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Subach OM, Piatkevich KD, Subach FV. Development of a genetically encoded NMT indicator for detection of mercury ions based on the green fluorescent protein mNeonGreen and metallothionein II from rat liver. Heliyon 2024; 10:e32814. [PMID: 38975119 PMCID: PMC11225830 DOI: 10.1016/j.heliyon.2024.e32814] [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: 04/14/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/09/2024] Open
Abstract
Heavy metals, particularly mercury, rank as some of the most hazardous systemic toxicants known to cause multiple organ damage, even at lower levels of exposure. Its detection in the environment and in the live cells is an actual task. Here, we engineered a novel genetically encoded fluorescent NMT indicator for mercury ions by inserting the metallothionein II domain from rat liver into the bright green-yellow fluorescent protein mNeonGreen, followed by directed molecular evolution of the resulting sensor prototype in bacteria. In solution, the NMT indicator was 1.7-fold brighter than the standard eGFP fluorescent protein and responded to the addition of even 10-18-10-19 M mercury ions by quenching fluorescence with a 5-fold fluorescence response and extremely high affinity to mercury ions characterized by the K d value of 0.50 ± 0.05 aM. We also characterized the selectivity of the NMT indicator to other metal cations. In cultured mammalian cells, the NMT indicator detected even an extracellular concentration of 0.1 fM mercury ions and achieved a 5.9-fold change in ΔF/F fluorescence intensity.
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Affiliation(s)
- Oksana M. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, 123182, 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
| | - Fedor V. Subach
- Complex of NBICS Technologies, National Research Center “Kurchatov Institute”, Moscow, 123182, Russia
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2
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Irfan, Soleja N, Mohsin M. FRET-based probe for ratiometric detection and imaging of folic acid in real-time. Anal Biochem 2023; 679:115285. [PMID: 37586674 DOI: 10.1016/j.ab.2023.115285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
Inadequate folic acid intake is linked to diseases such as megaloblastic anemia, neural tube defects, and hyperhomocysteinemia, increasing the risk of vascular disease and thrombosis. Folic acid, a cofactor in various enzymes, can be produced by plants and bacteria, but not by humans and other animals. L-5-methyl-tetrahydrofolate (L-5-methyl-THF) is the primary dietary folate form, transported in circulation for cellular metabolism. Traditional methods of determining folic acid levels are unreliable and time-consuming. SenFol (Sensor for folic acid) is a fluorescence resonance energy transfer (FRET)-based nanosensor that we have developed by inserting folic acid-binding protein (FolT) as the folate detecting domain between the pair of enhanced cyan fluorescent protein (ECFP) and Venus. The developed sensor is highly specific, produces a quick signal, which is pH stable, and delivers precise, ratiometric readings in cell-based experiments. The projected affinity score of folic acid with FolT was -7.4 kcal/mol. The apparent affinity (Kd) of SenFol for folic acid is 28.49 × 10-9 M, with a detection range of 5 × 10-9 M to 5 × 10-7 M, and a maximum FRET ratio change of 0.45. WT SenFol, a highly efficient folic acid nanosensor, can dynamically detect intracellular folic acid content in E. coli, yeast, and HEK-293 T cells, confirming its potential.
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Affiliation(s)
- Irfan
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India.
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3
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Torres-Ocampo AP, Palmer AE. Genetically encoded fluorescent sensors for metals in biology. Curr Opin Chem Biol 2023; 74:102284. [PMID: 36917910 PMCID: PMC10573084 DOI: 10.1016/j.cbpa.2023.102284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 03/14/2023]
Abstract
Metal ions intersect a wide range of biological processes. Some metal ions are essential and hence absolutely required for the growth and health of an organism, others are toxic and there is great interest in understanding mechanisms of toxicity. Genetically encoded fluorescent sensors are powerful tools that enable the visualization, quantification, and tracking of dynamics of metal ions in biological systems. Here, we review recent advances in the development of genetically encoded fluorescent sensors for metal ions. We broadly focus on 5 classes of sensors: single fluorescent protein, FRET-based, chemigenetic, DNAzymes, and RNA-based. We highlight recent developments in the past few years and where these developments stand concerning the rest of the field.
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Affiliation(s)
- Ana P Torres-Ocampo
- BioFrontiers Institute, University of Colorado, Boulder, 3415 Colorado Ave, CO, 80303, Boulder, United States
| | - Amy E Palmer
- Department of Biochemistry, University of Colorado, Boulder, 3415 Colorado Ave, CO, 80303, Boulder, United States; BioFrontiers Institute, University of Colorado, Boulder, 3415 Colorado Ave, CO, 80303, Boulder, United States.
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4
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Bano R, Mohsin M, Zeyaullah M, Khan MS. Real-Time Monitoring of Selenium in Living Cells by Fluorescence Resonance Energy Transfer-Based Genetically Encoded Ratiometric Nanosensors. ACS OMEGA 2023; 8:8625-8633. [PMID: 36910985 PMCID: PMC9996594 DOI: 10.1021/acsomega.2c07809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Selenium is a component of selenoproteins, which plays a crucial role in cellular redox homeostasis, thyroid metabolism, and DNA synthesis. Selenium has pleiotropic effects like antioxidant and anti-inflammatory activities; however, excess intake of selenium can imbalance such processes. The effects of selenium on human health are numerous and complex, demanding additional research to monitor the flux rate of selenium. Here, we have created a noninvasive and highly efficient genetically encoded fluorescence resonance energy transfer (FRET)-based nanosensor, SelFS (Selenium FRET-Sensor), for real-time monitoring of selenium at the cellular and subcellular levels. The construct of the nanosensor contains a selenium-binding protein (SeBP) as the selenium-detecting element inserted between the green fluorescent protein variants enhanced cyan fluorescent protein and Venus. In the presence of selenium, SelFS brings a conformational change, which is seen in the form of FRET. In vitro studies showed that SelFS is highly specific and selective for selenium and stable at an altered pH range from 5.0 to 8.0. SelFS is a flexible and dynamic tool for the detection of selenium in both prokaryotes and eukaryotes in a noninvasive way, with a binding constant (K d) of 0.198 × 10-6 M as compared to its mutants. The developed nanosensor can provide us a reporter tool for a wide range of industrial and environmental applications, which will help us to understand its functions in biological systems.
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Affiliation(s)
- Reshma Bano
- Department
of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohd Mohsin
- Department
of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohammad Zeyaullah
- Department
of Basic Medical Science, College of Applied Medical Sciences, King Khalid University, Khamis Mushayt Campus, Abha, Asir 61421, Saudi Arabia
| | - Mohammad Suhail Khan
- Department
of Public Health, College of Applied Medical Sciences, King Khalid University, Khamis Mushayt Campus, Abha, Asir 61421, Saudi Arabia
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5
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Designing of nanosensor and its applications for spatiotemporal visualization and real time quantification of biotin in biological samples. Biochem Eng J 2023. [DOI: 10.1016/j.bej.2023.108899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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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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7
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Soni GK, Wangoo N, Cokca C, Peneva K, Sharma RK. Ultrasensitive aptasensor for arsenic detection using quantum dots and guanylated Poly(methacrylamide). Anal Chim Acta 2022; 1209:339854. [DOI: 10.1016/j.aca.2022.339854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/04/2022] [Accepted: 04/16/2022] [Indexed: 11/16/2022]
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8
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Sargazi S, Fatima I, Hassan Kiani M, Mohammadzadeh V, Arshad R, Bilal M, Rahdar A, Díez-Pascual AM, Behzadmehr R. Fluorescent-based nanosensors for selective detection of a wide range of biological macromolecules: A comprehensive review. Int J Biol Macromol 2022; 206:115-147. [PMID: 35231532 DOI: 10.1016/j.ijbiomac.2022.02.137] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/01/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
Abstract
Thanks to their unique attributes, such as good sensitivity, selectivity, high surface-to-volume ratio, and versatile optical and electronic properties, fluorescent-based bioprobes have been used to create highly sensitive nanobiosensors to detect various biological and chemical agents. These sensors are superior to other analytical instrumentation techniques like gas chromatography, high-performance liquid chromatography, and capillary electrophoresis for being biodegradable, eco-friendly, and more economical, operational, and cost-effective. Moreover, several reports have also highlighted their application in the early detection of biomarkers associated with drug-induced organ damage such as liver, kidney, or lungs. In the present work, we comprehensively overviewed the electrochemical sensors that employ nanomaterials (nanoparticles/colloids or quantum dots, carbon dots, or nanoscaled metal-organic frameworks, etc.) to detect a variety of biological macromolecules based on fluorescent emission spectra. In addition, the most important mechanisms and methods to sense amino acids, protein, peptides, enzymes, carbohydrates, neurotransmitters, nucleic acids, vitamins, ions, metals, and electrolytes, blood gases, drugs (i.e., anti-inflammatory agents and antibiotics), toxins, alkaloids, antioxidants, cancer biomarkers, urinary metabolites (i.e., urea, uric acid, and creatinine), and pathogenic microorganisms were outlined and compared in terms of their selectivity and sensitivity. Altogether, the small dimensions and capability of these nanosensors for sensitive, label-free, real-time sensing of chemical, biological, and pharmaceutical agents could be used in array-based screening and in-vitro or in-vivo diagnostics. Although fluorescent nanoprobes are widely applied in determining biological macromolecules, unfortunately, they present many challenges and limitations. Efforts must be made to minimize such limitations in utilizing such nanobiosensors with an emphasis on their commercial developments. We believe that the current review can foster the wider incorporation of nanomedicine and will be of particular interest to researchers working on fluorescence technology, material chemistry, coordination polymers, and related research areas.
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Affiliation(s)
- Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, 98167-43463 Zahedan, Iran
| | - Iqra Fatima
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Maria Hassan Kiani
- Department of Pharmacy, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Vahideh Mohammadzadeh
- Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Science, Mashhad 1313199137, Iran
| | - Rabia Arshad
- Faculty of Pharmacy, University of Lahore, Lahore 45320, Pakistan
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, P. O. Box. 98613-35856, Iran.
| | - Ana M Díez-Pascual
- Universidad de Alcalá, Facultad de Ciencias, Departamento de Química Analítica, Química Física e Ingeniería Química, Ctra. Madrid-Barcelona, Km. 33.6, 28805 Alcalá de Henares, Madrid, Spain.
| | - Razieh Behzadmehr
- Department of Radiology, Zabol University of Medical Sciences, Zabol, Iran
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Wu SY, Shen Y, Shkolnikov I, Campbell RE. Fluorescent Indicators For Biological Imaging of Monatomic Ions. Front Cell Dev Biol 2022; 10:885440. [PMID: 35573682 PMCID: PMC9093666 DOI: 10.3389/fcell.2022.885440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/04/2022] [Indexed: 11/13/2022] Open
Abstract
Monatomic ions play critical biological roles including maintaining the cellular osmotic pressure, transmitting signals, and catalyzing redox reactions as cofactors in enzymes. The ability to visualize monatomic ion concentration, and dynamic changes in the concentration, is essential to understanding their many biological functions. A growing number of genetically encodable and synthetic indicators enable the visualization and detection of monatomic ions in biological systems. With this review, we aim to provide a survey of the current landscape of reported indicators. We hope this review will be a useful guide to researchers who are interested in using indicators for biological applications and to tool developers seeking opportunities to create new and improved indicators.
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Affiliation(s)
- Sheng-Yi Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Yi Shen
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - Irene Shkolnikov
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Robert E. Campbell
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Chemistry, The University of Tokyo, Tokyo, Japan
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10
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Nazir R, Mohsin M, Siddiqi TO. Real time optical detection of gold in living cells through genetically-encoded probe. RSC Adv 2022; 12:23193-23203. [PMID: 36090423 PMCID: PMC9380193 DOI: 10.1039/d2ra02574d] [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: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022] Open
Abstract
To study the efflux of gold (Au) in living cells, a genetically encoded fluorescence resonance energy transfer (FRET)-based sensor has been developed. The gold-sensing domain GolB from Salmonella typhimurium has been fused to the N- and C-termini of the FRET pair enhanced cyan fluorescent protein (ECFP) and Venus respectively. In living cells, this probe is highly selective and sensitive to gold and it can withstand changes in variable pH ranges. GolSeN-25, the most efficient sensor variant, binds gold with an affinity (Kd) of 0.3 × 10−6 M, covering gold concentrations of nM to μM, and can be used for non-invasive real-time in vivo gold measurement in living cells. A simple and sensitive FRET probe was designed for the detection of gold with high selectivity and can be applied to the analysis of real samples. To study the efflux of gold (Au) in living cells, a genetically encoded fluorescence resonance energy transfer (FRET)-based sensor has been developed.![]()
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Affiliation(s)
- Rahila Nazir
- Metabolic Engineering Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Mohd Mohsin
- Metabolic Engineering Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi 110025, India
| | - Tariq Omar Siddiqi
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
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11
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Design and Prototyping of Genetically Encoded Arsenic Biosensors Based on Transcriptional Regulator AfArsR. Biomolecules 2021; 11:biom11091276. [PMID: 34572489 PMCID: PMC8470949 DOI: 10.3390/biom11091276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 12/12/2022] Open
Abstract
Genetically encoded biosensors based on engineered fluorescent proteins (FPs) are essential tools for monitoring the dynamics of specific ions and molecules in biological systems. Arsenic ion in the +3 oxidation state (As3+) is highly toxic to cells due to its ability to bind to protein thiol groups, leading to inhibition of protein function, disruption of protein–protein interactions, and eventually to cell death. A genetically encoded biosensor for the detection of As3+ could potentially facilitate the investigation of such toxicity both in vitro and in vivo. Here, we designed and developed two prototype genetically encoded arsenic biosensors (GEARs), based on a bacterial As3+ responsive transcriptional factor AfArsR from Acidithiobacillus ferrooxidans. We constructed FRET-based GEAR biosensors by insertion of AfArsR between FP acceptor/donor FRET pairs. We further designed and engineered single FP-based GEAR biosensors by insertion of AfArsR into GFP. These constructs represent prototypes for a new family of biosensors based on the ArsR transcriptional factor scaffold. Further improvements of the GEAR biosensor family could lead to variants with suitable performance for detection of As3+ in various biological and environmental systems.
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Agrawal N, Soleja N, Bano R, Nazir R, Siddiqi TO, Mohsin M. FRET-Based Genetically Encoded Sensor to Monitor Silver Ions. ACS OMEGA 2021; 6:14164-14173. [PMID: 34124439 PMCID: PMC8190795 DOI: 10.1021/acsomega.1c00741] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Silver is commonly used in wound dressing, photography, health care products, laboratories, pharmacy, biomedical devices, and several industrial purposes. Silver (Ag+) ions are more toxic pollutants widely scattered in the open environment by natural processes and dispersed in soil, air, and water bodies. Ag+ binds with metallothionein, macroglobulins, and albumins, which may lead to the alteration of various enzymatic metabolic pathways. To analyze the uptake and metabolism of silver ions in vitro as well as in cells, a range of high-affinity fluorescence-based nanosensors has been constructed using a periplasmic protein CusF, a part of the CusCFBA efflux complex, which is involved in providing resistance against copper and silver ions in Escherichia coli. This nanosensor was constructed by combining of two fluorescent proteins (donor and acceptor) at the N- and C-terminus of the silver-binding protein (CusF), respectively. SenSil (WT) with a binding constant (K d) of 5.171 μM was more efficient than its mutant variants (H36D and F71W). This nanosensor allows monitoring the level of silver ions in real time in prokaryotes and eukaryotes without any disruption of cells or tissues.
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Affiliation(s)
- Neha Agrawal
- Department
of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Neha Soleja
- Department
of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Reshma Bano
- Department
of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rahila Nazir
- Department
of Botany, Jamia Hamdard, New Delhi 110062, India
| | | | - Mohd Mohsin
- Department
of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
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14
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Soleja N, Irfan, Mohsin M. Ratiometric imaging of flux dynamics of cobalt with an optical sensor. J Photochem Photobiol A Chem 2020. [DOI: 10.1016/j.jphotochem.2020.112699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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