51
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Sheng C, Zhao J, Yu F, Li L. Enzyme Translocation-Mediated Signal Amplification for Spatially Selective Aptasensing of ATP in Inflammatory Cells. Angew Chem Int Ed Engl 2023; 62:e202217551. [PMID: 36750407 DOI: 10.1002/anie.202217551] [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: 11/29/2022] [Revised: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 02/09/2023]
Abstract
Amplified ATP imaging in inflammatory cells is highly desirable. However, the spatial selectivity of current amplification methods is limited, that is, signal amplification is performed systemically and not in a disease site-specific manner. Here we present a versatile strategy, termed enzymatically triggerable, aptamer-based signal amplification (ETA-SA), that enables inflammatory cell-specific imaging of ATP through spatially-resolved signal amplification. The ETA-SA leverages a translocated enzyme in inflammatory cells to activate DNA aptamer probes and further drive cascade reactions through the consumption of hairpin fuels, which, however, exerts no ATP response activity in normal cells, leading to a significantly improved sensitivity and spatial specificity for the inflammation-specific ATP imaging in vivo. Benefiting from the improved spatial selectivity, enhanced signal-to-background ratios were achieved for ATP imaging during acute hepatitis.
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Affiliation(s)
- Chuangui Sheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fangzhi Yu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lele Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
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52
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Complete Genome Sequences of Bioluminescent Staphylococcus aureus Strains Xen31 and Xen36, Derived from Two Clinical Isolates. Microbiol Resour Announc 2023; 12:e0002423. [PMID: 36840571 PMCID: PMC10019319 DOI: 10.1128/mra.00024-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Here, we report complete genome sequences of two clinical isolates of Staphylococcus aureus, namely, Xen31 and Xen36, which have been genetically modified to express an optimized Photorhabdus luminescens luciferase operon. Xen31 and Xen36 are bioluminescent strains used widely for investigation of bacterial pathogenesis, drug discovery, and development of novel therapies.
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53
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Jiang T, Song J, Zhang Y. Coelenterazine-Type Bioluminescence-Induced Optical Probes for Sensing and Controlling Biological Processes. Int J Mol Sci 2023; 24:ijms24065074. [PMID: 36982148 PMCID: PMC10049153 DOI: 10.3390/ijms24065074] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Bioluminescence-based probes have long been used to quantify and visualize biological processes in vitro and in vivo. Over the past years, we have witnessed the trend of bioluminescence-driven optogenetic systems. Typically, bioluminescence emitted from coelenterazine-type luciferin–luciferase reactions activate light-sensitive proteins, which induce downstream events. The development of coelenterazine-type bioluminescence-induced photosensory domain-based probes has been applied in the imaging, sensing, and control of cellular activities, signaling pathways, and synthetic genetic circuits in vitro and in vivo. This strategy can not only shed light on the mechanisms of diseases, but also promote interrelated therapy development. Here, this review provides an overview of these optical probes for sensing and controlling biological processes, highlights their applications and optimizations, and discusses the possible future directions.
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Affiliation(s)
- Tianyu Jiang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Shenzhen Research Institute of Shandong University, Shenzhen 518000, China
- Correspondence: (T.J.); (Y.Z.)
| | - Jingwen Song
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- School of Life Sciences, Shandong University, Qingdao 266237, China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Correspondence: (T.J.); (Y.Z.)
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54
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Morozova EP, Smoliarova TE, Lukyanenko KA, Kirillova MA, Volochaev MN, Kichkailo AS, Ranjan R, Kratasyuk VA. Metal-enhanced bioluminescence by detergent stabilized Ag and Au nanoparticles. Talanta 2023; 254:124157. [PMID: 36470014 DOI: 10.1016/j.talanta.2022.124157] [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: 08/16/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
The assessment of microbial contamination is an important aspect of ensuring human food safety. One of the modern methods for the evaluation of microbial contamination is the estimation of the amount of ATP using firefly luciferase. In this case, the choice of an effective composition of the extraction buffer is crucial. In this study, we examined the influence of silver and gold nanoparticles on the firefly bioluminescent system during the ATP extraction process. It was found that gold nanoparticles stabilized with benzalkonium chloride and Triton X-100 enhanced bioluminescent system signal intensity due to metal-enhanced bioluminescence. Moreover, silver and gold nanoparticles could be used as extracting agents. So, using gold nanoparticles stabilized with BAC and Triton X-100 as ATP extraction agents with further detection by a bioluminescent system makes it possible to develop an ATP biosensor with higher sensitivity.
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Affiliation(s)
- Elizaveta P Morozova
- Siberian Federal University, Krasnoyarsk 660041, Russia; Federal Research Center KSC SB RAS, Krasnoyarsk 660036, Russia; Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia
| | | | - Kirill A Lukyanenko
- Siberian Federal University, Krasnoyarsk 660041, Russia; Federal Research Center KSC SB RAS, Krasnoyarsk 660036, Russia; Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia
| | | | | | - Anna S Kichkailo
- Federal Research Center KSC SB RAS, Krasnoyarsk 660036, Russia; Krasnoyarsk State Medical University, Krasnoyarsk, 660022, Russia
| | - Rajeev Ranjan
- Siberian Federal University, Krasnoyarsk 660041, Russia
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55
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Li Y, Li H, Gao J, Niu B, Wang H, Wang W. Visualizing the Intermittent Gating of Na + /H + Antiporters in Single Native Bioluminescent Bacteria. Angew Chem Int Ed Engl 2023; 62:e202215800. [PMID: 36562656 DOI: 10.1002/anie.202215800] [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: 10/27/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/24/2022]
Abstract
While the intermittent gating of ion channels has been well studied for decades, dynamics of the action of secondary transporters, another major pathway for ion transmembrane transports, remains largely unexplored in living cells. Herein, intermittent blinking of the spontaneous bioluminescence (BL) from single native bacteria, P. phosphoreum, was reported, investigated and attributed to the intermittent gating of sodium/proton antiporters (NhaA) between the active and inactive conformations. Each gating event caused the rapid depolarization and recovery of membrane potential within several seconds, accompanying with the apparent BL blinking due to the transient inhibitions on the activity of the respiratory chain. Temperature-dependent measurements further obtained an activation energy barrier of the conformational change of 20.3 kJ mol-1 .
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Affiliation(s)
- Yaohua Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Haoran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Ben Niu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Huan Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, ChemBIC (Chemistry and Biomedicine Innovation Center), Nanjing University, Nanjing, 210023, China
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Cerezo J, García-Iriepa C, Santoro F, Navizet I, Prampolini G. Unraveling the contributions to the spectral shape of flexible dyes in solution: insights on the absorption spectrum of an oxyluciferin analogue. Phys Chem Chem Phys 2023; 25:5007-5020. [PMID: 36722876 DOI: 10.1039/d2cp05701h] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We present a computational investigation of the absorption spectrum in water of 5,5-spirocyclopropyl-oxyluciferin (5,5-CprOxyLH), an analogue of the emitter compound responsible for the bioluminescence in fireflies. Several factors participate in determining the 5,5-CprOxyLH's spectral shape: (i) the contribution of the four close-energy excited states, which show significant non-adiabatic couplings, (ii) the flexible molecular structure and (iii) the specific interactions established with the surrounding environment, which strongly couple the protic solvent dynamics with the dye's spectral response. To tackle the challenge to capture and dissect the role of all these effects we preliminarily investigate the role of non-adiabatic couplings with quantum dynamics simulations and a linear vibronic coupling model in the gas phase. Then, we account for both the molecular flexibility and solvent interactions by resorting to a mixed quantum classical protocol, named Adiabatic Molecular Dynamics generalized Vertical Gradient (Ad-MD|gVG), which is built on a method recently proposed by some of us. It is rooted in the partition between stiff degrees of freedom of the dye, accounted for at the vibronic level within the harmonic approximation, and flexible degrees of freedom of the solute (and of the solvent), described classically through a sampling based on Molecular Dynamics (MD). Ad-MD|gVG avoids spurious effects arising in the excited state Hessians due to non-adiabatic couplings, and can therefore be applied to account for the contributions of the first four excited states to the 5,5-CprOxyLH absorption spectrum. The final simulated spectrum is in very good agreement with the experiment, especially when the MD is driven by a refined quantum-mechanically derived force-field. More importantly, the origin of each separate contribution to the spectral shape is appropriately accounted for, paving the way to future applications of the method to more complex systems or alternative spectroscopies, as emission or circular dichroism.
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Affiliation(s)
- Javier Cerezo
- Departamento de Química and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain. .,CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Cristina García-Iriepa
- Universidad de Alcalá, Departamento de Química Analítica, Química Física e Ingeniería Química, Grupo de Reactividad y Estructura Molecular (RESMOL), 28806 Alcalá de Henares (Madrid), Spain. .,Universidad de Alcalá, Instituto de Investigación Química "Andrés M. del Río" (IQAR), 28806 Alcalá de Henares (Madrid), Spain
| | - Fabrizio Santoro
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - Isabelle Navizet
- Univ Gustave Eiffel, Univ Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
| | - Giacomo Prampolini
- CNR - Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
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Niwa K, Kubota H, Enomoto T, Ichino Y, Ohmiya Y. Quantitative Analysis of Bioluminescence Optical Signal. BIOSENSORS 2023; 13:223. [PMID: 36831989 PMCID: PMC9953788 DOI: 10.3390/bios13020223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Bioluminescence is light emission based on the luciferin-luciferase enzymatic reaction in living organisms. Optical signals from bioluminescence (BL) reactions are available for bioanalysis and bioreporters for gene expression, in vitro, in vivo, and ex vivo bioimaging, immunoassay, and other applications. Although there are numerous bioanalysis methods based on BL signal measurements, the BL signal is measured as a relative value, and not as an absolute value. Recently, some approaches have been established to completely quantify the BL signal, resulting in, for instance, the redetermination of the quantum yield of the BL reaction and counting the photon number of the BL signal at the single-cell level. Reliable and reproducible understanding of biological events in the bioanalysis and bioreporter fields can be achieved by means of standardized absolute optical signal measurements, which is described in an International Organization for Standardization (ISO) document.
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Affiliation(s)
- Kazuki Niwa
- National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8563, Japan
| | | | | | - Yoshiro Ichino
- National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8563, Japan
| | - Yoshihiro Ohmiya
- National Institute of Advanced Industrial Science & Technology (AIST), Tsukuba 305-8563, Japan
- Osaka Institute of Technology (OIT), Osaka 535-8585, Japan
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58
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Shi X, Won M, Tang C, Ding Q, Sharma A, Wang F, Kim JS. RNA splicing based on reporter genes system: Detection, imaging and applications. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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59
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Yeh AHW, Norn C, Kipnis Y, Tischer D, Pellock SJ, Evans D, Ma P, Lee GR, Zhang JZ, Anishchenko I, Coventry B, Cao L, Dauparas J, Halabiya S, DeWitt M, Carter L, Houk KN, Baker D. De novo design of luciferases using deep learning. Nature 2023; 614:774-780. [PMID: 36813896 PMCID: PMC9946828 DOI: 10.1038/s41586-023-05696-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 105.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 01/03/2023] [Indexed: 02/24/2023]
Abstract
De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds1,2, but has been limited by a lack of suitable protein structures and the complexity of native protein sequence-structure relationships. Here we describe a deep-learning-based 'family-wide hallucination' approach that generates large numbers of idealized protein structures containing diverse pocket shapes and designed sequences that encode them. We use these scaffolds to design artificial luciferases that selectively catalyse the oxidative chemiluminescence of the synthetic luciferin substrates diphenylterazine3 and 2-deoxycoelenterazine. The designed active sites position an arginine guanidinium group adjacent to an anion that develops during the reaction in a binding pocket with high shape complementarity. For both luciferin substrates, we obtain designed luciferases with high selectivity; the most active of these is a small (13.9 kDa) and thermostable (with a melting temperature higher than 95 °C) enzyme that has a catalytic efficiency on diphenylterazine (kcat/Km = 106 M-1 s-1) comparable to that of native luciferases, but a much higher substrate specificity. The creation of highly active and specific biocatalysts from scratch with broad applications in biomedicine is a key milestone for computational enzyme design, and our approach should enable generation of a wide range of luciferases and other enzymes.
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Affiliation(s)
- Andy Hsien-Wei Yeh
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA.
| | - Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Yakov Kipnis
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Doug Tischer
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Samuel J Pellock
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Declan Evans
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Pengchen Ma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- School of Chemistry, Xi'an Key Laboratory of Sustainable Energy Materials Chemistry, MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, Xi'an Jiaotong University, Xi'an, China
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Jason Z Zhang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Brian Coventry
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Longxing Cao
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Samer Halabiya
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Michelle DeWitt
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Lauren Carter
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA.
- Institute for Protein Design, University of Washington, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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60
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Mi L, Yu Q, Mudiyanselage APK, Wu R, Sun Z, Zheng R, Ren K, You M. Genetically Encoded RNA-Based Bioluminescence Resonance Energy Transfer (BRET) Sensors. ACS Sens 2023; 8:308-316. [PMID: 36608281 PMCID: PMC10630924 DOI: 10.1021/acssensors.2c02213] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
RNA-based nanostructures and molecular devices have become popular for developing biosensors and genetic regulators. These programmable RNA nanodevices can be genetically encoded and modularly engineered to detect various cellular targets and then induce output signals, most often a fluorescence readout. Although powerful, the high reliance of fluorescence on the external excitation light raises concerns about its high background, photobleaching, and phototoxicity. Bioluminescence signals can be an ideal complementary readout for these genetically encoded RNA nanodevices. However, RNA-based real-time bioluminescent reporters have been rarely developed. In this study, we reported the first type of genetically encoded RNA-based bioluminescence resonance energy transfer (BRET) sensors that can be used for real-time target detection in living cells. By coupling a luciferase bioluminescence donor with a fluorogenic RNA-based acceptor, our BRET system can be modularly designed to image and detect various cellular analytes. We expect that this novel RNA-based bioluminescent system can be potentially used broadly in bioanalysis and nanomedicine for engineering biosensors, characterizing cellular RNA-protein interactions, and high-throughput screening or in vivo imaging.
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Affiliation(s)
- Lan Mi
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Qikun Yu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | | | - Rigumula Wu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Zhining Sun
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Ru Zheng
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
| | - Kewei Ren
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, China
| | - Mingxu You
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA
- Molecular and Cellular Biology Program, University of Massachusetts, Amherst, MA 01003, USA
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61
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Li S, Wang K, Wang Z, Zhang W, Liu Z, Cheng Y, Zhu J, Zhong M, Hu S, Zhang Y. Application and trend of bioluminescence imaging in metabolic syndrome research. Front Chem 2023; 10:1113546. [PMID: 36700071 PMCID: PMC9868317 DOI: 10.3389/fchem.2022.1113546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Bioluminescence imaging is a non-invasive technology used to visualize physiological processes in animals and is useful for studying the dynamics of metabolic syndrome. Metabolic syndrome is a broad spectrum of diseases which are rapidly increasing in prevalence, and is closely associated with obesity, type 2 diabetes, nonalcoholic fatty liver disease, and circadian rhythm disorder. To better serve metabolic syndrome research, researchers have established a variety of animal models expressing luciferase, while also committing to finding more suitable luciferase promoters and developing more efficient luciferase-luciferin systems. In this review, we systematically summarize the applications of different models for bioluminescence imaging in the study of metabolic syndrome.
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Affiliation(s)
- Shirui Li
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Kang Wang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,Postgraduate Department, Shandong First Medical University, Jinan, China
| | - Zeyu Wang
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,Postgraduate Department, Shandong First Medical University, Jinan, China
| | - Wenjie Zhang
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Zenglin Liu
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China
| | - Yugang Cheng
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Jiankang Zhu
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Mingwei Zhong
- Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Sanyuan Hu
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China,Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,*Correspondence: Sanyuan Hu, ; Yun Zhang,
| | - Yun Zhang
- Department of General Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, China,Department of General Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,*Correspondence: Sanyuan Hu, ; Yun Zhang,
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62
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Catalytic mechanism for Renilla-type luciferases. Nat Catal 2023. [DOI: 10.1038/s41929-022-00895-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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63
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Baljinnyam B, Ronzetti M, Simeonov A. Advances in luminescence-based technologies for drug discovery. Expert Opin Drug Discov 2023; 18:25-35. [PMID: 36562206 PMCID: PMC9892298 DOI: 10.1080/17460441.2023.2160441] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Luminescence-based technologies, specifically bioluminescence and chemiluminescence, are powerful tools with extensive use in drug discovery. Production of light during chemiluminescence and bioluminescence, unlike fluorescence, doesn't require an excitation light source, resulting in high signal-to-noise ratio, less background interference, and no issues from phototoxicity and photobleaching. These characteristics of luminescence technologies offer unique advantages for experimental designs, allowing for greater flexibility to target a wide range of proteins and biological processes for drug discovery at different stages. AREAS COVERED This review provides a basic overview of luciferase-based technologies and details recent advances and use cases of luciferase and luciferin variations and their applicability in the drug discovery toolset. The authors expand upon specific applications of luciferase technologies, including chemiluminescent and bioluminescent-based microscopy. Finally, the authors lay out forward-looking statements on the field of luminescence and how it may shape the translational scientists' work moving forward. EXPERT OPINION The demand for improved luciferase and luciferin pairs correlates strongly with efforts to improve the sensitivity and robustness of high-throughput assays. As luminescent reporter systems improve, so will the expansion of use cases for luminescence-based technologies in early-stage drug discovery. With the synthesis of novel, non-enzymatic chemiluminescence-based probes, which previously were restrained to only basic research applications, they may now be readily implemented in drug discovery campaigns.
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Affiliation(s)
- Bolormaa Baljinnyam
- Staff Scientist, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Michael Ronzetti
- Predoctoral IRTA Fellow, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Anton Simeonov
- Group Leader, Scientific Director, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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Cui WL, Wang MH, Yang YH, Wang JY, Zhu X, Zhang H, Ji X. Recent advances and perspectives in reaction-based fluorescent probes for imaging peroxynitrite in biological systems. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Becerra-García RE, Cruz-Valderrama JE, Cerbantez-Bueno VE, Marsch-Martínez N, de Folter S. A NanoLuc-Based Transactivation Assay in Plants. Methods Mol Biol 2023; 2686:553-565. [PMID: 37540377 DOI: 10.1007/978-1-0716-3299-4_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Protein-DNA interactions are determinant of the regulation of gene expression in living organisms. Luminescence studies have been used in a wide range of techniques to identify how gene transcription can be regulated by proteins such as transcription factors (TFs). Despite the great advances in the use of luciferases as reporters in the performance of this mechanism, some of them still have disadvantages that have been tried to be solved by the generation of new luciferases that induce a more stable and perfectly visualizable reaction. NanoLuc is a recently described luciferase that has been characterized by its efficient, stable, and powerful luminescence. These qualities have been considered to create a new and efficient reporter system to detect protein-DNA interactions. In this chapter, we take advantage of NanoLuc and describe its use in a reliable procedure to detect protein-DNA interactions in Nicotiana benthamiana extracts and entire leaves.
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Affiliation(s)
- Rosa Esmeralda Becerra-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato, Guanajuato, Mexico
| | - José Erik Cruz-Valderrama
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Vincent E Cerbantez-Bueno
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, Mexico.
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66
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Kolesnik OV, Rozhko TV, Kudryasheva NS. Marine Bacteria under Low-Intensity Radioactive Exposure: Model Experiments. Int J Mol Sci 2022; 24:ijms24010410. [PMID: 36613854 PMCID: PMC9820739 DOI: 10.3390/ijms24010410] [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: 11/04/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Radioactive contaminants create problems all over world, involving marine ecosystems, with their ecological importance increasing in the future. The review focuses on bioeffects of a series of alpha and beta emitting radioisotopes (americium-241, uranium-(235 + 238), thorium-232, and tritium) and gamma radiation. Low-intensity exposures are under special consideration. Great attention has been paid to luminous marine bacteria as representatives of marine microorganisms and a conventional bioassay system. This bioassay uses bacterial bioluminescence intensity as the main testing physiological parameter; currently, it is widely applied due to its simplicity and sensitivity. Dependences of the bacterial luminescence response on the exposure time and irradiation intensity were reviewed, and applicability of hormetic or threshold models was discussed. A number of aspects of molecular intracellular processes under exposure to low-intensity radiation were analyzed: (a) changes in the rates of enzymatic processes in bacteria with the bioluminescent system of coupled enzymatic reactions of NADH:FMN-oxidoreductase and bacterial luciferase taken as an example; (b) consumption of an intracellular reducer, NADH; (c) active role of reactive oxygen species; (d) repairing of the DNA damage. The results presented confirm the function of humic substances as natural radioprotectors.
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Affiliation(s)
- Olga V. Kolesnik
- Institute of Biophysics SB RAS, Federal Research Center ‘Krasnoyarsk Science Center SB RAS’, 660036 Krasnoyarsk, Russia
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Tatiana V. Rozhko
- FSBEI HE V.F. Voino-Yasenetsky KrasSMU MOH, 660022 Krasnoyarsk, Russia
| | - Nadezhda S. Kudryasheva
- Institute of Biophysics SB RAS, Federal Research Center ‘Krasnoyarsk Science Center SB RAS’, 660036 Krasnoyarsk, Russia
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Correspondence:
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67
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Gräwe A, Merkx M. Bioluminescence Goes Dark: Boosting the Performance of Bioluminescent Sensor Proteins Using Complementation Inhibitors. ACS Sens 2022; 7:3800-3808. [PMID: 36450135 PMCID: PMC9791688 DOI: 10.1021/acssensors.2c01726] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Bioluminescent sensor proteins have recently gained popularity in both basic research and point-of-care diagnostics. Sensor proteins based on intramolecular complementation of split NanoLuc are particularly attractive because their intrinsic modular design enables for systematic tuning of sensor properties. Here we show how the sensitivity of these sensors can be enhanced by the introduction of catalytically inactive variants of the small SmBiT subunit (DarkBiTs) as intramolecular inhibitors. Starting from previously developed bioluminescent antibody sensor proteins (LUMABS), we developed single component, biomolecular switches with a strongly reduced background signal for the detection of three clinically relevant antibodies, anti-HIV1-p17, cetuximab (CTX), and an RSV neutralizing antibody (101F). These new dark-LUMABS sensors showed 5-13-fold increases in sensitivity which translated into lower limits of detection. The use of DarkBiTs as competitive intramolecular inhibitor domains is not limited to the LUMABS sensor family and might be used to boost the performance of other bioluminescent sensor proteins based on split luciferase complementation.
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68
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Brennan CK, Yao Z, Ionkina AA, Rathbun CM, Sathishkumar B, Prescher JA. Multiplexed bioluminescence imaging with a substrate unmixing platform. Cell Chem Biol 2022; 29:1649-1660.e4. [PMID: 36283402 PMCID: PMC9675729 DOI: 10.1016/j.chembiol.2022.10.004] [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: 03/08/2022] [Revised: 08/31/2022] [Accepted: 09/30/2022] [Indexed: 01/31/2023]
Abstract
Bioluminescent tools can illuminate cellular features in whole organisms. Multi-component tracking remains challenging, though, owing to a lack of well-resolved probes and long imaging times. To address the need for more rapid, quantitative, and multiplexed bioluminescent readouts, we developed an analysis pipeline featuring sequential substrate administration and serial image acquisition. Light output from each luciferin is layered on top of the previous image, with minimal delay between substrate delivery. A MATLAB algorithm was written to analyze bioluminescent images generated from the rapid imaging protocol and deconvolute (i.e., unmix) signals from luciferase-luciferin pairs. Mixtures comprising three to five luciferase reporters were readily distinguished in under 50 min; this same experiment would require days using conventional workflows. We further showed that the algorithm can be used to accurately quantify luciferase levels in heterogeneous mixtures. Based on its speed and versatility, the multiplexed imaging platform will expand the scope of bioluminescence technology.
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Affiliation(s)
- Caroline K Brennan
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Zi Yao
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Anastasia A Ionkina
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA
| | - Colin M Rathbun
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA
| | | | - Jennifer A Prescher
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697, USA; Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697, USA.
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69
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Bioluminescent Dinoflagellates as a Bioassay for Toxicity Assessment. Int J Mol Sci 2022; 23:ijms232113012. [DOI: 10.3390/ijms232113012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/19/2022] [Accepted: 09/24/2022] [Indexed: 11/16/2022] Open
Abstract
Dinoflagellates bioluminescence mechanism depends upon a luciferin–luciferase reaction that promotes blue light emission (480 nm) in specialized luminogenic organelles called scintillons. The scintillons contain luciferin, luciferase and, in some cases, a luciferin-binding protein (LBP), which prevents luciferin from non-enzymatic oxidation in vivo. Even though dinoflagellate bioluminescence has been studied since the 1950s, there is still a lack of mechanistic understanding on whether the light emission process involves a peroxidic intermediate or not. Still, bioassays employing luminous dinoflagellates, usually from Gonyaulax or Pyrocystis genus, can be used to assess the toxicity of metals or organic compounds. In these dinoflagellates, the response to toxicity is observed as a change in luminescence, which is linked to cellular respiration. As a result, these changes can be used to calculate a percentage of light inhibition that correlates directly with toxicity. This current approach, which lies in between fast bacterial assays and more complex toxicity tests involving vertebrates and invertebrates, can provide a valuable tool for detecting certain pollutants, e.g., metals, in marine sediment and seawater. Thus, the present review focuses on how the dinoflagellates bioluminescence can be applied to evaluate the risks caused by contaminants in the marine environment.
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70
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Afshari MJ, Li C, Zeng J, Cui J, Wu S, Gao M. Self-illuminating NIR-II bioluminescence imaging probe based on silver sulfide quantum dots. ACS NANO 2022; 16:16824-16832. [PMID: 36178795 DOI: 10.1021/acsnano.2c06667] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bioluminescence (BL) imaging has emerged to tackle the potential challenges of fluorescence (FL) imaging including the autofluorescence background, inhomogeneous illumination over a wide imaging field, and the light-induced overheating effect. Taking advantage of the bioluminescence resonance energy transfer (BRET) mechanism between a conventional luciferin compound and a suitable acceptor, the visible light of the former can be extended to photons with longer wavelengths emitting from the latter. Although BRET-based self-illuminating imaging probes have already been prepared, employing potentially cytotoxic elements as the acceptor with the emission wavelengths which hardly reach the first near-infrared (NIR-I) window, has limited their applications as safe and high performance in vivo imaging agents. Herein, we report a biocompatible, self-illuminating, and second near-infrared (NIR-II) emissive probe to address the cytotoxicity concerns as well as improve the penetration depth and spatiotemporal resolution of BL imaging. To this end, NanoLuc luciferase enzyme molecules were immobilized on the surface of silver sulfide quantum dots to oxidize its luciferin substrate and initiate a single-step BRET mechanism, resulting in NIR-II photons from the quantum dots. The resulting dual modality (BL/FL) probes were successfully applied to in vivo tumor imaging in mice, demonstrating that NIR-II BL signals could be easily detected from the tumor sites, giving rise to ∼2 times higher signal-to-noise ratios compared to those obtained under FL mode. The results indicated that nontoxic NIR-II emitting nanocrystals deserve more attention to be tailored to fill the growing demands of preparing appropriate agents for high quality BL imaging.
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Affiliation(s)
- Mohammad Javad Afshari
- Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Cang Li
- Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Jianfeng Zeng
- Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Jiabin Cui
- Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Shuwang Wu
- Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
| | - Mingyuan Gao
- Key Laboratory of Radiation Medicine and Protection, School for Radiological and Interdisciplinary Sciences (RAD-X), Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, P. R. China
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71
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Yoon S, Cheon SY, Park S, Lee D, Lee Y, Han S, Kim M, Koo H. Recent advances in optical imaging through deep tissue: imaging probes and techniques. Biomater Res 2022; 26:57. [PMID: 36273205 PMCID: PMC9587606 DOI: 10.1186/s40824-022-00303-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/22/2022] [Indexed: 12/04/2022] Open
Abstract
Optical imaging has been essential for scientific observations to date, however its biomedical applications has been restricted due to its poor penetration through tissues. In living tissue, signal attenuation and limited imaging depth caused by the wave distortion occur because of scattering and absorption of light by various molecules including hemoglobin, pigments, and water. To overcome this, methodologies have been proposed in the various fields, which can be mainly categorized into two stategies: developing new imaging probes and optical techniques. For example, imaging probes with long wavelength like NIR-II region are advantageous in tissue penetration. Bioluminescence and chemiluminescence can generate light without excitation, minimizing background signals. Afterglow imaging also has high a signal-to-background ratio because excitation light is off during imaging. Methodologies of adaptive optics (AO) and studies of complex media have been established and have produced various techniques such as direct wavefront sensing to rapidly measure and correct the wave distortion and indirect wavefront sensing involving modal and zonal methods to correct complex aberrations. Matrix-based approaches have been used to correct the high-order optical modes by numerical post-processing without any hardware feedback. These newly developed imaging probes and optical techniques enable successful optical imaging through deep tissue. In this review, we discuss recent advances for multi-scale optical imaging within deep tissue, which can provide reseachers multi-disciplinary understanding and broad perspectives in diverse fields including biophotonics for the purpose of translational medicine and convergence science.
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Affiliation(s)
- Seokchan Yoon
- School of Biomedical Convergence Engineering, Pusan National University, Yangsan, 50612, Republic of Korea
| | - Seo Young Cheon
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Sangjun Park
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Donghyun Lee
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Yeeun Lee
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea
| | - Seokyoung Han
- Department of Mechanical Engineering, University of Louisville, Louisville, KY, 40208, USA
| | - Moonseok Kim
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
| | - Heebeom Koo
- Department of Medical Life Sciences and Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea. .,Catholic Photomedicine Research Institute, College of Medicine, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
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72
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Chen M, Zhou K, Dai SY, Tadepalli S, Balakrishnan PB, Xie J, Rami FEI, Dai T, Cui L, Idoyaga J, Rao J. In vivo bioluminescence imaging of granzyme B activity in tumor response to cancer immunotherapy. Cell Chem Biol 2022; 29:1556-1567.e6. [PMID: 36103874 PMCID: PMC9588750 DOI: 10.1016/j.chembiol.2022.08.006] [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: 07/23/2021] [Revised: 03/31/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022]
Abstract
Cancer immunotherapy has revolutionized the treatment of cancer, but only a small subset of patients benefits from this new treatment regime. Imaging tools are useful for early detection of tumor response to immunotherapy and probing the dynamic and complex immune system. Here, we report a bioluminescence probe (GBLI-2) for non-invasive, real-time, longitudinal imaging of granzyme B activity in tumors receiving immune checkpoint inhibitors. GBLI-2 is made of the mouse granzyme B tetrapeptide IEFD substrate conjugated to D-luciferin through a self-immolative group. GBLI-2 was evaluated for imaging the dynamics of the granzyme B activity and predicting therapeutic efficacy in a syngeneic mouse model of CT26 murine colorectal carcinoma. The GBLI-2 signal correlated with the change in the population of PD-1- and granzyme B-expressing CD8+ T cells in tumors.
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Affiliation(s)
- Min Chen
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kaixiang Zhou
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sheng-Yao Dai
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sirimuvva Tadepalli
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Preethi Bala Balakrishnan
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jinghang Xie
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Fadi E I Rami
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tingting Dai
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Liyang Cui
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Juliana Idoyaga
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jianghong Rao
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
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73
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Komuro H, Aminova S, Lauro K, Harada M. Advances of engineered extracellular vesicles-based therapeutics strategy. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2022; 23:655-681. [PMID: 36277506 PMCID: PMC9586594 DOI: 10.1080/14686996.2022.2133342] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 05/09/2023]
Abstract
Extracellular vesicles (EVs) are a heterogeneous population of lipid bilayer membrane-bound vesicles which encapsulate bioactive molecules, such as nucleic acids, proteins, and lipids. They mediate intercellular communication through transporting internally packaged molecules, making them attractive therapeutics carriers. Over the last decades, a significant amount of research has implied the potential of EVs servings as drug delivery vehicles for nuclear acids, proteins, and small molecular drugs. However, several challenges remain unresolved before the clinical application of EV-based therapeutics, including lack of specificity, stability, biodistribution, storage, large-scale manufacturing, and the comprehensive analysis of EV composition. Technical development is essential to overcome these issues and enhance the pre-clinical therapeutic effects. In this review, we summarize the current advancements in EV engineering which demonstrate their therapeutic potential.
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Affiliation(s)
- Hiroaki Komuro
- Institute for Quantitative Health Science and Engineering (IQ), Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Shakhlo Aminova
- Institute for Quantitative Health Science and Engineering (IQ), Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Katherine Lauro
- Institute for Quantitative Health Science and Engineering (IQ), Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Masako Harada
- Institute for Quantitative Health Science and Engineering (IQ), Michigan State University, East Lansing, MI, USA
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
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74
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Longitudinal bioluminescence imaging to monitor breast tumor growth and treatment response using the chick chorioallantoic membrane model. Sci Rep 2022; 12:17192. [PMID: 36229503 PMCID: PMC9562337 DOI: 10.1038/s41598-022-20854-9] [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: 06/20/2022] [Accepted: 09/20/2022] [Indexed: 01/05/2023] Open
Abstract
The development of successful treatment regimens for breast cancer requires strong pre-clinical data generated in physiologically relevant pre-clinical models. Here we report the development of the chick embryo chorioallantoic membrane (CAM) model to study tumor growth and angiogenesis using breast cancer cell lines. MDA-MB-231 and MCF7 tumor cell lines were engrafted onto the chick embryo CAM to study tumor growth and treatment response. Tumor growth was evaluated through bioluminescence imaging and a significant increase in tumor size and vascularization was found over a 9-day period. We then evaluated the impact of anti-angiogenic drugs, axitinib and bevacizumab, on tumor growth and angiogenesis. Drug treatment significantly reduced tumor vascularization and size. Overall, our findings demonstrate that the chick embryo CAM is a clinically relevant model to monitor therapeutic response in breast cancer and can be used as a platform for drug screening to evaluate not only gross changes in tumor burden but physiological processes such as angiogenesis.
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75
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Li CC, Liu WX, Jiang S, Liu M, Luo X, Zhang CY. Construction of Bioluminescent Sensors for Label-Free, Template-Free, Separation-Free, and Sequence-Independent Detection of both Clustered and Isolated Damage in Genomic DNA. Anal Chem 2022; 94:14716-14724. [PMID: 36223141 DOI: 10.1021/acs.analchem.2c03134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA damage induced by endogenous/exogenous factors may cause various diseases, and the genomic DNA damage has become an important biomarker for clinical diagnosis and risk assessment, but it remains a great challenge to accurately quantify both clustered and isolated damage because of their random locations, large diversity, and low abundance. Herein, we demonstrate the development of bioluminescent sensors for label-free, template-free, separation-free, and sequence-independent detection of both clustered and isolated damage in genomic DNA based on the base-excision repair (BER) pathway and terminal transferase (TdT)-initiated template-free isothermal cyclic amplification. The damaged bases are cleaved by DNA glycosylase to generate a new 3'-OH terminus, and subsequently, TdT catalyzes the repeated incorporation of dTTPs into the 3'-OH terminus to produce poly-T structures which can hybridize with the signal probe to form a poly-T sequence/signal probe duplex. Under the lambda exonuclease hydrolysis, a large number of adenosine monophosphate (AMP) molecules are produced to generate a high bioluminescence signal through the cyclic interconversion of AMP-adenosine triphosphate (ATP)-AMP in the presence of luciferin and firefly luciferase. Moreover, the introduction of APE1-induced cyclic cleavage signal amplification can greatly improve the detection sensitivity. The proposed strategy can detect both clustered and isolated damage in genomic DNA with extremely high sensitivity and excellent specificity, and it can even distinguish 0.001% DNA damage in the mixture. Importantly, it can detect the cellular DNA damage with a detection limit of 0.011 ng and further extend to measure various DNA damage with the integration of appropriate DNA repair enzymes.
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Affiliation(s)
- Chen-Chen Li
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Wan-Xin Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China.,Zichuan Experimental Middle School, Zibo 255100, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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76
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Ng KK, Prescher JA. Generalized Bioluminescent Platform To Observe and Track Cellular Interactions. Bioconjug Chem 2022; 33:1876-1884. [PMID: 36166258 DOI: 10.1021/acs.bioconjchem.2c00348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cell-to-cell communications are critical to biological processes ranging from embryonic development to cancer progression. Several imaging strategies have been developed to capture such interactions, but many are challenging to deploy in thick tissues and other complex environments. Here, we report a platform termed Luminescence to Observe and Track Intercellular Interactions (LOTIIS). The approach features split fragments of a luciferase enzyme that reassemble when target cells come into proximity. One fragment is secreted by "sender" cells, and the complementary piece is secreted by "receiver" cells. Split reporter assembly is facilitated by a single chain variable fragment (scFv)-peptide interaction on the receiver cell, resulting in localized light production. We demonstrate that LOTIIS can rapidly label cells in close proximity in a time- and distance-dependent fashion. The platform is also compatible with bioluminescence resonance energy transfer probes for multiplexed imaging. Collectively, these data suggest that LOTIIS will enable a variety of cellular interactions to be tracked in biological settings.
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Affiliation(s)
- Kevin K Ng
- Departments of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Jennifer A Prescher
- Departments of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States.,Departments of Chemistry, University of California, Irvine, California 92697, United States.,Molecular Biology and Biochemistry, University of California, Irvine, California 92697, United States
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A Luciferase Mutant with Improved Brightness and Stability for Whole-Cell Bioluminescent Biosensors and In Vitro Biosensing. BIOSENSORS 2022; 12:bios12090742. [PMID: 36140127 PMCID: PMC9496056 DOI: 10.3390/bios12090742] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022]
Abstract
The availability of new bioluminescent proteins with tuned properties, both in terms of emission wavelength, kinetics and protein stability, is highly valuable in the bioanalytical field, with the potential to improve the sensitivity and analytical performance of the currently used methods for ATP detection, whole-cell biosensors, and viability assays among others. We present a new luciferase mutant, called BgLuc, suitable for developing whole-cell biosensors and in vitro biosensors characterized by a bioluminescence maximum of 548 nm, narrow emission bandwidth, favorable kinetic properties, and excellent pH- and thermo-stabilities at 37 and 45 °C and pH from 5.0 to 8.0. We assessed the suitability of this new luciferase for whole-cell biosensing with a cell-based bioreporter assay for Nuclear Factor-kappa B (NF-kB) signal transduction pathway using 2D and 3D human embryonic kidney (HEK293T) cells, and for ATP detection with the purified enzyme. In both cases the luciferase showed suitable for sensitive detection of the target analytes, with better or similar performance than the commercial counterparts.
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78
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Xie X, He Z, Qu C, Sun Z, Cao H, Liu X. Nanobody/NanoBiT system-mediated bioluminescence immunosensor for one-step homogeneous detection of trace ochratoxin A in food. JOURNAL OF HAZARDOUS MATERIALS 2022; 437:129435. [PMID: 35753304 DOI: 10.1016/j.jhazmat.2022.129435] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/09/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Hazardous small molecules in food and environment seriously threatens human health, which requires sensitive and rapid tools for monitoring. Using a previously identified nanobody against ochratoxin A (OTA), we herein proposed a homogeneous sensing platform "nanobody/NanoLuc Binary Technology (NanoBiT) system" and developed a nanobody/NanoBiT system-mediated bioluminescence immunosensor (NBL-Immunosens) for OTA using LgBiT (Lg) and SmBiT (Sm), two subunits of the split nanoluciferase (NanoLuc). The core elements of NBL-Immunosens include Lg-nanobody fusion (NLg) and Sm-labeled OTA-bovine serum albumin conjugate (OSm). The antigen-antibody interaction between NLg and OSm triggers the reconstitution of NanoLuc for generating luminescence signals. Moreover, free OTA can compete with OSm for binding to NLg, resulting the decrease of dose-dependent signals. NBL-Immunosens can detect OTA in a one-step assay of 5 min without washing and exhibit a limit of detection of 0.01 ng/mL with a linear range of 0.04-2.23 ng/mL. It shows high selectivity for OTA and has good accuracy and precision in the spiking-and-recovery experiments. Furthermore, its effectiveness was evaluated with real cereal samples and confirmed by liquid chromatography tandem mass spectrometry and commercial ELISA kits. Hence, the NBL-Immunosens is a very promising tool for rapid, accurate, and selective detection of trace OTA in food.
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Affiliation(s)
- Xiaoxia Xie
- School of Food Science and Engineering, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China
| | - Zhenyun He
- School of Food Science and Engineering, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China
| | - Chaoshuang Qu
- School of Food Science and Engineering, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China
| | - Zhichang Sun
- School of Food Science and Engineering, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China
| | - Hongmei Cao
- School of Food Science and Engineering, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China
| | - Xing Liu
- School of Food Science and Engineering, Key Laboratory of Tropical Fruits and Vegetables Quality and Safety for State Market Regulation, Hainan University, Haikou 570228, China.
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79
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Liu YJ. Understanding the complete bioluminescence cycle from a multiscale computational perspective: A review. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C: PHOTOCHEMISTRY REVIEWS 2022. [DOI: 10.1016/j.jphotochemrev.2022.100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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80
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Jia H, Liu Y, Hu JJ, Li G, Lou X, Xia F. Lifetime-Based Responsive Probes: Design and Applications in Biological Analysis. Chem Asian J 2022; 17:e202200563. [PMID: 35916038 DOI: 10.1002/asia.202200563] [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: 05/30/2022] [Revised: 07/26/2022] [Indexed: 11/10/2022]
Abstract
With the development of modern biomedicine, biological analysis and detection are very important in disease diagnosis, detection of curative effect, prognosis and prediction of tumor recurrence. Compared with the currently widely used optical probes based on intensity signals, the lifetime signal does not depend on the influence of conditions such as the concentration of luminophore, tissue penetration depth and measurement method. Therefore, biological detection methods based on lifetime-based responsive probes have attracted great attention from the scientific community. Here, we briefly review the key advances in lifetime-based responsive probes in recent years (2017-2022). The review focuses on the design strategies of lifetime-based responsive probes and the research progress of their applications in the field of bioanalysis, and discusses the challenges they face. We hope it will further promote the development of lifetime-based responsive probes in the field of bioanalysis. With the development of modern biomedicine, biological analysis and detection are very important in disease diagnosis, detection of curative effect, prognosis and prediction of tumor recurrence. Compared with the currently widely used optical probes based on intensity signals, the lifetime signal does not depend on the influence of conditions such as the concentration of luminophore, tissue penetration depth and measurement method. Therefore, biological detection methods based on lifetime-based responsive probes have attracted great attention from the scientific community. Here, we briefly review the key advances in lifetime-based responsive probes in recent years (2017-2022). The review focuses on the design strategies of lifetime-based responsive probes and the research progress of their applications in the field of bioanalysis, and discusses the challenges they face. We hope it will further promote the development of lifetime-based responsive probes in the field of bioanalysis.
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Affiliation(s)
- Hui Jia
- China University of Geosciences, Faculty of Materials Science and Chemistry, CHINA
| | - Yiheng Liu
- China University of Geosciences, Faculty of Materials Science and Chemistry, CHINA
| | - Jing-Jing Hu
- China University of Geosciences, Faculty of Materials Science and Chemistry, CHINA
| | - Guogang Li
- China University of Geosciences, Faculty of Materials Science and Chemistry, CHINA
| | - Xiaoding Lou
- China University of Geosciences, Faculty of Materials Science and Chemistry, 388 Lumo Road, Wuhan 430074, P. R. China, 430074, wuhan, CHINA
| | - Fan Xia
- China University of Geosciences, Faculty of Materials Science and Chemistry, CHINA
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81
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Electrochemically switchable and tunable luciferase bioluminescence. Bioelectrochemistry 2022; 146:108109. [DOI: 10.1016/j.bioelechem.2022.108109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/10/2022] [Accepted: 03/22/2022] [Indexed: 11/21/2022]
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82
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Bioluminescent test systems based on firefly luciferase for studying stress effects on living cells. Biophys Rev 2022; 14:887-892. [PMID: 36124280 PMCID: PMC9481846 DOI: 10.1007/s12551-022-00978-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022] Open
Abstract
The bioluminescent luciferin-luciferase reaction is based on the oxidation of D-luciferin by oxygen in the presence of ATP and magnesium ions, catalyzed by firefly luciferase. The possibilities of using this reaction to study the influence of external effectors of a physical and chemical nature (temperature exposure, additions of drugs, membrane-active compounds, etc.) on living cells (prokaryotes and eukaryotes) are considered. Examples of the use of test systems based on living cells producing thermostable firefly luciferase for monitoring cellular homeostasis are given. The study of the kinetics of changes in the concentration of ATP and luciferase inside and outside cells made it possible to determine in dynamics the metabolic activity, cytotoxicity, and survival of cells under conditions of cellular stress, to study the processes of ATP synthesis/hydrolysis, and to evaluate the effectiveness of lytic agents in changing the permeability of the cell membrane.
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83
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Multiplexed bioluminescence microscopy via phasor analysis. Nat Methods 2022; 19:893-898. [PMID: 35739310 DOI: 10.1038/s41592-022-01529-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 05/18/2022] [Indexed: 12/19/2022]
Abstract
Bioluminescence imaging with luciferase-luciferin pairs is a well-established technique for visualizing biological processes across tissues and whole organisms. Applications at the microscale, by contrast, have been hindered by a lack of detection platforms and easily resolved probes. We addressed this limitation by combining bioluminescence with phasor analysis, a method commonly used to distinguish spectrally similar fluorophores. We built a camera-based microscope equipped with special optical filters to directly assign phasor locations to unique luciferase-luciferin pairs. Six bioluminescent reporters were easily resolved in live cells, and the readouts were quantitative and instantaneous. Multiplexed imaging was also performed over extended time periods. Bioluminescent phasor further provided direct measures of resonance energy transfer in single cells, setting the stage for dynamic measures of cellular and molecular features. The merger of bioluminescence with phasor analysis fills a long-standing void in imaging capabilities, and will bolster future efforts to visualize biological events in real time and over multiple length scales.
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84
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Bioluminescence Sensing in 3D Spherical Microtissues for Multiple Bioactivity Analysis of Environmental Samples. SENSORS 2022; 22:s22124568. [PMID: 35746350 PMCID: PMC9229012 DOI: 10.3390/s22124568] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023]
Abstract
The development of predictive in vitro sensing tools able to provide rapid information on the different bioactivities of a sample is of pivotal importance, not only to monitor environmental toxicants, but also to understand their mechanisms of action on diverse molecular pathways. This mechanistic understanding is highly important for the characterization of toxicological hazards, and for the risk assessment of chemicals and environmental samples such as surface waters and effluents. Prompted by this need, we developed and optimized a straightforward bioluminescent multiplexed assay which enables the measurement of four bioactivities, selected for their relevance from a toxicological perspective, in bioluminescent microtissues. The assay was developed to monitor inflammatory, antioxidant, and toxic activity, and the presence of heavy metals, and was successfully applied to the analysis of river water samples, showing potential applicability for environmental analyses. The assay, which does not require advanced equipment, can be easily implemented in general laboratories equipped with basic cell culture facilities and a luminometer.
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85
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Viviani VR, Pelentir GF, Bevilaqua VR. Bioluminescence Color-Tuning Firefly Luciferases: Engineering and Prospects for Real-Time Intracellular pH Imaging and Heavy Metal Biosensing. BIOSENSORS 2022; 12:400. [PMID: 35735548 PMCID: PMC9221268 DOI: 10.3390/bios12060400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Firefly luciferases catalyze the efficient production of yellow-green light under normal physiological conditions, having been extensively used for bioanalytical purposes for over 5 decades. Under acidic conditions, high temperatures and the presence of heavy metals, they produce red light, a property that is called pH-sensitivity or pH-dependency. Despite the demand for physiological intracellular biosensors for pH and heavy metals, firefly luciferase pH and metal sensitivities were considered drawbacks in analytical assays. We first demonstrated that firefly luciferases and their pH and metal sensitivities can be harnessed to estimate intracellular pH variations and toxic metal concentrations through ratiometric analysis. Using Macrolampis sp2 firefly luciferase, the intracellular pH could be ratiometrically estimated in bacteria and then in mammalian cells. The luciferases of Macrolampis sp2 and Cratomorphus distinctus fireflies were also harnessed to ratiometrically estimate zinc, mercury and other toxic metal concentrations in the micromolar range. The temperature was also ratiometrically estimated using firefly luciferases. The identification and engineering of metal-binding sites have allowed the development of novel luciferases that are more specific to certain metals. The luciferase of the Amydetes viviani firefly was selected for its special sensitivity to cadmium and mercury, and for its stability at higher temperatures. These color-tuning luciferases can potentially be used with smartphones for hands-on field analysis of water contamination and biochemistry teaching assays. Thus, firefly luciferases are novel color-tuning sensors for intracellular pH and toxic metals. Furthermore, a single luciferase gene is potentially useful as a dual bioluminescent reporter to simultaneously report intracellular ATP and/or luciferase concentrations luminometrically, and pH or metal concentrations ratiometrically, providing a useful tool for real-time imaging of intracellular dynamics and stress.
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Affiliation(s)
- Vadim R. Viviani
- Department of Physics, Chemistry and Mathematics, Federal University of São Carlos (UFSCar), Sorocaba 18052-780, Brazil
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), Sorocaba 18052-780, Brazil;
| | - Gabriel F. Pelentir
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), Sorocaba 18052-780, Brazil;
| | - Vanessa R. Bevilaqua
- Faculty of Medical and Health Sciences, Pontifical Catholic University of São Paulo (PUC), Sorocaba 05014-901, Brazil;
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86
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
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87
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Mazraeh D, Di Ventura B. Synthetic microbiology applications powered by light. Curr Opin Microbiol 2022; 68:102158. [PMID: 35660240 DOI: 10.1016/j.mib.2022.102158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 11/17/2022]
Abstract
Synthetic biology is a field of research in which molecular parts (mostly nucleic acids and proteins) are de novo created or modified and then used either alone or in combination to achieve new functions that can help solve the problems of our modern society. In synthetic microbiology, microbes are employed rather than other organisms or cell-free systems. Optogenetics, a relatively recently established technology that relies on the use of genetically encoded photosensitive proteins to control biological processes with high spatiotemporal precision, offers the possibility to empower synthetic (micro)biology applications due to the many positive features that light has as an external trigger. In this review, we describe recent synthetic microbiology applications that made use of optogenetics after briefly introducing the molecular mechanism behind some of the most employed optogenetic tools. We highlight the power and versatility of this technique, which opens up new horizons for both research and industry.
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Affiliation(s)
- Daniel Mazraeh
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Barbara Di Ventura
- Signaling Research Centres BIOSS and CIBSS, and Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany.
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88
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Tian Q, Wu J, Xu H, Hu Z, Huo Y, Wang L. Cryo-EM structure of the fatty acid reductase LuxC-LuxE complex provides insights into bacterial bioluminescence. J Biol Chem 2022; 298:102006. [PMID: 35504354 PMCID: PMC9157457 DOI: 10.1016/j.jbc.2022.102006] [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: 01/21/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/25/2022] Open
Abstract
The discovery of reduced flavin mononucleotide and fatty aldehydes as essential factors of light emission facilitated study of bacterial luminescence. Although the molecular mechanisms underlying bacterial luminescence have been studied for more than 60 years, the structure of the bacterial fatty acid reductase complex remains unclear. Here, we report the cryo-EM structure of the Photobacterium phosphoreum fatty acid reductase complex LuxC–LuxE to a resolution of 2.79 Å. We show that the active site Lys238/Arg355 pair of LuxE is >30 Å from the active site Cys296 of LuxC, implying that catalysis relies on a large conformational change. Furthermore, mutagenesis and biochemical experiments support that the L-shaped cleft inside LuxC plays an important role in substrate binding and reaction. We obtained a series of mutants with significantly improved activity as measured by in vitro bioluminescence assays and demonstrated that the double mutant W111A/F483K displayed the highest activity (370% of the WT). Our results indicated that the activity of LuxC significantly affects the bacterial bioluminescence reaction. Finally, we expressed this mutated lux operon in Escherichia coli but observed that the in vivo concentrations of ATP and NADPH limited the enzyme activity; thus, we conclude that the luminous intensity mainly depends on the level of metabolic energy.
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Affiliation(s)
- Qingwei Tian
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China; Key Laboratory of Optoelectronic Devices and Systems, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Jingting Wu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Haifeng Xu
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Zhangli Hu
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China; Key Laboratory of Optoelectronic Devices and Systems, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yangao Huo
- National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
| | - Liyan Wang
- Shenzhen Key Laboratory of Marine Bioresource and Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China.
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89
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Shen Y, Zhou Q, Li W, Yuan L. Advances in Optical Imaging of Nonalcoholic Fatty Liver Disease. Chem Asian J 2022; 17:e202200320. [PMID: 35420707 DOI: 10.1002/asia.202200320] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/13/2022] [Indexed: 01/10/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD), emerging as one of the most common chronic liver diseases including simple steatosis and non-alcoholic steatohepatitis (NASH), is likely to progress to liver fibrosis and hepatic carcinoma if not treated in time. Therefore, early diagnosis and treatment of NAFLD are necessary. Currently, liver biopsy, as the gold standard for clinical diagnosis of NAFLD, is not widely accepted by patients due to its invasiveness. However, other non-invasive methods that had been reported for NAFLD (such as magnetic resonance imaging, positron emission tomography, and ultrasound) still suffer from low resolution and sensitivity, which are available as a guide for liver biopsy sometimes. As a non-invasive modality with high spatiotemporal resolution and superior sensitivity, optical imaging methods have been widely favored in recent years, mainly including fluorescence imaging, photoacoustic imaging, and bioluminescence imaging. With these optical imaging approaches, a series of optical probes based on optical and molecular-specific design have been developed for the biomarker diagnosis and research of diseases. In this review, we summarize the existing non-invasive optical imaging probes for the detection of biomarkers in NAFLD, including microenvironment (viscosity, polarity), ROS, RSS, ions, proteins, and nucleic acids. Design strategies for optical imaging probes and their applications in NAFLD bioimaging are discussed and focused on. We also highlight the potential challenges and prospects of designing new generations of optical imaging probes in NAFLD studies, which will further enhance the diversity, practicality, and clinical feasibility of NAFLD research.
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Affiliation(s)
| | | | - Wei Li
- Hunan University, chemistry, CHINA
| | - Lin Yuan
- Hunan University, College of Chemistry and Chemical Engineering, NO372, Lushan Rd. Yuelu District., 410082, Changsha, CHINA
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90
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Watthaisong P, Kamutira P, Kesornpun C, Pongsupasa V, Phonbuppha J, Tinikul R, Maenpuen S, Wongnate T, Nishihara R, Ohmiya Y, Chaiyen P. Luciferin Synthesis and Pesticide Detection by Luminescence Enzymatic Cascades. Angew Chem Int Ed Engl 2022; 61:e202116908. [PMID: 35138676 DOI: 10.1002/anie.202116908] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Indexed: 12/24/2022]
Abstract
D-Luciferin (D-LH2 ), a substrate of firefly luciferase (Fluc), is important for a wide range of bioluminescence applications. This work reports a new and green method using enzymatic reactions (HELP, HadA Enzyme for Luciferin Preparation) to convert 19 phenolic derivatives to 8 D-LH2 analogues with ≈51 % yield. The method can synthesize the novel 5'-methyl-D-LH2 and 4',5'-dimethyl-D-LH2 , which have never been synthesized or found in nature. 5'-Methyl-D-LH2 emits brighter and longer wavelength light than the D-LH2 . Using HELP, we further developed LUMOS (Luminescence Measurement of Organophosphate and Derivatives) technology for in situ detection of organophosphate pesticides (OPs) including parathion, methyl parathion, EPN, profenofos, and fenitrothion by coupling the reactions of OPs hydrolase and Fluc. The LUMOS technology can detect these OPs at parts per trillion (ppt) levels. The method can directly detect OPs in food and biological samples without requiring sample pretreatment.
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Affiliation(s)
- Pratchaya Watthaisong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, 21210, Thailand
| | - Philaiwarong Kamutira
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, 21210, Thailand
| | - Vinutsada Pongsupasa
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, 21210, Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, 21210, Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, 10400, Thailand
| | - Somchart Maenpuen
- Department of Biochemistry, Faculty of Science, Burapha University, Chonburi, 20131, Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, 21210, Thailand
| | - Ryo Nishihara
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Yoshihiro Ohmiya
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, 305-8566, Japan
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Wangchan Valley, Rayong, 21210, Thailand
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91
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Othman A, Smutok O, Kim Y, Minko S, Melman A, Katz E. A magneto-controlled biocatalytic cascade with a fluorescent output. Org Biomol Chem 2022; 20:1869-1873. [PMID: 35156979 DOI: 10.1039/d1ob02313f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A biocatalytic cascade based on concerted operation of pyruvate kinase and luciferase with a bioluminescent output was switched reversibly between low and high activity by applying an external magnetic field at different positions or removing it. The enzymes participating in the reaction cascade were bound to magnetic nanoparticles to allow their translocation or aggregation/dispersion to be controlled by the magnetic field. The reaction intensity, measured as the bioluminescent output, was dependent on the effective distances between the enzymes transported on the magnetic nanoparticles controlled by the magnets.
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Affiliation(s)
- Ali Othman
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | - Yongwook Kim
- Nanostructured Materials Lab, University of Georgia, Athens, GA 30602, USA
| | - Sergiy Minko
- Nanostructured Materials Lab, University of Georgia, Athens, GA 30602, USA
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY 13699-5810, USA.
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92
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Watthaisong P, Kamutira P, Kesornpun C, Pongsupasa V, Phonbuppha J, Tinikul R, Maenpuen S, Wongnate T, Nishihara R, Ohmiya Y, Chaiyen P. Luciferin Synthesis and Pesticide Detection by Luminescence Enzymatic Cascades. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Pratchaya Watthaisong
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Philaiwarong Kamutira
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Vinutsada Pongsupasa
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Ruchanok Tinikul
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology Faculty of Science Mahidol University Bangkok 10400 Thailand
| | - Somchart Maenpuen
- Department of Biochemistry Faculty of Science Burapha University Chonburi 20131 Thailand
| | - Thanyaporn Wongnate
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
| | - Ryo Nishihara
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki 305-8566 Japan
| | - Yoshihiro Ohmiya
- National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Ibaraki 305-8566 Japan
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering Vidyasirimedhi Institute of Science and Technology (VISTEC) Wangchan Valley Rayong 21210 Thailand
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93
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Lomakina GY, Ugarova NN. Application of Bioluminescent Methods to Study the Effect of the Membrane-active Antibiotic Colistin on Bacterial Cells. Photochem Photobiol 2022; 98:1077-1083. [PMID: 35132643 DOI: 10.1111/php.13606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/04/2022] [Indexed: 11/28/2022]
Abstract
For the first time, recombinant Escherichia coli cells expressing thermostable Luciola mingrelica firefly luciferase were used to study the effect of the membrane-active antibiotic colistin on live cells. Simple, fast and highly sensitive bioluminescent methods were developed for measurement of luciferase activity and ATP concentration inside and outside E. coli cells incubated in a nutrient medium, or in saline. Luciferase proved to be an informative protein marker for detecting the irreversible changes in cell membrane permeability. The study of kinetics of intra- and extracellular ATP concentration at different concentrations of colistin showed that the rate of decrease in intracellular ATP concentration significantly exceeded the rate of accumulation of extracellular ATP concentration. This fact could not be explained only by the release of ATP from the cell with an increase in the permeability of the outer cell membrane under the action of colistin. The loss of a significant part of intracellular ATP in presence of the colistin is probably due to a decrease in the activity of the respiratory chain enzymes and ATP synthase which operate in the cytoplasmic cell membrane, which leads to a decrease in the rate of ATP synthesis or even to its halt.
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Affiliation(s)
- Galina Yu Lomakina
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia.,Bauman Moscow State Technical University, Moscow, Russia
| | - Natalia N Ugarova
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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94
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Calabretta MM, Lopreside A, Montali L, Zangheri M, Evangelisti L, D'Elia M, Michelini E. Portable light detectors for bioluminescence biosensing applications: A comprehensive review from the analytical chemist's perspective. Anal Chim Acta 2022; 1200:339583. [DOI: 10.1016/j.aca.2022.339583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/11/2022]
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95
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Quadri Z, Elsherbini A, Bieberich E. Extracellular vesicles in pharmacology: Novel approaches in diagnostics and therapy. Pharmacol Res 2022; 175:105980. [PMID: 34863822 PMCID: PMC8760625 DOI: 10.1016/j.phrs.2021.105980] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023]
Abstract
Exosomes are nano-sized lipid vesicles that are produced by all eukaryotic cells, and they typically range in size from 30 to 150 nm. Exosomes were discovered almost 40 years ago; however, the last two decades have attracted considerable attention due to exosomes' inherent abilities to shuttle nucleic acids, lipids and proteins between cells, along with their natural affinity to exosome target cells. From a pharmaceutical perspective, exosomes are regarded as naturally produced nanoparticle drug delivery vehicles. The application of exosomes as a means of drug delivery offers critical advantages compared to other nanoparticulate drug delivery systems, such as liposomes and polymeric nanoparticles. These advantages are due to the exosomes' intrinsic features, such as low immunogenicity, biocompatibility, stability, and their ability to overcome biological barriers. Herein, we outline the structure and origin of exosomes, as well as their biological functions. We also touch upon recent advances in exosome labeling, imaging and drug loading. Finally, we discuss exosomes in targeted drug delivery and clinical trial development.
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Affiliation(s)
- Zainuddin Quadri
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, United States; Veterans Affairs Medical Center, Lexington, KY 40502, United States
| | - Ahmed Elsherbini
- Veterans Affairs Medical Center, Lexington, KY 40502, United States
| | - Erhard Bieberich
- Department of Physiology, University of Kentucky College of Medicine, Lexington, KY 40536, United States; Veterans Affairs Medical Center, Lexington, KY 40502, United States.
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96
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Liu YL, Guo ZY. The NanoBiT-Based Homogenous Ligand-Receptor Binding Assay. Methods Mol Biol 2022; 2525:139-153. [PMID: 35836065 DOI: 10.1007/978-1-0716-2473-9_10] [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] [Indexed: 06/15/2023]
Abstract
NanoLuc Binary Technology (NanoBiT) was recently developed by Promega, based on a large NanoLuc fragment (LgBiT) and two small complementation tags, the low-affinity SmBiT tag and the high-affinity HiBiT tag. In recent studies, we applied NanoBiT to ligand-binding assays of some G protein-coupled receptors via genetic fusion of a secretory LgBiT (sLgBiT) to the extracellular N-terminus of the receptors and covalent attachment of the low-affinity SmBiT tag to an appropriate position of their peptide ligands. The NanoBiT-based homogenous ligand-receptor binding assay is convenient for use and suitable for both the wild-type and mutant receptors, representing a novel tool for interaction mechanism studies of these receptors with their ligands. In the present chapter, we provide detailed protocols for setting up the NanoBiT-based homogenous binding assay using growth hormone secretagogue receptor type 1a (GHSR1a) and its endogenous agonist and antagonist as a representative model system.
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Affiliation(s)
- Ya-Li Liu
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhan-Yun Guo
- Research Center for Translational Medicine at East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China.
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97
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Sato K. Bioluminescence Imaging for Evaluation of Antitumor Effect In Vitro and In Vivo in Mice Xenografted Tumor Models. Methods Mol Biol 2022; 2524:307-315. [PMID: 35821482 DOI: 10.1007/978-1-0716-2453-1_24] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bioluminescence imaging (BLI) enables real-time imaging in vitro and in vivo; it is widely used in laboratories. In vitro, the bioluminescence is commonly used as a reporter for the transfection. In vivo, BLI is employed to evaluate cell expression, migration, and proliferation inside animal bodies and visualize specific cells in various fields. Here, this chapter introduces BLI protocols for assaying the efficacy of in vivo BLI in monitoring cancer treatment using mice orthotopic models.
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Affiliation(s)
- Kazuhide Sato
- Respiratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan.
- Nagoya University Institute for Advanced Research, B3-Unit, Advanced Analytical and Diagnostic Imaging Center (AADIC)/Medical Engineering Unit (MEU), S-YLC, Nagoya, Japan.
- FOREST-Souhatsu, CREST, JST, Nagoya, Japan.
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98
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Yang Y, Zhang M, Zhang W, Chen Y, Zhang T, Chen S, Yuan Y, Liang G, Zhang S. Sensitive sensing of alkaline phosphatase and γ-glutamyltranspeptidase activity for tumor imaging. Analyst 2022; 147:1544-1550. [DOI: 10.1039/d2an00163b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mechanism of bioluminescence phenomenon of the probe P-Bz-Luc in the presence of ALP or GGT.
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Affiliation(s)
- Yanyun Yang
- College of Chemistry, Zhengzhou University, 100 Kexue Road, Zhengzhou, Henan 450001, China
| | - Miaomiao Zhang
- College of Chemistry, Zhengzhou University, 100 Kexue Road, Zhengzhou, Henan 450001, China
| | - Wenting Zhang
- School of Ecology and Environment, Zhengzhou University, 100 Kexue Road, Zhengzhou, Henan 450001, China
| | - Yinglu Chen
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Tong Zhang
- School of Life Sciences, University of Science and Technology of China, Huangshan Road, Hefei, Anhui 230027, China
| | - Sheng Chen
- College of Chemistry, Zhengzhou University, 100 Kexue Road, Zhengzhou, Henan 450001, China
| | - Yue Yuan
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Gaolin Liang
- Department of Chemistry, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Shusheng Zhang
- College of Chemistry, Zhengzhou University, 100 Kexue Road, Zhengzhou, Henan 450001, China
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99
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Tsai SJ, Atai NA, Cacciottolo M, Nice J, Salehi A, Guo C, Sedgwick A, Kanagavelu S, Gould SJ. Exosome-mediated mRNA delivery in vivo is safe and can be used to induce SARS-CoV-2 immunity. J Biol Chem 2021; 297:101266. [PMID: 34600888 PMCID: PMC8483990 DOI: 10.1016/j.jbc.2021.101266] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 12/15/2022] Open
Abstract
Functional delivery of mRNA has high clinical potential. Previous studies established that mRNAs can be delivered to cells in vitro and in vivo via RNA-loaded lipid nanoparticles (LNPs). Here we describe an alternative approach using exosomes, the only biologically normal nanovesicle. In contrast to LNPs, which elicited pronounced cellular toxicity, exosomes had no adverse effects in vitro or in vivo at any dose tested. Moreover, mRNA-loaded exosomes were characterized by efficient mRNA encapsulation (∼90%), high mRNA content, consistent size, and a polydispersity index under 0.2. Using an mRNA encoding the red light-emitting luciferase Antares2, we observed that mRNA-loaded exosomes were superior to mRNA-loaded LNPs at delivering functional mRNA into human cells in vitro. Injection of Antares2 mRNA-loaded exosomes also led to strong light emission following injection into the vitreous fluid of the eye or into the tissue of skeletal muscle in mice. Furthermore, we show that repeated injection of Antares2 mRNA-loaded exosomes drove sustained luciferase expression across six injections spanning at least 10 weeks, without evidence of signal attenuation or adverse injection site responses. Consistent with these findings, we observed that exosomes loaded with mRNAs encoding immunogenic forms of the SARS-CoV-2 Spike and Nucleocapsid proteins induced long-lasting cellular and humoral responses to both. Taken together, these results demonstrate that exosomes can be used to deliver functional mRNA to and into cells in vivo.
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Affiliation(s)
- Shang Jui Tsai
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nadia A Atai
- Capricor Therapeutics, Inc, Beverly Hills, California, USA
| | | | - Justin Nice
- Capricor Therapeutics, Inc, Beverly Hills, California, USA
| | - Arjang Salehi
- Capricor Therapeutics, Inc, Beverly Hills, California, USA
| | - Chenxu Guo
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Stephen J Gould
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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100
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Purtov KV, Petushkov VN, Rodionova NS, Chepurnykh TV, Kozhemyako VB, Zagitova RI, Shcheglov AS, Ziganshin RH, Tsarkova AS. Similarities and differences between the Chaetopterus variopedatus polychaete luciferases depending on the type of habitat. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2021. [DOI: 10.24075/brsmu.2021.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The marine polychaete Chaetopterus variopedatus (Renier) (family Chaetopteridae) is a cosmopolitan species complex, consisting of distinct populations/ subspecies. The worms release glowing (460 nm) clouds of mucus when disturbed, and their parapodia often glow brightly. Currently, it is still unclear how exactly the bioluminescence system of these polychaetes functions. It has been previously assumed that the C. variopedatus luciferase may be used for detection of ferroptosis, the recently explored pathway of programmed cell death, resulting from accumulation of the ferrous ions. This study was aimed to extract and characterize the C. variopedatus luciferases, as well as to compare luciferases obtained from C. variopedatus of different populations. When extracting the enzyme responsible for bioluminescence from the frozen samples of Brazilian C. variopedatus using the improved method, two active luciferases, L1 and L2, were obtained. We assumed that one of the listed above luciferases was responsible for luminescence of the mucus and the other luciferase was responsible for luminescence in parapodia, and used the method for the distinct samples of mucus and parapodia of the living Far Eastern C. variopedatus. However, mucus of the latter turned out to be non-glowing. It is shown that luciferase L2 is responsible for luminescence in the parapodia of the C. variopedatus polychaete, since this luciferase has been found in the total biomass of Brazilian polychaetes and parapodia of Far Eastern polychaetes. Luminescence of the Brazilian C. variopedatus mucus is attributed to the functioning of luciferase L1, which is lacking in the mucus of the Far Eastern subspecies. The range of luciferase isoforms in polychaetes C. variopedatus depends on the place of origin.
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Affiliation(s)
- KV Purtov
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - VN Petushkov
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - NS Rodionova
- Institute of Biophysics, Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Sciences
| | - TV Chepurnykh
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - VB Kozhemyako
- Pacific State Medical University, Vladivostok, Russia
| | - RI Zagitova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - AS Shcheglov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - RH Ziganshin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - AS Tsarkova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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