1
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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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2
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Bodén A, Ollech D, York AG, Millett-Sikking A, Testa I. Super-sectioning with multi-sheet reversible saturable optical fluorescence transitions (RESOLFT) microscopy. Nat Methods 2024; 21:882-888. [PMID: 38395993 PMCID: PMC11093742 DOI: 10.1038/s41592-024-02196-8] [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: 07/11/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Light-sheet fluorescence microscopy is an invaluable tool for four-dimensional biological imaging of multicellular systems due to the rapid volumetric imaging and minimal illumination dosage. However, it is challenging to retrieve fine subcellular information, especially in living cells, due to the width of the sheet of light (>1 μm). Here, using reversibly switchable fluorescent proteins (RSFPs) and a periodic light pattern for photoswitching, we demonstrate a super-resolution imaging method for rapid volumetric imaging of subcellular structures called multi-sheet RESOLFT. Multiple emission-sheets with a width that is far below the diffraction limit are created in parallel increasing recording speed (1-2 Hz) to provide super-sectioning ability (<100 nm). Our technology is compatible with various RSFPs due to its minimal requirement in the number of switching cycles and can be used to study a plethora of cellular structures. We track cellular processes such as cell division, actin motion and the dynamics of virus-like particles in three dimensions.
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Affiliation(s)
- Andreas Bodén
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dirk Ollech
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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3
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Maity A, Wulffelé J, Ayala I, Favier A, Adam V, Bourgeois D, Brutscher B. Structural Heterogeneity in a Phototransformable Fluorescent Protein Impacts its Photochemical Properties. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306272. [PMID: 38146132 PMCID: PMC10933604 DOI: 10.1002/advs.202306272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/29/2023] [Indexed: 12/27/2023]
Abstract
Photoconvertible fluorescent proteins (PCFP) are important cellular markers in advanced imaging modalities such as photoactivatable localization microscopy (PALM). However, their complex photophysical and photochemical behavior hampers applications such as quantitative and single-particle-tracking PALM. This work employs multidimensional NMR combined with ensemble fluorescence measurements to show that the popular mEos4b in its Green state populates two conformations (A and B), differing in side-chain protonation of the conserved residues E212 and H62, altering the hydrogen-bond network in the chromophore pocket. The interconversion (protonation/deprotonation) between these two states, which occurs on the minutes time scale in the dark, becomes strongly accelerated in the presence of UV light, leading to a population shift. This work shows that the reversible photoswitching and Green-to-Red photoconversion properties differ between the A and B states. The chromophore in the A-state photoswitches more efficiently and is proposed to be more prone to photoconversion, while the B-state shows a higher level of photobleaching. Altogether, this data highlights the central role of conformational heterogeneity in fluorescent protein photochemistry.
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Affiliation(s)
- Arijit Maity
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Jip Wulffelé
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Isabel Ayala
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Adrien Favier
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Virgile Adam
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Dominique Bourgeois
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
| | - Bernhard Brutscher
- CEACNRSInstitut de Biologie Structurale (IBS)Université Grenoble Alpes71 avenue des Martyrs, Cedex 9Grenoble38044France
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4
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Dzuvor CKO, Shen HH, Haritos VS, He L. Coassembled Multicomponent Protein Nanoparticles Elicit Enhanced Antibacterial Activity. ACS NANO 2024; 18:4478-4494. [PMID: 38266175 DOI: 10.1021/acsnano.3c11179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
The waning pipeline of the useful antibacterial arsenal has necessitated the urgent development of more effective antibacterial strategies with distinct mechanisms to rival the continuing emergence of resistant pathogens, particularly Gram-negative bacteria, due to their explicit drug-impermeable, two-membrane-sandwiched cell wall envelope. Herein, we have developed multicomponent coassembled nanoparticles with strong bactericidal activity and simultaneous bacterial cell envelope targeting using a peptide coassembly strategy. Compared to the single-component self-assembled nanoparticle counterparts or cocktail mixtures of these at a similar concentration, coassembled multicomponent nanoparticles showed higher bacterial killing efficiency against Acinetobacter baumannii, Pseudomonas aeruginosa, and Escherichia coli by several orders of magnitude (about 100-1,000,000-fold increase). Comprehensive confocal and electron microscopy suggest that the superior antibacterial activity of the coassembled nanoparticles proceeds via multiple complementary mechanisms of action, including membrane destabilization, disruption, and cell wall hydrolysis, actions that were not observed with the single nanoparticle counterparts. To understand the fundamental working mechanisms behind the improved performance of coassembled nanoparticles, we utilized a "dilution effect" system where the antibacterial components are intermolecularly mixed and coassembled with a non-antibacterial protein in the nanoparticles. We suggest that coassembled nanoparticles mediate enhanced bacterial killing activity by attributes such as optimized local concentration, high avidity, cooperativity, and synergy. The nanoparticles showed no cytotoxic or hemolytic activity against tested eukaryotic cells and erythrocytes. Collectively, these findings reveal potential strategies for disrupting the impermeable barrier that Gram-negative pathogens leverage to restrict antibacterial access and may serve as a platform technology for potential nano-antibacterial design to strengthen the declining antibiotic arsenal.
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Affiliation(s)
- Christian K O Dzuvor
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Hsin-Hui Shen
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
- Monash Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University Clayton, Victoria 3800, Australia
| | - Victoria S Haritos
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Lizhong He
- Bioengineering Laboratory, Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
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5
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Torii K, Benson S, Hori Y, Vendrell M, Kikuchi K. No-wash fluorogenic labeling of proteins for reversible photoswitching in live cells. Chem Sci 2024; 15:1393-1401. [PMID: 38274070 PMCID: PMC10806661 DOI: 10.1039/d3sc04953a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/16/2023] [Indexed: 01/27/2024] Open
Abstract
Photoswitchable fluorescent molecules (PSFMs) are positioned as valuable tools for biomolecule localization tracking and super-resolution imaging technologies due to their unique ability to reversibly control fluorescence intensity upon light irradiation. Despite the high demand for PSFMs that are suitable for live-cell imaging, no general method has been reported that enables reversible fluorescence control on proteins of interest in living cells. Herein, we have established a platform to realize reversible fluorescence switching in living cells by adapting a protein labeling system. We have developed a new PSFM, named HTL-Trp-BODIPY-FF, which exhibits strong fluorogenicity upon recognition of Halo-tag protein and reversible fluorescence photoswitching in living cells. This is the first example of a PSFM that can be applicable to a general-purpose Halo-tag protein labeling system for no-wash live-cell imaging.
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Affiliation(s)
- Kenji Torii
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
| | - Sam Benson
- Centre for Inflammation Research, The University of Edinburgh Edinburgh EH16 4UU UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh Edinburgh EH16 4UU UK
| | - Yuichiro Hori
- Faculty of Science, Kyushu University Fukuoka Fukuoka 819-0395 Japan
| | - Marc Vendrell
- Centre for Inflammation Research, The University of Edinburgh Edinburgh EH16 4UU UK
- IRR Chemistry Hub, Institute for Regeneration and Repair, The University of Edinburgh Edinburgh EH16 4UU UK
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University Suita Osaka 565-0871 Japan
- Immunology Frontier Research Center, Osaka University Suita Osaka 565-0871 Japan
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6
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Bourges AC, Moeyaert B, Bui TYH, Bierbuesse F, Vandenberg W, Dedecker P. Quantitative determination of the full switching cycle of photochromic fluorescent proteins. Chem Commun (Camb) 2023. [PMID: 37377004 DOI: 10.1039/d3cc01617j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
In this study, we develop a general analytical model of the photochromism of fluorescent proteins and apply it to spectroscopic measurements performed on six different labels. Our approach provides quantitative explanations for phenomena such as the existence of positive and negative switching, limitations in the photochromism contrast, and the fact that initial switching cycles may differ from subsequent ones. It also allows us to perform the very first measurement of all four isomerization quantum yields involved in the switching process.
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7
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Hargreaves R, Duwé S, Rozario AM, Funston AM, Tabor RF, Dedecker P, Whelan DR, Bell TDM. Live-Cell SOFI Correlation with SMLM and AFM Imaging. ACS BIO & MED CHEM AU 2023; 3:261-269. [PMID: 37363082 PMCID: PMC10288496 DOI: 10.1021/acsbiomedchemau.2c00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/09/2023] [Accepted: 03/10/2023] [Indexed: 06/28/2023]
Abstract
Standard optical imaging is diffraction-limited and lacks the resolving power to visualize many of the organelles and proteins found within the cell. The advent of super-resolution techniques overcame this barrier, enabling observation of subcellular structures down to tens of nanometers in size; however these techniques require or are typically applied to fixed samples. This raises the question of how well a fixed-cell image represents the system prior to fixation. Here we present the addition of live-cell Super-Resolution Optical Fluctuation Imaging (SOFI) to a previously reported correlative process using Single Molecule Localization Microscopy (SMLM) and Atomic Force Microscopy (AFM). SOFI was used with fluorescent proteins and low laser power to observe cellular ultrastructure in live COS-7 cells. SOFI-SMLM-AFM of microtubules showed minimal changes to the microtubule network in the 20 min between live-cell SOFI and fixation. Microtubule diameters were also analyzed through all microscopies; SOFI found diameters of 249 ± 68 nm and SMLM was 71 ± 33 nm. AFM height measurements found microtubules to protrude 26 ± 13 nm above the surrounding cellular material. The correlation of SMLM and AFM was extended to two-color SMLM to image both microtubules and actin. Two target SOFI was performed with various fluorescent protein combinations. rsGreen1-rsKAME, rsGreen1-Dronpa, and ffDronpaF-rsKAME fluorescent protein combinations were determined to be suitable for two target SOFI imaging. This correlative application of super-resolution live-cell and fixed-cell imaging revealed minimal artifacts created for the imaged target structures through the sample preparation procedure and emphasizes the power of correlative microscopy.
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Affiliation(s)
| | - Sam Duwé
- Advanced
Optical Microscopy Centre, Hasselt University, Diepenbeek 3590, Belgium
| | - Ashley M. Rozario
- Department
of Rural Clinical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo 3552, Victoria, Australia
| | - Alison M. Funston
- School
of Chemistry, Monash University, Melbourne, Victoria 3800, Australia
- ARC
Centre of Excellence in Exciton Science, Monash University, Clayton, Victoria 3800, Australia
| | - Rico F. Tabor
- School
of Chemistry, Monash University, Melbourne, Victoria 3800, Australia
| | - Peter Dedecker
- Department
of Chemistry, KU Leuven, Leuven 3001, Belgium
| | - Donna R. Whelan
- Department
of Rural Clinical Sciences, La Trobe Institute for Molecular Science, La Trobe University, Bendigo 3552, Victoria, Australia
| | - Toby D. M. Bell
- School
of Chemistry, Monash University, Melbourne, Victoria 3800, Australia
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8
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Chatterjee S, Kramer SN, Wellnitz B, Kim A, Kisley L. Spatially Resolving Size Effects on Diffusivity in Nanoporous Extracellular Matrix-like Materials with Fluorescence Correlation Spectroscopy Super-Resolution Optical Fluctuation Imaging. J Phys Chem B 2023; 127:4430-4440. [PMID: 37167609 DOI: 10.1021/acs.jpcb.3c00941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
It is well documented that the nanoscale structures within porous microenvironments greatly impact the diffusion dynamics of molecules. However, how the interaction between the environment and molecules influences the diffusion dynamics has not been thoroughly explored. Here, we show that fluorescence correlation spectroscopy super-resolution optical fluctuation imaging (fcsSOFI) can be used to accurately measure the diffusion dynamics of molecules within varying matrices such as nanopatterned surfaces and porous agarose hydrogels. Our data demonstrate the robustness of fcsSOFI, where it is possible not only to quantify the diffusion speeds of molecules in heterogeneous media but also to recover the matrix structure with resolution on the order of 100 nm. Using dextran molecules of varying sizes, we show that the diffusion coefficient is sensitive to the change in the molecular hydrodynamic radius. fcsSOFI images further reveal that smaller dextran molecules can freely move through the small pores of the hydrogel and report the detailed porous structure and local diffusion heterogeneities not captured by the average diffusion coefficient. Conversely, bigger dextran molecules are confined and unable to freely move through the hydrogel, highlighting only the larger pore structures. These findings establish fcsSOFI as a powerful tool to characterize spatial and diffusion information of diverse macromolecules within biorelevant matrices.
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Affiliation(s)
- Surajit Chatterjee
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Stephanie N Kramer
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Benjamin Wellnitz
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Albert Kim
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
| | - Lydia Kisley
- Department of Physics, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7079, United States
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9
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Bui TYH, De Zitter E, Moeyaert B, Pecqueur L, Srinivasu BY, Economou A, Fontecave M, Van Meervelt L, Dedecker P, Pedre B. Oxygen-induced chromophore degradation in the photoswitchable red fluorescent protein rsCherry. Int J Biol Macromol 2023; 239:124179. [PMID: 36972828 DOI: 10.1016/j.ijbiomac.2023.124179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/11/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023]
Abstract
Reversibly switchable monomeric Cherry (rsCherry) is a photoswitchable variant of the red fluorescent protein mCherry. We report that this protein gradually and irreversibly loses its red fluorescence in the dark over a period of months at 4 °C and a few days at 37 °C. We also find that its ancestor, mCherry, undergoes a similar fluorescence loss but at a slower rate. X-ray crystallography and mass spectrometry reveal that this is caused by the cleavage of the p-hydroxyphenyl ring from the chromophore and the formation of two novel types of cyclic structures at the remaining chromophore moiety. Overall, our work sheds light on a new process occurring within fluorescent proteins, further adding to the chemical diversity and versatility of these molecules.
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Affiliation(s)
- Thi Yen Hang Bui
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium
| | - Elke De Zitter
- Université Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Benjamien Moeyaert
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium
| | - Ludovic Pecqueur
- Laboratoire de Chimie des Processus Biologiques, Collège de France, UMR 8229 CNRS, Sorbonne Université, PSL University, Paris, France
| | - Bindu Y Srinivasu
- Laboratory of Molecular Bacteriology, Rega Institute, KU, Leuven, Belgium
| | | | - Marc Fontecave
- Laboratoire de Chimie des Processus Biologiques, Collège de France, UMR 8229 CNRS, Sorbonne Université, PSL University, Paris, France
| | - Luc Van Meervelt
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium
| | - Peter Dedecker
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium.
| | - Brandán Pedre
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU, Leuven, Belgium.
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10
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Bui TYH, Dedecker P, Van Meervelt L. An unusual disulfide-linked dimerization in the fluorescent protein rsCherryRev1.4. Acta Crystallogr F Struct Biol Commun 2023; 79:38-44. [PMID: 36748340 PMCID: PMC9903139 DOI: 10.1107/s2053230x23000572] [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: 11/22/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
rsCherryRev1.4 has been reported as one of the reversibly photoswitchable variants of mCherry, and is an improved version with a faster off-switching speed and lower switching fatigue at high light intensities than its precursor rsCherryRev. However, rsCherryRev1.4 still has some limitations such as a tendency to dimerize as well as complex photophysical properties. Here, the crystal structure of rsCherryRev1.4 was determined at a resolution of 2 Å and it was discovered that it forms a dimer that shows disulfide bonding between the protomers. Mutagenesis, gel electrophoresis and size-exclusion chromatography strongly implicate Cys24 in this process. Replacing Cys24 in rsCherryRev1.4 resulted in a much lower tendency towards dimerization, while introducing Cys24 into mCherry correspondingly increased its dimerization. In principle, this finding opens the possibility of developing redox sensors based on controlled dimerization via disulfide cross-linking in fluorescent proteins, even though the actual application of engineering such sensors still requires additional research.
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Affiliation(s)
- Thi Yen Hang Bui
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Peter Dedecker
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Luc Van Meervelt
- Biochemistry, Molecular and Structural Biology, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
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11
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Van Thillo T, Van Deuren V, Dedecker P. Smart genetically-encoded biosensors for the chemical monitoring of living systems. Chem Commun (Camb) 2023; 59:520-534. [PMID: 36519509 DOI: 10.1039/d2cc05363b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetically-encoded biosensors provide the all-optical and non-invasive visualization of dynamic biochemical events within living systems, which has allowed the discovery of profound new insights. Twenty-five years of biosensor development has steadily improved their performance and has provided us with an ever increasing biosensor repertoire. In this feature article, we present recent advances made in biosensor development and provide a perspective on the future direction of the field.
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Affiliation(s)
- Toon Van Thillo
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Vincent Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
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12
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Adam V, Hadjidemetriou K, Jensen N, Shoeman RL, Woodhouse J, Aquila A, Banneville AS, Barends TRM, Bezchastnov V, Boutet S, Byrdin M, Cammarata M, Carbajo S, Eleni Christou N, Coquelle N, De la Mora E, El Khatib M, Moreno Chicano T, Bruce Doak R, Fieschi F, Foucar L, Glushonkov O, Gorel A, Grünbein ML, Hilpert M, Hunter M, Kloos M, Koglin JE, Lane TJ, Liang M, Mantovanelli A, Nass K, Nass Kovacs G, Owada S, Roome CM, Schirò G, Seaberg M, Stricker M, Thépaut M, Tono K, Ueda K, Uriarte LM, You D, Zala N, Domratcheva T, Jakobs S, Sliwa M, Schlichting I, Colletier JP, Bourgeois D, Weik M. Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement. Chemphyschem 2022; 23:e202200192. [PMID: 35959919 DOI: 10.1002/cphc.202200192] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/25/2022] [Indexed: 01/07/2023]
Abstract
Reversibly photoswitchable fluorescent proteins are essential markers for advanced biological imaging, and optimization of their photophysical properties underlies improved performance and novel applications. Here we establish a link between photoswitching contrast, one of the key parameters that dictate the achievable resolution in nanoscopy applications, and chromophore conformation in the non-fluorescent state of rsEGFP2, a widely employed label in REversible Saturable OpticaL Fluorescence Transitions (RESOLFT) microscopy. Upon illumination, the cis chromophore of rsEGFP2 isomerizes to two distinct off-state conformations, trans1 and trans2, located on either side of the V151 side chain. Reducing or enlarging the side chain at this position (V151A and V151L variants) leads to single off-state conformations that exhibit higher and lower switching contrast, respectively, compared to the rsEGFP2 parent. The combination of structural information obtained by serial femtosecond crystallography with high-level quantum chemical calculations and with spectroscopic and photophysical data determined in vitro suggests that the changes in switching contrast arise from blue- and red-shifts of the absorption bands associated to trans1 and trans2, respectively. Thus, due to elimination of trans2, the V151A variants of rsEGFP2 and its superfolding variant rsFolder2 display a more than two-fold higher switching contrast than their respective parent proteins, both in vitro and in E. coli cells. The application of the rsFolder2-V151A variant is demonstrated in RESOLFT nanoscopy. Our study rationalizes the connection between structural and photophysical chromophore properties and suggests a means to rationally improve fluorescent proteins for nanoscopy applications.
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Affiliation(s)
- Virgile Adam
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | | | - Nickels Jensen
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany and University Medical Center of Göttingen, Clinic for Neurology, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Robert L Shoeman
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Joyce Woodhouse
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Andrew Aquila
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Anne-Sophie Banneville
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Thomas R M Barends
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Victor Bezchastnov
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Martin Byrdin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Marco Cammarata
- Department of Physics, UMR UR1-CNRS 6251, University of Rennes 1, Rennes, France
| | - Sergio Carbajo
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Nina Eleni Christou
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Nicolas Coquelle
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Eugenio De la Mora
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Mariam El Khatib
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Tadeo Moreno Chicano
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - R Bruce Doak
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Franck Fieschi
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Lutz Foucar
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Oleksandr Glushonkov
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Alexander Gorel
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Marie Luise Grünbein
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Mark Hunter
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Marco Kloos
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Thomas J Lane
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Angela Mantovanelli
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Karol Nass
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Gabriela Nass Kovacs
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Shigeki Owada
- RIKEN SPring-8 Center, Sayo, Japan.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Christopher M Roome
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Matthew Seaberg
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575, Sand Hill Road, Menlo Park, CA, 94025, USA
| | - Miriam Stricker
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Michel Thépaut
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Kensuke Tono
- RIKEN SPring-8 Center, Sayo, Japan.,Japan Synchrotron Radiation Research Institute, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5198, Japan
| | - Kiyoshi Ueda
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan
| | - Lucas M Uriarte
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille, 59000, France
| | - Daehyun You
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, 980-8577, Japan
| | - Ninon Zala
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Tatiana Domratcheva
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany.,Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany and University Medical Center of Göttingen, Clinic for Neurology, Göttingen, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Göttingen, Germany
| | - Michel Sliwa
- Univ. Lille, CNRS, UMR 8516, LASIR, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille, 59000, France
| | - Ilme Schlichting
- Max-Planck-Institut für medizinische Forschung, Jahnstrasse 29, 69120, Heidelberg, Germany
| | | | - Dominique Bourgeois
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044, Grenoble, France
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13
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Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification. Nat Commun 2022; 13:1850. [PMID: 35387971 PMCID: PMC8986857 DOI: 10.1038/s41467-022-29508-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/18/2022] [Indexed: 11/20/2022] Open
Abstract
Genetically-encoded biosensors based on a single fluorescent protein are widely used to visualize analyte levels or enzymatic activities in cells, though usually to monitor relative changes rather than absolute values. We report photochromism-enabled absolute quantification (PEAQ) biosensing, a method that leverages the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity. We develop proof-of-concept photochromic variants of the popular GCaMP family of Ca2+ biosensors, and show that these can be used to resolve dynamic changes in the absolute Ca2+ concentration in live cells. We also develop intermittent quantification, a technique that combines absolute aquisitions with fast fluorescence acquisitions to deliver fast but fully quantitative measurements. We also show how the photochromism-based measurements can be expanded to situations where the absolute illumination intensities are unknown. In principle, PEAQ biosensing can be applied to other biosensors with photochromic properties, thereby expanding the possibilities for fully quantitative measurements in complex and dynamic systems. Biosensors often report relative rather than absolute values. Here the authors report a method that utilises the photochromic properties of biosensors to provide an absolute measure of the analyte concentration or activity: photochromism-enabled absolute quantification (PEAQ) biosensing.
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14
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Uriarte LM, Vitale R, Niziński S, Hadjidemetriou K, Zala N, Lukacs A, Greetham GM, Sazanovich IV, Weik M, Ruckebusch C, Meech SR, Sliwa M. Structural Information about the trans-to- cis Isomerization Mechanism of the Photoswitchable Fluorescent Protein rsEGFP2 Revealed by Multiscale Infrared Transient Absorption. J Phys Chem Lett 2022; 13:1194-1202. [PMID: 35085441 DOI: 10.1021/acs.jpclett.1c02920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
RsEGFP2 is a reversibly photoswitchable fluorescent protein used in super-resolved optical microscopies, which can be toggled between a fluorescent On state and a nonfluorescent Off state. Previous time-resolved ultraviolet-visible spectroscopic studies have shown that the Off-to-On photoactivation extends over the femto- to millisecond time scale and involves two picosecond lifetime excited states and four ground state intermediates, reflecting a trans-to-cis excited state isomerization, a millisecond deprotonation, and protein structural reorganizations. Femto- to millisecond time-resolved multiple-probe infrared spectroscopy (TRMPS-IR) can reveal structural aspects of intermediate species. Here we apply TRMPS-IR to rsEGFP2 and implement a Savitzky-Golay derivative analysis to correct for baseline drift. The results reveal that a subpicosecond twisted excited state precursor controls the trans-to-cis isomerization and the chromophore reaches its final position in the protein pocket within 100 ps. A new step with a time constant of 42 ns is reported and assigned to structural relaxation of the protein that occurs prior to the deprotonation of the chromophore on the millisecond time scale.
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Affiliation(s)
- Lucas M Uriarte
- Univ. Lille, CNRS, UMR 8516, LASIRE, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille 59000, France
| | - Raffaele Vitale
- Univ. Lille, CNRS, UMR 8516, LASIRE, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille 59000, France
| | - Stanisław Niziński
- Univ. Lille, CNRS, UMR 8516, LASIRE, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille 59000, France
- Quantum Electronics Laboratory, Faculty of Physics, Adam Mickiewicz University, Uniwersytetu Poznańskiego 2, Poznan 61-614, Poland
| | | | - Ninon Zala
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pecs, Szigeti ut 12, 7624 Pecs, Hungary
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Martin Weik
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, 38000 Grenoble, France
| | - Cyril Ruckebusch
- Univ. Lille, CNRS, UMR 8516, LASIRE, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille 59000, France
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Michel Sliwa
- Univ. Lille, CNRS, UMR 8516, LASIRE, Laboratoire de Spectroscopie pour les Interactions, la Réactivité et l'Environnement, Lille 59000, France
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15
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Lin W, Mo GCH, Mehta S, Zhang J. DrFLINC Contextualizes Super-resolution Activity Imaging. J Am Chem Soc 2021; 143:14951-14955. [PMID: 34516108 DOI: 10.1021/jacs.1c05530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Super-resolution activity imaging maps the biochemical architecture of living cells yet currently overlooks the locations of collaborating regulators/effectors. Building on the fluorescence fluctuation increase by contact (FLINC) principle, here we devise Dronpa-chromophore-removed FLINC (DrFLINC), where the nonfluorescent Dronpa can nevertheless enhance TagRFP-T fluorescence fluctuations. Exploiting DrFLINC, we develop a superior red label and a next-generation activity sensor for context-rich super-resolution biosensing.
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Affiliation(s)
- Wei Lin
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Gary C H Mo
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Sohum Mehta
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States
| | - Jin Zhang
- Department of Pharmacology, University of California, San Diego, La Jolla, California 92093, United States.,Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, United States.,Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, United States
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16
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Konen T, Stumpf D, Grotjohann T, Jansen I, Bossi M, Weber M, Jensen N, Hell SW, Jakobs S. The Positive Switching Fluorescent Protein Padron2 Enables Live-Cell Reversible Saturable Optical Linear Fluorescence Transitions (RESOLFT) Nanoscopy without Sequential Illumination Steps. ACS NANO 2021; 15:9509-9521. [PMID: 34019380 PMCID: PMC8291764 DOI: 10.1021/acsnano.0c08207] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Reversibly switchable fluorescent proteins (RSFPs) can be repeatedly transferred between a fluorescent on- and a nonfluorescent off-state by illumination with light of different wavelengths. Negative switching RSFPs are switched from the on- to the off-state with the same wavelength that also excites fluorescence. Positive switching RSFPs have a reversed light response, where the fluorescence excitation wavelength induces the transition from the off- to the on-state. Reversible saturable optical linear (fluorescence) transitions (RESOLFT) nanoscopy utilizes these switching states to achieve diffraction-unlimited resolution but so far has primarily relied on negative switching RSFPs by using time sequential switching schemes. On the basis of the green fluorescent RSFP Padron, we engineered the positive switching RSFP Padron2. Compared to its predecessor, it can undergo 50-fold more switching cycles while displaying a contrast ratio between the on- and the off-states of more than 100:1. Because of its robust switching behavior, Padron2 supports a RESOLFT imaging scheme that entirely refrains from sequential switching as it only requires beam scanning of two spatially overlaid light distributions. Using Padron2, we demonstrate live-cell RESOLFT nanoscopy without sequential illumination steps.
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Affiliation(s)
- Timo Konen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Daniel Stumpf
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Tim Grotjohann
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Isabelle Jansen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Mariano Bossi
- Department
of Optical Nanoscopy, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Michael Weber
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Nickels Jensen
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
- Department
of Optical Nanoscopy, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany
| | - Stefan Jakobs
- Department
of NanoBiophotonics, Max Planck Institute
for Biophysical Chemistry, 37077 Göttingen, Germany
- Clinic
of Neurology, University of Göttingen, 37075 Göttingen, Germany
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17
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De Zitter E, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Van Meervelt L, Dedecker P. Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*. Angew Chem Int Ed Engl 2021; 60:10073-10081. [PMID: 33543524 DOI: 10.1002/anie.202015201] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Indexed: 11/05/2022]
Abstract
Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.
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Affiliation(s)
- Elke De Zitter
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium.,Present address: University Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, 38000, Grenoble, France
| | - Siewert Hugelier
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Sam Duwé
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium.,Present address: Advanced Optical Microscopy Centre, Hasselt University, Agoralaan building C, 3590, Diepenbeek, Belgium
| | - Wim Vandenberg
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Alison G Tebo
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia, 20147, USA
| | - Luc Van Meervelt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
| | - Peter Dedecker
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G - box 2403, 3001, Leuven, Belgium
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18
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De Zitter E, Hugelier S, Duwé S, Vandenberg W, Tebo AG, Van Meervelt L, Dedecker P. Structure–Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015201] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elke De Zitter
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
- Present address: University Grenoble Alpes CEA CNRS IBS 71 Avenue des Martyrs 38000 Grenoble France
| | - Siewert Hugelier
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Sam Duwé
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
- Present address: Advanced Optical Microscopy Centre Hasselt University Agoralaan building C 3590 Diepenbeek Belgium
| | - Wim Vandenberg
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Alison G. Tebo
- Janelia Research Campus Howard Hughes Medical Institute 19700 Helix Drive Ashburn Virginia 20147 USA
| | - Luc Van Meervelt
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
| | - Peter Dedecker
- Department of Chemistry KU Leuven Celestijnenlaan 200G – box 2403 3001 Leuven Belgium
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19
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Glogger M, Spahn C, Enderlein J, Heilemann M. Multi‐Color, Bleaching‐Resistant Super‐Resolution Optical Fluctuation Imaging with Oligonucleotide‐Based Exchangeable Fluorophores. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013166] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Marius Glogger
- Institute of Physical and Theoretical Chemistry Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Christoph Spahn
- Institute of Physical and Theoretical Chemistry Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
| | - Jörg Enderlein
- Third Institute of Physics—Biophysics Georg August University 37077 Göttingen Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC) Georg August University Göttingen Germany
| | - Mike Heilemann
- Institute of Physical and Theoretical Chemistry Goethe-University Frankfurt Max-von-Laue Str. 7 60438 Frankfurt Germany
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20
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Glogger M, Spahn C, Enderlein J, Heilemann M. Multi-Color, Bleaching-Resistant Super-Resolution Optical Fluctuation Imaging with Oligonucleotide-Based Exchangeable Fluorophores. Angew Chem Int Ed Engl 2021; 60:6310-6313. [PMID: 33301653 PMCID: PMC7986781 DOI: 10.1002/anie.202013166] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/07/2020] [Indexed: 11/17/2022]
Abstract
Super‐resolution optical fluctuation imaging (SOFI) is a super‐resolution microscopy technique that overcomes the diffraction limit by analyzing intensity fluctuations of statistically independent emitters in a time series of images. The final images are background‐free and show confocality and enhanced spatial resolution (super‐resolution). Fluorophore photobleaching, however, is a key limitation for recording long time series of images that will allow for the calculation of higher order SOFI results with correspondingly increased resolution. Here, we demonstrate that photobleaching can be circumvented by using fluorophore labels that reversibly and transiently bind to a target, and which are being replenished from a buffer which serves as a reservoir. Using fluorophore‐labeled short DNA oligonucleotides, we labeled cellular structures with target‐specific antibodies that contain complementary DNA sequences and record the fluctuation events caused by transient emitter binding. We show that this concept bypasses extensive photobleaching and facilitates two‐color imaging of cellular structures with SOFI.
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Affiliation(s)
- Marius Glogger
- Institute of Physical and Theoretical ChemistryGoethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Christoph Spahn
- Institute of Physical and Theoretical ChemistryGoethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
| | - Jörg Enderlein
- Third Institute of Physics—BiophysicsGeorg August University37077GöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)Georg August UniversityGöttingenGermany
| | - Mike Heilemann
- Institute of Physical and Theoretical ChemistryGoethe-University FrankfurtMax-von-Laue Str. 760438FrankfurtGermany
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21
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Khrenova MG, Mulashkin FD, Bulavko ES, Zakharova TM, Nemukhin AV. Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores. J Chem Inf Model 2020; 60:6288-6297. [PMID: 33206518 DOI: 10.1021/acs.jcim.0c01028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We propose a quantitative structure-property relationship (QSPR) model for prediction of spectral tuning in cyan, green, orange, and red fluorescent proteins, which are engineered by motifs of the green fluorescent protein. Protein variants, in which their chromophores are involved in the π-stacking interaction with amino acid residues tyrosine, phenylalanine, and histidine, are prospective markers useful in bioimaging and super-resolution microscopy. In this work, we constructed training sets of the π-stacked complexes of four fluorescent protein chromophores (of the green, orange, red, and cyan series) with various substituted benzenes and imidazoles and tested the use of dipole moment variation upon excitation (DMV) as a descriptor to evaluate the vertical excitation energies in these systems. To validate this approach, we computed and analyzed electron density distributions of the π-stacked complexes and correlated the QSPR predictions with the reference values of the transition energies obtained using the high-level ab initio quantum chemistry methods. According to our results, the use of the DMV descriptor allows one to predict excitation energies in the π-stacked complexes with errors not exceeding 0.1 eV, which makes this model a practically useful tool in the development of efficient fluorescent markers for in vivo imaging.
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Affiliation(s)
- Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology" of the Russian Academy of Sciences, Moscow 119071, Russian Federation
| | - Fedor D Mulashkin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Egor S Bulavko
- Department of Biology, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Tatiana M Zakharova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russian Federation.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russian Federation
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22
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Lee B, Lee H, Huh J, Yoon CJ, Oh SJ, Song K, Jeong S, Kim J, Lee K, Shin BS, Jeong JH, Kim TW, Lee J. Human Ferritin Platform and Its Optimized Structures to Enhance Anti‐Cancer Immunity. ADVANCED THERAPEUTICS 2020. [DOI: 10.1002/adtp.202000208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Bo‐Ram Lee
- Department of Chemical and Biological Engineering Korea University Seoul 136–713 Republic of Korea
| | - Hyo‐Jung Lee
- Laboratory of Tumor Immunology Department of Biomedical Sciences Graduate School of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biochemistry and Molecular Biology College of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biomedical Science College of Medicine Korea University Seoul 136–713 Republic of Korea
| | - June Huh
- Department of Chemical and Biological Engineering Korea University Seoul 136–713 Republic of Korea
| | - Chul Joo Yoon
- Department of Chemical and Biological Engineering Korea University Seoul 136–713 Republic of Korea
| | - Se Jin Oh
- Laboratory of Tumor Immunology Department of Biomedical Sciences Graduate School of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biochemistry and Molecular Biology College of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biomedical Science College of Medicine Korea University Seoul 136–713 Republic of Korea
| | - Kwon‐Ho Song
- Laboratory of Tumor Immunology Department of Biomedical Sciences Graduate School of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biochemistry and Molecular Biology College of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biomedical Science College of Medicine Korea University Seoul 136–713 Republic of Korea
| | - Sojin Jeong
- Department of Chemical and Biological Engineering Korea University Seoul 136–713 Republic of Korea
| | - Jungwon Kim
- Department of Biochemistry and Molecular Biology College of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biomedical Science College of Medicine Korea University Seoul 136–713 Republic of Korea
| | - Kyung‐Mi Lee
- Department of Biochemistry and Molecular Biology College of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biomedical Science College of Medicine Korea University Seoul 136–713 Republic of Korea
| | - Beom Soo Shin
- School of Pharmacy Sungkyunkwan University Suwon 16419 Republic of Korea
| | - Ji Hoon Jeong
- School of Pharmacy Sungkyunkwan University Suwon 16419 Republic of Korea
| | - Tae Woo Kim
- Laboratory of Tumor Immunology Department of Biomedical Sciences Graduate School of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biochemistry and Molecular Biology College of Medicine Korea University Seoul 136–713 Republic of Korea
- Department of Biomedical Science College of Medicine Korea University Seoul 136–713 Republic of Korea
- Translational Research Institute for Incurable Diseases College of Medicine Korea University Seoul 136–713 Republic of Korea
| | - Jeewon Lee
- Department of Chemical and Biological Engineering Korea University Seoul 136–713 Republic of Korea
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23
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Campbell BC, Nabel EM, Murdock MH, Lao-Peregrin C, Tsoulfas P, Blackmore MG, Lee FS, Liston C, Morishita H, Petsko GA. mGreenLantern: a bright monomeric fluorescent protein with rapid expression and cell filling properties for neuronal imaging. Proc Natl Acad Sci U S A 2020; 117:30710-30721. [PMID: 33208539 PMCID: PMC7720163 DOI: 10.1073/pnas.2000942117] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Although ubiquitous in biological studies, the enhanced green and yellow fluorescent proteins (EGFP and EYFP) were not specifically optimized for neuroscience, and their underwhelming brightness and slow expression in brain tissue limits the fidelity of dendritic spine analysis and other indispensable techniques for studying neurodevelopment and plasticity. We hypothesized that EGFP's low solubility in mammalian systems must limit the total fluorescence output of whole cells, and that improving folding efficiency could therefore translate into greater brightness of expressing neurons. By introducing rationally selected combinations of folding-enhancing mutations into GFP templates and screening for brightness and expression rate in human cells, we developed mGreenLantern, a fluorescent protein having up to sixfold greater brightness in cells than EGFP. mGreenLantern illuminates neurons in the mouse brain within 72 h, dramatically reducing lag time between viral transduction and imaging, while its high brightness improves detection of neuronal morphology using widefield, confocal, and two-photon microscopy. When virally expressed to projection neurons in vivo, mGreenLantern fluorescence developed four times faster than EYFP and highlighted long-range processes that were poorly detectable in EYFP-labeled cells. Additionally, mGreenLantern retains strong fluorescence after tissue clearing and expansion microscopy, thereby facilitating superresolution and whole-brain imaging without immunohistochemistry. mGreenLantern can directly replace EGFP/EYFP in diverse systems due to its compatibility with GFP filter sets, recognition by EGFP antibodies, and excellent performance in mouse, human, and bacterial cells. Our screening and rational engineering approach is broadly applicable and suggests that greater potential of fluorescent proteins, including biosensors, could be unlocked using a similar strategy.
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Affiliation(s)
- Benjamin C Campbell
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021;
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021
| | - Elisa M Nabel
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Mitchell H Murdock
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021
| | - Cristina Lao-Peregrin
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY 10021
| | - Pantelis Tsoulfas
- Department of Biomedical Sciences, Marquette University, Milwaukee, WI 53211
| | - Murray G Blackmore
- Department of Neurological Surgery, Miami Project to Cure Paralysis, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Francis S Lee
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY 10021
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY 10021
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY 10021
| | - Conor Liston
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021
- Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY 10021
- Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, Cornell University, New York, NY 10021
| | - Hirofumi Morishita
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Gregory A Petsko
- Helen and Robert Appel Alzheimer's Disease Research Institute, Weill Cornell Medicine, New York, NY 10021;
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021
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24
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Liu Z, Liu J, Wang X, Mi F, Wang D, Wu C. Fluorescent Bioconjugates for Super-Resolution Optical Nanoscopy. Bioconjug Chem 2020; 31:1857-1872. [DOI: 10.1021/acs.bioconjchem.0c00320] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Zhihe Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
| | - Jie Liu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
| | - Xiaodong Wang
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
| | - Feixue Mi
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
| | - Dan Wang
- Key Laboratory of Functional Inorganic Material Chemistry, Ministry of Education, School of Chemistry and Materials Science, Heilongjiang University, Harbin 150080, China
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, Guangdong 510855, China
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25
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De Zitter E, Ridard J, Thédié D, Adam V, Lévy B, Byrdin M, Gotthard G, Van Meervelt L, Dedecker P, Demachy I, Bourgeois D. Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State. J Am Chem Soc 2020; 142:10978-10988. [PMID: 32463688 DOI: 10.1021/jacs.0c01880] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Green-to-red photoconvertible fluorescent proteins (PCFPs) are key players in advanced microscopy schemes such as photoactivated localization microscopy (PALM). Whereas photoconversion and red-state blinking in PCFPs have been studied intensively, their green-state photophysical behavior has received less attention. Yet dark states in green PCFPs can become strongly populated in PALM schemes and exert an indirect but considerable influence on the quality of data recorded in the red channel. Furthermore, green-state photoswitching in PCFPs can be used directly for PALM and has been engineered to design highly efficient reversibly switchable fluorescent proteins (RSFPs) amenable to various nanoscopy schemes. Here, we demonstrate that green mEos4b efficiently switches to a long-lived dark state through cis-trans isomerization of its chromophore, as do most RSFPs. However, by combining kinetic crystallography, molecular dynamics simulations, and Raman spectroscopy, we find that the dark state in green mEos4b is much more dynamic than that seen in switched-off green IrisFP, a biphotochromic PCFP engineered from the common EosFP parent. Our data suggest that H-bonding patterns maintained by the chromophore in green PCFPs and RSFPs in both their on- and off-states collectively control photoswitching quantum yields. The reduced number of H-bonds maintained by the dynamic dark chromophore in green mEos4b thus largely accounts for the observed lower switching contrast as compared to that of IrisFP. We also compare the long-lived dark states reached from green and red mEos4b, on the basis of their X-ray structures and Raman signatures. Altogether, these data provide a unifying picture of the complex photophysics of PCFPs and RSFPs.
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Affiliation(s)
- Elke De Zitter
- Department of Chemistry, KU Leuven, Heverlee 3001, Belgium
| | - Jacqueline Ridard
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Daniel Thédié
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Bernard Lévy
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
| | - Guillaume Gotthard
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | | | - Peter Dedecker
- Department of Chemistry, KU Leuven, Heverlee 3001, Belgium
| | - Isabelle Demachy
- Institut de Chimie Physique UMR8000, Université Paris-Saclay, CNRS, Orsay 91405, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble 38044, France
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26
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Serganova I, Blasberg RG. Molecular Imaging with Reporter Genes: Has Its Promise Been Delivered? J Nucl Med 2020; 60:1665-1681. [PMID: 31792128 DOI: 10.2967/jnumed.118.220004] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
The first reporter systems were developed in the early 1980s and were based on measuring the activity of an enzyme-as a surrogate measure of promoter-driven transcriptional activity-which is now known as a reporter gene system. The initial objective and application of reporter techniques was to analyze the activity of a specific promoter (namely, the expression of a gene that is under the regulation of the specific promoter that is linked to the reporter gene). This system allows visualization of specific promoter activity with great sensitivity. In general, there are 2 classes of reporter systems: constitutively expressed (always-on) reporter constructs used for cell tracking, and inducible reporter systems sensitive to endogenous signaling molecules and transcription factors that characterize specific tissues, tumors, or signaling pathways.This review traces the development of different reporter systems, using fluorescent and bioluminescent proteins as well as radionuclide-based reporter systems. The development and application of radionuclide-based reporter systems is the focus of this review. The question at the end of the review is whether the "promise" of reporter gene imaging has been realized. What is required for moving forward with radionuclide-based reporter systems, and what is required for successful translation to clinical applications?
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Affiliation(s)
- Inna Serganova
- Department of Neurology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronald G Blasberg
- Department of Neurology, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York .,Department of Radiology, Memorial Hospital, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York; and.,Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
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27
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Moeyaert B, Dedecker P. A comprehensive dataset of image sequences covering 20 fluorescent protein labels and 12 imaging conditions for use in super-resolution imaging. Data Brief 2020; 29:105273. [PMID: 32149169 PMCID: PMC7033320 DOI: 10.1016/j.dib.2020.105273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 12/05/2022] Open
Abstract
Super-resolution fluorescence microscopy techniques allow imaging fluorescently labelled structures with a resolution that surpasses the diffraction limit of light (approx. 200nm). The quality and, thus, reliability of each of these techniques is strongly dependent on (1) the quality of the optics, (2) the fitness of the specific fluorescent label for the given technique and (3) the algorithms being used. Of these, the fitness of the labels is most subjective, as fitness metrics are scarce, and generating samples with different labels and imaging them is laborious. This prevent rigorous fitness assessment of fluorescent labels. We have developed a mathematical framework for assessing the quality of SOFI data [1], [2], which we used to assess the fitness of 20 different fluorescent protein labels for SOFI imaging. Here, we report this dataset of 2240 image sequences, representing 10 fields of view each of transfected Cos7 cells expressing each of the 20 different fluorescent proteins under 4-12 imaging conditions. The labels span the visible spectrum and include non-photo-transforming and photo-transforming fluorescent proteins. The imaging conditions consist of 4 different excitation powers, each with three different powers of 405 nm light added (except for the blue labels that are excited with 405 nm light). Though this data was in essence generated to assess which labels are best suited for SOFI imaging, it can be used as a benchmark for further development of the SOFI algorithm, or for the development of other super-resolution imaging modalities that benefit from similar input data.
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28
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Unzueta U, Roldán M, Pesarrodona M, Benitez R, Sánchez-Chardi A, Conchillo-Solé O, Mangues R, Villaverde A, Vázquez E. Self-assembling as regular nanoparticles dramatically minimizes photobleaching of tumour-targeted GFP. Acta Biomater 2020; 103:272-280. [PMID: 31812843 DOI: 10.1016/j.actbio.2019.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022]
Abstract
Fluorescent proteins are useful imaging and theranostic agents, but their potential superiority over alternative dyes is weakened by substantial photobleaching under irradiation. Enhancing protein photostability has been attempted through diverse strategies, with irregular results and limited applicability. In this context, we wondered if the controlled oligomerization of Green Fluorescent Protein (GFP) as nanoscale supramolecular complexes could stabilize the fluorophore through the newly formed protein-protein contacts, and thus, enhance its global photostability. For that, we have here analyzed the photobleaching profile of several GFP versions, engineered to self-assemble as tumour-homing nanoparticles with different targeting, size and structural stability. This has been done under prolonged irradiation in confocal laser scanning microscopy and by small-angle X-ray scattering. The results show that the oligomerization of GFP at the nanoscale enhances, by more than seven-fold, the stability of fluorescence emission. Interestingly, GFP nanoparticles are much more resistant to X-ray damage than the building block counterparts, indicating that the gained photostability is linked to enhanced structural resistance to radiation. Therefore, the controlled oligomerization of self-assembling fluorescent proteins as protein nanoparticles is a simple, versatile and powerful method to enhance their photostability for uses in precision imaging and therapy. STATEMENT OF SIGNIFICANCE: Fluorescent protein assembly into regular and highly symmetric nanoscale structures has been identified to confer enhanced structural stability against radiation stresses dramatically reducing their photobleaching. Being this the main bottleneck in the use of fluorescent proteins for imaging and theranostics, this protein architecture engineering principle appears as a powerful method to enhance their photostability for a broad applicability in precision imaging, drug delivery and theranostics.
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29
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Moeyaert B, Vandenberg W, Dedecker P. SOFIevaluator: a strategy for the quantitative quality assessment of SOFI data. BIOMEDICAL OPTICS EXPRESS 2020; 11:636-648. [PMID: 32133218 PMCID: PMC7041449 DOI: 10.1364/boe.382278] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 05/21/2023]
Abstract
Super-resolution fluorescence imaging techniques allow optical imaging of specimens beyond the diffraction limit of light. Super-resolution optical fluctuation imaging (SOFI) relies on computational analysis of stochastic blinking events to obtain a super-resolved image. As with some other super-resolution methods, this strong dependency on computational analysis can make it difficult to gauge how well the resulting images reflect the underlying sample structure. We herein report SOFIevaluator, an unbiased and parameter-free algorithm for calculating a set of metrics that describes the quality of super-resolution fluorescence imaging data for SOFI. We additionally demonstrate how SOFIevaluator can be used to identify fluorescent proteins that perform well for SOFI imaging under different imaging conditions.
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Affiliation(s)
- Benjamien Moeyaert
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Wim Vandenberg
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
| | - Peter Dedecker
- Laboratory for NanoBiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Heverlee, Belgium
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30
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Fluorescent Protein-Based Indicators for Functional Super-Resolution Imaging of Biomolecular Activities in Living Cells. Int J Mol Sci 2019; 20:ijms20225784. [PMID: 31744242 PMCID: PMC6887983 DOI: 10.3390/ijms20225784] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/15/2019] [Accepted: 11/15/2019] [Indexed: 11/16/2022] Open
Abstract
Super-resolution light microscopy (SRM) offers a unique opportunity for diffraction-unlimited imaging of biomolecular activities in living cells. To realize such potential, genetically encoded indicators were developed recently from fluorescent proteins (FPs) that exhibit phototransformation behaviors including photoactivation, photoconversion, and photoswitching, etc. Super-resolution observations of biomolecule interactions and biochemical activities have been demonstrated by exploiting the principles of bimolecular fluorescence complementation (BiFC), points accumulation for imaging nanoscale topography (PAINT), and fluorescence fluctuation increase by contact (FLINC), etc. To improve functional nanoscopy with the technology of genetically encoded indicators, it is essential to fully decipher the photo-induced chemistry of FPs and opt for innovative indicator designs that utilize not only fluorescence intensity but also multi-parametric readouts such as phototransformation kinetics. In parallel, technical improvements to both the microscopy optics and image analysis pipeline are promising avenues to increase the sensitivity and versatility of functional SRM.
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31
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Christou NE, Ayala I, Giandoreggio-Barranco K, Byrdin M, Adam V, Bourgeois D, Brutscher B. NMR Reveals Light-Induced Changes in the Dynamics of a Photoswitchable Fluorescent Protein. Biophys J 2019; 117:2087-2100. [PMID: 31733726 DOI: 10.1016/j.bpj.2019.10.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/20/2019] [Accepted: 10/25/2019] [Indexed: 12/22/2022] Open
Abstract
The availability of fluorescent proteins with distinct phototransformation properties is crucial for a wide range of applications in advanced fluorescence microscopy and biotechnology. To rationally design new variants optimized for specific applications, a detailed understanding of the mechanistic features underlying phototransformation is essential. At present, little is known about the conformational dynamics of fluorescent proteins at physiological temperature and how these dynamics contribute to the observed phototransformation properties. Here, we apply high-resolution NMR spectroscopy in solution combined with in situ sample illumination at different wavelengths to investigate the conformational dynamics of rsFolder, a GFP-derived protein that can be reversibly switched between a green fluorescent state and a nonfluorescent state. Our results add a dynamic view to the static structures obtained by x-ray crystallography. Including a custom-tailored NMR toolbox in fluorescent protein research provides new opportunities for investigating the effect of mutations or changes in the environmental conditions on the conformational dynamics of phototransformable fluorescent proteins and their correlation with the observed photochemical and photophysical properties.
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Affiliation(s)
- Nina-Eleni Christou
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Isabel Ayala
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | - Martin Byrdin
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Virgile Adam
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Dominique Bourgeois
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Bernhard Brutscher
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
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32
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Shinoda H, Lu K, Nakashima R, Wazawa T, Noguchi K, Matsuda T, Nagai T. Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions. Cell Chem Biol 2019; 26:1469-1479.e6. [DOI: 10.1016/j.chembiol.2019.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 06/13/2019] [Accepted: 07/23/2019] [Indexed: 02/08/2023]
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33
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Vandenberg W, Leutenegger M, Duwé S, Dedecker P. An extended quantitative model for super-resolution optical fluctuation imaging (SOFI). OPTICS EXPRESS 2019; 27:25749-25766. [PMID: 31510441 DOI: 10.1364/oe.27.025749] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/20/2019] [Indexed: 05/21/2023]
Abstract
Super-resolution optical fluctuation imaging (SOFI) provides super-resolution (SR) fluorescence imaging by analyzing fluctuations in the fluorophore emission. The technique has been used both to acquire quantitative SR images and to provide SR biosensing by monitoring changes in fluorophore blinking dynamics. Proper analysis of such data relies on a fully quantitative model of the imaging. However, previous SOFI imaging models made several assumptions that can not be realized in practice. In this work we address these limitations by developing and verifying a fully quantitative model that better approximates real-world imaging conditions. Our model shows that (i) SOFI images are free of bias, or can be made so, if the signal is stationary and fluorophores blink independently, (ii) allows a fully quantitative description of the link between SOFI imaging and probe dynamics, and (iii) paves the way for more advanced SOFI image reconstruction by offering a computationally fast way to calculate SOFI images for arbitrary probe, sample and instrumental properties.
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34
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Optimizing the fluorescent protein toolbox and its use. Curr Opin Biotechnol 2019; 58:183-191. [DOI: 10.1016/j.copbio.2019.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/24/2019] [Indexed: 01/07/2023]
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35
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Mechanistic investigation of mEos4b reveals a strategy to reduce track interruptions in sptPALM. Nat Methods 2019; 16:707-710. [PMID: 31285624 DOI: 10.1038/s41592-019-0462-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/24/2019] [Indexed: 11/09/2022]
Abstract
Green-to-red photoconvertible fluorescent proteins repeatedly enter dark states, causing interrupted tracks in single-particle-tracking localization microscopy (sptPALM). We identified a long-lived dark state in photoconverted mEos4b that results from isomerization of the chromophore and efficiently absorbs cyan light. Addition of weak 488-nm light swiftly reverts this dark state to the fluorescent state. This strategy largely eliminates slow blinking and enables the recording of longer tracks in sptPALM with minimum effort.
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36
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Kim HJ, Huh J, Kwon YW, Park D, Yu Y, Jang YE, Lee BR, Jo E, Lee EJ, Heo Y, Lee W, Lee J. Biological conversion of methane to methanol through genetic reassembly of native catalytic domains. Nat Catal 2019. [DOI: 10.1038/s41929-019-0255-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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37
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Wang S, Shuai Y, Sun C, Xue B, Hou Y, Su X, Sun Y. Lighting Up Live Cells with Smart Genetically Encoded Fluorescence Probes from GMars Family. ACS Sens 2018; 3:2269-2277. [PMID: 30346738 DOI: 10.1021/acssensors.8b00449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As a special kind of delicate light-controllable genetically encoded optical device, reversibly photoswitchable fluorescent proteins (RSFPs) have been widely applied in many fields, especially various kinds of advanced nanoscopy approaches in recent years. However, there are still necessities for exploring novel RSFPs with specific biochemical or photophysical properties not only for bioimaging or biosensing applications but also for fluorescent protein (FP) mechanisms study and further knowledge-based molecular sensors or optical actuators' rational design and evolution. Besides previously reported GMars-Q and GMars-T variants, herein, we reported the development and applications of other RSFPs from GMars family, especially some featured RSFPs with desired optical properties. In the current work, in vitro FP purification, spectra measurements, and live-cell RESOLFT nanoscopy approaches were applied to characterize the basic properties and test the imaging performances of the selected RSFPs. As demonstrated, GMars variants such as GMars-A, GMars-G, or remarkable photofatigue-resistant GMars-L were found with beneficial properties to be capable of parallelized RESOLFT nanoscopy in living cells, while other featured GMars variants such as dark GMars-P may be a good candidate for further biosensor or actuator design and applications.
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Affiliation(s)
- Sheng Wang
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Yao Shuai
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Chaoying Sun
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Boxin Xue
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Yingping Hou
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
| | - Xiaodong Su
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Yujie Sun
- Biomedical Pioneering Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China
- State Key Laboratory of Membrane Biology, Peking University, Beijing 100871, China
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38
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Wang S, Ding M, Xue B, Hou Y, Sun Y. Spying on protein interactions in living cells with reconstituted scarlet light. Analyst 2018; 143:5161-5169. [PMID: 30255175 DOI: 10.1039/c8an01223g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The BiFC (bimolecular fluorescence complementation) assay and BiFC combined with FRET (fluorescence resonance energy transfer) technique have become important tools for molecular interaction studies in live cells. However, the real detection and cellular imaging performances of most existing red fluorescent protein-derived BiFC assays still suffer from relatively low ensemble brightness, high cytotoxicity, the red fluorescent proteins being prone-to-aggregation or severe residual dimerization, inefficient complementation and slow maturation at 37 °C physiological temperature in live mammalian cells. We developed a BiFC assay based on a recently evolved truly monomeric red fluorescent protein (FP) mScarlet-I with excellent cellular performances such as low cytotoxicity, fast and efficient chromophore maturation and the highest in-cell brightness among all previously reported monomeric red fluorescent proteins. In this work, a classic β-Fos/β-Jun constitutive heterodimerization model and a rapamycin-inducible FRB/FKBP interaction system were used to establish and test the performance of the mScarlet-I-based BiFC assay in live mammalian cells. Furthermore, simply by adopting the large-Stokes-shift fluorescent protein mAmetrine as the donor, β-Jun-β-Fos-NFAT1 ternary protein complex formation could be readily and efficiently detected and visualized with minimal spectral cross-talk in live HeLa cells by combining live-cell sensitized-emission FRET measurement with the mScarlet-I-based BiFC assay. The currently established BiFC assay in this work was also shown to be able to detect and visualize various protein-protein interactions (PPIs) at different subcellular compartments with high specificity and sensitivity at 37 °C physiological temperature in live mammalian cells.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Membrane Biology, Biomedical pioneering innovation center (BIOPIC), School of Life Sciences, Peking University, Beijing 100871, China.
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39
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moxMaple3: a Photoswitchable Fluorescent Protein for PALM and Protein Highlighting in Oxidizing Cellular Environments. Sci Rep 2018; 8:14738. [PMID: 30283009 PMCID: PMC6170497 DOI: 10.1038/s41598-018-32955-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/19/2018] [Indexed: 11/09/2022] Open
Abstract
The ability of fluorescent proteins (FPs) to fold robustly is fundamental to the autocatalytic formation of the chromophore. While the importance of the tertiary protein structure is well appreciated, the impact of individual amino acid mutations for FPs is often not intuitive and requires direct testing. In this study, we describe the engineering of a monomeric photoswitchable FP, moxMaple3, for use in oxidizing cellular environments, especially the eukaryotic secretory pathway. Surprisingly, a point mutation to replace a cysteine substantially improved the yield of correctly folded FP capable of chromophore formation, regardless of cellular environment. The improved folding of moxMaple3 increases the fraction of visibly tagged fusion proteins, as well as FP performance in PALM super-resolution microscopy, and thus makes moxMaple3 a robust monomeric FP choice for PALM and optical highlighting applications.
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40
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Manna P, Hung ST, Mukherjee S, Friis P, Simpson DM, Lo MN, Palmer AE, Jimenez R. Directed evolution of excited state lifetime and brightness in FusionRed using a microfluidic sorter. Integr Biol (Camb) 2018; 10:516-526. [PMID: 30094420 PMCID: PMC6141309 DOI: 10.1039/c8ib00103k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Green fluorescent proteins (GFP) and their blue, cyan and red counterparts offer unprecedented advantages as biological markers owing to their genetic encodability and straightforward expression in different organisms. Although significant advancements have been made towards engineering the key photo-physical properties of red fluorescent proteins (RFPs), they continue to perform sub-optimally relative to GFP variants. Advanced engineering strategies are needed for further evolution of RFPs in the pursuit of improving their photo-physics. In this report, a microfluidic sorter that discriminates members of a cell-based library based on their excited state lifetime and fluorescence intensity is used for the directed evolution of the photo-physical properties of FusionRed. In-flow measurements of the fluorescence lifetime are performed in a frequency-domain approach with sub-millisecond sampling times. Promising clones are sorted by optical force trapping with an infrared laser. Using this microfluidic sorter, mutants are generated with longer lifetimes than their precursor, FusionRed. This improvement in the excited state lifetime of the mutants leads to an increase in their fluorescence quantum yield up to 1.8-fold. In the course of evolution, we also identified one key mutation (L177M), which generated a mutant (FusionRed-M) that displayed ∼2-fold higher brightness than its precursor upon expression in mammalian (HeLa) cells. Photo-physical and mutational analyses of clones isolated at the different stages of mutagenesis reveal the photo-physical evolution towards higher in vivo brightness.
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Affiliation(s)
- Premashis Manna
- JILA, NIST and University of Colorado, Boulder, Colorado 80309, USA.
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41
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Pennacchietti F, Serebrovskaya EO, Faro AR, Shemyakina II, Bozhanova NG, Kotlobay AA, Gurskaya NG, Bodén A, Dreier J, Chudakov DM, Lukyanov KA, Verkhusha VV, Mishin AS, Testa I. Fast reversibly photoswitching red fluorescent proteins for live-cell RESOLFT nanoscopy. Nat Methods 2018; 15:601-604. [PMID: 29988095 DOI: 10.1038/s41592-018-0052-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 05/18/2018] [Indexed: 11/09/2022]
Abstract
Reversibly photoswitchable fluorescent proteins (rsFPs) are gaining popularity as tags for optical nanoscopy because they make it possible to image with lower light doses. However, green rsFPs need violet-blue light for photoswitching, which is potentially phototoxic and highly scattering. We developed new rsFPs based on FusionRed that are reversibly photoswitchable with green-orange light. The rsFusionReds are bright and exhibit rapid photoswitching, thereby enabling nanoscale imaging of living cells.
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Affiliation(s)
- Francesca Pennacchietti
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ekaterina O Serebrovskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Aline R Faro
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Irina I Shemyakina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nina G Bozhanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexey A Kotlobay
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Nadya G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Andreas Bodén
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jes Dreier
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dmitry M Chudakov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Konstantin A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Vladislav V Verkhusha
- Department of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation.
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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42
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Wang S, Chen X, Chang L, Ding M, Xue R, Duan H, Sun Y. GMars-T Enabling Multimodal Subdiffraction Structural and Functional Fluorescence Imaging in Live Cells. Anal Chem 2018; 90:6626-6634. [PMID: 29722976 DOI: 10.1021/acs.analchem.8b00418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Fluorescent probes with multimodal and multilevel imaging capabilities are highly valuable as imaging with such probes not only can obtain new layers of information but also enable cross-validation of results under different experimental conditions. In recent years, the development of genetically encoded reversibly photoswitchable fluorescent proteins (RSFPs) has greatly promoted the application of various kinds of live-cell nanoscopy approaches, including reversible saturable optical fluorescence transitions (RESOLFT) and stochastic optical fluctuation imaging (SOFI). However, these two classes of live-cell nanoscopy approaches require different optical characteristics of specific RSFPs. In this work, we developed GMars-T, a monomeric bright green RSFP which can satisfy both RESOLFT and photochromic SOFI (pcSOFI) imaging in live cells. We further generated biosensor based on bimolecular fluorescence complementation (BiFC) of GMars-T which offers high specificity and sensitivity in detecting and visualizing various protein-protein interactions (PPIs) in different subcellular compartments under physiological conditions (e.g., 37 °C) in live mammalian cells. Thus, the newly developed GMars-T can serve as both structural imaging probe with multimodal super-resolution imaging capability and functional imaging probe for reporting PPIs with high specificity and sensitivity based on its derived biosensor.
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Affiliation(s)
- Sheng Wang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Xuanze Chen
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China.,Department of Biomedical Engineering, College of Engineering , Peking University , Beijing 100871 , China.,Cowin Venture Shanghai 200040 , China
| | - Lei Chang
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Miao Ding
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Ruiying Xue
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Haifeng Duan
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences , Peking University , Beijing 100871 , China
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Vangindertael J, Camacho R, Sempels W, Mizuno H, Dedecker P, Janssen KPF. An introduction to optical super-resolution microscopy for the adventurous biologist. Methods Appl Fluoresc 2018; 6:022003. [DOI: 10.1088/2050-6120/aaae0c] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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44
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Chen Z, Yuan H, Liang H, Lu C, Liu X. Synthesis of a cationic poly(p-phenylenevinylene) derivative for lysosome-specific and long-term imaging. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.09.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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45
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Lee HB, Cong A, Leopold H, Currie M, Boersma AJ, Sheets ED, Heikal AA. Rotational and translational diffusion of size-dependent fluorescent probes in homogeneous and heterogeneous environments. Phys Chem Chem Phys 2018; 20:24045-24057. [DOI: 10.1039/c8cp03873b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Macromolecular crowding effects on diffusion depend on the fluorophore structure, the concentration of crowding agents, and the technique employed.
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Affiliation(s)
- Hong Bok Lee
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Anh Cong
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Hannah Leopold
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Megan Currie
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | | | - Erin D. Sheets
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
| | - Ahmed A. Heikal
- Department of Chemistry and Biochemistry
- Swenson College of Science and Engineering
- University of Minnesota Duluth
- Duluth
- USA
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46
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Lei L, Ma H, Qin Y, Yang M, Ma Y, Wang T, Yang Y, Lei Z, Lu D, Guan X. AIE-active florescent polymers: The design, synthesis and the cell imaging application. POLYMER 2017. [DOI: 10.1016/j.polymer.2017.11.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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47
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Localization-based super-resolution imaging meets high-content screening. Nat Methods 2017; 14:1184-1190. [PMID: 29083400 DOI: 10.1038/nmeth.4486] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 09/26/2017] [Indexed: 11/08/2022]
Abstract
Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.
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48
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Roebroek T, Duwé S, Vandenberg W, Dedecker P. Reduced Fluorescent Protein Switching Fatigue by Binding-Induced Emissive State Stabilization. Int J Mol Sci 2017; 18:ijms18092015. [PMID: 28930199 PMCID: PMC5618663 DOI: 10.3390/ijms18092015] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/08/2017] [Accepted: 09/11/2017] [Indexed: 01/12/2023] Open
Abstract
Reversibly switchable fluorescent proteins (RSFPs) enable advanced fluorescence imaging, though the performance of this imaging crucially depends on the properties of the labels. We report on the use of an existing small binding peptide, named Enhancer, to modulate the spectroscopic properties of the recently developed rsGreen series of RSFPs. Fusion constructs of Enhancer with rsGreen1 and rsGreenF revealed an increased molecular brightness and pH stability, although expression in living E. coli or HeLa cells resulted in a decrease of the overall emission. Surprisingly, Enhancer binding also increased off-switching speed and resistance to switching fatigue. Further investigation suggested that the RSFPs can interconvert between fast- and slow-switching emissive states, with the overall protein population gradually converting to the slow-switching state through irradiation. The Enhancer modulates the spectroscopic properties of both states, but also preferentially stabilizes the fast-switching state, supporting the increased fatigue resistance. This work demonstrates how the photo-physical properties of RSFPs can be influenced by their binding to other small proteins, which opens up new horizons for applications that may require such modulation. Furthermore, we provide new insights into the photoswitching kinetics that should be of general consideration when developing new RSFPs with improved or different photochromic properties.
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Affiliation(s)
- Thijs Roebroek
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Sam Duwé
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Wim Vandenberg
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
| | - Peter Dedecker
- Laboratory for Nanobiology, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.
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49
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Correcting for photodestruction in super-resolution optical fluctuation imaging. Sci Rep 2017; 7:10470. [PMID: 28874717 PMCID: PMC5585228 DOI: 10.1038/s41598-017-09666-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/24/2017] [Indexed: 12/03/2022] Open
Abstract
Super-resolution optical fluctuation imaging overcomes the diffraction limit by analyzing fluctuations in the fluorophore emission. A key assumption of the imaging is that the fluorophores are independent, though this is invalidated in the presence of photodestruction. In this work, we evaluate the effect of photodestruction on SOFI imaging using theoretical considerations and computer simulations. We find that photodestruction gives rise to an additional signal that does not present an easily interpretable view of the sample structure. This additional signal is strong and the resulting images typically exhibit less noise. Accordingly, these images may be mis-interpreted as being more visually pleasing or more informative. To address this uncertainty, we develop a procedure that can robustly estimate to what extent any particular experiment is affected by photodestruction. We also develop a detailed assessment methodology and use it to evaluate the performance of several correction algorithms. We identify two approaches that can correct for the presence of even strong photodestruction, one of which can be implemented directly in the SOFI calculation software.
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50
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Chen X, Liu Z, Li R, Shan C, Zeng Z, Xue B, Yuan W, Mo C, Xi P, Wu C, Sun Y. Multicolor Super-resolution Fluorescence Microscopy with Blue and Carmine Small Photoblinking Polymer Dots. ACS NANO 2017; 11:8084-8091. [PMID: 28696661 DOI: 10.1021/acsnano.7b02893] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Advances in the development of small photoblinking semiconducting polymer dots (Pdots) have attracted great interest for use in super-resolution microscopy. However, multicolor super-resolution imaging using conventional small photoblinking Pdots remains a challenge due to their limited color choice, broad emission spectrum, and heavy spectrum crosstalk. Here, we introduce two types of small photoblinking Pdots with different colors and relatively narrow emission spectra: blue PFO Pdots and carmine PFTBT5 Pdots for blinking-based statistical nanoscopy. Both of these probes feature ultrahigh single-particle brightness, very strong photostability, superior biocompatibility, and robust fluorescence fluctuation. In addition, these small photoblinking Pdots serve as excellent labels for dual-color super-resolution optical fluctuation imaging (SOFI) of specific subcellular structures, indicating their promise for long-term multicolor SOFI nanoscopy with high spatiotemporal resolution.
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Affiliation(s)
- Xuanze Chen
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Zhihe Liu
- Department of Biomedical Engineering, Southern University of Science and Technology , Shenzhen, Guangdong 510855, China
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University , Changchun 130012, China
| | - Rongqin Li
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Chunyan Shan
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Zhiping Zeng
- College of Physics and Information Engineering, Fuzhou University , Fuzhou 350116, China
| | - Boxin Xue
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Weihong Yuan
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Chi Mo
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Peng Xi
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
| | - Changfeng Wu
- Department of Biomedical Engineering, Southern University of Science and Technology , Shenzhen, Guangdong 510855, China
| | - Yujie Sun
- State Key Laboratory of Membrane Biology, Biodynamic Optical Imaging Center (BIOPIC), School of Life Sciences, and Department of Biomedical Engineering, College of Engineering, Peking University , Beijing 100871, China
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