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Recent Advances in Bioluminescence
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Recent Advances in Bioluminescence

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 9978

Special Issue Editor

Dr. Liudmila P. Burakova

E-Mail Website
Guest Editor
1. Photobiology Laboratory, Institute of Biophysics SB RAS, Federal Research Center "Krasnoyarsk Science Center SB RAS", Krasnoyarsk, Russia
2. Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk 660000, Russia
Interests: ctenophora photoproteins bioluminescence

Special Issue Information

Dear Colleagues,

Bioluminescence is a widespread phenomenon in nature, especially in the depths of the ocean. Representatives of luminous organisms are found among bacteria, fungi, protozoa, coelenterates, worms, molluscs, insects, and fish. Bioluminescence is a special case of a chemiluminescent reaction in which the substrate, luciferin, is oxidized, catalyzed by a specific enzyme, luciferase. Luciferins and luciferases of different organisms are different compounds and their similarity is often only functional. The interest of researchers in these objects is due not only to fundamental problems and the need to identify the general patterns underlying the conversion of the energy of the chemical bonds of the substrate into visible light energy, but also to the possibility of using bioluminescent proteins as marker molecules in various analytical applications. Coelenterazine is one of the most common substrates in marine glowing organisms and works with both luciferases and photoproteins, and firefly luciferase has a high quantum yield, so these bioluminescent proteins are the most abundant in analytics. At the same time, the search for new enzymes and substrates is constantly ongoing, as well as various modifications of already known bioluminescent proteins with desired properties are being created. The Special Issue “Recent Advances in Bioluminescence” will be devoted to the fundamental and applied problems of bioluminescence.

Potential topics include, but are not limited to:

  • Study of molecular mechanisms of functioning of bioluminescent systems;
  • Synthesis and application of luciferin analogues;
  • Creation of analytical tools based on bioluminescent and fluorescent proteins;
  • Search for new bioluminescent organisms;
  • Modification of known bioluminescent proteins and substrates;
  • Creation of artificial bioluminescent proteins with desired properties.

The Special Issue are now open for submissions. Prospective authors should first send a short abstract or tentative title to the Editorial Office. If the editors deem the topic to be appropriate for inclusion in one of the Special Issues, the author will be encouraged to submit a full manuscript.

Dr. Liudmila P. Burakova
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • bioluminescence
  • fluorescence
  • luciferases
  • photoproteins
  • luciferins
  • energy transfer
  • fused proteins
  • biosensors
  • bioimaging
  • glowing creatures

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Published Papers (5 papers)

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Research

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16 pages, 2242 KiB  
Article
Design of Ctenophore Ca2+-Regulated Photoprotein Berovin Capable of Being Converted into Active Protein Under Physiological Conditions: Computational and Experimental Approaches
by Ludmila P. Burakova, Nikita V. Ivanisenko, Natalia V. Rukosueva, Vladimir A. Ivanisenko and Eugene S. Vysotski
Life 2024, 14(11), 1508; https://doi.org/10.3390/life14111508 - 19 Nov 2024
Viewed by 249
Abstract
Here, we describe (1) the AlphaFold-based structural modeling approach to identify amino acids of the photoprotein berovin that are crucial for coelenterazine binding, and (2) the production and characterization of berovin mutants with substitutions of the identified residues regarding their effects on the [...] Read more.
Here, we describe (1) the AlphaFold-based structural modeling approach to identify amino acids of the photoprotein berovin that are crucial for coelenterazine binding, and (2) the production and characterization of berovin mutants with substitutions of the identified residues regarding their effects on the ability to form an active photoprotein under physiological conditions and stability to light irradiation. The combination of mutations K90M, N107S, and W103F is demonstrated to cause a shift of optimal conditions for the conversion of apo-berovin into active photoprotein towards near-neutral pH and low ionic strength, and to reduce the sensitivity of active berovin to light. According to the berovin spatial structure model, these residues are found in close proximity to the 6-(p-hydroxy)-phenyl group of the coelenterazine peroxyanion. Full article
(This article belongs to the Special Issue Recent Advances in Bioluminescence)
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13 pages, 2036 KiB  
Article
Catecholamine Involvement in the Bioluminescence Control of Two Species of Anthozoans
by Laurent Duchatelet, Constance Coubris, Christopher Pels, Sam T. Dupont and Jérôme Mallefet
Life 2023, 13(9), 1798; https://doi.org/10.3390/life13091798 - 23 Aug 2023
Cited by 3 | Viewed by 2494
Abstract
Bioluminescence, the ability of living organisms to emit visible light, is an important ecological feature for many marine species. To fulfil the ecological role (defence, offence, or communication), bioluminescence needs to be finely controlled. While many benthic anthozoans are luminous, the physiological control [...] Read more.
Bioluminescence, the ability of living organisms to emit visible light, is an important ecological feature for many marine species. To fulfil the ecological role (defence, offence, or communication), bioluminescence needs to be finely controlled. While many benthic anthozoans are luminous, the physiological control of light emission has only been investigated in the sea pansy, Renilla koellikeri. Through pharmacological investigations, a nervous catecholaminergic bioluminescence control was demonstrated for the common sea pen, Pennatula phosphorea, and the tall sea pen, Funiculina quadrangularis. Results highlight the involvement of adrenaline as the main neuroeffector triggering clusters of luminescent flashes. While noradrenaline and octopamine elicit flashes in P. phosphorea, these two biogenic amines do not trigger significant light production in F. quadrangularis. All these neurotransmitters act on both the endodermal photocytes located at the base and crown of autozooids and specific chambers of water-pumping siphonozooids. Combined with previous data on R. koellikeri, our results suggest that a catecholaminergic control mechanisms of bioluminescence may be conserved in Anthozoans. Full article
(This article belongs to the Special Issue Recent Advances in Bioluminescence)
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21 pages, 5897 KiB  
Article
The Role of Cosolvent–Water Interactions in Effects of the Media on Functionality of Enzymes: A Case Study of Photobacterium leiognathi Luciferase
by Albert E. Lisitsa, Lev A. Sukovatyi, Anna A. Deeva, Dmitry V. Gulnov, Elena N. Esimbekova, Valentina A. Kratasyuk and Elena V. Nemtseva
Life 2023, 13(6), 1384; https://doi.org/10.3390/life13061384 - 13 Jun 2023
Cited by 2 | Viewed by 1456
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Recent Advances in Bioluminescence)
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15 pages, 2318 KiB  
Article
Localization of the Catalytic Domain of Copepod Luciferases: Analysis of Truncated Mutants of the Metridia longa Luciferase
by Svetlana V. Markova, Marina D. Larionova, Igor A. Korotov and Eugene S. Vysotski
Life 2023, 13(5), 1222; https://doi.org/10.3390/life13051222 - 21 May 2023
Viewed by 1891
Abstract
Luciferases from copepods Metridia longa and Gaussia princeps are successfully used as bioluminescent reporters for in vivo and in vitro assays. Here, we report the minimal sequence of copepod luciferases required for bioluminescence activity that was revealed by gradual deletions of sequence encoding [...] Read more.
Luciferases from copepods Metridia longa and Gaussia princeps are successfully used as bioluminescent reporters for in vivo and in vitro assays. Here, we report the minimal sequence of copepod luciferases required for bioluminescence activity that was revealed by gradual deletions of sequence encoding the smallest MLuc7 isoform of M. longa luciferase. The single catalytic domain is shown to reside within the G32-A149 MLuc7 sequence and to be formed by both non-identical repeats, including 10 conserved Cys residues. Because this part of MLuc7 displays high homology with those of other copepod luciferases, our suggestion is that the determined boundaries of the catalytic domain are the same for all known copepod luciferases. The involvement of the flexible C-terminus in the retention of the bioluminescent reaction product in the substrate-binding cavity was confirmed by structural modeling and kinetics study. We also demonstrate that the ML7-N10 mutant (15.4 kDa) with deletion of ten amino acid residues at the N-terminus can be successfully used as a miniature bioluminescent reporter in living cells. Application of a shortened reporter may surely reduce the metabolic load on the host cells and decrease steric and functional interference at its use as a part of hybrid proteins. Full article
(This article belongs to the Special Issue Recent Advances in Bioluminescence)
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Review

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16 pages, 1256 KiB  
Review
Systematic Distribution of Bioluminescence in Marine Animals: A Species-Level Inventory
by Julien M. Claes, Steven H. D. Haddock, Constance Coubris and Jérôme Mallefet
Life 2024, 14(4), 432; https://doi.org/10.3390/life14040432 - 24 Mar 2024
Cited by 1 | Viewed by 3023
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Recent Advances in Bioluminescence)
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