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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; 23:997-1010. [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] [MESH Headings] [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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2
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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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3
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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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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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5
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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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6
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Implementation of the Bio-Inspired Metaheuristic Firefly Algorithm (FA) Applied to Maximum Power Point Tracking of Photovoltaic Systems. ENERGIES 2022. [DOI: 10.3390/en15155338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
In this paper, an algorithm for the maximum extraction of energy generated by photovoltaic (PV) systems was presented. The tracking of the global maximum point of the system is complex due to the non-linearity of the current-voltage (I-V) characteristic curve of the photovoltaic modules, as they vary according to the temperature and solar irradiation in the module. To obtain the best energy efficiency in these systems, it is important that the generation is delivering the maximum power available through the arrangement. In order to solve such problems, in this work an efficient MPPT-FA method was proposed, which showed good traceability when compared to traditional methods. Most traditional MPPT techniques are not able to find the global maximum point to extract the maximum power provided by the PV system. Finally, the Firefly Metaheuristic MPPT method proved to be robust against several partial shading scenarios. Simulations were presented to demonstrate the effectiveness of the proposal when compared to the traditional MPPT-PO method.
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7
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Bioluminescence Color-Tuning Firefly Luciferases: Engineering and Prospects for Real-Time Intracellular pH Imaging and Heavy Metal Biosensing. BIOSENSORS 2022; 12:bios12060400. [PMID: 35735548 PMCID: PMC9221268 DOI: 10.3390/bios12060400] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/18/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022]
Abstract
Firefly luciferases catalyze the efficient production of yellow-green light under normal physiological conditions, having been extensively used for bioanalytical purposes for over 5 decades. Under acidic conditions, high temperatures and the presence of heavy metals, they produce red light, a property that is called pH-sensitivity or pH-dependency. Despite the demand for physiological intracellular biosensors for pH and heavy metals, firefly luciferase pH and metal sensitivities were considered drawbacks in analytical assays. We first demonstrated that firefly luciferases and their pH and metal sensitivities can be harnessed to estimate intracellular pH variations and toxic metal concentrations through ratiometric analysis. Using Macrolampis sp2 firefly luciferase, the intracellular pH could be ratiometrically estimated in bacteria and then in mammalian cells. The luciferases of Macrolampis sp2 and Cratomorphus distinctus fireflies were also harnessed to ratiometrically estimate zinc, mercury and other toxic metal concentrations in the micromolar range. The temperature was also ratiometrically estimated using firefly luciferases. The identification and engineering of metal-binding sites have allowed the development of novel luciferases that are more specific to certain metals. The luciferase of the Amydetes viviani firefly was selected for its special sensitivity to cadmium and mercury, and for its stability at higher temperatures. These color-tuning luciferases can potentially be used with smartphones for hands-on field analysis of water contamination and biochemistry teaching assays. Thus, firefly luciferases are novel color-tuning sensors for intracellular pH and toxic metals. Furthermore, a single luciferase gene is potentially useful as a dual bioluminescent reporter to simultaneously report intracellular ATP and/or luciferase concentrations luminometrically, and pH or metal concentrations ratiometrically, providing a useful tool for real-time imaging of intracellular dynamics and stress.
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8
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Jathoul AP, Branchini BR, Anderson JC, Murray JAH. A higher spectral range of beetle bioluminescence with infraluciferin. Front Bioeng Biotechnol 2022; 10:897272. [PMID: 36091447 PMCID: PMC9459109 DOI: 10.3389/fbioe.2022.897272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
Coleopteran bioluminescence is unique in that beetle luciferases emit colors ranging between green (ca.550 nm) and red (ca.600 nm), including intermediate colors such as yellow and orange, allowing up to 3 simultaneous parameters to be resolved in vitro with natural luciferin (D-LH2). Here, we report a more than doubling of the maximum bioluminescence wavelength range using a single synthetic substrate, infraluciferin (iLH2). We report that different luciferases can emit colors ranging from visible green to near-infrared (nIR) with iLH2, including in human cells. iLH2 was designed for dual color far-red to nIR bioluminescence imaging (BLI) in small animals and has been utilized in different mouse models of cancer (including a metastatic hepatic model showing detailed hepatic morphology) and for robust dual parameter imaging in vivo (including in systemic hematological models). Here, we report the properties of different enzymes with iLH2: Lampyrid wild-type (WT) Photinus pyralis (Ppy) firefly luciferase, Ppy-based derivatives previously engineered to be thermostable with D-LH2, and also color-shifted Elaterid-based enzymes: blue-shifted Pyrearinus termitilluminans derivative Eluc (reported D-LH2 λmax = 538 nm) and red-shifted Pyrophorus plagiopthalamus derivative click beetle red (CBR) luciferase (D-LH2 λmax = 618 nm). As purified enzyme, in bacteria or in human cells, Eluc emitted green light (λmax = 536 nm) with DL-iLH2 whereas Ppy Fluc (λmax = 689 nm), x2 Fluc (λmax = 704 nm), x5 Fluc (λmax = 694 nm), x11 Fluc (λmax = 694 nm) and CBR (λmax = 721 nm) produced far-red to nIR peak wavelengths. Therefore, with iLH2, enzyme λmaxes can be separated by ca.185nm, giving almost non-overlapping spectra. This is the first report of single-substrate bioluminescence color emission ranging from visible green to nIR in cells and may help shed light on the color tuning mechanism of beetle luciferases. We also report on the reason for the improvement in activity of x11 Fluc with iLH2 and engineer an improved infraluciferase (iluc) based on this mutant.
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Affiliation(s)
- Amit P Jathoul
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom.,Bioflares Ltd., Trowbridge, Wiltshire, United Kingdom
| | | | - James C Anderson
- Department of Chemistry, University College London, London, United Kingdom
| | - James A H Murray
- School of Biosciences, University of Cardiff, Cardiff, United Kingdom
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9
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Belleti E, Bevilaqua VR, Brito AMM, Modesto DA, Lanfredi AJC, Viviani VR, Nantes-Cardoso IL. Synthesis of bioluminescent gold nanoparticle-luciferase hybrid systems for technological applications. Photochem Photobiol Sci 2021; 20:1439-1453. [PMID: 34613602 PMCID: PMC8493054 DOI: 10.1007/s43630-021-00111-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/27/2021] [Indexed: 11/01/2022]
Abstract
Bioluminescent gold nanoparticles (AuNPs) were synthesized in situ using dithiol-terminated polyethylene glycol (PEG(SH)2) as reducer and stabilizing agents. Hybrid Au/F3O4 nanoparticles were also produced in a variation of synthesis, and both types of nanostructures had the polymer capping replaced by L-cysteine (Cys). The four types of nanoparticles, PEG(SH)2AuNPs, PEG(SH)2Au/F3O4NPs, CysAuNPs, and CysAu/F3O4NPs were associated with purified recombinant Pyrearinus termitilluminans green emitting click beetle luciferase (PyLuc) and Phrixotrix hirtus (RELuc) red-emitting railroad worm luciferase. Enzyme association with PEG(SH)2 was also investigated as a control. Luciferases were chosen because they catalyze bioluminescent reactions used in a wide range of bioanalytical applications, including ATP assays, gene reporting, high-throughput screening, bioluminescence imaging, biosensors and other bioluminescence-based assays. The immobilization of PyLuc and RELuc promoted partial suppression of the enzyme luminescence activity in a functionalization-dependent way. Association of PyLuc and RELuc with AuNPs increased the enzyme operational stability in relation to the free enzyme, as evidenced by the luminescence intensity from 0 to 7 h after substrate addition. The stability of the immobilized enzymes was also functionalization-dependent and the association with CysAuNPs was the condition that combined more sustained luminescent activity with a low degree of luminescence quenching. The higher enzymatic stability and sustained luminescence of luciferases associated with nanoparticles may improve the applicability of bioluminescence for bioimaging and biosensing purposes.
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Affiliation(s)
- Elisângela Belleti
- Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Bairro Bangu, Santo André, SP, 09210-580, Brazil
| | - Vanessa R Bevilaqua
- Graduate School of Evolutive Genetics and Molecular Biology (UFSCar), São Carlos, SP, Brazil
| | - Adrianne M M Brito
- Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Bairro Bangu, Santo André, SP, 09210-580, Brazil
| | - Diego A Modesto
- Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Bairro Bangu, Santo André, SP, 09210-580, Brazil
| | - Alexandre J C Lanfredi
- Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Bairro Bangu, Santo André, SP, 09210-580, Brazil
| | - Vadim R Viviani
- Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Bairro Bangu, Santo André, SP, 09210-580, Brazil
- Graduate School of Biotechnology and Environmental Monitoring (UFSCar), Sorocaba, SP, Brazil
| | - Iseli L Nantes-Cardoso
- Universidade Federal do ABC (UFABC), Av. dos Estados, 5001, Bairro Bangu, Santo André, SP, 09210-580, Brazil.
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10
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Yao Z, Caldwell DR, Love AC, Kolbaba-Kartchner B, Mills JH, Schnermann MJ, Prescher JA. Coumarin luciferins and mutant luciferases for robust multi-component bioluminescence imaging. Chem Sci 2021; 12:11684-11691. [PMID: 34659703 PMCID: PMC8442684 DOI: 10.1039/d1sc03114g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/20/2021] [Indexed: 12/21/2022] Open
Abstract
Multi-component bioluminescence imaging requires an expanded collection of luciferase-luciferin pairs that emit far-red or near-infrared light. Toward this end, we prepared a new class of luciferins based on a red-shifted coumarin scaffold. These probes (CouLuc-1s) were accessed in a two-step sequence via direct modification of commercial dyes. The bioluminescent properties of the CouLuc-1 analogs were also characterized, and complementary luciferase enzymes were identified using a two-pronged screening strategy. The optimized enzyme-substrate pairs displayed robust photon outputs and emitted a significant portion of near-infrared light. The CouLuc-1 scaffolds are also structurally distinct from existing probes, enabling rapid multi-component imaging. Collectively, this work provides novel bioluminescent tools along with a blueprint for crafting additional fluorophore-derived probes for multiplexed imaging.
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Affiliation(s)
- Zi Yao
- Department of Chemistry, University of California Irvine CA USA
| | - Donald R Caldwell
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Anna C Love
- Department of Chemistry, University of California Irvine CA USA
| | - Bethany Kolbaba-Kartchner
- School of Molecular Sciences, Arizona State University Tempe AZ USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University Tempe AZ USA
| | - Jeremy H Mills
- School of Molecular Sciences, Arizona State University Tempe AZ USA
- The Biodesign Center for Molecular Design and Biomimetics, Arizona State University Tempe AZ USA
| | - Martin J Schnermann
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute Frederick MD USA
| | - Jennifer A Prescher
- Department of Chemistry, University of California Irvine CA USA
- Department of Molecular Biology & Biochemistry, University of California Irvine CA USA
- Department of Pharmaceutical Sciences, University of California Irvine CA USA
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11
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Viviani VR, Bevilaqua VR, de Souza DR, Pelentir GF, Kakiuchi M, Hirano T. A Very Bright Far-Red Bioluminescence Emitting Combination Based on Engineered Railroad Worm Luciferase and 6'-Amino-Analogs for Bioimaging Purposes. Int J Mol Sci 2020; 22:E303. [PMID: 33396708 PMCID: PMC7794784 DOI: 10.3390/ijms22010303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 12/18/2022] Open
Abstract
Beetle luciferases produce bioluminescence (BL) colors ranging from green to red, having been extensively used for many bioanalytical purposes, including bioimaging of pathogen infections and metastasis proliferation in living animal models and cell culture. For bioimaging purposes in mammalian tissues, red bioluminescence is preferred, due to the lower self-absorption of light at longer wavelengths by hemoglobin, myoglobin and melanin. Red bioluminescence is naturally produced only by Phrixothrix hirtus railroad worm luciferase (PxRE), and by some engineered beetle luciferases. However, Far-Red (FR) and Near-Infrared (NIR) bioluminescence is best suited for bioimaging in mammalian tissues due to its higher penetrability. Although some FR and NIR emitting luciferin analogs have been already developed, they usually emit much lower bioluminescence activity when compared to the original luciferin-luciferases. Using site-directed mutagenesis of PxRE luciferase in combination with 6'-modified amino-luciferin analogs, we finally selected novel FR combinations displaying BL ranging from 636-655 nm. Among them, the combination of PxRE-R215K mutant with 6'-(1-pyrrolidinyl)luciferin proved to be the best combination, displaying the highest BL activity with a catalytic efficiency ~2.5 times higher than the combination with native firefly luciferin, producing the second most FR-shifted bioluminescence (650 nm), being several orders of magnitude brighter than commercial AkaLumine with firefly luciferase. Such combination also showed higher thermostability, slower BL decay time and better penetrability across bacterial cell membranes, resulting in ~3 times higher in vivo BL activity in bacterial cells than with firefly luciferin. Overall, this is the brightest FR emitting combination ever reported, and is very promising for bioimaging purposes in mammalian tissues.
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Affiliation(s)
- Vadim R. Viviani
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), 18052-780 São Carlos, São Paulo, Brazil;
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), 18119-001 Sorocaba, São Paulo, Brazil;
| | - Vanessa R. Bevilaqua
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), 18052-780 São Carlos, São Paulo, Brazil;
| | - Daniel R. de Souza
- Graduate Program of Biotechnology and Environmental Monitoring, Federal University of São Carlos (UFSCar), 18119-001 Sorocaba, São Paulo, Brazil;
| | - Gabriel F. Pelentir
- Department of Physics, Chemistry and Mathematics, Federal University of São Carlos (UFSCar), 18052-780 São Carlos, São Paulo, Brazil;
| | - Michio Kakiuchi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585, Japan; (M.K.); (T.H.)
| | - Takashi Hirano
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585, Japan; (M.K.); (T.H.)
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12
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Zambito G, Hall MP, Wood MG, Gaspar N, Ridwan Y, Stellari FF, Shi C, Kirkland TA, Encell LP, Löwik C, Mezzanotte L. Red-shifted click beetle luciferase mutant expands the multicolor bioluminescent palette for deep tissue imaging. iScience 2020; 24:101986. [PMID: 33490896 PMCID: PMC7811125 DOI: 10.1016/j.isci.2020.101986] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/07/2020] [Accepted: 12/21/2020] [Indexed: 12/21/2022] Open
Abstract
For in vivo multicolor bioluminescence applications, red and near-infrared signals are desirable over shorter wavelength signals because they are not as susceptible to light attenuation by blood and tissue. Herein, we describe the development of a new click beetle luciferase mutant, CBG2, with a red-shifted color emission. When paired with NH2-NpLH2 luciferin, CBG2 (λ = 660 nm) and CBR2 (λ = 730 nm) luciferases can be used for simultaneous dual-color bioluminescence imaging in deep tissue. Using a spectral unmixing algorithm tool it is possible to distinguish each spectral contribution. Ultimately, this enzyme pair can expand the near-infrared bioluminescent toolbox to enable rapid visualization of multiple biological processes in deep tissue using a single substrate. CBG2 is a new click beetle mutant derived from CBG99 luciferase It has a far red-shifted bioluminescent emission with NH2-NpLH2 luciferin (λ = 660 nm) CBG2 with CBR2 luciferase and NH2-NpLH2 allows fast acquisition of data in deep tissue
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Affiliation(s)
- Giorgia Zambito
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, 3015 CE, the Netherlands.,Erasmus Medical Center, Molecular Genetics, Rotterdam, 3015 CE, the Netherlands.,Medres Medical Research GmBH, Cologne 50931, Germany
| | | | | | - Natasa Gaspar
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, 3015 CE, the Netherlands.,Erasmus Medical Center, Molecular Genetics, Rotterdam, 3015 CE, the Netherlands.,Percuros B.V., Leiden, 1333 CL, the Netherlands
| | - Yanto Ridwan
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, 3015 CE, the Netherlands.,Erasmus Medical Center, Molecular Genetics, Rotterdam, 3015 CE, the Netherlands
| | | | - Ce Shi
- Promega Biosciences Incorporated, San Luis Obispo, CA 93401, USA
| | | | | | - Clemens Löwik
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, 3015 CE, the Netherlands.,Erasmus Medical Center, Molecular Genetics, Rotterdam, 3015 CE, the Netherlands.,CHUV Department of Oncology, University of Lausanne, 461011 Lausanne, Switzerland
| | - Laura Mezzanotte
- Erasmus Medical Center, Radiology and Nuclear Medicine, Rotterdam, 3015 CE, the Netherlands.,Erasmus Medical Center, Molecular Genetics, Rotterdam, 3015 CE, the Netherlands
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13
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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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14
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Yao Z, Zhang BS, Steinhardt RC, Mills JH, Prescher JA. Multicomponent Bioluminescence Imaging with a π-Extended Luciferin. J Am Chem Soc 2020; 142:14080-14089. [PMID: 32787261 PMCID: PMC7867379 DOI: 10.1021/jacs.0c01064] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Bioluminescence imaging with luciferase-luciferin pairs is commonly used for monitoring biological processes in cells and whole organisms. Traditional bioluminescent probes are limited in scope, though, as they cannot be easily distinguished in biological environments, precluding efforts to visualize multicellular processes. Additionally, many luciferase-luciferin pairs emit light that is poorly tissue penetrant, hindering efforts to visualize targets in deep tissues. To address these issues, we synthesized a set of π-extended luciferins that were predicted to be red-shifted luminophores. The scaffolds were designed to be rotationally labile such that they produced light only when paired with luciferases capable of enforcing planarity. A luciferin comprising an intramolecular "lock" was identified as a viable light-emitting probe. Native luciferases were unable to efficiently process the analog, but a complementary luciferase was identified via Rosetta-guided enzyme design. The unique enzyme-substrate pair is red-shifted compared to well-known bioluminescent tools. The probe set is also orthogonal to other luciferase-luciferin probes and can be used for multicomponent imaging. Four substrate-resolved luciferases were imaged in a single session. Collectively, this work provides the first example of Rosetta-guided design in engineering bioluminescent tools and expands the scope of orthogonal imaging probes.
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Affiliation(s)
- Zi Yao
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Brendan S. Zhang
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Rachel C. Steinhardt
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Jeremy H. Mills
- Department of Chemistry and Biochemistry, Arizona State University, Tempe AZ, USA
- The Center for Molecular Design and Biomimetics, Arizona State University, Tempe AZ, USA
- The Biodesign Institute, Arizona State University, Tempe AZ, USA
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697, United States
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
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15
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Yu M, Liu YJ. Same Luciferin in Different Luciferases Emitting Different-Color Light. A Theoretical Study on Beetle Bioluminescence. J Chem Theory Comput 2020; 16:3904-3909. [PMID: 32396347 DOI: 10.1021/acs.jctc.0c00074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bioluminescent beetles, firefly, click beetle, and railroad worm, naturally emit different-color light via the identical luciferin and bioluminescence (BL) mechanisms. Railroad worm especially emits two colors of light in its dorsal-lateral and cephalic lanterns. Four computational models of bioluminophore (oLu) in luciferases of red-emitting, yellow-green-emitting, red-emitting with additional loop, and red-emitting without C-terminal were built in this paper. To unveil the details of this luciferase effect at the molecular and electronic-state levels, second-order multiconfigurational perturbation calculations were performed following molecular dynamic simulations and time-dependent density functional calculations for the above four oLu-luciferase systems. Via a systematic analysis on properties of oLu at the first singlet state (S1-oLu) in different luciferases, one clearly see the details of the microenvironment and secondary structure of luciferase affecting the excited-state property of S1-oLu, which ultimately result in the variant color of light emission. Typically, the increase in charge transfer of S1-oLu leads to the longer wavelength BL.
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Affiliation(s)
- Mohan Yu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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16
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Branchini BR, Fontaine DM, Southworth TL, Huta BP, Racela A, Patel KD, Gulick AM. Mutagenesis and Structural Studies Reveal the Basis for the Activity and Stability Properties That Distinguish the Photinus Luciferases scintillans and pyralis. Biochemistry 2019; 58:4293-4303. [PMID: 31560532 DOI: 10.1021/acs.biochem.9b00719] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The dazzling yellow-green light emission of the common North American firefly Photinus pyralis and other bioluminescent organisms has provided a wide variety of prominent research applications like reporter gene assays and in vivo imaging methods. While the P. pyralis enzyme has been extensively studied, only recently has a second Photinus luciferase been cloned from the species scintillans. Even though the enzymes share very high sequence identity (89.8%), the color of the light they emit, their specific activity and their stability to heat, pH, and chemical denaturation are quite different with the scintillans luciferase being generally more resistant. Through the construction and evaluation of the properties of chimeric domain swapped, single point, and various combined variants, we have determined that only six amino acid changes are necessary to confer all of the properties of the scintillans enzyme to wild-type P. pyralis luciferase. Altered stability properties were attributed to four of the amino acid changes (T214N/S276T/H332N/E354N), and single mutations each predominantly changed emission color (Y255F) and specific activity (A222C). Results of a crystallographic study of the P. pyralis enzyme containing the six changes (Pps6) provide some insight into the structural basis for some of the documented property differences.
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Affiliation(s)
- Bruce R Branchini
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Danielle M Fontaine
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Tara L Southworth
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Brian P Huta
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Allison Racela
- Department of Chemistry , Connecticut College , New London , Connecticut 06320 , United States
| | - Ketan D Patel
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
| | - Andrew M Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo , Buffalo , New York 14203 , United States
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17
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Oliveira G, Viviani VR. Temperature effect on the bioluminescence spectra of firefly luciferases: potential applicability for ratiometric biosensing of temperature and pH. Photochem Photobiol Sci 2019; 18:2682-2687. [PMID: 31528963 DOI: 10.1039/c9pp00257j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioluminescence spectra of firefly luciferases are affected by pH, heavy metals and high temperatures. Previously, we compared the effect of pH and heavy metals on the bioluminescence spectra of different firefly luciferases and showed that such spectral sensitivity can be harnessed to ratiometrically estimate the pH inside cells and metal concentration. Here, we compared the effect of temperature on the spectral sensitivity of four firefly luciferases (Amydetes vivianii: 539 nm; Cratomorphus distinctus: 548 nm; Photinus pyralis: 558 nm and Macrolampis sp2: 594 nm) and investigated whether a ratiometric curve could be used to estimate temperature. The ratio of intensities of bioluminescence at two wavelengths (green and red) at different temperatures (5-35 °C) was determined. The results confirm that, in the case of pH-sensitive luciferases, the more blue-shifted the bioluminescence spectrum, the more thermostable the enzyme and the less sensitive the emission spectrum to temperature. An almost linear relationship between temperature and the ratio of bioluminescence intensities in the green and red region of the spectrum was found for the four luciferases: the more blue-shifted and less sensitive luciferases exhibit a smaller slope and the more red-shifted luciferases exhibit a steeper slope in the following order: Amy < Crt < Ppy < Mac. This relationship offers the possibility of using firefly luciferases as ratiometric indicators of temperature and may allow the compensation of the effect of temperature in the ratiometric analysis of intracellular pH and heavy metal concentration for each enzyme.
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Affiliation(s)
- Gabriela Oliveira
- Laboratory of Biochemistry and Biotechnology of Bioluminescence, Graduate Program of Biotechnology and Environmental Monitoring, Department of Chemistry, Physics and Mathematics, Federal University of São Carlos (UFSCar), Campus of Sorocaba, Sorocaba, SP, Brazil. and Department of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
| | - Vadim R Viviani
- Laboratory of Biochemistry and Biotechnology of Bioluminescence, Graduate Program of Biotechnology and Environmental Monitoring, Department of Chemistry, Physics and Mathematics, Federal University of São Carlos (UFSCar), Campus of Sorocaba, Sorocaba, SP, Brazil. and Department of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
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18
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Pelentir GF, Bevilaqua VR, Viviani VR. A highly efficient, thermostable and cadmium selective firefly luciferase suitable for ratiometric metal and pH biosensing and for sensitive ATP assays. Photochem Photobiol Sci 2019; 18:2061-2070. [PMID: 31339127 DOI: 10.1039/c9pp00174c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Firefly luciferases have been widely used for bioanalytical purposes during the last 5 decades. They usually emit yellow-green bioluminescence and are pH-sensitive, displaying a color change to red at acidic pH and higher temperature and in the presence of heavy metals. Besides the usual applications as bioanalytical reagents and as reporter genes, firefly luciferases' pH- and metal-sensitivities have been recently harnessed for intracellular metal and pH biosensing. Previously we cloned the luciferase of the Brazilian Amydetes vivianii firefly which displays the most blue-shifted color among known firefly luciferases. Here we purified it, characterized and investigated the kinetic properties and the pH, metal and thermal sensitivities of this firefly luciferase. This luciferase displays the lowest reported KM for ATP, the highest catalytic efficiencies, and the highest thermostability among the studied recombinant beetle luciferases, making this enzyme and its cDNA an ideal reagent for sensitive ATP assays and reporter gene. The blue-shifted spectrum, higher thermostability, lower pH- and thermal-sensitivities and protein fluorescence studies indicate a more rigid active site during light emission. This enzyme displays an unmatched selective spectral sensitivity for cadmium and mercury, making it a promising ratiometric indicator of such toxic metals. Finally, the weaker thermal-sensitivity compared to other firefly luciferases makes this enzyme a better ratiometric pH indicator at temperatures above 30 °C, suitable for mammalian cell assays.
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Affiliation(s)
- G F Pelentir
- Graduate School of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, São Paulo, Brazil.
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19
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Bevilaqua VR, Matsuhashi T, Oliveira G, Oliveira PSL, Hirano T, Viviani VR. Phrixotrix luciferase and 6'-aminoluciferins reveal a larger luciferin phenolate binding site and provide novel far-red combinations for bioimaging purposes. Sci Rep 2019; 9:8998. [PMID: 31227722 PMCID: PMC6588592 DOI: 10.1038/s41598-019-44534-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/14/2019] [Indexed: 11/20/2022] Open
Abstract
How the unique luciferase of Phrixothrix hirtus (PxRE) railroad worm catalyzes the emission of red bioluminescence using the same luciferin of fireflies, remains a mystery. Although PxRE luciferase is a very attractive tool for bioanalysis and bioimaging in hemoglobin rich tissues, it displays lower quantum yield (15%) when compared to green emitting luciferases (>40%). To identify which parts of PxRE luciferin binding site (LBS) determine bioluminescence color, and to develop brighter and more red-shifted emitting luciferases, we compared the effects of site-directed mutagenesis and of larger 6′-substituted aminoluciferin analogues (6′-morpholino- and 6′-pyrrolidinyl-LH) on the bioluminescence properties of PxRE and green-yellow emitting beetle luciferases. The effects of mutations in the benzothiazolyl and thiazolyl parts of PxRE LBS on the KM and catalytic efficiencies, indicated their importance for luciferin binding and catalysis. However, the absence of effects on the bioluminescence spectrum indicated a less interactive LBS in PxRE during light emission. Mutations at the bottom of LBS of PxRE blue-shifted the spectra and increased catalytic efficiency, suggesting that lack of interactions of this part of LBS with excited oxyluciferin phenolate underlie red light emission. The much higher bioluminescence activity and red-shifted spectra of PxRE luciferase with 6′-morpholino- (634 nm) and 6′-pyrrolidinyl-luciferins (644 nm), when compared to other beetle luciferases, revealed a larger luciferin phenolate binding pocket. The size and orientation of the side-chains of L/I/H348 are critical for amino-analogues accommodation and modulate bioluminescence color, affecting the interactions and mobility of excited oxyluciferin phenolate. The PxRE luciferase and 6′-aminoluciferins provide potential far-red combinations for bioimaging applications.
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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, SP, Brazil
| | - T Matsuhashi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo, 182-8585, Japan
| | - G Oliveira
- Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil
| | - P S L Oliveira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Zip Code 13083-970, Campinas, Sao Paulo, Brazil
| | - T Hirano
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo, 182-8585, Japan
| | - 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. .,Graduate Program of Evolutive Genetics and Molecular Biology, Federal University of São Carlos (UFSCar), São Carlos, SP, Brazil.
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20
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Effect of Protein Conformation and AMP Protonation State on Fireflies' Bioluminescent Emission. Molecules 2019; 24:molecules24081565. [PMID: 31009993 PMCID: PMC6514813 DOI: 10.3390/molecules24081565] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 04/12/2019] [Accepted: 04/17/2019] [Indexed: 12/12/2022] Open
Abstract
The emitted color in fireflies’ bioluminescent systems depends on the beetle species the system is extracted from and on different external factors (pH, temperature…) among others. Controlling the energy of the emitted light (i.e., color) is of crucial interest for the use of such bioluminescent systems. For instance, in the biomedical field, red emitted light is desirable because of its larger tissue penetration and lower energies. In order to investigate the influence of the protein environment and the AMP protonation state on the emitted color, the emission spectra of the phenolate-keto and phenolate-enol oxyluciferin forms have been simulated by means of MD simulations and QM/MM calculations, considering: two different protein conformations (with an open or closed C-terminal domain with respect to the N-terminal) and two protonation states of AMP. The results show that the emission spectra when considering the protein characterized by a closed conformation are blue-shifted compared to the open conformation. Moreover, the complete deprotonation of AMP phosphate group (AMP2−) can also lead to a blue-shift of the emission spectra but only when considering the closed protein conformation (open form is not sensitive to changes of AMP protonation state). These findings can be reasoned by the different interactions (hydrogen-bonds) found between oxyluciferin and the surrounding (protein, AMP and water molecules). This study gets partial insight into the possible origin of the emitted color modulation by changes of the pH or luciferase conformations.
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21
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Lui NM, Schramm S, Naumov P. pH-Dependent fluorescence from firefly oxyluciferin in agarose thin films. NEW J CHEM 2019. [DOI: 10.1039/c8nj05469j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The emitter of the firefly bioluminescence, oxyluciferin, and its derivatives were incorporated in agarose matrix to obtain self-supporting, lightweight fluorescent acidochromic thin films. This study demonstrates an alternative approach to investigating environmental effects on bioluminescent molecules.
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Affiliation(s)
- Nathan M. Lui
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
- Department of Chemistry and Chemical Biology, Baker Laboratory
- Cornell University
| | - Stefan Schramm
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
| | - Panče Naumov
- New York University Abu Dhabi
- Abu Dhabi
- United Arab Emirates
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22
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The proton and metal binding sites responsible for the pH-dependent green-red bioluminescence color tuning in firefly luciferases. Sci Rep 2018; 8:17594. [PMID: 30514851 PMCID: PMC6279810 DOI: 10.1038/s41598-018-33252-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 09/19/2018] [Indexed: 11/17/2022] Open
Abstract
Firefly luciferases produce yellow-green light under physiological and alkaline conditions, however at acidic pH, higher temperatures or in the presence of heavy metals the color changes to red, a property called pH-sensitivity. Despite many decades of studies, the proton and metal binding sites responsible for pH-sensitivity remain enigmatic. Previously we suggested that the salt bridge E311/R337 keeps a closed conformation of the luciferin phenolate binding site. Here we further investigated the effect of this salt bridge and mutations of the neighbor residues H310 and E/N354, on metal and pH-sensitivity of firefly luciferases emitting distinct bioluminescence colors (Cratomorphus distinctus: 548 nm; Macrolampis sp2: 569 nm). The substitutions of H310 and E/N354 modulate metal sensitivity, whereas the carboxylate of E311 may work as the catalytic base essential for green bioluminescence and pH-sensitivity. Modeling studies showed that H310, E311 and E354 side-chains coordinate Zinc, constituting the metal binding site and the pH-sensor. Electrostatic potential and pKa calculations suggest that the external couple H310/E354 is affected by pH, whereas E311/R337 make a stabilized internal pair which retains excited oxyluciferin ejected proton near its phenolate group into a high energy state, promoting yellow-green bioluminescence. Protonation or metal binding weaken these electrostatic gates and their ability to retain the excited oxyluciferin released proton near its phenolate, promoting red light emission.
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23
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Carrasco-López C, Ferreira JC, Lui NM, Schramm S, Berraud-Pache R, Navizet I, Panjikar S, Naumov P, Rabeh WM. Beetle luciferases with naturally red- and blue-shifted emission. Life Sci Alliance 2018; 1:e201800072. [PMID: 30456363 PMCID: PMC6238593 DOI: 10.26508/lsa.201800072] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 01/23/2023] Open
Abstract
New crystal structures of red- and green blue–shifted beetle luciferases reveal that the color emission mechanism is dependent on the active site microenvironment affected by the conformation of loop regions. The different colors of light emitted by bioluminescent beetles that use an identical substrate and chemiexcitation reaction sequence to generate light remain a challenging and controversial mechanistic conundrum. The crystal structures of two beetle luciferases with red- and blue-shifted light relative to the green yellow light of the common firefly species provide direct insight into the molecular origin of the bioluminescence color. The structure of a blue-shifted green-emitting luciferase from the firefly Amydetes vivianii is monomeric with a structural fold similar to the previously reported firefly luciferases. The only known naturally red-emitting luciferase from the glow-worm Phrixothrix hirtus exists as tetramers and octamers. Structural and computational analyses reveal varying aperture between the two domains enclosing the active site. Mutagenesis analysis identified two conserved loops that contribute to the color of the emitted light. These results are expected to advance comparative computational studies into the conformational landscape of the luciferase reaction sequence.
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Affiliation(s)
| | | | - Nathan M Lui
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Stefan Schramm
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Romain Berraud-Pache
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, Marne-la-Vallée, France
| | - Isabelle Navizet
- Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, Marne-la-Vallée, France
| | - Santosh Panjikar
- Australian Synchrotron, Clayton, Australia.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Australia
| | - Panče Naumov
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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24
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Cheng YY, Liu YJ. Theoretical Development of Near-Infrared Bioluminescent Systems. Chemistry 2018; 24:9340-9352. [PMID: 29710377 DOI: 10.1002/chem.201800416] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Indexed: 12/16/2022]
Abstract
The luciferin/luciferase system of the firefly has been used in bioluminescent imaging to monitor biological processes. In order to enhance the efficiency and expand the application range, some efforts have been made to tune the light emission, especially the effort to obtain NIR light. However, those case-by-case studies have not together revealed the nature and mechanism of the color tuning. In this paper, we theoretically investigated the fluorescence of all kinds of typical oxyluciferin analogues. The present systematical modifications of both oxyluciferin and luciferase indicate that the essential factor affecting the emission color is the charge distribution (or the electric dipole moment) on the oxyluciferin, which impacts on the charge transfer to form the light emitter and, subsequently, influence the strength and wavelength of the emission light. More negative charge distributed on the "thiazolone moiety" of the oxyluciferin or its analogues leads to a redshift. Based on this conclusion, we theoretically designed optimal pairs of luciferin analogue and luciferase for emitting NIR light, which could inspire new synthetic procedures and practical applications.
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Affiliation(s)
- Yuan-Yuan Cheng
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Ya-Jun Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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25
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Kakiuchi M, Ito S, Kiyama M, Goto F, Matsuhashi T, Yamaji M, Maki S, Hirano T. Electronic and Steric Effects of Cyclic Amino Substituents of Luciferin Analogues on a Firefly Luciferin–Luciferase Reaction. CHEM LETT 2017. [DOI: 10.1246/cl.170361] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Michio Kakiuchi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585
| | - Soichiro Ito
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585
| | - Masahiro Kiyama
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585
| | - Fumiya Goto
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585
| | - Takuto Matsuhashi
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585
| | - Minoru Yamaji
- Division of Molecular Science, Graduate School of Science and Engineering, Gunma University, Kiryu, Gunma 376-8515
| | - Shojiro Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585
| | - Takashi Hirano
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585
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26
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Branchini BR, Southworth TL, Fontaine DM, Murtiashaw MH, McGurk A, Talukder MH, Qureshi R, Yetil D, Sundlov JA, Gulick AM. Cloning of the Orange Light-Producing Luciferase from Photinus scintillans-A New Proposal on how Bioluminescence Color is Determined. Photochem Photobiol 2017; 93:479-485. [PMID: 27861940 DOI: 10.1111/php.12671] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 10/04/2016] [Indexed: 11/29/2022]
Abstract
Unlike the enchanting yellow-green flashes of light produced on warm summer evenings by Photinus pyralis, the most common firefly species in North America, the orange lights of Photinus scintillans are infrequently observed. These Photinus species, and likely all bioluminescent beetles, use the same substrates beetle luciferin, ATP and oxygen to produce light. It is the structure of the particular luciferase enzyme that is the key to determining the color of the emitted light. We report here the molecular cloning of the P. scintillans luc gene and the expression and characterization of the corresponding novel recombinant luciferase enzyme. A comparison of the amino acid sequence with that of the highly similar P. pyralis enzyme and subsequent mutagenesis studies revealed that the single conservative amino acid change tyrosine to phenylalanine at position 255 accounted for the entire emission color difference. Additional mutagenesis and crystallographic studies were performed on a H-bond network, which includes the position 255 residue and five other stringently conserved beetle luciferase residues, that is proximal to the substrate/emitter binding site. The results are interpreted in the context of a speculative proposal that this network is key to the understanding of bioluminescence color determination.
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Affiliation(s)
| | | | | | | | - Alex McGurk
- Department of Chemistry, Connecticut College, New London, CT
| | | | - Rakhshi Qureshi
- Department of Chemistry, Connecticut College, New London, CT
| | - Deniz Yetil
- Department of Chemistry, Connecticut College, New London, CT
| | - Jesse A Sundlov
- Hauptman-Woodward Institute, Buffalo, NY.,Department of Structural Biology, University of Buffalo, Buffalo, NY
| | - Andrew M Gulick
- Hauptman-Woodward Institute, Buffalo, NY.,Department of Structural Biology, University of Buffalo, Buffalo, NY
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27
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Kakiuchi M, Ito S, Yamaji M, Viviani VR, Maki S, Hirano T. Spectroscopic Properties of Amine-substituted Analogues of Firefly Luciferin and Oxyluciferin. Photochem Photobiol 2016; 93:486-494. [DOI: 10.1111/php.12654] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 09/07/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Michio Kakiuchi
- Department of Engineering Science; Graduate School of Informatics and Engineering; The University of Electro-Communications; Chofu Tokyo Japan
| | - Soichiro Ito
- Department of Engineering Science; Graduate School of Informatics and Engineering; The University of Electro-Communications; Chofu Tokyo Japan
| | - Minoru Yamaji
- Division of Molecular Science; Graduate School of Science and Engineering; Gunma University; Kiryu Gunma Japan
| | - Vadim R. Viviani
- Department of Physics, Chemistry and Mathematics; Graduate Program of Biotechnology and Environmental Monitoring; Federal University of São Carlos (UFSCAR); Itinga Sorocaba SP Brazil
- Graduate Program of Evolutive Genetics and Molecular Biology; Federal University of São Carlos (UFSCAR); São Carlos SP Brazil
| | - Shojiro Maki
- Department of Engineering Science; Graduate School of Informatics and Engineering; The University of Electro-Communications; Chofu Tokyo Japan
| | - Takashi Hirano
- Department of Engineering Science; Graduate School of Informatics and Engineering; The University of Electro-Communications; Chofu Tokyo Japan
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