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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Voronina MV, Frolova AS, Kolesova EP, Kuldyushev NA, Parodi A, Zamyatnin AA. The Intricate Balance between Life and Death: ROS, Cathepsins, and Their Interplay in Cell Death and Autophagy. Int J Mol Sci 2024; 25:4087. [PMID: 38612897 PMCID: PMC11012956 DOI: 10.3390/ijms25074087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024] Open
Abstract
Cellular survival hinges on a delicate balance between accumulating damages and repair mechanisms. In this intricate equilibrium, oxidants, currently considered physiological molecules, can compromise vital cellular components, ultimately triggering cell death. On the other hand, cells possess countermeasures, such as autophagy, which degrades and recycles damaged molecules and organelles, restoring homeostasis. Lysosomes and their enzymatic arsenal, including cathepsins, play critical roles in this balance, influencing the cell's fate toward either apoptosis and other mechanisms of regulated cell death or autophagy. However, the interplay between reactive oxygen species (ROS) and cathepsins in these life-or-death pathways transcends a simple cause-and-effect relationship. These elements directly and indirectly influence each other's activities, creating a complex web of interactions. This review delves into the inner workings of regulated cell death and autophagy, highlighting the pivotal role of ROS and cathepsins in these pathways and their intricate interplay.
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Affiliation(s)
- Maya V. Voronina
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia; (M.V.V.); (A.S.F.); (E.P.K.); (N.A.K.); (A.P.)
| | - Anastasia S. Frolova
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia; (M.V.V.); (A.S.F.); (E.P.K.); (N.A.K.); (A.P.)
- Institute of Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Ekaterina P. Kolesova
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia; (M.V.V.); (A.S.F.); (E.P.K.); (N.A.K.); (A.P.)
| | - Nikita A. Kuldyushev
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia; (M.V.V.); (A.S.F.); (E.P.K.); (N.A.K.); (A.P.)
| | - Alessandro Parodi
- Research Center for Translational Medicine, Sirius University of Science and Technology, 354340 Sochi, Russia; (M.V.V.); (A.S.F.); (E.P.K.); (N.A.K.); (A.P.)
| | - Andrey A. Zamyatnin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
- Department of Biological Chemistry, Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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Zhang X, Xiao W, Xie S, Fan G, Shi X, Meng H, Yang H. Low-density Pt nanoarray-based hydrogen peroxide sensing platform and its application in trace sarcosine detection. Electrochim Acta 2023. [DOI: 10.1016/j.electacta.2023.141952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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Yoo HJ, Choi DW, Roh YJ, Lee YM, Lim JH, Eo S, Lee HJ, Kim NY, Kim S, Cho S, Im G, Lee BC, Kim JH. MsrB1-regulated GAPDH oxidation plays programmatic roles in shaping metabolic and inflammatory signatures during macrophage activation. Cell Rep 2022; 41:111598. [DOI: 10.1016/j.celrep.2022.111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/02/2022] [Accepted: 10/13/2022] [Indexed: 11/09/2022] Open
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Tarrago L, Kaya A, Kim HY, Manta B, Lee BC, Gladyshev VN. The selenoprotein methionine sulfoxide reductase B1 (MSRB1). Free Radic Biol Med 2022; 191:228-240. [PMID: 36084791 DOI: 10.1016/j.freeradbiomed.2022.08.043] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/11/2022] [Accepted: 08/31/2022] [Indexed: 11/24/2022]
Abstract
Methionine (Met) can be oxidized to methionine sulfoxide (MetO), which exist as R- and S-diastereomers. Present in all three domains of life, methionine sulfoxide reductases (MSR) are the enzymes that reduce MetO back to Met. Most characterized among them are MSRA and MSRB, which are strictly stereospecific for the S- and R-diastereomers of MetO, respectively. While the majority of MSRs use a catalytic Cys to reduce their substrates, some employ selenocysteine. This is the case of mammalian MSRB1, which was initially discovered as selenoprotein SELR or SELX and later was found to exhibit an MSRB activity. Genomic analyses demonstrated its occurrence in most animal lineages, and biochemical and structural analyses uncovered its catalytic mechanism. The use of transgenic mice and mammalian cell culture revealed its physiological importance in the protection against oxidative stress, maintenance of neuronal cells, cognition, cancer cell proliferation, and the immune response. Coincident with the discovery of Met oxidizing MICAL enzymes, recent findings of MSRB1 regulating the innate immunity response through reversible stereospecific Met-R-oxidation of cytoskeletal actin opened up new avenues for biological importance of MSRB1 and its role in disease. In this review, we discuss the current state of research on MSRB1, compare it with other animal Msrs, and offer a perspective on further understanding of biological functions of this selenoprotein.
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Affiliation(s)
- Lionel Tarrago
- UMR 1163, Biodiversité et Biotechnologie Fongiques, INRAE, Aix-Marseille Université, 13009, Marseille, France.
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Bruno Manta
- Laboratorio de Genomica Microbiana, Institut Pasteur de Montevideo, Mataojo 2020, 11440, Montevideo, Uruguay; Catedra de Fisiopatología, Facultad de Odontología, Universidad de la República, Las Heras 1925, 11600, Montevideo, Uruguay
| | - Byung-Cheon Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, 02115, USA.
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Kuldyushev N, Schönherr R, Coburger I, Ahmed M, Hussein RA, Wiesel E, Godbole A, Pfirrmann T, Hoshi T, Heinemann SH. A GFP-based ratiometric sensor for cellular methionine oxidation. Talanta 2022; 243:123332. [PMID: 35276500 DOI: 10.1016/j.talanta.2022.123332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/17/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022]
Abstract
Methionine oxidation is a reversible post-translational protein modification, affecting protein function, and implicated in aging and degenerative diseases. The detection of accumulating methionine oxidation in living cells or organisms, however, has not been achieved. Here we introduce a genetically encoded probe for methionine oxidation (GEPMO), based on the super-folder green fluorescent protein (sfGFP), as a specific, versatile, and integrating sensor for methionine oxidation. Placed at amino-acid position 147 in an otherwise methionine-less sfGFP, the oxidation of this specific methionine to methionine sulfoxide results in a ratiometric fluorescence change when excited with ∼400 and ∼470 nm light. The strength and homogeneity of the sensor expression is suited for live-cell imaging as well as fluorescence-activated cell sorting (FACS) experiments using standard laser wavelengths (405/488 nm). Expressed in mammalian cells and also in S. cerevisiae, the sensor protein faithfully reports on the status of methionine oxidation in an integrating manner. Variants targeted to membranes and the mitochondria provide subcellular resolution of methionine oxidation, e.g. reporting on site-specific oxidation by illumination of endogenous protoporphyrin IX.
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Affiliation(s)
- Nikita Kuldyushev
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Roland Schönherr
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Ina Coburger
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Marwa Ahmed
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Rama A Hussein
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Eric Wiesel
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Amod Godbole
- Center for Molecular Biomedicine, Institute for Molecular Cell Biology, Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany
| | - Thorsten Pfirrmann
- Institute for Physiological Chemistry, Martin Luther University Halle-Wittenberg, Hollystr. 1, 06144, Halle/Saale, Germany; Department of Medicine, Health and Medical University, Olympischer Weg 1, 14471 Potsdam, Germany
| | - Toshinori Hoshi
- Department of Physiology, University of Pennsylvania, Philadelphia, PA, 19104-6085, USA
| | - Stefan H Heinemann
- Center for Molecular Biomedicine, Department of Biophysics, Friedrich Schiller University Jena and Jena University Hospital, Hans-Knöll-Str. 2, 07745, Jena, Germany.
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Lee HM, Choi DW, Kim S, Lee A, Kim M, Roh YJ, Jo YH, Cho HY, Lee HJ, Lee SR, Tarrago L, Gladyshev VN, Kim JH, Lee BC. Biosensor-Linked Immunosorbent Assay for the Quantification of Methionine Oxidation in Target Proteins. ACS Sens 2022; 7:131-141. [PMID: 34936330 DOI: 10.1021/acssensors.1c01819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Methionine oxidation is involved in regulating the protein activity and often leads to protein malfunction. However, tools for quantitative analyses of protein-specific methionine oxidation are currently unavailable. In this work, we developed a biological sensor that quantifies oxidized methionine in the form of methionine-R-sulfoxide in target proteins. The biosensor "tpMetROG" consists of methionine sulfoxide reductase B (MsrB), circularly permuted yellow fluorescent protein (cpYFP), thioredoxin, and protein G. Protein G binds to the constant region of antibodies against target proteins, specifically capturing them. Then, MsrB reduces the oxidized methionine in these proteins, leading to cpYFP fluorescence changes. We assessed this biosensor for quantitative analysis of methionine-R-sulfoxide in various proteins, such as calmodulin, IDLO, LegP, Sacde, and actin. We further developed an immunosorbent assay using the biosensor to quantify methionine oxidation in specific proteins such as calmodulin in animal tissues. The biosensor-linked immunosorbent assay proves to be an indispensable tool for detecting methionine oxidation in a protein-specific manner. This is a versatile tool for studying the redox biology of methionine oxidation in proteins.
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Affiliation(s)
- Hae Min Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Dong Wook Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Seahyun Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Aro Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Minseo Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Yeon Jin Roh
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Young Ho Jo
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Hwa Yeon Cho
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Ho-Jae Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Seung-Rock Lee
- Department of Biochemistry, Research Center for Aging and Geriatrics, Chonnam National University Medical School, Gwangju 61186, Republic of Korea
| | - Lionel Tarrago
- INRAE, Aix Marseille University, BBF, Marseille F13108, France
| | - Vadim N. Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Ji Hyung Kim
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Byung Cheon Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 02841, Republic of Korea
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