1
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Bogdanova YA, Solovyev ID, Baleeva NS, Myasnyanko IN, Gorshkova AA, Gorbachev DA, Gilvanov AR, Goncharuk SA, Goncharuk MV, Mineev KS, Arseniev AS, Bogdanov AM, Savitsky AP, Baranov MS. Fluorescence lifetime multiplexing with fluorogen activating protein FAST variants. Commun Biol 2024; 7:799. [PMID: 38956304 PMCID: PMC11219735 DOI: 10.1038/s42003-024-06501-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 06/24/2024] [Indexed: 07/04/2024] Open
Abstract
In this paper, we propose a fluorescence-lifetime imaging microscopy (FLIM) multiplexing system based on the fluorogen-activating protein FAST. This genetically encoded fluorescent labeling platform employs FAST mutants that activate the same fluorogen but provide different fluorescence lifetimes for each specific protein-dye pair. All the proposed probes with varying lifetimes possess nearly identical and the smallest-in-class size, along with quite similar steady-state optical properties. In live mammalian cells, we target these chemogenetic tags to two intracellular structures simultaneously, where their fluorescence signals are clearly distinguished by FLIM. Due to the unique structure of certain fluorogens under study, their complexes with FAST mutants display a monophasic fluorescence decay, which may facilitate enhanced multiplexing efficiency by reducing signal cross-talks and providing optimal prerequisites for signal separation upon co-localized and/or spatially overlapped labeling.
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Affiliation(s)
- Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Ilya D Solovyev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia
| | - Anastasia A Gorshkova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Dmitriy A Gorbachev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Goethe University Frankfurt, Frankfurt am Main, 60433, Germany
| | - Alexander S Arseniev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alexey M Bogdanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Department of Photonics, İzmir Institute of Technology, 35430, İzmir, Turkey
| | - Alexander P Savitsky
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, 119071, Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997, Moscow, Russia.
- Pirogov Russian National Research Medical University, Ostrovitianov 1, Moscow, 117997, Russia.
- Department of Biology, Lomonosov Moscow State University, Moscow, 119991 Russia, 121205, Moscow, Russia.
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2
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Baleeva NS, Bogdanova YA, Goncharuk MV, Sokolov AI, Myasnyanko IN, Kublitski VS, Smirnov AY, Gilvanov AR, Goncharuk SA, Mineev KS, Baranov MS. A Combination of Library Screening and Rational Mutagenesis Expands the Available Color Palette of the Smallest Fluorogen-Activating Protein Tag nanoFAST. Int J Mol Sci 2024; 25:3054. [PMID: 38474299 DOI: 10.3390/ijms25053054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/14/2024] Open
Abstract
NanoFAST is the smallest fluorogen-activating protein, consisting of only 98 amino acids, used as a genetically encoded fluorescent tag. Previously, only a single fluorogen with an orange color was revealed for this protein. In the present paper, using rational mutagenesis and in vitro screening of fluorogens libraries, we expanded the color palette of this tag. We discovered that E46Q is one of the key substitutions enabling the range of possible fluorogens to be expanded. The introduction of this and several other substitutions has made it possible to use not only orange but also red and green fluorogens with the modified protein.
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Affiliation(s)
- Nadezhda S Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Yulia A Bogdanova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Marina V Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Anatolii I Sokolov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Ivan N Myasnyanko
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Vadim S Kublitski
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Alexander Yu Smirnov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
| | - Aidar R Gilvanov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Sergey A Goncharuk
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Konstantin S Mineev
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
| | - Mikhail S Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia
- Laboratory of Medicinal Substances Chemistry, Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovitianov 1, 117997 Moscow, Russia
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3
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Starling T, Carlon-Andres I, Iliopoulou M, Kraemer B, Loidolt-Krueger M, Williamson DJ, Padilla-Parra S. Multicolor lifetime imaging and its application to HIV-1 uptake. Nat Commun 2023; 14:4994. [PMID: 37591879 PMCID: PMC10435470 DOI: 10.1038/s41467-023-40731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/04/2023] [Indexed: 08/19/2023] Open
Abstract
Simultaneous imaging of nine fluorescent proteins is demonstrated in a single acquisition using fluorescence lifetime imaging microscopy combined with pulsed interleaved excitation of three laser lines. Multicolor imaging employing genetically encodable fluorescent proteins permits spatio-temporal live cell imaging of multiple cues. Here, we show that multicolor lifetime imaging allows visualization of quadruple labelled human immunodeficiency viruses on host cells that in turn are also labelled with genetically encodable fluorescent proteins. This strategy permits to simultaneously visualize different sub-cellular organelles (mitochondria, cytoskeleton, and nucleus) during the process of virus entry with the potential of imaging up to nine different spectral channels in living cells.
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Affiliation(s)
- Tobias Starling
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK
| | - Irene Carlon-Andres
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK
| | - Maro Iliopoulou
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- Randall Division of Cell and Molecular Biophysics and Department of Physics, King's College London, London, UK
| | - Benedikt Kraemer
- PicoQuant GmbH, Rudower Chaussee 29 (IGZ), 12489, Berlin, Germany
| | | | - David J Williamson
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK
| | - Sergi Padilla-Parra
- Department of Infectious Diseases, King's College London, Faculty of Life Sciences & Medicine, London, UK.
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
- Randall Division of Cell and Molecular Biophysics, King's College London, London, UK.
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4
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Goryacheva E, Efremov R, Krylov N, Artemyev I, Bogdanov A, Mamontova A, Pletnev S, Pletneva N, Pletnev V. Crystal Structure of Bright Fluorescent Protein BrUSLEE with Subnanosecond Fluorescence Lifetime; Electric and Dynamic Properties. Int J Mol Sci 2023; 24:ijms24076403. [PMID: 37047378 PMCID: PMC10094611 DOI: 10.3390/ijms24076403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023] Open
Abstract
The rapid development of new microscopy techniques for cell biology has exposed the need for genetically encoded fluorescent tags with special properties. Fluorescent biomarkers of the same color and spectral range and different fluorescent lifetimes (FLs) became useful for fluorescent lifetime image microscopy (FLIM). One such tag, the green fluorescent protein BrUSLEE (Bright Ultimately Short Lifetime Enhanced Emitter), having an extremely short subnanosecond component of fluorescence lifetime (FL~0.66 ns) and exceptional fluorescence brightness, was designed for FLIM experiments. Here, we present the X-ray structure and discuss the structure-functional relations of BrUSLEE. Its development from the EGFP (enhanced green fluorescent proteins) precursor (FL~2.83 ns) resulted in a change of the chromophore microenvironment due to a significant alteration in the side chain conformations. To get further insight into molecular details explaining the observed differences in the photophysical properties of these proteins, we studied their structural, dynamic, and electric properties by all-atom molecular-dynamics simulations in an aqueous solution. It has been shown that compared to BrUSLEE, the mobility of the chromophore in the EGFP is noticeably limited by nonbonded interactions (mainly H-bonds) with the neighboring residues.
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5
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Lecinski S, Shepherd JW, Bunting K, Dresser L, Quinn SD, MacDonald C, Leake MC. Correlating viscosity and molecular crowding with fluorescent nanobeads and molecular probes: in vitro and in vivo. Interface Focus 2022; 12:20220042. [PMID: 36330320 PMCID: PMC9560789 DOI: 10.1098/rsfs.2022.0042] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/05/2022] [Indexed: 02/02/2023] Open
Abstract
In eukaryotes, intracellular physico-chemical properties like macromolecular crowding and cytoplasmic viscoelasticity influence key processes such as metabolic activities, molecular diffusion and protein folding. However, mapping crowding and viscoelasticity in living cells remains challenging. One approach uses passive rheology in which diffusion of exogenous fluorescent particles internalized in cells is tracked and physico-chemical properties inferred from derived mean square displacement relations. Recently, the crGE2.3 Förster resonance energy transfer biosensor was developed to quantify crowding in cells, though it is unclear how this readout depends on viscoelasticity and the molecular weight of the crowder. Here, we present correlative, multi-dimensional data to explore diffusion and molecular crowding characteristics of molecular crowding agents using super-resolved fluorescence microscopy and ensemble time-resolved spectroscopy. We firstly characterize in vitro and then apply these insights to live cells of budding yeast Saccharomyces cerevisiae. It is to our knowledge the first time this has been attempted. We demonstrate that these are usable both in vitro and in the case of endogenously expressed sensors in live cells. Finally, we present a method to internalize fluorescent beads as in situ viscoelasticity markers in the cytoplasm of live yeast cells and discuss limitations of this approach including impairment of cellular function.
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Affiliation(s)
- Sarah Lecinski
- Department of Physics, University of York, York YO10 5DD, UK
| | - Jack W. Shepherd
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
| | - Kate Bunting
- Department of Biology, University of York, York YO10 5DD, UK
| | - Lara Dresser
- Department of Physics, University of York, York YO10 5DD, UK
| | - Steven D. Quinn
- Department of Physics, University of York, York YO10 5DD, UK
| | - Chris MacDonald
- Department of Biology, University of York, York YO10 5DD, UK
| | - Mark C. Leake
- Department of Physics, University of York, York YO10 5DD, UK
- Department of Biology, University of York, York YO10 5DD, UK
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6
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Lukyanov KA. Fluorescent proteins for a brighter science. Biochem Biophys Res Commun 2022; 633:29-32. [DOI: 10.1016/j.bbrc.2022.08.089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 08/29/2022] [Indexed: 11/06/2022]
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7
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Mamontova AV, Simonyan TR, Lukyanov KA, Bogdanov AM. Circular Permutants of BrUSLEE Protein as Fluorescent pH Indicators. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022. [DOI: 10.1134/s106816202204015x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Abstract—
Two variants of circularly permuted BrUSLEE, a green fluorescent protein with a short fluorescence lifetime, have been engineered. We characterized the pH-dependence of fluorescence decay kinetics of these fluorophores. It was shown that both permutants (cpBrUS and cpBrUS-145) exhibit three-component fluorescence decay kinetics, with the lifetime of the one component varying within the ~3000–300 ps range upon pH shift from 5.5 to 9.0. At the same time, the original BrUSLEE does not show a significant change in the fluorescence decay kinetics within the physiologically relevant pH-range of 6.0–8.5. The described pH-dependence allows considering the BrUSLEE permutants as pH indicators with the fluorescence lifetime readout.
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8
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Mukherjee S, Manna P, Hung ST, Vietmeyer F, Friis P, Palmer AE, Jimenez R. Directed Evolution of a Bright Variant of mCherry: Suppression of Nonradiative Decay by Fluorescence Lifetime Selections. J Phys Chem B 2022; 126:4659-4668. [PMID: 35709514 DOI: 10.1021/acs.jpcb.2c01956] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The approximately linear scaling of fluorescence quantum yield (ϕ) with fluorescence lifetime (τ) in fluorescent proteins (FPs) has inspired engineering of brighter fluorophores based on screening for increased lifetimes. Several recently developed FPs such as mTurquoise2, mScarlet, and FusionRed-MQV which have become useful for live cell imaging are products of lifetime selection strategies. However, the underlying photophysical basis of the improved brightness has not been scrutinized. In this study, we focused on understanding the outcome of lifetime-based directed evolution of mCherry, which is a popular red-FP (RFP). We identified four positions (W143, I161, Q163, and I197) near the FP chromophore that can be mutated to create mCherry-XL (eXtended Lifetime: ϕ = 0.70; τ = 3.9 ns). The 3-fold higher quantum yield of mCherry-XL is on par with that of the brightest RFP to date, mScarlet. We examined selected variants within the evolution trajectory and found a near-linear scaling of lifetime with quantum yield and consistent blue-shifts of the absorption and emission spectra. We find that the improvement in brightness is primarily due to a decrease in the nonradiative decay of the excited state. In addition, our analysis revealed the decrease in nonradiative rate is not limited to the blue-shift of the energy gap and changes in the excited state reorganization energy. Our findings suggest that nonradiative mechanisms beyond the scope of energy-gap models such the Englman-Jortner model are suppressed in this lifetime evolution trajectory.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Premashis Manna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sheng-Ting Hung
- Department of Physics, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Felix Vietmeyer
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Pia Friis
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, Colorado 80309, United States.,BioFrontiers Institute, University of Colorado, Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado, Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States.,Department of Chemistry, University of Colorado, Boulder, 215 UCB, Boulder, Colorado 80309, United States
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9
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Mukherjee S, Jimenez R. Photophysical Engineering of Fluorescent Proteins: Accomplishments and Challenges of Physical Chemistry Strategies. J Phys Chem B 2022; 126:735-750. [DOI: 10.1021/acs.jpcb.1c05629] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
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10
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Koh SP, Pham NP, Piekny A. Seeing is believing: tools to study the role of Rho GTPases during cytokinesis. Small GTPases 2022; 13:211-224. [PMID: 34405757 PMCID: PMC9707540 DOI: 10.1080/21541248.2021.1957384] [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] [Indexed: 02/06/2023] Open
Abstract
Cytokinesis is required to cleave the daughter cells at the end of mitosis and relies on the spatiotemporal control of RhoA GTPase. Cytokinesis failure can lead to changes in cell fate or aneuploidy, which can be detrimental during development and/or can lead to cancer. However, our knowledge of the pathways that regulate RhoA during cytokinesis is limited, and the role of other Rho family GTPases is not clear. This is largely because the study of Rho GTPases presents unique challenges using traditional cell biological and biochemical methods, and they have pleiotropic functions making genetic studies difficult to interpret. The recent generation of optogenetic tools and biosensors that control and detect active Rho has overcome some of these challenges and is helping to elucidate the role of RhoA in cytokinesis. However, improvements are needed to reveal the role of other Rho GTPases in cytokinesis, and to identify the molecular mechanisms that control Rho activity. This review examines some of the outstanding questions in cytokinesis, and explores tools for the imaging and control of Rho GTPases.
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Affiliation(s)
- Su Pin Koh
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Nhat Phi Pham
- Department of Biology, Concordia University, Montreal, QC, Canada
| | - Alisa Piekny
- Department of Biology, Concordia University, Montreal, QC, Canada,CONTACT Alisa Piekny Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montreal, QC, Canada
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11
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Schilling K, Zhai Y, Zhou Z, Zhou B, Brown E, Zhang X. High-resolution imaging of the osteogenic and angiogenic interface at the site of murine cranial bone defect repair via multiphoton microscopy. eLife 2022; 11:83146. [PMID: 36326085 PMCID: PMC9678361 DOI: 10.7554/elife.83146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022] Open
Abstract
The spatiotemporal blood vessel formation and specification at the osteogenic and angiogenic interface of murine cranial bone defect repair were examined utilizing a high-resolution multiphoton-based imaging platform in conjunction with advanced optical techniques that allow interrogation of the oxygen microenvironment and cellular energy metabolism in living animals. Our study demonstrates the dynamic changes of vessel types, that is, arterial, venous, and capillary vessel networks at the superior and dura periosteum of cranial bone defect, suggesting a differential coupling of the vessel type with osteoblast expansion and bone tissue deposition/remodeling during repair. Employing transgenic reporter mouse models that label distinct types of vessels at the site of repair, we further show that oxygen distributions in capillary vessels at the healing site are heterogeneous as well as time- and location-dependent. The endothelial cells coupling to osteoblasts prefer glycolysis and are less sensitive to microenvironmental oxygen changes than osteoblasts. In comparison, osteoblasts utilize relatively more OxPhos and potentially consume more oxygen at the site of repair. Taken together, our study highlights the dynamics and functional significance of blood vessel types at the site of defect repair, opening up opportunities for further delineating the oxygen and metabolic microenvironment at the interface of bone tissue regeneration.
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Affiliation(s)
- Kevin Schilling
- Center for Musculoskeletal Research, University of Rochester, School of Medicine and DentistryRochesterUnited States,Department of Biomedical Engineering, University of RochesterRochesterUnited States
| | - Yuankn Zhai
- Center for Musculoskeletal Research, University of Rochester, School of Medicine and DentistryRochesterUnited States
| | - Zhuang Zhou
- Center for Musculoskeletal Research, University of Rochester, School of Medicine and DentistryRochesterUnited States
| | - Bin Zhou
- Shanghai Institutes for Biological SciencesShanghaiChina
| | - Edward Brown
- Department of Biomedical Engineering, University of RochesterRochesterUnited States
| | - Xinping Zhang
- Center for Musculoskeletal Research, University of Rochester, School of Medicine and DentistryRochesterUnited States
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12
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Schilling K, Brown E, Zhang X. NAD(P)H autofluorescence lifetime imaging enables single cell analyses of cellular metabolism of osteoblasts in vitro and in vivo via two-photon microscopy. Bone 2022; 154:116257. [PMID: 34781049 PMCID: PMC8671374 DOI: 10.1016/j.bone.2021.116257] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023]
Abstract
Two-photon fluorescence lifetime microscopy (2P-FLIM) is a non-invasive optical technique that can obtain cellular metabolism information based on the intrinsic autofluorescence lifetimes of free and enzyme-bound NAD(P)H, which reflect the metabolic state of single cells within the native microenvironment of the living tissue. NAD(P)H 2P-FLIM was initially performed in bone marrow stromal cell (BMSC) cultures established from Col (I) 2.3GFP or OSX-mCherry mouse models, in which osteoblastic lineage cells were labelled with green or red fluorescence protein, respectively. Measurement of the mean NAD(P)H lifetime, τM, demonstrated that osteoblasts in osteogenic media had a progressively increased τM compared to cells in regular media, suggesting that osteoblasts undergoing mineralization had higher NAD+/NAD(P)H ratio and may utilize more oxidative phosphorylation (OxPhos). In vivo NAD(P)H 2P-FLIM was conducted in conjunction with two-photon phosphorescence lifetime microscopy (2P-PLIM) to evaluate cellular metabolism of GFP+ osteoblasts as well as bone tissue oxygen at different locations of the native cranial bone in Col (I) 2.3GFP mice. Our data showed that osteocytes dwelling within lacunae had higher τM than osteoblasts at the bone edge of suture and marrow space. Measurement of pO2 showed poor correlation of pO2 and τM in native bone. However, when NAD(P)H 2P-FLIM was used to examine osteoblast cellular metabolism at the leading edge of the cranial defects during repair in Col (I) 2.3GFP mouse model, a significantly lower τM was recorded, which was associated with lower pO2 at an early stage of healing, indicating an impact of hypoxia on energy metabolism during bone tissue repair. Taken together, our current study demonstrates the feasibility of using non-invasive optical NAD(P)H 2P-FLIM technique to examine cellular energy metabolism at single cell resolution in living animals. Our data further support that both glycolysis and OxPhos are being used in the osteoblasts, with more mature osteoblasts exhibiting higher ratio of NAD+/NAD(P)H, indicating a potential change of energy mode during differentiation. Further experiments utilizing animals with genetic modification of cellular metabolism could enhance our understanding of energy metabolism in various cell types in living bone microenvironment.
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Affiliation(s)
- Kevin Schilling
- Center for Musculoskeletal Research, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642, USA
| | - Edward Brown
- Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642, USA
| | - Xinping Zhang
- Center for Musculoskeletal Research, University of Rochester, School of Medicine and Dentistry, Rochester, NY 14642, USA; Department of Biomedical Engineering, University of Rochester, Rochester, NY 14642, USA.
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13
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Live imaging Arabidopsis thaliana embryos under different hydration conditions. STAR Protoc 2021; 2:101025. [PMID: 34977672 PMCID: PMC8683761 DOI: 10.1016/j.xpro.2021.101025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Despite the ecological and agronomical importance of seed germination, how seeds integrate environmental signals to trigger germination remains enigmatic. Recently we reported that a protein called FLOE1 is involved in sensing and responding to water availability during germination. Here, we present a live-imaging protocol to assess the subcellular localization of a protein of interest during imbibition of desiccated Arabidopsis thaliana seeds with the goal of understanding protein dynamics during the early stages of water uptake. For complete details on the use and execution of this profile, please refer to Dorone et al. (2021).
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Saydmohammed M, Jha A, Mahajan V, Gavlock D, Shun TY, DeBiasio R, Lefever D, Li X, Reese C, Kershaw EE, Yechoor V, Behari J, Soto-Gutierrez A, Vernetti L, Stern A, Gough A, Miedel MT, Lansing Taylor D. Quantifying the progression of non-alcoholic fatty liver disease in human biomimetic liver microphysiology systems with fluorescent protein biosensors. Exp Biol Med (Maywood) 2021; 246:2420-2441. [PMID: 33957803 PMCID: PMC8606957 DOI: 10.1177/15353702211009228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
Metabolic syndrome is a complex disease that involves multiple organ systems including a critical role for the liver. Non-alcoholic fatty liver disease (NAFLD) is a key component of the metabolic syndrome and fatty liver is linked to a range of metabolic dysfunctions that occur in approximately 25% of the population. A panel of experts recently agreed that the acronym, NAFLD, did not properly characterize this heterogeneous disease given the associated metabolic abnormalities such as type 2 diabetes mellitus (T2D), obesity, and hypertension. Therefore, metabolic dysfunction-associated fatty liver disease (MAFLD) has been proposed as the new term to cover the heterogeneity identified in the NAFLD patient population. Although many rodent models of NAFLD/NASH have been developed, they do not recapitulate the full disease spectrum in patients. Therefore, a platform has evolved initially focused on human biomimetic liver microphysiology systems that integrates fluorescent protein biosensors along with other key metrics, the microphysiology systems database, and quantitative systems pharmacology. Quantitative systems pharmacology is being applied to investigate the mechanisms of NAFLD/MAFLD progression to select molecular targets for fluorescent protein biosensors, to integrate computational and experimental methods to predict drugs for repurposing, and to facilitate novel drug development. Fluorescent protein biosensors are critical components of the platform since they enable monitoring of the pathophysiology of disease progression by defining and quantifying the temporal and spatial dynamics of protein functions in the biosensor cells, and serve as minimally invasive biomarkers of the physiological state of the microphysiology system experimental disease models. Here, we summarize the progress in developing human microphysiology system disease models of NAFLD/MAFLD from several laboratories, developing fluorescent protein biosensors to monitor and to measure NAFLD/MAFLD disease progression and implementation of quantitative systems pharmacology with the goal of repurposing drugs and guiding the creation of novel therapeutics.
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Affiliation(s)
- Manush Saydmohammed
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Anupma Jha
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vineet Mahajan
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Dillon Gavlock
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Tong Ying Shun
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Richard DeBiasio
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Daniel Lefever
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Xiang Li
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Celeste Reese
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Erin E Kershaw
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Vijay Yechoor
- Department of Medicine, Division of Endocrinology and Metabolism, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Jaideep Behari
- Department of Medicine, Division of Gastroenterology, Hepatology and Nutrition, Pittsburgh, PA 15261, USA
- UPMC Liver Clinic, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Alejandro Soto-Gutierrez
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Larry Vernetti
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Andrew Stern
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Albert Gough
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Mark T Miedel
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - D Lansing Taylor
- University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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15
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Bogdanov AM, Gorbachev DA, Zaitseva ER, Smirnov AY, Baleeva NS, Baranov MS. Lability of Stationary and Time-Resolved Optical Properties of the Conformationally Locked CFP Chromophore Derivative. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021030043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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17
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Peng B, Dikdan R, Hill SE, Patterson-Orazem AC, Lieberman RL, Fahrni CJ, Dickson RM. Optically Modulated and Optically Activated Delayed Fluorescent Proteins through Dark State Engineering. J Phys Chem B 2021; 125:5200-5209. [PMID: 33978414 DOI: 10.1021/acs.jpcb.1c00649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Modulating fluorescent protein emission holds great potential for increasing readout sensitivity for applications in biological imaging and detection. Here, we identify and engineer optically modulated yellow fluorescent proteins (EYFP, originally 10C, but renamed EYFP later, and mVenus) to yield new emitters with distinct modulation profiles and unique, optically gated, delayed fluorescence. The parent YFPs are individually modulatable through secondary illumination, depopulating a long-lived dark state to dynamically increase fluorescence. A single point mutation introduced near the chromophore in each of these YFPs provides access to a second, even longer-lived modulatable dark state, while a different double mutant renders EYFP unmodulatable. The naturally occurring dark state in the parent YFPs yields strong fluorescence modulation upon long-wavelength-induced dark state depopulation, allowing selective detection at the frequency at which the long wavelength secondary laser is intensity modulated. Distinct from photoswitches, however, this near IR secondary coexcitation repumps the emissive S1 level from the long-lived triplet state, resulting in optically activated delayed fluorescence (OADF). This OADF results from secondary laser-induced, reverse intersystem crossing (RISC), producing additional nanosecond-lived, visible fluorescence that is delayed by many microseconds after the primary excitation has turned off. Mutation of the parent chromophore environment opens an additional modulation pathway that avoids the OADF-producing triplet state, resulting in a second, much longer-lived, modulatable dark state. These Optically Modulated and Optically Activated Delayed Fluorescent Proteins (OMFPs and OADFPs) are thus excellent for background- and reference-free, high sensitivity cellular imaging, but time-gated OADF offers a second modality for true background-free detection. Our combined structural and spectroscopic data not only gives additional mechanistic details for designing optically modulated fluorescent proteins but also provides the opportunity to distinguish similarly emitting OMFPs through OADF and through their unique modulation spectra.
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Affiliation(s)
- Baijie Peng
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Ryan Dikdan
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Shannon E Hill
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Athéna C Patterson-Orazem
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Raquel L Lieberman
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Christoph J Fahrni
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Robert M Dickson
- School of Chemistry & Biochemistry and Petit Institute for Biosciences and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
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18
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Pletneva NV, Maksimov EG, Protasova EA, Mamontova AV, Simonyan TR, Ziganshin RH, Lukyanov KA, Muslinkina L, Pletnev S, Bogdanov AM, Pletnev VZ. Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design. Comput Struct Biotechnol J 2021; 19:2950-2959. [PMID: 34136094 PMCID: PMC8163865 DOI: 10.1016/j.csbj.2021.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 01/07/2023] Open
Abstract
For the whole GFP family, a few cases, when a single mutation in the chromophore environment strongly inhibits maturation, were described. Here we study EYFP-F165G - a variant of the enhanced yellow fluorescent protein - obtained by a single F165G replacement, and demonstrated multiple fluorescent states represented by the minor emission peaks in blue and yellow ranges (~470 and ~530 nm), and the major peak at ~330 nm. The latter has been assigned to tryptophan fluorescence, quenched due to excitation energy transfer to the mature chromophore in the parental EYFP protein. EYFP-F165G crystal structure revealed two general independent routes of post-translational chemistry, resulting in two main states of the polypeptide chain with the intact chromophore forming triad (~85%) and mature chromophore (~15%). Our experiments thus highlighted important stereochemical role of the 165th position strongly affecting spectral characteristics of the protein. On the basis of the determined EYFP-F165G three-dimensional structure, new variants with ~ 2-fold improved brightness were engineered.
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Key Words
- Ala (A), alanine
- Arg (R), arginine
- Asn (R), asparagine
- Chromophore maturation
- DTT, dithiothreitol
- EC, extinction coefficient
- EET, excitation energy transfer
- EGFP, enhanced green fluorescent protein
- ESET, excited-state electron transfer
- EYFP
- EYFP, enhanced yellow fluorescent protein
- Excitation energy transfer
- FLIM, fluorescence lifetime imaging microscopy
- FP, fluorescent protein
- FQY, fluorescence quantum yield
- FRET, Förster resonance energy transfer
- FTIR, Fourier-transform infrared (spectroscopy
- Femtosecond spectroscopy
- Fluorescent proteins
- GFP, green fluorescent protein
- GYG, glycine-tyrosine-glycine
- Gln (Q), glutamine
- Glu (E), glutamic acid
- Gly (G), glycine
- His (H), histidine
- IVA-cloning, in vivo assembly cloning
- Leu (L), leucine
- PBS, phosphate buffered saline
- PCR, polymerase chain reaction
- Phe (F), phenylalanine
- REACh, resonance energy-accepting chromoprotein
- Ser (S), serine
- Structure-guided mutagenesis
- Trp (W), tryptophan
- Tryptophan fluorescence
- Tyr (Y), tyrosine
- Val (V), valine
- X-ray structure
- avGFP, Aequorea victoria green fluorescent protein
- sfGFP, superfolder GFP
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Affiliation(s)
- Nadya V. Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Elena A. Protasova
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Tatiana R. Simonyan
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
| | - Vladimir Z. Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
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19
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Shirmanova MV, Gorbachev DA, Sarkisyan KS, Parnes AP, Gavrina AI, Polozova AV, Kovaleva TF, Snopova LB, Dudenkova VV, Zagaynova EV, Lukyanov KA. FUCCI-Red: a single-color cell cycle indicator for fluorescence lifetime imaging. Cell Mol Life Sci 2021; 78:3467-3476. [PMID: 33555392 PMCID: PMC11073227 DOI: 10.1007/s00018-020-03712-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/23/2020] [Accepted: 11/16/2020] [Indexed: 01/23/2023]
Abstract
The phase of the cell cycle determines numerous aspects of cancer cell behaviour including invasiveness, ability to migrate and responsiveness to cytotoxic drugs. To non-invasively monitor progression of cell cycle in vivo, a family of genetically encoded fluorescent indicators, FUCCI (fluorescent ubiquitination-based cell cycle indicator), has been developed. Existing versions of FUCCI are based on fluorescent proteins of two or more different colors fused to cell-cycle-dependent degradation motifs. Thus, FUCCI-expressing cells emit light of different colors in different phases providing a robust way to monitor cell cycle progression by fluorescence microscopy and flow cytometry but limiting the possibility to simultaneously visualize other markers. To overcome this limitation, we developed a single-color variant of FUCCI, called FUCCI-Red, which utilizes two red fluorescent proteins with distinct fluorescence lifetimes, mCherry and mKate2. Similarly to FUCCI, these proteins carry cell cycle-dependent degradation motifs to resolve G1 and S/G2/M phases. We showed utility of FUCCI-Red by visualizing cell cycle progression of cancer cells in 2D and 3D cultures and monitoring development of tumors in vivo by confocal and fluorescence lifetime imaging microscopy (FLIM). Single-channel registration and red-shifted spectra make FUCCI-Red sensor a promising instrument for multiparameter in vivo imaging applications, which was demonstrated by simultaneous detection of cellular metabolic state using endogenous fluorescence in the blue range.
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Affiliation(s)
- Marina V Shirmanova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Dmitry A Gorbachev
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205, Moscow, Russia
| | - Karen S Sarkisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alina P Parnes
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - Alena I Gavrina
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Anastasia V Polozova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Tatyana F Kovaleva
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Ludmila B Snopova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Varvara V Dudenkova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
| | - Elena V Zagaynova
- Privolzhsky Research Medical University, Minin and Pozharsky Sq. 10/1, 603005, Nizhny Novgorod, Russia
- Lobachevsky State University of Nizhny Novgorod, Gagarin Ave. 23, 603950, Nizhny Novgorod, Russia
| | - Konstantin A Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, 121205, Moscow, Russia.
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20
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Mamontova AV, Shakhov AM, Lukyanov KA, Bogdanov AM. Deciphering the Role of Positions 145 and 165 in Fluorescence Lifetime Shortening in the EGFP Variants. Biomolecules 2020; 10:biom10111547. [PMID: 33202759 PMCID: PMC7696298 DOI: 10.3390/biom10111547] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/05/2020] [Accepted: 11/10/2020] [Indexed: 01/15/2023] Open
Abstract
The bright ultimately short lifetime enhanced emitter (BrUSLEE) green fluorescent protein, which differs from the enhanced green fluorescent protein (EGFP) in three mutations, exhibits an extremely short fluorescence lifetime at a relatively high brightness. An important contribution to shortening the BrUSLEE fluorescence lifetime compared to EGFP is provided by the T65G substitution of chromophore-forming residue and the Y145M mutation touching the chromophore environment. Although the influence of the T65G mutation was studied previously, the role of the 145th position in determining the GFPs physicochemical characteristics remains unclear. In this work, we show that the Y145M substitution, both alone and in combination with the F165Y mutation, does not shorten the fluorescence lifetime of EGFP-derived mutants. Thus, the unlocking of Y145M as an important determinant of lifetime tuning is possible only cooperatively with mutations at position 65. We also show here that the introduction of a T65G substitution into EGFP causes complex photobehavior of the respective mutants in the lifetime domain, namely, the appearance of two fluorescent states with different lifetimes, preserved in any combination with the Y145M and F165Y substitutions.
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Affiliation(s)
- Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | | | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, 121205 Moscow, Russia; (A.V.M.); (K.A.L.)
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia
- Correspondence:
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21
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Mukherjee S, Hung ST, Douglas N, Manna P, Thomas C, Ekrem A, Palmer AE, Jimenez R. Engineering of a Brighter Variant of the FusionRed Fluorescent Protein Using Lifetime Flow Cytometry and Structure-Guided Mutations. Biochemistry 2020; 59:3669-3682. [PMID: 32914619 DOI: 10.1021/acs.biochem.0c00484] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of fluorescent proteins (FPs) has revolutionized biological imaging. FusionRed, a monomeric red FP (RFP), is known for its low cytotoxicity and correct localization of target fusion proteins in mammalian cells but is limited in application by low fluorescence brightness. We report a brighter variant of FusionRed, "FR-MQV," which exhibits an extended fluorescence lifetime (2.8 ns), enhanced quantum yield (0.53), higher extinction coefficient (∼140 000 M-1 cm-1), increased radiative rate constant, and reduced nonradiative rate constant with respect to its precursor. The properties of FR-MQV derive from three mutations-M42Q, C159V, and the previously identified L175M. A structure-guided approach was used to identify and mutate candidate residues around the para-hydroxyphenyl and the acylimine sites of the chromophore. The C159V mutation was identified via lifetime-based flow cytometry screening of a library in which multiple residues adjacent to the para-hydroxyphenyl site of the chromophore were mutated. The M42Q mutation is located near the acylimine moiety of the chromophore and was discovered using site-directed mutagenesis guided by X-ray crystal structures. FR-MQV exhibits a 3.4-fold higher molecular brightness and a 5-fold increase in the cellular brightness in HeLa cells [based on fluorescence-activated cell sorting (FACS)] compared to FusionRed. It also retains the low cytotoxicity and high-fidelity localization of FusionRed, as demonstrated through assays in mammalian cells. These properties make FR-MQV a promising template for further engineering into a new family of RFPs.
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Affiliation(s)
- Srijit Mukherjee
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
| | - Sheng-Ting Hung
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Nancy Douglas
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Premashis Manna
- Department of Chemistry, MIT, 77 Massachusetts Avenue, 18-084, Cambridge, Massachusetts 02139, United States
| | - Connor Thomas
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Annika Ekrem
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado at Boulder, 596 UCB, Boulder, Colorado 80309, United States
- BioFrontiers Institute, University of Colorado, Boulder, 596 UCB, Boulder, Colorado 80309, United States
| | - Ralph Jimenez
- JILA, University of Colorado at Boulder and National Institute of Standards and Technology, 440 UCB, Boulder, Colorado 80309, United States
- Department of Chemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, United States
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Influence of the First Chromophore-Forming Residue on Photobleaching and Oxidative Photoconversion of EGFP and EYFP. Int J Mol Sci 2019; 20:ijms20205229. [PMID: 31652505 PMCID: PMC6829896 DOI: 10.3390/ijms20205229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 12/21/2022] Open
Abstract
Enhanced green fluorescent protein (EGFP)—one of the most widely applied genetically encoded fluorescent probes—carries the threonine-tyrosine-glycine (TYG) chromophore. EGFP efficiently undergoes green-to-red oxidative photoconversion (“redding”) with electron acceptors. Enhanced yellow fluorescent protein (EYFP), a close EGFP homologue (five amino acid substitutions), has a glycine-tyrosine-glycine (GYG) chromophore and is much less susceptible to redding, requiring halide ions in addition to the oxidants. In this contribution we aim to clarify the role of the first chromophore-forming amino acid in photoinduced behavior of these fluorescent proteins. To that end, we compared photobleaching and redding kinetics of EGFP, EYFP, and their mutants with reciprocally substituted chromophore residues, EGFP-T65G and EYFP-G65T. Measurements showed that T65G mutation significantly increases EGFP photostability and inhibits its excited-state oxidation efficiency. Remarkably, while EYFP-G65T demonstrated highly increased spectral sensitivity to chloride, it is also able to undergo redding chloride-independently. Atomistic calculations reveal that the GYG chromophore has an increased flexibility, which facilitates radiationless relaxation leading to the reduced fluorescence quantum yield in the T65G mutant. The GYG chromophore also has larger oscillator strength as compared to TYG, which leads to a shorter radiative lifetime (i.e., a faster rate of fluorescence). The faster fluorescence rate partially compensates for the loss of quantum efficiency due to radiationless relaxation. The shorter excited-state lifetime of the GYG chromophore is responsible for its increased photostability and resistance to redding. In EYFP and EYFP-G65T, the chromophore is stabilized by π-stacking with Tyr203, which suppresses its twisting motions relative to EGFP.
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23
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Chen M, Zhang S, Xing Y, Li X, He Y, Wang Y, Oberholzer J, Ai HW. Genetically Encoded, Photostable Indicators to Image Dynamic Zn 2+ Secretion of Pancreatic Islets. Anal Chem 2019; 91:12212-12219. [PMID: 31475537 PMCID: PMC6773511 DOI: 10.1021/acs.analchem.9b01802] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As an essential element for living organisms, zinc (Zn2+) exerts its biological functions both intracellularly and extracellularly. Previous studies have reported a number of genetically encoded Zn2+ indicators (GEZIs), which have been widely used to monitor Zn2+ in the cytosol and intracellular organelles. However, it is challenging to localize existing GEZIs to the extracellular space to detect secreted Zn2+. Herein, we report two photostable, green fluorescent protein (GFP) based indicators, ZIBG1 and ZIBG2, which respond to Zn2+ selectively and have affinities suited for detecting Zn2+ secretion from intracellular vesicles. In particular, ZIBG2 can be effectively targeted to the extracellular side of plasma membrane. We applied cell surface-localized ZIBG2 to monitor glucose-induced dynamic Zn2+ secretion from mouse insulinoma MIN6 cells and primary mouse and human pancreatic islets. Because Zn2+ is co-released with insulin from β-cells, the fluorescence of cell surface-localized ZIBG2 was shown to be a strong indicator for the functional potency of islets. Our work here has thus expanded the use of GEZIs to image dynamic Zn2+ secretion in live tissue. Because it is convenient to use genetically encoded indicators for expression over extended periods and for in vivo delivery, we envision future applications of ZIBG2 in development of induced β-cells or islets to advance cell replacement therapies for diabetes and in direct imaging of Zn2+ secretion dynamics in vivo.
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Affiliation(s)
- Minghai Chen
- Center for Membrane and Cell Physiology, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Shen Zhang
- Center for Membrane and Cell Physiology, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- Department of Chemistry, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Yuan Xing
- Department of Surgery, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Xinyu Li
- Center for Membrane and Cell Physiology, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Yi He
- Department of Surgery, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Yong Wang
- Department of Surgery, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - José Oberholzer
- Department of Surgery, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- Department of Bioengineering, and , University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
| | - Hui-wang Ai
- Center for Membrane and Cell Physiology, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- Department of Molecular Physiology and Biological Physics, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- Department of Chemistry, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- Department of Bioengineering, and , University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
- UVA Cancer Center, University of Virginia, 1340 Jefferson Park Avenue, Charlottesville, Virginia 22908, United States
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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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