative function wherein it forms a cage surrounding the extruded chromatin in female meiosis and is required for polar body extrusion (PBE). As this is a highly unexpected finding for protein that normally binds DNA, we tested whether ORC4 can actually form larger, higher order structures, which would be necessary to form a cage-like structure. We generated two fluorescent constructs of mouse ORC4, mORC4-EGFP and mORC4-FlAsH, to examine its spatial dynamics during oocyte activation in live cells. We show that both constructs were primarily monomeric throughout the embryo but self-association into larger units was detected with both probes. However, mORC4-FlAsH clearly showed higher order self-association and unique spatial distribution while mORC4-EGFP failed to form large structures during Anaphase II. Interestingly, both variants were found in the pronuclei suggesting that its role in DNA licensing is still functional. Our results with both constructs support the prediction that ORC4 can form higher order structures in the cytoplasm, suggesting that it is possible to form a cage-like structure. The finding that FlAsH labeled ORC4 formed demonstrably larger higher order structures than ORC4-GFP suggests that ORC4 oligomerization is sensitive to the bulky addition of GFP at its carboxy terminus.
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Affiliation(s)
- Hieu Nguyen
- Department of Anatomy, Biochemistry, and Physiology, John A. Burns School of Medicine, 1960 East-West Rd., University of Hawaii, Honolulu, HI 96822, United States of America
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47
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Obashi K, Matsuda A, Inoue Y, Okabe S. Precise Temporal Regulation of Molecular Diffusion within Dendritic Spines by Actin Polymers during Structural Plasticity. Cell Rep 2019; 27:1503-1515.e8. [DOI: 10.1016/j.celrep.2019.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 02/22/2019] [Accepted: 03/29/2019] [Indexed: 10/26/2022] Open
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48
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Levi M, Gratton E. Visualizing the regulation of SLC34 proteins at the apical membrane. Pflugers Arch 2019; 471:533-542. [PMID: 30613865 PMCID: PMC6436987 DOI: 10.1007/s00424-018-02249-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 12/19/2018] [Accepted: 12/20/2018] [Indexed: 10/27/2022]
Abstract
The cloning of the renal NaPi-2a (SLC34A1) and NaPi-2c (SLC34A3) phosphate transporters has made it possible to characterize the molecular and biophysical regulation of renal proximal tubular reabsorption of inorganic phosphate (Pi). Dietary factors, such as Pi and K, and several hormones and phosphatonins, including parathyroid hormone (PTH), fibroblast growth factor 23 (FGF23), and glucocorticoids, regulate the transporters through various transcriptional, translational, and post-translational mechanisms that involve acute trafficking via endocytosis or exocytosis, interactions with PDZ domain proteins, lipid microdomains, and diffusion and clustering in the apical brush border membrane. The visualization of these trafficking events by means of novel microscopy techniques that includes fluorescence lifetime imaging microscopy (FLIM), Förster resonance energy transfer (FRET), fluctuation correlation spectroscopy (FCS), and modulation tracking (MT), is the primary focus of this review.
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Affiliation(s)
- Moshe Levi
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA.
| | - Enrico Gratton
- Department of Biomedical Engineering, Laboratory for Fluorescence Dynamics, University of California at Irvine, Irvine, CA, USA
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49
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Sezgin E, Schneider F, Galiani S, Urbančič I, Waithe D, Lagerholm BC, Eggeling C. Measuring nanoscale diffusion dynamics in cellular membranes with super-resolution STED-FCS. Nat Protoc 2019; 14:1054-1083. [PMID: 30842616 DOI: 10.1038/s41596-019-0127-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/04/2019] [Indexed: 11/08/2022]
Abstract
Super-resolution microscopy techniques enable optical imaging in live cells with unprecedented spatial resolution. They unfortunately lack the temporal resolution required to directly investigate cellular dynamics at scales sufficient to measure molecular diffusion. These fast time scales are, on the other hand, routinely accessible by spectroscopic techniques such as fluorescence correlation spectroscopy (FCS). To enable the direct investigation of fast dynamics at the relevant spatial scales, FCS has been combined with super-resolution stimulated emission depletion (STED) microscopy. STED-FCS has been applied in point or scanning mode to reveal nanoscale diffusion behavior of molecules in live cells. In this protocol, we describe the technical details of performing point STED-FCS (pSTED-FCS) and scanning STED-FCS (sSTED-FCS) measurements, from calibration and sample preparation to data acquisition and analysis. We give particular emphasis to 2D diffusion dynamics in cellular membranes, using molecules tagged with organic fluorophores. These measurements can be accomplished within 4-6 h by those proficient in fluorescence imaging.
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Affiliation(s)
- Erdinc Sezgin
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Falk Schneider
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Silvia Galiani
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Iztok Urbančič
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Solid State Physics Department, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Dominic Waithe
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- MRC Centre for Computational Biology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - B Christoffer Lagerholm
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Christian Eggeling
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Wolfson Imaging Centre, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
- Institute of Applied Optics, Friedrich-Schiller-University Jena, Jena, Germany.
- Department of Biophysical Imaging, Leibniz Institute of Photonic Technology e.V., Jena, Germany.
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50
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Collini M, Radaelli F, Sironi L, Ceffa NG, D’Alfonso L, Bouzin M, Chirico G. Adaptive optics microspectrometer for cross-correlation measurement of microfluidic flows. JOURNAL OF BIOMEDICAL OPTICS 2019; 24:1-15. [PMID: 30816029 PMCID: PMC6987636 DOI: 10.1117/1.jbo.24.2.025004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/04/2018] [Indexed: 05/17/2023]
Abstract
Mapping flows in vivo is essential for the investigation of cardiovascular pathologies in animal models. The limitation of optical-based methods, such as space-time cross correlation, is the scattering of light by the connective and fat components and the direct wave front distortion by large inhomogeneities in the tissue. Nonlinear excitation of the sample fluorescence helps us by reducing light scattering in excitation. However, there is still a limitation on the signal-background due to the wave front distortion. We develop a diffractive optical microscope based on a single spatial light modulator (SLM) with no movable parts. We combine the correction of wave front distortions to the cross-correlation analysis of the flow dynamics. We use the SLM to shine arbitrary patterns of spots on the sample, to correct their optical aberrations, to shift the aberration corrected spot array on the sample for the collection of fluorescence images, and to measure flow velocities from the cross-correlation functions computed between couples of spots. The setup and the algorithms are tested on various microfluidic devices. By applying the adaptive optics correction algorithm, it is possible to increase up to 5 times the signal-to-background ratio and to reduce approximately of the same ratio the uncertainty of the flow speed measurement. By working on grids of spots, we can correct different aberrations in different portions of the field of view, a feature that allows for anisoplanatic aberrations correction. Finally, being more efficient in the excitation, we increase the accuracy of the speed measurement by employing a larger number of spots in the grid despite the fact that the two-photon excitation efficiency scales as the fourth power of this number: we achieve a twofold decrease of the uncertainty and a threefold increase of the accuracy in the evaluation of the flow speed.
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Affiliation(s)
- Maddalena Collini
- University of Milano-Bicocca, Department of Physics, Milan, Italy
- University of Milano-Bicocca, Nanomedicine Center, Milan, Italy
- Institute of Applied Sciences and Intelligent Systems, National Research Council of Italy, Pozzuoli, Italy
| | | | - Laura Sironi
- University of Milano-Bicocca, Department of Physics, Milan, Italy
| | - Nicolo G. Ceffa
- University of Milano-Bicocca, Department of Physics, Milan, Italy
| | - Laura D’Alfonso
- University of Milano-Bicocca, Department of Physics, Milan, Italy
| | - Margaux Bouzin
- University of Milano-Bicocca, Department of Physics, Milan, Italy
| | - Giuseppe Chirico
- University of Milano-Bicocca, Department of Physics, Milan, Italy
- University of Milano-Bicocca, Nanomedicine Center, Milan, Italy
- Institute of Applied Sciences and Intelligent Systems, National Research Council of Italy, Pozzuoli, Italy
- Address all correspondence to Giuseppe Chirico, E-mail:
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