1
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Yang J, Chen Z, Yang Y, Zheng B, Zhu Y, Wu F, Xiong H. Visualization of Endogenous Hypochlorite in Drug-Induced Liver Injury Mice via a Bioluminescent Probe Combined with Firefly Luciferase mRNA-Loaded Lipid Nanoparticles. Anal Chem 2024; 96:6978-6985. [PMID: 38652863 DOI: 10.1021/acs.analchem.4c00008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Drug-induced liver injury (DILI) is a common liver disease with a high rate of morbidity, and its pathogenesis is closely associated with the overproduction of highly reactive hypochlorite (ClO-) in the liver. However, bioluminescence imaging of endogenous hypochlorite in nontransgenic natural mice remains challenging. Herein, to address this issue, we report a strategy for imaging ClO- in living cells and DILI mice by harnessing a bioluminescent probe formylhydrazine luciferin (ClO-Luc) combined with firefly luciferase (fLuc) mRNA-loaded lipid nanoparticles (LNPs). LNPs could efficiently deliver fLuc mRNA into living cells and in vivo, expressing abundant luciferase in the cytoplasm in situ. In the presence of ClO-, probe ClO-Luc locked by formylhydrazine could release cage-free d-luciferin through oxidation and follow-up hydrolysis reactions, further allowing for bioluminescence imaging. Moreover, based on the luciferase-luciferin system, it was able to sensitively and selectively detect ClO- in vitro with a limit of detection of 0.59 μM and successfully monitor the endogenous hypochlorite generation in the DILI mouse model for the first time. We postulate that this work provides a new method to elucidate the roles of ClO- in related diseases via bioluminescence imaging.
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Affiliation(s)
- Jieyu Yang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhaoming Chen
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yuexia Yang
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Bingbing Zheng
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Yu Zhu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Fapu Wu
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hu Xiong
- Research Center for Analytical Sciences, Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University, Tianjin 300071, China
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2
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Pelentir GF, Tomazini A, Bevilaqua VR, Viviani VR. Role of Histidine 310 in Amydetes vivianii firefly luciferase pH and metal sensitivities and improvement of its color tuning properties. Photochem Photobiol Sci 2024:10.1007/s43630-024-00570-1. [PMID: 38693447 DOI: 10.1007/s43630-024-00570-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/28/2024] [Indexed: 05/03/2024]
Abstract
Firefly luciferases emit yellow-green light and are pH-sensitive, changing the bioluminescence color to red in the presence of heavy metals, acidic pH and high temperatures. These pH and metal-sensitivities have been recently harnessed for intracellular pH indication and toxic metal biosensing. However, whereas the structure of the pH sensor and the metal binding site, which consists mainly of two salt bridges that close the active site (E311/R337 and H310/E354), has been identified, the specific role of residue H310 in pH and metal sensing is still under debate. The Amydetes vivianii firefly luciferase has one of the lowest pH sensitivities among the group of pH-sensitive firefly luciferases, displaying high bioluminescent activity and special spectral selectivity for cadmium and mercury, which makes it a promising analytical reagent. Using site-directed mutagenesis, we have investigated in detail the role of residue H310 on pH and metal sensitivity in this luciferase. Negatively charged residues at position 310 increase the pH sensitivity and metal sensitivity; H310G considerably increases the size of the cavity, severely impacting the activity, H310R closes the cavity, and H310F considerably decreases both pH and metal sensitivities. However, no substitution completely abolished pH and metal sensitivities. The results indicate that the presence of negatively charged and basic side chains at position 310 is important for pH sensitivity and metals coordination, but not essential, indicating that the remaining side chains of E311 and E354 may still coordinate some metals in this site. Furthermore, a metal binding site search predicted that H310 mutations decrease the affinity mainly for Zn, Ni and Hg but less for Cd, and revealed the possible existence of additional binding sites for Zn, Ni and Hg.
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Affiliation(s)
- Gabriel F Pelentir
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, Brazil
| | - Atílio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 9190401, Jerusalem, Israel
| | - Vanessa R Bevilaqua
- Biomaterials Laboratory, Pontifical Catholic University-PUC, Sorocaba, SP, Brazil
| | - Vadim R Viviani
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, Brazil.
- Department of Physics, Chemistry and Mathematics, Center for Sustainable Sciences and Technologies (CCTS), UFSCar, Sorocaba, SP, Brazil.
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3
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Colee C, Oberlag NM, Simon M, Chapman OS, Flanagan LC, Reid-McLaughlin ES, Gewing-Mullins JA, Maiche S, Patel DF, Cavalcanti ARO, Leconte AM. Discovery of Red-Shifting Mutations in Firefly Luciferase Using High-Throughput Biochemistry. Biochemistry 2024; 63:733-742. [PMID: 38437583 PMCID: PMC10956436 DOI: 10.1021/acs.biochem.3c00708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/03/2024] [Accepted: 02/20/2024] [Indexed: 03/06/2024]
Abstract
Photinus pyralis luciferase (FLuc) has proven a valuable tool for bioluminescence imaging, but much of the light emitted from the native enzyme is absorbed by endogenous biomolecules. Thus, luciferases displaying red-shifted emission enable higher resolution during deep-tissue imaging. A robust model of how protein structure determines emission color would greatly aid the engineering of red-shifted mutants, but no consensus has been reached to date. In this work, we applied deep mutational scanning to systematically assess 20 functionally important amino acid positions on FLuc for red-shifting mutations, predicting that an unbiased approach would enable novel contributions to this debate. We report dozens of red-shifting mutations as a result, a large majority of which have not been previously identified. Further characterization revealed that mutations N229T and T352M, in particular, bring about unimodal emission with the majority of photons being >600 nm. The red-shifting mutations identified by this high-throughput approach provide strong biochemical evidence for the multiple-emitter mechanism of color determination and point to the importance of a water network in the enzyme binding pocket for altering the emitter ratio. This work provides a broadly applicable mutational data set tying FLuc structure to emission color that contributes to our mechanistic understanding of emission color determination and should facilitate further engineering of improved probes for deep-tissue imaging.
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Affiliation(s)
- Clair
M. Colee
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | - Nicole M. Oberlag
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | - Marcell Simon
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | - Owen S. Chapman
- Department
of Biology, Pomona College, Claremont, California 91711, United States
| | - Lyndsey C. Flanagan
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | - Edison S. Reid-McLaughlin
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | - Jordan A. Gewing-Mullins
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | - Synaida Maiche
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | - Devi F. Patel
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
| | | | - Aaron M. Leconte
- W.M.
Keck Science Department of Claremont McKenna, Pitzer, and Scripps
Colleges, Claremont, California 91711, United States
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4
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Sima W, Yang Y, Sun P, Shi Y, Yuan T, Yang M, Xiong H, Tang X, Niu C. Self-Reporting Microsensors Inspired by Noctiluca Scintillans for Small-Defect Positioning and Electrical-Stress Visualization in Polymers. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2313254. [PMID: 38459423 DOI: 10.1002/adma.202313254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 02/08/2024] [Indexed: 03/10/2024]
Abstract
Small defects induce concentrated electrical stress in dielectric polymers, leading to premature failure of materials. Existing sensing methods fail to effectively visualize these defects owing to the invisible-energy state of the electric field. Thus, it is necessary to establish a nondestructive method for the real-time detection of small defects in dielectric polymers. In this study, a self-reporting microsensor (SRM) inspired by Noctiluca scintillans is designed to endow materials with the ability of self-detection for defects and electrical stress. The SRM leverages the energy of a nearby electric field to emit measurable fluorescence, enabling defect localization and diagnosis as well as electrical-stress visualization. A controllable dielectric microsphere is constructed to achieve an adjustable electroluminescence threshold for the SRM, thereby increasing its detection accuracy while decreasing the electroluminescence threshold. The potential degradation in the polymer performance owing to SRM implantation is addressed by assembling long molecular chains on the SRM surface to spontaneously generate an interpenetrating network. Results of finite element analyses and experiments demonstrate that the SRM can effectively realize nondestructive visualization and positioning of small defects and concentrated electrical stress in polymers, positioning it as a promising sensing method for monitoring the electric field and charge distribution in materials.
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Affiliation(s)
- Wenxia Sima
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Yuhang Yang
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Potao Sun
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Yuning Shi
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Tao Yuan
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Ming Yang
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Hongbo Xiong
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Xinyu Tang
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
| | - Chaolu Niu
- State Key Laboratory of Power Transmission Equipment Technology, School of Electrical Engineering, Chongqing University, Chongqing, 400044, China
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5
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Viviani VR, Benites GR, Souza DR, Pelentir GF, Reis RM, Bechara EJH, Tomazini A. The orange light emitting luciferase from the rare Euryopa clarindae adult railroadworm (Coleoptera:Phengodidae): structural/functional and evolutionary relationship with green and red emitting luciferases. Photochem Photobiol Sci 2024; 23:257-269. [PMID: 38141147 DOI: 10.1007/s43630-023-00515-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Railroadworms luciferases emit the widest range of bioluminescence colors among beetles, ranging from green to red, being model enzymes to investigate the structure and bioluminescence colors relationships. Only three active railroadworms luciferases from the larval stage have been cloned and investigated: the Phrixothrix hirtus head lanterns red-emitting luciferase (PhRE); the Phrixothrix vivianii lateral lanterns green emitting luciferases (PvGR) and the Phengodes sp. dorsal lanterns yellow-green emitting luciferase (Ph). No active luciferase emitting in the yellow-orange region, however, has been cloned yet. Here we report the cloning and characterization of the orange emitting luciferase from the adult males of a rare Brazilian Cerrado railroadworm, Euryopa clarindae, and the transcriptional identification of two isozymes from the Amazon forest Mastinomorphus sp. railroadworm. The luciferase of E. clarindae has 548 residues, emits orange bioluminescence (600 nm), and displays intermediate kinetic values [KM(luciferin) = 50 µM, KM(ATP) ~ 170 µM] between those reported for green-emitting lateral lanterns and red emitting head lanterns luciferases. It displays 74-78% identity with the lateral lanterns luciferases of other railroadworms and 70% with the head lantern PhRE luciferase, and 96% with the larval Mastinomorphus sp. Mast-1, suggesting that this larva could be from the Euryopa genus. The phylogenetic analysis and kinetic/functional properties, place this orange-emitting enzyme as an intermediate form between the green-emitting lateral lanterns and red-emitting head lanterns luciferases. Major structural differences that could be associated with bioluminescence color determination are a relatively larger cavity size, and substitutions in the loops 223-235 and 311-316, especially N/C/T311, and their interactions which may help to close the bottom of LBS.
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Affiliation(s)
- V R Viviani
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil.
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil.
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos, Sorocaba, Brazil.
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), São Carlos, Brazil.
| | - G R Benites
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - D R Souza
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos, Sorocaba, Brazil
| | - G F Pelentir
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Biotechnology, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Raone M Reis
- Departamento de Física, Química e Matemática, CCTS, Federal University of Sao Carlos: Universidade Federal de Sao Carlos, Sorocaba, SP, Brazil
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos, Sorocaba, Brazil
| | | | - Atilio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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6
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Kudo Y, Kumaki F, Nagasaka M, Adachi JI, Noguchi Y, Koga N, Itabashi H, Hiyama M. Experimental and Theoretical Study for Core Excitation of Firefly Luciferin in Carbon K-Edge Spectra. J Phys Chem A 2024; 128:611-617. [PMID: 38227306 DOI: 10.1021/acs.jpca.3c07504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Carbon (C) K-edge X-ray absorption spectra for firefly luciferin were measured and assigned using time-dependent density functional theoretical calculations for luciferin anion and dianion to elucidate the effect of hydroxy-group deprotonation. It was found that the C K-edge spectra for luciferin had four characteristic peaks. The effect of deprotonation of the hydroxy group appears in the energy difference of the first and second peaks of these spectra. This energy difference is 1.0 eV at pH 7 and 2.3 eV at pH 10. The deprotonation of the hydroxy group can be distinguished based on the soft X-ray absorption spectra.
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Affiliation(s)
- Yuto Kudo
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
| | - Fumitoshi Kumaki
- Department of Materials Structure Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Masanari Nagasaka
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
- Department of Functional Molecular Science, School of Physical Sciences, SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
| | - Jun-Ichi Adachi
- Department of Materials Structure Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Yoshifumi Noguchi
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Johoku 3-5-1, Hamamatsu, Shizuoka 432-8561, Japan
| | - Nobuaki Koga
- Graduate School of Informatics, Nagoya University, Nagoya 464-8601, Japan
| | - Hideyuki Itabashi
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
- Gunma University Center for Food Science and Wellness, Maebashi, Gunma 371-8510, Japan
| | - Miyabi Hiyama
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma 376-8515, Japan
- Gunma University Center for Food Science and Wellness, Maebashi, Gunma 371-8510, Japan
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7
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Ugarova NN, Lomakina GY. The role of protein globule in firefly luciferase catalysis. Photochem Photobiol 2024. [PMID: 38235806 DOI: 10.1111/php.13909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/12/2023] [Accepted: 01/04/2024] [Indexed: 01/19/2024]
Abstract
The important role of the dynamic structure of firefly luciferase in enzyme functioning is a subject of this literature review. Due to the domain alternation, the optimal configuration of the active site is created for each stage of the luciferin oxidation. The diversity of bioluminescence spectra is explained by the combined emission of several coexisting forms of electronically excited oxyluciferin. The superposition of two or three emitter forms recorded in the bioluminescence spectra indicates that different luciferase conformers coexist in the reaction medium in dynamic equilibrium. The relationship between the thermal stability of the protein globule and the bioluminescence spectra is also discussed.
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Affiliation(s)
- Natalia N Ugarova
- Faculty of Chemistry, Lomonossov Moscow State University, Moscow, Russia
| | - Galina Yu Lomakina
- Faculty of Chemistry, Lomonossov Moscow State University, Moscow, Russia
- Bauman Moscow State Technical University, Moscow, Russia
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8
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Gerbig D, Schreiner PR. Preparation and Spectroscopic Identification of the Cyclic CO 2 Dimer 1,2-Dioxetanedione. J Am Chem Soc 2023; 145:22341-22346. [PMID: 37812656 DOI: 10.1021/jacs.3c08894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
We report the preparation and infrared spectroscopic identification of 1,2-dioxetanedione, which is one of the two possible cyclic dimers of carbon dioxide. We prepared this hitherto experimentally incompletely characterized species in a solid nitrogen matrix at 3 K from the reaction of oxalyl dichloride with the urea·hydrogen peroxide complex. Surprisingly, irradiation at 254 nm does not lead to its dissociation into carbon dioxide but rather yields cyclic carbon trioxide. We further assert our spectroscopic assignments by 18O isotopic labeling and high-level N-electron valence state perturbation theory and coupled-cluster computations. The successful isolation of 1,2-dioxetanedione supports its viability as the postulated high-energy intermediate in the well-known and ubiquitously exploited "peroxyoxalate" chemiluminescent system.
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Affiliation(s)
- Dennis Gerbig
- Institute of Organic Chemistry, Justus Liebig University, 35392 Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, 35392 Giessen, Germany
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9
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Adams ST, Zephyr J, Bohn MF, Schiffer CA, Miller SC. FruitFire: a luciferase based on a fruit fly metabolic enzyme. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547126. [PMID: 37425765 PMCID: PMC10327219 DOI: 10.1101/2023.06.30.547126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Firefly luciferase is homologous to fatty acyl-CoA synthetases from insects that are not bioluminescent. Here, we determined the crystal structure of the fruit fly fatty acyl-CoA synthetase CG6178 to 2.5 Å. Based on this structure, we mutated a steric protrusion in the active site to create the artificial luciferase FruitFire, which prefers the synthetic luciferin CycLuc2 to d-luciferin by >1000-fold. FruitFire enabled in vivo bioluminescence imaging in the brains of mice using the pro-luciferin CycLuc2-amide. The conversion of a fruit fly enzyme into a luciferase capable of in vivo imaging underscores the potential for bioluminescence with a range of adenylating enzymes from nonluminescent organisms, and the possibilities for application-focused design of enzyme-substrate pairs.
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Affiliation(s)
- Spencer T. Adams
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, 364 Plantation St, Worcester, MA 01605
| | - Jacqueto Zephyr
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, 364 Plantation St, Worcester, MA 01605
| | - Markus F. Bohn
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, 364 Plantation St, Worcester, MA 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, 364 Plantation St, Worcester, MA 01605
| | - Stephen C. Miller
- Department of Biochemistry and Molecular Biotechnology, UMass Chan Medical School, 364 Plantation St, Worcester, MA 01605
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10
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Wu R, Meng B, Corredig M, Griffiths MW. Rapid Detection of Hepatitis A Virus in Foods Using a Bioluminescent Assay in Real-Time (BART) and Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Technology. FOOD AND ENVIRONMENTAL VIROLOGY 2023; 15:144-157. [PMID: 36640204 PMCID: PMC9839959 DOI: 10.1007/s12560-022-09548-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 12/30/2022] [Indexed: 06/13/2023]
Abstract
Foodborne hepatitis A infections have been considered as a major threat for public health worldwide. Increased incidences of hepatitis A virus (HAV) infection has been associated with growing global trade of food products. Rapid and sensitive detection of HAV in foods is very essential for investigating the outbreaks. Real-time RT-PCR has been most widely used for the detection of HAV by far. However, the technology relies on fluorescence determination of the amplicon and requires sophisticated, high-cost instruments and trained personnel, limiting its use in low resource settings. In this study, a robust, affordable, and simple assay, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in combination with a bioluminescence-based determination of amplification in real-time (BART), was developed for the detection of HAV in different food matrices, including green onion, strawberry, mussel, and milk. The efficiencies of a one-step RT-LAMP-BART and a two-step RT-LAMP-BART were investigated for the detection of HAV in different food matrices and was compared with that of real-time RT-PCR. The sensitivity of the RT-LAMP-BART assay was significantly affected by Mg2+ concentration (P < 0.05), in addition to primer quality. The optimal Mg2+ concentration was 2 mM for one-step RT-LAMP-BART and 4 mM for two-step RT-LAMP-BART. Compared with cartridge-purified primers, HPLC-purified primers could greatly improve the sensitivity of the RT-LAMP-BART assay (P < 0.05). For detecting HAV in different food matrices, the performance of two-step RT-LAMP-BART was comparable with that of real-time RT-PCR and was better than that of one-step RT-LAMP-BART. The detection limit of the two-step RT-LAMP-BART for HAV in green onion, strawberry, mussel, and milk was 8.3 × 100 PFU/15 g, 8.3 × 101 PFU/50 g, 8.3 × 100 PFU/5 g, and 8.3 × 100 PFU/40 mL, respectively. The developed RT-LAMP-BART was an effective, simple, sensitive, and robust method for foodborne HAV detection.
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Affiliation(s)
- Ruiqin Wu
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada.
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Milena Corredig
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Mansel W Griffiths
- Department of Food Science, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
- Canadian Research Institute for Food Safety, 43 McGilvray Street, Guelph, ON, N1G 2W1, Canada
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11
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Liu R, Yan ZG, Zhu H, Jia F, Feng X. Energy Stability Property of the CPR Method Based on Subcell Second-Order CNNW Limiting in Solving Conservation Laws. ENTROPY (BASEL, SWITZERLAND) 2023; 25:e25050729. [PMID: 37238484 DOI: 10.3390/e25050729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023]
Abstract
This paper studies the energy stability property of the correction procedure via reconstruction (CPR) method with staggered flux points based on second-order subcell limiting. The CPR method with staggered flux points uses the Gauss point as the solution point, dividing flux points based on Gauss weights, with the flux points being one more point than the solution points. For subcell limiting, a shock indicator is used to detect troubled cells where discontinuities may exist. Troubled cells are calculated by the second-order subcell compact nonuniform nonlinear weighted (CNNW2) scheme, which has the same solution points as the CPR method. The smooth cells are calculated by the CPR method. The linear energy stability of the linear CNNW2 scheme is proven theoretically. Through various numerical experiments, we demonstrate that the CNNW2 scheme and CPR method based on subcell linear CNNW2 limiting are energy-stable and that the CPR method based on subcell nonlinear CNNW2 limiting is nonlinearly stable.
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Affiliation(s)
- Ran Liu
- School of Mathematics and Systems Science, Xinjiang University, Urumqi 830017, China
- State Key Laboratory of Aerodynamics, China Aerodynamics Research and Development Center, Mianyang 621000, China
| | - Zhen-Guo Yan
- State Key Laboratory of Aerodynamics, China Aerodynamics Research and Development Center, Mianyang 621000, China
| | - Huajun Zhu
- State Key Laboratory of Aerodynamics, China Aerodynamics Research and Development Center, Mianyang 621000, China
| | - Feiran Jia
- State Key Laboratory of Aerodynamics, China Aerodynamics Research and Development Center, Mianyang 621000, China
- School of Power and Energy, Northwestern Polytechnical University, Xi'an 710000, China
| | - Xinlong Feng
- School of Mathematics and Systems Science, Xinjiang University, Urumqi 830017, China
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12
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Beyond luciferase-luciferin system: Modification, improved imaging and biomedical application. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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13
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Chang CH, Gómez S, Fontaine DM, Fikas P, Branchini BR, Anderson JC. Bioluminescence, photophysical, computational and molecular docking studies of fully conformationally restricted enamine infraluciferin. Org Biomol Chem 2023; 21:2941-2949. [PMID: 36928464 DOI: 10.1039/d3ob00247k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
A new rationally designed fully rotationally restricted luciferin has been synthesised. This synthetic luciferin, based upon the structure of infraluciferin, has two intramolecular H-bonds to reduce degrees of freedom, an amine group to enhance ICT process, and an alkenyl group to increase π-conjugation. In the spectroscopic measurements and computational calculations, enamine luciferin showed more red-shifted absorption and fluorescence emission than LH2 and iLH2. With PpyWT luciferase enamine luciferin gave bioluminescence at 564 nm which is similar to LH2 at 561 nm. Further investigation by docking studies revealed that the emission wavelength of enamine luciferin might be attributed to the unwanted twisted structure caused by Asp531 within the enzyme. With mutant luciferase FlucRed, the major emission peak was shifted to 606 nm, a distinct shoulder above 700 nm, and 21% of its spectrum located in the nIR range.
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Affiliation(s)
- Chia-Hao Chang
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Sandra Gómez
- Departamento de Quimica Fisica, University of Salamanca, 37008, Spain
| | | | - Panagiotis Fikas
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
| | - Bruce R Branchini
- Department of Chemistry, Connecticut College, New London, CT 06320, USA
| | - James C Anderson
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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14
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Abstract
The genetically encoded fluorescent sensors convert chemical and physical signals into light. They are powerful tools for the visualisation of physiological processes in living cells and freely moving animals. The fluorescent protein is the reporter module of a genetically encoded biosensor. In this study, we first review the history of the fluorescent protein in full emission spectra on a structural basis. Then, we discuss the design of the genetically encoded biosensor. Finally, we briefly review several major types of genetically encoded biosensors that are currently widely used based on their design and molecular targets, which may be useful for the future design of fluorescent biosensors.
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Affiliation(s)
- Minji Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yifan Da
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, No. 3663 Zhong Shan Road North, Shanghai, 200062, China
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15
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Practical Guidance for Developing Small-Molecule Optical Probes for In Vivo Imaging. Mol Imaging Biol 2023; 25:240-264. [PMID: 36745354 DOI: 10.1007/s11307-023-01800-1] [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: 08/23/2022] [Revised: 12/31/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023]
Abstract
The WMIS Education Committee (2019-2022) reached a consensus that white papers on molecular imaging could be beneficial for practitioners of molecular imaging at their early career stages and other scientists who are interested in molecular imaging. With this consensus, the committee plans to publish a series of white papers on topics related to the daily practice of molecular imaging. In this white paper, we aim to provide practical guidance that could be helpful for optical molecular imaging, particularly for small molecule probe development and validation in vitro and in vivo. The focus of this paper is preclinical animal studies with small-molecule optical probes. Near-infrared fluorescence imaging, bioluminescence imaging, chemiluminescence imaging, image-guided surgery, and Cerenkov luminescence imaging are discussed in this white paper.
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16
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Effect of pH on the secondary structure and thermostability of beetle luciferases: structural origin of pH-insensitivity. PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES : OFFICIAL JOURNAL OF THE EUROPEAN PHOTOCHEMISTRY ASSOCIATION AND THE EUROPEAN SOCIETY FOR PHOTOBIOLOGY 2023; 22:893-904. [PMID: 36681778 DOI: 10.1007/s43630-022-00360-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 12/27/2022] [Indexed: 01/22/2023]
Abstract
Beetle luciferases were classified into three functional groups: (1) pH-sensitive yellow-green-emitting (fireflies) which change the bioluminescence color to red at acidic pH, high temperatures and presence of heavy metals; (2) the pH-insensitive green-yellow-emitting (click beetles, railroad worms and firefly isozymes) which are not affected by these factors, and (3) pH-insensitive red-emitting. Although the pH-sensing site in firefly luciferases was recently identified, it is unclear why some luciferases are pH-insensitive despite the presence of some conserved pH-sensing residues. Through circular dichroism, we compared the secondary structural changes and unfolding temperature of luciferases of representatives of these three groups: (1) pH-sensitive green-yellow-emitting Macrolampis sp2 (Mac) and Amydetes vivianii (Amy) firefly luciferases; (2) the pH-insensitive green-emitting Pyrearinus termitilluminans larval click beetle (Pte) and Aspisoma lineatum (Al2) larval firefly luciferases, and (3) the pH-insensitive red-emitting Phrixotrix hirtus railroadworm (PxRE) luciferase. The most blue-shifted luciferases, independently of pH sensitivity, are thermally more stable at different pHs than the red-shifted ones. The pH-sensitive luciferases undergo increases of α-helices and thermal stability above pH 6. The pH-insensitive Pte luciferase secondary structure remains stable between pH 6 and 8, whereas the Al2 luciferase displays an increase of the β-sheet at pH 8. The PxRE luciferase also displays an increase of α-helices at pH 8. The results indicate that green-yellow emission in beetle luciferases can be attained by: (1) a structurally rigid scaffold which stabilizes a single closed active site conformation in the pH-insensitive luciferases, and (2) active site compaction above pH 7.0 in the more flexible pH-sensitive luciferases.
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17
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Satalkar V, Benassi E, Mao Y, Pan X, Ran C, Chen X, Shao Y. Computational Investigation of Substituent Effects on the Fluorescence Wavelengths of Oxyluciferin Analogs. J Photochem Photobiol A Chem 2022; 431:114018. [PMID: 36407037 PMCID: PMC9673899 DOI: 10.1016/j.jphotochem.2022.114018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxyluciferin, which is the light emitter for firefly bioluminescence, has been subjected to extensive chemical modifications to tune its emission wavelength and quantum yield. However, the exact mechanisms for various electron-donating and withdrawing groups to perturb the photophysical properties of oxyluciferin analogs are still not fully understood. To elucidate the substituent effects on the fluorescence wavelength of oxyluciferin analogs, we applied the absolutely localized molecular orbitals (ALMO)-based frontier orbital analysis to assess various types of interactions (i.e. permanent electrostatics/exchange repulsion, polarization, occupied-occupied orbital mixing, virtual-virtual orbital mixing, and charge-transfer) between the oxyluciferin and substituent orbitals. We suggested two distinct mechanisms that can lead to red-shifted oxyluciferin emission wavelength, a design objective that can help increase the tissue penetration of bioluminescence emission. Within the first mechanism, an electron-donating group (such as an amino or dimethylamino group) can contribute its highest occupied molecular orbital (HOMO) to an out-of-phase combination with oxyluciferin's HOMO, thus raising the HOMO energy of the substituted analog and narrowing its HOMO-LUMO gap. Alternatively, an electron-withdrawing group (such as a nitro or cyano group) can participate in an in-phase virtual-virtual orbital mixing of fragment LUMOs, thus lowering the LUMO energy of the substituted analog. Such an ALMO-based frontier orbital analysis is expected to lead to intuitive principles for designing analogs of not only the oxyluciferin molecule, but also many other functional dyes.
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Affiliation(s)
- Vardhan Satalkar
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Enrico Benassi
- Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
| | - Chongzhao Ran
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Charlestown, Boston, MA 02129, USA
| | - Xiaoyuan Chen
- Yong Loo Lin School of Medicine and Faculty of Engineering, National University of Singapore, 117597, Singapore
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA
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18
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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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19
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Al-Handawi MB, Polavaram S, Kurlevskaya A, Commins P, Schramm S, Carrasco-López C, Lui NM, Solntsev KM, Laptenok SP, Navizet I, Naumov P. Spectrochemistry of Firefly Bioluminescence. Chem Rev 2022; 122:13207-13234. [PMID: 35926147 DOI: 10.1021/acs.chemrev.1c01047] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The chemical reactions underlying the emission of light in fireflies and other bioluminescent beetles are some of the most thoroughly studied processes by scientists worldwide. Despite these remarkable efforts, fierce academic arguments continue around even some of the most fundamental aspects of the reaction mechanism behind the beetle bioluminescence. In an attempt to reach a consensus, we made an exhaustive search of the available literature and compiled the key discoveries on the fluorescence and chemiluminescence spectrochemistry of the emitting molecule, the firefly oxyluciferin, and its chemical analogues reported over the past 50+ years. The factors that affect the light emission, including intermolecular interactions, solvent polarity, and electronic effects, were analyzed in the context of both the reaction mechanism and the different colors of light emitted by different luciferases. The collective data points toward a combined emission of multiple coexistent forms of oxyluciferin as the most probable explanation for the variation in color of the emitted light. We also highlight realistic research directions to eventually address some of the remaining questions related to firefly bioluminescence. It is our hope that this extensive compilation of data and detailed analysis will not only consolidate the existing body of knowledge on this important phenomenon but will also aid in reaching a wider consensus on some of the mechanistic details of firefly bioluminescence.
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Affiliation(s)
- Marieh B Al-Handawi
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Srujana Polavaram
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Anastasiya Kurlevskaya
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Patrick Commins
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Stefan Schramm
- Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany
| | - César Carrasco-López
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Nathan M Lui
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Kyril M Solntsev
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Sergey P Laptenok
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Isabelle Navizet
- Univ. Gustave Eiffel, Univ. Paris Est Creteil, CNRS, UMR 8208, MSME, F-77454 Marne-la-Vallée, France
| | - Panče Naumov
- Smart Materials Lab (SML), New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.,Molecular Design Institute, Department of Chemistry, New York University, 100 Washington Square East, New York, New York 10003, United States
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20
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Jara MDL, Alvarez LAC, Guimarães MCC, Antunes PWP, de Oliveira JP. Lateral flow assay applied to pesticides detection: recent trends and progress. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:46487-46508. [PMID: 35507227 PMCID: PMC9067001 DOI: 10.1007/s11356-022-20426-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 04/20/2022] [Indexed: 06/14/2023]
Abstract
Devices based on lateral flow assay (LFA) have been gaining more and more space in the detection market mainly due to their simplicity, speed, and low cost. These devices have excellent sensing format versatility and make these strips an ideal choice for field applications. The COVID-19 pandemic boosted the democratization of this method as a "point of care testing" (POCT), and the trend is that these devices become protagonists for the monitoring of pesticides in the environment. However, designing LFA devices for detecting and monitoring pesticides in the environment is still a challenge. This is because analytes are small molecules and have only one antigenic determinant, which makes it difficult to apply direct immunoassays. Furthermore, most LFA devices provide only qualitative or semi-quantitative results and have a limited number of applications in multi-residue analysis. Here, we present the state of the art on the use of LFA in the environmental monitoring of pesticides. Based on well-documented results, we review all available LFA formats and strategies for pesticide detection, which may have important implications for the future of monitoring pesticides in the environment. The main advances, challenges, and perspectives of these devices for a direction in this field of study are also presented.
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Affiliation(s)
- Marcia Daniela Lazo Jara
- Department of Morphology, Federal University of Espirito Santo, Av Marechal Campos1468, Vitória, ES, 29.040-090, Brazil
| | | | - Marco C C Guimarães
- Department of Morphology, Federal University of Espirito Santo, Av Marechal Campos1468, Vitória, ES, 29.040-090, Brazil
| | - Paulo Wagnner Pereira Antunes
- Bioengen Consulting, Engineering and Environmental Planning, R. Belo Horizonte, Lote 05-Quadra W - Alterosas, Serra, ES, 29168-068, Brazil
| | - Jairo Pinto de Oliveira
- Department of Morphology, Federal University of Espirito Santo, Av Marechal Campos1468, Vitória, ES, 29.040-090, Brazil.
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21
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Cloning and molecular properties of a novel luciferase from the Brazilian Bicellonycha lividipennis (Lampyridae: Photurinae) firefly: comparison with other firefly luciferases. Photochem Photobiol Sci 2022; 21:1559-1571. [PMID: 35590087 DOI: 10.1007/s43630-022-00240-0] [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: 03/02/2022] [Accepted: 04/25/2022] [Indexed: 10/18/2022]
Abstract
Several firefly luciferases eliciting light emission in the yellow-green range of the spectrum and with distinct kinetic properties have been already cloned, sequenced, and characterized. Some of them are currently being applied as analytical reagents and reporter genes for bioimaging and biosensors, and more recently as potential color tuning indicators of intracellular pH and toxic metals. They were cloned from the subfamilies Lampyrinae (Photinini: Photinus pyralis, Macrolampis sp2; Cratomorphini: Cratomorphus distinctus), Photurinae (Photuris pennsylvanica), Luciolinae (Luciola cruciata, L. lateralis, L. mingrelica, L. italica, Hotaria parvula), and Amydetinae (Amydetes vivianii) occurring in different parts of the world. The largest number has been cloned from fireflies occurring in Brazilian biomes. Taking advantage of the large biodiversity of fireflies occurring in the Brazilian Atlantic rainforest, here we report the cloning and characterization of a novel luciferase cDNA from the Photurinae subfamily, Bicellonycha lividipennis, which is a very common firefly in marshlands in Brazil. As expected, multialignements and phylogenetic analysis show that this luciferase clusters with Photuris pennsylvanica adult isozyme, and with other adult lantern firefly luciferases, in reasonable agreement with traditional phylogenetic analysis. The luciferase elicits light emission in the yellow-green region, has kinetics properties similar to other adult lantern firefly luciferases, including pH- and metal sensitivities, but displays a lower sensitivity to nickel, which is suggested to be caused by the natural substitution of H310Y.
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22
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Cao Z, Li D, Zhao L, Liu M, Ma P, Luo Y, Yang X. Bioorthogonal in situ assembly of nanomedicines as drug depots for extracellular drug delivery. Nat Commun 2022; 13:2038. [PMID: 35440570 PMCID: PMC9018704 DOI: 10.1038/s41467-022-29693-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 03/29/2022] [Indexed: 12/11/2022] Open
Abstract
Developing precise nanomedicines to improve the transport of anticancer drugs into tumor tissue and to the final action site remains a critical challenge. Here, we present a bioorthogonal in situ assembly strategy for prolonged retention of nanomedicines within tumor areas to act as drug depots. After extravasating into the tumor site, the slightly acidic microenvironment induces the exposure of cysteine on the nanoparticle surface, which subsequently undergoes a bioorthogonal reaction with the 2-cyanobenzothiazole group of another neighboring nanoparticle, enabling the formation of micro-sized drug depots to enhance drug retention and enrichment. This in situ nanoparticle assembly strategy remarkably improves the antimetastatic efficacy of extracellular-targeted drug batimastat, and also leads to the simultaneous enhanced retention and sustained release of multiple agents for combined cocktail chemoimmunotherapy to finally elicit a potent antitumor immune response. Such in situ assembly of nanomedicines represents a generalizable strategy towards extracellular drug delivery and cocktail chemoimmunotherapy. Delivering the correct concentration of drugs to the correct location is a challenge in cancer therapy. Here, the authors generate a drug loaded nanoparticle that enlarges following contact with the internal tumour cell environment, resulting in the retention of the nanoparticle and loaded drugs in cancer cells.
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Affiliation(s)
- Ziyang Cao
- Department of General Surgery, Guangzhou First People's Hospital, South China University of Technology, 510006, Guangzhou, P. R. China.,School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, 511442, Guangzhou, P. R. China
| | - Dongdong Li
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, 511442, Guangzhou, P. R. China
| | - Liang Zhao
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, 511442, Guangzhou, P. R. China.,National Engineering Research Center for Tissue Restoration and Reconstruction, and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, 510006, Guangzhou, P. R. China
| | - Mengting Liu
- School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, 511442, Guangzhou, P. R. China
| | - Pengyue Ma
- Department of General Surgery, Guangzhou First People's Hospital, South China University of Technology, 510006, Guangzhou, P. R. China
| | - Yingli Luo
- National Engineering Research Center for Tissue Restoration and Reconstruction, and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, 510006, Guangzhou, P. R. China.,Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, and Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, 510006, Guangzhou, P. R. China
| | - Xianzhu Yang
- Department of General Surgery, Guangzhou First People's Hospital, South China University of Technology, 510006, Guangzhou, P. R. China. .,School of Biomedical Sciences and Engineering, South China University of Technology, Guangzhou International Campus, 511442, Guangzhou, P. R. China. .,National Engineering Research Center for Tissue Restoration and Reconstruction, and Key Laboratory of Biomedical Engineering of Guangdong Province, South China University of Technology, 510006, Guangzhou, P. R. China. .,Key Laboratory of Biomedical Materials and Engineering of the Ministry of Education, and Innovation Center for Tissue Restoration and Reconstruction, South China University of Technology, 510006, Guangzhou, P. R. China.
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23
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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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24
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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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25
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Liu C, Chen C, Tu C, Hung S, Chao C. Structure colorants based on cross‐linked cholesteric liquid crystalline polymeric slices. J Appl Polym Sci 2022. [DOI: 10.1002/app.51717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Chun‐Yen Liu
- Department of Materials Science and Engineering National Cheng Kung University Tainan City Taiwan
| | - Cheng‐Chieh Chen
- Department of Chemical Engineering National Cheng Kung University Tainan City Taiwan
| | - Chia‐Ming Tu
- Department of Materials Science and Engineering National Cheng Kung University Tainan City Taiwan
| | - Sheng‐Chi Hung
- Department of Materials Science and Engineering National Cheng Kung University Tainan City Taiwan
| | - Chia‐Hui Chao
- Department of Materials Science and Engineering National Cheng Kung University Tainan City Taiwan
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Kim SB, Fujii R, Miller S, Tanabe M. Molecular Tension Probe for In Vitro Bioassays. Methods Mol Biol 2022; 2524:91-103. [PMID: 35821465 DOI: 10.1007/978-1-0716-2453-1_7] [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
Cell-free bioassays (CFBs) provide their own distinctive merits over cell-based bioassays (CBBs) including (i) rapid and on-site applicability, (ii) long-term utility, and (iii) bioanalytical versatility. The authors previously introduced a unique bioluminescent imaging probe for illuminating molecular tension appended by protein-protein interactions (PPIs) of interest. In this chapter, we exemplify that a full-length artificial luciferase is sandwiched between FRB (FKBP-rapamycin-binding domain of FKBP12-rapamycin-associated protein) and FKBP (FK506-binding protein) via minimal flexible linkers, named FRB-A23-FKBP. The rapamycin-activated PPIs between FRB and FKBP append molecular tension to the sandwiched luciferase, enhancing the enzymatic activity in a quantitative manner. The fusion protein, FRB-A23-FKBP, is three-step column-purified and the bioanalytical utility is characterized in various CFB conditions. This chapter guides the detailed protocols from the purification to the practical bioassays of FRB-A23-FKBP.
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Affiliation(s)
- Sung-Bae Kim
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan.
| | - Rika Fujii
- Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi, Japan
| | - Mikio Tanabe
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki, Japan
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27
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Liu Y, Huang Z, Li Z. Molecular Imaging of Tumor Progression and Angiogenesis by Dual Bioluminescence. Methods Mol Biol 2022; 2524:457-469. [PMID: 35821492 DOI: 10.1007/978-1-0716-2453-1_34] [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
Angiogenesis is a prerequisite for tumor growth and invasion, and anti-angiogenesis has become a highlight in tumor treatment research. However, so far, there is no reliable solution for how to simultaneously visualize the relationship between tumor progression and angiogenesis. Bioluminescence imaging (BLI) has been broadly utilized and is a very promising non-invasive imaging technique with the advantages of low cost, high sensitivity, and robust specificity. In this chapter, we describe a dual bioluminescence imaging BLI protocol for tumor progression and angiogenesis through implanting murine breast cancer cell line 4T1 which stably expressing Renilla luciferase (RLuc) into the transgenic mice with angiogenesis-induced firefly luciferase (FLuc) expression. This modality enables us to synchronously monitor the tumor progression and angiogenesis in the same mouse, which has broad applicability in oncology studies.
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Affiliation(s)
- Yue Liu
- School of Medicine, Nankai University, Tianjin, China
- The Key Laboratory of Bioactive Materials, The College of Life Science, Ministry of Education, Nankai University, Tianjin, China
| | - Ziyu Huang
- School of Medicine, Nankai University, Tianjin, China
- The Key Laboratory of Bioactive Materials, The College of Life Science, Ministry of Education, Nankai University, Tianjin, China
| | - Zongjin Li
- School of Medicine, Nankai University, Tianjin, China.
- The Key Laboratory of Bioactive Materials, The College of Life Science, Ministry of Education, Nankai University, Tianjin, China.
- Tianjin Key Laboratory of Human Development and Reproductive Regulation, Nankai University Affiliated Hospital of Obstetrics and Gynecology, Tianjin, China.
- State Key Laboratory of Kidney Diseases, Chinese PLA General Hospital, Beijing, China.
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28
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Liang Y, Li Z. Split-Luciferase Complementation for Analysis of Virus-Host Protein Interactions. Methods Mol Biol 2022; 2400:55-62. [PMID: 34905190 DOI: 10.1007/978-1-0716-1835-6_6] [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: 06/14/2023]
Abstract
Productive viral infection entails highly regulated and sequential protein-protein interactions between viral factors and between virus and host factors. Deciphering such interactions is of paramount importance for a better understanding of virus infection cycles and the development of new strategies for virus prevention and control. In this protocol, we describe a split-luciferase complementation (SLC ) assay for the detection of protein-protein interaction in Nicotiana benthamiana leaves following agroinfiltration-mediated transient protein expression. In this assay, the firefly luciferase protein is divided into two halves, each expressed as a fusion to a prey or bait protein, respectively. Interaction of the two candidate proteins brings the two otherwise nonfunctional halves into close proximity to restore the luciferase activity, which catalyzes the substrate D-luciferin to emit luminescence. The SLC assay allows for noninvasive, quantitative measurement of dynamic protein interactions in living cells within their native cellular compartments.
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Affiliation(s)
- Yan Liang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhenghe Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
- Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Zhejiang University, Hangzhou, China.
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29
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Abstract
An efficient construction of amides through NHC-mediated oxidation of imines is described. This work has the advantages of wide scope, fast assembly and high yield, and can avoid the use of coupling agents, such as HATU, DCC, etc.
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Affiliation(s)
- Shaofa Sun
- College of Chemistry and Biological Sciences, Hubei University of Science and Technology, Hubei, 437100, China
| | - Donghui Guo
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Fangyi Li
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, P. R. China
| | - Jian Wang
- College of Chemistry and Biological Sciences, Hubei University of Science and Technology, Hubei, 437100, China
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, P. R. China
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30
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Sarrion-Perdigones A, Gonzalez Y, Chang L, Gallego-Flores T, Young DW, Venken KJT. Multiplex Hextuple Luciferase Assaying. Methods Mol Biol 2022; 2524:433-456. [PMID: 35821491 PMCID: PMC10157609 DOI: 10.1007/978-1-0716-2453-1_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We recently expanded the commonly used dual luciferase assaying method toward multiplex hextuple luciferase assaying, allowing monitoring the activity of five experimental pathways against one control at the same time. In doing so, while our expanded assay utilizes a total of six orthogonal luciferases instead of two, this assay, conveniently, still utilizes the well-established reagents and principles of the widely used dual luciferase assay. Three quenchable D-luciferin-consuming luciferases are measured after addition of D-Luciferin substrate, followed by quenching of their bioluminescence (BL) and the measurement of three coelenterazine (CTZ)-consuming luciferases after addition of CTZ substrate, all in the same vessel. Here, we provide detailed protocols on how to perform such multiplex hextuple luciferase assaying to monitor cellular signal processing upstream of five transcription factors and their corresponding transcription factor-binding motifs, using a constitutive promoter as normalization control. The first protocol is provided on how to perform cell culture in preparation toward genetic or pharmaceutical perturbations, as well as transfecting a multiplex hextuple luciferase reporter vector encoding all luciferase reporter units needed for multiplex hextuple luciferase assaying. The second protocol details on how to execute multiplex hextuple luciferase assaying using a microplate reader appropriately equipped to detect the different BLs emitted by all six luciferases. Finally, the third protocol provides details on analyzing, plotting, and interpreting the data obtained by the microplate reader.
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Affiliation(s)
- Alejandro Sarrion-Perdigones
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Yezabel Gonzalez
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Lyra Chang
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA
| | - Tatiana Gallego-Flores
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Max Planck Institute for Brain Research, Frankfurt am Main, Germany
| | - Damian W Young
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Koen J T Venken
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA.
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX, USA.
- Center for Drug Discovery, Baylor College of Medicine, Houston, TX, USA.
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- McNair Medical Institute at The Robert and Janice McNair Foundation, Baylor College of Medicine, Houston, TX, USA.
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31
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Azad T, Janse van Rensburg HJ, Morgan J, Rezaei R, Crupi MJF, Chen R, Ghahremani M, Jamalkhah M, Forbes N, Ilkow C, Bell JC. Luciferase-Based Biosensors in the Era of the COVID-19 Pandemic. ACS NANOSCIENCE AU 2021; 1:15-37. [PMID: 37579261 PMCID: PMC8370122 DOI: 10.1021/acsnanoscienceau.1c00009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Luciferase-based biosensors have a wide range of applications and assay formats, including their relatively recent use in the study of viruses. Split luciferase, bioluminescence resonance energy transfer, circularly permuted luciferase, cyclic luciferase, and dual luciferase systems have all been used to interrogate the structure and function of prominent viruses infecting humans, animals, and plants. The utility of these assays is demonstrated by numerous studies which have not only successfully characterized interactions between viral and host cell proteins but that have also used these systems to identify viral inhibitors. In the present COVID-19 pandemic, luciferase-based biosensors are already playing a critical role in the study of the culprit virus SARS-CoV-2 as well as in the development of serological assays and drug development via high-throughput screening. In this review paper, we provide a summary of existing luciferase-based biosensors and their applications in virology.
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Affiliation(s)
- Taha Azad
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | | | - Jessica Morgan
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Reza Rezaei
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mathieu J. F. Crupi
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Rui Chen
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Mina Ghahremani
- Canada
Department of Biology, University of Ottawa, Ottawa K1N 6N5, Canada
| | - Monire Jamalkhah
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Nicole Forbes
- Centre
for Communicable Diseases and Infection Control, Public Health Agency of Canada, Ottawa K2E 1B6, Canada
| | - Carolina Ilkow
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
| | - John C. Bell
- Centre
for Innovative Cancer Research, Ottawa Hospital
Research Institute, Ottawa K1H 8L6, Canada
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa K1H 8M5, Canada
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32
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de Vries S, Fürst-Jansen JMR, Irisarri I, Dhabalia Ashok A, Ischebeck T, Feussner K, Abreu IN, Petersen M, Feussner I, de Vries J. The evolution of the phenylpropanoid pathway entailed pronounced radiations and divergences of enzyme families. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:975-1002. [PMID: 34165823 DOI: 10.1111/tpj.15387] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/11/2021] [Accepted: 06/21/2021] [Indexed: 05/20/2023]
Abstract
Land plants constantly respond to fluctuations in their environment. Part of their response is the production of a diverse repertoire of specialized metabolites. One of the foremost sources for metabolites relevant to environmental responses is the phenylpropanoid pathway, which was long thought to be a land-plant-specific adaptation shaped by selective forces in the terrestrial habitat. Recent data have, however, revealed that streptophyte algae, the algal relatives of land plants, have candidates for the genetic toolkit for phenylpropanoid biosynthesis and produce phenylpropanoid-derived metabolites. Using phylogenetic and sequence analyses, we here show that the enzyme families that orchestrate pivotal steps in phenylpropanoid biosynthesis have independently undergone pronounced radiations and divergence in multiple lineages of major groups of land plants; sister to many of these radiated gene families are streptophyte algal candidates for these enzymes. These radiations suggest a high evolutionary versatility in the enzyme families involved in the phenylpropanoid-derived metabolism across embryophytes. We suggest that this versatility likely translates into functional divergence, and may explain the key to one of the defining traits of embryophytes: a rich specialized metabolism.
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Affiliation(s)
- Sophie de Vries
- Population Genetics, Heinrich-Heine University Düsseldorf, Universitätsstr. 1, 40225, Düsseldorf, Germany
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Janine M R Fürst-Jansen
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Iker Irisarri
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077, Goettingen, Germany
| | - Amra Dhabalia Ashok
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
| | - Till Ischebeck
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Kirstin Feussner
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Ilka N Abreu
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Maike Petersen
- Institut für Pharmazeutische Biologie und Biotechnologie, Philipps-Universität Marburg, Robert-Koch-Str. 4, 35037, Marburg, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, University of Goettingen, Albrecht-von-Haller-Institute for Plant Sciences, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Goettingen Center for Molecular Biosciences (GZMB), Goettingen Metabolomics and Lipidomics Laboratory, University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Justus-von-Liebig Weg 11, 37077, Goettingen, Germany
| | - Jan de Vries
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Goettingen, Goldschmidtstr. 1, 37077, Goettingen, Germany
- University of Goettingen, Campus Institute Data Science (CIDAS), Goldschmidstr. 1, 37077, Goettingen, Germany
- Department of Applied Bioinformatics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goldschmidtsr. 1, 37077, Goettingen, Germany
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Xie J, Wang Y, Choi W, Jangili P, Ge Y, Xu Y, Kang J, Liu L, Zhang B, Xie Z, He J, Xie N, Nie G, Zhang H, Kim JS. Overcoming barriers in photodynamic therapy harnessing nano-formulation strategies. Chem Soc Rev 2021; 50:9152-9201. [PMID: 34223847 DOI: 10.1039/d0cs01370f] [Citation(s) in RCA: 186] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Photodynamic therapy (PDT) has been extensively investigated for decades for tumor treatment because of its non-invasiveness, spatiotemporal selectivity, lower side-effects, and immune activation ability. It can be a promising treatment modality in several medical fields, including oncology, immunology, urology, dermatology, ophthalmology, cardiology, pneumology, and dentistry. Nevertheless, the clinical application of PDT is largely restricted by the drawbacks of traditional photosensitizers, limited tissue penetrability of light, inefficient induction of tumor cell death, tumor resistance to the therapy, and the severe pain induced by the therapy. Recently, various photosensitizer formulations and therapy strategies have been developed to overcome these barriers. Significantly, the introduction of nanomaterials in PDT, as carriers or photosensitizers, may overcome the drawbacks of traditional photosensitizers. Based on this, nanocomposites excited by various light sources are applied in the PDT of deep-seated tumors. Modulation of cell death pathways with co-delivered reagents promotes PDT induced tumor cell death. Relief of tumor resistance to PDT with combined therapy strategies further promotes tumor inhibition. Also, the optimization of photosensitizer formulations and therapy procedures reduces pain in PDT. Here, a systematic summary of recent advances in the fabrication of photosensitizers and the design of therapy strategies to overcome barriers in PDT is presented. Several aspects important for the clinical application of PDT in cancer treatment are also discussed.
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Affiliation(s)
- Jianlei Xie
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, Institute of Microscale Optoelectronics, and Otolaryngology Department and Biobank of the First Affiliated Hospital, Shenzhen Second People's Hospital, Health Science Center, Shenzhen University, Shenzhen 518060, P. R. China.
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34
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Light from a firefly at temperatures considerably higher and lower than normal. Sci Rep 2021; 11:12498. [PMID: 34127729 PMCID: PMC8203691 DOI: 10.1038/s41598-021-91839-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/24/2021] [Indexed: 11/08/2022] Open
Abstract
Bioluminescence emissions from a few species of fireflies have been studied at different temperatures. Variations in the flash-duration have been observed and interesting conclusions drawn in those studies. Here we investigate steady-state and pulsed emissions from male specimens of the Indian species Sclerotia substriata at temperatures considerably higher and lower than the ones at which they normally flash. When the temperature is raised to 34 °C, the peak wavelength gets red-shifted and the emitted pulses become the narrowest which broaden considerably thereafter for small increases in temperature; this probably indicates denaturation of the enzyme luciferase catalyzing the light-producing reaction. When the temperature is decreased to the region of 10.5-9 °C, the peak gets blue-shifted and the flash-duration increased abnormally with large fluctuation; this possibly implies cold denaturation of the luciferase. We conclude that the first or hot effect is very likely to be the reason of the species being dark-active on hot days, and the second or cold one is the probable reason for its disappearance at the onset of the winter. Our study makes the inference that these two happenings determine the temperature-tolerance, which plays a major role in the selection of the habitat for the firefly.
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35
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Noguchi Y, Hiyama M, Shiga M, Akiyama H, Sugino O. Quantum-mechanical hydration plays critical role in the stability of firefly oxyluciferin isomers: State-of-the-art calculations of the excited states. J Chem Phys 2021; 153:201103. [PMID: 33261487 DOI: 10.1063/5.0031356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Stabilizing mechanisms of three possible isomers (phenolate-keto, phenolate-enol, and phenol-enolate) of the oxyluciferin anion hydrated with quantum explicit water molecules in the first singlet excited state were investigated using first-principles Born-Oppenheimer molecular dynamics simulations for up to 1.8 ns (or 3.7 × 106 MD steps), revealing that the surrounding water molecules were distributed to form clear single-layered structures for phenolate-keto and multi-layered structures for phenolate-enol and phenol-enolate isomers. The isomers employed different stabilizing mechanisms compared to the ground state. Only the phenolate-keto isomer became attracted to the water molecules in its excited state and was stabilized by increasing the number of hydrogen bonds with nearby water molecules. The most stable isomer in the excited state was the phenolate-keto, and the phenolate-enol and phenol-enolate isomers were higher in energy by ∼0.38 eV and 0.57 eV, respectively, than the phenolate-keto. This was in contrast to the case of ground state in which the phenolate-enol was the most stable isomer.
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Affiliation(s)
- Yoshifumi Noguchi
- Department of Applied Chemistry and Biochemical Engineering, Graduate School of Engineering, Shizuoka University, Johoku 3-5-1, Hamamatsu, Shizuoka 432-8561, Japan
| | - Miyabi Hiyama
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Motoyuki Shiga
- Center for Computational Science and E-Systems, Japan Atomic Energy Agency, 148-4 Kashiwanoha Campus, 178-4 Wakashiba, Kashiwa, Chiba 277-0871, Japan
| | - Hidefumi Akiyama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Osamu Sugino
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
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Bevilaqua VR, Carvalho MC, Pelentir GF, Tomazini A, Murakami M, Viviani VR. Influence of the C-terminal domain on the bioluminescence activity and color determination in green and red emitting beetle luciferases and luciferase-like enzyme. Photochem Photobiol Sci 2021; 20:113-122. [PMID: 33721241 DOI: 10.1007/s43630-020-00007-5] [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: 11/04/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
Beetle luciferases catalyze the bioluminescent oxidation of D-luciferin, producing bioluminescence colors ranging from green to red, using two catalytic steps: adenylation of D-luciferin to produce D-luciferyl-adenylate and PPi, and oxidation of D-luciferyl-adenylate, yielding AMP, CO2, and excited oxyluciferin, the emitter. Luciferases and CoA-ligases display a similar fold, with a large N-terminal domain, and a small C-terminal domain which undergoes rotation, closing the active site and promoting both adenylation and oxidative reactions. The effect of C-terminal domain deletion was already investigated for Photinus pyralis firefly luciferase, resulting in a red-emitting mutant with severely impacted luminescence activity. However, the contribution of C-terminal in the bioluminescence activities and colors of other beetle luciferases and related ancestral luciferases were not investigated yet. Here we compared the effects of the C-terminal domain deletion on green-emitting luciferases of Pyrearinus termitilluminans (Pte) click beetle and Phrixothrix vivianii railroadworm, and on the red-emitting luciferase of Phrixothrix hirtus railroadworm and luciferase-like enzyme of Zophobas morio. In all cases, the domain deletion severely impacted the overall bioluminescence activities and, slightly less, the oxidative activities, and usually red-shifted the bioluminescence colors. The results support the involvement of the C-terminal in shielding the active site from the solvent during the light emitting step. However, in Pte luciferase, the deletion caused only a 10 nm red-shift, indicating a distinctive active site which remains more shielded, independently of the C'-terminal. Altogether, the results confirm the main contribution of the C-terminal for the catalysis of the adenylation reaction and for active site shielding during the light emitting step.
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Affiliation(s)
- V R Bevilaqua
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Mariele C Carvalho
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil
| | - Gabriel F Pelentir
- Department of Physics, Chemistry and Mathematics, Federal University of São Carlos (UFSCar), Sorocaba, Brazil
| | - Atílio Tomazini
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Mario Murakami
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - Vadim R Viviani
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil. .,Department of Physics, Chemistry and Mathematics, Federal University of São Carlos (UFSCar), Sorocaba, Brazil. .,Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Rod. João Leme Dos Santos, SP 264, Km 110, Itinga, Sorocaba, SP, Brazil.
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37
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Liu CX, Liu QB, Dong K, Huang SJ, Yang XK, Ren AM, Min CG, Liu G. Theoretically obtained insight into the effect of basic amino acids on Cypridina bioluminescence. J Photochem Photobiol A Chem 2021. [DOI: 10.1016/j.jphotochem.2020.113000] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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38
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Li S, Ruan Z, Zhang H, Xu H. Recent achievements of bioluminescence imaging based on firefly luciferin-luciferase system. Eur J Med Chem 2020; 211:113111. [PMID: 33360804 DOI: 10.1016/j.ejmech.2020.113111] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/26/2020] [Accepted: 12/13/2020] [Indexed: 02/06/2023]
Abstract
Bioluminescence imaging (BLI) is a newly developed noninvasive visual approach which facilitates the understanding of a plethora of biological processes in vitro and in vivo due to the high sensitivity, resolution and selectivity, low background signal, and the lack of external light excitation. BLI based on firefly luciferin-luciferase system has been widely used for the activity evaluation of tumor-specific enzymes, for the detection of diseases-related bioactive small molecules and metal ions, and for the diagnosis and therapy of diseases including the studies of drug transport, the research of immune response, and the evaluation of drug potency and tissue distribution. In this review, we highlight the recent achievements in luciferin derivatives with red-shifted emission spectra, mutant luciferase-luciferin pairs, and the diagnostic and therapeutic application of BLI based on firefly luciferin-luciferase system. The development and application of BLI will expand our knowledge of the occurrence and development of diseases and shed light on the diagnosis and treatment of various diseases.
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Affiliation(s)
- Shufeng Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Zhiyang Ruan
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Hang Zhang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China.
| | - Haiwei Xu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Co-innovation Center of Henan Province for New Drug R&D and Preclinical Safety, and School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, 450001, China.
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Shi C, Killoran MP, Hall MP, Otto P, Wood MG, Strauss E, Encell LP, Machleidt T, Wood KV, Kirkland TA. 5,5-Dialkylluciferins are thermal stable substrates for bioluminescence-based detection systems. PLoS One 2020; 15:e0243747. [PMID: 33315907 PMCID: PMC7735563 DOI: 10.1371/journal.pone.0243747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/26/2020] [Indexed: 11/18/2022] Open
Abstract
Firefly luciferase-based ATP detection assays are frequently used as a sensitive, cost-efficient method for monitoring hygiene in many industrial settings. Solutions of detection reagent, containing a mixture of a substrate and luciferase enzyme that produces photons in the presence of ATP, are relatively unstable and maintain only a limited shelf life even under refrigerated conditions. It is therefore common for the individual performing a hygiene test to manually prepare fresh reagent at the time of monitoring. To simplify sample processing, a liquid detection reagent with improved thermal stability is needed. The engineered firefly luciferase, Ultra-Glo™, fulfills one aspect of this need and has been valuable for hygiene monitoring because of its high resistance to chemical and thermal inactivation. However, solutions containing both Ultra-Glo™ luciferase and its substrate luciferin gradually lose the ability to effectively detect ATP over time. We demonstrate here that dehydroluciferin, a prevalent oxidative breakdown product of luciferin, is a potent inhibitor of Ultra-Glo™ luciferase and that its formation in the detection reagent is responsible for the decreased ability to detect ATP. We subsequently found that dialkylation at the 5-position of luciferin (e.g., 5,5-dimethylluciferin) prevents degradation to dehydroluciferin and improves substrate thermostability in solution. However, since 5,5-dialkylluciferins are poorly utilized by Ultra-Glo™ luciferase as substrates, we used structural optimization of the luciferin dialkyl modification and protein engineering of Ultra-Glo™ to develop a luciferase/luciferin pair that shows improved total reagent stability in solution at ambient temperature. The results of our studies outline a novel luciferase/luciferin system that could serve as foundations for the next generation of bioluminescence ATP detection assays with desirable reagent stability.
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Affiliation(s)
- Ce Shi
- Promega Biosciences, Inc., San Luis Obispo, California, United States of America
| | | | - Mary P. Hall
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Paul Otto
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Monika G. Wood
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Ethan Strauss
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Lance P. Encell
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Thomas Machleidt
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Keith V. Wood
- Promega Corporation, Madison, Wisconsin, United States of America
| | - Thomas A. Kirkland
- Promega Biosciences, Inc., San Luis Obispo, California, United States of America
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Carrasco-López C, Lui NM, Schramm S, Naumov P. The elusive relationship between structure and colour emission in beetle luciferases. Nat Rev Chem 2020; 5:4-20. [PMID: 37118106 DOI: 10.1038/s41570-020-00238-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2020] [Indexed: 12/23/2022]
Abstract
In beetles, luciferase enzymes catalyse the conversion of chemical energy into light through bioluminescence. The principles of this process have become a fundamental biotechnological tool that revolutionized biological research. Different beetle species can emit different colours of light, despite using the same substrate and highly homologous luciferases. The chemical reasons for these different colours are hotly debated yet remain unresolved. This Review summarizes the structural, biochemical and spectrochemical data on beetle bioluminescence reported over the past three decades. We identify the factors that govern what colour is emitted by wild-type and mutant luciferases. This topic is controversial, but, in general, we note that green emission requires cationic residues in a specific position near the benzothiazole fragment of the emitting molecule, oxyluciferin. The commonly emitted green-yellow light can be readily changed to red by introducing a variety of individual and multiple mutations. However, complete switching of the emitted light from red to green has not been accomplished and the synergistic effects of combined mutations remain unexplored. The minor colour shifts produced by most known mutations could be important in establishing a 'mutational catalogue' to fine-tune emission of beetle luciferases, thereby expanding the scope of their applications.
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Oba Y, Konishi K, Yano D, Shibata H, Kato D, Shirai T. Resurrecting the ancient glow of the fireflies. SCIENCE ADVANCES 2020; 6:6/49/eabc5705. [PMID: 33268373 PMCID: PMC7710365 DOI: 10.1126/sciadv.abc5705] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 10/20/2020] [Indexed: 06/12/2023]
Abstract
The color of firefly bioluminescence is determined by the structure of luciferase. Firefly luciferase genes have been isolated from more than 30 species, producing light ranging in color from green to orange-yellow. Here, we reconstructed seven ancestral firefly luciferase genes, characterized the enzymatic properties of the recombinant proteins, and determined the crystal structures of the gene from ancestral Lampyridae. Results showed that the synthetic luciferase for the last common firefly ancestor exhibited green light caused by a spatial constraint on the luciferin molecule in enzyme, while fatty acyl-CoA synthetic activity, an original function of firefly luciferase, was diminished in exchange. All known firefly species are bioluminescent in the larvae, with a common ancestor arising approximately 100 million years ago. Combined, our findings propose that, within the mid-Cretaceous forest, the common ancestor of fireflies evolved green light luciferase via trade-off of the original function, which was likely aposematic warning display against nocturnal predation.
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Affiliation(s)
- Y Oba
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Japan.
| | - K Konishi
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - D Yano
- Department of Environmental Biology, Chubu University, Kasugai 487-8501, Japan
| | - H Shibata
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - D Kato
- Graduate School of Science and Engineering, Kagoshima University, Kagoshima 890-0065, Japan
| | - T Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama 526-0829, Japan.
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Carvalho MC, Tomazini A, Amaral DT, Murakami MT, Viviani VR. Luciferase isozymes from the Brazilian Aspisoma lineatum (Lampyridae) firefly: origin of efficient pH-sensitive lantern luciferases from fat body pH-insensitive ancestors. Photochem Photobiol Sci 2020; 19:1750-1764. [PMID: 33241249 DOI: 10.1039/d0pp00272k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Firefly luciferases usually emit green-yellow bioluminescence at physiological pH values. However, under acidic conditions, in the presence of heavy metals and, at high temperatures they emit red bioluminescence. To understand the structural origin of bioluminescence colors and pH-sensitivity, about 20 firefly luciferases have been cloned, sequenced and investigated. The proton and metal-binding site responsible for pH- and metal sensitivity in firefly luciferases was shown to involve the residues H310, E311 and E354 in firefly luciferases. However, it is still unclear how and why pH-sensitivity arose and evolved in firefly luciferases. Here, we cloned and characterized two novel luciferase cDNAs from the fat body and lanterns of the Brazilian firefly Aspisoma lineatum. The larval fat body isozyme (AL2) has 545 residues, and displays very slow luminescence kinetics and a pH-insensitive spectrum. The adult lantern isozyme (AL1) has 548 residues, displays flash-like kinetics and pH and metal sensitive bioluminescence spectra, and is at least 10 times catalytically more efficient than AL2. Thermostability and CD studies showed that AL2 is much more stable and rigid than the AL1 isozyme. Multialignment and modelling studies show that the E310Q substitution (E310 in AL2 and Q310 in AL1) may have been critical for the origin of pH-sensitivity in firefly luciferases. The results indicate that the lantern efficient flash-emitting pH-sensitive luciferases arose from less efficient glow-type pH-insensitive luciferases found in the fat body of ancestral larval fireflies by enzyme structure flexibilization and substitution at position 310.
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Affiliation(s)
- M C Carvalho
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, Brazil.
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de Paiva FCR, Chan K, Samborskyy M, Silber AM, Leadlay PF, Dias MVB. The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:1201-1210. [DOI: 10.1107/s2059798320013431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 10/07/2020] [Indexed: 11/10/2022]
Abstract
Adenylate-forming enzymes (AFEs) are a mechanistic superfamily of proteins that are involved in many cellular roles. In the biosynthesis of benzoxazole antibiotics, an AFE has been reported to play a key role in the condensation of cyclic molecules. In the biosynthetic gene cluster for the benzoxazole AJI9561, AjiA1 catalyzes the condensation of two 3-hydroxyanthranilic acid (3-HAA) molecules using ATP as a co-substrate. Here, the enzymatic activity of AjiA1 is reported together with a structural analysis of its apo form. The structure of AjiA1 was solved at 2.0 Å resolution and shows a conserved fold with other AFE family members. AjiA1 exhibits activity in the presence of 3-HAA (K
m = 77.86 ± 28.36, k
cat = 0.04 ± 0.004) and also with the alternative substrate 3-hydroxybenzoic acid (3-HBA; K
m = 22.12 ± 31.35, k
cat = 0.08 ± 0.005). The structure of AjiA1 in the apo form also reveals crucial conformational changes that occur during the catalytic cycle of this enzyme which have not been described for any other AFE member. Consequently, the results shown here provide insights into this protein family and a new subgroup is proposed for enzymes that are involved in benzoxazole-ring formation.
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Viviani VR, Pelentir GF, Oliveira G, Tomazini A, Bevilaqua VR. Role of E270 in pH- and metal-sensitivities of firefly luciferases. Photochem Photobiol Sci 2020; 19:1548-1558. [PMID: 33146219 DOI: 10.1039/d0pp00190b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Firefly luciferases display a typical change in bioluminescence color to red at acidic pH, high temperatures and in the presence of heavy metals. Recently, the proton and metal sensing site responsible for the pH-sensitivity of firefly luciferases, which involves the salt bridges between E311-R337 and H310-E354, was identified. However, it is unclear what other residues contribute to the distinct degrees of pH-sensitivity observed in other firefly luciferases. A multialignment of primary structures of a large set of pH-sensitive and pH-insensitive beetle luciferases showed that the conserved E270 among adult firefly luciferases is substituted by Gly (railroad worms)/Gln (click-beetles) in pH-insensitive ones. Site-directed mutagenesis studies using Macrolampis sp2 and Amydetes vivianii firefly luciferases indeed showed that E270 is important for the pH-dependent activity and spectral profiles: the substitution E270A/G drastically decreases the spectral pH-sensitivity, and extends the activity profile above pH 9.0. These mutations also decrease the sensitivity to metals such as zinc, mercury and cadmium. Modelling studies showed that the residue E270 is located in a three-glutamate motif (269EEE271) at the N-terminal of α-helix-10. The results suggest that at acidic pH, the protonation of E270 carboxylate may extend a turn of the helix at the N-terminal, misaligning the pH-sensor and luciferin phenolate binding site residues: S286, I288 and E311. In contrast, the substitution of E270A/G may unwind a turn of the α-helix-10, indirectly increasing the interaction of the pH-sensor and other residues at the bottom of the luciferin binding site, stabilizing the green light emitting conformation.
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Affiliation(s)
- V R Viviani
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, Itinga, Sorocaba, SP, Brazil. and Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
| | - G F Pelentir
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), Rodovia João Leme dos Santos, Km 110, Itinga, Sorocaba, SP, Brazil.
| | - G Oliveira
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
| | - A Tomazini
- Brazilian Biorenewables Energy National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | - V R Bevilaqua
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
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de Almeida Barbosa NM, Gosset P, Réal E, Ledentu V, Didier P, Ferré N. pH-Dependent absorption spectrum of oxyluciferin analogues in the active site of firefly luciferase. Phys Chem Chem Phys 2020; 22:21731-21740. [PMID: 32985625 DOI: 10.1039/d0cp02514c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the quest for the identification of the light emitter(s) responsible for the firefly bioluminescence, the study of oxyluciferin analogues with controlled chemical and electronic structures is of particular importance. In this article, we report the results of our experimental and computational investigation of the pH-dependent absorption spectra characterizing three analogues bound into the luciferase cavity, together with adenosine-monophosphate (AMP). While the analogue microscopic pKa values do not differ much from their reference values, it turns out that the AMP protonation state is analogue-dependent and never doubly-deprotonated. A careful analysis of the interactions evidences the main role of E344 glutamic acid, as well as the flexibility of the cavity which can accommodate any oxyluciferin analogue. The consideration of the absorption spectra suggests that the oxyluciferin enolate form has to be excluded from the list of the bioluminescence reaction products.
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Affiliation(s)
| | - Pauline Gosset
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
| | - Eléonore Réal
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
| | | | - Pascal Didier
- Université de Strasbourg, UMR 7021 CNRS, Laboratoire de Bioimagerie et Pathologies, Strasbourg, France
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46
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Recent progress in the design principles, sensing mechanisms, and applications of small-molecule probes for nitroreductases. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213460] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Zhang R, He J, Dong Z, Liu G, Yin Y, Zhang X, Li Q, Ren Y, Yang Y, Liu W, Chen X, Xia W, Duan K, Hao F, Lin Z, Yang J, Chang Z, Zhao R, Wan W, Lu S, Peng Y, Ge S, Wang W, Li X. Genomic and experimental data provide new insights into luciferin biosynthesis and bioluminescence evolution in fireflies. Sci Rep 2020; 10:15882. [PMID: 32985577 PMCID: PMC7522259 DOI: 10.1038/s41598-020-72900-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 09/09/2020] [Indexed: 02/08/2023] Open
Abstract
Fireflies are among the most charismatic insects for their spectacular bioluminescence, but the origin and evolution of bioluminescence remain elusive. Especially, the genic basis of luciferin (D-luciferin) biosynthesis and light patterns is largely unknown. Here, we present the high-quality reference genomes of two fireflies Lamprigera yunnana (1053 Mb) and Abscondita terminalis (501 Mb) with great differences in both morphology and luminous behavior. We sequenced the transcriptomes and proteomes of luminous organs of two species. We created the CRISPR/Cas9-induced mutants of Abdominal B gene without luminous organs in the larvae of A. terminalis and sequenced the transcriptomes of mutants and wild-types. Combining gene expression analyses with comparative genomics, we propose a more complete luciferin synthesis pathway, and confirm the convergent evolution of bioluminescence in insects. Using experiments, the function of the firefly acyl-CoA thioesterase (ACOT1) to convert L-luciferin to D-luciferin was validated for the first time. Comparisons of three-dimension reconstruction of luminous organs and their differentially expressed genes among two species suggest that two positive genes in the calcium signaling pathway and structural difference of luminous organs may play an important role in the evolution of flash pattern. Altogether, our results provide important resources for further exploring bioluminescence in insects.
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Affiliation(s)
- Ru Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Jinwu He
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Zhiwei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Guichun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yuan Yin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Xinying Zhang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qi Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Yandong Ren
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Yongzhi Yang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Xianqing Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Wenhao Xia
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Kang Duan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Fei Hao
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Zeshan Lin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Jie Yang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Zhou Chang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Ruoping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Wenting Wan
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China
| | - Sihan Lu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China
| | - Yanqiong Peng
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China
| | - Siqin Ge
- Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, Shaanxi, China.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
- Center for Excellence in Animal Evolution and Genetics, Kunming, 650223, Yunnan, China.
| | - Xueyan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, Yunnan, China.
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Abstract
Bioluminescence (BL) is an excellent optical readout platform that has great potential to be utilized in various bioassays and molecular imaging. The advantages of BL-based bioassays include the long dynamic range, minimal background, high signal-to-noise ratios, biocompatibility for use in cell-based assays, no need of external light source for excitation, simplicity in the measurement system, and versatility in the assay design. The recent intensive research in BL has greatly diversified the available luciferase-luciferin systems in the bioassay toolbox. However, the wide variety does not promise their successful utilization in various bioassays as new tools. This is mainly due to complexity and confusion with the diversity, and the unavailability of defined standards. This review is intended to provide an overview of recent basic developments and applications in BL studies, and showcases the bioanalytical utilities. We hope that this review can be used as an instant reference on BL and provides useful guidance for readers in narrowing down their potential options in their own assay designs.
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Affiliation(s)
- Sung-Bae Kim
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST)
| | - Ramasamy Paulmurugan
- Molecular Imaging Program at Stanford, Bio-X Program, Stanford University School of Medicine
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49
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Endo M, Ozawa T. Advanced Bioluminescence System for In Vivo Imaging with Brighter and Red-Shifted Light Emission. Int J Mol Sci 2020; 21:E6538. [PMID: 32906768 PMCID: PMC7555964 DOI: 10.3390/ijms21186538] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/03/2020] [Accepted: 09/04/2020] [Indexed: 01/04/2023] Open
Abstract
In vivo bioluminescence imaging (BLI), which is based on luminescence emitted by the luciferase-luciferin reaction, has enabled continuous monitoring of various biochemical processes in living animals. Bright luminescence with a high signal-to-background ratio, ideally red or near-infrared light as the emission maximum, is necessary for in vivo animal experiments. Various attempts have been undertaken to achieve this goal, including genetic engineering of luciferase, chemical modulation of luciferin, and utilization of bioluminescence resonance energy transfer (BRET). In this review, we overview a recent advance in the development of a bioluminescence system for in vivo BLI. We also specifically examine the improvement in bioluminescence intensity by mutagenic or chemical modulation on several beetle and marine luciferase bioluminescence systems. We further describe that intramolecular BRET enhances luminescence emission, with recent attempts for the development of red-shifted bioluminescence system, showing great potency in in vivo BLI. Perspectives for future improvement of bioluminescence systems are discussed.
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Affiliation(s)
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
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50
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Davis CR, Johnson CH, Robertson JB. A bioluminescent reporter for the halophilic archaeon Haloferax volcanii. Extremophiles 2020; 24:773-785. [PMID: 32749548 PMCID: PMC7462420 DOI: 10.1007/s00792-020-01193-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/21/2020] [Indexed: 12/19/2022]
Abstract
Haloarchaea have evolved to thrive in hypersaline environments. Haloferax volcanii is of particular interest due to its genetic tractability; however, few in vivo reporters exist for halophiles. Haloarchaeal proteins evolved characteristics that promote proper folding and function at high salt concentrations, but many mesophilic reporter proteins lack these characteristics. Mesophilic proteins that acquire salt-stabilizing mutations, however, can lead to proper function in haloarchaea. Using laboratory-directed evolution, we developed and demonstrated an in vivo luciferase that functions in the hypersaline cytosol of H. volcanii.
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Affiliation(s)
- Chris R Davis
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA
| | - Carl H Johnson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - J Brian Robertson
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, USA.
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