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Eguchi M, Yoshimura H, Ueda Y, Ozawa T. Split Luciferase-Fragment Reconstitution for Unveiling RNA Localization and Dynamics in Live Cells. ACS Sens 2023; 8:4055-4063. [PMID: 37889477 DOI: 10.1021/acssensors.3c01080] [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: 10/28/2023]
Abstract
The intracellular distribution and dynamics of RNAs play pivotal roles in various physiological phenomena. The ability to monitor the amount and localization of endogenous RNAs in living cells allows for elucidating the mechanisms of various intracellular events. Protein-based fluorescent RNA probes are now widely used to visualize and analyze RNAs in living cells. However, continuously monitoring the temporal changes in RNA localization and dynamics in living cells is challenging. In this study, we developed a bioluminescent probe for spatiotemporal monitoring of RNAs in living cells by using a split-luciferase reconstitution technique. The probe consists of split fragments of a bioluminescent protein, NanoLuc, connected with RNA-binding protein domains generated from a custom-made mutation of a PUM-HD. The probe showed rapid luminescence intensity changes in response to an increase or decrease in the amount of a target RNA in vitro. In live-cell imaging, temporal alteration of the intracellular distribution of endogenous β-actin mRNA was visualized in response to extracellular stimulation. Furthermore, the application of the probe to the visualization of the specific localization of β-actin mRNA in primary hippocampal neurons was conducted. These results demonstrate the capability of the bioluminescent RNA probe to monitor the changes in localization, dynamics, and the amount of target RNA in living cells.
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Affiliation(s)
- Masatoshi Eguchi
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hideaki Yoshimura
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yoshibumi Ueda
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Ni Y, Arts R, Merkx M. Ratiometric Bioluminescent Sensor Proteins Based on Intramolecular Split Luciferase Complementation. ACS Sens 2019; 4:20-25. [PMID: 30525479 PMCID: PMC6350203 DOI: 10.1021/acssensors.8b01381] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bioluminescent sensor proteins provide attractive tools for applications ranging from in vivo imaging to point-of-care testing. Here we introduce a new class of ratiometric bioluminescent sensor proteins that do not rely on direct modulation of BRET efficiency, but are based on competitive intramolecular complementation of split NanoLuc luciferase. Proof of concept for the feasibility of this sensor principle was provided by developing a blue-red light emitting sensor protein for the detection of anti-HIV1-p17 antibodies with a 500% change in emission ratio and a Kd of 10 pM. The new sensor design also improved the dynamic response of a sensor for the therapeutic antibody cetuximab 4-fold, allowing the direct quantification of this anti-EGFR antibody in undiluted blood plasma. The modular sensor architecture allows easy and systematic tuning of a sensor's dynamic range and should be generally applicable to allow rational engineering of bioluminescent sensor proteins.
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Affiliation(s)
- Yan Ni
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Remco Arts
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Maarten Merkx
- Laboratory of Chemical Biology and Institute for Complex Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
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Li Q, Yoshimura H, Komiya M, Tajiri K, Uesugi M, Hata Y, Ozawa T. A robust split-luciferase-based cell fusion screening for discovering myogenesis-promoting molecules. Analyst 2018; 143:3472-3480. [DOI: 10.1039/c8an00285a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Screening by the luciferase complementation-based cell fusion assay discovered two myogenesis-promoting chemicals.
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Affiliation(s)
- Qiaojing Li
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Hideaki Yoshimura
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Maki Komiya
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
| | - Ken Tajiri
- Institute for Integrated Cell-Material Sciences (iCeMS)/Institute for Chemical Research (ICR)
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Motonari Uesugi
- Institute for Integrated Cell-Material Sciences (iCeMS)/Institute for Chemical Research (ICR)
- Kyoto University
- Kyoto 611-0011
- Japan
| | - Yutaka Hata
- Graduate School of Medical and Dental Sciences
- Tokyo Medical and Dental University
- Tokyo 113-8510
- Japan
| | - Takeaki Ozawa
- Department of Chemistry
- School of Science
- The University of Tokyo
- Tokyo 113-0033
- Japan
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4
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Kim SO, Jackman JA, Elazar M, Cho SJ, Glenn JS, Cho NJ. Quantitative Evaluation of Viral Protein Binding to Phosphoinositide Receptors and Pharmacological Inhibition. Anal Chem 2017; 89:9742-9750. [PMID: 28809547 PMCID: PMC5724528 DOI: 10.1021/acs.analchem.7b01568] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There is significant interest in developing analytical methods to characterize molecular recognition events between proteins and phosphoinositides, which are a medically important class of carbohydrate-functionalized lipids. Within this scope, one area of high priority involves quantitatively evaluating drug candidates that pharmacologically inhibit protein-phosphoinositide interactions. As full-length proteins are often difficult to produce, establishing methods to study these interactions with shorter, bioactive peptides would be advantageous. Herein, we report an atomic force microscopy (AFM)-based force spectroscopic approach to detect the specific interaction between an amphipathic, α-helical (AH) peptide derived from the hepatitis C virus NS5A protein and its biological target, the phosphatidylinositol (4,5)-bisphosphate [PI(4,5)P2] phosphoinositide receptor. After optimization of the peptide tethering strategy and measurement parameters, the binding specificity of AH peptide for PI(4,5)P2 receptors was comparatively evaluated across a panel of phosphoinositides and the influence of ionic strength on AH-PI(4,5)P2 binding strength was tested. Importantly, these capabilities were translated into the development of a novel experimental methodology to determine the inhibitory activity of a small-molecule drug candidate acting against the AH-PI(4,5)P2 interaction, and extracted kinetic parameters agree well with literature values obtained by conventional biochemical methods. Taken together, our findings provide a nanomechanical basis for explaining the high binding specificity of the NS5A AH to PI(4,5)P2 receptors, in turn establishing an analytical framework to study phosphoinositide-binding viral peptides and proteins as well as a broadly applicable approach to evaluate candidate inhibitors of protein-phosphoinositide interactions.
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Affiliation(s)
- Seong-Oh Kim
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Drive, 637553 Singapore
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Drive, 637553 Singapore.,Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Menashe Elazar
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine , Stanford, California 94305, United States
| | - Sang-Joon Cho
- Advanced Institute of Convergence Technology, Seoul National University , Suwon 443-270, South Korea
| | - Jeffrey S Glenn
- Division of Gastroenterology and Hepatology, Department of Medicine, Stanford University School of Medicine , Stanford, California 94305, United States.,Veterans Administration Medical Center , Palo Alto, California 94304, United States
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Drive, 637553 Singapore.,School of Chemical and Biomedical Engineering, Nanyang Technological University , 62 Nanyang Drive, 637459 Singapore
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AWAIS M, VORONINA SG, SUTTON R. An Efficient Method is Required to Transfect Non-dividing Cells with Genetically Encoded Optical Probes for Molecular Imaging. ANAL SCI 2015; 31:293-8. [DOI: 10.2116/analsci.31.293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Muhammad AWAIS
- NIHR Liverpool Pancreas Biomedical Research Unit, Institute of Translational Medicine, The University of Liverpool, Royal Liverpool University Hospital
| | - Svetlana G VORONINA
- Department of Cellular and Molecular Physiology, The University of Liverpool
| | - Robert SUTTON
- NIHR Liverpool Pancreas Biomedical Research Unit, Institute of Translational Medicine, The University of Liverpool, Royal Liverpool University Hospital
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6
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Hattori M, Ozawa T. Bioluminescent tools for the analysis of G-protein-coupled receptor and arrestin interactions. RSC Adv 2015. [DOI: 10.1039/c4ra14979c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
New protein-based bioluminescent probes for monitoring GPCR interaction with β-arrestin are presented.
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Affiliation(s)
- Mitsuru Hattori
- Department of Chemistry
- School of Science
- The University of Tokyo
- Bunkyo-ku
- Japan
| | - Takeaki Ozawa
- Department of Chemistry
- School of Science
- The University of Tokyo
- Bunkyo-ku
- Japan
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7
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Idevall-Hagren O, De Camilli P. Detection and manipulation of phosphoinositides. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1851:736-45. [PMID: 25514766 DOI: 10.1016/j.bbalip.2014.12.008] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 11/27/2014] [Accepted: 12/09/2014] [Indexed: 12/23/2022]
Abstract
Phosphoinositides (PIs) are minor components of cell membranes, but play key roles in cell function. Recent refinements in techniques for their detection, together with imaging methods to study their distribution and changes, have greatly facilitated the study of these lipids. Such methods have been complemented by the parallel development of techniques for the acute manipulation of their levels, which in turn allow bypassing the long-term adaptive changes implicit in genetic perturbations. Collectively, these advancements have helped elucidate the role of PIs in physiology and the impact of the dysfunction of their metabolism in disease. Combining methods for detection and manipulation enables the identification of specific roles played by each of the PIs and may eventually lead to the complete deconstruction of the PI signaling network. Here, we review current techniques used for the study and manipulation of cellular PIs and also discuss advantages and disadvantages associated with the various methods. This article is part of a Special Issue entitled Phosphoinositides.
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Affiliation(s)
- Olof Idevall-Hagren
- Department of Medical Cell Biology, Uppsala University, BMC Box 571, 75123 Uppsala, Sweden.
| | - Pietro De Camilli
- Department of Cell Biology, Howard Hughes Medical Institute and Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT 06510, USA.
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Wakelam MJO. The uses and limitations of the analysis of cellular phosphoinositides by lipidomic and imaging methodologies. Biochim Biophys Acta Mol Cell Biol Lipids 2014; 1841:1102-7. [PMID: 24769341 DOI: 10.1016/j.bbalip.2014.04.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 04/14/2014] [Accepted: 04/17/2014] [Indexed: 01/24/2023]
Abstract
The advent of mass spectrometric methods has facilitated the determination of multiple molecular species of cellular lipid classes including the polyphosphoinositides, though to date methods to analyse and quantify each of the individual three PtdInsP and three PtdInsP2 species are lacking. The use of imaging methods has allowed intracellular localization of the phosphoinositide classes but this methodology does not determine the acyl structures. The range of molecular species suggests a greater complexity in polyphosphoinositide signaling than yet defined but elucidating this will require further method development to be achieved. This article is part of a Special Issue entitled Tools to study lipid functions.
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HATTORI M, OZAWA T. Split Luciferase Complementation for Analysis of Intracellular Signaling. ANAL SCI 2014; 30:539-44. [DOI: 10.2116/analsci.30.539] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Mitsuru HATTORI
- Department of Chemistry, School of Science, The University of Tokyo
| | - Takeaki OZAWA
- Department of Chemistry, School of Science, The University of Tokyo
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