1
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Coïs J, Niepon ML, Wittwer M, Sepasi Tehrani H, Bun P, Mallet JM, Vialou V, Dumat B. A Fluorogenic Chemogenetic pH Sensor for Imaging Protein Exocytosis. ACS Sens 2024. [PMID: 39145986 DOI: 10.1021/acssensors.4c01057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
Fluorescent protein-based pH biosensors enable the tracking of pH changes during protein trafficking and, in particular, exocytosis. The recent development of chemogenetic reporters combining synthetic fluorophores with self-labeling protein tags offers a versatile alternative to fluorescent proteins that combines the diversity of chemical probes and indicators with the selectivity of the genetic encoding. However, this hybrid protein labeling strategy does not avoid common drawbacks of organic fluorophores such as the risk of off-target signal due to unbound molecules. Here, we describe a novel fluorogenic and chemogenetic pH sensor based on a cell-permeable molecular pH indicator called pHluo-Halo-1, whose fluorescence can be locally activated in cells by reaction with HaloTag, ensuring excellent signal selectivity in wash-free imaging experiments. pHluo-Halo-1 was selected out of a series of four fluorogenic molecular rotor structures based on protein chromophore analogues. It displays good pH sensitivity with a pKa of 6.3 well-suited to monitor pH variations during exocytosis and an excellent labeling selectivity in cells. It was applied to follow the secretion of CD63-HaloTag fusion proteins using TIRF microscopy. We anticipate that this strategy based on the combination of a tunable and chemically accessible fluorogenic probe with a well-established protein tag will open new possibilities for the development of versatile alternatives to fluorescent proteins for elucidating the dynamics and regulatory mechanisms of proteins in living cells.
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Affiliation(s)
- Justine Coïs
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
- Laboratoire Neurosciences Paris Seine, Sorbonne Université, CNRS, INSERM, Paris 75005, France
| | - Marie-Laure Niepon
- Laboratoire Neurosciences Paris Seine, Sorbonne Université, CNRS, INSERM, Paris 75005, France
| | - Manon Wittwer
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Hessam Sepasi Tehrani
- PASTEUR, Département de chimie, École normale supérieure, CNRS, PSL University, Sorbonne Université, Paris 75005, France
| | - Philippe Bun
- Institute of Psychiatry and Neuroscience of Paris (IPNP), INSERM U1266, NeurImag Imaging Core Facility, Université Paris Cité, Paris 75014, France
| | - Jean-Maurice Mallet
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Vincent Vialou
- Laboratoire Neurosciences Paris Seine, Sorbonne Université, CNRS, INSERM, Paris 75005, France
| | - Blaise Dumat
- Laboratoire des biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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2
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Frei MS, Mehta S, Zhang J. Next-Generation Genetically Encoded Fluorescent Biosensors Illuminate Cell Signaling and Metabolism. Annu Rev Biophys 2024; 53:275-297. [PMID: 38346245 DOI: 10.1146/annurev-biophys-030722-021359] [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] [Indexed: 02/28/2024]
Abstract
Genetically encoded fluorescent biosensors have revolutionized the study of cell signaling and metabolism, as they allow for live-cell measurements with high spatiotemporal resolution. This success has spurred the development of tailor-made biosensors that enable the study of dynamic phenomena on different timescales and length scales. In this review, we discuss different approaches to enhancing and developing new biosensors. We summarize the technologies used to gain structural insights into biosensor design and comment on useful screening technologies. Furthermore, we give an overview of different applications where biosensors have led to key advances over recent years. Finally, we give our perspective on where future work is bound to make a large impact.
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Affiliation(s)
- Michelle S Frei
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Sohum Mehta
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
| | - Jin Zhang
- Department of Pharmacology, University of California San Diego, La Jolla, California, USA; , ,
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, California, USA
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA
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3
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Toke O, Batta G. Dynamic Structures of Bioactive Proteins as Determined by Nuclear Magnetic Resonance. Int J Mol Sci 2023; 25:295. [PMID: 38203465 PMCID: PMC10779278 DOI: 10.3390/ijms25010295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
According to "Panta rhei", a phrase by the ancient Greeks, you cannot enter the same river two times [...].
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Affiliation(s)
- Orsolya Toke
- NMR Research Laboratory, Centre for Structural Science, Research Centre for Natural Sciences, 2 Magyar tudósok körútja, H-1117 Budapest, Hungary
| | - Gyula Batta
- Department of Organic Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
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4
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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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5
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Vecchia MD, Conte-Daban A, Cappe B, Vandenberg W, Vandenabeele P, Riquet FB, Dedecker P. Spectrally Tunable Förster Resonance Energy Transfer-Based Biosensors Using Organic Dye Grafting. ACS Sens 2022; 7:2920-2927. [PMID: 36162130 DOI: 10.1021/acssensors.2c00066] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Biosensors based on Förster resonance energy transfer (FRET) have revolutionized cellular biology by allowing the direct measurement of biochemical processes in situ. Many genetically encoded sensors make use of fluorescent proteins that are limited in spectral versatility and that allow few ways to change the spectral properties once the construct has been created. In this work, we developed genetically encoded FRET biosensors based on the chemigenetic SNAP and HaloTag domains combined with matching organic fluorophores. We found that the resulting constructs can display comparable responses, kinetics, and reversibility compared to their fluorescent protein-based ancestors, but with the added advantage of spectral versatility, including the availability of red-shifted dye pairs. However, we also find that the introduction of these tags can alter the sensor readout, showing that careful validation is required before applying such constructs in practice. Overall, our approach delivers an innovative methodology that can readily expand the spectral variety and versatility of FRET-based biosensors.
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Affiliation(s)
- Marco Dalla Vecchia
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium.,Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | | | - Benjamin Cappe
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Wim Vandenberg
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium
| | - Franck B Riquet
- Molecular Signaling and Cell Death Unit, Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.,Cell Death and Inflammation Unit, VIB-UGent Center for Inflammation Research (IRC), Technologiepark 71, Zwijnaarde, 9052 Ghent, Belgium.,Université de Lille, CNRS, UMR 8523-PhLAM-Physique des Lasers Atomes et Molécules, 59000 Lille, France
| | - Peter Dedecker
- Lab for NanoBiology, Department of Chemistry, 3001 Leuven, Belgium
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6
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Theillet FX, Luchinat E. In-cell NMR: Why and how? PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:1-112. [PMID: 36496255 DOI: 10.1016/j.pnmrs.2022.04.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/17/2023]
Abstract
NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.
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Affiliation(s)
- Francois-Xavier Theillet
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France.
| | - Enrico Luchinat
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Alma Mater Studiorum - Università di Bologna, Piazza Goidanich 60, 47521 Cesena, Italy; CERM - Magnetic Resonance Center, and Neurofarba Department, Università degli Studi di Firenze, 50019 Sesto Fiorentino, Italy
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7
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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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8
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Goncharuk MV, Baleeva NS, Nolde DE, Gavrikov AS, Mishin AV, Mishin AS, Sosorev AY, Arseniev AS, Goncharuk SA, Borshchevskiy VI, Efremov RG, Mineev KS, Baranov MS. Structure-based rational design of an enhanced fluorogen-activating protein for fluorogens based on GFP chromophore. Commun Biol 2022; 5:706. [PMID: 35840781 PMCID: PMC9287381 DOI: 10.1038/s42003-022-03662-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
“Fluorescence-Activating and absorption-Shifting Tag” (FAST) is a well-studied fluorogen-activating protein with high brightness and low size, able to activate a wide range of fluorogens. This makes FAST a promising target for both protein and fluorogen optimization. Here, we describe the structure-based rational design of the enhanced FAST mutants, optimized for the N871b fluorogen. Using the spatial structure of the FAST/N871b complex, NMR relaxation analysis, and computer simulations, we identify the mobile regions in the complex and suggest mutations that could stabilize both the protein and the ligand. Two of our mutants appear brighter than the wild-type FAST, and these mutants provide up to 35% enhancement for several other fluorogens of similar structure, both in vitro and in vivo. Analysis of the mutants by NMR reveals that brighter mutants demonstrate the highest stability and lowest length of intermolecular H-bonds. Computer simulations provide the structural basis for such stabilization. Structural analyses guide the rational design of mutant fluorogen-activating proteins with enhanced fluorescence.
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Affiliation(s)
- Marina V Goncharuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia
| | - Nadezhda S Baleeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia
| | - Dmitry E Nolde
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia.,National Research University Higher School of Economics, Moscow, 101000, Russia
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia
| | - Alexey V Mishin
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia
| | - Andrey Y Sosorev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia
| | - Alexander S Arseniev
- 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, Dolgoprudny, 141701, Russia
| | | | - Roman G Efremov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia.,National Research University Higher School of Economics, Moscow, 101000, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
| | - Mikhail S Baranov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, 117997, Russia. .,Pirogov Russian National Research Medical University, Moscow, 117997, Russia.
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9
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Farrants H, Tebo AG. Fluorescent chemigenetic actuators and indicators for use in living animals. Curr Opin Pharmacol 2022; 62:159-167. [DOI: 10.1016/j.coph.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/03/2021] [Accepted: 12/12/2021] [Indexed: 11/28/2022]
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10
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El Hajji L, Benaissa H, Gautier A. Isolating and Engineering Fluorescence-Activating Proteins Using Yeast Surface Display. Methods Mol Biol 2022; 2491:593-626. [PMID: 35482206 DOI: 10.1007/978-1-0716-2285-8_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This protocol describes the workflow to isolate and engineer fluorescence-activating proteins by yeast surface display. Fluorescence-activating proteins are an emerging class of fluorescent chemogenetic reporters for monitoring gene expression and protein localization in living cells and organisms. They become fluorescent upon binding exogenously applied fluorogenic organic dyes. Efficient fluorescence-activating proteins can be selected from yeast-displayed libraries by iterative rounds of fluorescence-activated cell sorting. The overall strategy is described, as well as a strategy for characterizing the affinity and spectroscopic properties of the selected clones.
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Affiliation(s)
- Lina El Hajji
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des biomolécules, LBM, Paris, France
| | - Hela Benaissa
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des biomolécules, LBM, Paris, France
| | - Arnaud Gautier
- Sorbonne Université, École Normale Supérieure, Université PSL, CNRS, Laboratoire des biomolécules, LBM, Paris, France.
- Institut Universitaire de, Paris, France.
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11
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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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Kolesov DV, Sokolinskaya EL, Lukyanov KA, Bogdanov AM. Molecular Tools for Targeted Control of Nerve Cell Electrical Activity. Part II. Acta Naturae 2021; 13:17-32. [PMID: 35127143 PMCID: PMC8807539 DOI: 10.32607/actanaturae.11415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 05/14/2021] [Indexed: 01/01/2023] Open
Abstract
In modern life sciences, the issue of a specific, exogenously directed manipulation of a cell's biochemistry is a highly topical one. In the case of electrically excitable cells, the aim of the manipulation is to control the cells' electrical activity, with the result being either excitation with subsequent generation of an action potential or inhibition and suppression of the excitatory currents. The techniques of electrical activity stimulation are of particular significance in tackling the most challenging basic problem: figuring out how the nervous system of higher multicellular organisms functions. At this juncture, when neuroscience is gradually abandoning the reductionist approach in favor of the direct investigation of complex neuronal systems, minimally invasive methods for brain tissue stimulation are becoming the basic element in the toolbox of those involved in the field. In this review, we describe three approaches that are based on the delivery of exogenous, genetically encoded molecules sensitive to external stimuli into the nervous tissue. These approaches include optogenetics (overviewed in Part I), as well as chemogenetics and thermogenetics (described here, in Part II), which is significantly different not only in the nature of the stimuli and structure of the appropriate effector proteins, but also in the details of experimental applications. The latter circumstance is an indication that these are rather complementary than competing techniques.
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Affiliation(s)
- D. V. Kolesov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - E. L. Sokolinskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - K. A. Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
| | - A. M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997 Russia
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Baek K, Ji K, Peng W, Liyanaarachchi SM, Dodani SC. The design and evolution of fluorescent protein-based sensors for monoatomic ions in biology. Protein Eng Des Sel 2021; 34:gzab023. [PMID: 34581820 PMCID: PMC8477612 DOI: 10.1093/protein/gzab023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 08/18/2021] [Accepted: 08/18/2021] [Indexed: 12/15/2022] Open
Abstract
Living cells rely on a finely tuned symphony of inorganic ion gradients composed of both cations and anions. This delicate balance is maintained by biological receptors all acting in concert to selectively recognize and position ions for homeostasis. These dynamic processes can be intercepted and visualized with optical microscopy at the organismal, tissue, cellular and subcellular levels using fluorescent protein-based biosensors. Since the first report of such tool for calcium (Ca2+) in 1997, outstanding biological questions and innovations in protein engineering along with associated fields have driven the development of new biosensors for Ca2+ and beyond. In this Review, we summarize a workflow that can be used to generate fluorescent protein-based biosensors to study monoatomic ions in biology. To showcase the scope of this approach, we highlight recent advances reported for Ca2+ biosensors and in detail discuss representative case studies of biosensors reported in the last four years for potassium (K+), magnesium (Mg2+), copper (Cu2+/+), lanthanide (Ln3+) and chloride (Cl-) ions.
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Affiliation(s)
- Kiheon Baek
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Ke Ji
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Weicheng Peng
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Sureshee M Liyanaarachchi
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
| | - Sheel C Dodani
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, 800 West Campbell Road, Richardson, TX 75080, USA
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Montecinos-Franjola F, Lin JY, Rodriguez EA. Fluorescent proteins for in vivo imaging, where's the biliverdin? Biochem Soc Trans 2020; 48:2657-2667. [PMID: 33196077 DOI: 10.1042/bst20200444] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/20/2020] [Accepted: 10/26/2020] [Indexed: 12/13/2022]
Abstract
Noninvasive fluorescent imaging requires far-red and near-infrared fluorescent proteins for deeper imaging. Near-infrared light penetrates biological tissue with blood vessels due to low absorbance, scattering, and reflection of light and has a greater signal-to-noise due to less autofluorescence. Far-red and near-infrared fluorescent proteins absorb light >600 nm to expand the color palette for imaging multiple biosensors and noninvasive in vivo imaging. The ideal fluorescent proteins are bright, photobleach minimally, express well in the desired cells, do not oligomerize, and generate or incorporate exogenous fluorophores efficiently. Coral-derived red fluorescent proteins require oxygen for fluorophore formation and release two hydrogen peroxide molecules. New fluorescent proteins based on phytochrome and phycobiliproteins use biliverdin IXα as fluorophores, do not require oxygen for maturation to image anaerobic organisms and tumor core, and do not generate hydrogen peroxide. The small Ultra-Red Fluorescent Protein (smURFP) was evolved from a cyanobacterial phycobiliprotein to covalently attach biliverdin as an exogenous fluorophore. The small Ultra-Red Fluorescent Protein is biophysically as bright as the enhanced green fluorescent protein, is exceptionally photostable, used for biosensor development, and visible in living mice. Novel applications of smURFP include in vitro protein diagnostics with attomolar (10-18 M) sensitivity, encapsulation in viral particles, and fluorescent protein nanoparticles. However, the availability of biliverdin limits the fluorescence of biliverdin-attaching fluorescent proteins; hence, extra biliverdin is needed to enhance brightness. New methods for improved biliverdin bioavailability are necessary to develop improved bright far-red and near-infrared fluorescent proteins for noninvasive imaging in vivo.
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Affiliation(s)
| | - John Y Lin
- School of Medicine, University of Tasmania, Hobart, Tasmania 7000, Australia
| | - Erik A Rodriguez
- Department of Chemistry, The George Washington University, Washington, DC 20052, U.S.A
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