1
|
Pedre B. A guide to genetically-encoded redox biosensors: state of the art and opportunities. Arch Biochem Biophys 2024:110067. [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] [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.
Collapse
Affiliation(s)
- Brandán Pedre
- Biochemistry, Molecular and Structural Biology Unit, Department of Chemistry, KU Leuven, Belgium.
| |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Fernández-Puente E, Martín-Prieto E, Márquez CM, Palomero J. Effect of RONS-Induced Intracellular Redox Homeostasis in 6-NBDG/Glucose Uptake in C2C12 Myotubes and Single Isolated Skeletal Muscle Fibres. Int J Mol Sci 2023; 24:ijms24098082. [PMID: 37175789 PMCID: PMC10179233 DOI: 10.3390/ijms24098082] [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: 03/20/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
The glucose uptake in skeletal muscle is essential to produce energy through ATP, which is needed by this organ to maintain vital functions. The impairment of glucose uptake compromises the metabolism and function of skeletal muscle and other organs and is a feature of diabetes, obesity, and ageing. There is a need for research to uncover the mechanisms involved in the impairment of glucose uptake in skeletal muscle. In this study, we adapted, developed, optimised, and validated a methodology based on the fluorescence glucose analogue 6-NBDG, combined with a quantitative fluorescence microscopy image analysis, to determine the glucose uptake in two models of skeletal muscle cells: C2C12 myotubes and single fibres isolated from muscle. It was proposed that reactive oxygen and nitrogen species (RONS) and redox homeostasis play an important role in the modulation of intracellular redox signalling pathways associated with glucose uptake. In this study, we prove that the prooxidative intracellular redox environment under oxidative eustress produced by RONS such as hydrogen peroxide and nitric oxide improves glucose uptake in skeletal muscle cells. However, when oxidation is excessive, oxidative distress occurs, and cellular viability is compromised, although there might be an increase in the glucose uptake. Based on the results of this study, the determination of 6-NBDG/glucose uptake in myotubes and skeletal muscle cells is feasible, validated, and will contribute to improve future research.
Collapse
Affiliation(s)
- Escarlata Fernández-Puente
- Department of Physiology and Pharmacology, University of Salamanca, 37007 Salamanca, Spain
- Institute of Neurosciences of Castilla y León (INCyL), 37007 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
| | - Eva Martín-Prieto
- Department of Physiology and Pharmacology, University of Salamanca, 37007 Salamanca, Spain
- Institute of Neurosciences of Castilla y León (INCyL), 37007 Salamanca, Spain
| | - Carlos Manuel Márquez
- Department of Physiology and Pharmacology, University of Salamanca, 37007 Salamanca, Spain
| | - Jesús Palomero
- Department of Physiology and Pharmacology, University of Salamanca, 37007 Salamanca, Spain
- Institute of Neurosciences of Castilla y León (INCyL), 37007 Salamanca, Spain
- Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain
| |
Collapse
|
4
|
Fu N, Sugiura K, Kondo K, Nakamura S, Wakabayashi KI, Hisabori T. Monitoring cellular redox dynamics using newly developed BRET-based redox sensor proteins. J Biol Chem 2021; 297:101186. [PMID: 34517006 PMCID: PMC8487062 DOI: 10.1016/j.jbc.2021.101186] [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: 05/04/2021] [Revised: 08/30/2021] [Accepted: 09/07/2021] [Indexed: 11/06/2022] Open
Abstract
Reactive oxygen species are key factors that strongly affect the cellular redox state and regulate various physiological and cellular phenomena. To monitor changes in the redox state, we previously developed fluorescent redox sensors named Re-Q, the emissions of which are quenched under reduced conditions. However, such fluorescent probes are unsuitable for use in the cells of photosynthetic organisms because they require photoexcitation that may change intracellular conditions and induce autofluorescence, primarily in chlorophylls. In addition, the presence of various chromophore pigments may interfere with fluorescence-based measurements because of their strong absorbance. To overcome these problems, we adopted the bioluminescence resonance energy transfer (BRET) mechanism for the sensor and developed two BRET-based redox sensors by fusing cyan fluorescent protein–based or yellow fluorescent protein–based Re-Q with the luminescent protein Nluc. We named the resulting redox-sensitive BRET-based indicator probes “ROBINc” and “ROBINy.” ROBINc is pH insensitive, which is especially vital for observation in photosynthetic organisms. By using these sensors, we successfully observed dynamic redox changes caused by an anticancer agent in HeLa cells and light/dark-dependent redox changes in the cells of photosynthetic cyanobacterium Synechocystis sp. PCC 6803. Since the newly developed sensors do not require excitation light, they should be especially useful for visualizing intracellular phenomena caused by redox changes in cells containing colored pigments.
Collapse
Affiliation(s)
- Nae Fu
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kazunori Sugiura
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Kumiko Kondo
- Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Shungo Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Ken-Ichi Wakabayashi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama, Japan
| | - Toru Hisabori
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan; Laboratory for Chemistry and Life Science, Tokyo Institute of Technology, Yokohama, Japan.
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Real-time monitoring of the in vivo redox state transition using the ratiometric redox state sensor protein FROG/B. Proc Natl Acad Sci U S A 2020; 117:16019-16026. [PMID: 32576684 DOI: 10.1073/pnas.1918919117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The intracellular redox state is one of the key factors regulating various physiological phenomena in the cell. Monitoring this state is therefore important for understanding physiological homeostasis in cells. Various fluorescent sensor proteins have already been developed to monitor intracellular redox state. We also developed fluorescent redox sensor proteins named Oba-Q and Re-Q, the emissions of which are quenched under oxidized and reduced conditions, respectively. Although these sensors were useful to visualize the redox changes in the cell over time, they have the weakness that their emission signals are directly influenced by their in situ expression levels. To overcome this problem, we developed a redox sensor protein with a single excitation peak and dual variable emission peaks. This sensor protein shows green emission under oxidized conditions and blue emission under reduced conditions. We therefore named this sensor FROG/B, fluorescent protein with redox-dependent change in green/blue. By using this sensor, we successfully measured the changes in intracellular redox potentials in cyanobacterial cells quantitatively caused by light/dark transition just by calculating the ratio of emission between green and blue signals.
Collapse
|
7
|
Sugiura K, Yokochi Y, Fu N, Fukaya Y, Yoshida K, Mihara S, Hisabori T. The thioredoxin (Trx) redox state sensor protein can visualize Trx activities in the light/dark response in chloroplasts. J Biol Chem 2019; 294:12091-12098. [PMID: 31217277 DOI: 10.1074/jbc.ra119.007616] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 06/10/2019] [Indexed: 11/06/2022] Open
Abstract
Thiol-based redox regulation via ferredoxin-thioredoxin (Trx) reductase/Trx controls various functions in chloroplasts in response to light/dark changes. Trx is a key factor of this regulatory system, and five Trx subtypes, including 10 isoforms, have been identified as chloroplast-localized forms in Arabidopsis thaliana These subtypes display distinct target selectivity, and, consequently, they form a complicated redox regulation network in chloroplasts. In this study, we developed a FRET-based sensor protein by combining CFP, YFP, and the N-terminal region of CP12, a redox-sensitive regulatory and Trx-targeted protein in chloroplasts. This sensor protein enabled us to monitor the redox change of chloroplast thioredoxin in vivo, and we therefore designated this protein "change in redox state of Trx" (CROST). Using CP12 isoforms, we successfully prepared two types of CROST sensors that displayed different affinities for two major chloroplast Trx isoforms (f-type and m-type). These sensor proteins helped unravel the real-time redox dynamics of Trx molecules in chloroplasts during the light/dark transition.
Collapse
Affiliation(s)
- Kazunori Sugiura
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan
| | - Yuichi Yokochi
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan
| | - Nae Fu
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan
| | - Yuki Fukaya
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan
| | - Keisuke Yoshida
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan
| | - Shoko Mihara
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan
| | - Toru Hisabori
- Laboratory for Chemistry and Life Science, Institute of Innovative Science, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan; School of Life Science and Technology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8503, Japan.
| |
Collapse
|