1
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Torrey ZR, Halbers LP, Scipioni L, Tedeschi G, Digman MA, Prescher JA. A versatile bioluminescent probe with tunable color. RSC Chem Biol 2024:d4cb00101j. [PMID: 39308479 PMCID: PMC11414822 DOI: 10.1039/d4cb00101j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Accepted: 09/06/2024] [Indexed: 09/25/2024] Open
Abstract
Bioluminescence is a powerful method for imaging in vivo, but applications at the microscale are far from routine. This is due, in part, to a lack of versatile tools for visualizing dynamic events. To address this void, we developed a new platform-Bioluminescence Resonance Energy mAKe over with a Fluorescence-Activating absorption-Shifting Tag (BREAKFAST). BREAKFAST features a bright luciferase combined with a chemogenetic tag (pFAST) for rapid color switching. In the presence of luciferin and a discrete fluorogenic ligand, signal is observed via resonance energy transfer. We evaluated spectral outputs with various fluorogens and established the utility of BREAKFAST for combined fluorescence and bioluminescence imaging. Dynamic, four-color visualization was achieved with sequential ligand addition and spectral phasor analysis. We further showed selective signal quenching with a dark fluorogen. Collectively, this work establishes a new method for bioluminescence imaging at the cellular scale and sets the stage for continued probe development.
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Affiliation(s)
- Zachary R Torrey
- Department of Chemistry, University of California Irvine Irvine CA 92697 USA
| | - Lila P Halbers
- Department of Pharmaceutical Sciences, University of California Irvine Irvine CA 92697 USA
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California Irvine Irvine CA 92697 USA
| | - Giulia Tedeschi
- Department of Biomedical Engineering, University of California Irvine Irvine CA 92697 USA
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California Irvine Irvine CA 92697 USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California Irvine Irvine CA 92697 USA
- Department of Pharmaceutical Sciences, University of California Irvine Irvine CA 92697 USA
- Department of Molecular Biology & Biochemistry, University of California Irvine Irvine CA 92697 USA
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2
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Pedre B. A guide to genetically-encoded redox biosensors: State of the art and opportunities. Arch Biochem Biophys 2024; 758:110067. [PMID: 38908743 DOI: 10.1016/j.abb.2024.110067] [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] [Received: 05/13/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 06/24/2024]
Abstract
Genetically-encoded redox biosensors have become invaluable tools for monitoring cellular redox processes with high spatiotemporal resolution, coupling the presence of the redox-active analyte with a change in fluorescence signal that can be easily recorded. This review summarizes the available fluorescence recording methods and presents an in-depth classification of the redox biosensors, organized by the analytes they respond to. In addition to the fluorescent protein-based architectures, this review also describes the recent advances on fluorescent, chemigenetic-based redox biosensors and other emerging chemigenetic strategies. This review examines how these biosensors are designed, the biosensors sensing mechanism, and their practical advantages and disadvantages.
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Affiliation(s)
- Brandán Pedre
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU Leuven, Belgium.
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3
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Bogdanova YA, Solovyev ID, Baleeva NS, Myasnyanko IN, Gorshkova AA, Gorbachev DA, Gilvanov AR, Goncharuk SA, Goncharuk MV, Mineev KS, Arseniev AS, Bogdanov AM, Savitsky AP, Baranov MS. Fluorescence lifetime multiplexing with fluorogen activating protein FAST variants. Commun Biol 2024; 7:799. [PMID: 38956304 PMCID: PMC11219735 DOI: 10.1038/s42003-024-06501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 06/24/2024] [Indexed: 07/04/2024] Open
Abstract
In this paper, we propose a fluorescence-lifetime imaging microscopy (FLIM) multiplexing system based on the fluorogen-activating protein FAST. This genetically encoded fluorescent labeling platform employs FAST mutants that activate the same fluorogen but provide different fluorescence lifetimes for each specific protein-dye pair. All the proposed probes with varying lifetimes possess nearly identical and the smallest-in-class size, along with quite similar steady-state optical properties. In live mammalian cells, we target these chemogenetic tags to two intracellular structures simultaneously, where their fluorescence signals are clearly distinguished by FLIM. Due to the unique structure of certain fluorogens under study, their complexes with FAST mutants display a monophasic fluorescence decay, which may facilitate enhanced multiplexing efficiency by reducing signal cross-talks and providing optimal prerequisites for signal separation upon co-localized and/or spatially overlapped labeling.
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Affiliation(s)
- Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ilya D Solovyev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Anastasia A Gorshkova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Goethe University Frankfurt, Frankfurt am Main, 60433, Germany
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Department of Photonics, İzmir Institute of Technology, 35430, İzmir, Turkey
| | - Alexander P Savitsky
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, 119991 Russia, 121205, Moscow, Russia.
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4
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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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5
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Baleeva NS, Bogdanova YA, Goncharuk MV, Sokolov AI, Myasnyanko IN, Kublitski VS, Smirnov AY, Gilvanov AR, Goncharuk SA, Mineev KS, Baranov MS. A Combination of Library Screening and Rational Mutagenesis Expands the Available Color Palette of the Smallest Fluorogen-Activating Protein Tag nanoFAST. Int J Mol Sci 2024; 25:3054. [PMID: 38474299 DOI: 10.3390/ijms25053054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
NanoFAST is the smallest fluorogen-activating protein, consisting of only 98 amino acids, used as a genetically encoded fluorescent tag. Previously, only a single fluorogen with an orange color was revealed for this protein. In the present paper, using rational mutagenesis and in vitro screening of fluorogens libraries, we expanded the color palette of this tag. We discovered that E46Q is one of the key substitutions enabling the range of possible fluorogens to be expanded. The introduction of this and several other substitutions has made it possible to use not only orange but also red and green fluorogens with the modified protein.
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Affiliation(s)
- Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
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6
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Rakotoarison LM, Tebo AG, Böken D, Board S, El Hajji L, Gautier A. Improving Split Reporters of Protein-Protein Interactions through Orthology-Based Protein Engineering. ACS Chem Biol 2024; 19:428-441. [PMID: 38289242 DOI: 10.1021/acschembio.3c00631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Protein-protein interactions (PPIs) can be detected through selective complementation of split fluorescent reporters made of two complementary fragments that reassemble into a functional fluorescent reporter when in close proximity. We previously introduced splitFAST, a chemogenetic PPI reporter with rapid and reversible complementation. Here, we present the engineering of splitFAST2, an improved reporter displaying higher brightness, lower self-complementation, and higher dynamic range for optimal monitoring of PPI using an original protein engineering strategy that exploits proteins with orthology relationships. Our study allowed the identification of a system with improved properties and enabled a better understanding of the molecular features controlling the complementation properties. Because of the rapidity and reversibility of its complementation, its low self-complementation, high dynamic range, and improved brightness, splitFAST2 is well suited to study PPI with high spatial and temporal resolution, opening great prospects to decipher the role of PPI in various biological contexts.
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Affiliation(s)
- Louise-Marie Rakotoarison
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
| | - Alison G Tebo
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
| | - Dorothea Böken
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
| | - Stephanie Board
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
| | - Lina El Hajji
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
| | - Arnaud Gautier
- Laboratoire de Biomolécules, UMR 7203, Sorbonne Université - CNRS - École Normale Supérieure, 75005 Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005 Paris, France
- Institut Universitaire de France, 75231 Paris, France
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7
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Broch F, El Hajji L, Pietrancosta N, Gautier A. Engineering of Tunable Allosteric-like Fluorogenic Protein Sensors. ACS Sens 2023; 8:3933-3942. [PMID: 37830919 DOI: 10.1021/acssensors.3c01536] [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: 10/14/2023]
Abstract
Optical protein sensors that enable detection of relevant biomolecules of interest play central roles in biological research. Coupling fluorescent reporters with protein sensing units has enabled the development of a wide range of biosensors that recognize analytes with high selectivity. In these sensors, analyte recognition induces a conformational change in the protein sensing unit that can modulate the optical signal of the fluorescent reporter. Here, we explore various designs for the creation of tunable allosteric-like fluorogenic protein sensors through incorporation of sensing protein units within the chemogenetic fluorescence-activating and absorption-shifting tag (FAST) that selectively binds and stabilizes the fluorescent state of 4-hydroxybenzylidene rhodanine (HBR) analogs. Conformational coupling allowed us to design analyte-responsive optical protein sensors through allosteric-like modulation of fluorogen binding.
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Affiliation(s)
- Fanny Broch
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
| | - Nicolas Pietrancosta
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, 75005 Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France
- Institut Universitaire de France, 75231 Paris, France
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8
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Tchagang CF, Mah TF, Campbell-Valois FX. Anaerobic fluorescent reporters for live imaging of Pseudomonas aeruginosa. Front Microbiol 2023; 14:1245755. [PMID: 37928662 PMCID: PMC10623331 DOI: 10.3389/fmicb.2023.1245755] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Pseudomonas aeruginosa thrives in the airways of individuals with cystic fibrosis, in part by forming robust biofilms that are resistant to immune clearance or antibiotic treatment. In the cystic fibrosis lung, the thickened mucus layers create an oxygen gradient, often culminating with the formation of anoxic pockets. In this environment, P. aeruginosa can use nitrate instead of oxygen to grow. Current fluorescent reporters for studying P. aeruginosa are limited to the GFP and related analogs. However, these reporters require oxygen for the maturation of their chromophore, making them unsuitable for the study of anaerobically grown P. aeruginosa. To overcome this limitation, we evaluated seven alternative fluorescent proteins, including iLOV, phiLOV2.1, evoglow-Bs2, LucY, UnaG, Fluorescence-Activating and Absorption-Shifting Tag (FAST), and iRFP670, which have been reported to emit light under oxygen-limiting conditions. We generated a series of plasmids encoding these proteins and validated their fluorescence using plate reader assays and confocal microscopy. Six of these proteins successfully labeled P. aeruginosa in anoxia. In particular, phiLOV2.1 and FAST provided superior fluorescence stability and enabled dual-color imaging of both planktonic and biofilm cultures. This study provides a set of fluorescent reporters for monitoring P. aeruginosa under low-oxygen conditions. These reporters will facilitate studies of P. aeruginosa in biofilms or other contexts relevant to its pathogenesis, such as those found in cystic fibrosis airways. Due to the broad host range of our expression vector, the phiLOV2.1 and FAST-based reporters may be applicable to the study of other Gram-negative bacteria that inhabit similar low-oxygen niches.
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Affiliation(s)
- Caetanie F. Tchagang
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
- Host-Microbe Interactions Laboratory, Center for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
| | - Thien-Fah Mah
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - François-Xavier Campbell-Valois
- Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Centre for Infection, Immunity, and Inflammation, University of Ottawa, Ottawa, ON, Canada
- Host-Microbe Interactions Laboratory, Center for Chemical and Synthetic Biology, Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada
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9
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Hesse S. Synthesis of 5-arylidenerhodanines in L-proline-based deep eutectic solvent. Beilstein J Org Chem 2023; 19:1537-1544. [PMID: 37822921 PMCID: PMC10562643 DOI: 10.3762/bjoc.19.110] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
Rhodanines and their derivatives are known to have many pharmacological activities that can be modulated through different functionalization sites. One of the most studied modification in those scaffolds is the introduction of a benzylidene moiety on C5 via a Knoevenagel reaction. Here, a facile synthesis of 5-arylidenerhodanines via a Knoevenagel reaction in an ʟ-proline-based deep eutectic solvent (DES) is reported. This method is fast (1 h at 60 °C), easy, catalyst-free and sustainable as no classical organic solvents were used. The expected compounds are recovered by a simple filtration after hydrolysis and no purification is required. Those derivatives were studied for their antioxidant activities and the results are consistent with those reported in the literature indicating that phenolic compounds are the more active ones.
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10
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Anderson DM, Logan MG, Patty SS, Kendall AJ, Borland CZ, Pfeifer CS, Kreth J, Merritt JL. Microbiome imaging goes à la carte: Incorporating click chemistry into the fluorescence-activating and absorption-shifting tag (FAST) imaging platform. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560575. [PMID: 37873282 PMCID: PMC10592883 DOI: 10.1101/2023.10.02.560575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The human microbiome is predominantly composed of facultative and obligate anaerobic bacteria that live in hypoxic/anoxic polymicrobial biofilm communities. Given the oxidative sensitivity of large fractions of the human microbiota, green fluorescent protein (GFP) and related genetically-encoded fluorophores only offer limited utility for live cell imaging due the oxygen requirement for chromophore maturation. Consequently, new fluorescent imaging modalities are needed to study polymicrobial interactions and microbiome-host interactions within anaerobic environments. The fluorescence-activating and absorption shifting tag (FAST) is a rapidly developing genetically-encoded fluorescent imaging technology that exhibits tremendous potential to address this need. In the FAST system, fluorescence only occurs when the FAST protein is complexed with one of a suite of cognate small molecule fluorogens. To expand the utility of FAST imaging, we sought to develop a modular platform (Click-FAST) to democratize fluorogen engineering for personalized use cases. Using Click-FAST, investigators can quickly and affordably sample a vast chemical space of compounds, potentially imparting a broad range of desired functionalities to the parental fluorogen. In this work, we demonstrate the utility of the Click-FAST platform using a novel fluorogen, PLBlaze-alkyne, which incorporates the widely available small molecule ethylvanillin as the hydroxybenzylidine head group. Different azido reagents were clicked onto PLBlaze-alkyne and shown to impart useful characteristics to the fluorogen, such as selective bacterial labeling in mixed populations as well as fluorescent signal enhancement. Conjugation of an 80 Å PEG molecule to PLBlaze-alkyne illustrates the broad size range of functional fluorogen chimeras that can be employed. This PEGylated fluorogen also functions as an exquisitely selective membrane permeability marker capable of outperforming propidium iodide as a fluorescent marker of cell viability.
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Affiliation(s)
- David M Anderson
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Matthew G Logan
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Sara S Patty
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Alexander J Kendall
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Christina Z Borland
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Carmem S Pfeifer
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
| | - Jens Kreth
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
| | - Justin L Merritt
- Division of Biomaterial and Biomedical Sciences, Oregon Health & Science University, Portland, OR, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, OR, USA
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11
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Yu M, Hu S, Tang B, Yang H, Sun D. Engineering Escherichia coli Nissle 1917 as a microbial chassis for therapeutic and industrial applications. Biotechnol Adv 2023; 67:108202. [PMID: 37343690 DOI: 10.1016/j.biotechadv.2023.108202] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/19/2023] [Accepted: 06/17/2023] [Indexed: 06/23/2023]
Abstract
Genetically engineered microbes, especially Escherichia coli, have been widely used in the biosynthesis of proteins and metabolites for medical and industrial applications. As a traditional probiotic with a well-established safety record, E. coli Nissle 1917 (EcN) has recently emerged as a microbial chassis for generating living therapeutics, drug delivery vehicles, and microbial platforms for industrial production. Despite the availability of genetic tools for engineering laboratory E. coli K-12 and B strains, new genetic engineering systems are still greatly needed to expand the application range of EcN. In this review, we have summarized the latest progress in the development of genetic engineering systems in EcN, as well as their applications in the biosynthesis and delivery of valuable small molecules and biomacromolecules of medical and/or industrial interest, followed by a glimpse of how this rapidly growing field will evolve in the future.
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Affiliation(s)
- Mingjing Yu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Shilong Hu
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China
| | - Biao Tang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Hua Yang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Dongchang Sun
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, Zhejiang 310014, China.
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12
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Bottone S, Joliot O, Cakil ZV, El Hajji L, Rakotoarison LM, Boncompain G, Perez F, Gautier A. A fluorogenic chemically induced dimerization technology for controlling, imaging and sensing protein proximity. Nat Methods 2023; 20:1553-1562. [PMID: 37640938 DOI: 10.1038/s41592-023-01988-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 07/28/2023] [Indexed: 08/31/2023]
Abstract
Molecular tools enabling the control and observation of the proximity of proteins are essential for studying the functional role of physical distance between two proteins. Here we present CATCHFIRE (chemically assisted tethering of chimera by fluorogenic-induced recognition), a chemically induced proximity technology with intrinsic fluorescence imaging and sensing capabilities. CATCHFIRE relies on genetic fusion to small dimerizing domains that interact upon addition of fluorogenic inducers of proximity that fluoresce upon formation of the ternary assembly, allowing real-time monitoring of the chemically induced proximity. CATCHFIRE is rapid and fully reversible and allows the control and tracking of protein localization, protein trafficking, organelle transport and cellular processes, opening new avenues for studying or controlling biological processes with high spatiotemporal resolution. Its fluorogenic nature allows the design of a new class of biosensors for the study of processes such as signal transduction and apoptosis.
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Affiliation(s)
- Sara Bottone
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | | | - Zeyneb Vildan Cakil
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | - Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | - Louise-Marie Rakotoarison
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France
| | | | | | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, Paris, France.
- Institut Universitaire de France, Paris, France.
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13
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Hocq R, Bottone S, Gautier A, Pflügl S. A fluorescent reporter system for anaerobic thermophiles. Front Bioeng Biotechnol 2023; 11:1226889. [PMID: 37476481 PMCID: PMC10355840 DOI: 10.3389/fbioe.2023.1226889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023] Open
Abstract
Owing to their inherent capacity to make invisible biological processes visible and quantifiable, fluorescent reporter systems have numerous applications in biotechnology. For classical fluorescent protein systems (i.e., GFP and derivatives), chromophore maturation is O2-dependent, restricting their applications to aerobic organisms. In this work, we pioneered the use of the oxygen-independent system FAST (Fluorescence Activating and absorption Shifting tag) in the thermophilic anaerobe Thermoanaerobacter kivui. We developed a modular cloning system that was used to easily clone a library of FAST expression cassettes in an E. coli-Thermoanaerobacter shuttle plasmid. FAST-mediated fluorescence was then assessed in vivo in T. kivui, and we observed bright green and red fluorescence for cells grown at 55°C. Next, we took advantage of this functional reporter system to characterize a set of homologous and heterologous promoters by quantifying gene expression, expanding the T. kivui genetic toolbox. Low fluorescence at 66°C (Topt for T. kivui) was subsequently investigated at the single-cell level using flow cytometry and attributed to plasmid instability at higher temperatures. Adaptive laboratory evolution circumvented this issue and drastically enhanced fluorescence at 66°C. Whole plasmid sequencing revealed the evolved strain carried functional plasmids truncated at the Gram-positive origin of replication, that could however not be linked to the increased fluorescence displayed by the evolved strain. Collectively, our work demonstrates the applicability of the FAST fluorescent reporter systems to T. kivui, paving the way for further applications in thermophilic anaerobes.
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Affiliation(s)
- Rémi Hocq
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
| | - Sara Bottone
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Arnaud Gautier
- Laboratoire des Biomolécules (LBM), Centre National de la Recherche Scientifique (CNRS), Sorbonne Université, École Normale Supérieure, Université PSL, Paris, France
- Institut Universitaire de France, Paris, France
| | - Stefan Pflügl
- Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
- Christian Doppler Laboratory for Optimized Expression of Carbohydrate-Active Enzymes, Institute of Chemical, Environmental and Bioscience Engineering, Technische Universität Wien, Vienna, Austria
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14
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Tholen MME, Tas RP, Wang Y, Albertazzi L. Beyond DNA: new probes for PAINT super-resolution microscopy. Chem Commun (Camb) 2023; 59:8332-8342. [PMID: 37306078 PMCID: PMC10318573 DOI: 10.1039/d3cc00757j] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/26/2023] [Indexed: 06/13/2023]
Abstract
In the last decade, point accumulation for imaging in nanoscale topography (PAINT) has emerged as a versatile tool for single-molecule localization microscopy (SMLM). Currently, DNA-PAINT is the most widely used, in which a transient stochastically binding DNA docking-imaging pair is used to reconstruct specific characteristics of biological or synthetic materials on a single-molecule level. Slowly, the need for PAINT probes that are not dependent on DNA has emerged. These probes can be based on (i) endogenous interactions, (ii) engineered binders, (iii) fusion proteins, or (iv) synthetic molecules and provide complementary applications for SMLM. Therefore, researchers have been expanding the PAINT toolbox with new probes. In this review, we provide an overview of the currently existing probes that go beyond DNA and their applications and challenges.
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Affiliation(s)
- Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
| | - Roderick P Tas
- Department of Chemical Engineering and Chemistry, Laboratory of Self-Organizing Soft Matter, Eindhoven University of Technology, Eindhoven, 5612 AP, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Lorenzo Albertazzi
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, The Netherlands.
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15
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Cao Z, Liu R, Wang C, Lin S, Wang L, Pang Y. Fluorescence-Activating and Absorption-Shifting Nanoprobes for Anaerobic Tracking of Gut Microbiota Derived Vesicles. ACS NANO 2023; 17:2279-2293. [PMID: 36735721 DOI: 10.1021/acsnano.2c08780] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Outer membrane vesicles (OMVs) are crucial for bacterial intercellular communication and the crosstalk between the gut microbiota and its host. Methods capable of visualizing gut microbiota derived OMVs would be of great significance but have been rarely reported. Here, nanoprobes carrying a fluorescence-activating and absorption-shifting tag are prepared by combining genetic engineering and antibiotic-boosted vesicle formation and release. Benefiting from their natural structure and molecular oxygen-independent emission, the resulting nanovesicles can be applied as endogenous fluorescence probes to anaerobically track gut microbiota associated OMVs. These nanoprobes show flexibility in on-demand fluorescence turn-on/off and reversibly switchable emission bands for intelligent and dual-color imaging. With these special characteristics, the behaviors of microbiota OMVs to not only inhibit specific pathogenic strains through membrane fusion but also repair the intestinal barrier via entering intestinal epithelia and promoting the expressions of tight junctions are tracked and identified in the gut. Based on these discoveries, OMVs are disclosed to be able to remit inflammation in a murine model of colitis following transplantation to the intestine by oral delivery. This work provides an approach to visualize the dynamics of the gut microbiota and disclose potential targets for disease intervention.
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Affiliation(s)
- Zhenping Cao
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Rui Liu
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chuhan Wang
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
| | - Sisi Lin
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Lu Wang
- Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Institute of Molecular Medicine, State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yan Pang
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Department of Ophthalmology, Shanghai Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, China
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16
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de Moliner F, Konieczna Z, Mendive‐Tapia L, Saleeb RS, Morris K, Gonzalez‐Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. Angew Chem Int Ed Engl 2023; 62:e202216231. [PMID: 36412996 PMCID: PMC10108274 DOI: 10.1002/anie.202216231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
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Affiliation(s)
| | | | | | | | - Katie Morris
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain SciencesThe University of EdinburghUK
| | | | | | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghUK
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17
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de Moliner F, Konieczna Z, Mendive‐Tapia L, Saleeb RS, Morris K, Gonzalez‐Vera JA, Kaizuka T, Grant SGN, Horrocks MH, Vendrell M. Small Fluorogenic Amino Acids for Peptide-Guided Background-Free Imaging. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202216231. [PMID: 38515539 PMCID: PMC10952862 DOI: 10.1002/ange.202216231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Indexed: 11/23/2022]
Abstract
The multiple applications of super-resolution microscopy have prompted the need for minimally invasive labeling strategies for peptide-guided fluorescence imaging. Many fluorescent reporters display limitations (e.g., large and charged scaffolds, non-specific binding) as building blocks for the construction of fluorogenic peptides. Herein we have built a library of benzodiazole amino acids and systematically examined them as reporters for background-free fluorescence microscopy. We have identified amine-derivatized benzoselenadiazoles as scalable and photostable amino acids for the straightforward solid-phase synthesis of fluorescent peptides. Benzodiazole amino acids retain the binding capabilities of bioactive peptides and display excellent signal-to-background ratios. Furthermore, we have demonstrated their application in peptide-PAINT imaging of postsynaptic density protein-95 nanoclusters in the synaptosomes from mouse brain tissues.
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Affiliation(s)
| | | | | | | | - Katie Morris
- EaStCHEM School of ChemistryThe University of EdinburghUK
| | | | - Takeshi Kaizuka
- Centre for Clinical Brain SciencesThe University of EdinburghUK
| | | | | | - Marc Vendrell
- Centre for Inflammation ResearchThe University of EdinburghUK
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18
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Gautier A. Fluorescence-Activating and Absorption-Shifting Tags for Advanced Imaging and Biosensing. Acc Chem Res 2022; 55:3125-3135. [PMID: 36269101 DOI: 10.1021/acs.accounts.2c00098] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Fluorescent labels and biosensors play central roles in biological and medical research. Targeted to specific biomolecules or cells, they allow noninvasive imaging of the machinery that govern cells and organisms in real time. Recently, chemogenetic reporters made of organic dyes specifically anchored to genetic tags have challenged the paradigm of fully genetically encoded fluorescent proteins. Combining the advantage of synthetic fluorophores with the targeting selectivity of genetically encoded tags, these chemogenetic reporters open new exciting prospects for studying cell biochemistry and biology. In this Account, we present the growing toolbox of fluorescence-activating and absorption-shifting tags (FASTs), small monomeric proteins of 14 kDa (125 amino acids residues) that can be used as markers to monitor gene expression and protein localization in live cells and organisms. Engineered by directed protein evolution from the photoactive yellow protein (PYP) from the bacterium Halorhodospira halophila, prototypical FAST binds and stabilizes the fluorescent state of live-cell compatible hydroxybenzylidene rhodanine chromophores. This class of chromophores are normally dark when free in solution or in cells because they dissipate light energy through nonradiative processes. The protein cavity of FAST allows the stabilization of the deprotonated state of the chromophore and blocks the chromophore into a planar conformation, which leads to highly fluorescent protein-chromophore assemblies. The use of such fluorogenic dyes (also called fluorogens) enables the imaging of FAST fusion proteins in cells with high contrast without the need to remove unbound ligands through separate washing steps. Fluorogens with various spectral properties exist nowadays allowing investigators to adjust the spectral properties of FAST to their experimental conditions. Molecular engineering allowed furthermore to generate membrane-impermeant fluorogens for the selective labeling of cell-surface proteins. Over the years, we generated a collection of FAST variants with expanded spectral properties or fluorogen selectivity using a concerted strategy involving molecular engineering and directed protein evolution. Moreover, protein engineering allowed us to adapt FASTs for the design of fluorescent biosensors. Circular permutation enabled the generation of FAST variants with increased conformational flexibility for the design of biosensors in which fluorogen binding is conditioned to the recognition of a given analyte. Bisection of FASTs into two complementary fragments allowed us furthermore to create split variants with reversible complementation that allow the detection and imaging of dynamic protein-protein interactions. We provide, here, a general overview of the current state of development of these different systems and their applications for advanced live cell imaging and biosensing and discuss potential future directions.
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Affiliation(s)
- Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005 Paris, France.,Institut Universitaire de France, 75005 Paris, France
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19
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Sokolov AI, Baleeva NS, Baranov MS. Halogen-Containing 4-Hydroxybenzylidene-Rhodanines as Fast Protein Fluorogens. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022050247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Lushpa VA, Baleeva NS, Goncharuk SA, Goncharuk MV, Arseniev AS, Baranov MS, Mineev KS. Spatial Structure of nanoFAST in the Apo State and in Complex with its Fluorogen HBR-DOM2. Int J Mol Sci 2022; 23:ijms231911361. [PMID: 36232662 PMCID: PMC9570328 DOI: 10.3390/ijms231911361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/22/2022] Open
Abstract
NanoFAST is a fluorogen-activating protein and can be considered one of the smallest encodable fluorescent tags. Being a shortened variant of another fluorescent tag, FAST, nanoFAST works nicely only with one out of all known FAST ligands. This substantially limits the applicability of this protein. To find the reason for such a behavior, we investigated the spatial structure and dynamics of nanoFAST, both in the apo state and in the complex with its fluorogen molecule, using the solution NMR spectroscopy. We showed that the truncation of FAST did not affect the structure of the remaining part of the protein. Our data suggest that the deleted N-terminus of FAST destabilizes the C-terminal domain in the apo state. While it does not contact the fluorogen directly, it serves as a free energy reservoir that enhances the ligand binding propensity of the protein. The structure of nanoFAST/HBR-DOM2 complex reveals the atomistic details of nanoFAST interactions with the rhodanine-based ligands and explains the ligand specificity. NanoFAST selects ligands with the lowest dissociation constants, 2,5-disubstituted 4-hydroxybenzyldienerhodainines, which allow the non-canonical intermolecular CH–N hydrogen bonding and provide the optimal packing of the ligand within the hydrophobic cavity of the protein.
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Affiliation(s)
- Vladislav A. Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
| | - Nadezhda S. Baleeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | - Sergey A. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
| | - Marina V. Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
| | | | - Mikhail S. Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Correspondence: (M.S.B.); (K.S.M.)
| | - Konstantin S. Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow 117997, Russia
- Moscow Institute of Physics and Technology, School of Biological and Medical Physics, Dolgoprudny 141701, Russia
- Correspondence: (M.S.B.); (K.S.M.)
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21
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Khrulev AA, Baleeva NS, Kamzeeva PN, Baranov MS, Aralov AV. Cyanine Dyes as Fluorogens for FAST and NanoFAST Proteins. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s1068162022040112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Wu X, Tan D, Qiao Q, Yin W, Xu Z, Liu X. Molecular origins of the multi-donor strategy in inducing bathochromic shifts and enlarging Stokes shifts of fluorescent proteins. Phys Chem Chem Phys 2022; 24:15937-15944. [PMID: 35727090 DOI: 10.1039/d2cp00759b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Long-wavelength fluorescent proteins (LWFPs) and LWFP-based sensors are indispensable tools for bioimaging and biosensing applications. However, it remains challenging to develop LWFPs with outstanding brightness and/or sensitivities, largely due to the lack of simple and effective molecular design strategies. Herein, we rationalized the molecular origins of a multi-donor strategy that affords significant bathochromic shifts and large Stokes shifts with minimal structural changes in the resulting protein fluorophores. We analyzed three key factors that affect the spectral properties of these fluorophores, including the (1) substituent position, (2) electron-donating strength, and (3) number of electron-donating groups. We further demonstrated that this simple design strategy is generalizable to various fluorophore families. We expect that this work can provide rational guidelines for developing fluorescent proteins (and small-molecule fluorophores) with long emission wavelengths and large Stokes shifts.
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Affiliation(s)
- Xia Wu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore.
| | - Davin Tan
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore.
| | - Qinglong Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Wenting Yin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Zhaochao Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China.
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore.
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The Fluorescence-Activating and Absorption-Shifting Tag (FAST) Enables Live-Cell Fluorescence Imaging of Methanococcus maripaludis. J Bacteriol 2022; 204:e0012022. [PMID: 35657707 DOI: 10.1128/jb.00120-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Live-cell fluorescence imaging of methanogenic archaea has been limited due to the strictly anoxic conditions required for growth and issues with autofluorescence associated with electron carriers in central metabolism. Here, we show that the fluorescence-activating and absorption-shifting tag (FAST) complexed with the fluorogenic ligand 4-hydroxy-3-methylbenzylidene-rhodanine (HMBR) overcomes these issues and displays robust fluorescence in Methanococcus maripaludis. We also describe a mechanism to visualize cells under anoxic conditions using a fluorescence microscope. Derivatives of FAST were successfully applied for protein abundance analysis, subcellular localization analysis, and determination of protein-protein interactions. FAST fusions to both formate dehydrogenase (Fdh) and F420-reducing hydrogenase (Fru) displayed increased fluorescence in cells grown on formate-containing medium, consistent with previous studies suggesting the increased abundance of these proteins in the absence of H2. Additionally, FAST fusions to both Fru and the ATPase associated with the archaellum (FlaI) showed a membrane localization in single cells observed using anoxic fluorescence microscopy. Finally, a split reporter translationally fused to the alpha and beta subunits of Fdh reconstituted a functionally fluorescent molecule in vivo via bimolecular fluorescence complementation. Together, these observations demonstrate the utility of FAST as a tool for studying members of the methanogenic archaea. IMPORTANCE Methanogenic archaea are important members of anaerobic microbial communities where they catalyze essential reactions in the degradation of organic matter. Developing additional tools for studying the cell biology of these organisms is essential to understanding them at a mechanistic level. Here, we show that FAST, in combination with the fluorogenic ligand HMBR, can be used to monitor protein dynamics in live cells of M. maripaludis. The application of FAST holds promise for future studies focused on the metabolism and physiology of methanogenic archaea.
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Cao Z, Wang L, Liu R, Lin S, Wu F, Liu J. Encoding with a fluorescence-activating and absorption-shifting tag generates living bacterial probes for mammalian microbiota imaging. Mater Today Bio 2022; 15:100311. [PMID: 35711290 PMCID: PMC9194656 DOI: 10.1016/j.mtbio.2022.100311] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 05/28/2022] [Accepted: 05/28/2022] [Indexed: 12/12/2022] Open
Abstract
The mammalian microbiota plays essential roles in health. A primary determinant to understand the interaction with the host is the distribution and viability of its key microorganisms. Here, a strategy of encoding with a fluorescence-activating and absorption-shifting tag (FAST) is reported to prepare living bacterial probes for real-time dynamic, dual-modal, and molecular oxygen-independent imaging of the host microbiota. Carrying FAST endows bacteria with rapid on-demand turn on-off fluorescence by adding or removal of corresponding fluorogens. Encoded bacteria are able to reversibly switch emission bands for dual-color fluorescence imaging via fluorogen exchange. Due to molecular oxygen-independent emission of FAST, encoded bacteria can emit fluorescence under anaerobic environments including the gut and tumor. These living probes demonstrate the applicability to quantify the vitality of bacteria transplanted to the gut microbiota. This work proposes a unique fluorescence probe for investigating the dynamics of the host microbiota. Living bacterial probes for real-time dynamic, dual-modal, and molecular oxygen-independent imaging of mammalian microbiota. Engineered bacteria showing on-demand turn on-off fluorescence by adding or removal of corresponding fluorogens. Fluorescence emission under anaerobic in vivo environments including the gut and tumor. A fluorescence probe to determine the vitality of transplanted bacteria and investigate the dynamics of the host microbiota.
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25
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Flaiz M, Baur T, Gaibler J, Kröly C, Dürre P. Establishment of Green- and Red-Fluorescent Reporter Proteins Based on the Fluorescence-Activating and Absorption-Shifting Tag for Use in Acetogenic and Solventogenic Anaerobes. ACS Synth Biol 2022; 11:953-967. [PMID: 35081709 DOI: 10.1021/acssynbio.1c00554] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anaerobic bacteria are promising biocatalysts to produce industrially relevant products from nonfood feedstocks. Several anaerobes are genetically accessible, and various molecular tools for metabolic engineering are available. Still, the use of bright fluorescent reporters, which are commonly used in molecular biological approaches is limited under anaerobic conditions. Therefore, the establishment of different anaerobic fluorescent reporter proteins is of great interest. Here, we present the establishment of the green- and red-fluorescent reporter proteins greenFAST and redFAST for use in different solventogenic and acetogenic bacteria. Green fluorescence of greenFAST was bright in Clostridium saccharoperbutylacetonicum, Clostridium acetobutylicum, Acetobacterium woodii, and Eubacterium limosum, while only C. saccharoperbutylacetonicum showed bright red fluorescence when producing redFAST. We used both reporter proteins in C. saccharoperbutylacetonicum for multicolor approaches. These include the investigation of the co-culture dynamics of metabolically engineered strains. Moreover, we established a tightly regulated inducible two-plasmid system and used greenFAST and redFAST to track the coexistence and interaction of both plasmids under anaerobic conditions in C. saccharoperbutylacetonicum. The establishment of greenFAST and redFAST as fluorescent reporters opens the door for further multicolor approaches to investigate cell dynamics, gene expression, or protein localization under anaerobic conditions.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tina Baur
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Jana Gaibler
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Christian Kröly
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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Autotrophic lactate production from H2 + CO2 using recombinant and fluorescent FAST-tagged Acetobacterium woodii strains. Appl Microbiol Biotechnol 2022; 106:1447-1458. [PMID: 35092454 PMCID: PMC8882112 DOI: 10.1007/s00253-022-11770-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/23/2021] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
AbstractLactate has various uses as industrial platform chemical, poly-lactic acid precursor or feedstock for anaerobic co-cultivations. The aim of this study was to construct and characterise Acetobacterium woodii strains capable of autotrophic lactate production. Therefore, the lctBCD genes, encoding the native Lct dehydrogenase complex, responsible for lactate consumption, were knocked out. Subsequently, a gene encoding a d-lactate dehydrogenase (LDHD) originating from Leuconostoc mesenteroides was expressed in A. woodii, either under the control of the anhydrotetracycline-inducible promoter Ptet or under the lactose-inducible promoter PbgaL. Moreover, LDHD was N-terminally fused to the oxygen-independent fluorescence-activating and absorption-shifting tag (FAST) and expressed in respective A. woodii strains. Cells that produced the LDHD fusion protein were capable of lactate production of up to 18.8 mM in autotrophic batch experiments using H2 + CO2 as energy and carbon source. Furthermore, cells showed a clear and bright fluorescence during exponential growth, as well as in the stationary phase after induction, mediated by the N-terminal FAST. Flow cytometry at the single-cell level revealed phenotypic heterogeneities for cells expressing the FAST-tagged LDHD fusion protein. This study shows that FAST provides a new reporter tool to quickly analyze gene expression over the course of growth experiments of A. woodii. Consequently, fluorescence-based reporters allow for faster and more targeted optimization of production strains.Key points
•Autotrophic lactate production was achieved with A. woodii.
•FAST functions as fluorescent marker protein in A. woodii.
•Fluorescence measurements on single-cell level revealed population heterogeneity.
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Recent Advancements in Tracking Bacterial Effector Protein Translocation. Microorganisms 2022; 10:microorganisms10020260. [PMID: 35208715 PMCID: PMC8876096 DOI: 10.3390/microorganisms10020260] [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: 12/15/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 11/17/2022] Open
Abstract
Bacteria-host interactions are characterized by the delivery of bacterial virulence factors, i.e., effectors, into host cells where they counteract host immunity and exploit host responses allowing bacterial survival and spreading. These effectors are translocated into host cells by means of dedicated secretion systems such as the type 3 secretion system (T3SS). A comprehensive understanding of effector translocation in a spatio-temporal manner is of critical importance to gain insights into an effector’s mode of action. Various approaches have been developed to understand timing and order of effector translocation, quantities of translocated effectors and their subcellular localization upon translocation into host cells. Recently, the existing toolset has been expanded by newly developed state-of-the art methods to monitor bacterial effector translocation and dynamics. In this review, we elaborate on reported methods and discuss recent advances and shortcomings in this area of tracking bacterial effector translocation.
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Chen P, Wang R, Wang K, Han JN, Kuang S, Nie Z, Huang Y. Multifunctional stimuli-responsive chemogenetic platform for conditional multicolor cell-selective labeling. Chem Sci 2022; 13:12187-12197. [PMID: 36349109 PMCID: PMC9601257 DOI: 10.1039/d2sc03100k] [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: 06/03/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022] Open
Abstract
Multicolor conditional labeling is a powerful tool that can simultaneously and selectively visualize multiple targets for bioimaging analysis of complex biological processes and cellular features. We herein report a multifunctional stimuli-responsive Fluorescence-Activating and absorption-Shifting Tag (srFAST) chemogenetic platform for multicolor cell-selective labeling. This platform comprises stimuli-responsive fluorogenic ligands and the organelle-localizable FAST. The physicochemical properties of the srFAST ligands can be tailored by modifying the optical-tunable hydroxyl group with diverse reactive groups, and their chemical decaging process caused by cell-specific stimuli induces a conditionally activatable fluorescent labeling upon binding with the FAST. Thus, the resulting switch-on srFASTs were designed for on-demand labeling of cells of interest by spatiotemporally precise photo-stimulation or unique cellular feature-dependent activation, including specific endogenous metabolites or enzyme profiles. Furthermore, diverse enzyme-activatable srFAST ligands with distinct colors were constructed and simultaneously exploited for multicolor cell-selective labeling, which allow discriminating and orthogonal labeling of three different cell types with the same protein tag. Our method provides a promising strategy for designing a stimuli-responsive chemogenetic labeling platform via facile molecular engineering of the synthetic ligands, which has great potential for conditional multicolor cell-selective labeling and cellular heterogeneity evaluation. Comparison of the stimuli-responsive FAST platform (srFAST) proposed in this work with the reported original FAST system (O-FAST). The srFAST could achieve not only conditional selective labeling, but also multicolor selective labeling.![]()
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Affiliation(s)
- Pengfei Chen
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Rui Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Ke Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Jiao-Na Han
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Shi Kuang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Zhou Nie
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
| | - Yan Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, 410082, P. R. China
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29
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Benaissa H, Ounoughi K, Aujard I, Fischer E, Goïame R, Nguyen J, Tebo AG, Li C, Le Saux T, Bertolin G, Tramier M, Danglot L, Pietrancosta N, Morin X, Jullien L, Gautier A. Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging. Nat Commun 2021; 12:6989. [PMID: 34848727 PMCID: PMC8633346 DOI: 10.1038/s41467-021-27334-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 11/12/2021] [Indexed: 11/09/2022] Open
Abstract
Biocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing Förster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.
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Affiliation(s)
- Hela Benaissa
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France
| | - Karim Ounoughi
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France
| | - Isabelle Aujard
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France
| | - Evelyne Fischer
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Rosette Goïame
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Julie Nguyen
- Université de Paris, NeurImag Imaging Facility, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, 75014, Paris, France
| | - Alison G Tebo
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, 20147, USA
| | - Chenge Li
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Thomas Le Saux
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France
| | - Giulia Bertolin
- University of Rennes, Centre National de la Recherche Scientifique (CNRS), (IGDR) Institute of Genetics and Development of Rennes, Unité Mixte de Recherche (UMR) 6290, F-35000, Rennes, France
| | - Marc Tramier
- University of Rennes, Centre National de la Recherche Scientifique (CNRS), (IGDR) Institute of Genetics and Development of Rennes, Unité Mixte de Recherche (UMR) 6290, F-35000, Rennes, France
| | - Lydia Danglot
- Université de Paris, NeurImag Imaging Facility, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, 75014, Paris, France
- Université de Paris, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Membrane Traffic in Healthy & Diseased Brain, 75014, Paris, France
| | - Nicolas Pietrancosta
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France
- Neuroscience Paris Seine-Institut de Biologie Paris Seine (NPS-IBPS) INSERM, CNRS, Sorbonne Université, Paris, France
| | - Xavier Morin
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Ludovic Jullien
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, 75005, Paris, France.
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, 75005, Paris, France.
- Institut Universitaire de France, Paris, France.
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30
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Perfilov MM, Gavrikov AS, Lukyanov KA, Mishin AS. Transient Fluorescence Labeling: Low Affinity-High Benefits. Int J Mol Sci 2021; 22:11799. [PMID: 34769228 PMCID: PMC8583718 DOI: 10.3390/ijms222111799] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
Fluorescent labeling is an established method for visualizing cellular structures and dynamics. The fundamental diffraction limit in image resolution was recently bypassed with the development of super-resolution microscopy. Notably, both localization microscopy and stimulated emission depletion (STED) microscopy impose tight restrictions on the physico-chemical properties of labels. One of them-the requirement for high photostability-can be satisfied by transiently interacting labels: a constant supply of transient labels from a medium replenishes the loss in the signal caused by photobleaching. Moreover, exchangeable tags are less likely to hinder the intrinsic dynamics and cellular functions of labeled molecules. Low-affinity labels may be used both for fixed and living cells in a range of nanoscopy modalities. Nevertheless, the design of optimal labeling and imaging protocols with these novel tags remains tricky. In this review, we highlight the pros and cons of a wide variety of transiently interacting labels. We further discuss the state of the art and future perspectives of low-affinity labeling methods.
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Affiliation(s)
| | | | | | - Alexander S. Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia; (M.M.P.); (A.S.G.); (K.A.L.)
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31
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Baleeva NS, Smirnov AY, Myasnyanko IN, Gavrikov AS, Baranov MS. A Thiophene Analog of the GFP Chromophore As Fluorogen for FAST Protein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021050198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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32
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Gautier A, Jullien L, Li C, Plamont MA, Tebo AG, Thauvin M, Volovitch M, Vriz S. Versatile On-Demand Fluorescent Labeling of Fusion Proteins Using Fluorescence-Activating and Absorption-Shifting Tag (FAST). Methods Mol Biol 2021; 2350:253-265. [PMID: 34331290 DOI: 10.1007/978-1-0716-1593-5_16] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Observing the localization, the concentration, and the distribution of proteins in cells or organisms is essential to understand theirs functions. General and versatile methods allowing multiplexed imaging of proteins under a large variety of experimental conditions are thus essential for deciphering the inner workings of cells and organisms. Here, we present a general method based on the non-covalent labeling of a small protein tag, named FAST (fluorescence-activating and absorption-shifting tag), with various fluorogenic ligands that light up upon labeling, which makes the simple, robust, and versatile on-demand labeling of fusion proteins in a wide range of experimental systems possible.
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Affiliation(s)
- Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, Paris, France.
- Institut Universitaire de France, Paris, France.
| | - Ludovic Jullien
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Chenge Li
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
- Department of Obstetrics and Gynecology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Marie-Aude Plamont
- PASTEUR, Department of Chemistry, École Normale Supérieure, Université PSL, Sorbonne Université, CNRS, Paris, France
| | - Alison G Tebo
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, Paris, France
- Janelia Farms Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Marion Thauvin
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Department of Biology, École Normale Supérieure, Université PSL, Paris, France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERM, Université PSL, Paris, France
- Faculty of Science, Université de Paris, Paris, France
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33
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Anaerobic fluorescent reporters for cell identification, microbial cell biology and high-throughput screening of microbiota and genomic libraries. Curr Opin Biotechnol 2021; 71:151-163. [PMID: 34375813 DOI: 10.1016/j.copbio.2021.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/08/2021] [Indexed: 11/23/2022]
Abstract
The lack of real-time reporters in obligate anaerobes has limited studies in gene expression, promoter characterization, library screening, population dynamics, and cell biology in these organisms. While the use of enzymatic, colorimetric, and luminescent reporters has been reported, the need for reliable anaerobic fluorescent proteins is widely acknowledged. Recently, the fluorescent proteins HaloTag, SNAP-tag and FAST have been established as reliable reporters in Clostridium spp., thus suggesting that these reporters can be adopted widely for many obligate anaerobes. With a multitude of labeling options, these anaerobic fluorescent proteins hold a great potential for screening promoters, terminators, and RBS sites, tracking population dynamics in complex multi-species co-cultures, such as microbiomes, screening libraries, and in cell biology studies of protein localization and interactions using high-resolution microscopy.
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34
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Iyer A, Baranov M, Foster AJ, Chordia S, Roelfes G, Vlijm R, van den Bogaart G, Poolman B. Chemogenetic Tags with Probe Exchange for Live-Cell Fluorescence Microscopy. ACS Chem Biol 2021; 16:891-904. [PMID: 33913682 PMCID: PMC8154248 DOI: 10.1021/acschembio.1c00100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/15/2021] [Indexed: 11/29/2022]
Abstract
Fluorogenic protein tagging systems have been less developed for prokaryotes than for eukaryotic cell systems. Here, we extend the concept of noncovalent fluorogenic protein tags in bacteria by introducing transcription factor-based tags, namely, LmrR and RamR, for probe binding and fluorescence readout under aerobic and anaerobic conditions. We developed two chemogenetic protein tags that impart fluorogenicity and a longer fluorescence lifetime to reversibly bound organic fluorophores, hence the name Chemogenetic Tags with Probe Exchange (CTPEs). We present an extensive characterization of 30 fluorophores reversibly interacting with the two different CTPEs and conclude that aromatic planar structures bind with high specificity to the hydrophobic pockets of these tags. The reversible binding of organic fluorophores to the CTPEs and the superior photophysical properties of organic fluorophores enable long-term fluorescence microscopy of living bacterial cells. Our protein tags provide a general tool for investigating (sub)cellular protein localization and dynamics, protein-protein interactions, and prolonged live-cell microscopy, even under oxygen-free conditions.
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Affiliation(s)
- Aditya Iyer
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Maxim Baranov
- Department
of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Alexander J. Foster
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Shreyans Chordia
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Gerard Roelfes
- Stratingh
Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Rifka Vlijm
- Molecular
Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Geert van den Bogaart
- Department
of Molecular Immunology, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bert Poolman
- Department
of Biochemistry, Groningen Biomolecular Sciences and Biotechnology
Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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35
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Chen C, Tachibana SR, Baleeva NS, Myasnyanko IN, Bogdanov AM, Gavrikov AS, Mishin AS, Malyshevskaya KK, Baranov MS, Fang C. Developing Bright Green Fluorescent Protein (GFP)-like Fluorogens for Live-Cell Imaging with Nonpolar Protein-Chromophore Interactions. Chemistry 2021; 27:8946-8950. [PMID: 33938061 DOI: 10.1002/chem.202101250] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Indexed: 11/09/2022]
Abstract
Fluorescence-activating proteins (FAPs) that bind a chromophore and activate its fluorescence have gained popularity in bioimaging. The fluorescence-activating and absorption-shifting tag (FAST) is a light-weight FAP that enables fast reversible fluorogen binding, thus advancing multiplex and super-resolution imaging. However, the rational design of FAST-specific fluorogens with large fluorescence enhancement (FE) remains challenging. Herein, a new fluorogen directly engineered from green fluorescent protein (GFP) chromophore by a unique double-donor-one-acceptor strategy, which exhibits an over 550-fold FE upon FAST binding and a high extinction coefficient of approximately 100,000 M-1 cm-1 , is reported. Correlation analysis of the excited state nonradiative decay rates and environmental factors reveal that the large FE is caused by nonpolar protein-fluorogen interactions. Our deep insights into structure-function relationships could guide the rational design of bright fluorogens for live-cell imaging with extended spectral properties such as redder emissions.
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Affiliation(s)
- Cheng Chen
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Sean R Tachibana
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Kseniya K Malyshevskaya
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, Moscow, 117997, Russia.,Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR 97331-4003, USA
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36
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Flaiz M, Ludwig G, Bengelsdorf FR, Dürre P. Production of the biocommodities butanol and acetone from methanol with fluorescent FAST-tagged proteins using metabolically engineered strains of Eubacterium limosum. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:117. [PMID: 33971948 PMCID: PMC8111989 DOI: 10.1186/s13068-021-01966-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/29/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND The interest in using methanol as a substrate to cultivate acetogens increased in recent years since it can be sustainably produced from syngas and has the additional benefit of reducing greenhouse gas emissions. Eubacterium limosum is one of the few acetogens that can utilize methanol, is genetically accessible and, therefore, a promising candidate for the recombinant production of biocommodities from this C1 carbon source. Although several genetic tools are already available for certain acetogens including E. limosum, the use of brightly fluorescent reporter proteins is still limited. RESULTS In this study, we expanded the genetic toolbox of E. limosum by implementing the fluorescence-activating and absorption shifting tag (FAST) as a fluorescent reporter protein. Recombinant E. limosum strains that expressed the gene encoding FAST in an inducible and constitutive manner were constructed. Cultivation of these recombinant strains resulted in brightly fluorescent cells even under anaerobic conditions. Moreover, we produced the biocommodities butanol and acetone from methanol with recombinant E. limosum strains. Therefore, we used E. limosum cultures that produced FAST-tagged fusion proteins of the bifunctional acetaldehyde/alcohol dehydrogenase or the acetoacetate decarboxylase, respectively, and determined the fluorescence intensity and product concentrations during growth. CONCLUSIONS The addition of FAST as an oxygen-independent fluorescent reporter protein expands the genetic toolbox of E. limosum. Moreover, our results show that FAST-tagged fusion proteins can be constructed without negatively impacting the stability, functionality, and productivity of the resulting enzyme. Finally, butanol and acetone can be produced from methanol using recombinant E. limosum strains expressing genes encoding fluorescent FAST-tagged fusion proteins.
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Affiliation(s)
- Maximilian Flaiz
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.
| | - Gideon Ludwig
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Frank R Bengelsdorf
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Peter Dürre
- Institute of Microbiology and Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany
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37
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Mineev KS, Goncharuk SA, Goncharuk MV, Povarova NV, Sokolov AI, Baleeva NS, Smirnov AY, Myasnyanko IN, Ruchkin DA, Bukhdruker S, Remeeva A, Mishin A, Borshchevskiy V, Gordeliy V, Arseniev AS, Gorbachev DA, Gavrikov AS, Mishin AS, Baranov MS. NanoFAST: structure-based design of a small fluorogen-activating protein with only 98 amino acids. Chem Sci 2021; 12:6719-6725. [PMID: 34040747 PMCID: PMC8132994 DOI: 10.1039/d1sc01454d] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/08/2021] [Indexed: 12/31/2022] Open
Abstract
One of the essential characteristics of any tag used in bioscience and medical applications is its size. The larger the label, the more it may affect the studied object, and the more it may distort its behavior. In this paper, using NMR spectroscopy and X-ray crystallography, we have studied the structure of fluorogen-activating protein FAST both in the apo form and in complex with the fluorogen. We showed that significant change in the protein occurs upon interaction with the ligand. While the protein is completely ordered in the complex, its apo form is characterized by higher mobility and disordering of its N-terminus. We used structural information to design the shortened FAST (which we named nanoFAST) by truncating 26 N-terminal residues. Thus, we created the shortest genetically encoded tag among all known fluorescent and fluorogen-activating proteins, which is composed of only 98 amino acids.
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Affiliation(s)
- Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Natalia V Povarova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitry A Ruchkin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Sergey Bukhdruker
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- ESRF - The European Synchrotron Grenoble 38000 France
| | - Alina Remeeva
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
| | - Valentin Borshchevskiy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology Dolgoprudny 141701 Russia
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH Jülich 52425 Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH Jülich 52425 Germany
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes, CEA, CNRS Grenoble France
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S Gavrikov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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Myasnyanko IN, Gavrikov AS, Zaitseva SO, Smirnov AY, Zaitseva ER, Sokolov AI, Malyshevskaya KK, Baleeva NS, Mishin AS, Baranov MS. Color Tuning of Fluorogens for FAST Fluorogen‐Activating Protein. Chemistry 2021; 27:3986-3990. [DOI: 10.1002/chem.202004760] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/16/2020] [Indexed: 01/04/2023]
Affiliation(s)
- Ivan N. Myasnyanko
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexey S. Gavrikov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Snizhana O. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander Yu. Smirnov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Elvira R. Zaitseva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Anatolii I. Sokolov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Kseniya K. Malyshevskaya
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Nadezhda S. Baleeva
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Alexander S. Mishin
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
| | - Mikhail S. Baranov
- Institute of Bioorganic Chemistry Russian Academy of Sciences Miklukho-Maklaya 16/10 117997 Moscow Russia
- Pirogov Russian National Research Medical University Ostrovitianov 1 Moscow 117997 Russia
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Sokolov AI, Myasnyanko IN, Baleeva NS, Baranov MS. Styrene Derivatives of Indole and Pyranone as Fluorogenic Substrates for FAST Protein. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021010234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Peron-Cane C, Fernandez JC, Leblanc J, Wingertsmann L, Gautier A, Desprat N, Lebreton A. Fluorescent secreted bacterial effectors reveal active intravacuolar proliferation of Listeria monocytogenes in epithelial cells. PLoS Pathog 2020; 16:e1009001. [PMID: 33045003 PMCID: PMC7580998 DOI: 10.1371/journal.ppat.1009001] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 10/22/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022] Open
Abstract
Real-time imaging of bacterial virulence factor dynamics is hampered by the limited number of fluorescent tools suitable for tagging secreted effectors. Here, we demonstrated that the fluorogenic reporter FAST could be used to tag secreted proteins, and we implemented it to monitor infection dynamics in epithelial cells exposed to the human pathogen Listeria monocytogenes (Lm). By tracking individual FAST-labelled vacuoles after Lm internalisation into cells, we unveiled the heterogeneity of residence time inside entry vacuoles. Although half of the bacterial population escaped within 13 minutes after entry, 12% of bacteria remained entrapped over an hour inside long term vacuoles, and sometimes much longer, regardless of the secretion of the pore-forming toxin listeriolysin O (LLO). We imaged LLO-FAST in these long-term vacuoles, and showed that LLO enabled Lm to proliferate inside these compartments, reminiscent of what had been previously observed for Spacious Listeria-containing phagosomes (SLAPs). Unexpectedly, inside epithelial SLAP-like vacuoles (eSLAPs), Lm proliferated as fast as in the host cytosol. eSLAPs thus constitute an alternative replication niche in epithelial cells that might promote the colonization of host tissues. Bacterial pathogens secrete virulence factors to subvert their hosts; however, monitoring bacterial secretion in real-time remains challenging. Here, we developed a convenient method that enabled fluorescent imaging of secreted proteins in live microscopy, and applied it to the human pathogen Listeria monocytogenes. Listeria has been described to invade cells and proliferate in their cytosol; it is first internalized inside vacuoles, from where it escapes thanks to the secretion of virulence factors that disrupt membranes. Our work revealed the existence, in human epithelial cells, of a population of Listeria that failed to escape vacuoles but instead multiplied efficiently therein, despite—and in fact, thanks to—the active secretion of a toxin that permeates membranes. This intravacuolar niche may provide Listeria with an alternative strategy to colonize its host.
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Affiliation(s)
- Caroline Peron-Cane
- Laboratoire de Physique de l’École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, Paris, France
- Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - José-Carlos Fernandez
- Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Julien Leblanc
- Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Laure Wingertsmann
- Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École normale supérieure, Université PSL, CNRS, Laboratoire des Biomolécules, LBM, Paris, France
- Institut Universitaire de France
| | - Nicolas Desprat
- Laboratoire de Physique de l’École normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, Paris, France
- Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- UFR de Physique, Université Paris-Diderot, Université de Paris, Paris, France
- * E-mail: (ND); (AL)
| | - Alice Lebreton
- Institut de biologie de l’ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, France
- INRAE, IBENS, Paris, France
- * E-mail: (ND); (AL)
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41
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Chekli Y, Peron-Cane C, Dell'Arciprete D, Allemand JF, Li C, Ghigo JM, Gautier A, Lebreton A, Desprat N, Beloin C. Visualizing the dynamics of exported bacterial proteins with the chemogenetic fluorescent reporter FAST. Sci Rep 2020; 10:15791. [PMID: 32978420 PMCID: PMC7519654 DOI: 10.1038/s41598-020-72498-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Bacterial proteins exported to the cell surface play key cellular functions. However, despite the interest to study the localisation of surface proteins such as adhesins, transporters or hydrolases, monitoring their dynamics in live imaging remains challenging, due to the limited availability of fluorescent probes remaining functional after secretion. In this work, we used the Escherichia coli intimin and the Listeria monocytogenes InlB invasin as surface exposed scaffolds fused with the recently developed chemogenetic fluorescent reporter protein FAST. Using both membrane permeant (HBR-3,5DM) and non-permeant (HBRAA-3E) fluorogens that fluoresce upon binding to FAST, we demonstrated that fully functional FAST can be exposed at the cell surface and used to specifically tag the external side of the bacterial envelop in both diderm and monoderm bacteria. Our work opens new avenues to study the organization and dynamics of the bacterial cell surface proteins.
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Affiliation(s)
- Yankel Chekli
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Caroline Peron-Cane
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Dario Dell'Arciprete
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
| | - Jean-François Allemand
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Chenge Li
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
| | - Jean-Marc Ghigo
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France
| | - Arnaud Gautier
- École Normale Supérieure, Université PSL, CNRS, Laboratoire Des Biomolécules (LBM), Sorbonne Université, 75005, Paris, France
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France
- Institut Universitaire de France, Paris, France
| | - Alice Lebreton
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
- INRAE, IBENS, 75005, Paris, France
| | - Nicolas Desprat
- Laboratoire de Physique de L'ENS, École Normale Supérieure, Université PSL, CNRS, Sorbonne Université, Université de Paris, 75005, Paris, France.
- Institut de Biologie de I'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Christophe Beloin
- Genetics of Biofilms Laboratory, Institut Pasteur, UMR CNRS2001, 75015, Paris, France.
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42
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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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43
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Li C, Tebo AG, Thauvin M, Plamont M, Volovitch M, Morin X, Vriz S, Gautier A. A Far‐Red Emitting Fluorescent Chemogenetic Reporter for In Vivo Molecular Imaging. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chenge Li
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Present address: Department of Obstetrics and Gynecology Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
| | - Alison G. Tebo
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
| | - Marion Thauvin
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Sorbonne Université Paris France
| | - Marie‐Aude Plamont
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- École Normale Supérieure Université PSL Department of biology Paris France
| | - Xavier Morin
- Institut de Biologie de l'ENS (IBENS) École Normale Supérieure CNRS INSERM Université PSL 75005 Paris France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Université de Paris Faculty of Science 75006 Paris France
| | - Arnaud Gautier
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
- Institut Universitaire de France France
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44
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Li C, Tebo AG, Thauvin M, Plamont M, Volovitch M, Morin X, Vriz S, Gautier A. A Far‐Red Emitting Fluorescent Chemogenetic Reporter for In Vivo Molecular Imaging. Angew Chem Int Ed Engl 2020; 59:17917-17923. [DOI: 10.1002/anie.202006576] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 11/08/2022]
Affiliation(s)
- Chenge Li
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Present address: Department of Obstetrics and Gynecology Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
- State Key Laboratory of Oncogenes and Related Genes Shanghai Cancer Institute Ren Ji Hospital School of Medicine Shanghai Jiao Tong University China
| | - Alison G. Tebo
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
| | - Marion Thauvin
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Sorbonne Université Paris France
| | - Marie‐Aude Plamont
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
| | - Michel Volovitch
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- École Normale Supérieure Université PSL Department of biology Paris France
| | - Xavier Morin
- Institut de Biologie de l'ENS (IBENS) École Normale Supérieure CNRS INSERM Université PSL 75005 Paris France
| | - Sophie Vriz
- Center for Interdisciplinary Research in Biology (CIRB) Collège de France CNRS INSERM Université PSL Paris France
- Université de Paris Faculty of Science 75006 Paris France
| | - Arnaud Gautier
- PASTEUR Department of Chemistry École Normale Supérieure Université PSL Sorbonne Université CNRS 75005 Paris France
- Sorbonne Université École Normale Supérieure Université PSL CNRS, Laboratoire des biomolécules, LBM 75005 Paris France
- Institut Universitaire de France France
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45
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Tebo AG, Moeyaert B, Thauvin M, Carlon-Andres I, Böken D, Volovitch M, Padilla-Parra S, Dedecker P, Vriz S, Gautier A. Orthogonal fluorescent chemogenetic reporters for multicolor imaging. Nat Chem Biol 2020; 17:30-38. [PMID: 32778846 PMCID: PMC7610487 DOI: 10.1038/s41589-020-0611-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/02/2020] [Indexed: 12/24/2022]
Abstract
Spectrally separated fluorophores allow the observation of multiple targets simultaneously inside living cells, leading to a deeper understanding of the molecular interplay that regulates cell function and fate. Chemogenetic systems combining a tag and a synthetic fluorophore provide certain advantages over fluorescent proteins since there is no requirement for chromophore maturation. Here, we present the engineering of a set of spectrally orthogonal fluorogen activating tags based on the Fluorescence Activating and absorption Shifting Tag (FAST), that are compatible with two-color, live cell imaging. The resulting tags, greenFAST and redFAST, demonstrate orthogonality not only in their fluorogen recognition capabilities, but also in their one- and two-photon absorption profiles. This pair of orthogonal tags allowed the creation of a two-color cell cycle sensor capable of detecting very short, early cell cycles in zebrafish development, and the development of split complementation systems capable of detecting multiple protein-protein interactions by live cell fluorescence microscopy.
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Affiliation(s)
- Alison G Tebo
- Sorbonne University, École Normale Supérieure, PSL University, CNRS, Laboratoire des biomolécules (LBM), Paris, France.,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France.,Janelia Farms Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Benjamien Moeyaert
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Marion Thauvin
- Center for Interdisciplinary Research, Collège de France, CNRS, INSERM, PSL University, Paris, France.,Sorbonne University, Paris, France
| | - Irene Carlon-Andres
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK
| | - Dorothea Böken
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France
| | - Michel Volovitch
- Center for Interdisciplinary Research, Collège de France, CNRS, INSERM, PSL University, Paris, France.,Department of Biology, École Normale Supérieure, PSL University, Paris, France
| | - Sergi Padilla-Parra
- Division of Structural Biology, University of Oxford, Wellcome Centre for Human Genetics, Oxford, UK.,Department of Infectious Diseases, Faculty of Life Sciences & Medicine, King's College London, London, UK.,Randall Centre for Cell and Molecular Biology, King's College London, London, UK
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Heverlee, Belgium
| | - Sophie Vriz
- Center for Interdisciplinary Research, Collège de France, CNRS, INSERM, PSL University, Paris, France.,Faculty of Sciences, Université de Paris, Paris, France
| | - Arnaud Gautier
- Sorbonne University, École Normale Supérieure, PSL University, CNRS, Laboratoire des biomolécules (LBM), Paris, France. .,PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne University, CNRS, Paris, France. .,Institut Universitaire de France, Paris, France.
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46
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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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47
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Perkins LA, Bruchez MP. Fluorogen activating protein toolset for protein trafficking measurements. Traffic 2020; 21:333-348. [PMID: 32080949 PMCID: PMC7462100 DOI: 10.1111/tra.12722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 12/11/2022]
Abstract
Throughout the past decade the use of fluorogen activating proteins (FAPs) has expanded with several unique reporter dyes that support a variety of methods to specifically quantify protein trafficking events. The platform's capabilities have been demonstrated in several systems and shared for widespread use. This review will highlight the current FAP labeling techniques for protein traffic measurements and focus on the use of the different designed fluorogenic dyes for selective and specific labeling applications.
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Affiliation(s)
- Lydia A. Perkins
- School of MedicineUniversity of PittsburghPittsburghPennsylvaniaUSA
| | - Marcel P. Bruchez
- The Department of Biological SciencesCarnegie MellonPittsburghPennsylvaniaUSA
- Department of ChemistryCarnegie MellonPittsburghPennsylvaniaUSA
- Molecular and Biosensor Imaging CenterCarnegie MellonPittsburghPennsylvaniaUSA
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Ozbakir HF, Anderson NT, Fan KC, Mukherjee A. Beyond the Green Fluorescent Protein: Biomolecular Reporters for Anaerobic and Deep-Tissue Imaging. Bioconjug Chem 2020; 31:293-302. [PMID: 31794658 PMCID: PMC7033020 DOI: 10.1021/acs.bioconjchem.9b00688] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescence imaging represents cornerstone technology for studying biological function at the cellular and molecular levels. The technology's centerpiece is a prolific collection of genetic reporters based on the green fluorescent protein (GFP) and related analogs. More than two decades of protein engineering have endowed the GFP repertoire with an incredible assortment of fluorescent proteins, allowing scientists immense latitude in choosing reporters tailored to various cellular and environmental contexts. Nevertheless, GFP and derivative reporters have specific limitations that hinder their unrestricted use for molecular imaging. These challenges have inspired the development of new reporter proteins and imaging mechanisms. Here, we review how these developments are expanding the frontiers of reporter gene techniques to enable nondestructive studies of cell function in anaerobic environments and deep inside intact animals-two important biological contexts that are fundamentally incompatible with the use of GFP-based reporters.
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Affiliation(s)
- Harun F. Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Nolan T. Anderson
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Kang-Ching Fan
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
| | - Arnab Mukherjee
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, United States
- Department of Chemistry, University of California, Santa Barbara, California 93106, United States
- Neuroscience Research Institute, University of California, Santa Barbara, California 93106, United States
- Center for Bioengineering, University of California, Santa Barbara, California 93106, United States
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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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50
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Endesfelder U. From single bacterial cell imaging towards in vivo single-molecule biochemistry studies. Essays Biochem 2019; 63:187-196. [PMID: 31197072 PMCID: PMC6610453 DOI: 10.1042/ebc20190002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 12/12/2022]
Abstract
Bacteria as single-cell organisms are important model systems to study cellular mechanisms and functions. In recent years and with the help of advanced fluorescence microscopy techniques, immense progress has been made in characterizing and quantifying the behavior of single bacterial cells on the basis of molecular interactions and assemblies in the complex environment of live cultures. Importantly, single-molecule imaging enables the in vivo determination of the stoichiometry and molecular architecture of subcellular structures, yielding detailed, quantitative, spatiotemporally resolved molecular maps and unraveling dynamic heterogeneities and subpopulations on the subcellular level. Nevertheless, open challenges remain. Here, we review the past and current status of the field, discuss example applications and give insights into future trends.
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Affiliation(s)
- Ulrike Endesfelder
- Department of Systems and Synthetic Microbiology, Max Planck Institute for Terrestrial Microbiology and LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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