1
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Kamikawa T, Hashimoto A, Yamazaki N, Adachi J, Matsushima A, Kikuchi K, Hori Y. Bioisostere-conjugated fluorescent probes for live-cell protein imaging without non-specific organelle accumulation. Chem Sci 2024; 15:8097-8105. [PMID: 38817570 PMCID: PMC11134342 DOI: 10.1039/d3sc06957e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 04/26/2024] [Indexed: 06/01/2024] Open
Abstract
Specific labeling of proteins using membrane-permeable fluorescent probes is a powerful technique for bioimaging. Cationic fluorescent dyes with high fluorescence quantum yield, photostability, and water solubility provide highly useful scaffolds for protein-labeling probes. However, cationic probes generally show undesired accumulation in organelles, which causes a false-positive signal in localization analysis. Herein, we report a design strategy for probes that suppress undesired organelle accumulation using a bioisostere for intracellular protein imaging in living cells. Our design allows the protein labeling probes to possess both membrane permeability and suppress non-specific accumulation and has been shown to use several protein labeling systems, such as PYP-tag and Halo tag systems. We further developed a fluorogenic PYP-tag labeling probe for intracellular proteins and used it to visualize multiple localizations of target proteins in the intracellular system. Our strategy offers a versatile design for undesired accumulation-suppressed probes with cationic dye scaffolds and provides a valuable tool for intracellular protein imaging.
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Affiliation(s)
- Takuya Kamikawa
- Graduate School of Science, Kyushu University 744 Motooka Nishi Fukuoka 819-0395 Japan
| | - Akari Hashimoto
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Nozomi Yamazaki
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Junya Adachi
- Faculty of Science, Kyushu University, Fukuoka Fukuoka 819-0395 Japan
| | - Ayami Matsushima
- Faculty of Science, Kyushu University, Fukuoka Fukuoka 819-0395 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Faculty of Science, Kyushu University, Fukuoka Fukuoka 819-0395 Japan
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2
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Minoshima M, Reja SI, Hashimoto R, Iijima K, Kikuchi K. Hybrid Small-Molecule/Protein Fluorescent Probes. Chem Rev 2024; 124:6198-6270. [PMID: 38717865 DOI: 10.1021/acs.chemrev.3c00549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Hybrid small-molecule/protein fluorescent probes are powerful tools for visualizing protein localization and function in living cells. These hybrid probes are constructed by diverse site-specific chemical protein labeling approaches through chemical reactions to exogenous peptide/small protein tags, enzymatic post-translational modifications, bioorthogonal reactions for genetically incorporated unnatural amino acids, and ligand-directed chemical reactions. The hybrid small-molecule/protein fluorescent probes are employed for imaging protein trafficking, conformational changes, and bioanalytes surrounding proteins. In addition, fluorescent hybrid probes facilitate visualization of protein dynamics at the single-molecule level and the defined structure with super-resolution imaging. In this review, we discuss development and the bioimaging applications of fluorescent probes based on small-molecule/protein hybrids.
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Affiliation(s)
- Masafumi Minoshima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Shahi Imam Reja
- Immunology Frontier Research Center, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Ryu Hashimoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kohei Iijima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1, Yamadaoka, Suita, Osaka 5650871, Japan
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3
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Nishiura M, Hori Y, Umeno M, Kikuchi K. Visualization of multiple localizations of GLUT4 by fluorescent probes of PYP-tag with designed unnatural warhead. Chem Sci 2023; 14:5925-5935. [PMID: 37293637 PMCID: PMC10246691 DOI: 10.1039/d3sc00724c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/08/2023] [Indexed: 06/10/2023] Open
Abstract
Within a cell, multiple copies of the same protein coexist in different pathways and behave differently. Being able to individually analyze the constant actions of proteins in a cell is crucial to know the pathways through which they pass and which physiological functions they are deeply involved in. However, until now, it has been difficult to distinguish protein copies with distinct translocation properties by fluorescence labeling with different colors in living cells. In this study, we have created an unnatural ligand with an unprecedented protein-tag labeling property in living cells and overcome the above-mentioned problem. Of special interest is that some fluorescent probes with the ligand can selectively and efficiently label intracellular proteins without binding to cell-surface proteins, even if the proteins are present on the cell membrane. We also developed a cell-membrane impermeable fluorescent probe that selectively labels cell-surface proteins without labeling of intracellular proteins. These localization-selective properties enabled us to visually discriminate two kinetically distinct glucose transporter 4 (GLUT4) molecules that show different multiple subcellular localization and translocation dynamics in live cells. Taking advantage of the probes, we revealed that N-glycosylation of GLUT4 influences intracellular localization. Furthermore, we were able to visually distinguish active GLUT4 molecules that underwent membrane translocation at least twice within an hour from those that remained intracellularly, discovering previously unrecognized dynamic behaviors of GLUT4. This technology provides not only a valuable tool for study on multiple localization and dynamics of proteins but also important information on diseases caused by protein translocation dysfunction.
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Affiliation(s)
- Miyako Nishiura
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Department of Chemistry, Faculty of Science, Kyushu University Fukuoka Fukuoka 819-0395 Japan
| | - Maho Umeno
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Department of Applied Chemistry, Graduate School of Engineering, and Division of Applied Chemistry, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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4
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Milanesi F, Unione L, Ardá A, Nativi C, Jiménez-Barbero J, Roelens S, Francesconi O. Biomimetic Tweezers for N-Glycans: Selective Recognition of the Core GlcNAc 2 Disaccharide of the Sialylglycopeptide SGP. Chemistry 2023; 29:e202203591. [PMID: 36597924 DOI: 10.1002/chem.202203591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/05/2023]
Abstract
In recent years, glycomics have shown how pervasive the role of carbohydrates in biological systems is and how chemical tools are essential to investigate glycan function and modulate carbohydrate-mediated processes. Biomimetic receptors for carbohydrates can carry out this task but, although significant affinities and selectivities toward simple saccharides have been achieved, targeting complex glycoconjugates remains a goal yet unattained. In this work we report the unprecedented recognition of a complex biantennary sialylglycopeptide (SGP) by a tweezers-shaped biomimetic receptor, which selectively binds to the core GlcNAc2 disaccharide of the N-glycan with an affinity of 170 μM. Because of the simple structure and the remarkable binding ability, this biomimetic receptor can represent a versatile tool for glycoscience, opening the way to useful applications.
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Affiliation(s)
- Francesco Milanesi
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, University of Florence, Polo Scientifico e Tecnologico, I-50019 Sesto Fiorentino, Firenze, Italy.,Magnetic Resonance Center CERM, University of Florence, Via L. Sacconi 6, I-50019, Sesto Fiorentino, Firenze, Italy
| | - Luca Unione
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Bizkaia, Spain
| | - Ana Ardá
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Bizkaia, Spain
| | - Cristina Nativi
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, University of Florence, Polo Scientifico e Tecnologico, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Jesús Jiménez-Barbero
- CICbioGUNE, Basque Research & Technology Alliance (BRTA), Bizkaia Technology Park, Building 800, 48160, Derio, Bizkaia, Spain.,Ikerbasque, Basque Foundation for Science, Maria Diaz de Haro 3, 48013, Bilbao, Bizkaia, Spain.,Department of Organic Chemistry, II Faculty of Science and Technology, University of the Basque Country, EHU-UPV, 48940, Leioa, Spain.,Centro de Investigación Biomédica En Red de Enfermedades Respiratorias, Madrid, Spain
| | - Stefano Roelens
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, University of Florence, Polo Scientifico e Tecnologico, I-50019 Sesto Fiorentino, Firenze, Italy
| | - Oscar Francesconi
- Department of Chemistry "Ugo Schiff" DICUS and INSTM, University of Florence, Polo Scientifico e Tecnologico, I-50019 Sesto Fiorentino, Firenze, Italy
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5
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Reja SI, Hori Y, Kamikawa T, Yamasaki K, Nishiura M, Bull SD, Kikuchi K. An “OFF–ON–OFF” fluorescence protein-labeling probe for real-time visualization of the degradation of short-lived proteins in cellular systems. Chem Sci 2022; 13:1419-1427. [PMID: 35222926 PMCID: PMC8809410 DOI: 10.1039/d1sc06274c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 01/11/2022] [Indexed: 12/19/2022] Open
Abstract
The ability to monitor proteolytic pathways that remove unwanted and damaged proteins from cells is essential for understanding the multiple processes used to maintain cellular homeostasis. In this study, we have developed a new protein-labeling probe that employs an ‘OFF–ON–OFF’ fluorescence switch to enable real-time imaging of the expression (fluorescence ON) and degradation (fluorescence OFF) of PYP-tagged protein constructs in living cells. Fluorescence switching is modulated by intramolecular contact quenching interactions in the unbound probe (fluorescence OFF) being disrupted upon binding to the PYP-tag protein, which turns fluorescence ON. Quenching is then restored when the PYP-tag–probe complex undergoes proteolytic degradation, which results in fluorescence being turned OFF. Optimization of probe structures and PYP-tag mutants has enabled this fast reacting ‘OFF–ON–OFF’ probe to be used to fluorescently image the expression and degradation of short-lived proteins. An “OFF–ON–OFF” fluorescence probe for real-time imaging of the expression (fluorescence ‘OFF’) and degradation (fluorescence ‘ON’) of short lived PYP-tag proteins in cellular systems.![]()
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Affiliation(s)
- Shahi Imam Reja
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuichiro Hori
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Takuya Kamikawa
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kohei Yamasaki
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miyako Nishiura
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Steven D. Bull
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Kazuya Kikuchi
- Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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6
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Xu Y, Gao Z, Hu R, Wang Y, Wang Y, Su Z, Zhang X, Yang J, Mei M, Ren Y, Li M, Zhou X. PD-L2 glycosylation promotes immune evasion and predicts anti-EGFR efficacy. J Immunother Cancer 2021; 9:jitc-2021-002699. [PMID: 34697216 PMCID: PMC8547513 DOI: 10.1136/jitc-2021-002699] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2021] [Indexed: 12/25/2022] Open
Abstract
Background Combination therapy has been explored for advanced head and neck squamous cell carcinoma (HNSCC) owing to the limited efficacy of anti-epidermal growth factor receptor (EGFR) therapy. Increased expression and glycosylation of immune checkpoint molecules in tumors are responsible for cetuximab therapy refractoriness. The role of programmed death ligand 2 (PD-L2), a ligand of PD-1, in the immune function is unclear. Here, we examined the regulatory mechanism of PD-L2 glycosylation and its role in antitumor immunity and cetuximab therapy. Methods Single-cell RNA sequencing and immunohistochemical staining were used to investigate PD-L2 expression in cetuximab-resistant/sensitive HNSCC tissues. The mechanism of PD-L2 glycosylation regulation was explored in vitro. The effects of PD-L2 glycosylation on immune evasion and cetuximab efficacy were verified in vitro and using mice bearing orthotopic SCC7 tumors. Results The PD-L2 levels were elevated and N-glycosylated in patients with cetuximab-resistant HNSCC. Glycosylated PD-L2 formed a complex with EGFR, which resulted in the activation of EGFR/signal transducer and activator of transcription 3 (STAT3) signaling and decreased the cetuximab binding affinity to EGFR. The N-glycosyltransferase fucosyltransferase (FUT8), a transcriptional target of STAT3, was required for PD-L2 glycosylation. Moreover, glycosylation modification stabilized PD-L2 by blocking ubiquitin-dependent lysosomal degradation, which consequently promoted its binding to PD-1 and immune evasion. Inhibition of PD-L2 glycosylation using Stattic, a specific STAT3 inhibitor, or PD-L2 mutation blocking its binding to FUT8, increased cytotoxic T lymphocyte activity and augmented response to cetuximab. Conclusions Increased expression and glycosylation of PD-L2 in tumors are an important mechanism for cetuximab therapy refractoriness. Thus, the combination of PD-L2 glycosylation inhibition and cetuximab is a potential therapeutic strategy for cancer.
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Affiliation(s)
- Yiqi Xu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China.,Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Zhenyue Gao
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China.,Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Ruxin Hu
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yuqing Wang
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yuhong Wang
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Zheng Su
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Xiaoyue Zhang
- Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
| | - Jingxuan Yang
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Mei Mei
- Department of Cell Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Yu Ren
- Department of Genetics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, People's Republic of China
| | - Min Li
- Department of Medicine, Department of Surgery, The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA
| | - Xuan Zhou
- Department of Maxillofacial and Otorhinolaryngology Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, People's Republic of China
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7
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Pe KBA, Yatsuzuka K, Hakariya H, Kida T, Katsuda Y, Fukuda M, Sato SI. RNA-based cooperative protein labeling that permits direct monitoring of the intracellular concentration change of an endogenous protein. Nucleic Acids Res 2021; 49:e132. [PMID: 34581825 PMCID: PMC8682759 DOI: 10.1093/nar/gkab839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 08/24/2021] [Accepted: 09/09/2021] [Indexed: 11/13/2022] Open
Abstract
Imaging the dynamics of proteins in living cells is a powerful means for understanding cellular functions at a deeper level. Here, we report a versatile method for spatiotemporal imaging of specific endogenous proteins in living mammalian cells. The method employs a bifunctional aptamer capable of selective protein recognition and fluorescent probe-binding, which is induced only when the aptamer specifically binds to its target protein. An aptamer for β-actin protein preferentially recognizes its monomer forms over filamentous forms, resulting in selective G-actin staining in both fixed and living cells. Through actin-drug treatment, the method permitted direct monitoring of the intracellular concentration change of endogenous G-actin. This protein-labeling method, which is highly selective and non-covalent, provides rich insights into the study of spatiotemporal protein dynamics in living cells.
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Affiliation(s)
| | - Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hayase Hakariya
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Tomoki Kida
- Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Yousuke Katsuda
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Division of Materials Science and Chemistry, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555, Japan
| | - Masatora Fukuda
- Department of Chemistry, Faculty of Science, Fukuoka University, 8-19-1 Nanakuma, Jonan-ku, Fukuoka 814-0180, Japan
| | - Shin-Ichi Sato
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
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8
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de Moliner F, Knox K, Gordon D, Lee M, Tipping WJ, Geddis A, Reinders A, Ward JM, Oparka K, Vendrell M. A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 133:7715-7720. [PMID: 38505234 PMCID: PMC10946860 DOI: 10.1002/ange.202016802] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/19/2022]
Abstract
Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.
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Affiliation(s)
| | - Kirsten Knox
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University ofEdinburghUK
| | - Martin Lee
- Cancer Research (UK) Edinburgh CentreThe University of EdinburghUK
| | - William J. Tipping
- EaStCHEM School of ChemistryThe University of EdinburghUK
- Centre for Molecular NanometrologyUniversity of StrathclydeUK
| | - Ailsa Geddis
- Centre for Inflammation ResearchThe University ofEdinburghUK
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | - Anke Reinders
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - John M. Ward
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - Karl Oparka
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University ofEdinburghUK
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9
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de Moliner F, Knox K, Gordon D, Lee M, Tipping WJ, Geddis A, Reinders A, Ward JM, Oparka K, Vendrell M. A Palette of Minimally Tagged Sucrose Analogues for Real-Time Raman Imaging of Intracellular Plant Metabolism. Angew Chem Int Ed Engl 2021; 60:7637-7642. [PMID: 33491852 PMCID: PMC8048481 DOI: 10.1002/anie.202016802] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Indexed: 12/20/2022]
Abstract
Sucrose is the main saccharide used for long-distance transport in plants and plays an essential role in energy metabolism; however, there are no analogues for real-time imaging in live cells. We have optimised a synthetic approach to prepare sucrose analogues including very small (≈50 Da or less) Raman tags in the fructose moiety. Spectroscopic analysis identified the alkyne-tagged compound 6 as a sucrose analogue recognised by endogenous transporters in live cells and with higher Raman intensity than other sucrose derivatives. Herein, we demonstrate the application of compound 6 as the first optical probe to visualise real-time uptake and intracellular localisation of sucrose in live plant cells using Raman microscopy.
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Affiliation(s)
| | - Kirsten Knox
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Doireann Gordon
- Centre for Inflammation ResearchThe University ofEdinburghUK
| | - Martin Lee
- Cancer Research (UK) Edinburgh CentreThe University of EdinburghUK
| | - William J. Tipping
- EaStCHEM School of ChemistryThe University of EdinburghUK
- Centre for Molecular NanometrologyUniversity of StrathclydeUK
| | - Ailsa Geddis
- Centre for Inflammation ResearchThe University ofEdinburghUK
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | - Anke Reinders
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - John M. Ward
- Department of Plant and Microbial BiologyUniversity of MinnesotaUSA
| | - Karl Oparka
- Institute of Molecular Plant SciencesThe University of EdinburghUK
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University ofEdinburghUK
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10
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Ojima K, Shiraiwa K, Soga K, Doura T, Takato M, Komatsu K, Yuzaki M, Hamachi I, Kiyonaka S. Ligand-directed two-step labeling to quantify neuronal glutamate receptor trafficking. Nat Commun 2021; 12:831. [PMID: 33547306 PMCID: PMC7864911 DOI: 10.1038/s41467-021-21082-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022] Open
Abstract
The regulation of glutamate receptor localization is critical for development and synaptic plasticity in the central nervous system. Conventional biochemical and molecular biological approaches have been widely used to analyze glutamate receptor trafficking, especially for α-amino-3-hydroxy-5-methyl-4-isoxazole-propionate-type glutamate receptors (AMPARs). However, conflicting findings have been reported because of a lack of useful tools for analyzing endogenous AMPARs. Here, we develop a method for the rapid and selective labeling of AMPARs with chemical probes, by combining affinity-based protein labeling and bioorthogonal click chemistry under physiological temperature in culture medium. This method allows us to quantify AMPAR distribution and trafficking, which reveals some unique features of AMPARs, such as a long lifetime and a rapid recycling in neurons. This method is also successfully expanded to selectively label N-methyl-D-aspartate-type glutamate receptors. Thus, bioorthogonal two-step labeling may be a versatile tool for investigating the physiological and pathophysiological roles of glutamate receptors in neurons. The analysis of AMPA-type glutamate receptor (AMPAR) trafficking is essential for understanding molecular mechanisms of learning and memory, but the analytical tools are currently limited. Here, the authors report a method that combines affinity-based receptor labeling and bioorthogonal click chemistry to quantify AMPAR distribution and trafficking under physiological conditions.
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Affiliation(s)
- Kento Ojima
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Kazuki Shiraiwa
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Kyohei Soga
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Tomohiro Doura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Mikiko Takato
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Kazuhiro Komatsu
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan
| | - Michisuke Yuzaki
- Department of Physiology, School of Medicine, Keio University, Tokyo, 160-8582, Japan
| | - Itaru Hamachi
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Kyoto, 615-8510, Japan.
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan.
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11
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Near-infrared fluorescent probes: a next-generation tool for protein-labeling applications. Chem Sci 2020; 12:3437-3447. [PMID: 34163617 PMCID: PMC8179524 DOI: 10.1039/d0sc04792a] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/18/2020] [Indexed: 12/21/2022] Open
Abstract
The development of near-infrared (NIR) fluorescent probes over the past few decades has changed the way that biomolecules are imaged, and thus represents one of the most rapidly progressing areas of research. Presently, NIR fluorescent probes are routinely used to visualize and understand intracellular activities. The ability to penetrate tissues deeply, reduced photodamage to living organisms, and a high signal-to-noise ratio characterize NIR fluorescent probes as efficient next-generation tools for elucidating various biological events. The coupling of self-labeling protein tags with synthetic fluorescent probes is one of the most promising research areas in chemical biology. Indeed, at present, protein-labeling techniques are not only used to monitor the dynamics and localization of proteins but also play a more diverse role in imaging applications. For instance, one of the dominant technologies employed in the visualization of protein activity and regulation is based on protein tags and their associated NIR fluorescent probes. In this mini-review, we will discuss the development of several NIR fluorescent probes used for various protein-tag systems.
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Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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12
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Aissa HB, Gautier A. Engineering Glowing Chemogenetic Hybrids for Spying on Cells. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Hela Ben Aissa
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
| | - Arnaud Gautier
- École normale supérieure PSL University CNRS, Laboratoire des biomolécules, LBM Sorbonne Université 75005 Paris France
- Institut Universitaire de France Paris France
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13
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Hu M, Han Q, Lyu L, Tong Y, Dong S, Loh ZH, Xing B. Luminescent molecules towards precise cellular event regulation. Chem Commun (Camb) 2020; 56:10231-10234. [PMID: 32749396 DOI: 10.1039/d0cc01923b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A unique lanthanide complex which responds to near-infrared (NIR) stimulation was developed for remote regulation of cellular events. This molecule can be localized specifically on the cell surface. Upon NIR stimulation, strong emission of the complex can successfully modulate the activities of light-gated membrane channels and regulate the ion flux in vivo.
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Affiliation(s)
- Ming Hu
- Division of Chemistry and Biological Chemistry, School of Physical & Mathematical Sciences, Nanyang Technological University, 21 Nanyang link, 637371, Singapore.
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14
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Torii K, Hori Y, Watabe K, Kikuchi K. Development of Photoswitchable Fluorescent Molecules Using Arylazopyrazole. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20200077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kenji Torii
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Keiichiro Watabe
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
- Quantum Information and Quantum Biology Division, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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15
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Broch F, Gautier A. Illuminating Cellular Biochemistry: Fluorogenic Chemogenetic Biosensors for Biological Imaging. Chempluschem 2020; 85:1487-1497. [PMID: 32644262 DOI: 10.1002/cplu.202000413] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/18/2020] [Indexed: 12/19/2022]
Abstract
Cellular activity is defined by the precise spatiotemporal regulation of various components, such as ions, small molecules, or proteins. Studying cell physiology consequently requires the optical recording of these processes, notably by using fluorescent biosensors. The recent development of various fluorogenic systems greatly expanded the palette of reporters to be included in these sensors design. Fluorogenic reporters consist of a protein or RNA tag that can complex either an endogenous or a synthetic fluorogenic dye (so-called fluorogen). The intrinsic nature of these tags, along with the high tunability of their cognate chromophore provide interesting features such as far-red to near-infrared emission, oxygen independence, or unprecedented color versatility. These engineered photoreceptors, self-labelling proteins, or noncovalent aptamers and protein tags were rapidly identified as promising reporters to observe biological events. This Minireview focuses on the new perspectives they offer to design unique and innovative biosensors, thus pushing the boundaries of cellular imaging.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, PSL University, CNRS Laboratoire des biomolécules, LBM, 75005, Paris, France.,Institut Universitaire de France, France
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16
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Glucose transporters in adipose tissue, liver, and skeletal muscle in metabolic health and disease. Pflugers Arch 2020; 472:1273-1298. [PMID: 32591906 PMCID: PMC7462924 DOI: 10.1007/s00424-020-02417-x] [Citation(s) in RCA: 193] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/01/2020] [Accepted: 06/05/2020] [Indexed: 12/13/2022]
Abstract
A family of facilitative glucose transporters (GLUTs) is involved in regulating tissue-specific glucose uptake and metabolism in the liver, skeletal muscle, and adipose tissue to ensure homeostatic control of blood glucose levels. Reduced glucose transport activity results in aberrant use of energy substrates and is associated with insulin resistance and type 2 diabetes. It is well established that GLUT2, the main regulator of hepatic hexose flux, and GLUT4, the workhorse in insulin- and contraction-stimulated glucose uptake in skeletal muscle, are critical contributors in the control of whole-body glycemia. However, the molecular mechanism how insulin controls glucose transport across membranes and its relation to impaired glycemic control in type 2 diabetes remains not sufficiently understood. An array of circulating metabolites and hormone-like molecules and potential supplementary glucose transporters play roles in fine-tuning glucose flux between the different organs in response to an altered energy demand.
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17
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A New Pathway Promotes Adaptation of Human Glioblastoma Cells to Glucose Starvation. Cells 2020; 9:cells9051249. [PMID: 32443613 PMCID: PMC7290719 DOI: 10.3390/cells9051249] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 12/13/2022] Open
Abstract
Adaptation of glioblastoma to caloric restriction induces compensatory changes in tumor metabolism that are incompletely known. Here we show that in human glioblastoma cells maintained in exhausted medium, SHC adaptor protein 3 (SHC3) increases due to down-regulation of SHC3 protein degradation. This effect is reversed by glucose addition and is not present in normal astrocytes. Increased SHC3 levels are associated to increased glucose uptake mediated by changes in membrane trafficking of glucose transporters of the solute carrier 2A superfamily (GLUT/SLC2A). We found that the effects on vesicle trafficking are mediated by SHC3 interactions with adaptor protein complex 1 and 2 (AP), BMP-2-inducible protein kinase and a fraction of poly ADP-ribose polymerase 1 (PARP1) associated to vesicles containing GLUT/SLC2As. In glioblastoma cells, PARP1 inhibitor veliparib mimics glucose starvation in enhancing glucose uptake. Furthermore, cytosol extracted from glioblastoma cells inhibits PARP1 enzymatic activity in vitro while immunodepletion of SHC3 from the cytosol significantly relieves this inhibition. The identification of a new pathway controlling glucose uptake in high grade gliomas represents an opportunity for repositioning existing drugs and designing new ones.
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18
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Kumar N, Hori Y, Nishiura M, Kikuchi K. Rapid no-wash labeling of PYP-tag proteins with reactive fluorogenic ligands affords stable fluorescent protein conjugates for long-term cell imaging studies. Chem Sci 2020; 11:3694-3701. [PMID: 34094058 PMCID: PMC8152630 DOI: 10.1039/d0sc00499e] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Covalent labeling systems that employ protein-tags or chemical probes to convert proteins into fluorescent conjugates are powerful tools for carrying out real time imaging and pulse-chase tracking studies that enable the spatiotemporal role of proteins in complex biological systems to be investigated. In this study, we have covalently modified a specific nucleophilic cysteine residue of the PYP-tag protein with weakly fluorescent α,β-unsaturated ketone (conjugate addition) and α-halomethyl ketone (SN2 reaction) acceptors to afford highly fluorescent PYP-tag-dimethylaminocoumarin (DMAC) conjugates, whose ligands are covalently bound to the PYP-protein through stable thioether linkers. A chloromethylketone derived DMAC-CMK reagent was found to afford the best kinetic and stability profile for labeling the PYP-tag in cellular systems, with in vitro studies demonstrating that PYP-DMAC-CMK conjugates exhibit excellent photostability and cellular stability profiles which enables them to be used for long-term protein imaging studies in cellular systems. The potential of using this no wash fluorescent labeling PYP-tag-DMAC system to visualise dividing cells undergoing mitosis and for imaging a PYP-tag fused telomere binding protein bound to chromatin in cell nuclei has been demonstrated.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
| | - Miyako Nishiura
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
- Quantum Information and Quantum Biology Division, Osaka University Suita Osaka 565-0871 Japan
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19
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Gao J, Hori Y, Nishiura M, Bordy M, Hasserodt J, Kikuchi K. Engineered Protein-tag for Rapid Live-cell Fluorogenic Visualization of Proteins by Anionic Probes. CHEM LETT 2020. [DOI: 10.1246/cl.190875] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Jingchi Gao
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuichiro Hori
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Miyako Nishiura
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Mathieu Bordy
- Laboratoie de Chimie, ENS de Lyon, 46 allée d'Italie, Lyon Cedex 07, France 69364
| | - Jens Hasserodt
- Laboratoie de Chimie, ENS de Lyon, 46 allée d'Italie, Lyon Cedex 07, France 69364
| | - Kazuya Kikuchi
- Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- WPI-Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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20
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Gao J, Hori Y, Takeuchi O, Kikuchi K. Live-Cell Imaging of Protein Degradation Utilizing Designed Protein-Tag Mutant and Fluorescent Probe with Turn-Off Switch. Bioconjug Chem 2019; 31:577-583. [DOI: 10.1021/acs.bioconjchem.9b00696] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
| | | | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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21
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Péresse T, Gautier A. Next-Generation Fluorogen-Based Reporters and Biosensors for Advanced Bioimaging. Int J Mol Sci 2019; 20:E6142. [PMID: 31817528 PMCID: PMC6940837 DOI: 10.3390/ijms20246142] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/04/2019] [Accepted: 12/04/2019] [Indexed: 12/17/2022] Open
Abstract
Our ability to observe biochemical events with high spatial and temporal resolution is essential for understanding the functioning of living systems. Intrinsically fluorescent proteins such as the green fluorescent protein (GFP) have revolutionized the way biologists study cells and organisms. The fluorescence toolbox has been recently extended with new fluorescent reporters composed of a genetically encoded tag that binds endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activates their fluorescence. This review presents the toolbox of fluorogen-based reporters and biosensors available to biologists. Various applications are detailed to illustrate the possible uses and opportunities offered by this new generation of fluorescent probes and sensors for advanced bioimaging.
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Affiliation(s)
- Tiphaine Péresse
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France;
- Institut Universitaire de France (IUF), 1 rue Descartes, 75005 Paris, France
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22
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Gao J, Hori Y, Shimomura T, Bordy M, Hasserodt J, Kikuchi K. Development of Fluorogenic Probes for Rapid High‐Contrast Imaging of Transient Nuclear Localization of Sirtuin 3. Chembiochem 2019; 21:656-662. [DOI: 10.1002/cbic.201900568] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Jingchi Gao
- Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita, Osaka 565-0871 Japan
| | - Yuichiro Hori
- Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita, Osaka 565-0871 Japan
- Immunology Frontier Research Center Osaka University, 3-1 Yamada-oka Suita Osaka 565-0871 Japan
| | - Takashi Shimomura
- Dojindo Laboratories Tabaru 2025-5, Mashiki-machi Kumamoto 561-2202 Japan
| | - Mathieu Bordy
- Laboratoie de Chimie ENS de Lyon 46 allée d'Italie 69364 Lyon Cedex 07 France
| | - Jens Hasserodt
- Laboratoie de Chimie ENS de Lyon 46 allée d'Italie 69364 Lyon Cedex 07 France
| | - Kazuya Kikuchi
- Graduate School of Engineering Osaka University 2-1 Yamada-oka Suita, Osaka 565-0871 Japan
- Immunology Frontier Research Center Osaka University, 3-1 Yamada-oka Suita Osaka 565-0871 Japan
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23
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Hori Y, Kikuchi K. Chemical Tools with Fluorescence Switches for Verifying Epigenetic Modifications. Acc Chem Res 2019; 52:2849-2857. [PMID: 31577127 DOI: 10.1021/acs.accounts.9b00349] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Epigenetic DNA and histone modifications alter chromatin conformation and regulate gene expression. A major DNA modification is methylation, which is catalyzed by DNA methyltransferase (Dnmt) and results in gene suppression. Compared to DNA, histones undergo a greater variety of modification types, one of which is the acetylation of lysine. While histone acetyltransferase (HAT) catalyzes acetylation and activates gene expression, histone deacetylase (HDAC) removes the modification and causes gene suppression. As precise regulation of these epigenetic marks on DNA and histones is critical for cellular functions, their dysregulation causes various diseases including cancer, metabolic syndromes, immune diseases, and psychiatric diseases. Therefore, elucidation of the epigenetic phenomena is important not only in the field of biology but also in medical and pharmaceutical sciences. Furthermore, this field is also attracting industrial interest, because small-molecule inhibitors modulate enzymatic activity for epigenetic modification and are used for cancer treatment. Under these circumstances, various methods for detecting epigenetic modifications have been developed. However, most methods require cell lysis, which is not suitable for real-time detection of enzymatic activity. Since fluorescent probes are attractive chemical tools to solve this issue, chemists made considerable efforts to create fluorescent probes for epigenetics. To date, we have particularly focused on HDAC activity and DNA methylation and have developed fluorescent probes for their detection. The first part of this review describes our recent efforts to develop fluorescent probes for detecting HDAC activity. Since the discovery of HDAC activity in the late 1960s, no fluorescent probe has been developed that can detect enzymatic reactions in a simple, one-step procedure despite its biological and medical importance. We designed fluorescent probes to overcome this limitation by devising two different types of fluorescence switching mechanisms, which are based on aggregation-induced emission (AIE) and intramolecular transesterification. Using these probes, we detected HDAC activity simply by mixing the probes and HDAC for the first time. In the second part, a hybrid approach using a protein-labeling system was employed to detect DNA methylation in living cells. So far, live-cell detection of DNA methylation was conducted by imaging the localization of Fluorescent Proteins (FPs) fused to a methylated DNA-binding domain. However, FP lacks a fluorescence switch and emits fluorescence without binding to methylated DNA. We created a hybrid probe that comprises a fluorogen and a protein and enhances fluorescence intensity upon binding to methylated DNA. To create the hybrid probe, we applied our protein labeling system using the PYP-tag that we previously developed. This method successfully visualized methylated DNA in living cells and verified its dynamics during cell division. Both of the above-mentioned fluorescent probes have great potential for use not only in HDAC and DNA methylation but also in other epigenetics-associated modifications. For example, the mechanism of the HDAC probes can be used to detect histone demethylation. The hybrid probe can be converted to a sensor for imaging acetylated or methylated histones. In this review, we mainly describe how we designed the probes using chemical principles and solved the current obstacles with the probe design and discuss the future prospects of these probes.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering and Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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24
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Kumar N, Hori Y, Kikuchi K. Photoactive yellow protein and its chemical probes: an approach to protein labelling in living cells. J Biochem 2019; 166:121-127. [PMID: 31340005 DOI: 10.1093/jb/mvz051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 07/20/2019] [Indexed: 01/18/2023] Open
Abstract
Labelling technologies developed over the past few years have changed the way of looking at biomolecules and have made a considerable contribution to our understanding of the functions and regulation of dynamic biological processes. One of the robust technologies employed to image proteins in a cellular environment is based on the use of chemical tags and their fluorescent probes, which provides flexibility in developing probes with a wide range of synthetic fluorophores. A variety of chemical tags, ranging from short amino acid sequences to small proteins, have been employed to generate protein-labelling systems. One such chemical tag is the photoactive yellow protein (PYP)-tag, which is a small bacterial protein, developed for the selective labelling and imaging of proteins. Herein, we briefly discuss the protein-labelling system developed based on PYP-tag technology, with a focus on the design strategy for PYP-tag labelling probes and their applications in protein imaging.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka, Japan.,Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
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25
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Reja SI, Minoshima M, Hori Y, Kikuchi K. Development of an effective protein-labeling system based on smart fluorogenic probes. J Biol Inorg Chem 2019; 24:443-455. [PMID: 31152238 DOI: 10.1007/s00775-019-01669-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/15/2019] [Indexed: 12/23/2022]
Abstract
Proteins are an important component of living systems and play a crucial role in various physiological functions. Fluorescence imaging of proteins is a powerful tool for monitoring protein dynamics. Fluorescent protein (FP)-based labeling methods are frequently used to monitor the movement and interaction of cellular proteins. However, alternative methods have also been developed that allow the use of synthetic fluorescent probes to target a protein of interest (POI). Synthetic fluorescent probes have various advantages over FP-based labeling methods. They are smaller in size than the fluorescent proteins, offer a wide variety of colors and have improved photochemical properties. There are various chemical recognition-based labeling techniques that can be used for labeling a POI with a synthetic probe. In this review, we focus on the development of protein-labeling systems, particularly the SNAP-tag, BL-tag, and PYP-tag systems, and understanding the fluorescence behavior of the fluorescently labeled target protein in these systems. We also discuss the smart fluorogenic probes for these protein-labeling systems and their applications. The fluorogenic protein labeling will be a useful tool to investigate complex biological phenomena in future work on cell biology.
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Affiliation(s)
- Shahi Imam Reja
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masafumi Minoshima
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka, 565-0871, Japan.
- Immunology Frontier Research Center (IFReC), Osaka University, Suita, Osaka, 565-0871, Japan.
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26
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Benson S, Fernandez A, Barth ND, de Moliner F, Horrocks MH, Herrington CS, Abad JL, Delgado A, Kelly L, Chang Z, Feng Y, Nishiura M, Hori Y, Kikuchi K, Vendrell M. SCOTfluors: Small, Conjugatable, Orthogonal, and Tunable Fluorophores for In Vivo Imaging of Cell Metabolism. Angew Chem Int Ed Engl 2019; 58:6911-6915. [PMID: 30924239 PMCID: PMC6563150 DOI: 10.1002/anie.201900465] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Indexed: 12/11/2022]
Abstract
The transport and trafficking of metabolites are critical for the correct functioning of live cells. However, in situ metabolic imaging studies are hampered by the lack of fluorescent chemical structures that allow direct monitoring of small metabolites under physiological conditions with high spatial and temporal resolution. Herein, we describe SCOTfluors as novel small-sized multi-colored fluorophores for real-time tracking of essential metabolites in live cells and in vivo and for the acquisition of metabolic profiles from human cancer cells of variable origin.
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Affiliation(s)
- Sam Benson
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Antonio Fernandez
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Fabio de Moliner
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Mathew H. Horrocks
- UK Dementia Research Institute and EaStCHEM School of ChemistryThe University of EdinburghEH9 3FJEdinburghUK
| | | | - Jose Luis Abad
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia08034BarcelonaSpain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit)BarcelonaSpain
| | - Antonio Delgado
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia08034BarcelonaSpain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit)BarcelonaSpain
| | - Lisa Kelly
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Ziyuan Chang
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | - Yi Feng
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
| | | | - Yuichiro Hori
- Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Kazuya Kikuchi
- Graduate School of EngineeringOsaka UniversitySuitaJapan
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghEH16 4TJEdinburghUK
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27
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Benson S, Fernandez A, Barth ND, de Moliner F, Horrocks MH, Herrington CS, Abad JL, Delgado A, Kelly L, Chang Z, Feng Y, Nishiura M, Hori Y, Kikuchi K, Vendrell M. SCOTfluors: Small, Conjugatable, Orthogonal, and Tunable Fluorophores for In Vivo Imaging of Cell Metabolism. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900465] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Sam Benson
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Antonio Fernandez
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Nicole D. Barth
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Fabio de Moliner
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Mathew H. Horrocks
- UK Dementia Research Institute and EaStCHEM School of ChemistryThe University of Edinburgh EH9 3FJ Edinburgh UK
| | | | - Jose Luis Abad
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia 08034 Barcelona Spain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit) Barcelona Spain
| | - Antonio Delgado
- Research Unit on Bioactive MoleculesInstitute for Advanced Chemistry of Catalonia 08034 Barcelona Spain
- University of BarcelonaFaculty of Pharmacy, Unit of Pharmaceutical Chemistry (CSIC Associated Unit) Barcelona Spain
| | - Lisa Kelly
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Ziyuan Chang
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | - Yi Feng
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
| | | | - Yuichiro Hori
- Graduate School of EngineeringOsaka University Suita Japan
| | - Kazuya Kikuchi
- Graduate School of EngineeringOsaka University Suita Japan
| | - Marc Vendrell
- Centre for Inflammation ResearchThe University of Edinburgh EH16 4TJ Edinburgh UK
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28
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Li Y, Shi D, Yang F, Chen X, Xing Y, Liang Z, Zhuang J, Liu W, Gong Y, Jiang J, Wei Y. Complex N-glycan promotes CD133 mono-ubiquitination and secretion. FEBS Lett 2019; 593:719-731. [PMID: 30873590 DOI: 10.1002/1873-3468.13358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/03/2019] [Accepted: 03/05/2019] [Indexed: 12/20/2022]
Abstract
CD133 is a widely used cell surface marker of cancer stem cells that plays an important role in tumor initiation and metastasis. Increasing evidence shows that CD133 is secreted to the extracellular space. However, the underlying mechanisms of CD133 secretion remain largely unknown. In this study, we report that secreted CD133 has a complex-type N-glycosylation and is modified by beta1,6GlcNAc N-glycan. We found that inhibition of CD133 complex-type N-glycosylation by swainsonine does not affect the membrane localization of CD133, but significantly reduces CD133 secretion and promotes its accumulation in early endosomes. Moreover, swainsonine reduces CD133 secretion by reducing its mono-ubiquitination and inhibiting the interaction between CD133 and Tsg101. These findings reveal a new mechanism of glycosylation-dependent secretion of CD133.
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Affiliation(s)
- Yinan Li
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | - Danfang Shi
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | - Fan Yang
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | - Xiaoning Chen
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | - Yang Xing
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | - Ziwei Liang
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | | | - Weitao Liu
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | - Ye Gong
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Jianhai Jiang
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
| | - Yuanyan Wei
- NHC Key Laboratory of Glycoconjugates Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, China
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29
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Liu SY, Xiong H, Li RR, Yang WC, Yang GF. Activity-Based Near-Infrared Fluorogenic Probe for Enabling in Vitro and in Vivo Profiling of Neutrophil Elastase. Anal Chem 2019; 91:3877-3884. [DOI: 10.1021/acs.analchem.8b04455] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Shi-Yu Liu
- Key Laboratory
of Pesticide and Chemical Biology of Ministry of Education, International
Joint Research Center for Intelligent Biosensor Technology and Health,
and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Hao Xiong
- Key Laboratory
of Pesticide and Chemical Biology of Ministry of Education, International
Joint Research Center for Intelligent Biosensor Technology and Health,
and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Rong-Rong Li
- Key Laboratory
of Pesticide and Chemical Biology of Ministry of Education, International
Joint Research Center for Intelligent Biosensor Technology and Health,
and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Wen-Chao Yang
- Key Laboratory
of Pesticide and Chemical Biology of Ministry of Education, International
Joint Research Center for Intelligent Biosensor Technology and Health,
and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
| | - Guang-Fu Yang
- Key Laboratory
of Pesticide and Chemical Biology of Ministry of Education, International
Joint Research Center for Intelligent Biosensor Technology and Health,
and Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan 430079, People’s Republic of China
- Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 30071, People’s Republic of China
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30
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Gautier A, Tebo AG. Fluorogenic Protein‐Based Strategies for Detection, Actuation, and Sensing. Bioessays 2018; 40:e1800118. [DOI: 10.1002/bies.201800118] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/01/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
| | - Alison G. Tebo
- PASTEUR, Département de Chimie, École Normale SupérieurePSL University, Sorbonne Université, CNRS75005 ParisFrance
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31
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de Moliner F, King A, Dias GG, de Lima GF, de Simone CA, da Silva Júnior EN, Vendrell M. Quinone-Derived π-Extended Phenazines as New Fluorogenic Probes for Live-Cell Imaging of Lipid Droplets. Front Chem 2018; 6:339. [PMID: 30151362 PMCID: PMC6099520 DOI: 10.3389/fchem.2018.00339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 07/19/2018] [Indexed: 01/14/2023] Open
Abstract
We describe a new synthetic methodology for the preparation of fluorescent π-extended phenazines from the naturally-occurring naphthoquinone lapachol. These novel structures represent the first fluorogenic probes based on the phenazine scaffold for imaging of lipid droplets in live cells. Systematic characterization and analysis of the compounds in vitro and in cells led to the identification of key structural features responsible for the fluorescent behavior of quinone-derived π-extended phenazines. Furthermore, live-cell imaging experiments identified one compound (P1) as a marker for intracellular lipid droplets with minimal background and enhanced performance over the lipophilic tracker Nile Red.
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Affiliation(s)
- Fabio de Moliner
- Medical Research Council Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Aaron King
- Medical Research Council Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
| | - Gleiston G. Dias
- Institute of Exact Sciences, Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Guilherme F. de Lima
- Institute of Exact Sciences, Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Eufrânio N. da Silva Júnior
- Institute of Exact Sciences, Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Marc Vendrell
- Medical Research Council Centre for Inflammation Research, The University of Edinburgh, Edinburgh, United Kingdom
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32
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Yatsuzuka K, Sato SI, Pe KB, Katsuda Y, Takashima I, Watanabe M, Uesugi M. Live-cell imaging of multiple endogenous mRNAs permits the direct observation of RNA granule dynamics. Chem Commun (Camb) 2018; 54:7151-7154. [PMID: 29882951 DOI: 10.1039/c8cc03805h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Here, we developed two pairs of high-contrast chemical probes and their RNA aptamers with distinct readout channels that permitted simultaneous live-cell imaging of endogenous β-actin and cortactin mRNAs. Application of this technology allowed the direct observation of the formation process of stress granules, protein-RNA assemblies essential for cellular response to the environment.
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Affiliation(s)
- Kenji Yatsuzuka
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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33
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Li C, Mourton A, Plamont MA, Rodrigues V, Aujard I, Volovitch M, Le Saux T, Perez F, Vriz S, Jullien L, Joliot A, Gautier A. Fluorogenic Probing of Membrane Protein Trafficking. Bioconjug Chem 2018; 29:1823-1828. [PMID: 29791141 DOI: 10.1021/acs.bioconjchem.8b00180] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Methods to differentially label cell-surface and intracellular membrane proteins are indispensable for understanding their function and the regulation of their trafficking. We present an efficient strategy for the rapid and selective fluorescent labeling of membrane proteins based on the chemical-genetic fluorescent marker FAST (fluorescence-activating and absorption-shifting tag). Cell-surface FAST-tagged proteins could be selectively and rapidly labeled using fluorogenic membrane-impermeant 4-hydroxybenzylidene rhodanine (HBR) analogs. This approach allows the study of protein trafficking at the plasma membrane with various fluorometric techniques, and opens exciting prospects for the high-throughput screening of small molecules able to restore disease-related trafficking defects.
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Affiliation(s)
- Chenge Li
- PASTEUR, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Aurélien Mourton
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France , CNRS, INSERM, PSL Research University , 75231 Paris , France
- PSL Research University , 75006 Paris , France
| | - Marie-Aude Plamont
- PASTEUR, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Vanessa Rodrigues
- PASTEUR, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Isabelle Aujard
- PASTEUR, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France , CNRS, INSERM, PSL Research University , 75231 Paris , France
- École Normale Supérieure, Department of Biology , PSL Research University , 75005 Paris , France
| | - Thomas Le Saux
- PASTEUR, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Franck Perez
- Institut Curie, PSL Research University, CNRS UMR144 , 26 rue d'Ulm , 75248 Paris Cedex 05, France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France , CNRS, INSERM, PSL Research University , 75231 Paris , France
- Université Paris Diderot, Sorbonne Paris Cité , Biology Department , 75205 Paris Cedex 13, France
| | - Ludovic Jullien
- PASTEUR, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Alain Joliot
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France , CNRS, INSERM, PSL Research University , 75231 Paris , France
| | - Arnaud Gautier
- PASTEUR, Département de Chimie, École Normale Supérieure , PSL University, Sorbonne Université, CNRS , 75005 Paris , France
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34
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Kumar N, Hori Y, Kikuchi K. Live-Cell Imaging of DNA Methylation Based on Synthetic-Molecule/Protein Hybrid Probe. CHEM REC 2018; 18:1672-1680. [PMID: 29863802 DOI: 10.1002/tcr.201800039] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 05/18/2018] [Indexed: 12/15/2022]
Abstract
The epigenetic modification of DNA involves the conversion of cytosine to 5-methylcytosine, also known as DNA methylation. DNA methylation is important in modulating gene expression and thus, regulating genome and cellular functions. Recent studies have shown that aberrations in DNA methylation are associated with various epigenetic disorders or diseases including cancer. This stimulates great interest in the development of methods that can detect and visualize DNA methylation. For instance, fluorescent proteins (FPs) in conjugation with methyl-CpG-binding domain (MBD) have been employed for live-cell imaging of DNA methylation. However, the FP-based approach showed fluorescence signals for both the DNA-bound and -unbound states and thus differentiation between these states is difficult. Synthetic-molecule/protein hybrid probes can provide an alternative to overcome this restriction. In this article, we discuss the synthetic-molecule/protein hybrid probe that we developed recently for live-cell imaging of DNA methylation, which exhibited fluorescence enhancement only after binding to methylated DNA.
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Affiliation(s)
- Naresh Kumar
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan
| | - Yuichiro Hori
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita, Osaka, 565-0871, Japan.,Immunology Fontier Research Center, Osaka University Suita, Osaka, 565-0871, Japan
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35
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Hori Y, Otomura N, Nishida A, Nishiura M, Umeno M, Suetake I, Kikuchi K. Synthetic-Molecule/Protein Hybrid Probe with Fluorogenic Switch for Live-Cell Imaging of DNA Methylation. J Am Chem Soc 2018; 140:1686-1690. [PMID: 29381073 DOI: 10.1021/jacs.7b09713] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hybrid probes consisting of synthetic molecules and proteins are powerful tools for detecting biological molecules and signals in living cells. To date, most targets of the hybrid probes have been limited to pH and small analytes. Although biomacromolecules are essential to the physiological function of cells, the hybrid-probe-based approach has been scarcely employed for live-cell detection of biomacromolecules. Here, we developed a hybrid probe with a chemical switch for live-cell imaging of methylated DNA, an important macromolecule in the repression of gene expression. Using a protein labeling technique, we created a hybrid probe containing a DNA-binding fluorogen and a methylated-DNA-binding domain. The hybrid probe enhanced fluorescence intensity upon binding to methylated DNA and successfully monitored methylated DNA during mitosis. The hybrid probe offers notable advantages absent from probes based on small molecules or fluorescent proteins and is useful for live-cell analyses of epigenetic phenomena and diseases related to DNA methylation.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Norimichi Otomura
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Ayuko Nishida
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Miyako Nishiura
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Maho Umeno
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University , Suita, Osaka 565-0871, Japan.,Center for Twin Research, Graduate School of Medicine, Osaka University , Suita, Osaka 565-0871, Japan.,College of Nutrition, Koshien University , Takaraduka, Hyogo 665-0006, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
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36
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Abstract
The facilitative glucose transporter (GLUT) family plays a key role in metabolic homeostasis, controlling the absorption rates and rapid response to changing carbohydrate levels. The facilitative GLUT2 transporter is uniquely expressed in metabolic epithelial cells of the intestine, pancreas, liver, and kidney. GLUT2 dysfunction is associated with several pathologies, including Fanconi-Bickel syndrome, a glycogen storage disease, characterized by growth retardation and renal dysfunction. Interestingly, GLUT2 activity is modulated by its cellular localization. Membrane translocation specifically regulates GLUT2 activity in enterocytes, pancreatic β-cells, hepatocytes, and proximal tubule cells. We have established a system to visualize and quantify GLUT2 translocation, and its dynamics, by live imaging of a mCherry-hGLUT2 fusion protein in polarized epithelial cells. This system enables testing of putative modulators of GLUT2 translocation, which are potential drugs for conditions of impaired glucose homeostasis and associated nephropathy.
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Affiliation(s)
- Sabina Tsytkin-Kirschenzweig
- Alexander Grass Center for Bioengineering, The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Merav Cohen
- Alexander Grass Center for Bioengineering, The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
- Department of Cell and Developmental Biology, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Yaakov Nahmias
- Alexander Grass Center for Bioengineering, The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
- Department of Cell and Developmental Biology, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel.
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37
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Hori Y, Hirayama S, Kikuchi K. Development of cyanine probes with dinitrobenzene quencher for rapid fluorogenic protein labelling. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2017; 375:rsta.2017.0018. [PMID: 29038376 PMCID: PMC5647265 DOI: 10.1098/rsta.2017.0018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/08/2017] [Indexed: 06/07/2023]
Abstract
A multicolour protein labelling technique using a protein tag and fluorogenic probes is a powerful approach for spatio-temporal analyses of proteins in living cells. Since cyanine fluorophores have attractive properties for multicolour imaging of proteins, there is a huge demand to develop fluorogenic cyanine probes for specific protein labelling in living cells. Herein, we develop fluorogenic cyanine probes for labelling a protein tag by using a dinitrobenzene fluorescence quencher. The probes enhanced fluorescence intensity upon labelling reactions and emitted orange or far-red fluorescence. Intramolecular interactions between the cyanine fluorophores and the dinitrobenzene quencher led not only to fluorescence quenching of the probes in the free state but also to promotion of labelling reactions. Furthermore, the probes successfully imaged cell-surface proteins without a washing process. These findings offer valuable information on the design of fluorogenic cyanine probes and indicate that the probes are useful as novel live-cell imaging tools.This article is part of the themed issue 'Challenges for chemistry in molecular imaging'.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shinya Hirayama
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan
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38
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Hong YR, Lam CH, Tan KT. Fluorogenic Protein Labeling Probes to Study the Morphological Interplay between PreLamin and Mature Lamin. Bioconjug Chem 2017; 28:2895-2902. [DOI: 10.1021/acs.bioconjchem.7b00611] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi-Ru Hong
- Department of Chemistry and ‡Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang Fu Rd, Hsinchu 30013, Taiwan (ROC)
| | - Chak Hin Lam
- Department of Chemistry and ‡Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang Fu Rd, Hsinchu 30013, Taiwan (ROC)
| | - Kui-Thong Tan
- Department of Chemistry and ‡Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, 101 Sec.
2, Kuang Fu Rd, Hsinchu 30013, Taiwan (ROC)
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39
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Li C, Tebo AG, Gautier A. Fluorogenic Labeling Strategies for Biological Imaging. Int J Mol Sci 2017; 18:ijms18071473. [PMID: 28698494 PMCID: PMC5535964 DOI: 10.3390/ijms18071473] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/03/2017] [Accepted: 07/06/2017] [Indexed: 12/27/2022] Open
Abstract
The spatiotemporal fluorescence imaging of biological processes requires effective tools to label intracellular biomolecules in living systems. This review presents a brief overview of recent labeling strategies that permits one to make protein and RNA strongly fluorescent using synthetic fluorogenic probes. Genetically encoded tags selectively binding the exogenously applied molecules ensure high labeling selectivity, while high imaging contrast is achieved using fluorogenic chromophores that are fluorescent only when bound to their cognate tag, and are otherwise dark. Beyond avoiding the need for removal of unbound synthetic dyes, these approaches allow the development of sophisticated imaging assays, and open exciting prospects for advanced imaging, particularly for multiplexed imaging and super-resolution microscopy.
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Affiliation(s)
- Chenge Li
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
| | - Alison G Tebo
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
| | - Arnaud Gautier
- École Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, 24 rue Lhomond, 75005 Paris, France.
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, 75005 Paris, France.
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