1
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King CR, Dodge MJ, MacNeil KM, Tessier TM, Mymryk JS, Mehle A. Expanding the adenovirus toolbox: reporter viruses for studying the dynamics of human adenovirus replication. J Virol 2024:e0020724. [PMID: 38639487 DOI: 10.1128/jvi.00207-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024] Open
Abstract
To streamline standard virological assays, we developed a suite of nine fluorescent or bioluminescent replication competent human species C5 adenovirus reporter viruses that mimic their parental wild-type counterpart. These reporter viruses provide a rapid and quantitative readout of various aspects of viral infection and replication based on EGFP, mCherry, or NanoLuc measurement. Moreover, they permit real-time non-invasive measures of viral load, replication dynamics, and infection kinetics over the entire course of infection, allowing measurements that were not previously possible. This suite of replication competent reporter viruses increases the ease, speed, and adaptability of standard assays and has the potential to accelerate multiple areas of human adenovirus research.IMPORTANCEIn this work, we developed a versatile toolbox of nine HAdV-C5 reporter viruses and validated their functions in cell culture. These reporter viruses provide a rapid and quantitative readout of various aspects of viral infection and replication based on EGFP, mCherry, or NanoLuc measurement. The utility of these reporter viruses could also be extended for use in 3D cell culture, organoids, live cell imaging, or animal models, and provides a conceptual framework for the development of new reporter viruses representing other clinically relevant HAdV species.
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Affiliation(s)
- Cason R King
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mackenzie J Dodge
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Katelyn M MacNeil
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
| | - Tanner M Tessier
- Division of Protective Immunity, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Joe S Mymryk
- Department of Microbiology and Immunology, University of Western Ontario, London, Ontario, Canada
- Department of Oncology, University of Western Ontario, London, Ontario, Canada
- Department of Otolaryngology, University of Western Ontario, London, Ontario, Canada
- London Regional Cancer Program, Lawson Health Research Institute, London, Ontario, Canada
| | - Andrew Mehle
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Makrakis D, Dambri OA, Hafid AS. Design of Bio-Optical Transceiver for In Vivo Biomedical Sensor Applications. Sensors (Basel) 2024; 24:2584. [PMID: 38676201 DOI: 10.3390/s24082584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/27/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
This paper presents an enhanced version of our previously developed bio-optical transceiver, presenting a significant advancement in nanosensor technology. Using self-assembled polymers, this nanodevice is capable of electron detection while maintaining biocompatibility, an essential feature for in vivo medical biosensors. This enhancement finds significance in the field of infectious disease control, particularly in the early detection of respiratory viruses, including high-threat pathogens such as SARS-CoV-2. The proposed system harnesses bioluminescence by converting electric signaling to visible blue light, effectively opening the path of linking nano-sized mechanisms to larger-scale systems, thereby pushing the boundaries of in vivo biomedical sensing. The performance evaluation of our technology is analytical and is based on the use of Markov chains, through which we assess the bit error probability. The calculated improvements indicate that this technology qualifies as a forerunner in terms of supporting the communication needs of smaller, safer, and more efficient manufactured sensor technologies for in vivo medical applications.
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Affiliation(s)
- Dimitrios Makrakis
- School of Electrical Engineering and Computer Science, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | | | - Abdelhakim Senhaji Hafid
- Department of Computer Science and Operations Research, University of Montreal, Montreal, QC H3T 1J4, Canada
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3
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Björefeldt A, Murphy J, Crespo EL, Lambert GG, Prakash M, Ikefuama EC, Friedman N, Brown TM, Lipscombe D, Moore CI, Hochgeschwender U, Shaner NC. Efficient opto- and chemogenetic control in a single molecule driven by FRET-modified bioluminescence. Neurophotonics 2024; 11:021005. [PMID: 38450294 PMCID: PMC10917299 DOI: 10.1117/1.nph.11.2.021005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 03/08/2024]
Abstract
Significance Bioluminescent optogenetics (BL-OG) offers a unique and powerful approach to manipulate neural activity both opto- and chemogenetically using a single actuator molecule (a LuMinOpsin, LMO). Aim To further enhance the utility of BL-OG by improving the efficacy of chemogenetic (bioluminescence-driven) LMO activation. Approach We developed novel luciferases optimized for Förster resonance energy transfer when fused to the fluorescent protein mNeonGreen, generating bright bioluminescent (BL) emitters spectrally tuned to Volvox Channelrhodopsin 1 (VChR1). Results A new LMO generated from this approach (LMO7) showed significantly stronger BL-driven opsin activation compared to previous and other new variants. We extensively benchmarked LMO7 against LMO3 (current standard) and found significantly stronger neuronal activity modulation ex vivo and in vivo, and efficient modulation of behavior. Conclusions We report a robust new option for achieving multiple modes of control in a single actuator and a promising engineering strategy for continued improvement of BL-OG.
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Affiliation(s)
- Andreas Björefeldt
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
- University of Gothenburg, Institute of Neuroscience and Physiology, Department of Physiology, Gothenburg, Sweden
| | - Jeremy Murphy
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Emmanuel L. Crespo
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cell, and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
| | - Gerard G. Lambert
- University of California, San Diego, School of Medicine, Department of Neurosciences, La Jolla, California, United States
| | - Mansi Prakash
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Ebenezer C. Ikefuama
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Neuroscience Graduate Program, Mount Pleasant, Michigan, United States
| | - Nina Friedman
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Tariq M. Brown
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Diane Lipscombe
- Brown University, Carney Institute for Brain Science, Providence, Rhode Island, United States
| | - Christopher I. Moore
- Brown University, Carney Institute for Brain Science, Providence, Rhode Island, United States
| | - Ute Hochgeschwender
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cell, and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
- Central Michigan University, Neuroscience Graduate Program, Mount Pleasant, Michigan, United States
| | - Nathan C. Shaner
- University of California, San Diego, School of Medicine, Department of Neurosciences, La Jolla, California, United States
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4
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Slaviero AN, Gorantla N, Simkins J, Crespo EL, Ikefuama EC, Tree MO, Prakash M, Björefeldt A, Barnett LM, Lambert GG, Lipscombe D, Moore CI, Shaner NC, Hochgeschwender U. Engineering luminopsins with improved coupling efficiencies. Neurophotonics 2024; 11:024208. [PMID: 38559366 PMCID: PMC10980360 DOI: 10.1117/1.nph.11.2.024208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 03/13/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Significance Luminopsins (LMOs) are bioluminescent-optogenetic tools with a luciferase fused to an opsin that allow bimodal control of neurons by providing both optogenetic and chemogenetic access. Determining which design features contribute to the efficacy of LMOs will be beneficial for further improving LMOs for use in research. Aim We investigated the relative impact of luciferase brightness, opsin sensitivity, pairing of emission and absorption wavelength, and arrangement of moieties on the function of LMOs. Approach We quantified efficacy of LMOs through whole cell patch clamp recordings in HEK293 cells by determining coupling efficiency, the percentage of maximum LED induced photocurrent achieved with bioluminescent activation of an opsin. We confirmed key results by multielectrode array recordings in primary neurons. Results Luciferase brightness and opsin sensitivity had the most impact on the efficacy of LMOs, and N-terminal fusions of luciferases to opsins performed better than C-terminal and multi-terminal fusions. Precise paring of luciferase emission and opsin absorption spectra appeared to be less critical. Conclusions Whole cell patch clamp recordings allowed us to quantify the impact of different characteristics of LMOs on their function. Our results suggest that coupling brighter bioluminescent sources to more sensitive opsins will improve LMO function. As bioluminescent activation of opsins is most likely based on Förster resonance energy transfer, the most effective strategy for improving LMOs further will be molecular evolution of luciferase-fluorescent protein-opsin fusions.
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Affiliation(s)
- Ashley N. Slaviero
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cellular and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
| | - Nipun Gorantla
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Jacob Simkins
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Emmanuel L. Crespo
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cellular and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
| | - Ebenezer C. Ikefuama
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Neuroscience Graduate Program, Mount Pleasant, Michigan, United States
| | - Maya O. Tree
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Mansi Prakash
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Andreas Björefeldt
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Lauren M. Barnett
- University of California San Diego, Department of Neurosciences, La Jolla, California, United States
| | - Gerard G. Lambert
- University of California San Diego, Department of Neurosciences, La Jolla, California, United States
| | - Diane Lipscombe
- Brown University, Carney Institute for Brain Science, Providence, Rhode Island, United States
| | - Christopher I. Moore
- Brown University, Carney Institute for Brain Science, Providence, Rhode Island, United States
| | - Nathan C. Shaner
- University of California San Diego, Department of Neurosciences, La Jolla, California, United States
| | - Ute Hochgeschwender
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cellular and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
- Central Michigan University, Neuroscience Graduate Program, Mount Pleasant, Michigan, United States
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5
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Porta-de-la-Riva M, Morales-Curiel LF, Carolina Gonzalez A, Krieg M. Bioluminescence as a functional tool for visualizing and controlling neuronal activity in vivo. Neurophotonics 2024; 11:024203. [PMID: 38348359 PMCID: PMC10861157 DOI: 10.1117/1.nph.11.2.024203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/15/2024]
Abstract
The use of bioluminescence as a reporter for physiology in neuroscience is as old as the discovery of the calcium-dependent photon emission of aequorin. Over the years, luciferases have been largely replaced by fluorescent reporters, but recently, the field has seen a renaissance of bioluminescent probes, catalyzed by unique developments in imaging technology, bioengineering, and biochemistry to produce luciferases with previously unseen colors and intensity. This is not surprising as the advantages of bioluminescence make luciferases very attractive for noninvasive, longitudinal in vivo observations without the need of an excitation light source. Here, we review how the development of dedicated and specific sensor-luciferases afforded, among others, transcranial imaging of calcium and neurotransmitters, or cellular metabolites and physical quantities such as forces and membrane voltage. Further, the increased versatility and light output of luciferases have paved the way for a new field of functional bioluminescence optogenetics, in which the photon emission of the luciferase is coupled to the gating of a photosensor, e.g., a channelrhodopsin and we review how they have been successfully used to engineer synthetic neuronal connections. Finally, we provide a primer to consider important factors in setting up functional bioluminescence experiments, with a particular focus on the genetic model Caenorhabditis elegans, and discuss the leading challenges that the field needs to overcome to regain a competitive advantage over fluorescence modalities. Together, our paper caters to experienced users of bioluminescence as well as novices who would like to experience the advantages of luciferases in their own hand.
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Affiliation(s)
- Montserrat Porta-de-la-Riva
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Luis-Felipe Morales-Curiel
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Adriana Carolina Gonzalez
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Michael Krieg
- ICFO—Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
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6
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Townsend KM, Prescher JA. Recent advances in bioluminescent probes for neurobiology. Neurophotonics 2024; 11:024204. [PMID: 38390217 PMCID: PMC10883388 DOI: 10.1117/1.nph.11.2.024204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024]
Abstract
Bioluminescence is a popular modality for imaging in living organisms. The platform relies on enzymatically (luciferase) generated light via the oxidation of small molecule luciferins. Since no external light is needed for photon production, there are no concerns with background autofluorescence or photobleaching over time-features that have historically limited other optical readouts. Bioluminescence is thus routinely used for longitudinal tracking across whole animals. Applications in the brain, though, have been more challenging due to a lack of sufficiently bioavailable, bright, and easily multiplexed probes. Recent years have seen the development of designer luciferase and luciferin pairs that address these issues, providing more sensitive and real-time readouts of biochemical features relevant to neurobiology. This review highlights many of the advances in bioluminescent probe design, with a focus on the small molecule light emitter, the luciferin. Specific efforts to improve luciferin pharmacokinetics and tissue-penetrant emission are covered, in addition to applications that such probes have enabled. The continued development of improved bioluminescent probes will aid in illuminating critical neurochemical processes in the brain.
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Affiliation(s)
- Katherine M Townsend
- University of California, Irvine, Department of Chemistry, Irvine, California, United States
| | - Jennifer A Prescher
- University of California, Irvine, Department of Chemistry, Irvine, California, United States
- University of California, Irvine, Department of Molecular Biology and Biochemistry, Irvine, California, United States
- University of California, Irvine, Department of Pharmaceutical Sciences, Irvine, California, United States
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7
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Grady CJ, Castellanos Franco EA, Schossau J, Ashbaugh RC, Pelled G, Gilad AA. A putative design for the electromagnetic activation of split proteins for molecular and cellular manipulation. Front Bioeng Biotechnol 2024; 12:1355915. [PMID: 38605993 PMCID: PMC11007078 DOI: 10.3389/fbioe.2024.1355915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/05/2024] [Indexed: 04/13/2024] Open
Abstract
The ability to manipulate cellular function using an external stimulus is a powerful strategy for studying complex biological phenomena. One approach to modulate the function of the cellular environment is split proteins. In this method, a biologically active protein or an enzyme is fragmented so that it reassembles only upon a specific stimulus. Although many tools are available to induce these systems, nature has provided other mechanisms to expand the split protein toolbox. Here, we show a novel method for reconstituting split proteins using magnetic stimulation. We found that the electromagnetic perceptive gene (EPG) changes conformation due to magnetic field stimulation. By fusing split fragments of a certain protein to both termini of the EPG, the fragments can be reassembled into a functional protein under magnetic stimulation due to conformational change. We show this effect with three separate split proteins: NanoLuc, APEX2, and herpes simplex virus type-1 thymidine kinase. Our results show, for the first time, that reconstitution of split proteins can be achieved only with magnetic fields. We anticipate that this study will be a starting point for future magnetically inducible split protein designs for cellular perturbation and manipulation. With this technology, we can help expand the toolbox of the split protein platform and allow better elucidation of complex biological systems.
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Affiliation(s)
- Connor J. Grady
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI, United States
| | | | - Jory Schossau
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, United States
- Department of Computer Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Ryan C. Ashbaugh
- Department of Electrical and Computer Engineering, Michigan State University, East Lansing, MI, United States
| | - Galit Pelled
- Department of Mechanical Engineering, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
| | - Assaf A. Gilad
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, United States
- Department of Radiology, Michigan State University, East Lansing, MI, United States
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Claes JM, Haddock SHD, Coubris C, Mallefet J. Systematic Distribution of Bioluminescence in Marine Animals: A Species-Level Inventory. Life (Basel) 2024; 14:432. [PMID: 38672704 DOI: 10.3390/life14040432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Bioluminescence is the production of visible light by an organism. This phenomenon is particularly widespread in marine animals, especially in the deep sea. While the luminescent status of numerous marine animals has been recently clarified thanks to advancements in deep-sea exploration technologies and phylogenetics, that of others has become more obscure due to dramatic changes in systematics (themselves triggered by molecular phylogenies). Here, we combined a comprehensive literature review with unpublished data to establish a catalogue of marine luminescent animals. Inventoried animals were identified to species level in over 97% of the cases and were associated with a score reflecting the robustness of their luminescence record. While luminescence capability has been established in 695 genera of marine animals, luminescence reports from 99 additional genera need further confirmation. Altogether, these luminescent and potentially luminescent genera encompass 9405 species, of which 2781 are luminescent, 136 are potentially luminescent (e.g., suggested luminescence in those species needs further confirmation), 99 are non-luminescent, and 6389 have an unknown luminescent status. Comparative analyses reveal new insights into the occurrence of luminescence among marine animal groups and highlight promising research areas. This work will provide a solid foundation for future studies related to the field of marine bioluminescence.
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Affiliation(s)
- Julien M Claes
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Steven H D Haddock
- Monterey Bay Aquarium Research Institute, 7700 Sandholdt Road, Moss Landing, CA 95039, USA
| | - Constance Coubris
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Jérôme Mallefet
- Marine Biology Laboratory, Earth and Life Institute, Université catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
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Sutormin OS, Nemtseva EV, Gulnov DV, Sukovatyi LA, Tyrtyshnaya YS, Lisitsa AE, Kratasyuk VA. Coupling of NAD(P)H:FMN-oxidoreductase and luciferase from luminous bacteria in a viscous medium: Finding the weakest link in the chain. Photochem Photobiol 2024; 100:465-476. [PMID: 37583116 DOI: 10.1111/php.13845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/15/2023] [Accepted: 07/31/2023] [Indexed: 08/17/2023]
Abstract
The study aims at revealing the mechanisms of the viscous medium effects on the kinetic features of NAD(P)H:FMN-oxidoreductase from luminous bacteria (Red), which are exhibited in a single enzyme assay and in coupling with bacterial luciferase (BLuc). Different concentrations of glycerol and sucrose were used to vary the medium viscosity. The activity of Red, alone and in the presence of BLuc, was analyzed, as well as BLuc activity in the presence of Red, whereas in the absence of BLuc, the Red activity was suppressed in viscous medium, and in the presence of BLuc, the increase in Red activity was observed at low glycerol concentrations (5-20 wt%). The interaction of glycerol and sucrose with Red substrates FMN and NADH was studied using absorption spectroscopy and molecular dynamics. Glycerol was found to form hydrogen bonds with the phosphate groups of the substrates, unlike sucrose. A mechanism for the activation of Red in the presence of BLuc in glycerol solutions through the acceleration of FMN reoxidation was proposed. Thus, it was concluded that, under the conditions used, the weakest link of the coupled enzyme system BLuc-Red in viscous medium is the FMN concentration, which depends on Red activity and the medium viscosity.
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Affiliation(s)
- Oleg S Sutormin
- Department of Chemistry, Institute of Natural and Technical Sciences, Surgut State University, Surgut, Russia
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Krasnoyarsk, Russia
| | - Dmitry V Gulnov
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Lev A Sukovatyi
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Yekaterina S Tyrtyshnaya
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Albert E Lisitsa
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
| | - Valentina A Kratasyuk
- Department of Biophysics, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Photobiology Laboratory, Institute of Biophysics, Russian Academy of Sciences, Krasnoyarsk, Russia
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10
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Ahmadi Y, Jafarian V, Shirdel A. Site-specific mutagenesis on Mnemiopsin 2: Calcium coordination and substrate binding properties of new variants. LUMINESCENCE 2024; 39:e4707. [PMID: 38497361 DOI: 10.1002/bio.4707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/19/2024]
Abstract
We used site-specific mutagenesis by targeting E179 and F190 on the structure of photoprotein Mnemiopsin 2 (Mn2) from Mnemiopsis leidyi. The tertiary structure of E179S and F190L mutants was made by the MODELLER program. Far-ultraviolet circular dichroism data showed that the overall secondary structural content of photoprotein is not changed upon mutation, however the helicity and stabilizing interactions in helical structure decreases in mutants as compared with the wild-type (WT) photoprotein. Fluorescence spectra data revealed that the tertiary structure of the mutants is more compact than that of WT Mn2. According to the heat-induced denaturation experiments data, the melting temperature (Tm ) for the unfolding of tertiary structure of the F190L variant increases by 3°C compared with that of the WT and E179S mutant. Interestingly, the conformational enthalpy of the F190L mutant (86 kcal mol-1 ) is considerably lower than those in the WT photoprotein (102 kcal mol-1 ) and E179S mutant (106 kcal mol-1 ). The significant difference in the enthalpy of the thermal unfolding process could be explained by considering that the thermally denatured state of the F190L mutant is structurally less expanded than the WT and E179S variants. Bioluminescence activity data showed that the maximum characteristic wavelengths of the mutants undergo blue shift as compared with the WT protein. Initial intensity of the F190L and E179S variants was recorded to be 137.5% and 55.9% of the WT protein, respectively.
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Affiliation(s)
- Yasaman Ahmadi
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
| | - Vahab Jafarian
- Department of Biology, Faculty of Science, University of Guilan, Rasht, Iran
| | - Akram Shirdel
- Department of Biology, Faculty of Sciences, University of Zanjan, Zanjan, Iran
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11
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Kanie S, Wu C, Kihira K, Yasuno R, Mitani Y, Ohmiya Y. Bioluminescence of ( R)-Cypridina Luciferin with Cypridina Luciferase. Int J Mol Sci 2024; 25:2699. [PMID: 38473946 DOI: 10.3390/ijms25052699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Cypridina luciferin (CypL) is a marine natural product that functions as the luminous substrate for the enzyme Cypridina luciferase (CypLase). CypL has two enantiomers, (R)- and (S)-CypL, due to its one chiral center at the sec-butyl moiety. Previous studies reported that (S)-CypL or racemic CypL with CypLase produced light, but the luminescence of (R)-CypL with CypLase has not been investigated. Here, we examined the luminescence of (R)-CypL, which had undergone chiral separation from the enantiomeric mixture, with a recombinant CypLase. Our luminescence measurements demonstrated that (R)-CypL with CypLase produced light, indicating that (R)-CypL must be considered as the luminous substrate for CypLase, as in the case of (S)-CypL, rather than a competitive inhibitor for CypLase. Additionally, we found that the maximum luminescence intensity from the reaction of (R)-CypL with CypLase was approximately 10 fold lower than that of (S)-CypL with CypLase, but our kinetic analysis of CypLase showed that the Km value of CypLase for (R)-CypL was approximately 3 fold lower than that for (S)-CypL. Furthermore, the chiral high-performance liquid chromatography (HPLC) analysis of the reaction mixture of racemic CypL with CypLase showed that (R)-CypL was consumed more slowly than (S)-CypL. These results indicate that the turnover rate of CypLase for (R)-CypL was lower than that for (S)-CypL, which caused the less efficient luminescence of (R)-CypL with CypLase.
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Affiliation(s)
- Shusei Kanie
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Chun Wu
- Biomedical Research Institute, AIST, Kansai Center, 1-8-31 Midorigaoka, Ikeda 563-8577, Japan
| | - Kiyohito Kihira
- Japan Aerospace Exploration Agency (JAXA), Tsukuba Space Center, 2-1-1 Sengen, Tsukuba 305-8505, Japan
| | - Rie Yasuno
- Cellular and Molecular Biotechnology Research Institute, AIST, Tsukuba Center, 1-1-1 Higashi, Tsukuba 305-8566, Japan
| | - Yasuo Mitani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, 2-17-2-1 Tsukisamu-Higashi, Toyohira-ku, Sapporo 062-8517, Japan
| | - Yoshihiro Ohmiya
- Biomedical Research Institute, AIST, Kansai Center, 1-8-31 Midorigaoka, Ikeda 563-8577, Japan
- Department of Biomedical Engineering, Osaka Institute of Technology (OIT), 5-16-1 Ohmiya, Asahi-ku, Osaka 535-8585, Japan
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12
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Magalhães CM, Esteves da Silva JCG, Pinto da Silva L. Investigation of the Chemiluminescent Reaction of a Fluorinated Analog of Marine Coelenterazine. Materials (Basel) 2024; 17:868. [PMID: 38399119 PMCID: PMC10890627 DOI: 10.3390/ma17040868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024]
Abstract
Bioluminescence (BL) and chemiluminescence (CL) are remarkable processes in which light is emitted due to (bio)chemical reactions. These reactions have attracted significant attention for various applications, such as biosensing, bioimaging, and biomedicine. Some of the most relevant and well-studied BL/CL systems are that of marine imidazopyrazine-based compounds, among which Coelenterazine is a prime example. Understanding the mechanisms behind efficient chemiexcitation is essential for the optimization and development of practical applications for these systems. Here, the CL of a fluorinated Coelenterazine analog was studied using experimental and theoretical approaches to obtain insight into these processes. Experimental analysis revealed that CL is more efficient under basic conditions than under acidic ones, which could be attributed to the higher relative chemiexcitation efficiency of an anionic dioxetanone intermediate over a corresponding neutral species. However, theoretical calculations indicated that the reactions of both species are similarly associated with both electron and charge transfer processes, which are typically used to explain efficiency chemiexcitation. So, neither process appears to be able to explain the relative chemiexcitation efficiencies observed. In conclusion, this study provides further insight into the mechanisms behind the chemiexcitation of imidazopyrazinone-based systems.
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Affiliation(s)
| | | | - Luís Pinto da Silva
- Centro de Investigação em Química (CIQUP), Instituto de Ciências Moleculares (IMS), Departamento de Geociências, Ambiente e Ordenamento do Território, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal; (C.M.M.); (J.C.G.E.d.S.)
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13
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Sever EA, Aybakan E, Beşli Y, Karatuna O, Kocagoz T. A novel rapid bioluminescence-based antimicrobial susceptibility testing method based on adenosine triphosphate consumption. Front Microbiol 2024; 15:1357680. [PMID: 38404596 PMCID: PMC10885693 DOI: 10.3389/fmicb.2024.1357680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 01/19/2024] [Indexed: 02/27/2024] Open
Abstract
Introduction Standard, phenotypic antimicrobial susceptibility testing (AST) methods require 16-20 h of incubation and are considered as the bottleneck in providing timely input for appropriate antimicrobial treatment. In this study, a novel adenosine triphosphate (ATP)-bioluminescence-based method which allows rapid AST within 3 h was described. Methods Standard AST was performed for 56 Enterobacterales isolates using EUCAST disk diffusion (DD) methodology. For the bioluminescence-based rapid AST, suspensions of bacteria were prepared using Mueller-Hinton broth to obtain a turbidity of 0.5 McFarland. The suspensions were distributed into 96-well microtiter plates. ATP (20 mM) and fixed concentrations of different antibiotics were added. Following incubation at 37°C for 1 h, a luminescent reaction mixture, including the substrate luciferin and luciferase enzyme solutions, was added. The chemiluminescence was monitored using an imaging system. Light production demonstrated the presence of ATP, indicating that the isolate was susceptible to the antibiotic in the well. Absence or decrease of light intensity, compared with the growth control well, indicated the use of ATP as an indirect measure of bacterial growth, and therefore resistance to the antibiotic in the well. Results The novel AST method was tested using a total of 348 test wells. Concordance was achieved for 290 (83.3%) of the tests, whereas 52 (14.9%) and 6 (1.7%) tests caused minor and major errors, respectively. Discussion In this study, a bioluminescence-based rapid AST was developed based on the consumption of ATP by bacteria. Our method's uniqueness relies on determining ATP consumption by microorganisms in the presence or absence of an antibiotic. The novel AST method described in this study lays the groundwork for obtaining rapid results, which should be considered as a proof of concept. With further optimization studies, this novel method can provide higher accuracy and be introduced into clinical practice as a routine AST method.
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Affiliation(s)
- Elif Arik Sever
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
- Department of Biostatistics and Bioinformatics, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
| | - Esma Aybakan
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
| | - Yeşim Beşli
- American Hospital Clinical Laboratory, Istanbul, Türkiye
| | - Onur Karatuna
- EUCAST Development Laboratory, Clinical Microbiology, Central Hospital, Växjö, Sweden
| | - Tanil Kocagoz
- Department of Medical Biotechnology, Institute of Health Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
- Department of Medical Microbiology, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Türkiye
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14
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Jaroensuk J, Sutthaphirom C, Phonbuppha J, Chinantuya W, Kesornpun C, Akeratchatapan N, Kittipanukul N, Phatinuwat K, Atichartpongkul S, Fuangthong M, Pongtharangkul T, Hollmann F, Chaiyen P. A versatile in situ cofactor enhancing system for meeting cellular demands for engineered metabolic pathways. J Biol Chem 2024; 300:105598. [PMID: 38159859 PMCID: PMC10850783 DOI: 10.1016/j.jbc.2023.105598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/02/2023] [Accepted: 12/18/2023] [Indexed: 01/03/2024] Open
Abstract
Cofactor imbalance obstructs the productivities of metabolically engineered cells. Herein, we employed a minimally perturbing system, xylose reductase and lactose (XR/lactose), to increase the levels of a pool of sugar phosphates which are connected to the biosynthesis of NAD(P)H, FAD, FMN, and ATP in Escherichia coli. The XR/lactose system could increase the amounts of the precursors of these cofactors and was tested with three different metabolically engineered cell systems (fatty alcohol biosynthesis, bioluminescence light generation, and alkane biosynthesis) with different cofactor demands. Productivities of these cells were increased 2-4-fold by the XR/lactose system. Untargeted metabolomic analysis revealed different metabolite patterns among these cells, demonstrating that only metabolites involved in relevant cofactor biosynthesis were altered. The results were also confirmed by transcriptomic analysis. Another sugar reducing system (glucose dehydrogenase) could also be used to increase fatty alcohol production but resulted in less yield enhancement than XR. This work demonstrates that the approach of increasing cellular sugar phosphates can be a generic tool to increase in vivo cofactor generation upon cellular demand for synthetic biology.
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Affiliation(s)
- Juthamas Jaroensuk
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chalermroj Sutthaphirom
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Jittima Phonbuppha
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Wachirawit Chinantuya
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand; Faculty of Science, Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Mahidol University, Bangkok, Thailand
| | - Chatchai Kesornpun
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Nattanon Akeratchatapan
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Narongyot Kittipanukul
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Kamonwan Phatinuwat
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand
| | | | - Mayuree Fuangthong
- Program in Applied Biological Sciences, Chulabhorn Graduate Institute, Bangkok, Thailand; Laboratory of Biotechnology, Chulabhorn Research Institute, Bangkok, Thailand
| | | | - Frank Hollmann
- Department of Biotechnology, Delft University of Technology, Delft, Netherlands
| | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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15
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Apostolidou D, Zhang P, Pandya D, Bock K, Liu Q, Yang W, Marszalek PE. Tandem repeats of highly bioluminescent NanoLuc are refolded noncanonically by the Hsp70 machinery. Protein Sci 2024; 33:e4895. [PMID: 38284490 PMCID: PMC10804678 DOI: 10.1002/pro.4895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Chaperones are a large family of proteins crucial for maintaining cellular protein homeostasis. One such chaperone is the 70 kDa heat shock protein (Hsp70), which plays a crucial role in protein (re)folding, stability, functionality, and translocation. While the key events in the Hsp70 chaperone cycle are well established, a relatively small number of distinct substrates were repetitively investigated. This is despite Hsp70 engaging with a plethora of cellular proteins of various structural properties and folding pathways. Here we analyzed novel Hsp70 substrates, based on tandem repeats of NanoLuc (Nluc), a small and highly bioluminescent protein with unique structural characteristics. In previous mechanical unfolding and refolding studies, we have identified interesting misfolding propensities of these Nluc-based tandem repeats. In this study, we further investigate these properties through in vitro bulk experiments. Similar to monomeric Nluc, engineered Nluc dyads and triads proved to be highly bioluminescent. Using the bioluminescence signal as the proxy for their structural integrity, we determined that heat-denatured Nluc dyads and triads can be efficiently refolded by the E. coli Hsp70 chaperone system, which comprises DnaK, DnaJ, and GrpE. In contrast to previous studies with other substrates, we observed that Nluc repeats can be efficiently refolded by DnaK and DnaJ, even in the absence of GrpE co-chaperone. Taken together, our study offers a new powerful substrate for chaperone research and raises intriguing questions about the Hsp70 mechanisms, particularly in the context of structurally diverse proteins.
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Affiliation(s)
- Dimitra Apostolidou
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
| | - Pan Zhang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Devanshi Pandya
- Department of Electrical and Computer EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Kaden Bock
- Department of Biomedical EngineeringDuke UniversityDurhamNorth CarolinaUnited States
| | - Qinglian Liu
- Department of Physiology and Biophysics, School of MedicineVirginia Commonwealth UniversityRichmondVirginiaUnited States
| | - Weitao Yang
- Department of ChemistryDuke UniversityDurhamNorth CarolinaUnited States
| | - Piotr E. Marszalek
- Department of Mechanical Engineering and Materials ScienceDuke UniversityDurhamNorth CarolinaUnited States
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Demby A, Zaccolo M. Investigating G-protein coupled receptor signalling with light-emitting biosensors. Front Physiol 2024; 14:1310197. [PMID: 38260094 PMCID: PMC10801095 DOI: 10.3389/fphys.2023.1310197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are the most frequent target of currently approved drugs and play a central role in both physiological and pathophysiological processes. Beyond the canonical understanding of GPCR signal transduction, the importance of receptor conformation, beta-arrestin (β-arr) biased signalling, and signalling from intracellular locations other than the plasma membrane is becoming more apparent, along with the tight spatiotemporal compartmentalisation of downstream signals. Fluorescent and bioluminescent biosensors have played a pivotal role in elucidating GPCR signalling events in live cells. To understand the mechanisms of action of the GPCR-targeted drugs currently available, and to develop new and better GPCR-targeted therapeutics, understanding these novel aspects of GPCR signalling is critical. In this review, we present some of the tools available to interrogate each of these features of GPCR signalling, we illustrate some of the key findings which have been made possible by these tools and we discuss their limitations and possible developments.
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Affiliation(s)
| | - Manuela Zaccolo
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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18
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Stepin EA, Sushko ES, Vnukova NG, Churilov GN, Rogova AV, Tomilin FN, Kudryasheva NS. Effects of Endohedral Gd-Containing Fullerenols with a Different Number of Oxygen Substituents on Bacterial Bioluminescence. Int J Mol Sci 2024; 25:708. [PMID: 38255785 PMCID: PMC10815327 DOI: 10.3390/ijms25020708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Gadolinium (Gd)-containing fullerenols are perspective agents for magnetic resonance imaging and cancer research. They combine the unique paramagnetic properties of Gd with solubility in water, low toxicity and antiradical activity of fullerenols. We compared the bioeffects of two Gd-containing fullerenols with a different number of oxygen groups-20 and 42: Gd@C82O20H14 and Gd@C82O42H32. The bioluminescent bacteria-based assay was applied to monitor the toxicity of fullerenols, bioluminescence was applied as a signal physiological parameter, and bacterial enzyme-based assay was used to evaluate the fullerenol effects on enzymatic intracellular processes. Chemiluminescence luminol assay was applied to monitor the content of reactive oxygen species (ROS) in bacterial and enzymatic media. It was shown that Gd@C82O42H32 and Gd@C82O20H14 inhibited bacterial bioluminescence at >10-1 and >10-2 gL-1, respectively, revealing a lower toxicity of Gd@C82O42H32. Low-concentration (10-3-10-1 gL-1) bacterial bioluminescence activation by Gd@C82O42H32 was observed, while this activation was not found under exposure to Gd@C82O20H14. Additional carboxyl groups in the structure of Gd@C82O42H32 were determined by infrared spectroscopy and confirmed by quantum chemical calculations. The groups were supposed to endow Gd@C82O42H32 with higher penetration ability through the cellular membrane, activation ability, lower toxicity, balancing of the ROS content in the bacterial suspensions, and lower aggregation in aqueous media.
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Affiliation(s)
- Evsei A. Stepin
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
| | - Ekaterina S. Sushko
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
- Institute of Biophysics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
| | - Natalia G. Vnukova
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Solid State Physics and Nanotechnology, School of Engineering Physics and Radioelectronics, Siberian Federal University, 660074 Krasnoyarsk, Russia
| | - Grigoriy N. Churilov
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Solid State Physics and Nanotechnology, School of Engineering Physics and Radioelectronics, Siberian Federal University, 660074 Krasnoyarsk, Russia
| | - Anastasia V. Rogova
- Department of Physical and Inorganic Chemistry, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660025 Krasnoyarsk, Russia;
- Laboratory for Digital Controlled Drugs and Theranostics, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - Felix N. Tomilin
- Institute of Physics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia; (N.G.V.); (G.N.C.); (F.N.T.)
- Department of Physical and Inorganic Chemistry, School of Non-Ferrous Metals and Materials Science, Siberian Federal University, 660025 Krasnoyarsk, Russia;
- Laboratory for Digital Controlled Drugs and Theranostics, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
| | - Nadezhda S. Kudryasheva
- Biophysics Department, School of Fundamental Biology and Biotechnology, Siberian Federal University, 660041 Krasnoyarsk, Russia; (E.A.S.); (E.S.S.)
- Institute of Biophysics SB RAS, FRC KSC SB RAS, 660036 Krasnoyarsk, Russia
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19
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He J, Li J, Zhang R, Dong Z, Liu G, Chang Z, Bi W, Ruan Y, Yang Y, Liu H, Qiu L, Zhao R, Wan W, Li Z, Chen L, Li Y, Li X. Multiple Origins of Bioluminescence in Beetles and Evolution of Luciferase Function. Mol Biol Evol 2024; 41:msad287. [PMID: 38174583 PMCID: PMC10798137 DOI: 10.1093/molbev/msad287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 12/15/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024] Open
Abstract
Bioluminescence in beetles has long fascinated biologists, with diverse applications in biotechnology. To date, however, our understanding of its evolutionary origin and functional variation mechanisms remains poor. To address these questions, we obtained high-quality reference genomes of luminous and nonluminous beetles in 6 Elateroidea families. We then reconstructed a robust phylogenetic relationship for all luminous families and related nonluminous families. Comparative genomic analyses and biochemical functional experiments suggested that gene evolution within Elateroidea played a crucial role in the origin of bioluminescence, with multiple parallel origins observed in the luminous beetle families. While most luciferase-like proteins exhibited a conserved nonluminous amino acid pattern (TLA346 to 348) in the luciferin-binding sites, luciferases in the different luminous beetle families showed divergent luminous patterns at these sites (TSA/CCA/CSA/LVA). Comparisons of the structural and enzymatic properties of ancestral, extant, and site-directed mutant luciferases further reinforced the important role of these sites in the trade-off between acyl-CoA synthetase and luciferase activities. Furthermore, the evolution of bioluminescent color demonstrated a tendency toward hypsochromic shifts and variations among the luminous families. Taken together, our results revealed multiple parallel origins of bioluminescence and functional divergence within the beetle bioluminescent system.
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Affiliation(s)
- Jinwu He
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Jun Li
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Kunming College of Life Science, University of the Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ru Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Zhiwei Dong
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Guichun Liu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zhou Chang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wenxuan Bi
- Room 401, No. 2, Lane 155, Lianhua South Road, Shanghai 201100, China
| | - Yongying Ruan
- Plant Protection Research Center, Shenzhen Polytechnic University, Shenzhen 518055, China
| | - Yuxia Yang
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Haoyu Liu
- Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Lu Qiu
- Engineering Research Center for Forest and Grassland Disaster Prevention and Reduction, Mianyang Normal University, 621000 Mianyang, China
| | - Ruoping Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wenting Wan
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Zihe Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shaanxi 710072, China
| | - Yuanning Li
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Xueyan Li
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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20
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Navarro MX, Brennan CK, Love AC, Prescher JA. Caged luciferins enable rapid multicomponent bioluminescence imaging. Photochem Photobiol 2024; 100:67-74. [PMID: 37259257 PMCID: PMC10687313 DOI: 10.1111/php.13814] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Bioluminescence is a sensitive technique for imaging biological features over time. Historically, though, the modality has been challenging to employ for multiplexed tracking due to a lack of resolvable luciferase-luciferin pairs. Recent years have seen the development of numerous orthogonal probes for multi-parameter imaging. While successful, generating such tools often requires complex syntheses and lengthy enzyme evolution campaigns. This work showcases an alternative strategy for multiplexed bioluminescence that takes advantage of already-orthogonal caged luciferins and established uncaging enzymes. These probes generate unique bioluminescent signals that can be distinguished via a linear unmixing algorithm. Caged luciferins enabled two- and three-component imaging on the minutes time scale. We further showed that the tools can be used in conjunction with endogenous enzymes for multiplexed studies. Collectively, this approach lowers the barrier to multicomponent bioluminescence imaging and can be readily adopted by the broader community.
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Affiliation(s)
- Mariana X. Navarro
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
| | - Caroline K. Brennan
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
| | - Anna C. Love
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine 1120 Natural Science II, Irvine, CA 92617 (USA)
- Department of Molecular Biology and Biochemistry, University of California, Irvine, 3205 McGaugh Hall, Irvine, CA 92716 (USA)
- Department of Pharmaceutical Sciences, University of California, Irvine, 101 Theory, Suite 100, Irvine, CA 92617 (USA)
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21
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Arima T, Sugimoto K, Taniwaki T, Maeda K, Shibata Y, Tateyama M, Karasugi T, Tokunaga T, Sueyoshi T, Hisanaga S, Masuda T, Uehara Y, Yugami M, Matsushita K, Yonemitsu R, Kawakami J, Yoshimura N, Tanimura S, Kato H, Ito N, Inoue K, Bando K, Nakamura T, Miyamoto T. Cartilage tissues regulate systemic aging via ectonucleotide pyrophosphatase/phosphodiesterase 1 in mice. J Biol Chem 2024; 300:105512. [PMID: 38042486 PMCID: PMC10777000 DOI: 10.1016/j.jbc.2023.105512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/09/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Aging presents fundamental health concerns worldwide; however, mechanisms underlying how aging is regulated are not fully understood. Here, we show that cartilage regulates aging by controlling phosphate metabolism via ectonucleotide pyrophosphatase/phosphodiesterase 1 (Enpp1). We newly established an Enpp1 reporter mouse, in which an EGFP-luciferase sequence was knocked-in at the Enpp1 gene start codon (Enpp1/EGFP-luciferase), enabling detection of Enpp1 expression in cartilage tissues of resultant mice. We then established a cartilage-specific Enpp1 conditional knockout mouse (Enpp1 cKO) by generating Enpp1 flox mice and crossing them with cartilage-specific type 2 collagen Cre mice. Relative to WT controls, Enpp1 cKO mice exhibited phenotypes resembling human aging, such as short life span, ectopic calcifications, and osteoporosis, as well as significantly lower serum pyrophosphate levels. We also observed significant weight loss and worsening of osteoporosis in Enpp1 cKO mice under phosphate overload conditions, similar to global Enpp1-deficient mice. Aging phenotypes seen in Enpp1 cKO mice under phosphate overload conditions were rescued by a low vitamin D diet, even under high phosphate conditions. These findings suggest overall that cartilage tissue plays an important role in regulating systemic aging via Enpp1.
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Affiliation(s)
- Takahiro Arima
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuki Sugimoto
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takuya Taniwaki
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kazuya Maeda
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yuto Shibata
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Makoto Tateyama
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tatsuki Karasugi
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takuya Tokunaga
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Takanao Sueyoshi
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Satoshi Hisanaga
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Tetsuro Masuda
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yusuke Uehara
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Masaki Yugami
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kozo Matsushita
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Ryuji Yonemitsu
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Junki Kawakami
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naoto Yoshimura
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Shuntaro Tanimura
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Hajime Kato
- Division of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan
| | - Nobuaki Ito
- Division of Nephrology and Endocrinology, The University of Tokyo Hospital, Tokyo, Japan
| | - Kenichi Inoue
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Kana Bando
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan
| | - Takayuki Nakamura
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
| | - Takeshi Miyamoto
- Department of Orthopedic Surgery, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
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22
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Klein MA, Lazarev S, Gervasi C, Cowan C, Machleidt T, Friedman Ohana R. Luciferase Calibrants Enable Absolute Quantitation of Bioluminescence Power. ACS Meas Sci Au 2023; 3:496-503. [PMID: 38145021 PMCID: PMC10740115 DOI: 10.1021/acsmeasuresciau.3c00036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 12/26/2023]
Abstract
Bioluminescence emitted from a luciferase-catalyzed oxidation of luciferin has been broadly utilized to report on biological events, predominantly through relative changes in the light output. Recent advances in protein engineering and synthetic chemistry have yielded bioluminescent systems with markedly improved brightness and bioavailability. These developments have enabled not only the detection of biological events at far lower expression levels but also new opportunities utilizing bioluminescence to power photochemistry in cells. Regardless of the application, bioluminescence analyses have leaned heavily on the use of luminometers to measure the light output of a system. Current luminometers report the light output of a sample in relative units, limiting the ability to compare data between instruments and preventing the absolute power of a bioluminescent system from being quantified. Luminescent solution calibrants comprising luciferases and their cognate luciferins that have been characterized for absolute light output would enable calibration of any given luminometer for absolute photon counting. To this end, we have built a custom light detection apparatus and used it alongside wavelength-matched LED light sources emitting at 450 and 561 nm to characterize the absolute power of a series of NanoLuc and firefly luciferase solutions, respectively. This approach revealed that these two common luciferases produce 3.72 × 10-18 and 7.25 × 10-20 watts/molecule, respectively. Components of these luminescent solution calibrants are commercially available and produce stable bioluminescent signals over 2-5 min, enabling any luminometer to be calibrated for power measurements of bioluminescence emitted by these two luciferases in units of watts or photons per second.
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Affiliation(s)
- Mark A. Klein
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Sergey Lazarev
- Promega Corporation, Madison, Wisconsin 53711, United States
| | - Charles Gervasi
- Promega Corporation, Madison, Wisconsin 53711, United States
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23
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Chang CH, Fontaine DM, Gómez S, Branchini BR, Anderson JC. Synthesis and Bioluminescence of 'V'-Shaped Firefly Luciferin Analogues Based on A Novel Benzobisthiazole Core. Chemistry 2023; 29:e202302204. [PMID: 37743319 DOI: 10.1002/chem.202302204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/21/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023]
Abstract
The design of π-extended conjugation 'V'-shaped red shifted bioluminescent D-luciferin analogues based on a novel benzobisthiazole core is described. The divergent synthetic route allowed access to a range of amine donor substituents through an SN Ar reaction. In spectroscopic studies, the 'V'-shaped luciferins exhibited narrower optical band gaps, more red-shifted absorption and emission spectra than D-luciferin. Their bioluminescence characteristics were recorded against four different luciferases (PpyLuc, FlucRed, CBR2 and PLR3). With native luciferase PpyLuc, the 'V'-shaped luciferins demonstrated more red-shifted emissions than D-luciferin (λbl =561 nm) by 60 to 80 nm. In addition, the benzobisthiazole luciferins showed a wide range of bioluminescence spectra from the visible light region (λbl =500 nm) to the nIR window (>650 nm). The computational results validate the design concept which can be used as a guide for further novel D-luciferin analogues based upon other 'V'-shaped heterocyclic cores.
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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, Salamanca, 37008, Spain
| | - 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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Jiang Z, Yang Z, Li W. Self-Luminous Probe with One-Step Energy Conversion from Bioluminescence to NIR-IIb. Adv Healthc Mater 2023; 12:e2302089. [PMID: 37812813 DOI: 10.1002/adhm.202302089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 09/07/2023] [Indexed: 10/11/2023]
Abstract
Self-luminous probes with near-infrared (NIR) emission are powerful tools for deep-penetration and autofluorescence-free imaging, owing to the joint optimization of both excitation and emission. However, the limited emission wavelength and requirement for multistep energy transfer limit its potency. In this study, the concept of direct wavelength conversion is established from visible light (vis) to NIR-IIb using an exquisitely designed sensitizer-activator ion pair. The manipulation of the doping hosts enables a pair of energy levels between the sensitizer and activator. Based on this a class of broadband vis-responsive nanocrystals with intense NIR-II emission is prepared. The stability and quantum yield (up to 7.4%) of the nanocrystals are further enhanced by ZnS passivation via coherent epitaxial growth. By coupling luciferase, the self-luminous probe can convert bioluminescence to NIR-IIb luminescence (>1500 nm) through a one-step energy transfer. A maximum penetrable thickness of 6 mm is achieved in the porcine tissue model. Collectively, the distinctive photon-conversion performance of this probe offers the prospect of high-resolution labeling of deep-seated lesions.
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Affiliation(s)
- Zhao Jiang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Zhiwen Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Wanwan Li
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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25
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Gould AL, Henderson JB. Comparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences. Microb Genom 2023; 9:001161. [PMID: 38112751 PMCID: PMC10763503 DOI: 10.1099/mgen.0.001161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for P. leiognathi and its subspecies P. 'mandapamensis', enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, Photobacterium acropomis sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the P. leiognathi and P. 'mandapamensis' strains. A comparison of the P. leiognathi and P. 'mandapamensis' lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the lux-rib operon, responsible for light production, indicated congruence between the presence of luxF and host family, challenging its role in differentiating P. 'mandapamensis' from P. leiognathi. Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in P. leiognathi as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of Photobacterium genome evolution, highlighting subtle differences between closely related lineages, specifically P. leiognathi and P. 'mandapamensis'. These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.
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Affiliation(s)
- Alison L. Gould
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr. San Francisco, CA 94118, California, USA
| | - James B. Henderson
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, 55 Music Concourse Dr. San Francisco, CA 94118, California, USA
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26
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Hensley NM, Rivers TJ, Gerrish GA, Saha R, Oakley TH. Collective synchrony of mating signals modulated by ecological cues and social signals in bioluminescent sea fireflies. Proc Biol Sci 2023; 290:20232311. [PMID: 38018106 PMCID: PMC10685132 DOI: 10.1098/rspb.2023.2311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/06/2023] [Indexed: 11/30/2023] Open
Abstract
Individuals often employ simple rules that can emergently synchronize behaviour. Some collective behaviours are intuitively beneficial, but others like mate signalling in leks occur across taxa despite theoretical individual costs. Whether disparate instances of synchronous signalling are similarly organized is unknown, largely due to challenges observing many individuals simultaneously. Recording field collectives and ex situ playback experiments, we describe principles of synchronous bioluminescent signals produced by marine ostracods (Crustacea; Luxorina) that seem behaviorally convergent with terrestrial fireflies, and with whom they last shared a common ancestor over 500 Mya. Like synchronous fireflies, groups of signalling males use visual cues (intensity and duration of light) to decide when to signal. Individual ostracods also modulate their signal based on the distance to nearest neighbours. During peak darkness, luminescent 'waves' of synchronous displays emerge and ripple across the sea floor approximately every 60 s, but such periodicity decays within and between nights after the full moon. Our data reveal these bioluminescent aggregations are sensitive to both ecological and social light sources. Because the function of collective signals is difficult to dissect, evolutionary convergence, like in the synchronous visual displays of diverse arthropods, provides natural replicates to understand the generalities that produce emergent group behaviour.
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Affiliation(s)
- Nicholai M. Hensley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
| | - Trevor J. Rivers
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66405, USA
| | - Gretchen A. Gerrish
- Center for Limnology, Trout Lake Station, University of Wisconsin, Boulder Junction, Madison, WI 54512, USA
| | - Raj Saha
- Roux Institute, Northeastern University, Portland, ME 04101, USA
| | - Todd H. Oakley
- Department of Ecology, Evolution, and Marine Biology, University of California Santa Barbara, Santa Barbara, CA 93106-9620, USA
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27
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Slaviero A, Gorantla N, Simkins J, Crespo EL, Ikefuama EC, Tree MO, Prakash M, Björefeldt A, Barnett LM, Lambert GG, Lipscombe D, Moore CI, Shaner NC, Hochgeschwender U. Engineering luminopsins with improved coupling efficiencies. bioRxiv 2023:2023.11.22.568342. [PMID: 38045286 PMCID: PMC10690276 DOI: 10.1101/2023.11.22.568342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Significance Luminopsins (LMOs) are bioluminescent-optogenetic tools with a luciferase fused to an opsin that allow bimodal control of neurons by providing both optogenetic and chemogenetic access. Determining which design features contribute to the efficacy of LMOs will be beneficial for further improving LMOs for use in research. Aim We investigated the relative impact of luciferase brightness, opsin sensitivity, pairing of emission and absorption wavelength, and arrangement of moieties on the function of LMOs. Approach We quantified efficacy of LMOs through whole cell patch clamp recordings in HEK293 cells by determining coupling efficiency, the percentage of maximum LED induced photocurrent achieved with bioluminescent activation of an opsin. We confirmed key results by multielectrode array (MEAs) recordings in primary neurons. Results Luciferase brightness and opsin sensitivity had the most impact on the efficacy of LMOs, and N-terminal fusions of luciferases to opsins performed better than C-terminal and multi-terminal fusions. Precise paring of luciferase emission and opsin absorption spectra appeared to be less critical. Conclusions Whole cell patch clamp recordings allowed us to quantify the impact of different characteristics of LMOs on their function. Our results suggest that coupling brighter bioluminescent sources to more sensitive opsins will improve LMO function. As bioluminescent activation of opsins is most likely based on Förster resonance energy transfer (FRET), the most effective strategy for improving LMOs further will be molecular evolution of luciferase-fluorescent protein-opsin fusions.
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Affiliation(s)
- Ashley Slaviero
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cellular and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
| | - Nipun Gorantla
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Jacob Simkins
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Emmanuel L Crespo
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cellular and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
| | - Ebenezer C Ikefuama
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Neuroscience Graduate Program, Mount Pleasant, Michigan, United States
| | - Maya O Tree
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Mansi Prakash
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Andreas Björefeldt
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
| | - Lauren M Barnett
- University of California San Diego, Department of Neurosciences, La Jolla, California, United States
| | - Gerard G Lambert
- University of California San Diego, Department of Neurosciences, La Jolla, California, United States
| | - Diane Lipscombe
- Brown University, Carney Institute for Brain Science, Providence, Rhode Island, United States
| | - Christopher I Moore
- Brown University, Carney Institute for Brain Science, Providence, Rhode Island, United States
| | - Nathan C Shaner
- University of California San Diego, Department of Neurosciences, La Jolla, California, United States
| | - Ute Hochgeschwender
- Central Michigan University, College of Medicine, Mount Pleasant, Michigan, United States
- Central Michigan University, Biochemistry, Cellular and Molecular Biology Graduate Program, Mount Pleasant, Michigan, United States
- Central Michigan University, Neuroscience Graduate Program, Mount Pleasant, Michigan, United States
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28
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Cui X, Li X, Peng C, Qiu Y, Shi Y, Liu Y, Fei JF. Beyond External Light: On-Spot Light Generation or Light Delivery for Highly Penetrated Photodynamic Therapy. ACS Nano 2023; 17:20776-20803. [PMID: 37874930 DOI: 10.1021/acsnano.3c05619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
External light sources, such as lasers, light emitting diodes (LEDs) and lamps, are widely applied in photodynamic therapy (PDT); however, their use is severely limited by the nature of shallow tissue penetration depth. The recent exploration of light delivery or local generation on tumor sites has attracted much attention, owing to the fact that these systems are significantly endowed with high tissue penetration. In this review, we briefly introduced the principle of "on-spot light generation or delivery systems" in PDT. These systems are divided into different categories: (1) implantable luminescence, (2) mechanoluminescence, (3) electrochemiluminescence, (4) Cerenkov luminescence, (5) chemiluminescence, and (6) bioluminescence. Finally, their applications, advantages, and disadvantages in PDT will be appropriately summarized and further discussed in detail. We believe that this review will provide general guidance for the further design of light generation or delivery systems and clinical studies for PDT-mediated cancer treatments with unparalleled merits.
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Affiliation(s)
- Xiao Cui
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, People's Republic of China
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, People's Republic of China
| | - Xiang Li
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, People's Republic of China
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, People's Republic of China
| | - Cheng Peng
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Yuanhui Qiu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Yu Shi
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Yanmei Liu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China, Institute for Brain Research and Rehabilitation, and Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, 510631, People's Republic of China
| | - Ji-Feng Fei
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510080, People's Republic of China
- Department of Pathology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, Guangdong 510080, People's Republic of China
- School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, People's Republic of China
- School of Medicine, South China University of Technology, Guangzhou, Guangdong 510006, People's Republic of China
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29
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Bakhshi T, Zafar S. Hybrid Deep Learning Techniques for Securing Bioluminescent Interfaces in Internet of Bio Nano Things. Sensors (Basel) 2023; 23:8972. [PMID: 37960671 PMCID: PMC10648166 DOI: 10.3390/s23218972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/27/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
The Internet of bio-nano things (IoBNT) is an emerging paradigm employing nanoscale (~1-100 nm) biological transceivers to collect in vivo signaling information from the human body and communicate it to healthcare providers over the Internet. Bio-nano-things (BNT) offer external actuation of in-body molecular communication (MC) for targeted drug delivery to otherwise inaccessible parts of the human tissue. BNTs are inter-connected using chemical diffusion channels, forming an in vivo bio-nano network, connected to an external ex vivo environment such as the Internet using bio-cyber interfaces. Bio-luminescent bio-cyber interfacing (BBI) has proven to be promising in realizing IoBNT systems due to their non-obtrusive and low-cost implementation. BBI security, however, is a key concern during practical implementation since Internet connectivity exposes the interfaces to external threat vectors, and accurate classification of anomalous BBI traffic patterns is required to offer mitigation. However, parameter complexity and underlying intricate correlations among BBI traffic characteristics limit the use of existing machine-learning (ML) based anomaly detection methods typically requiring hand-crafted feature designing. To this end, the present work investigates the employment of deep learning (DL) algorithms allowing dynamic and scalable feature engineering to discriminate between normal and anomalous BBI traffic. During extensive validation using singular and multi-dimensional models on the generated dataset, our hybrid convolutional and recurrent ensemble (CNN + LSTM) reported an accuracy of approximately ~93.51% over other deep and shallow structures. Furthermore, employing a hybrid DL network allowed automated extraction of normal as well as temporal features in BBI data, eliminating manual selection and crafting of input features for accurate prediction. Finally, we recommend deployment primitives of the extracted optimal classifier in conventional intrusion detection systems as well as evolving non-Von Neumann architectures for real-time anomaly detection.
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Affiliation(s)
- Taimur Bakhshi
- School of Built Environment, Engineering & Computing, Leeds Beckett University, Leeds LS1 3HE, UK
| | - Sidra Zafar
- Department of Computer Science, Kinnaird College for Women, Lahore 54000, Pakistan;
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30
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Irwin S, Wang T, Bolam SM, Alvares S, Swift S, Cornish J, Williams DL, Ashton NN, Matthews BG. Rat model of recalcitrant prosthetic joint infection using biofilm inocula. J Orthop Res 2023; 41:2462-2473. [PMID: 37132080 DOI: 10.1002/jor.25587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 04/04/2023] [Accepted: 05/01/2023] [Indexed: 05/04/2023]
Abstract
Prosthetic joint infection (PJI) is a rare but devastating complication of joint arthroplasty. Biofilm formation around the prosthesis confers tolerance to antibiotics so that treatment is challenging. Most animal models of PJI use planktonic bacteria to establish the infection which fails to reproduce the pathology of chronic infection. We aimed to establish a rat model of Staphylococcus aureus PJI in male Sprague-Dawley rats using biofilm inocula and demonstrate its tolerance to frontline antibiotics. Pilot studies indicated that infection could be introduced to the knee joint by a biofilm-coated pin but that handling the prosthetic without disturbing the biofilm was difficult. We, therefore, developed a pin with a slotted end and used a miniature-biofilm reactor to develop mature biofilm in this niche. These biofilm-laden pins consistently produced infection of the bone and joint space. Treatment with high dose cefazolin, 250 mg/kg, starting the day of surgery reduced or cleared pin-adherent bioburden within 7 days, however when escalation from 25 to 250 mg/kg cefazolin treatment was delayed for 48 h, rats were unable to clear the infection. To track infections, we used bioluminescent bacteria, however, the bioluminescent signal did not accurately track the degree of infection in the bone and joint space as the signal did not penetrate the bone. In conclusion, we demonstrate that using a custom prosthetic pin, we can generate biofilm in a specific niche using a novel bioreactor setup and initiate a rat PJI that rapidly develops tolerance to supra-clinical doses of cefazolin.
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Affiliation(s)
- Stuart Irwin
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Tao Wang
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Scott M Bolam
- Department of Surgery, University of Auckland, Auckland, New Zealand
| | - Sydel Alvares
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Simon Swift
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Jillian Cornish
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Dustin L Williams
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah, USA
- Department of Pathology, University of Utah, Salt Lake City, Utah, USA
- Department of Bioengineering, University of Utah, Salt Lake City, Utah, USA
- Department of Physical Medicine and Rehabilitation, Uniformed Services University, Bethesda, Maryland, USA
| | - Nicholas N Ashton
- Department of Orthopaedics, University of Utah, Salt Lake City, Utah, USA
| | - Brya G Matthews
- Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
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31
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Xu Y, Vertrees D, He Y, Momben-Abolfath S, Li X, Brewah YA, Scott DE, Konduru K, Rios M, Struble EB. Nanoluciferase Reporter Zika Viruses as Tools for Assessing Infection Kinetics and Antibody Potency. Viruses 2023; 15:2190. [PMID: 38005868 PMCID: PMC10674863 DOI: 10.3390/v15112190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
Zika virus (ZIKV) has become endemic in multiple tropical and subtropical regions and has the potential to become widespread in countries with limited prior exposure to this infection. One of the most concerning sequelae of ZIKV infection is the teratogenic effect on the developing fetus, with the mechanisms of viral spread to and across the placenta remaining largely unknown. Although vaccine trials and prophylactic or therapeutic treatments are being studied, there are no approved treatments or vaccines for ZIKV. Appropriate tests, including potency and in vivo assays to assess the safety and efficacy of these modalities, can greatly aid both the research of the pathophysiology of the infection and the development of anti-ZIKV therapeutics. Building on previous work, we tested reporter ZIKV variants that express nanoluciferase in cell culture and in vivo assays. We found that these variants can propagate in cells shown to be susceptible to the widely used clinical isolate PRVABC59, including Vero and human placenta cell lines. When used in neutralization assays with bioluminescence as readout, these variants gave rise to neutralization curves similar to those produced by PRVABC59, while being better suited for performing high-throughput assays. In addition, the engineered reporter variants can be useful research tools when used in other in vitro and in vivo assays, as we illustrated in transcytosis experiments and a pilot study in guinea pigs.
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Affiliation(s)
- Yanqun Xu
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
| | - Devin Vertrees
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
| | - Yong He
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
| | - Sanaz Momben-Abolfath
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
| | - Xiaohong Li
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
| | - Yambasu A. Brewah
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
| | - Dorothy E. Scott
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
| | - Krishnamurthy Konduru
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (K.K.); (M.R.)
| | - Maria Rios
- Laboratory of Molecular Virology, Division of Emerging and Transfusion Transmitted Diseases, Office of Blood Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Silver Spring, MD 20993, USA; (K.K.); (M.R.)
| | - Evi B. Struble
- Laboratory of Plasma Derivatives, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (Y.X.); (D.V.); (Y.H.); (X.L.); (Y.A.B.); (D.E.S.)
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Choi IY, Oh JH, Wang Z, van Pijkeren JP. Bioluminescent monitoring of recombinant lactic acid bacteria and their products. mBio 2023; 14:e0119723. [PMID: 37668408 PMCID: PMC10653940 DOI: 10.1128/mbio.01197-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/29/2023] [Indexed: 09/06/2023] Open
Abstract
IMPORTANCE Lactic acid bacteria constitute a genetically diverse group of microorganisms with significant roles in the food industry, biotechnology, agriculture, and medicine. A core understanding of bacterial physiology in diverse environments is crucial to select and develop bacteria for industrial and medical applications. However, there is a lack of versatile tools to track (recombinant) protein production in lactic acid bacteria. In this study, we adapted a peptide-based bioluminescent tagging system that is functional across multiple genera and species. This system enables tracking of tagged proteins both in vitro and in situ, while it also can be used to enumerate recombinant bacteria from the mouse gastrointestinal tract with accuracy comparable to that of conventional plate counts. Our work expands the lactic acid bacteria genetic toolbox and will facilitate researchers in industry and academia with opportunities to monitor microbes and proteins under different physiologically relevant conditions.
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Affiliation(s)
- In Young Choi
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zhiying Wang
- Department of Food Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
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Nguyen HT, Venter H, Woolford L, Young KA, McCluskey A, Garg S, Sapula SS, Page SW, Ogunniyi AD, Trott DJ. Oral administration of a 2-aminopyrimidine robenidine analogue (NCL195) significantly reduces Staphylococcus aureus infection and reduces Escherichia coli infection in combination with sub-inhibitory colistin concentrations in a bioluminescent mouse model. Antimicrob Agents Chemother 2023; 67:e0042423. [PMID: 37695304 PMCID: PMC10583667 DOI: 10.1128/aac.00424-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/06/2023] [Indexed: 09/12/2023] Open
Abstract
We have previously reported promising in vivo activity of the first-generation 2-aminopyramidine robenidine analogue NCL195 against Gram-positive bacteria (GPB) when administered via the systemic route. In this study, we examined the efficacy of oral treatment with NCL195 (± low-dose colistin) in comparison to oral moxifloxacin in bioluminescent Staphylococcus aureus and Escherichia coli peritonitis-sepsis models. Four oral doses of 50 mg/kg NCL195, commencing immediately post-infection, were administered at 4 h intervals in the S. aureus peritonitis-sepsis model. We used a combination of four oral doses of 50 mg/kg NCL195 and four intraperitoneal doses of colistin at 0.125 mg/kg, 0.25 mg/kg, or 0.5 mg/kg in the E. coli peritonitis-sepsis model. Subsequently, the dose rates of four intraperitoneal doses of colistin were increased to 0.5 mg/kg, 1 mg/kg, or 2 mg/kg at 4 h intervals to treat a colistin-resistant E. coli infection. In the S. aureus infection model, oral treatment of mice with NCL195 resulted in significantly reduced S. aureus infection loads (P < 0.01) and longer survival times (P < 0.001) than vehicle-only treated mice. In the E. coli infection model, co-administration of NCL195 and graded doses of colistin resulted in a dose-dependent significant reduction in colistin-susceptible (P < 0.01) or colistin-resistant (P < 0.05) E. coli loads compared to treatment with colistin alone at similar concentrations. Our results confirm that NCL195 is a potential candidate for further preclinical development as a specific treatment for multidrug-resistant infections, either as a stand-alone antibiotic for GPB or in combination with sub-inhibitory concentrations of colistin for Gram-negative bacteria.
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Affiliation(s)
- Hang Thi Nguyen
- Australian Center for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Pharmacology, Toxicology, Internal Medicine and Diagnostics, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Henrietta Venter
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Lucy Woolford
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kelly A. Young
- Chemistry, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Adam McCluskey
- Chemistry, School of Environmental and Life Sciences, University of Newcastle, Callaghan, New South Wales, Australia
| | - Sanjay Garg
- Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Sylvia S. Sapula
- Health and Biomedical Innovation, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | | | - Abiodun David Ogunniyi
- Australian Center for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Darren J. Trott
- Australian Center for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, South Australia, Australia
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Silva-Filho AGS, Mombert A, Nascimento CC, Nóbrega BB, Soares DMM, Martins AGS, Domingos AHR, Santos I, Della-Torre OHP, Perry BA, Desjardin DE, Stevani CV, Menolli N. Eoscyphella luciurceolata gen. and sp. nov. (Agaricomycetes) Shed Light on Cyphellopsidaceae with a New Lineage of Bioluminescent Fungi. J Fungi (Basel) 2023; 9:1004. [PMID: 37888262 PMCID: PMC10608165 DOI: 10.3390/jof9101004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/22/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023] Open
Abstract
During nocturnal field expeditions in the Brazilian Atlantic Rainforest, an unexpected bioluminescent fungus with reduced form was found. Based on morphological data, the taxon was first identified as belonging to the cyphelloid genus Maireina, but in our phylogenetic analyses, Maireina was recovered and confirmed as a paraphyletic group related to genera Merismodes and Cyphellopsis. Maireina filipendula, Ma. monacha, and Ma. subsphaerospora are herein transferred to Merismodes. Based upon morphological and molecular characters, the bioluminescent cyphelloid taxon is described as the new genus Eoscyphella, characterized by a vasiform to urceolate basidiomata, subglobose to broadly ellipsoid basidiospores, being pigmented, weakly to densely encrusted external hyphae, regularly bi-spored basidia, unclamped hyphae, and an absence of both conspicuous long external hairs and hymenial cystidia. Phylogenetic analyses based on ITS rDNA and LSU rDNA support the proposal of the new genus and confirm its position in Cyphellopsidaceae. Eoscyphella luciurceolata represents a new lineage of bioluminescent basidiomycetes with reduced forms.
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Affiliation(s)
- Alexandre G. S. Silva-Filho
- IFungiLab, Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Campus São Paulo (SPO), São Paulo 01109-010, SP, Brazil; (A.G.S.S.-F.); (C.C.N.)
| | | | - Cristiano C. Nascimento
- IFungiLab, Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Campus São Paulo (SPO), São Paulo 01109-010, SP, Brazil; (A.G.S.S.-F.); (C.C.N.)
| | - Bianca B. Nóbrega
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Douglas M. M. Soares
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Ana G. S. Martins
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Adão H. R. Domingos
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Isaias Santos
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Olavo H. P. Della-Torre
- Instituto de Pesquisa da Biodiversidade (IPBio), Iporanga 18330-000, SP, Brazil; (A.G.S.M.); (A.H.R.D.); (I.S.); (O.H.P.D.-T.)
| | - Brian A. Perry
- Department of Biological Sciences, California State University, East Bay, Hayward, CA 94542, USA;
| | - Dennis E. Desjardin
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA;
| | - Cassius V. Stevani
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, São Paulo 05508-000, SP, Brazil;
| | - Nelson Menolli
- IFungiLab, Departamento de Ciências da Natureza e Matemática (DCM), Subárea de Biologia (SAB), Instituto Federal de Educação, Ciência e Tecnologia de São Paulo (IFSP), Campus São Paulo (SPO), São Paulo 01109-010, SP, Brazil; (A.G.S.S.-F.); (C.C.N.)
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35
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Hernandez Pichardo A, Littlewood J, Taylor A, Wilm B, Lévy R, Murray P. Multispectral optoacoustic tomography is more sensitive than micro-computed tomography for tracking gold nanorod labelled mesenchymal stromal cells. J Biophotonics 2023; 16:e202300109. [PMID: 37431566 DOI: 10.1002/jbio.202300109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/28/2023] [Accepted: 06/30/2023] [Indexed: 07/12/2023]
Abstract
Tracking the fate of therapeutic cell types is important for assessing their safety and efficacy. Bioluminescence imaging (BLI) is an effective cell tracking technique, but poor spatial resolution means it has limited ability to precisely map cells in vivo in 3D. This can be overcome by using a bimodal imaging approach that combines BLI with a technique capable of generating high-resolution images. Here we compared the effectiveness of combining either multispectral optoacoustic tomography (MSOT) or micro-computed tomography (micro-CT) with BLI for tracking the fate of luciferase+ human mesenchymal stromal cells (MSCs) labelled with gold nanorods. Following subcutaneous administration in mice, the MSCs could be readily detected with MSOT but not with micro-CT. We conclude that MSOT is more sensitive than micro-CT for tracking gold nanorod-labelled cells in vivo and depending on the route of administration, can be used effectively with BLI to track MSC fate in mice.
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Affiliation(s)
- Alejandra Hernandez Pichardo
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Pre-clinical Imaging, University of Liverpool, Liverpool, UK
| | - James Littlewood
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- iThera Medical GmbH, Munich, Germany
| | - Arthur Taylor
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Pre-clinical Imaging, University of Liverpool, Liverpool, UK
| | - Bettina Wilm
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Pre-clinical Imaging, University of Liverpool, Liverpool, UK
| | - Raphaël Lévy
- Université Sorbonne Paris Nord and Université de Paris, INSERM, LVTS, Paris, France
| | - Patricia Murray
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Centre for Pre-clinical Imaging, University of Liverpool, Liverpool, UK
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36
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Ramírez Martínez C, Gómez-Pérez LS, Ordaz A, Torres-Huerta AL, Antonio-Perez A. Current Trends of Bacterial and Fungal Optoproteins for Novel Optical Applications. Int J Mol Sci 2023; 24:14741. [PMID: 37834188 PMCID: PMC10572898 DOI: 10.3390/ijms241914741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/13/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023] Open
Abstract
Photoproteins, luminescent proteins or optoproteins are a kind of light-response protein responsible for the conversion of light into biochemical energy that is used by some bacteria or fungi to regulate specific biological processes. Within these specific proteins, there are groups such as the photoreceptors that respond to a given light wavelength and generate reactions susceptible to being used for the development of high-novel applications, such as the optocontrol of metabolic pathways. Photoswitchable proteins play important roles during the development of new materials due to their capacity to change their conformational structure by providing/eliminating a specific light stimulus. Additionally, there are bioluminescent proteins that produce light during a heatless chemical reaction and are useful to be employed as biomarkers in several fields such as imaging, cell biology, disease tracking and pollutant detection. The classification of these optoproteins from bacteria and fungi as photoreceptors or photoresponse elements according to the excitation-emission spectrum (UV-Vis-IR), as well as their potential use in novel applications, is addressed in this article by providing a structured scheme for this broad area of knowledge.
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Affiliation(s)
| | | | | | | | - Aurora Antonio-Perez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Ciudad López Mateos, Atizapán de Zaragoza 52926, Estado de México, Mexico; (C.R.M.); (L.S.G.-P.); (A.O.); (A.L.T.-H.)
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37
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Ding R, Liu D, Feng Y, Liu H, Ji H, He L, Liu S. Unexcited Light Source Imaging for Biomedical Applications. Chemistry 2023; 29:e202301689. [PMID: 37401914 DOI: 10.1002/chem.202301689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/05/2023]
Abstract
Optical imaging has a wide range of applications in the biomedical field, allowing the visualization of physiological processes and helping in the diagnosis and treatment of diseases. Unexcited light source imaging technologies, such as chemiluminescence imaging, bioluminescence imaging and afterglow imaging have attracted great attention in recent years because of the absence of excitation light interference in their application and the advantages of high sensitivity and high signal-to-noise ratio. In this review, the latest advances in unexcited light source imaging technology for biomedical applications are highlighted. The design strategies of unexcited light source luminescent probes in improving luminescence brightness, penetration depth, quantum yield and targeting, and their applications in inflammation imaging, tumor imaging, liver and kidney injury imaging and bacterial infection imaging are introduced in detail. The research progress and future prospects of unexcited light source imaging for medical applications are further discussed.
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Affiliation(s)
- Ruihao Ding
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, 150040, Harbin, China
| | - Danqing Liu
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, 150040, Harbin, China
| | - Yu Feng
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, 150040, Harbin, China
| | - Haoxin Liu
- Augustana Faculty, University of Alberta, T4V2R3, Camrose, Canada
| | - Hongrui Ji
- School of Material Science and Chemical Engineering, Harbin University of Science and Technology, 150040, Harbin, China
| | - Liangcan He
- Key Laboratory of Micro-systems and, Micro-structures Manufacturing of Ministry of Education, Harbin Institute of Technology, 150001, Harbin, China
| | - Shaoqin Liu
- Key Laboratory of Micro-systems and, Micro-structures Manufacturing of Ministry of Education, Harbin Institute of Technology, 150001, Harbin, China
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38
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Nishida K, Wang G, Kobatake E, Mie M. Sensitive Detection of Tumor Cells Using Protein Nanoparticles with Multiple Displays of DNA Aptamers and Bioluminescent Reporters. ACS Biomater Sci Eng 2023; 9:5260-5269. [PMID: 37642536 DOI: 10.1021/acsbiomaterials.3c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Simple and effective detection methods for circulating tumor cells are essential for early detection and progression monitoring of tumors. The use of DNA aptamer and bioluminescence is expected to be a key tool for the simple, effective, and sensitive detection of tumor cells. Herein, we designed multifunctional protein nanoparticles for the detection of tumor cells using DNA aptamer and bioluminescence. Fusion proteins (ELP-poly(d)-POIs), composed of elastin-like polypeptide (ELP) fused with protein of interests (POIs) via poly(aspartic acid) (poly(d)), formed the protein nanoparticles based on the temperature responsivity of ELP sequences, leading to multiply displayed POIs on the protein nanoparticles. In the present study, we focused on porcine circovirus type 2 replication initiation protein (Rep), which covalently conjugated with DNA aptamers, and NanoLuc luciferase (Nluc), which emitted a strong bioluminescence, as POIs. ELP-poly(d)-Rep and ELP-poly(d)-Nluc were constructed and formed the protein nanoparticles with multiply displayed Nluc and Rep (DNA aptamer) that amplified the bioluminescence signal and tumor recognition ability. Mucin-1 (MUC1)-overexpressing human breast tumor MCF7 cells and MUC1-recognizing aptamer (MUC1 aptamer) were selected as models. The MUC1 aptamer-conjugated protein nanoparticles exhibited a 13.7-fold higher bioluminescence signal to MCF-7 cells than to human embryonic kidney 293 (HEK293) cells, which express low levels of MUC1. Furthermore, the protein nanoparticles could detect up to 70.7 cells/mL of MCF-7 cells from a cell suspension containing HEK-293. The protein nanoparticles with multiple Rep and Nluc show a great potential as a material for detecting CTCs.
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Affiliation(s)
- Kei Nishida
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
| | - Gaoyang Wang
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
| | - Eiry Kobatake
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
| | - Masayasu Mie
- Department of Life Science and Technology, School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8502, Japan
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39
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Mihai IT, Rudzitis-Auth J, Menger MD, Laschke MW. The Presence of Pre-Existing Endometriotic Lesions Promotes the Growth of New Lesions in the Peritoneal Cavity. Int J Mol Sci 2023; 24:13858. [PMID: 37762161 PMCID: PMC10531296 DOI: 10.3390/ijms241813858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
Endometriosis is a common gynecological disease which is characterized by endometriotic lesions outside the uterine cavity. In this study, we investigated whether the presence of pre-existing endometriotic lesions promotes the development of new lesions due to the exchange of cells and an altered peritoneal environment. For this purpose, uterine tissue samples from FVB/N wild-type donor mice were transplanted simultaneously or time-delayed with samples from transgenic FVB-Tg(CAG-luc-GFP)L2G85Chco/J donor mice into the abdominal cavity of FVB/N wild-type recipient mice. The formation of endometriotic lesions was analyzed by means of high-resolution ultrasound, bioluminescence imaging, histology and immunohistochemistry. Moreover, immune cells and inflammatory factors in the peritoneal fluid were assessed by flow cytometry and a cytokine array. These analyses revealed that the growth of newly developing endometriotic lesions is promoted by the presence of pre-existing ones. This is not due to an exchange of cells between both lesion types but rather caused by peritoneal inflammation induced by already established lesions. These findings indicate that, among other pathogenic mechanisms, the chronic nature of endometriosis may be driven by a lesion-induced inflammatory milieu in the peritoneal cavity, which creates favorable conditions for the development of new lesions.
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Affiliation(s)
| | | | | | - Matthias W. Laschke
- Institute for Clinical and Experimental Surgery, Saarland University, 66421 Homburg, Germany; (I.T.M.); (J.R.-A.); (M.D.M.)
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40
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Yang J, Zhu B, Ran C. The Application of Bio-orthogonality for In Vivo Animal Imaging. Chem Biomed Eng 2023; 1:434-447. [PMID: 37655167 PMCID: PMC10466453 DOI: 10.1021/cbmi.3c00033] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 09/02/2023]
Abstract
The application of bio-orthogonality has greatly facilitated numerous aspects of biological studies in recent years. In particular, bio-orthogonal chemistry has transformed biological research, including in vitro conjugate chemistry, target identification, and biomedical imaging. In this review, we highlighted examples of bio-orthogonal in vivo imaging published in recent years. We grouped the references into two major categories: bio-orthogonal chemistry-related imaging and in vivo imaging with bio-orthogonal nonconjugated pairing. Lastly, we discussed the challenges and opportunities of bio-orthogonality for in vivo imaging.
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Affiliation(s)
- Jun Yang
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129, United States
| | - Biyue Zhu
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129, United States
| | - Chongzhao Ran
- Athinoula
A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital/Harvard Medical School, Room 2301, Building 149, Charlestown, Boston, Massachusetts 02129, United States
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Reichard WD, Smith SE, Robertson JB. BLINCAR: a reusable bioluminescent and Cas9-based genetic toolset for repeatedly modifying wild-type Scheffersomyces stipitis. mSphere 2023; 8:e0022423. [PMID: 37345937 PMCID: PMC10449509 DOI: 10.1128/msphere.00224-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 05/09/2023] [Indexed: 06/23/2023] Open
Abstract
Scheffersomyces stipitis is a yeast that robustly ferments the 5-carbon sugar xylose, making the yeast a valuable candidate for lignocellulosic ethanol fermentation. However, the non-canonical codon usage of S. stipitis is an obstacle for implementing molecular tools that were developed for other yeast species, thereby limiting the molecular toolset available for S. stipitis. Here, we developed a series of molecular tools for S. stipitis including BLINCAR, a Bio-Luminescent Indicator that is Nullified by Cas9-Actuated Recombination, which can be used repeatedly to add different exogenous DNA payloads to the wild-type S. stipitis genome or used repeatedly to remove multiple native S. stipitis genes from the wild-type genome. Through the use of BLINCAR tools, one first produces antibiotic-resistant, bioluminescent colonies of S. stipitis whose bioluminescence highlights those clones that have been genetically modified; then second, once candidate clones have been confirmed, one uses a transient Cas9-producing plasmid to nullify the antibiotic resistance and bioluminescent markers from the prior introduction, thereby producing non-bioluminescent colonies that highlight those clones which have been re-sensitized to the antibiotic and are therefore susceptible to another round of BLINCAR implementation. IMPORTANCE Cellulose and hemicellulose that comprise a large portion of sawdust, leaves, and grass can be valuable sources of fermentable sugars for ethanol production. However, some of the sugars liberated from hemicellulose (like xylose) are not easily fermented using conventional glucose-fermenting yeast like Saccharomyces cerevisiae, so engineering robust xylose-fermenting yeast that is not inhibited by other components liberated from cellulose/hemicellulose will be important for maximizing yield and making lignocellulosic ethanol fermentation cost efficient. The yeast Scheffersomyces stipitis is one such yeast that can ferment xylose; however, it possesses several barriers to genetic manipulation. It is difficult to transform, has only a few antibiotic resistance markers, and uses an alternative genetic code from most other organisms. We developed a genetic toolset for S. stipitis that lowers these barriers and allows a user to deliver and/or delete multiple genetic elements to/from the wild-type genome, thereby expanding S. stipitis's potential.
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Affiliation(s)
- Walter D. Reichard
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - Serenah E. Smith
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
| | - J. Brian Robertson
- Department of Biology, Middle Tennessee State University, Murfreesboro, Tennessee, USA
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Ogunniyi AD, Nguyen HT, Hansford KA, Cooper MA, Trott DJ, Blaskovich MAT. Impact of the new membrane-targeting lipoglycopeptide antibiotic MCC5145 on the treatment of bacteremic pneumococcal pneumonia in mice. Microbiol Spectr 2023; 11:e0445922. [PMID: 37606382 PMCID: PMC10580989 DOI: 10.1128/spectrum.04459-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 07/06/2023] [Indexed: 08/23/2023] Open
Abstract
Bacteremic Streptococcus pneumoniae pneumonia is one of the most severe forms of invasive pneumococcal disease (IPD) and with particularly high case-fatality rates among the elderly and individuals with comorbidities, exacerbated by rising antibiotic resistance and time to initiation of therapy. Here, we examined the efficacy of the preclinical "vancapticin" glycopeptide MCC5145 against fulminant infection by S. pneumoniae serotype 2 strain D39 in a bioluminescent, neutropenic mouse model of bacteremic pneumonia. MCC5145 is a semisynthetic vancomycin derivative chemically modified at the C-terminus with a membrane-targeting motif designed to preferentially bind the anionic bacterial surface. We show that similar to vancomycin, subcutaneous administration of MCC5145 to mice 1 day after intranasal infection with a bioluminescent derivative of S. pneumoniae D39 elicited time and concentration-dependent reduction in total flux in the lungs and blood. Together, our finding supports the further development of MCC5145 as a potential new treatment option for pneumonia and/or bacteremic pneumonia in clinical settings, particularly for immunocompromised individuals. IMPORTANCE S. pneumoniae (the pneumococcus) causes severe community acquired lung and blood infection, especially among the elderly and people with underlying medical conditions and/or weakened immune systems. The rising incidence of antibiotic resistance and delays between diagnosis of infection and commencement of effective therapy make treatment difficult and result in high mortality rates. In this work, we show that a new derivative (MCC5145) of an existing antibiotic (vancomycin) rapidly eradicated lethal pneumococcal challenge from the lungs and blood of mice with a suppressed immune system. Our findings support that MCC5145 is a promising option for the treatment of lung and blood infections caused by the pneumococcus at point-of-care settings, particularly for the elderly and individuals with a weakened immune system.
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Affiliation(s)
- Abiodun D. Ogunniyi
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Hang Thi Nguyen
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Karl A. Hansford
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew A. Cooper
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Darren J. Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, South Australia, Australia
| | - Mark A. T. Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
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Mujawar A, Phadte P, Palkina KA, Markina NM, Mohammad A, Thakur BL, Sarkisyan KS, Balakireva AV, Ray P, Yamplosky I, De A. Triple Reporter Assay: A Non-Overlapping Luciferase Assay for the Measurement of Complex Macromolecular Regulation in Cancer Cells Using a New Mushroom Luciferase-Luciferin Pair. Sensors (Basel) 2023; 23:7313. [PMID: 37687774 PMCID: PMC10490530 DOI: 10.3390/s23177313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023]
Abstract
This study demonstrates the development of a humanized luciferase imaging reporter based on a recently discovered mushroom luciferase (Luz) from Neonothopanus nambi. In vitro and in vivo assessments showed that human-codon-optimized Luz (hLuz) has significantly higher activity than native Luz in various cancer cell types. The potential of hLuz in non-invasive bioluminescence imaging was demonstrated by human tumor xenografts subcutaneously and by the orthotopic lungs xenograft in immunocompromised mice. Luz enzyme or its unique 3OH-hispidin substrate was found to be non-cross-reacting with commonly used luciferase reporters such as Firefly (FLuc2), Renilla (RLuc), or nano-luciferase (NLuc). Based on this feature, a non-overlapping, multiplex luciferase assay using hLuz was envisioned to surpass the limitation of dual reporter assay. Multiplex reporter functionality was demonstrated by designing a new sensor construct to measure the NF-κB transcriptional activity using hLuz and utilized in conjunction with two available constructs, p53-NLuc and PIK3CA promoter-FLuc2. By expressing these constructs in the A2780 cell line, we unveiled a complex macromolecular regulation of high relevance in ovarian cancer. The assays performed elucidated the direct regulatory action of p53 or NF-κB on the PIK3CA promoter. However, only the multiplexed assessment revealed further complexities as stabilized p53 expression attenuates NF-κB transcriptional activity and thereby indirectly influences its regulation on the PIK3CA gene. Thus, this study suggests the importance of live cell multiplexed measurement of gene regulatory function using more than two luciferases to address more realistic situations in disease biology.
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Affiliation(s)
- Aaiyas Mujawar
- Molecular Functional Imaging Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India; (A.M.); (A.M.)
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
| | - Pratham Phadte
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
- Imaging Cell Signalling and Therapeutics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India
| | - Ksenia A. Palkina
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Planta LLC, Bolshoi Boulevard, 42 Street 1, Moscow 121205, Russia
| | - Nadezhda M. Markina
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Planta LLC, Bolshoi Boulevard, 42 Street 1, Moscow 121205, Russia
| | - Ameena Mohammad
- Molecular Functional Imaging Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India; (A.M.); (A.M.)
| | - Bhushan L. Thakur
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
- Imaging Cell Signalling and Therapeutics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India
| | - Karen S. Sarkisyan
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Synthetic Biology Group, MRC London Institute of Medical Sciences, London W12 0NN, UK
| | - Anastasia V. Balakireva
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
- Planta LLC, Bolshoi Boulevard, 42 Street 1, Moscow 121205, Russia
| | - Pritha Ray
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
- Imaging Cell Signalling and Therapeutics Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India
| | - Ilia Yamplosky
- Institute of Bioorganic Chemistry (IBCh), Russian Academy of Sciences, Moscow 119991, Russia; (K.A.P.); (N.M.M.); (K.S.S.); (A.V.B.)
| | - Abhijit De
- Molecular Functional Imaging Laboratory, Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai 410210, India; (A.M.); (A.M.)
- Faculty of Life Science, Homi Bhabha National Institute, Mumbai 400094, India; (P.P.); (B.L.T.); (P.R.)
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Gregucci D, Nazir F, Calabretta MM, Michelini E. Illuminating Progress: The Contribution of Bioluminescence to Sustainable Development Goal 6-Clean Water and Sanitation-Of the United Nations 2030 Agenda. Sensors (Basel) 2023; 23:7244. [PMID: 37631781 PMCID: PMC10458275 DOI: 10.3390/s23167244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023]
Abstract
The United Nations Agenda 2030 Sustainable Development Goal 6 (SDG 6) aims at ensuring the availability and sustainable management of water and sanitation. The routine monitoring of water contaminants requires accurate and rapid analytical techniques. Laboratory analyses and conventional methods of field sampling still require considerable labor and time with highly trained personnel and transport to a central facility with sophisticated equipment, which renders routine monitoring cumbersome, time-consuming, and costly. Moreover, these methods do not provide information about the actual toxicity of water, which is crucial for characterizing complex samples, such as urban wastewater and stormwater runoff. The unique properties of bioluminescence (BL) offer innovative approaches for developing advanced tools and technologies for holistic water monitoring. BL biosensors offer a promising solution by combining the natural BL phenomenon with cutting-edge technologies. This review provides an overview of the recent advances and significant contributions of BL to SDG 6, focusing attention on the potential use of the BL-based sensing platforms for advancing water management practices, protecting ecosystems, and ensuring the well-being of communities.
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Affiliation(s)
- Denise Gregucci
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy; (D.G.); (F.N.); (M.M.C.)
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | - Faisal Nazir
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy; (D.G.); (F.N.); (M.M.C.)
| | - Maria Maddalena Calabretta
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy; (D.G.); (F.N.); (M.M.C.)
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy; (D.G.); (F.N.); (M.M.C.)
- Center for Applied Biomedical Research (CRBA), Azienda Ospedaliero-Universitaria Policlinico S. Orsola-Malpighi, 40138 Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, 40126 Bologna, Italy
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Petersen ED, Lapan AP, Castellanos Franco EA, Fillion AJ, Crespo EL, Lambert GG, Grady CJ, Zanca AT, Orcutt R, Hochgeschwender U, Shaner NC, Gilad AA. Bioluminescent Genetically Encoded Glutamate Indicators for Molecular Imaging of Neuronal Activity. ACS Synth Biol 2023; 12:2301-2309. [PMID: 37450884 PMCID: PMC10443529 DOI: 10.1021/acssynbio.2c00687] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Indexed: 07/18/2023]
Abstract
Genetically encoded optical sensors and advancements in microscopy instrumentation and techniques have revolutionized the scientific toolbox available for probing complex biological processes such as release of specific neurotransmitters. Most genetically encoded optical sensors currently used are based on fluorescence and have been highly successful tools for single-cell imaging in superficial brain regions. However, there remains a need to develop new tools for reporting neuronal activity in vivo within deeper structures without the need for hardware such as lenses or fibers to be implanted within the brain. Our approach to this problem is to replace the fluorescent elements of the existing biosensors with bioluminescent elements. This eliminates the need of external light sources to illuminate the sensor, thus allowing deeper brain regions to be imaged noninvasively. Here, we report the development of the first genetically encoded neurotransmitter indicators based on bioluminescent light emission. These probes were optimized by high-throughput screening of linker libraries. The selected probes exhibit robust changes in light output in response to the extracellular presence of the excitatory neurotransmitter glutamate. We expect this new approach to neurotransmitter indicator design to enable the engineering of specific bioluminescent probes for multiple additional neurotransmitters in the future, ultimately allowing neuroscientists to monitor activity associated with a specific neurotransmitter as it relates to behavior in a variety of neuronal and psychiatric disorders, among many other applications.
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Affiliation(s)
- Eric D. Petersen
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
- College
of Medicine, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Alexandra P. Lapan
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | | | - Adam J. Fillion
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - Emmanuel L. Crespo
- College
of Medicine, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Gerard G. Lambert
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Connor J. Grady
- Department
of Biomedical Engineering, Michigan State
University, East Lansing, Michigan 48824, United States
| | - Albertina T. Zanca
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Richard Orcutt
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Ute Hochgeschwender
- College
of Medicine, Central Michigan University, Mount Pleasant, Michigan 48859, United States
| | - Nathan C. Shaner
- Department
of Neurosciences, University of California
San Diego School of Medicine, La Jolla, California 92093, United States
| | - Assaf A. Gilad
- Department
of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Radiology, Michigan State University, East Lansing, Michigan 48824, United States
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Rahavi SM, Aletaha M, Farrokhi A, Lorentzian A, Lange PF, Maxwell CA, Lim CJ, Reid GSD. Adaptation of the Th-MYCN Mouse Model of Neuroblastoma for Evaluation of Disseminated Disease. Int J Mol Sci 2023; 24:12071. [PMID: 37569447 PMCID: PMC10419036 DOI: 10.3390/ijms241512071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
High-risk neuroblastoma remains a profound clinical challenge that requires eradication of neuroblastoma cells from a variety of organ sites, including bone marrow, liver, and CNS, to achieve a cure. While preclinical modeling is a powerful tool for the development of novel cancer therapies, the lack of widely available models of metastatic neuroblastoma represents a significant barrier to the development of effective treatment strategies. To address this need, we report a novel luciferase-expressing derivative of the widely used Th-MYCN mouse. While our model recapitulates the non-metastatic neuroblastoma development seen in the parental transgenic strain, transplantation of primary tumor cells from disease-bearing mice enables longitudinal monitoring of neuroblastoma growth at distinct sites in immune-deficient or immune-competent recipients. The transplanted tumors retain GD2 expression through many rounds of serial transplantation and are sensitive to GD2-targeted immune therapy. With more diverse tissue localization than is seen with human cell line-derived xenografts, this novel model for high-risk neuroblastoma could contribute to the optimization of immune-based treatments for this deadly disease.
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Affiliation(s)
- Seyed M. Rahavi
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Maryam Aletaha
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Ali Farrokhi
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Department of Pediatrics, University of British Columbia, 950 W28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Amanda Lorentzian
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Philipp F. Lange
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Department of Pathology, University of British Columbia, 950 W28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Christopher A. Maxwell
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Department of Pediatrics, University of British Columbia, 950 W28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Chinten James Lim
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Department of Pediatrics, University of British Columbia, 950 W28th Avenue, Vancouver, BC V5Z 4H4, Canada
| | - Gregor S. D. Reid
- Michael Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
- Department of Pediatrics, University of British Columbia, 950 W28th Avenue, Vancouver, BC V5Z 4H4, Canada
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Kim SB, Furuta T, Kitada N, Maki SA. Creation of Artificial Luciferase 60s from Sequential Insights and Their Applications to Bioassays. Sensors (Basel) 2023; 23:6376. [PMID: 37514669 PMCID: PMC10384629 DOI: 10.3390/s23146376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/10/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
In this study, a series of new artificial luciferases (ALucs) was created using sequential insights on missing peptide blocks, which were revealed using the alignment of existing ALuc sequences. Through compensating for the missing peptide blocks in the alignment, 10 sibling sequences were artificially fabricated and named from ALuc55 to ALuc68. The phylogenetic analysis showed that the new ALucs formed an independent branch that was genetically isolated from other natural marine luciferases. The new ALucs successfully survived and luminesced with native coelenterazine (nCTZ) and its analogs in living mammalian cells. The results showed that the bioluminescence (BL) intensities of the ALucs were interestingly proportional to the length of the appended peptide blocks. The computational modeling revealed that the appended peptide blocks created a flexible region near the active site, potentially modulating the enzymatic activities. The new ALucs generated various colors with maximally approximately 90 nm redshifted BL spectra in orange upon reaction with the authors' previously reported 1- and 2-series coelenterazine analogs. The utilities of the new ALucs in bioassays were demonstrated through the construction of single-chain molecular strain probes and protein fragment complementation assay (PCA) probes. The success of this study can guide new insights into how we can engineer and functionalize marine luciferases to expand the toolbox of optical readouts for bioassays and molecular imaging.
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Affiliation(s)
- Sung-Bae Kim
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8569, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Nobuo Kitada
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
| | - Shojiro A Maki
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu 182-8585, Japan
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Lisitsa AE, Sukovatyi LA, Deeva AA, Gulnov DV, Esimbekova EN, Kratasyuk VA, Nemtseva EV. The Role of Cosolvent-Water Interactions in Effects of the Media on Functionality of Enzymes: A Case Study of Photobacterium leiognathi Luciferase. Life (Basel) 2023; 13:1384. [PMID: 37374166 DOI: 10.3390/life13061384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
A complex heterogeneous intracellular environment seems to affect enzymatic catalysis by changing the mobility of biomolecules, their stability, and their conformational states, as well as by facilitating or hindering continuously occurring interactions. The evaluation and description of the influence of the cytoplasmic matrix components on enzymatic activity are problems that remain unsolved. In this work, we aimed to determine the mechanisms of action of two-component media with cosolvents of various molecular sizes on the complex multi-stage bioluminescent reaction catalyzed by bacterial luciferase. Kinetic and structural effects of ethylene glycol, glycerol, sorbitol, glucose, sucrose, dextran, and polyethylene glycol on bacterial luciferase were studied using stopped-flow and fluorescence spectroscopy techniques and molecular dynamics simulations. We have found that diffusion limitations in the presence of cosolvents promote the stabilization of flavin substrate and peroxyflavin intermediate of the reaction, but do not provide any advantages in bioluminescence quantum yield, because substrate binding is slowed down as well. The catalytic constant of bacterial luciferase has been found to be viscosity-independent and correlated with parameters of water-cosolvent interactions (Norrish constant, van der Waals interaction energies). Crowding agents, in contrast to low-molecular-weight cosolvents, had little effect on peroxyflavin intermediate decay and enzyme catalytic constant. We attributed specific kinetic effects to the preferential interaction of the cosolvents with enzyme surface and their penetration into the active site.
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Affiliation(s)
- Albert E Lisitsa
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Lev A Sukovatyi
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Anna A Deeva
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Dmitry V Gulnov
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
| | - Elena N Esimbekova
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
| | - Valentina A Kratasyuk
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
| | - Elena V Nemtseva
- Biophysics Department, Siberian Federal University, 660041 Krasnoyarsk, Russia
- Institute of Biophysics, Siberian Branch of Russian Academy of Sciences, 660036 Krasnoyarsk, Russia
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Melnik A, Silakov M, Mashukova O, Melnik L. Research into bioluminescence of the Black Sea ctenophores Pleurobrachia pileus O.F. Müller, 1776. LUMINESCENCE 2023. [PMID: 37259886 DOI: 10.1002/bio.4529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
The work presents the findings of the laboratory and in situ studies of ctenophore Pleurobrachia pileus O.F. Müller, 1776 which have shown that this species has bioluminescent properties. These organisms were considered non-luminous before. P. pileus bioluminescence was studied on board RV Professor Vodyanitsky during its 116th voyage. Sampling live organisms was preceded by probing with the Salpa MA+ probe to register the daily maximum glow in redoxcline, which in this zone was recorded, as a rule, in the depth range of 60-70 m, where dense clusters of P. pileus were formed at that time. The samples of ctenophores were taken by a Bogorov-Rass plankton net. After the net was closed, it was lifted to the surface at a speed of 0.4-0.5 m·s-1 . It was shown that only at a temperature not exceeding 14°C, the P. pileus remained alive for 2-3 days. The data provided indicate that the temperature above 14°C is close to the maximum permissible for P. pileus, therefore, chemical and mechanical stimulation experiments were carried out at this temperature (14°C) to agitate ctenophores luminescence. Though, the nature of their signal was significantly different. The total percentage of luminous organisms from the entire catch was 32.43%, which unequivocally proves that P. pileus glows and makes a significant contribution to the intensity of the glow at great depths in redoxcline.
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Affiliation(s)
- Alexandr Melnik
- A.O.Kovalevsky Institute of Biology of the Southern Seas, Sevastopol, Russia
| | - Mikhail Silakov
- A.O.Kovalevsky Institute of Biology of the Southern Seas, Sevastopol, Russia
| | - Olga Mashukova
- A.O.Kovalevsky Institute of Biology of the Southern Seas, Sevastopol, Russia
| | - Lidia Melnik
- A.O.Kovalevsky Institute of Biology of the Southern Seas, Sevastopol, Russia
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Zagitova RI, Purtov KV, Shcheglov AS, Mineev KS, Dubinnyi MA, Myasnyanko IN, Belozerova OA, Pakhomova VG, Petushkov VN, Rodionova NS, Lushpa VA, Guglya EB, Kovalchuk S, Kozhemyako VB, Mirza JD, Oliveira AG, Yampolsky IV, Kaskova ZM, Tsarkova AS. Conjugated Dienoic Acid Peroxides as Substrates in Chaetopterus Bioluminescence System. Int J Mol Sci 2023; 24:ijms24119466. [PMID: 37298416 DOI: 10.3390/ijms24119466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/07/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Biochemistry of bioluminescence of the marine parchment tubeworm Chaetopterus has been in research focus for over a century; however, the results obtained by various groups contradict each other. Here, we report the isolation and structural elucidation of three compounds from Chaetomorpha linum algae, which demonstrate bioluminescence activity with Chaetopterus luciferase in the presence of Fe2+ ions. These compounds are derivatives of polyunsaturated fatty acid peroxides. We have also obtained their structural analogues and demonstrated their activity in the bioluminescence reaction, thus confirming the broad substrate specificity of the luciferase.
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Affiliation(s)
- Renata I Zagitova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Konstantin V Purtov
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Aleksandr S Shcheglov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Konstantin S Mineev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, 141700 Moscow, Russia
| | - Maxim A Dubinnyi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, 141700 Moscow, Russia
| | - Ivan N Myasnyanko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Olga A Belozerova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Vera G Pakhomova
- Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50, 660036 Krasnoyarsk, Russia
| | - Valentin N Petushkov
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Natalia S Rodionova
- Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Akademgorodok 50/50, 660036 Krasnoyarsk, Russia
| | - Vladislav A Lushpa
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 9 Institutskiy per., Dolgoprudny, 141700 Moscow, Russia
| | - Elena B Guglya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Sergey Kovalchuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
| | - Valeri B Kozhemyako
- Central Research Laboratory, Pacific State Medical University, Ostryakova 2, 690002 Vladivostok, Russia
| | - Jeremy D Mirza
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Anderson G Oliveira
- Department of Chemistry and Biochemistry, Yeshiva University, 245 Lexington Ave, New York, NY 10016, USA
| | - Ilia V Yampolsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Zinaida M Kaskova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Aleksandra S Tsarkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya, 16/10, 117997 Moscow, Russia
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
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