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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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Kostyuk AI, Rapota DD, Morozova KI, Fedotova AA, Jappy D, Semyanov AV, Belousov VV, Brazhe NA, Bilan DS. Modern optical approaches in redox biology: Genetically encoded sensors and Raman spectroscopy. Free Radic Biol Med 2024; 217:68-115. [PMID: 38508405 DOI: 10.1016/j.freeradbiomed.2024.03.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/10/2024] [Accepted: 03/13/2024] [Indexed: 03/22/2024]
Abstract
The objective of the current review is to summarize the current state of optical methods in redox biology. It consists of two parts, the first is dedicated to genetically encoded fluorescent indicators and the second to Raman spectroscopy. In the first part, we provide a detailed classification of the currently available redox biosensors based on their target analytes. We thoroughly discuss the main architecture types of these proteins, the underlying engineering strategies for their development, the biochemical properties of existing tools and their advantages and disadvantages from a practical point of view. Particular attention is paid to fluorescence lifetime imaging microscopy as a possible readout technique, since it is less prone to certain artifacts than traditional intensiometric measurements. In the second part, the characteristic Raman peaks of the most important redox intermediates are listed, and examples of how this knowledge can be implemented in biological studies are given. This part covers such fields as estimation of the redox states and concentrations of Fe-S clusters, cytochromes, other heme-containing proteins, oxidative derivatives of thiols, lipids, and nucleotides. Finally, we touch on the issue of multiparameter imaging, in which biosensors are combined with other visualization methods for simultaneous assessment of several cellular parameters.
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Affiliation(s)
- Alexander I Kostyuk
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia
| | - Diana D Rapota
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia
| | - Kseniia I Morozova
- Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Anna A Fedotova
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia
| | - David Jappy
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia
| | - Alexey V Semyanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia; Sechenov First Moscow State Medical University, Moscow, 119435, Russia; College of Medicine, Jiaxing University, Jiaxing, Zhejiang Province, 314001, China
| | - Vsevolod V Belousov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, 117997, Russia; Life Improvement by Future Technologies (LIFT) Center, Skolkovo, Moscow, 143025, Russia
| | - Nadezda A Brazhe
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Dmitry S Bilan
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia; Pirogov Russian National Research Medical University, 117997, Moscow, Russia.
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3
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Zhang H, Lesnov GD, Subach OM, Zhang W, Kuzmicheva TP, Vlaskina AV, Samygina VR, Chen L, Ye X, Nikolaeva AY, Gabdulkhakov A, Papadaki S, Qin W, Borshchevskiy V, Perfilov MM, Gavrikov AS, Drobizhev M, Mishin AS, Piatkevich KD, Subach FV. Bright and stable monomeric green fluorescent protein derived from StayGold. Nat Methods 2024; 21:657-665. [PMID: 38409224 DOI: 10.1038/s41592-024-02203-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 01/31/2024] [Indexed: 02/28/2024]
Abstract
The high brightness and photostability of the green fluorescent protein StayGold make it a particularly attractive probe for long-term live-cell imaging; however, its dimeric nature precludes its application as a fluorescent tag for some proteins. Here, we report the development and crystal structures of a monomeric variant of StayGold, named mBaoJin, which preserves the beneficial properties of its precursor, while serving as a tag for structural proteins and membranes. Systematic benchmarking of mBaoJin against popular green fluorescent proteins and other recently introduced monomeric and pseudomonomeric derivatives of StayGold established mBaoJin as a bright and photostable fluorescent protein, exhibiting rapid maturation and high pH/chemical stability. mBaoJin was also demonstrated for super-resolution, long-term live-cell imaging and expansion microscopy. We further showed the applicability of mBaoJin for neuronal labeling in model organisms, including Caenorhabditis elegans and mice.
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Affiliation(s)
- Hanbin Zhang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Gleb D Lesnov
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Oksana M Subach
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Wenhao Zhang
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tatyana P Kuzmicheva
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Anna V Vlaskina
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Valeriya R Samygina
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
- Institute of Crystallography of Federal Research Scientific Center 'Crystallography and Photonics' of the Russian Academy of Sciences, Moscow, Russia
| | - Liangyi Chen
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China
| | - Xianxin Ye
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Alena Yu Nikolaeva
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
| | - Stavrini Papadaki
- School of Life Sciences, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Wenming Qin
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute CAS, Shanghai, China
| | | | - Maxim M Perfilov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Gavrikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Drobizhev
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, USA
| | - Alexander S Mishin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kiryl D Piatkevich
- School of Life Sciences, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China.
| | - Fedor V Subach
- Complex of NBICS Technologies, National Research Center 'Kurchatov Institute', Moscow, Russia.
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4
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Yarkova ES, Grigor’eva EV, Medvedev SP, Tarasevich DA, Pavlova SV, Valetdinova KR, Minina JM, Zakian SM, Malakhova AA. Detection of ER Stress in iPSC-Derived Neurons Carrying the p.N370S Mutation in the GBA1 Gene. Biomedicines 2024; 12:744. [PMID: 38672099 PMCID: PMC11047942 DOI: 10.3390/biomedicines12040744] [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: 02/20/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Endoplasmic reticulum (ER) stress is involved in the pathogenesis of many human diseases, such as cancer, type 2 diabetes, kidney disease, atherosclerosis and neurodegenerative diseases, in particular Parkinson's disease (PD). Since there is currently no treatment for PD, a better understanding of the molecular mechanisms underlying its pathogenesis, including the mechanisms of the switch from adaptation in the form of unfolded protein response (UPR) to apoptosis under ER stress conditions, may help in the search for treatment methods. Genetically encoded biosensors based on fluorescent proteins are suitable tools that facilitate the study of living cells and visualization of molecular events in real time. The combination of technologies to generate patient-specific iPSC lines and genetically encoded biosensors allows the creation of cell models with new properties. Using CRISPR-Cas9-mediated homologous recombination at the AAVS1 locus of iPSC with the genetic variant p.N370S (rs76763715) in the GBA1 gene, we created a cell model designed to study the activation conditions of the IRE1-XBP1 cascade of the UPR system. The cell lines obtained have a doxycycline-dependent expression of the genetically encoded biosensor XBP1-TagRFP, possess all the properties of human pluripotent cells, and can be used to test physical conditions and chemical compounds that affect the development of ER stress, the functioning of the UPR system, and in particular, the IRE1-XBP1 cascade.
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Affiliation(s)
- Elena S. Yarkova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Elena V. Grigor’eva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Sergey P. Medvedev
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Denis A. Tarasevich
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
- Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Sophia V. Pavlova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Kamila R. Valetdinova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Julia M. Minina
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Suren M. Zakian
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
| | - Anastasia A. Malakhova
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk 630090, Russia (S.P.M.); (S.V.P.); (K.R.V.); (J.M.M.); (S.M.Z.); (A.A.M.)
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5
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Berndt A, Lee J, Won W, Kimball K, Neiswanger C, Schattauer S, Wang Y, Yeboah F, Ruiz M, Evitts K, Rappleye M, Bremner S, Chun C, Smith N, Mack D, Young J, Lee CJ, Chavkin C. Ultra-fast genetically encoded sensor for precise real-time monitoring of physiological and pathophysiological peroxide dynamics. RESEARCH SQUARE 2024:rs.3.rs-4048855. [PMID: 38585715 PMCID: PMC10996778 DOI: 10.21203/rs.3.rs-4048855/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Hydrogen Peroxide (H2O2) is a central oxidant in redox biology due to its pleiotropic role in physiology and pathology. However, real-time monitoring of H2O2 in living cells and tissues remains a challenge. We address this gap with the development of an optogenetic hydRogen perOxide Sensor (oROS), leveraging the bacterial peroxide binding domain OxyR. Previously engineered OxyR-based fluorescent peroxide sensors lack the necessary sensitivity and response speed for effective real-time monitoring. By structurally redesigning the fusion of Escherichia coli (E. coli) ecOxyR with a circularly permutated green fluorescent protein (cpGFP), we created a novel, green-fluorescent peroxide sensor oROS-G. oROS-G exhibits high sensitivity and fast on-and-off kinetics, ideal for monitoring intracellular H2O2 dynamics. We successfully tracked real-time transient and steady-state H2O2 levels in diverse biological systems, including human stem cell-derived neurons and cardiomyocytes, primary neurons and astrocytes, and mouse brain ex vivo and in vivo. These applications demonstrate oROS's capabilities to monitor H2O2 as a secondary response to pharmacologically induced oxidative stress and when adapting to varying metabolic stress. We showcased the increased oxidative stress in astrocytes via Aβ-putriscine-MAOB axis, highlighting the sensor's relevance in validating neurodegenerative disease models. Lastly, we demonstrated acute opioid-induced generation of H2O2 signal in vivo which highlights redox-based mechanisms of GPCR regulation. oROS is a versatile tool, offering a window into the dynamic landscape of H2O2 signaling. This advancement paves the way for a deeper understanding of redox physiology, with significant implications for understanding diseases associated with oxidative stress, such as cancer, neurodegenerative, and cardiovascular diseases.
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6
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Lee JD, Won W, Kimball K, Wang Y, Yeboah F, Evitts KM, Neiswanger C, Schattauer S, Rappleye M, Bremner SB, Chun C, Smith N, Mack DL, Young JE, Lee CJ, Chavkin C, Berndt A. Structure-guided engineering of a fast genetically encoded sensor for real-time H 2O 2 monitoring. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578117. [PMID: 38352381 PMCID: PMC10862829 DOI: 10.1101/2024.01.31.578117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Hydrogen Peroxide (H2O2) is a central oxidant in redox biology due to its pleiotropic role in physiology and pathology. However, real-time monitoring of H2O2 in living cells and tissues remains a challenge. We address this gap with the development of an optogenetic hydRogen perOxide Sensor (oROS), leveraging the bacterial peroxide binding domain OxyR. Previously engineered OxyR-based fluorescent peroxide sensors lack the necessary sensitivity or response speed for effective real-time monitoring. By structurally redesigning the fusion of Escherichia coli (E. coli) ecOxyR with a circularly permutated green fluorescent protein (cpGFP), we created a novel, green-fluorescent peroxide sensor oROS-G. oROS-G exhibits high sensitivity and fast on-and-off kinetics, ideal for monitoring intracellular H2O2 dynamics. We successfully tracked real-time transient and steady-state H2O2 levels in diverse biological systems, including human stem cell-derived neurons and cardiomyocytes, primary neurons and astrocytes, and mouse neurons and astrocytes in ex vivo brain slices. These applications demonstrate oROS's capabilities to monitor H2O2 as a secondary response to pharmacologically induced oxidative stress, G-protein coupled receptor (GPCR)-induced cell signaling, and when adapting to varying metabolic stress. We showcased the increased oxidative stress in astrocytes via Aβ-putriscine-MAOB axis, highlighting the sensor's relevance in validating neurodegenerative disease models. oROS is a versatile tool, offering a window into the dynamic landscape of H2O2 signaling. This advancement paves the way for a deeper understanding of redox physiology, with significant implications for diseases associated with oxidative stress, such as cancer, neurodegenerative disorders, and cardiovascular diseases.
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Affiliation(s)
- Justin Daho Lee
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Woojin Won
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, Republic of Korea
| | - Kandace Kimball
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Yihan Wang
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Fred Yeboah
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Kira M Evitts
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Carlie Neiswanger
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Selena Schattauer
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Michael Rappleye
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Samantha B Bremner
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Changho Chun
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Netta Smith
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - David L Mack
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Rehabilitation Medicine, University of Washington, Seattle, WA, USA
| | - Jessica E Young
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - C Justin Lee
- Center for Cognition and Sociality, Institute for Basic Science, Daejeon, Republic of Korea
| | - Charles Chavkin
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
| | - Andre Berndt
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
- Center for Neuroscience of Addiction, Pain and Emotion, University of Washington, Seattle, WA, USA
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7
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Marchetti M, Ronda L, Cozzi M, Bettati S, Bruno S. Genetically Encoded Biosensors for the Fluorescence Detection of O 2 and Reactive O 2 Species. SENSORS (BASEL, SWITZERLAND) 2023; 23:8517. [PMID: 37896609 PMCID: PMC10611200 DOI: 10.3390/s23208517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 10/29/2023]
Abstract
The intracellular concentrations of oxygen and reactive oxygen species (ROS) in living cells represent critical information for investigating physiological and pathological conditions. Real-time measurement often relies on genetically encoded proteins that are responsive to fluctuations in either oxygen or ROS concentrations. The direct binding or chemical reactions that occur in their presence either directly alter the fluorescence properties of the binding protein or alter the fluorescence properties of fusion partners, mostly consisting of variants of the green fluorescent protein. Oxygen sensing takes advantage of several mechanisms, including (i) the oxygen-dependent hydroxylation of a domain of the hypoxia-inducible factor-1, which, in turn, promotes its cellular degradation along with fluorescent fusion partners; (ii) the naturally oxygen-dependent maturation of the fluorophore of green fluorescent protein variants; and (iii) direct oxygen binding by proteins, including heme proteins, expressed in fusion with fluorescent partners, resulting in changes in fluorescence due to conformational alterations or fluorescence resonance energy transfer. ROS encompass a group of highly reactive chemicals that can interconvert through various chemical reactions within biological systems, posing challenges for their selective detection through genetically encoded sensors. However, their general reactivity, and particularly that of the relatively stable oxygen peroxide, can be exploited for ROS sensing through different mechanisms, including (i) the ROS-induced formation of disulfide bonds in engineered fluorescent proteins or fusion partners of fluorescent proteins, ultimately leading to fluorescence changes; and (ii) conformational changes of naturally occurring ROS-sensing domains, affecting the fluorescence properties of fusion partners. In this review, we will offer an overview of these genetically encoded biosensors.
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Affiliation(s)
- Marialaura Marchetti
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Luca Ronda
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Monica Cozzi
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
| | - Stefano Bettati
- Department of Medicine and Surgery, University of Parma, 43125 Parma, Italy; (M.M.); (L.R.); (M.C.)
- Institute of Biophysics, Italian National Research Council (CNR), 56124 Pisa, Italy
| | - Stefano Bruno
- Department of Food and Drug, University of Parma, 43124 Parma, Italy;
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8
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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9
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Subach OM, Vlaskina AV, Agapova YK, Nikolaeva AY, Anokhin KV, Piatkevich KD, Patrushev MV, Boyko KM, Subach FV. Blue-to-Red TagFT, mTagFT, mTsFT, and Green-to-FarRed mNeptusFT2 Proteins, Genetically Encoded True and Tandem Fluorescent Timers. Int J Mol Sci 2023; 24:ijms24043279. [PMID: 36834686 PMCID: PMC9963904 DOI: 10.3390/ijms24043279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
True genetically encoded monomeric fluorescent timers (tFTs) change their fluorescent color as a result of the complete transition of the blue form into the red form over time. Tandem FTs (tdFTs) change their color as a consequence of the fast and slow independent maturation of two forms with different colors. However, tFTs are limited to derivatives of the mCherry and mRuby red fluorescent proteins and have low brightness and photostability. The number of tdFTs is also limited, and there are no blue-to-red or green-to-far-red tdFTs. tFTs and tdFTs have not previously been directly compared. Here, we engineered novel blue-to-red tFTs, called TagFT and mTagFT, which were derived from the TagRFP protein. The main spectral and timing characteristics of the TagFT and mTagFT timers were determined in vitro. The brightnesses and photoconversions of the TagFT and mTagFT tFTs were characterized in live mammalian cells. The engineered split version of the TagFT timer matured in mammalian cells at 37 °C and allowed the detection of interactions between two proteins. The TagFT timer under the control of the minimal arc promoter, successfully visualized immediate-early gene induction in neuronal cultures. We also developed and optimized green-to-far-red and blue-to-red tdFTs, named mNeptusFT and mTsFT, which were based on mNeptune-sfGFP and mTagBFP2-mScarlet fusion proteins, respectively. We developed the FucciFT2 system based on the TagFT-hCdt1-100/mNeptusFT2-hGeminin combination, which could visualize the transitions between the G1 and S/G2/M phases of the cell cycle with better resolution than the conventional Fucci system because of the fluorescent color changes of the timers over time in different phases of the cell cycle. Finally, we determined the X-ray crystal structure of the mTagFT timer and analyzed it using directed mutagenesis.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Yulia K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Konstantin V. Anokhin
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia
| | - Kiryl D. Piatkevich
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maxim V. Patrushev
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow 123182, Russia
- Correspondence: ; Tel.: +7-499-196-7100-3389
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10
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LSSmScarlet2 and LSSmScarlet3, Chemically Stable Genetically Encoded Red Fluorescent Proteins with a Large Stokes’ Shift. Int J Mol Sci 2022; 23:ijms231911051. [PMID: 36232354 PMCID: PMC9569913 DOI: 10.3390/ijms231911051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/25/2022] Open
Abstract
Red fluorescent proteins with a large Stokes’ shift (LSSRFPs) are genetically encoded and efficiently excited by 488 nm light, allowing simultaneous dual-color one- and two-photon fluorescence imaging and fluorescence correlation spectroscopy in combination with green fluorescent proteins FPs. Recently, based on the conventional bright mScarlet RFP, we developed the LSSRFP LSSmScarlet. LSSmScarlet is characterized by two pKa values at pH values of 1.9 and 5.8. In this study, we developed improved versions of LSSmScarlet, named LSSmScarlet2 and LSSmScarlet3, which are characterized by a Stokes’ shift of 128 nm and extreme pH stability with a single pKa value of 2.2. LSSmScarlet2 and LSSmScarlet3 had 1.8-fold faster and 3-fold slower maturation than LSSmScarlet, respectively. In addition, both LSSRFPs were 1.5- to 1.6-fold more photostable and more chemically resistant to denaturation by guanidinium chloride and guanidinium thiocyanate. We also compared the susceptibility of the LSSmScarlet2, LSSmScarlet3, and other LSSRFPs to the reagents used for whole-mount imaging, expansion microscopy, and immunostaining techniques. Due to higher pH stability and faster maturation, the LSSmScarlet3-LAMP3 fusion was 2.2-fold brighter than LSSmScarlet-LAMP3 in lysosomes of mammalian cells. The LSSmScarlet3-hLAMP2A fusion was similar in brightness to LSSmScarlet-hLAMP2A in lysosomes. We successfully applied the monomeric LSSmScarlet2 and LSSmScarlet3 proteins for confocal imaging of structural proteins in live mammalian cells. We also solved the X-ray structure of the LSSmScarlet2 protein at a resolution of 1.41 Å. Site-directed mutagenesis of the LSSmScarlet2 protein demonstrated the key role of the T74 residue in improving the pH and chemical stability of the LSSmScarlet2 protein.
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11
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Yu Y, Pan M, Peng J, Hu D, Hao Y, Qian Z. A review on recent advances in hydrogen peroxide electrochemical sensors for applications in cell detection. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.02.045] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Erdogan YC, Altun HY, Secilmis M, Ata BN, Sevimli G, Cokluk Z, Zaki AG, Sezen S, Akgul Caglar T, Sevgen İ, Steinhorn B, Ai H, Öztürk G, Belousov VV, Michel T, Eroglu E. Complexities of the chemogenetic toolkit: Differential mDAAO activation by d-amino substrates and subcellular targeting. Free Radic Biol Med 2021; 177:132-142. [PMID: 34687864 PMCID: PMC8639799 DOI: 10.1016/j.freeradbiomed.2021.10.023] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/14/2021] [Accepted: 10/18/2021] [Indexed: 01/01/2023]
Abstract
A common approach to investigate oxidant-regulated intracellular pathways is to add exogenous H2O2 to living cells or tissues. However, the addition of H2O2 to the culture medium of cells or tissues approach does not accurately replicate intracellular redox-mediated cell responses. d-amino acid oxidase (DAAO)-based chemogenetic tools represent informative methodological advances that permit the generation of H2O2 on demand with a high spatiotemporal resolution by providing or withdrawing the DAAO substrate d-amino acids. Much has been learned about the intracellular transport of H2O2 through studies using DAAO, yet these valuable tools remain incompletely characterized in many cultured cells. In this study, we describe and characterize in detail the features of a new modified variant of DAAO (termed mDAAO) with improved catalytic activities. We tested mDAAO functionality in several cultured cell lines employing live-cell imaging techniques. Our imaging experiments show that mDAAO is suitable for the generation of H2O2 under hypoxic conditions imaged with the novel ultrasensitive H2O2 sensor (HyPer7). Moreover, this approach was suitable for generating H2O2 in a reversible and concentration-dependent manner in subcellular locales. Furthermore, we show that the choice of d-amino acids differentially affects mDAAO-dependent intracellular H2O2 generation. When paired with the hydrogen sulfide (H2S) sensor hsGFP, administration of the sulfur-containing amino acid d-cysteine to cells expressing mDAAO generates robust H2S signals. We also show that chemogenetic H2O2 generation in different cell types yields distinct HyPer7 profiles. These studies fully characterize the new mDAAO as a novel chemogenetic tool and provide multiparametric approaches for cell manipulation that may open new lines of investigations for redox biochemists to dissect the role of ROS signaling pathways with high spatial and temporal precision.
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Affiliation(s)
- Yusuf C Erdogan
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Hamza Y Altun
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melike Secilmis
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Busra N Ata
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Gulsah Sevimli
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Zeynep Cokluk
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Asal Ghaffari Zaki
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Serap Sezen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Tuba Akgul Caglar
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey
| | - İlker Sevgen
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Benjamin Steinhorn
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Huiwang Ai
- Department of Molecular Physiology and Biological Physics, Center for Membrane and Cell Physiology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Gürkan Öztürk
- Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Physiology Department, International School of Medicine, Istanbul Medipol University, Istanbul, Turkey
| | - Vsevelod V Belousov
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, 117997, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997, Moscow, Russia; Institute of Cardiovascular Physiology, Universitätsmedizin Göttingen, 37073, Göttingen, Germany
| | - Thomas Michel
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Emrah Eroglu
- Molecular Biology, Genetics and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey; Research Institute for Health Sciences and Technologies (SABITA), Istanbul Medipol University, Istanbul, Turkey; Molecular Biology and Biochemistry, Gottfried Schatz Research Center, Medical University of Graz, Austria; Nanotechnology Research and Application Center, Sabanci University, Istanbul, Turkey.
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13
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Subach OM, Vlaskina AV, Agapova YK, Dorovatovskii PV, Nikolaeva AY, Ivashkina OI, Popov VO, Piatkevich KD, Khrenova MG, Smirnova TA, Boyko KM, Subach FV. LSSmScarlet, dCyRFP2s, dCyOFP2s and CRISPRed2s, Genetically Encoded Red Fluorescent Proteins with a Large Stokes Shift. Int J Mol Sci 2021; 22:12887. [PMID: 34884694 PMCID: PMC8657457 DOI: 10.3390/ijms222312887] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 11/20/2021] [Accepted: 11/24/2021] [Indexed: 11/24/2022] Open
Abstract
Genetically encoded red fluorescent proteins with a large Stokes shift (LSSRFPs) can be efficiently co-excited with common green FPs both under single- and two-photon microscopy, thus enabling dual-color imaging using a single laser. Recent progress in protein development resulted in a great variety of novel LSSRFPs; however, the selection of the right LSSRFP for a given application is hampered by the lack of a side-by-side comparison of the LSSRFPs' performance. In this study, we employed rational design and random mutagenesis to convert conventional bright RFP mScarlet into LSSRFP, called LSSmScarlet, characterized by excitation/emission maxima at 470/598 nm. In addition, we utilized the previously reported LSSRFPs mCyRFP1, CyOFP1, and mCRISPRed as templates for directed molecular evolution to develop their optimized versions, called dCyRFP2s, dCyOFP2s and CRISPRed2s. We performed a quantitative assessment of the developed LSSRFPs and their precursors in vitro on purified proteins and compared their brightness at 488 nm excitation in the mammalian cells. The monomeric LSSmScarlet protein was successfully utilized for the confocal imaging of the structural proteins in live mammalian cells and multicolor confocal imaging in conjugation with other FPs. LSSmScarlet was successfully applied for dual-color two-photon imaging in live mammalian cells. We also solved the X-ray structure of the LSSmScarlet protein at the resolution of 1.4 Å that revealed a hydrogen bond network supporting excited-state proton transfer (ESPT). Quantum mechanics/molecular mechanics molecular dynamic simulations confirmed the ESPT mechanism of a large Stokes shift. Structure-guided mutagenesis revealed the role of R198 residue in ESPT that allowed us to generate a variant with improved pH stability. Finally, we showed that LSSmScarlet protein is not appropriate for STED microscopy as a consequence of LSSRed-to-Red photoconversion with high-power 775 nm depletion light.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Anna V. Vlaskina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Yuliya K. Agapova
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Pavel V. Dorovatovskii
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
| | - Alena Y. Nikolaeva
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Olga I. Ivashkina
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Laboratory for Neurobiology of Memory, P.K. Anokhin Research Institute of Normal Physiology, 125315 Moscow, Russia
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir O. Popov
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Faculty of Biology, M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Kiryl D. Piatkevich
- School of Life Sciences, Westlake University, Hangzhou 310024, China;
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China
| | - Maria G. Khrenova
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Tatiana A. Smirnova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia;
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Centre of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia; (M.G.K.); (K.M.B.)
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, 123182 Moscow, Russia; (O.M.S.); (A.V.V.); (Y.K.A.); (P.V.D.); (A.Y.N.); (O.I.I.); (V.O.P.)
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14
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Pang Y, Zhang H, Ai HW. Genetically Encoded Fluorescent Redox Indicators for Unveiling Redox Signaling and Oxidative Toxicity. Chem Res Toxicol 2021; 34:1826-1845. [PMID: 34284580 DOI: 10.1021/acs.chemrestox.1c00149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Redox-active molecules play essential roles in cell homeostasis, signaling, and other biological processes. Dysregulation of redox signaling can lead to toxic effects and subsequently cause diseases. Therefore, real-time tracking of specific redox-signaling molecules in live cells would be critical for deciphering their functional roles in pathophysiology. Fluorescent protein (FP)-based genetically encoded redox indicators (GERIs) have emerged as valuable tools for monitoring the redox states of various redox-active molecules from subcellular compartments to live organisms. In the first section of this review, we overview the background, focusing on the sensing mechanisms of various GERIs. Next, we review a list of selected GERIs according to their analytical targets and discuss their key biophysical and biochemical properties. In the third section, we provide several examples which applied GERIs to understanding redox signaling and oxidative toxicology in pathophysiological processes. Lastly, a summary and outlook section is included.
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Affiliation(s)
- Yu Pang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States.,Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Hao Zhang
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States.,Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Hui-Wang Ai
- Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, Virginia 22908, United States.,Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States.,The UVA Cancer Center, University of Virginia, Charlottesville, Virginia 22908, United States
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15
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Smolyarova DD, Podgorny OV, Bilan DS, Belousov VV. A guide to genetically encoded tools for the study of H 2 O 2. FEBS J 2021; 289:5382-5395. [PMID: 34173331 DOI: 10.1111/febs.16088] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 04/23/2021] [Accepted: 06/24/2021] [Indexed: 01/09/2023]
Abstract
Cell metabolism heavily relies on the redox reactions that inevitably generate reactive oxygen species (ROS). It is now well established that ROS fluctuations near basal levels coordinate numerous physiological processes in living organisms, thus exhibiting regulatory functions. Hydrogen peroxide, the most long-lived ROS, is a key contributor to ROS-dependent signal transduction in the cell. H2 O2 is known to impact various targets in the cell; therefore, the question of how H2 O2 modulates physiological processes in a highly specific manner is central in redox biology. To resolve this question, novel genetic tools have recently been created for detecting H2 O2 and emulating its generation in living organisms with unmatched spatiotemporal resolution. Here, we review H2 O2 -sensitive genetically encoded fluorescent sensors and opto- and chemogenetic tools for controlled H2 O2 generation.
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Affiliation(s)
- Daria D Smolyarova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Russia
| | - Oleg V Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia.,Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia.,Laboratory of Experimental Oncology, Pirogov Russian National Research Medical University, Moscow, Russia.,Federal Center of Brain Research and Neurotechnologies of the Federal Medical Biological Agency, Moscow, Russia.,Institute for Cardiovascular Physiology, Georg August University Göttingen, Germany
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16
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Limited Substrate Specificity of PS/γ-Secretase Is Supported by Novel Multiplexed FRET Analysis in Live Cells. BIOSENSORS-BASEL 2021; 11:bios11060169. [PMID: 34073182 PMCID: PMC8228125 DOI: 10.3390/bios11060169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/19/2021] [Accepted: 05/24/2021] [Indexed: 12/01/2022]
Abstract
Presenilin (PS)/γ-secretase is an aspartyl protease that processes a wide range of transmembrane proteins such as the amyloid precursor protein (APP) and Notch1, playing essential roles in normal biological events and diseases. However, whether there is a substrate preference for PS/γ-secretase processing in cells is not fully understood. Structural studies of PS/γ-secretase enfolding a fragment of APP or Notch1 showed that the two substrates engage the protease in broadly similar ways, suggesting the limited substrate specificity of PS/γ-secretase. In the present study, we developed a new multiplexed imaging platform that, for the first time, allowed us to quantitatively monitor how PS/γ-secretase processes two different substrates (e.g., APP vs. Notch1) in the same cell. In this assay, we utilized the recently reported, spectrally compatible visible and near-infrared (NIR)-range Förster resonance energy transfer (FRET) biosensors that permit quantitative recording of PS/γ-secretase activity in live cells. Here, we show that, overall, PS/γ-secretase similarly cleaves Notch1 N100, wild-type APP C99, and familial Alzheimer’s disease (FAD)-linked APP C99 mutants in Chinese hamster ovary (CHO) cells, which further supports the limited PS/γ-secretase substrate specificity. On the other hand, a cell-by-cell basis analysis demonstrates a certain degree of variability in substrate recognition and processing by PS/γ-secretase among different cells. Our new multiplexed FRET assay could be a useful tool to better understand how PS/γ-secretase processes its multiple substrates in normal and disease conditions in live, intact cells.
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17
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Kostyuk AI, Panova AS, Kokova AD, Kotova DA, Maltsev DI, Podgorny OV, Belousov VV, Bilan DS. In Vivo Imaging with Genetically Encoded Redox Biosensors. Int J Mol Sci 2020; 21:E8164. [PMID: 33142884 PMCID: PMC7662651 DOI: 10.3390/ijms21218164] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasiya S. Panova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Daria A. Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dmitry I. Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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18
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Gibhardt CS, Ezeriņa D, Sung HM, Messens J, Bogeski I. Redox regulation of the mitochondrial calcium transport machinery. CURRENT OPINION IN PHYSIOLOGY 2020. [DOI: 10.1016/j.cophys.2020.07.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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19
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Pal A, Tian L. Imaging voltage and brain chemistry with genetically encoded sensors and modulators. Curr Opin Chem Biol 2020; 57:166-176. [PMID: 32823064 DOI: 10.1016/j.cbpa.2020.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/21/2023]
Abstract
Neurons and glia are functionally organized into circuits and higher-order structures that allow the precise information processing required for complex behaviors. To better understand the structure and function of the brain, we must understand synaptic connectivity, action potential generation and propagation, as well as well-orchestrated molecular signaling. Recently, dramatically improved sensors for voltage, intracellular calcium, and neurotransmitters/modulators, combined with advanced microscopy provide new opportunities for in vivo dissection of cellular and circuit activity in awake, behaving animals. This review focuses on the current trends in genetically encoded sensors for molecules and cellular events and their potential applicability to the study of nervous system in health and disease.
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Affiliation(s)
- Akash Pal
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA.
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Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV. Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. Int J Mol Sci 2020; 21:ijms21051644. [PMID: 32121243 PMCID: PMC7084697 DOI: 10.3390/ijms21051644] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 02/25/2020] [Accepted: 02/25/2020] [Indexed: 12/21/2022] Open
Abstract
Green fluorescent genetically encoded calcium indicators (GECIs) are the most popular tool for visualization of calcium dynamics in vivo. However, most of them are based on the EGFP protein and have similar molecular brightnesses. The NTnC indicator, which is composed of the mNeonGreen fluorescent protein with the insertion of troponin C, has higher brightness as compared to EGFP-based GECIs, but shows a limited inverted response with an ΔF/F of 1. By insertion of a calmodulin/M13-peptide pair into the mNeonGreen protein, we developed a green GECI called NCaMP7. In vitro, NCaMP7 showed positive response with an ΔF/F of 27 and high affinity (Kd of 125 nM) to calcium ions. NCaMP7 demonstrated a 1.7-fold higher brightness and similar calcium-association/dissociation dynamics compared to the standard GCaMP6s GECI in vitro. According to fluorescence recovery after photobleaching (FRAP) experiments, the NCaMP7 design partially prevented interactions of NCaMP7 with the intracellular environment. The NCaMP7 crystal structure was obtained at 1.75 Å resolution to uncover the molecular basis of its calcium ions sensitivity. The NCaMP7 indicator retained a high and fast response when expressed in cultured HeLa and neuronal cells. Finally, we successfully utilized the NCaMP7 indicator for in vivo visualization of grating-evoked and place-dependent neuronal activity in the visual cortex and the hippocampus of mice using a two-photon microscope and an NVista miniscope, respectively.
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Affiliation(s)
- Oksana M. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir P. Sotskov
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Viktor V. Plusnin
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna M. Gruzdeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
| | - Natalia V. Barykina
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Olga I. Ivashkina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Konstantin V. Anokhin
- Institute for Advanced Brain Studies, M.V. Lomonosov Moscow State University, Moscow 119991, Russia; (V.P.S.); (K.V.A.)
- P.K. Anokhin Research Institute of Normal Physiology, Moscow 125315, Russia;
| | - Alena Y. Nikolaeva
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Dmitry A. Korzhenevskiy
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Anna V. Vlaskina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Vladimir A. Lazarenko
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
| | - Konstantin M. Boyko
- Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia;
| | - Tatiana V. Rakitina
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
| | - Anna M. Varizhuk
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Galina E. Pozmogova
- Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (A.M.V.); (G.E.P.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Moscow 119435, Russia
| | - Oleg V. Podgorny
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, RAS, Moscow 117997, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
- N.K. Koltzov Institute of Developmental Biology, RAS, Moscow 119334, Russia
| | - Kiryl D. Piatkevich
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
- School of Life Sciences, Westlake University, Hangzhou 310024, China
| | - Edward S. Boyden
- Massachusetts Institute of Technology, Cambridge, MA 02139, USA; (K.D.P.); (E.S.B.)
| | - Fedor V. Subach
- National Research Center “Kurchatov Institute”, Moscow 123182, Russia; (O.M.S.); (V.V.P.); (A.M.G.); (O.I.I.); (A.Y.N.); (D.A.K.); (A.V.V.); (V.A.L.); (T.V.R.)
- Correspondence: ; Tel.: +07-499-196 7100-3389
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Kostyuk AI, Demidovich AD, Kotova DA, Belousov VV, Bilan DS. Circularly Permuted Fluorescent Protein-Based Indicators: History, Principles, and Classification. Int J Mol Sci 2019; 20:E4200. [PMID: 31461959 PMCID: PMC6747460 DOI: 10.3390/ijms20174200] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 12/28/2022] Open
Abstract
Genetically encoded biosensors based on fluorescent proteins (FPs) are a reliable tool for studying the various biological processes in living systems. The circular permutation of single FPs led to the development of an extensive class of biosensors that allow the monitoring of many intracellular events. In circularly permuted FPs (cpFPs), the original N- and C-termini are fused using a peptide linker, while new termini are formed near the chromophore. Such a structure imparts greater mobility to the FP than that of the native variant, allowing greater lability of the spectral characteristics. One of the common principles of creating genetically encoded biosensors is based on the integration of a cpFP into a flexible region of a sensory domain or between two interacting domains, which are selected according to certain characteristics. Conformational rearrangements of the sensory domain associated with ligand interaction or changes in the cellular parameter are transferred to the cpFP, changing the chromophore environment. In this review, we highlight the basic principles of such sensors, the history of their creation, and a complete classification of the available biosensors.
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Affiliation(s)
- Alexander I Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | | | - Daria A Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Vsevolod V Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia.
- Pirogov Russian National Research Medical University, Moscow 117997, Russia.
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